diff --git a/RELEASE_NOTES b/RELEASE_NOTES index e687bf442f84..590c5db69f2d 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,8 +3,145 @@ For more detailed information, please see the git log. These release notes can also be consulted at https://docs.easybuild.io/en/latest/Release_notes.html. -The latest version of easybuild-easyconfig provides 19,985 easyconfig files, for 3,552 different software packages, -incl. 40 different (compiler) toolchains. +The latest version of easybuild-easyconfig provides 20,561 easyconfig files, for 3,656 different software packages, +incl. 41 different (compiler) toolchains. + + +v4.9.3 (14 September 2024) +-------------------------- + +update/bugfix release + +- added easyconfigs for foss/2024a (#21100) and intel/2024a (#21101) common toolchains +- new toolchain: gmpflf/2024.06 (#20882) +- added example easyconfig files for 107 new software packages: + - absl-py (#21039), accelerate (#21107), affogato (#20636), APOST3D (#21133), bayesian-optimization (#21301), + BayesOpt (#21261), BGEN-enkre (#15752), bitsandbytes (#21248), bliss (#21206), cfgrib (#21113), CLANS (#21099), + colorize (#20964), CORSIKA (#20693), COSTA (#20989), coxeter (#21254), Critic2 (#20833), crypt4gh (#20870), + dblatex (#21207), dictys (#21166), DL_POLY_Classic_GUI (#20819), EGA-QuickView (#20870, #20888), EMMAX (#21174), + empanada-dl (#20454), empanada-napari (#20454), ESIpy (#21006), fastfilters (#21003), fish (#21345, #21381), + flash-attention (#21083), Flax (#21039), fonttools (#21363), fsm-lite (#20503), GDMA (#21171), GeoDict (#20650), + GPflow (#21172), gtk-doc (#21207), Gubbins (#20413), Gymnasium (#20420), HERRO (#21252), IEntropy (#20808), + ilastik-napari (#21003), IMAGE (#20994), junos-eznc (#21166), jupyter-collaboration (#20741), + jupyter-vscode-proxy (#20876), langchain-mistralai (#20759), langchain-openai (#20711), LRBinner (#21310), + lrcalc (#21339), MAGIC (#20900), mallard-ducktype (#21127), MATES (#21229), MBX (#21155), mcqd (#21283), + MeshLab (#20806), meteogrid (#20921), micro-sam (#20636), miniprot (#21157), napari-denoiseg (#20934), + NECAT (#21359), nellie (#21267), NextPolish (#21265), nifty (#20636), ome-types (#21256), openai-python (#20711), + OpenForceField-Toolkit (#20852), orjson (#20880), PEcAn (#21227), PretextMap (#20790), PyBEL (#20953), + pyMBE (#21034), pystencils (#20889), python-blosc (#20636), python-elf (#20636), rankwidth (#20788), Rasqal (#21207), + Redland (#21227), Regenie (#15752), rMATS-long (#20916), Sagemath (#21365), scCustomize (#20907), SCENICplus (#21085), + scFEA (#20777), sdsl-lite (#20503), SharedMeatAxe (#21303), Single-cell-python-bundle (#20116), SIRIUS (#20989), + sirocco (#21304), SKA2 (#20411), SpFFT (#20989), spla (#11607), Stable-Baselines3 (#20884), submitit (#21103), + SVDSS2 (#20855), tdlib (#21305), torch-em (#20636), Umpire (#20989), Uni-Core (#21182), vigra (#20636), + Visit (#20981), weblogo (#20800), wradlib (#21110), xtb-IFF (#20783), yell (#20964), yelp-tools (#21127), + yelp-xsl (#21127), z5py (#20636), Zoltan (#21324) +- added additional easyconfigs for various supported software packages, including: + - AGAT 1.4.0, ASE 3.23.0, Abseil 20240722.0, Albumentations 1.4.0, AlphaPulldown 2.0.0b4, AlphaPulldown 2.0.0b4, + AmberTools 26.3, Arrow 16.1.0, alsa-lib 1.2.11, archspec 0.2.4, attr 2.5.2, BayesTraits 4.1.2, BeautifulSoup 4.12.3, + Biopython 1.84, Boost.MPI 1.83.0, bcl-convert 4.2.7-2, beagle-lib 4.0.1, biom-format 2.1.16, byacc 2.0.20240109, + CDO 2.3.0, CFITSIO 4.4.1, CUDA-Samples 12.2, CUDA 12.5.0 + 12.6.0, CUTLASS 3.4.0, Catch2 2.13.10, CellOracle 0.18.0, + Clang 18.1.8, Coreutils 9.5, chewBBACA 3.3.9, code-server 4.90.2, connected-components-3d 3.14.1, cooler 0.10.2, + cryptography 42.0.8, cutadapt 4.9, cyvcf2 0.31.1, dorado 0.7.3, dtcmp 1.1.5, ESMF 8.6.1, EvidentialGene 2023.07.15, + Extrae 4.2.0, ecBuild 3.8.5, elfutils 0.191, FFmpeg 7.0.2, FLAC 1.4.3, FUSE 3.16.2, Flask 3.0.3, Flye 2.9.4, + FriBidi 1.0.15, ffnvcodec 12.2.72.0, flatbuffers-python 24.3.25, flatbuffers 24.3.25, fmt 10.2.1, fpylll 0.6.1, + GCC 14.2.0, GDAL 3.9.0, GEOS 3.12.1, GHC 9.10.1, GLM 1.0.1, GLib 2.80.4, GLibmm 2.72.1 + 2.75.0 + 2.77.0 + 2.78.1, + GPAW 24.6.0, GetOrganelle 1.7.7.1, Guile 2.0.14 + 3.0.10, Gurobi 11.0.2, gap 4.13.0, genomepy 0.16.1, gensim 4.3.2, + gffutils 0.13, gh 2.52.0, git-annex 10.20240731, gmpy2 2.2.0, googletest 1.15.2, graph-tool 2.59, HDBSCAN 0.8.38.post1, + HOMER 4.11.1, HTSeq 2.0.7, HiCMatrix 17.2, Highway 1.2.0, Hypre 2.31.0, hatchling 1.24.2, histolab 0.7.0, + hypothesis 6.103.1, IQ-TREE 2.3.5, ImageMagick 7.1.1-34, Imath 3.1.11, IsoQuant 3.5.0, igraph 0.10.12, imageio 2.34.1, + imbalanced-learn 0.12.3, inferCNV 1.21.0, intervaltree 0.1, JsonCpp 1.9.5, Julia 1.10.4, jax 0.4.25, json-fortran 8.5.2, + Kent_tools 468, LLVM 18.1.8, LittleCMS 2.16, libdrm 2.4.122, libdwarf 0.10.1, libedit 20240517, libgeotiff 1.7.3, + libgit2 1.8.1, libopus 1.5.2, libsigc++ 3.6.0, libspatialindex 2.0.0, libunistring 1.2, libunwind 1.8.1, libwebp 1.4.0, + libxslt 1.1.42, libzip 1.10.1, lwgrp 1.0.6, lxml 5.3.0, MCR R2024a, MPICH 4.2.1, MUMPS 5.7.2, MariaDB 11.6.0, + Maven 3.9.7, Mercurial 6.8.1, Mesa 24.1.3, Miniconda3 23.10.0-1, MultiQC 1.22.3, makedepend 1.0.9, matplotlib 3.9.2, + maturin 1.6.0, medaka 1.12.1, meshio 5.3.5, meson-python 0.16.0, mm-common 1.0.6, NanoCaller 3.6.0, Normaliz 3.10.3, + n2v 0.3.3, nano 8.1, ncbi-vdb 3.1.1, nettle 3.10, nsync 1.29.2, numexpr 2.9.0, ORCA 6.0.0, OpenEXR 3.2.4, OpenFOAM 12, + OpenFOAM v2406, OpenJPEG 2.5.2, Optax 0.2.2, Optuna 3.6.1, PaStiX 6.3.2, Perl-bundle-CPAN 5.38.2, Pillow-SIMD 10.4.0, + Pint 0.24, Platypus-Opt 1.2.0, PostgreSQL 16.4, PyAEDT 0.9.9, PyCharm 2024.1.6, PyRosetta 4.release-384, + PyWavelets 1.7.0, PyYAML 6.0.2, Pygments 2.18.0, Pylint 3.2.5, Pyomo 6.7.3, Python-bundle-PyPI 2024.06, packmol 20.14.4, + pagmo 2.19.0, parallel 20240722, pixman 0.43.4, pod5-file-format 0.3.10, poetry 1.8.3, popt 1.19, pretty-yaml 24.7.0, + primecount 7.14, psycopg 3.2.1, pyGenomeTracks 3.9, pybind11 2.12.0, pycocotools 2.0.7, pydantic 2.7.4, pygmo 2.19.5, + pyperf 2.7.0, pyseer 1.3.12, pysteps 1.10.0, QuantumESPRESSO 7.3.1, Qwt 6.3.0, R-bundle-CRAN 2024.06, R 4.4.1, + RDKit 2024.03.3, RapidJSON 1.1.0-20240409, Ray-project 2.9.1, ReFrame 4.6.2, Rust 1.79.0, redis-py 5.0.9, + regionmask 0.12.1, rjags 4-15, rpmrebuild 2.18, SDL2 2.30.6, SHAP 0.43.0, SIP 6.8.3, SRA-Toolkit 3.1.1, + STAR 2.7.11b_alpha_2024-02-09, STRUMPACK 7.1.0, SVDSS2 2.0.0-alpha.3, Safetensors 0.4.3, Salmon 1.10.3, + SciPy-bundle 2024.05, SeqKit 2.8.2, SingleM 0.16.0, Sphinx-RTD-Theme 2.0.0, Stack 3.1.1, SuiteSparse 7.7.0, + SuperLU 6.0.1, SuperLU_DIST 8.2.1, scArches 0.6.1, scib-metrics 0.5.1, scvi-tools 1.1.2, sdsl-lite 2.0.3, + setuptools-rust 1.9.0, sirocco 2.1.0, slepc4py 3.20.2, smafa 0.8.0, snpEff 5.2c, spaCy 3.7.4, spektral 1.2.0, + spglib-python 2.5.0, spglib 2.5.0, TELEMAC-MASCARET 8p5r0, Tk 8.6.14, Tkinter 3.12.3, Trycycler 0.5.5, tiktoken 0.7.0, + timm 1.0.8, UCX-CUDA 1.16.0, unixODBC 2.3.12, utf8proc 2.9.0, VSEARCH 2.28.1, virtualenv 20.26.2, WRF 4.5.1, + Wayland 1.23.0, X11 20240607, XGBoost 2.1.1, XML-LibXML 2.0210, x264 20240513, x265 3.6, xarray 2024.5.0, xtb-IFF 1.1, + xtb 6.7.1, xtensor 0.24.7, yelp-xsl 42.1 +- minor enhancements, including: + - add internal CUDA header patch for PSM2 v12.0.1 (#20804) + - add patch for JupyterHub support to recent tensorboard easyconfigs (#20823) + - make sure that recent ImageMagick versions pick up the right pkgconf + improve sanity check for ImageMagick (#20900) + - also install utilities for recent versions of FUSE 3.x (#20918) + - add RISC-V support to x264 v20231019 (#20968) + - add RISC-v support to recent LAME easyconfigs by removing workaround for finding libncurses (#20970) + - enable PIC in recent x265 easyconfigs to solve compilation errors on RISC-V (#20971) + - add extensions to R-bundle-CRAN: missmDA (#21167, #21183). insight (#21260), performance + datwizard + bayestestR (#21272, #21285) + - add Qt support to VTK 9.3.0 (#21221) + - add `helper_scripts` to `$PATH` in easyconfig for ProteinMPNN v1.0.1-20230627 (#21289) + - also build & install the plugins with OpenFOAM v2406 (#21332) +- various bug fixes, including: + - fix easyconfigs for recent versions of QuantumESPRESSO (#20070) + - add wrapper for Julia with linking safeguards and delegate environment setup to JuliaPackage (#20103) + - fix typo in description of SuiteSparse v7.7.0 (#20567) + - add 'pic' flag to IML (#20789) + - add patch to recent SciPy-bundle easyconfigs to fix build error with numpy with some Fortran compilers (#20817) + - rename unpacked sources for components of EasyBuild v4.9.2, to ensure that '`--install-latest-eb-release`' works with older EasyBuild versions (#20818) + - fix build of OpenBLAS 0.3.24 on A64FX (#20820) + - remove maturin build dependency from langchain-antropic (#20825) + - add GMP and MPFR as dependencies to OpenFOAM v2306 and v2312 (#20841) + - add patch to SciPy-bundle 2024.05 that fixes numpy test failures on RISC-V (#20847) + - skip unreliable memory leak test in PyTorch 2.1.2 (#20874) + - use PyYAML 6.0.1 instead of 6.0 for recent ReFrame versions to fix problem with Cython 3.x (#20879) + - use PyPI source tarball and gfbf/2023a toolchain for pyBigWig (#20881) + - add fix for failing test on zen4 to Highway 1.0.4 (#20942) + - add patch to fix implicit function declaration in OpenMPI 4.1.4 (#20949) + - only use libxsmm as dependency for CP2K 2023.1 w/ `foss/2023a` on x86_64 (#20951) + - copy missing `rsem_perl_utils.pm` in DETONATE, since it's required by `rsem-eval-calculate-score` command (#20956) + - set `$SATSUMA2_PATH` so Satsuma2 can locate executables (#20957) + - disable auto-vectorizer (`-ftree-vectorize`) for OpenFOAM v10 + v11 when using toolchain that with GCC >= 11 (#20958) + - disable test step for WIEN2k 23.2 because files required by it can no longer be downloaded (#20969) + - add patch to fix Qt6 issues with ParaView v5.12.0, e.g. representation selection (#21002) + - update homepage in phonopy easyconfigs (#21014) + - make libunwind dependency architecture specific in Extrae 4.2.0 easyconfig (#21017) + - add `OPENSSL_ENABLE_SHA1_SIGNATURES` for building `ansys-pythonnet` (#21028) + - fix download URLs for old Intel software (2018-2023) by using `IRC_NAS` instead of `irc_nas` (#21108) + - update source and homepage URLs in Szip easyconfigs (#21129) + - rename source URL in HDF v4.2.16-2 easyconfig (#21130) + - consistently fix homeage + source URL for `HDF` + `h4toh5` (#21134) + - ensure that recent BioPerl easyconfigs use `Bundle` easyblock (#21136) + - fix checksum checks for easyconfigs using a `Bundle`-like easyblock in easyconfigs test suite (#21143) + - add pkgconf build dependency to scikit-misc v0.3.1 (#21144) + - explicitly disable use of MySQL in recent GDAL easyconfigs (#21156) + - fix easyconfig tensorflow-probability v0.20.0 to pass `pip check` (#21172) + - stop RStudio-Server 2023.09 from installing R packages (+ move to `foss/2023a` toolchain) (#21175) + - remove `Time::HiRes` from `Perl-bundle-CPAN` since there's newer version in `Perl` (#21198) + - fix build of STAR 2.7.11a + 2.7.11b on non-x86 architectures by avoiding use of `-maxv2` + add missing `xxd` build dependency (#21200) + - add missing cairo dependency for python-igraph v0.10.6 (#21211) + - add patch for xtb 6.7.0 to fix build failure due to changes in tblite (#21255) + - add patch for HDF5 v1.14.3 to suppress fp exceptions (#21280) + - update easyconfig for dorado 0.7.3 to properly use provided OpenSSL dependency, and not install external libraries into its own lib directory (#21297) + - use proper Python dependency for OTF2 (#21325) + - use source tarballs from GitHub for recent libdap easyconfigs (#21334) + - remove Highway build dependency in Brunsli easyconfigs, since it's not actually required at all (#21366) + - add alternative checksum for bold 1.3.0 extension in R-bundle-CRAN (#21370) +- other changes: + - archive outdated example easyconfigs for Fujitsu toolchain (#20781) + - upgrade rpmrebuild build dependency to version 2.18 in bcl-convert 4.2.7 easyconfig (#20861) + - use proper dependency for Safetensors in easyconfig for Transformers v4.39.3 (#20864) + - remove CMake Arrow flag as there is no Arrow dependency in recent GDAL easyconfigs (#20905) + - whitelist `ConfigureMakePythonPackage` for `sanity_check_paths` CI check (#20963) + - rename `gubbins-2.4.0.eb` to `Gubbins-2.4.0.eb` (#20995) + - make pytest v7.4.2 independent of Python-bundle-PyPI (#21004) + - reorganize Flax/JAX stack in 2023a: move `jax` + `Optax` to `gfbf/2023a` toolchain + use standalone `Flax` + `absl-py` as dependencies (#21038) + - use stand-alone absl-py as dependency for jax w/ `gfbf/2023a` (#21039) + - remove Cython dependency from Python-bundle-PyPI 2024.06 + add standalone easyconfig for Cython 3.0.10 (#21233) + - add Cython build dependency for SciPy-bundle v2024.05 (#21235) + - use top-level parameters for `use_pip` & co instead of `exts_default_options` for `PythonBundle` easyconfigs (#21292) v4.9.2 (12 June 2024) diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-FCC-4.5.0.eb b/easybuild/easyconfigs/__archive__/a/Autoconf/Autoconf-2.71-FCC-4.5.0.eb similarity index 100% rename from easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-FCC-4.5.0.eb rename to easybuild/easyconfigs/__archive__/a/Autoconf/Autoconf-2.71-FCC-4.5.0.eb diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.16.3-FCC-4.5.0.eb b/easybuild/easyconfigs/__archive__/a/Automake/Automake-1.16.3-FCC-4.5.0.eb similarity index 100% rename from easybuild/easyconfigs/a/Automake/Automake-1.16.3-FCC-4.5.0.eb rename to easybuild/easyconfigs/__archive__/a/Automake/Automake-1.16.3-FCC-4.5.0.eb diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-20210128-FCC-4.5.0.eb b/easybuild/easyconfigs/__archive__/a/Autotools/Autotools-20210128-FCC-4.5.0.eb similarity index 100% rename from easybuild/easyconfigs/a/Autotools/Autotools-20210128-FCC-4.5.0.eb rename to easybuild/easyconfigs/__archive__/a/Autotools/Autotools-20210128-FCC-4.5.0.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.7.6-FCC-4.5.0.eb b/easybuild/easyconfigs/__archive__/b/Bison/Bison-3.7.6-FCC-4.5.0.eb similarity index 100% rename from easybuild/easyconfigs/b/Bison/Bison-3.7.6-FCC-4.5.0.eb rename to easybuild/easyconfigs/__archive__/b/Bison/Bison-3.7.6-FCC-4.5.0.eb diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.36.1-FCC-4.5.0.eb b/easybuild/easyconfigs/__archive__/b/binutils/binutils-2.36.1-FCC-4.5.0.eb similarity index 100% rename from easybuild/easyconfigs/b/binutils/binutils-2.36.1-FCC-4.5.0.eb rename to easybuild/easyconfigs/__archive__/b/binutils/binutils-2.36.1-FCC-4.5.0.eb diff --git a/easybuild/easyconfigs/b/buildenv/buildenv-default-FCC-4.5.0.eb b/easybuild/easyconfigs/__archive__/b/buildenv/buildenv-default-FCC-4.5.0.eb similarity index 100% rename from easybuild/easyconfigs/b/buildenv/buildenv-default-FCC-4.5.0.eb rename to easybuild/easyconfigs/__archive__/b/buildenv/buildenv-default-FCC-4.5.0.eb diff --git 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rename to easybuild/easyconfigs/__archive__/f/ffmpi/ffmpi-4.5.0.eb diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4-FCC-4.5.0.eb b/easybuild/easyconfigs/__archive__/f/flex/flex-2.6.4-FCC-4.5.0.eb similarity index 100% rename from easybuild/easyconfigs/f/flex/flex-2.6.4-FCC-4.5.0.eb rename to easybuild/easyconfigs/__archive__/f/flex/flex-2.6.4-FCC-4.5.0.eb diff --git a/easybuild/easyconfigs/g/groff/groff-1.22.4-FCC-4.5.0.eb b/easybuild/easyconfigs/__archive__/g/groff/groff-1.22.4-FCC-4.5.0.eb similarity index 100% rename from easybuild/easyconfigs/g/groff/groff-1.22.4-FCC-4.5.0.eb rename to easybuild/easyconfigs/__archive__/g/groff/groff-1.22.4-FCC-4.5.0.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.3-Fujitsu-21.05.eb b/easybuild/easyconfigs/__archive__/h/HPL/HPL-2.3-Fujitsu-21.05.eb similarity index 100% rename from easybuild/easyconfigs/h/HPL/HPL-2.3-Fujitsu-21.05.eb rename to easybuild/easyconfigs/__archive__/h/HPL/HPL-2.3-Fujitsu-21.05.eb diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.48.3-FCC-4.5.0.eb b/easybuild/easyconfigs/__archive__/h/help2man/help2man-1.48.3-FCC-4.5.0.eb similarity index 100% rename from easybuild/easyconfigs/h/help2man/help2man-1.48.3-FCC-4.5.0.eb rename to easybuild/easyconfigs/__archive__/h/help2man/help2man-1.48.3-FCC-4.5.0.eb diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-8.1-FCC-4.5.0.eb b/easybuild/easyconfigs/__archive__/l/libreadline/libreadline-8.1-FCC-4.5.0.eb similarity index 100% rename from easybuild/easyconfigs/l/libreadline/libreadline-8.1-FCC-4.5.0.eb rename to easybuild/easyconfigs/__archive__/l/libreadline/libreadline-8.1-FCC-4.5.0.eb diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-FCC-4.5.0.eb b/easybuild/easyconfigs/__archive__/l/libtool/libtool-2.4.6-FCC-4.5.0.eb similarity index 100% rename from easybuild/easyconfigs/l/libtool/libtool-2.4.6-FCC-4.5.0.eb rename to easybuild/easyconfigs/__archive__/l/libtool/libtool-2.4.6-FCC-4.5.0.eb diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-FCC-4.5.0.eb b/easybuild/easyconfigs/__archive__/m/M4/M4-1.4.18-FCC-4.5.0.eb similarity index 100% rename from easybuild/easyconfigs/m/M4/M4-1.4.18-FCC-4.5.0.eb rename to easybuild/easyconfigs/__archive__/m/M4/M4-1.4.18-FCC-4.5.0.eb diff --git a/easybuild/easyconfigs/m/makeinfo/makeinfo-6.7-FCC-4.5.0.eb b/easybuild/easyconfigs/__archive__/m/makeinfo/makeinfo-6.7-FCC-4.5.0.eb similarity index 100% rename from easybuild/easyconfigs/m/makeinfo/makeinfo-6.7-FCC-4.5.0.eb rename to easybuild/easyconfigs/__archive__/m/makeinfo/makeinfo-6.7-FCC-4.5.0.eb diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.2-FCC-4.5.0.eb b/easybuild/easyconfigs/__archive__/n/ncurses/ncurses-6.2-FCC-4.5.0.eb similarity index 100% rename from easybuild/easyconfigs/n/ncurses/ncurses-6.2-FCC-4.5.0.eb rename to easybuild/easyconfigs/__archive__/n/ncurses/ncurses-6.2-FCC-4.5.0.eb diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-ffmpi-4.5.0.eb b/easybuild/easyconfigs/__archive__/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-ffmpi-4.5.0.eb similarity index 100% rename from easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-ffmpi-4.5.0.eb rename to easybuild/easyconfigs/__archive__/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-ffmpi-4.5.0.eb diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.32.1-FCC-4.5.0.eb b/easybuild/easyconfigs/__archive__/p/Perl/Perl-5.32.1-FCC-4.5.0.eb similarity index 100% rename from easybuild/easyconfigs/p/Perl/Perl-5.32.1-FCC-4.5.0.eb rename to easybuild/easyconfigs/__archive__/p/Perl/Perl-5.32.1-FCC-4.5.0.eb diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-FCC-4.5.0.eb b/easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.11-FCC-4.5.0.eb similarity index 100% rename from easybuild/easyconfigs/z/zlib/zlib-1.2.11-FCC-4.5.0.eb rename to easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.11-FCC-4.5.0.eb diff --git a/easybuild/easyconfigs/a/AGAT/AGAT-1.4.0-GCC-12.3.0.eb b/easybuild/easyconfigs/a/AGAT/AGAT-1.4.0-GCC-12.3.0.eb new file mode 100644 index 000000000000..2677e62fda13 --- /dev/null +++ b/easybuild/easyconfigs/a/AGAT/AGAT-1.4.0-GCC-12.3.0.eb @@ -0,0 +1,70 @@ +# easybuild easyconfig +# +# John Dey Fred Hutchinson Cancer Center +# Thomas Eylenbosch - Gluo NV +# Update: Petr Král (INUITS) +# +easyblock = 'Bundle' + +name = 'AGAT' +version = '1.4.0' + +homepage = 'https://agat.readthedocs.io/en/latest/' +description = """AGAT: Another GTF/GFF Analysis Toolkit. Suite of tools to handle gene annotations + in any GTF/GFF format.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('Perl', '5.36.1'), + ('BioPerl', '1.7.8'), +] + +exts_defaultclass = 'PerlModule' +exts_filter = ("perl -e 'require %(ext_name)s'", '') + +exts_list = [ + ('Set::Object', '1.42', { + 'source_tmpl': 'Set-Object-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RU/RURBAN'], + 'checksums': ['d18c5a8a233eabbd0206cf3da5b00fcdd7b37febf12a93dcc3d1c026e6fdec45'], + }), + ('File::Share', '0.27', { + 'source_tmpl': 'File-Share-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IN/INGY'], + 'checksums': ['d6e8f4b55ebd38e0bb45e44392e3fa27dc1fde16abc5d1ff53e157e19a5755be'], + }), + ('Sort::Naturally', '1.03', { + 'source_tmpl': 'Sort-Naturally-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': ['eaab1c5c87575a7826089304ab1f8ffa7f18e6cd8b3937623e998e865ec1e746'], + }), + ('Class::MethodMaker', '2.24', { + 'source_tmpl': 'Class-MethodMaker-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SC/SCHWIGON/class-methodmaker'], + 'checksums': ['5eef58ccb27ebd01bcde5b14bcc553b5347a0699e5c3e921c7780c3526890328'], + }), + ('Term::ProgressBar', '2.23', { + 'source_tmpl': 'Term-ProgressBar-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MANWAR'], + 'checksums': ['defc03fb9f4ac1c9df1359d312bff3c0865ddefbf3aba64cd42a69a86215d49d'], + }), + (name, version, { + 'modulename': 'AGAT::Utilities', + 'source_urls': ['https://github.com/NBISweden/AGAT/archive/refs/tags'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['d5e30db44b5d05ed51c606a823894c01c85c1ed85580148ad5473cb2f2b2ac77'], + }), +] + +modextrapaths = {'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin', 'lib/perl5/site_perl/%(perlver)s/%(name)s'], +} + +sanity_check_commands = ['agat_convert_bed2gff.pl --help'] +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-12.3.0-Java-11.eb b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-12.3.0-Java-11.eb new file mode 100644 index 000000000000..4f76242d899d --- /dev/null +++ b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-12.3.0-Java-11.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'ANTLR' +version = '2.7.7' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://www.antlr2.org/' +description = """ANTLR, ANother Tool for Language Recognition, (formerly PCCTS) + is a language tool that provides a framework for constructing recognizers, + compilers, and translators from grammatical descriptions containing + Java, C#, C++, or Python actions.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://www.antlr2.org/download/'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['%(name)s-%(version)s_includes.patch'] +checksums = [ + '853aeb021aef7586bda29e74a6b03006bcb565a755c86b66032d8ec31b67dbb9', # antlr-2.7.7.tar.gz + 'd167d3248a03301bc93efcb37d5df959aae6794968e42231af0b0dd26d6a2e66', # ANTLR-2.7.7_includes.patch +] + +builddependencies = [('binutils', '2.40')] + +dependencies = [('Java', '11', '', SYSTEM)] + +configopts = '--disable-examples --disable-csharp --disable-python' + +sanity_check_paths = { + 'files': ['bin/antlr', 'bin/antlr-config'], + 'dirs': ['include'], +} + +sanity_check_commands = ["antlr --help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/APOST3D/APOST3D-20240527-intel-compilers-2023.1.0.eb b/easybuild/easyconfigs/a/APOST3D/APOST3D-20240527-intel-compilers-2023.1.0.eb new file mode 100644 index 000000000000..c5c4c40ac5bc --- /dev/null +++ b/easybuild/easyconfigs/a/APOST3D/APOST3D-20240527-intel-compilers-2023.1.0.eb @@ -0,0 +1,51 @@ +easyblock = 'CmdCp' + +name = 'APOST3D' +version = '20240527' +local_commit = 'e06c8b0' + +description = """ +Open-source APOST-3D software features a large number of wavefunction analysis tools developed +over the past 20 years, aiming at connecting classical chemical concepts with the electronic +structure of molecules. APOST-3D relies on the identification of the atom in the molecule +(AIM), and several analysis tools are implemented in the most general way so that they can be +used in combination with any chosen AIM. +A Fortran-based code developed at the Universitat de Girona (UdG) by P. Salvador and collaborators. +""" +homepage = 'https://github.com/mgimferrer/APOST3D' + +toolchain = {'name': 'intel-compilers', 'version': '2023.1.0'} + +builddependencies = [ + ('make', '4.4.1'), +] + +source_urls = ['https://github.com/mgimferrer/APOST3D/archive'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['1eb9a0f97b4dd135b782b96cadc37b3acfc27c69521cf3aab6cc10d4fc9292af'] + +local_cmds = ' export APOST3D_PATH=%(start_dir)s && ' +# Compile provided Libxc version 4.2.3 +# (it is not possible to couple APOST-3D with newer Libxc libraries): +local_cmds += 'bash compile_libxc.sh && ' +# Compile +local_cmds += 'make -f Makefile_profgen && ' +# Run test calculations on single-processor: +local_cmds += 'bash compiler-runtest && ' +# Recompile using info geneated in previous step +local_cmds += 'make -f Makefile_profuse && ' +# Run test calculations in parallel: +local_cmds += 'bash compiler-runtest2' + +cmds_map = [('.*', local_cmds)] + +local_bin_files = ['apost3d', 'apost3d-eos', 'eos_aom'] + +files_to_copy = [(local_bin_files, 'bin')] + +sanity_check_paths = { + 'files': ['bin/%s' % f for f in local_bin_files], + 'dirs': [''], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/a/APR-util/APR-util-1.6.3-GCCcore-13.3.0.eb b/easybuild/easyconfigs/a/APR-util/APR-util-1.6.3-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..fc5f92c2b702 --- /dev/null +++ b/easybuild/easyconfigs/a/APR-util/APR-util-1.6.3-GCCcore-13.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'APR-util' +version = '1.6.3' + +homepage = 'https://apr.apache.org/' +description = "Apache Portable Runtime (APR) util libraries." + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://archive.apache.org/dist/apr/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['2b74d8932703826862ca305b094eef2983c27b39d5c9414442e9976a9acf1983'] + +builddependencies = [('binutils', '2.42')] + +dependencies = [ + ('APR', '1.7.4'), + ('SQLite', '3.45.3'), + ('expat', '2.6.2'), +] + +configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config --with-sqlite3=$EBROOTSQLITE --with-expat=$EBROOTEXPAT " + +sanity_check_paths = { + 'files': ["bin/apu-1-config", "lib/libaprutil-1.%s" % SHLIB_EXT, "lib/libaprutil-1.a"], + 'dirs': ["include/apr-1"], +} + +parallel = 1 + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/APR/APR-1.7.4-GCCcore-13.3.0.eb b/easybuild/easyconfigs/a/APR/APR-1.7.4-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..8ac5ed02a98f --- /dev/null +++ b/easybuild/easyconfigs/a/APR/APR-1.7.4-GCCcore-13.3.0.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'APR' +version = '1.7.4' + +homepage = 'https://apr.apache.org/' +description = "Apache Portable Runtime (APR) libraries." + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://archive.apache.org/dist/apr/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['a4137dd82a185076fa50ba54232d920a17c6469c30b0876569e1c2a05ff311d9'] + +builddependencies = [('binutils', '2.42')] + +sanity_check_paths = { + 'files': ["bin/apr-1-config", "lib/libapr-1.%s" % SHLIB_EXT, "lib/libapr-1.a"], + 'dirs': ["include/apr-1"], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.23.0-gfbf-2023a.eb b/easybuild/easyconfigs/a/ASE/ASE-3.23.0-gfbf-2023a.eb new file mode 100644 index 000000000000..554779e99cc1 --- /dev/null +++ b/easybuild/easyconfigs/a/ASE/ASE-3.23.0-gfbf-2023a.eb @@ -0,0 +1,48 @@ +easyblock = 'PythonBundle' + +name = 'ASE' +version = '3.23.0' + +homepage = 'https://wiki.fysik.dtu.dk/ase' +description = """ASE is a python package providing an open source Atomic Simulation Environment + in the Python scripting language. + +From version 3.20.1 we also include the ase-ext package, it contains optional reimplementations +in C of functions in ASE. ASE uses it automatically when installed.""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('Flask', '2.3.3'), + ('matplotlib', '3.7.2'), + ('Tkinter', '%(pyver)s'), # Needed by GUI of ASE + ('spglib-python', '2.1.0'), # optional +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('pytest-mock', '3.11.1', { + 'checksums': ['7f6b125602ac6d743e523ae0bfa71e1a697a2f5534064528c6ff84c2f7c2fc7f'], + }), + ('ase', version, { + 'checksums': ['91a2aa31d89bd90b0efdfe4a7e84264f32828b2abfc9f38e65e041ad76fec8ae'], + }), + ('ase-ext', '20.9.0', { + 'checksums': ['a348b0e42cf9fdd11f04b3df002b0bf150002c8df2698ff08d3c8fc7a1223aed'], + }), +] + +sanity_check_paths = { + 'files': ['bin/ase'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +# make sure Tkinter is available, otherwise 'ase gui' will not work +sanity_check_commands = ["python -c 'import tkinter' "] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.23.0-iimkl-2023a.eb b/easybuild/easyconfigs/a/ASE/ASE-3.23.0-iimkl-2023a.eb new file mode 100644 index 000000000000..f8bbed9f583a --- /dev/null +++ b/easybuild/easyconfigs/a/ASE/ASE-3.23.0-iimkl-2023a.eb @@ -0,0 +1,48 @@ +easyblock = 'PythonBundle' + +name = 'ASE' +version = '3.23.0' + +homepage = 'https://wiki.fysik.dtu.dk/ase' +description = """ASE is a python package providing an open source Atomic Simulation Environment + in the Python scripting language. + +From version 3.20.1 we also include the ase-ext package, it contains optional reimplementations +in C of functions in ASE. ASE uses it automatically when installed.""" + +toolchain = {'name': 'iimkl', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('Flask', '2.3.3'), + ('matplotlib', '3.7.2'), + ('Tkinter', '%(pyver)s'), # Needed by GUI of ASE + ('spglib-python', '2.1.0'), # optional +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('pytest-mock', '3.11.1', { + 'checksums': ['7f6b125602ac6d743e523ae0bfa71e1a697a2f5534064528c6ff84c2f7c2fc7f'], + }), + ('ase', version, { + 'checksums': ['91a2aa31d89bd90b0efdfe4a7e84264f32828b2abfc9f38e65e041ad76fec8ae'], + }), + ('ase-ext', '20.9.0', { + 'checksums': ['a348b0e42cf9fdd11f04b3df002b0bf150002c8df2698ff08d3c8fc7a1223aed'], + }), +] + +sanity_check_paths = { + 'files': ['bin/ase'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +# make sure Tkinter is available, otherwise 'ase gui' will not work +sanity_check_commands = ["python -c 'import tkinter' "] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/a/Abseil/Abseil-20240722.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/a/Abseil/Abseil-20240722.0-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..24951c68814c --- /dev/null +++ b/easybuild/easyconfigs/a/Abseil/Abseil-20240722.0-GCCcore-13.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'CMakeMake' + +name = 'Abseil' +version = '20240722.0' + +homepage = 'https://abseil.io/' +description = """Abseil is an open-source collection of C++ library code designed to augment the +C++ standard library. The Abseil library code is collected from Google's own +C++ code base, has been extensively tested and used in production, and is the +same code we depend on in our daily coding lives.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'https://github.com/%(namelower)s/%(namelower)s-cpp/archive/refs/tags'] +sources = ['%(version)s.tar.gz'] +checksums = ['f50e5ac311a81382da7fa75b97310e4b9006474f9560ac46f54a9967f07d4ae3'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] + +configopts = "-DABSL_PROPAGATE_CXX_STD=ON " + +build_shared_libs = True + +sanity_check_paths = { + 'files': ['lib/libabsl_base.' + SHLIB_EXT], + 'dirs': ['include/absl'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/a/Advisor/Advisor-2019_update2.eb b/easybuild/easyconfigs/a/Advisor/Advisor-2019_update2.eb index 24ce3fe1c317..2e121781a463 100644 --- a/easybuild/easyconfigs/a/Advisor/Advisor-2019_update2.eb +++ b/easybuild/easyconfigs/a/Advisor/Advisor-2019_update2.eb @@ -10,7 +10,7 @@ description = """Vectorization Optimization and Thread Prototyping toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15084/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15084/'] sources = ['advisor_%(version)s.tar.gz'] checksums = ['b63e11b0601013ad21789869ad76be5a836da566ee47c125dcda19ff8277de77'] diff --git a/easybuild/easyconfigs/a/Advisor/Advisor-2019_update3.eb b/easybuild/easyconfigs/a/Advisor/Advisor-2019_update3.eb index a9f9a8881546..7b0252873629 100644 --- a/easybuild/easyconfigs/a/Advisor/Advisor-2019_update3.eb +++ b/easybuild/easyconfigs/a/Advisor/Advisor-2019_update3.eb @@ -10,7 +10,7 @@ description = """Vectorization Optimization and Thread Prototyping toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15206/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15206/'] sources = ['advisor_%(version)s.tar.gz'] checksums = ['6597f165dee3c6444eb0f38a9069327d10584b09555f5d2c4ed86b8f84d980bb'] diff --git a/easybuild/easyconfigs/a/Advisor/Advisor-2019_update5.eb b/easybuild/easyconfigs/a/Advisor/Advisor-2019_update5.eb index 6a0d2fa4eced..cbcdab88d6e3 100644 --- a/easybuild/easyconfigs/a/Advisor/Advisor-2019_update5.eb +++ b/easybuild/easyconfigs/a/Advisor/Advisor-2019_update5.eb @@ -10,7 +10,7 @@ description = """Vectorization Optimization and Thread Prototyping toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15825/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15825/'] sources = ['advisor_%(version)s.tar.gz'] checksums = ['3f203ee63df37e87423fdd4cbeb5ec027b3d11e50c9121935f8b323dd635e866'] diff --git a/easybuild/easyconfigs/a/Advisor/Advisor-2021.2.0.eb b/easybuild/easyconfigs/a/Advisor/Advisor-2021.2.0.eb index 2a7de357e47a..144362e2eb70 100644 --- a/easybuild/easyconfigs/a/Advisor/Advisor-2021.2.0.eb +++ b/easybuild/easyconfigs/a/Advisor/Advisor-2021.2.0.eb @@ -13,7 +13,7 @@ description = """Vectorization Optimization and Thread Prototyping toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17730/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/17730/'] sources = ['l_oneapi_advisor_p_%(version)s.189_offline.sh'] checksums = ['9d9e9aa11819e6422f732de0e29e70a164e576254504857713cfec90b6b78664'] diff --git a/easybuild/easyconfigs/a/Advisor/Advisor-2021.4.0.eb b/easybuild/easyconfigs/a/Advisor/Advisor-2021.4.0.eb index 55354cc6e257..ec07e00e07ef 100644 --- a/easybuild/easyconfigs/a/Advisor/Advisor-2021.4.0.eb +++ b/easybuild/easyconfigs/a/Advisor/Advisor-2021.4.0.eb @@ -13,7 +13,7 @@ description = """Vectorization Optimization and Thread Prototyping toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18220/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18220/'] sources = ['l_oneapi_advisor_p_%(version)s.389_offline.sh'] checksums = ['dd948f7312629d9975e12a57664f736b8e011de948771b4c05ad444438532be8'] diff --git a/easybuild/easyconfigs/a/Advisor/Advisor-2022.1.0.eb b/easybuild/easyconfigs/a/Advisor/Advisor-2022.1.0.eb index 58235ccff908..34a2115a37c9 100644 --- a/easybuild/easyconfigs/a/Advisor/Advisor-2022.1.0.eb +++ b/easybuild/easyconfigs/a/Advisor/Advisor-2022.1.0.eb @@ -13,7 +13,7 @@ description = """Vectorization Optimization and Thread Prototyping toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18730/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18730/'] sources = ['l_oneapi_advisor_p_%(version)s.171_offline.sh'] checksums = ['b627dbfefa779b44e7ab40dfa37614e56caa6e245feaed402d51826e6a7cb73b'] diff --git a/easybuild/easyconfigs/a/Advisor/Advisor-2023.0.0.eb b/easybuild/easyconfigs/a/Advisor/Advisor-2023.0.0.eb index 187fcafa1806..e6d811a03a09 100644 --- a/easybuild/easyconfigs/a/Advisor/Advisor-2023.0.0.eb +++ b/easybuild/easyconfigs/a/Advisor/Advisor-2023.0.0.eb @@ -11,7 +11,7 @@ description = """Vectorization Optimization and Thread Prototyping toolchain = SYSTEM source_urls = [ - 'https://registrationcenter-download.intel.com/akdlm/irc_nas/19094/'] + 'https://registrationcenter-download.intel.com/akdlm/IRC_NAS/19094/'] sources = ['l_oneapi_advisor_p_%(version)s.25338_offline.sh'] checksums = ['5d8ef163f70ee3dc42b13642f321d974f49915d55914ba1ca9177ed29b100b9d'] diff --git a/easybuild/easyconfigs/a/Albumentations/Albumentations-1.4.0-foss-2023a.eb b/easybuild/easyconfigs/a/Albumentations/Albumentations-1.4.0-foss-2023a.eb new file mode 100644 index 000000000000..36b765ffdc84 --- /dev/null +++ b/easybuild/easyconfigs/a/Albumentations/Albumentations-1.4.0-foss-2023a.eb @@ -0,0 +1,36 @@ +easyblock = 'PythonBundle' + +name = 'Albumentations' +version = '1.4.0' + +homepage = 'https://albumentations.ai' +description = "Albumentations is a Python library for fast and flexible image augmentations" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('PyYAML', '6.0'), + ('scikit-image', '0.22.0'), + ('scikit-learn', '1.3.1'), + ('OpenCV', '4.8.1', '-contrib'), +] + +preinstallopts = "sed -i 's|CHOOSE_INSTALL_REQUIRES),|[]),|g' setup.py && " + +use_pip = True + +exts_list = [ + ('qudida', '0.0.4', { + 'checksums': ['db198e2887ab0c9aa0023e565afbff41dfb76b361f85fd5e13f780d75ba18cc8'], + }), + ('albumentations', version, { + 'checksums': ['649f8a14896f788b356ecc70083c4fb91bedab4ff4e2b39ad217a824e189ded0'], + }), +] + +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b2_fix-import-protein_letters_3to1.patch b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b2_fix-import-protein_letters_3to1.patch new file mode 100644 index 000000000000..34994664f805 --- /dev/null +++ b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b2_fix-import-protein_letters_3to1.patch @@ -0,0 +1,13 @@ +fix import of protein_letters_3to1 from Biopython +author: Kenneth Hoste (HPC-UGent) +--- AlphaPulldown/alphapulldown/utils/remove_clashes_low_plddt.py.orig 2024-06-05 09:30:16.114746286 +0200 ++++ AlphaPulldown/alphapulldown/utils/remove_clashes_low_plddt.py 2024-06-05 09:30:35.242665615 +0200 +@@ -4,7 +4,7 @@ + from alphafold.data.mmcif_parsing import parse + from alphafold.common.residue_constants import residue_atoms, atom_types + from Bio.PDB import NeighborSearch, PDBIO, MMCIFIO +-from Bio.PDB.Polypeptide import protein_letters_3to1 ++from Bio.Data.SCOPData import protein_letters_3to1 + from Bio import SeqIO + from colabfold.batch import convert_pdb_to_mmcif + from Bio.PDB import Structure, Model, Chain, Residue diff --git a/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b4-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b4-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 000000000000..492a787c919b --- /dev/null +++ b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b4-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,106 @@ +# created by Denis Kristak (Inuits) +easyblock = 'PythonBundle' + +name = 'AlphaPulldown' +version = '2.0.0b4' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/KosinskiLab/AlphaPulldown' +description = """AlphaPulldown is a Python package that streamlines protein-protein +interaction screens and high-throughput modelling of higher-order oligomers using AlphaFold-Multimer""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('Python', '3.10.4'), + ('OpenMM', '8.0.0'), + ('Kalign', '3.3.5'), + ('PyYAML', '6.0'), + ('jax', '0.3.25', versionsuffix), # also provides absl-py + ('Biopython', '1.79'), + ('h5py', '3.7.0'), + ('IPython', '8.5.0'), + ('JupyterLab', '3.5.0'), + ('matplotlib', '3.5.2'), + ('TensorFlow', '2.11.0', versionsuffix), + ('PyTorch', '1.12.0', versionsuffix), + ('tqdm', '4.64.0'), + ('dm-tree', '0.1.8'), + ('py3Dmol', '2.0.1.post1'), + ('HMMER', '3.3.2'), + ('HH-suite', '3.3.0'), + ('Uni-Core', '0.0.3', versionsuffix), +] + +use_pip = True + +exts_list = [ + ('importlib-resources', '5.13.0', { + 'modulename': 'importlib_resources', + 'source_tmpl': 'importlib_resources-%(version)s.tar.gz', + 'checksums': ['82d5c6cca930697dbbd86c93333bb2c2e72861d4789a11c2662b933e5ad2b528'], + }), + ('jmp', '0.0.4', { + 'checksums': ['5dfeb0fd7c7a9f72a70fff0aab9d0cbfae32a809c02f4037ff3485ceb33e1730'], + }), + ('dm-haiku', '0.0.9', { + 'modulename': 'haiku', + 'source_urls': ['https://github.com/deepmind/dm-haiku/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['d550f07f5891ede30ada5faafde98f549ed1b8ceadb7a601cca3d81db7d82414'], + }), + ('contextlib2', '21.6.0', { + 'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'], + }), + ('ml-collections', '0.1.1', { + 'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ", + 'sources': ['ml_collections-%(version)s.tar.gz'], + 'checksums': ['3fefcc72ec433aa1e5d32307a3e474bbb67f405be814ea52a2166bfc9dbe68cc'], + }), + ('PDBFixer', '1.9', { + 'source_urls': ['https://github.com/openmm/pdbfixer/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['88b9a77e50655f89d0eb2075093773e82c27a4cef842cb7d735c877b20cd39fb'], + }), + ('ihm', '1.3', { + 'checksums': ['09f69809fd81509cc26b60253c55b02ce79fc01fc8f4a068bca2953a7dfd33be'], + }), + ('modelcif', '1.0', { + 'checksums': ['e8375bc502a73dcfab0b7fbdd454d67d393bbb8969981eb52199d77192a3de56'], + }), + (name, version, { + 'sources': [{ + 'filename': SOURCE_TAR_GZ, + 'git_config': { + 'url': 'https://github.com/KosinskiLab', + 'repo_name': 'AlphaPulldown', + 'tag': version, + 'recursive': True, + }, + }], + 'patches': ['AlphaPulldown-2.0.0b2_fix-import-protein_letters_3to1.patch'], + 'checksums': [ + None, + 'd41247cd12f6ef8579adbc893f6c1af5fba051167ee838449974365f4bdccf06', + ], + # remove strict version requirements for Python dependencies + 'preinstallopts': "sed -i 's/[>=]=.*//g' setup.cfg && ", + }), +] + +fix_python_shebang_for = ['bin/*.py'] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/run_multimer_jobs.py', 'bin/rename_colab_search_a3m.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/alphapulldown'], +} + +sanity_check_commands = [ + "run_multimer_jobs.py --help | grep 'A script to perform structure prediction'", + "convert_to_modelcif.py --help | grep 'turn it into a ModelCIF'", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b4-foss-2022a.eb b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b4-foss-2022a.eb new file mode 100644 index 000000000000..f410c438e236 --- /dev/null +++ b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b4-foss-2022a.eb @@ -0,0 +1,104 @@ +# created by Denis Kristak (Inuits) +easyblock = 'PythonBundle' + +name = 'AlphaPulldown' +version = '2.0.0b4' + +homepage = 'https://github.com/KosinskiLab/AlphaPulldown' +description = """AlphaPulldown is a Python package that streamlines protein-protein +interaction screens and high-throughput modelling of higher-order oligomers using AlphaFold-Multimer""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('OpenMM', '8.0.0'), + ('Kalign', '3.3.5'), + ('PyYAML', '6.0'), + ('jax', '0.3.25'), # also provides absl-py + ('Biopython', '1.79'), + ('h5py', '3.7.0'), + ('IPython', '8.5.0'), + ('JupyterLab', '3.5.0'), + ('matplotlib', '3.5.2'), + ('TensorFlow', '2.11.0'), + ('PyTorch', '1.12.0'), + ('tqdm', '4.64.0'), + ('dm-tree', '0.1.8'), + ('py3Dmol', '2.0.1.post1'), + ('HMMER', '3.3.2'), + ('HH-suite', '3.3.0'), + ('Uni-Core', '0.0.3'), +] + +use_pip = True + +exts_list = [ + ('importlib-resources', '5.13.0', { + 'modulename': 'importlib_resources', + 'source_tmpl': 'importlib_resources-%(version)s.tar.gz', + 'checksums': ['82d5c6cca930697dbbd86c93333bb2c2e72861d4789a11c2662b933e5ad2b528'], + }), + ('jmp', '0.0.4', { + 'checksums': ['5dfeb0fd7c7a9f72a70fff0aab9d0cbfae32a809c02f4037ff3485ceb33e1730'], + }), + ('dm-haiku', '0.0.9', { + 'modulename': 'haiku', + 'source_urls': ['https://github.com/deepmind/dm-haiku/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['d550f07f5891ede30ada5faafde98f549ed1b8ceadb7a601cca3d81db7d82414'], + }), + ('contextlib2', '21.6.0', { + 'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'], + }), + ('ml-collections', '0.1.1', { + 'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ", + 'sources': ['ml_collections-%(version)s.tar.gz'], + 'checksums': ['3fefcc72ec433aa1e5d32307a3e474bbb67f405be814ea52a2166bfc9dbe68cc'], + }), + ('PDBFixer', '1.9', { + 'source_urls': ['https://github.com/openmm/pdbfixer/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['88b9a77e50655f89d0eb2075093773e82c27a4cef842cb7d735c877b20cd39fb'], + }), + ('ihm', '1.3', { + 'checksums': ['09f69809fd81509cc26b60253c55b02ce79fc01fc8f4a068bca2953a7dfd33be'], + }), + ('modelcif', '1.0', { + 'checksums': ['e8375bc502a73dcfab0b7fbdd454d67d393bbb8969981eb52199d77192a3de56'], + }), + (name, version, { + 'sources': [{ + 'filename': SOURCE_TAR_GZ, + 'git_config': { + 'url': 'https://github.com/KosinskiLab', + 'repo_name': 'AlphaPulldown', + 'tag': version, + 'recursive': True, + }, + }], + 'patches': ['AlphaPulldown-2.0.0b2_fix-import-protein_letters_3to1.patch'], + 'checksums': [ + None, + 'd41247cd12f6ef8579adbc893f6c1af5fba051167ee838449974365f4bdccf06', + ], + # remove strict version requirements for Python dependencies + 'preinstallopts': "sed -i 's/[>=]=.*//g' setup.cfg && ", + }), +] + +fix_python_shebang_for = ['bin/*.py'] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/run_multimer_jobs.py', 'bin/rename_colab_search_a3m.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/alphapulldown'], +} + +sanity_check_commands = [ + "run_multimer_jobs.py --help | grep 'A script to perform structure prediction'", + "convert_to_modelcif.py --help | grep 'turn it into a ModelCIF'", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/AmberTools/AmberTools-23.6-foss-2023a.eb b/easybuild/easyconfigs/a/AmberTools/AmberTools-23.6-foss-2023a.eb new file mode 100644 index 000000000000..ca7d8074aab1 --- /dev/null +++ b/easybuild/easyconfigs/a/AmberTools/AmberTools-23.6-foss-2023a.eb @@ -0,0 +1,86 @@ +easyblock = 'EB_Amber' + +name = 'AmberTools' +local_ambertools_ver = 23 +# Patch levels from http://ambermd.org/AmberPatches.php and http://ambermd.org/ATPatches.php +patchlevels = (6, 0) # (AmberTools, Amber) +version = '%s.%s' % (local_ambertools_ver, patchlevels[0]) + +homepage = 'https://ambermd.org/' +description = """AmberTools consists of several independently developed packages that work well by themselves, + and with Amber itself. The suite can also be used to carry out complete molecular dynamics simulations, + with either explicit water or generalized Born solvent models.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'usempi': True} + +# download requires registration +local_download_credentials = '?Name=Easybuild&Institution=Easybuild&City=Internet&State=Other&Country=Belgium' +source_urls = ['https://ambermd.org/cgi-bin/AmberTools%s-get.pl' % local_ambertools_ver] +sources = [{ + 'download_filename': local_download_credentials, + 'filename': 'AmberTools%s.tar.bz2' % local_ambertools_ver, +}] +patches = [ + 'AmberTools-20_cmake-locate-netcdf.patch', + 'AmberTools-20_fix_missing_MPI_LIBRARY_error.patch', + 'AmberTools-20_fix_xblas_missing_make_dependency.patch', + 'AmberTools-21_CMake-FlexiBLAS.patch', + 'AmberTools-21_fix_incorrect_dvout_call.patch', + 'AmberTools-21_fix_more_blas_argument_problems.patch', + 'AmberTools-21_fix_potential_use_before_init.patch', + 'AmberTools-21_fix_rism_argument_mismatch.patch', + 'AmberTools-21_fix_xray_fftpack_arg_mismatch.patch', + 'AmberTools-22_fix_test_missing_cuda_dir.patch', +] +checksums = [ + {'AmberTools23.tar.bz2': 'debb52e6ef2e1b4eaa917a8b4d4934bd2388659c660501a81ea044903bf9ee9d'}, + {'AmberTools-20_cmake-locate-netcdf.patch': '473e07c53b6f641d96d333974a6af2e03413fecef79f879d3fdecf7fecaab4d0'}, + {'AmberTools-20_fix_missing_MPI_LIBRARY_error.patch': + '0b89a0624167bc23876bcdefcb1055f591e38e3bd559a71d5749e342bd311acc'}, + {'AmberTools-20_fix_xblas_missing_make_dependency.patch': + 'ff25e91fdc72347a778c3837b581e174d6a8c71efa5b46e11391b18bca84fd65'}, + {'AmberTools-21_CMake-FlexiBLAS.patch': '9543812c24c4b7842f64f1f8abaf2c92b5c4c0fadcdbd9811e76b81a778f0d36'}, + {'AmberTools-21_fix_incorrect_dvout_call.patch': + '1054d4007f5c79126a41582e1e80514267cf406416ed6c471574cd708b16319b'}, + {'AmberTools-21_fix_more_blas_argument_problems.patch': + 'c6279b57752239184b942d37f760749494ae0eff95236f3368c76ac0d2726a7c'}, + {'AmberTools-21_fix_potential_use_before_init.patch': + '377e645b5bd2c91ebb4d0b6fbca0407a94289e5ddc5b1e7ed0cb0b0724ad2139'}, + {'AmberTools-21_fix_rism_argument_mismatch.patch': + '14255e5739cec39303df570f06820c7532f7395e1b73b1e4104377984e2c9fc1'}, + {'AmberTools-21_fix_xray_fftpack_arg_mismatch.patch': + '99c954e693659efc2a1d121f91510f56408006f0751d91595f45a34b03364e2f'}, + {'AmberTools-22_fix_test_missing_cuda_dir.patch': + 'fb1ab74314d7816169bb9f3f527b78085654aae2825c52cebf50a5760401b737'}, +] + +builddependencies = [ + ('CMake', '3.26.3'), + ('pkgconf', '1.9.5'), + ('Bison', '3.8.2'), + ('flex', '2.6.4'), + ('make', '4.4.1'), +] + +dependencies = [ + ('zlib', '1.2.13'), + ('bzip2', '1.0.8'), + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('Perl', '5.36.1'), + ('Perl-bundle-CPAN', '5.36.1'), + ('Boost', '1.82.0'), + ('libreadline', '8.2'), + ('matplotlib', '3.7.2'), + ('netCDF', '4.9.2'), + ('netCDF-Fortran', '4.6.1'), + ('PnetCDF', '1.12.3'), + ('Tkinter', '%(pyver)s'), + ('X11', '20230603'), + ('mpi4py', '3.1.4'), +] + +runtest = True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/a/Arcade-Learning-Environment/Arcade-Learning-Environment-0.8.1-foss-2023a.eb b/easybuild/easyconfigs/a/Arcade-Learning-Environment/Arcade-Learning-Environment-0.8.1-foss-2023a.eb new file mode 100644 index 000000000000..aca8f2dca72f --- /dev/null +++ b/easybuild/easyconfigs/a/Arcade-Learning-Environment/Arcade-Learning-Environment-0.8.1-foss-2023a.eb @@ -0,0 +1,63 @@ +easyblock = 'CMakeMake' + +name = 'Arcade-Learning-Environment' +version = '0.8.1' + +homepage = 'https://github.com/mgbellemare/Arcade-Learning-Environment' +description = """The Arcade Learning Environment (ALE) is a simple framework that allows +researchers and hobbyists to develop AI agents for Atari 2600 games. It is +built on top of the Atari 2600 emulator Stella and separates the details of +emulation from agent design. This video depicts over 50 games currently +supported in the ALE.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +github_account = 'mgbellemare' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['28960616cd89c18925ced7bbdeec01ab0b2ebd2d8ce5b7c88930e97381b4c3b5'] + +builddependencies = [ + ('CMake', '3.26.3'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('pybind11', '2.11.1'), + ('SciPy-bundle', '2023.07'), + ('SDL2', '2.28.2'), + ('zlib', '1.2.13'), +] + +# main build of C++ libraries +configopts = "-DBUILD_PYTHON_LIB=OFF" + +# install Python bindings and its dependencies +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'download_dep_fail': True, + 'use_pip': True, + 'sanity_pip_check': True, +} +exts_list = [ + ('ale-py', version, { + 'patches': ['%(name)s-%(version)s_fix_version.patch'], + 'preinstallopts': 'ALE_BUILD_VERSION=%(version)s', + 'source_tmpl': 'v%(version)s.tar.gz', + 'checksums': [ + {'v0.8.1.tar.gz': '28960616cd89c18925ced7bbdeec01ab0b2ebd2d8ce5b7c88930e97381b4c3b5'}, + {'ale-py-0.8.1_fix_version.patch': '3ad39a05eb82c3aacf34a6de562ad2d76c254a906963bdef6a810f0b5ce0d22f'}, + ], + }), +] + +sanity_check_paths = { + 'files': ['bin/ale-import-roms', 'lib64/libale.a'], + 'dirs': ['include/ale', 'lib/python%(pyshortver)s/site-packages/'], +} + +sanity_check_commands = ["ale-import-roms --help"] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-16.1.0-gfbf-2023b.eb b/easybuild/easyconfigs/a/Arrow/Arrow-16.1.0-gfbf-2023b.eb new file mode 100644 index 000000000000..87862215507b --- /dev/null +++ b/easybuild/easyconfigs/a/Arrow/Arrow-16.1.0-gfbf-2023b.eb @@ -0,0 +1,86 @@ +easyblock = 'CMakeMake' + +name = 'Arrow' +version = '16.1.0' + +homepage = 'https://arrow.apache.org' +description = """Apache Arrow (incl. PyArrow Python bindings), a cross-language development platform + for in-memory data.""" + +toolchain = {'name': 'gfbf', 'version': '2023b'} + +source_urls = ['https://archive.apache.org/dist/%(namelower)s/%(namelower)s-%(version)s'] +sources = ['apache-arrow-%(version)s.tar.gz'] +checksums = ['c9e60c7e87e59383d21b20dc874b17153729ee153264af6d21654b7dff2c60d7'] + +builddependencies = [ + ('CMake', '3.27.6'), + ('Autotools', '20220317'), + ('flex', '2.6.4'), + ('Bison', '3.8.2'), + ('pkgconf', '2.0.3'), +] + +# Arrow strongly prefers included jemalloc, so not including it as a dependency +dependencies = [ + ('Python', '3.11.5'), + ('SciPy-bundle', '2023.11'), # for numpy + ('Boost', '1.83.0'), + ('lz4', '1.9.4'), + ('zlib', '1.2.13'), + ('bzip2', '1.0.8'), + ('zstd', '1.5.5'), + ('snappy', '1.1.10'), + ('RapidJSON', '1.1.0-20240409'), + ('RE2', '2024-03-01'), + ('utf8proc', '2.9.0'), +] + +start_dir = 'cpp' + +# see https://arrow.apache.org/docs/developers/python.html +configopts = "-DARROW_DATASET=on -DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON " +configopts += "-DCMAKE_INSTALL_LIBDIR=lib -DPython3_ROOT_DIR=$EBROOTPYTHON " +configopts += "-DARROW_WITH_ZLIB=ON -DARROW_WITH_BZ2=ON -DARROW_WITH_ZSTD=ON -DARROW_WITH_LZ4=ON " +configopts += "-DZSTD_ROOT=$EBROOTZSTD " + +# install Python bindings +_pyarrow_preinstall_opts = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && " +_pyarrow_preinstall_opts += "export Arrow_DIR=%(installdir)s && export ArrowDataset_DIR=%(installdir)s && " +_pyarrow_preinstall_opts += "export ArrowAcero_DIR=%(installdir)s && export Parquet_DIR=%(installdir)s && " +_pyarrow_preinstall_opts += "export XDG_CACHE_HOME=$TMPDIR && " +_pyarrow_preinstall_opts += "sed -i 's/numpy==[0-9.]*/numpy/g' pyproject.toml && " +_pyarrow_preinstall_opts += "Python3_ROOT_DIR=$EBROOTPYTHON " +_pyarrow_preinstall_opts += "PYARROW_CMAKE_OPTIONS='-DZSTD_LIB=$EBROOTZSTD/lib/libzstd.%s ' " % SHLIB_EXT +_pyarrow_preinstall_opts += "PYARROW_WITH_DATASET=1 PYARROW_WITH_PARQUET=1 " + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'download_dep_fail': True, + 'use_pip': True, + 'sanity_pip_check': True, +} +exts_list = [ + ('pyarrow', version, { + 'sources': ['apache-arrow-%(version)s.tar.gz'], + 'checksums': ['c9e60c7e87e59383d21b20dc874b17153729ee153264af6d21654b7dff2c60d7'], + 'start_dir': '%(builddir)s/apache-arrow-%(version)s/python', + 'preinstallopts': _pyarrow_preinstall_opts, + }), +] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['lib/libarrow.a', 'lib/libarrow.%s' % SHLIB_EXT, + 'lib/python%%(pyshortver)s/site-packages/pyarrow/libarrow_python.%s' % SHLIB_EXT], + 'dirs': ['include/arrow', 'lib/cmake/Arrow', 'lib/pkgconfig', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "python -c 'import pyarrow'", + "python -c 'import pyarrow.dataset'", + "python -c 'import pyarrow.parquet'", +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/a/Autoconf-archive/Autoconf-archive-2023.02.20-GCCcore-12.2.0.eb b/easybuild/easyconfigs/a/Autoconf-archive/Autoconf-archive-2023.02.20-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..73e0608725bb --- /dev/null +++ b/easybuild/easyconfigs/a/Autoconf-archive/Autoconf-archive-2023.02.20-GCCcore-12.2.0.eb @@ -0,0 +1,53 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: GNU Free Documentation License +# +# Notes:: +## + +easyblock = 'ConfigureMake' + +name = 'Autoconf-archive' +version = '2023.02.20' + +homepage = "https://www.gnu.org/software/autoconf-archive" + +description = """ +The GNU Autoconf Archive is a collection of more than 500 macros for GNU Autoconf +that have been contributed as free software by friendly supporters of the cause from +all over the Internet. Every single one of those macros can be re-used without +imposing any restrictions whatsoever on the licensing of the generated configure script. +In particular, it is possible to use all those macros in configure scripts that +are meant for non-free software. This policy is unusual for a Free Software Foundation +project. The FSF firmly believes that software ought to be free, and software licenses +like the GPL are specifically designed to ensure that derivative work based on free +software must be free as well. In case of Autoconf, however, an exception has been made, +because Autoconf is at such a pivotal position in the software development tool chain +that the benefits from having this tool available as widely as possible outweigh the +disadvantage that some authors may choose to use it, too, for proprietary software. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['71d4048479ae28f1f5794619c3d72df9c01df49b1c628ef85fde37596dc31a33'] + +builddependencies = [ + ('binutils', '2.39'), + ('Autotools', '20220317'), + ('makeinfo', '7.0.3'), +] + +preconfigopts = 'autoreconf -i -f &&' + +sanity_check_paths = { + 'files': [], + 'dirs': ['share/%s' % x for x in + ['aclocal', 'doc', 'info']], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/absl-py/absl-py-2.1.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/a/absl-py/absl-py-2.1.0-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..faadde2a51d5 --- /dev/null +++ b/easybuild/easyconfigs/a/absl-py/absl-py-2.1.0-GCCcore-12.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonBundle' + +name = 'absl-py' +version = '2.1.0' + +homepage = 'https://github.com/abseil/abseil-py' +description = """absl-py is a collection of Python library code for building Python +applications. The code is collected from Google's own Python code base, and has +been extensively tested and used in production.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [('binutils', '2.40')] + +dependencies = [('Python', '3.11.3')] + +use_pip = True + +exts_list = [ + ('absl-py', version, { + 'modulename': 'absl', + 'checksums': ['7820790efbb316739cde8b4e19357243fc3608a152024288513dd968d7d959ff'], + }), +] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/accelerate/accelerate-0.33.0-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/a/accelerate/accelerate-0.33.0-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 000000000000..7f6d595a7c56 --- /dev/null +++ b/easybuild/easyconfigs/a/accelerate/accelerate-0.33.0-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonBundle' + +name = 'accelerate' +version = '0.33.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/huggingface/accelerate' +description = """A simple way to launch, train, and use PyTorch models on almost any device and +distributed configuration, automatic mixed precision (including fp8), +and easy-to-configure FSDP and DeepSpeed support.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('CUDA', '12.1.1', '', SYSTEM), + ('PyTorch-bundle', '2.1.2', versionsuffix), + ('PyYAML', '6.0'), + ('Safetensors', '0.4.3'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('huggingface-hub', '0.24.5', { + 'sources': ['huggingface_hub-%(version)s.tar.gz'], + 'checksums': ['7b45d6744dd53ce9cbf9880957de00e9d10a9ae837f1c9b7255fc8fa4e8264f3'], + }), + (name, version, { + 'checksums': ['11ba481ed6ea09191775df55ce464aeeba67a024bd0261a44b77b30fb439e26a'], + }), +] + +sanity_check_commands = ['accelerate test'] + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/a/adjustText/adjustText-0.7.3-foss-2022b.eb b/easybuild/easyconfigs/a/adjustText/adjustText-0.7.3-foss-2022b.eb new file mode 100644 index 000000000000..4c13c1210479 --- /dev/null +++ b/easybuild/easyconfigs/a/adjustText/adjustText-0.7.3-foss-2022b.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'adjustText' +version = '0.7.3' + +homepage = 'https://github.com/Phlya/adjustText' +description = "A small library for automatically adjustment of text position in matplotlib plots to minimize overlaps." + +toolchain = {'name': 'foss', 'version': '2022b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['b90e275a95b4d980cbbac7967914b8d66477c09bc346a0b3c9e2125bba664b06'] + +dependencies = [ + ('Python', '3.10.8'), + ('matplotlib', '3.7.0'), + ('SciPy-bundle', '2023.02'), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +options = {'modulename': 'adjustText'} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/affogato/affogato-0.3.3-foss-2023a.eb b/easybuild/easyconfigs/a/affogato/affogato-0.3.3-foss-2023a.eb new file mode 100644 index 000000000000..391f9d95eda1 --- /dev/null +++ b/easybuild/easyconfigs/a/affogato/affogato-0.3.3-foss-2023a.eb @@ -0,0 +1,40 @@ +easyblock = 'CMakeMakeCp' + +name = 'affogato' +version = '0.3.3' + +homepage = 'https://github.com/constantinpape/affogato/' +description = """Affinity based segmentation algorithms and tools.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/constantinpape/affogato/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['ad3bb1aca50ce9311d4e88e97e701237bce94faa6e79460f0bc2d2061f1484d2'] + +builddependencies = [('CMake', '3.26.3')] + +dependencies = [ + ('Python', '3.11.3'), + ('Boost', '1.82.0'), + ('SciPy-bundle', '2023.07'), + ('vigra', '1.11.2'), + ('xtensor', '0.24.7'), + ('h5py', '3.9.0'), +] + +configopts = '-DBUILD_PYTHON=ON ' +# Fix path to python executable - it finds v3.6.8 from /usr/bin/ without this fix +configopts += '-DPYTHON_EXECUTABLE="$EBROOTPYTHON/bin/python" ' + +files_to_copy = [(['python/affogato'], 'lib/python%(pyshortver)s/site-packages')] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/affogato'], +} +sanity_check_commands = ["python -c 'import affogato'"] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/a/alsa-lib/alsa-lib-1.2.11-GCCcore-13.2.0.eb b/easybuild/easyconfigs/a/alsa-lib/alsa-lib-1.2.11-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..fd05a43146f7 --- /dev/null +++ b/easybuild/easyconfigs/a/alsa-lib/alsa-lib-1.2.11-GCCcore-13.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'alsa-lib' +version = '1.2.11' + +homepage = 'https://www.alsa-project.org' +description = """The Advanced Linux Sound Architecture (ALSA) provides audio and MIDI functionality + to the Linux operating system.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://www.alsa-project.org/files/pub/lib/'] +sources = [SOURCE_TAR_BZ2] +checksums = ['9f3f2f69b995f9ad37359072fbc69a3a88bfba081fc83e9be30e14662795bb4d'] + +dependencies = [('binutils', '2.40')] + +configopts = ['--disable-shared --enable-static', '--enable-shared'] + +sanity_check_paths = { + 'files': ['bin/aserver', 'include/asoundlib.h', + 'lib64/libatopology.%s' % SHLIB_EXT, 'lib64/libasound.%s' % SHLIB_EXT, 'lib64/libasound.a'], + 'dirs': ['include/alsa', 'lib/pkgconfig', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/a/alsa-lib/alsa-lib-1.2.11-GCCcore-13.3.0.eb b/easybuild/easyconfigs/a/alsa-lib/alsa-lib-1.2.11-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..4333348a7411 --- /dev/null +++ b/easybuild/easyconfigs/a/alsa-lib/alsa-lib-1.2.11-GCCcore-13.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'alsa-lib' +version = '1.2.11' + +homepage = 'https://www.alsa-project.org' +description = """The Advanced Linux Sound Architecture (ALSA) provides audio and MIDI functionality + to the Linux operating system.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://www.alsa-project.org/files/pub/lib/'] +sources = [SOURCE_TAR_BZ2] +checksums = ['9f3f2f69b995f9ad37359072fbc69a3a88bfba081fc83e9be30e14662795bb4d'] + +dependencies = [('binutils', '2.42')] + +configopts = ['--disable-shared --enable-static', '--enable-shared'] + +sanity_check_paths = { + 'files': ['bin/aserver', 'include/asoundlib.h', + 'lib64/libatopology.%s' % SHLIB_EXT, 'lib64/libasound.%s' % SHLIB_EXT, 'lib64/libasound.a'], + 'dirs': ['include/alsa', 'lib/pkgconfig', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/a/archspec/archspec-0.2.4-GCCcore-13.3.0.eb b/easybuild/easyconfigs/a/archspec/archspec-0.2.4-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..5a4f3a288e93 --- /dev/null +++ b/easybuild/easyconfigs/a/archspec/archspec-0.2.4-GCCcore-13.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'archspec' +version = '0.2.4' + +homepage = 'https://github.com/archspec/archspec' +description = "A library for detecting, labeling, and reasoning about microarchitectures" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['eabbae22f315d24cc2ce786a092478ec8e245208c9877fb213c2172a6ecb9302'] + +builddependencies = [ + ('binutils', '2.42'), + ('poetry', '1.8.3'), +] + +dependencies = [('Python', '3.12.3')] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_commands = ["python -c 'from archspec.cpu import host; print(host())'"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/attr/attr-2.5.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/a/attr/attr-2.5.2-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..fcd6d723f166 --- /dev/null +++ b/easybuild/easyconfigs/a/attr/attr-2.5.2-GCCcore-13.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'attr' +version = '2.5.2' + +homepage = 'https://savannah.nongnu.org/projects/attr' + +description = """Commands for Manipulating Filesystem Extended Attributes""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['39bf67452fa41d0948c2197601053f48b3d78a029389734332a6309a680c6c87'] + +builddependencies = [('binutils', '2.42')] + +sanity_check_paths = { + 'files': ['bin/attr', 'bin/getfattr', 'bin/setfattr', + 'include/%(name)s/attributes.h', 'include/%(name)s/error_context.h', + 'include/%(name)s/libattr.h', 'lib/libattr.a', + 'lib/libattr.%s' % SHLIB_EXT], + 'dirs': ['share'], +} + +sanity_check_commands = ["getfattr --help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/BGEN-enkre/3rd-party-removal.patch b/easybuild/easyconfigs/b/BGEN-enkre/3rd-party-removal.patch new file mode 100644 index 000000000000..83f35651997b --- /dev/null +++ b/easybuild/easyconfigs/b/BGEN-enkre/3rd-party-removal.patch @@ -0,0 +1,176 @@ +Removal of sqlite3, boost and zstd from 3-party modules +Author: J. Sassmannshausen +diff --git a/bgen.tgz.orig/3rd_party/wscript b/bgen.tgz/3rd_party/wscript +index 220728a..e69de29 100644 +--- a/bgen.tgz.orig/3rd_party/wscript ++++ b/bgen.tgz/3rd_party/wscript +@@ -1,2 +0,0 @@ +-def build( bld ): +- bld.recurse( [ 'boost_1_55_0', 'sqlite3', 'zstd-1.1.0' ] ) +diff --git a/bgen.tgz.orig/Makefile b/bgen.tgz/Makefile +index a7b0ac8..c62ac16 100644 +--- a/bgen.tgz.orig/Makefile ++++ b/bgen.tgz/Makefile +@@ -1,14 +1,9 @@ + FLAGS = -g -std=c++11 -lz \ + -I genfile/include \ + -I db/include \ +--I 3rd_party/boost_1_55_0 \ +--I 3rd_party/zstd-1.1.0 \ +--I 3rd_party/zstd-1.1.0/lib \ +--I 3rd_party/zstd-1.1.0/lib/common \ +--I 3rd_party/zstd-1.1.0/lib/compress \ +--I 3rd_party/zstd-1.1.0/lib/decompress \ +--I 3rd_party/sqlite3 \ +--I include/3rd_party/sqlite3 \ ++-I ${EBBOST}/include \ ++-I ${EBDEVELZSTD}/include \ ++-I ${EBSQLITE3}/include \ + -D SQLITE_ENABLE_COLUMN_METADATA \ + -D SQLITE_ENABLE_STAT4 \ + -D SQLITE_MAX_EXPR_DEPTH=10000 \ +diff --git a/bgen.tgz.orig/db/include/db/SQLStatement.hpp b/bgen.tgz/db/include/db/SQLStatement.hpp +index e107bd2..fca5957 100644 +--- a/bgen.tgz.orig/db/include/db/SQLStatement.hpp ++++ b/bgen.tgz/db/include/db/SQLStatement.hpp +@@ -12,7 +12,7 @@ + #include + #include + #include +-#include "sqlite3/sqlite3.h" ++#include "sqlite3.h" + #include "db/SQLite3Connection.hpp" + + namespace db { +diff --git a/bgen.tgz.orig/db/include/db/SQLite3Connection.hpp b/bgen.tgz/db/include/db/SQLite3Connection.hpp +index b4bd219..cfbbd3a 100644 +--- a/bgen.tgz.orig/db/include/db/SQLite3Connection.hpp ++++ b/bgen.tgz/db/include/db/SQLite3Connection.hpp +@@ -10,7 +10,7 @@ + #include + #include + #include +-#include "sqlite3/sqlite3.h" ++#include "sqlite3.h" + #include "db/Connection.hpp" + #include "db/Transaction.hpp" + #include "db/Error.hpp" +diff --git a/bgen.tgz.orig/db/include/db/SQLite3Statement.hpp b/bgen.tgz/db/include/db/SQLite3Statement.hpp +index d41a710..76dbfb6 100644 +--- a/bgen.tgz.orig/db/include/db/SQLite3Statement.hpp ++++ b/bgen.tgz/db/include/db/SQLite3Statement.hpp +@@ -11,7 +11,7 @@ + #include + #include + +-#include "sqlite3/sqlite3.h" ++#include "sqlite3.h" + #include "db/SQLite3Connection.hpp" + #include "db/SQLStatement.hpp" + +diff --git a/bgen.tgz.orig/db/src/SQLStatement.cpp b/bgen.tgz/db/src/SQLStatement.cpp +index 60168c6..32576ca 100644 +--- a/bgen.tgz.orig/db/src/SQLStatement.cpp ++++ b/bgen.tgz/db/src/SQLStatement.cpp +@@ -7,7 +7,7 @@ + #include + #include + #include +-#include "sqlite3/sqlite3.h" ++#include "sqlite3.h" + #include "db/SQLStatement.hpp" + + namespace db { +diff --git a/bgen.tgz.orig/db/src/SQLite3Statement.cpp b/bgen.tgz/db/src/SQLite3Statement.cpp +index 84e0658..03b3d5e 100644 +--- a/bgen.tgz.orig/db/src/SQLite3Statement.cpp ++++ b/bgen.tgz/db/src/SQLite3Statement.cpp +@@ -9,7 +9,7 @@ + #include + #include + #include +-#include "sqlite3/sqlite3.h" ++#include "sqlite3.h" + #include "db/SQLite3Connection.hpp" + #include "db/SQLStatement.hpp" + #include "db/SQLite3Statement.hpp" +diff --git a/bgen.tgz.orig/db/wscript b/bgen.tgz/db/wscript +index 7b0b617..a3861f0 100644 +--- a/bgen.tgz.orig/db/wscript ++++ b/bgen.tgz/db/wscript +@@ -5,8 +5,8 @@ def build( bld ): + bld.stlib( + target = 'db', + source = sources, +- includes='./include', ++ includes='${EBSQLITE}/include ./include', + cxxflags = [], + use = 'boost sqlite3', +- export_includes = './include' ++ export_includes = '${EBSQLITE}/include ./include' + ) +diff --git a/bgen.tgz.orig/wscript b/bgen.tgz/wscript +index a6385d9..47b9fc9 100644 +--- a/bgen.tgz.orig/wscript ++++ b/bgen.tgz/wscript +@@ -63,7 +63,7 @@ def build( bld ): + use = 'zlib zstd sqlite3 db', + export_includes = 'genfile/include' + ) +- bld.recurse( [ '3rd_party', 'appcontext', 'genfile', 'db', 'apps', 'example', 'test', 'R' ] ) ++ bld.recurse( [ 'appcontext', 'genfile', 'db', 'apps', 'example', 'test', 'R' ] ) + # Copy files into rbgen package directory + for source in bgen_sources: + bld( rule = 'cp ${SRC} ${TGT}', source = source, target = 'R/rbgen/src/bgen/' + os.path.basename( source.abspath() ), always = True ) +@@ -126,12 +126,12 @@ class ReleaseBuilder: + shutil.copytree( 'R/package/', rbgen_dir ) + os.makedirs( os.path.join( rbgen_dir, "src", "include" )) + os.makedirs( os.path.join( rbgen_dir, "src", "include", "boost" )) +- os.makedirs( os.path.join( rbgen_dir, "src", "include", "zstd-1.1.0" )) ++ os.makedirs( os.path.join( rbgen_dir, "src", "include", "zstd" )) + os.makedirs( os.path.join( rbgen_dir, "src", "db" )) + os.makedirs( os.path.join( rbgen_dir, "src", "bgen" )) + os.makedirs( os.path.join( rbgen_dir, "src", "boost" )) + os.makedirs( os.path.join( rbgen_dir, "src", "sqlite3" )) +- os.makedirs( os.path.join( rbgen_dir, "src", "zstd-1.1.0" )) ++ os.makedirs( os.path.join( rbgen_dir, "src", "zstd" )) + + # Copy source files in + from glob import glob +@@ -141,11 +141,11 @@ class ReleaseBuilder: + for filename in glob( 'db/src/*.cpp' ): + shutil.copy( filename, os.path.join( rbgen_dir, "src", "db", os.path.basename( filename ) ) ) + +- for filename in glob( '3rd_party/sqlite3/sqlite3/sqlite3.c' ): +- shutil.copy( filename, os.path.join( rbgen_dir, "src", "sqlite3", os.path.basename( filename ) ) ) ++# for filename in glob( '3rd_party/sqlite3/sqlite3/sqlite3.c' ): ++# shutil.copy( filename, os.path.join( rbgen_dir, "src", "sqlite3", os.path.basename( filename ) ) ) + +- for filename in glob( '3rd_party/zstd-1.1.0/lib/common/*.c' ) + glob( '3rd_party/zstd-1.1.0/lib/compress/*.c' ) + glob( '3rd_party/zstd-1.1.0/lib/decompress/*.c' ): +- shutil.copy( filename, os.path.join( rbgen_dir, "src", "zstd-1.1.0", os.path.basename( filename ) ) ) ++# for filename in glob( '3rd_party/zstd-1.1.0/lib/common/*.c' ) + glob( '3rd_party/zstd-1.1.0/lib/compress/*.c' ) + glob( '3rd_party/zstd-1.1.0/lib/decompress/*.c' ): ++# shutil.copy( filename, os.path.join( rbgen_dir, "src", "zstd-1.1.0", os.path.basename( filename ) ) ) + + boostGlobs = [ + 'libs/system/src/*.cpp', +@@ -160,14 +160,14 @@ class ReleaseBuilder: + 'libs/chrono/src/*.cpp', + ] + +- for pattern in boostGlobs: +- for filename in glob( '3rd_party/boost_1_55_0/%s' % pattern ): +- shutil.copy( filename, os.path.join( rbgen_dir, "src", "boost", os.path.basename( filename ) ) ) ++# for pattern in boostGlobs: ++# for filename in glob( '3rd_party/boost_1_55_0/%s' % pattern ): ++# shutil.copy( filename, os.path.join( rbgen_dir, "src", "boost", os.path.basename( filename ) ) ) + + include_paths = [ +- "3rd_party/boost_1_55_0/boost/", +- "3rd_party/zstd-1.1.0/", +- "3rd_party/sqlite3/", ++ "${EBBOOST}", ++ "${EBROOTZSTD}", ++ "${EBROOTSQLITE}", + "genfile/include/genfile", + "db/include/db" + ] diff --git a/easybuild/easyconfigs/b/BGEN-enkre/BGEN-enkre-1.1.7-GCC-11.2.0.eb b/easybuild/easyconfigs/b/BGEN-enkre/BGEN-enkre-1.1.7-GCC-11.2.0.eb new file mode 100644 index 000000000000..b0c0bc1be02a --- /dev/null +++ b/easybuild/easyconfigs/b/BGEN-enkre/BGEN-enkre-1.1.7-GCC-11.2.0.eb @@ -0,0 +1,74 @@ +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen +# we recommend to use --download-timeout=1000 when fetching the files + +easyblock = 'CmdCp' + +name = 'BGEN-enkre' +version = '1.1.7' + +homepage = 'https://enkre.net/cgi-bin/code/bgen/dir?ci=trunk' +description = """This repository contains a reference implementation +of the BGEN format, written in C++. The library can be used as the +basis for BGEN support in other software, or as a reference for +developers writing their own implementations of the BGEN format. +Please cite: +Band, G. and Marchini, J., "BGEN: a binary file format for imputed genotype and haplotype data", +bioArxiv 308296; doi: https://doi.org/10.1101/308296 +""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://code.enkre.net/bgen/tarball/v%(version)s/'] +sources = ['v%(version)s.tgz'] +patches = [ + '3rd-party-removal.patch', + 'BGEN-enkre_streampos.patch', +] + +checksums = [ + ('6476b077af6c8e98e85fd7e09f58cb3fdf143ff91850c984248fd4dc2d74a8c3', # v1.1.7.tgz + 'b922ac22c1c0e365d0de6054f6ce2ad911bc81db5bcd8ca915bae750f57bd0a7'), + '0269b91d21976f38a9cf9bf7811375d16bf35be587d903ab1d846b2001b7d767', # 3rd-party-removal.patch + '61c05ae5f7363d5b7b6015f0a015b93f149dbda4b23b9f48f9517a6ce93d5869', # BGEN-enkre_streampos.patch +] + +builddependencies = [ + ('binutils', '2.37'), + ('Python', '3.9.6'), +] + +dependencies = [ + ('SQLite', '3.36'), + ('zstd', '1.5.0'), + ('Boost', '1.55.0'), +] + +cmds_map = [ + ('.*', "./waf configure && echo LIB_zstd = [\\'zstd\\'] >> build/c4che/_cache.py &&" + " echo LIB_sqlite3 = [\\'sqlite3\\'] >> build/c4che/_cache.py &&" + "echo LIB_boost = [\\'boost_system\\', \\'boost_filesystem\\', \\'boost_thread\\', \\'boost_timer\\'] " + " >> build/c4che/_cache.py && ./waf"), +] + +files_to_copy = [ + (['build/apps/edit-bgen', 'build/apps/bgenix', 'build/apps/cat-bgen'], 'bin'), + (['build/db/libdb.a', 'build/libbgen.a'], 'lib'), + (['genfile/include/*', 'db/include/*'], 'include'), +] + +postinstallcmds = ['./build/test/unit/test_bgen'] + +sanity_check_paths = { + 'files': ['bin/edit-bgen', 'bin/bgenix', 'bin/cat-bgen'], + 'dirs': ['bin', 'lib', 'include'], +} + +sanity_check_commands = [ + 'bgenix -help', + 'cat-bgen -help', + 'edit-bgen -help', +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BGEN-enkre/BGEN-enkre_streampos.patch b/easybuild/easyconfigs/b/BGEN-enkre/BGEN-enkre_streampos.patch new file mode 100644 index 000000000000..5d7c0e471c36 --- /dev/null +++ b/easybuild/easyconfigs/b/BGEN-enkre/BGEN-enkre_streampos.patch @@ -0,0 +1,12 @@ +diff -ruN 1.1.7.tgz.orig/src/View.cpp 1.1.7.tgz/src/View.cpp +--- 1.1.7.tgz.orig/src/View.cpp 2020-06-29 01:19:43.000000000 -0700 ++++ 1.1.7.tgz/src/View.cpp 2022-06-06 18:05:10.650577000 -0700 +@@ -177,7 +177,7 @@ + + // get file size + { +- std::ios::streampos origin = m_stream->tellg() ; ++ std::streampos origin = m_stream->tellg() ; + m_stream->seekg( 0, std::ios::end ) ; + m_file_metadata.size = m_stream->tellg() - origin ; + m_stream->seekg( 0, std::ios::beg ) ; diff --git a/easybuild/easyconfigs/b/BRiAl/BRiAl-1.2.12-GCC-13.2.0.eb b/easybuild/easyconfigs/b/BRiAl/BRiAl-1.2.12-GCC-13.2.0.eb new file mode 100644 index 000000000000..50bbeea16eef --- /dev/null +++ b/easybuild/easyconfigs/b/BRiAl/BRiAl-1.2.12-GCC-13.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'BRiAl' +version = '1.2.12' + +homepage = 'https://github.com/BRiAl/BRiAl' +description = """BRiAl is the legacy version of PolyBoRi maintained by sagemath developers.""" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +source_urls = ['https://github.com/BRiAl/BRiAl/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['ca009e3722dd3f0a60d15501caed1413146c80abced57423e32ae0116f407494'] + +dependencies = [ + ('Boost', '1.83.0'), + ('m4ri', '20200125'), + ('CUDD', '3.0.0'), +] + +configopts = "--with-boost=$EBROOTBOOST " + +runtest = 'check' + +sanity_check_paths = { + 'files': ['include/polybori.h'] + + ['lib/libbrial.%s' % e for e in ['a', SHLIB_EXT]], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/b/Bandage/Bandage-0.9.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/b/Bandage/Bandage-0.9.0-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..acdc093c96d2 --- /dev/null +++ b/easybuild/easyconfigs/b/Bandage/Bandage-0.9.0-GCCcore-12.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'MakeCp' + +name = 'Bandage' +version = '0.9.0' + +homepage = 'http://rrwick.github.io/Bandage' +description = "Bandage is a program for visualising de novo assembly graphs" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/rrwick/Bandage/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['04de8152d8bf5e5aa32b41a63cf1c23e1fee7b67ccd9f1407db8dc2824ca4e30'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [('Qt5', '5.15.10')] + +prebuildopts = "qmake Bandage.pro && " + +files_to_copy = [(['Bandage'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/Bandage'], + 'dirs': [], +} + +sanity_check_commands = ["Bandage --help && ldd $(which Bandage)"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BayesOpt/BayesOpt-0.9-GCC-12.3.0.eb b/easybuild/easyconfigs/b/BayesOpt/BayesOpt-0.9-GCC-12.3.0.eb new file mode 100644 index 000000000000..2e20ceba9042 --- /dev/null +++ b/easybuild/easyconfigs/b/BayesOpt/BayesOpt-0.9-GCC-12.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'CMakeMake' + +name = 'BayesOpt' +version = '0.9' + +homepage = 'https://rmcantin.github.io/bayesopt' +description = """BayesOpt is an efficient implementation of the Bayesian optimization methodology for +nonlinear-optimization, experimental design, stochastic bandits and hyperparameter tunning""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/rmcantin/bayesopt/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['f4e60cfac380eccd2d1adc805b752b5bd22a1d8a27dc6aeb630c403adc04f28c'] + +builddependencies = [ + ('CMake', '3.26.3'), +] + +dependencies = [ + ('Boost', '1.82.0'), + ('NLopt', '2.7.1'), +] + +# don't build included version of NLopt (use provided dependency) +configopts = "-DNLOPT_BUILD=OFF" + +sanity_check_paths = { + 'files': ['lib/libbayesopt.a'], + 'dirs': ['include/bayesopt'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/b/BayesTraits/BayesTraits-4.1.2-Linux.eb b/easybuild/easyconfigs/b/BayesTraits/BayesTraits-4.1.2-Linux.eb new file mode 100644 index 000000000000..541dedf129e3 --- /dev/null +++ b/easybuild/easyconfigs/b/BayesTraits/BayesTraits-4.1.2-Linux.eb @@ -0,0 +1,40 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +# Updated by +# Author: Alex Salois +# Research Cyberinfrastructure +# Montana State University + +easyblock = "Tarball" + +name = 'BayesTraits' +version = '4.1.2' +versionsuffix = '-Linux' + +homepage = 'https://www.evolution.reading.ac.uk/SoftwareMain.html' +description = """ BayesTraits is a computer package for performing analyses of trait + evolution among groups of species for which a phylogeny or sample of phylogenies is + available. This new package incoporates our earlier and separate programes Multistate, + Discrete and Continuous. BayesTraits can be applied to the analysis of traits that adopt + a finite number of discrete states, or to the analysis of continuously varying traits. + Hypotheses can be tested about models of evolution, about ancestral states and about + correlations among pairs of traits. """ + +toolchain = SYSTEM + +source_urls = ['https://www.evolution.reading.ac.uk/BayesTraitsV%(version)s/Files/'] +sources = ['BayesTraitsV%(version)s%(versionsuffix)s.tar.gz'] +checksums = ['d5251c2b256405fc63c55caf8371b267530a3c4ebd11cbfd3ebd4013c9d49db0'] + +sanity_check_paths = { + 'files': ['BayesTraitsV4', 'Artiodactyl.trees', 'Bird.trees', 'Mammal.trees', + 'Marsupials.trees', 'NortheastBantu.trees', 'Primates.trees'], + 'dirs': [], +} + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BeautifulSoup/BeautifulSoup-4.12.3-GCCcore-13.3.0.eb b/easybuild/easyconfigs/b/BeautifulSoup/BeautifulSoup-4.12.3-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..95cb6cf32282 --- /dev/null +++ b/easybuild/easyconfigs/b/BeautifulSoup/BeautifulSoup-4.12.3-GCCcore-13.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonBundle' + +name = 'BeautifulSoup' +version = '4.12.3' + +homepage = 'https://www.crummy.com/software/BeautifulSoup' +description = "Beautiful Soup is a Python library designed for quick turnaround projects like screen-scraping." + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('binutils', '2.42'), + ('hatchling', '1.24.2'), +] + +dependencies = [ + ('Python', '3.12.3'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('soupsieve', '2.5', { + 'checksums': ['5663d5a7b3bfaeee0bc4372e7fc48f9cff4940b3eec54a6451cc5299f1097690'], + }), + (name, version, { + 'modulename': 'bs4', + 'source_tmpl': 'beautifulsoup4-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/b/beautifulsoup4'], + 'checksums': ['74e3d1928edc070d21748185c46e3fb33490f22f52a3addee9aee0f4f7781051'], + }), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-12.2.0.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-12.2.0.eb index 8caddd5df221..e8e52099b07f 100644 --- a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-12.2.0.eb @@ -5,7 +5,7 @@ # Fred Hutchinson Cancer Research Center # Thomas Eylenbosch - Gluo NV -easyblock = 'PerlModule' +easyblock = 'Bundle' name = 'BioPerl' version = '1.7.8' diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-12.3.0.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-12.3.0.eb index b47216124f89..4212570abb1d 100644 --- a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-12.3.0.eb @@ -5,7 +5,7 @@ # Fred Hutchinson Cancer Research Center # Thomas Eylenbosch - Gluo NV -easyblock = 'PerlModule' +easyblock = 'Bundle' name = 'BioPerl' version = '1.7.8' diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-13.3.0.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..ba3029a6a413 --- /dev/null +++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-13.3.0.eb @@ -0,0 +1,58 @@ +# easybuild easyconfig +# +# John Dey jfdey@fredhutch.org +# +# Fred Hutchinson Cancer Research Center +# Thomas Eylenbosch - Gluo NV + +easyblock = 'Bundle' + +name = 'BioPerl' +version = '1.7.8' + +homepage = 'https://bioperl.org/' +description = """Bioperl is the product of a community effort to produce Perl code which is useful in biology. + Examples include Sequence objects, Alignment objects and database searching objects.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [('binutils', '2.42')] + +dependencies = [ + ('Perl', '5.38.2'), + ('Perl-bundle-CPAN', '5.38.2'), + ('XML-LibXML', '2.0210'), + ('DB_File', '1.859'), +] + +exts_defaultclass = 'PerlModule' +exts_filter = ("perldoc -lm %(ext_name)s ", "") + +exts_list = [ + ('XML::Writer', '0.900', { + 'source_tmpl': 'XML-Writer-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JO/JOSEPHW'], + 'checksums': ['73c8f5bd3ecf2b350f4adae6d6676d52e08ecc2d7df4a9f089fa68360d400d1f'], + }), + (name, version, { + 'source_tmpl': '%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/'], + 'checksums': ['c490a3be7715ea6e4305efd9710e5edab82dabc55fd786b6505b550a30d71738'], + }), + ('Bio::Procedural', '1.7.4', { + 'source_tmpl': 'Bio-Procedural-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/'], + 'checksums': ['d2bd9cfbb091eee2d80ed6cf812ac3813b1c8a1aaca20671037f5f225d31d1da'], + }), +] + +modextrapaths = { + 'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/', +} + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin', 'lib/perl5/site_perl/%(perlver)s/Bio'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.84-foss-2023b.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.84-foss-2023b.eb new file mode 100644 index 000000000000..03c23f41186c --- /dev/null +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.84-foss-2023b.eb @@ -0,0 +1,46 @@ +# Updated from previous easyconfig +# Author: Robert Mijakovic +# Update: Pavel Tománek (INUITS) + +easyblock = 'PythonPackage' + +name = 'Biopython' +version = '1.84' + +homepage = 'https://www.biopython.org' +description = """Biopython is a set of freely available tools for biological + computation written in Python by an international team of developers. It is + a distributed collaborative effort to develop Python libraries and + applications which address the needs of current and future work in + bioinformatics. """ + +toolchain = {'name': 'foss', 'version': '2023b'} + +source_urls = ['https://biopython.org/DIST'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['60fbe6f996e8a6866a42698c17e552127d99a9aab3259d6249fbaabd0e0cc7b4'] + +dependencies = [ + ('Python', '3.11.5'), + ('SciPy-bundle', '2023.11'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +# Run only tests that don't require internet connection +runtest = 'python setup.py test --offline' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/Bio', + 'lib/python%(pyshortver)s/site-packages/BioSQL'] +} + +# extra check to ensure numpy dependency is available +sanity_check_commands = ["python -c 'import Bio.MarkovModel'"] + +options = {'modulename': 'Bio'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-14.2.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-14.2.0.eb new file mode 100644 index 000000000000..427ebbbe2b7c --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-14.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.8.2' + +homepage = 'https://www.gnu.org/software/bison' +description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar + into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" + +toolchain = {'name': 'GCCcore', 'version': '14.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['06c9e13bdf7eb24d4ceb6b59205a4f67c2c7e7213119644430fe82fbd14a0abb'] + +builddependencies = [ + ('M4', '1.4.19'), + # use same binutils version that was used when building GCCcore toolchain + ('binutils', '2.42', '', SYSTEM), +] + + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bison', 'yacc']] + [('lib/liby.a', 'lib64/liby.a')], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/b/Boost.MPI/Boost.MPI-1.83.0-gompi-2023b.eb b/easybuild/easyconfigs/b/Boost.MPI/Boost.MPI-1.83.0-gompi-2023b.eb new file mode 100644 index 000000000000..2378bf71abb5 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost.MPI/Boost.MPI-1.83.0-gompi-2023b.eb @@ -0,0 +1,29 @@ +easyblock = 'EB_Boost' + +name = 'Boost.MPI' +version = '1.83.0' + +homepage = 'https://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'gompi', 'version': '2023b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://boostorg.jfrog.io/artifactory/main/release/%(version)s/source/'] +sources = ['boost_%s.tar.gz' % '_'.join(version.split('.'))] +checksums = ['c0685b68dd44cc46574cce86c4e17c0f611b15e195be9848dfd0769a0a207628'] + +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.13'), + ('XZ', '5.4.4'), + ('zstd', '1.5.5'), + ('ICU', '74.1'), +] + +configopts = '--without-libraries=python' + +boost_mpi = True +tagged_layout = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.82.0-GCC-12.3.0.eb b/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.82.0-GCC-12.3.0.eb new file mode 100644 index 000000000000..ee38c6983cde --- /dev/null +++ b/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.82.0-GCC-12.3.0.eb @@ -0,0 +1,24 @@ +easyblock = 'EB_Boost' + +name = 'Boost.Python' +version = '1.82.0' + +homepage = 'https://boostorg.github.io/python' +description = """Boost.Python is a C++ library which enables seamless interoperability between C++ + and the Python programming language.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://boostorg.jfrog.io/artifactory/main/release/%(version)s/source/'] +sources = ['boost_1_82_0.tar.gz'] +checksums = ['66a469b6e608a51f8347236f4912e27dc5c60c60d7d53ae9bfe4683316c6f04c'] + +dependencies = [ + ('Boost', version), + ('Python', '3.11.3'), +] + +only_python_bindings = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.55.0-GCC-11.2.0.eb b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-GCC-11.2.0.eb new file mode 100644 index 000000000000..1814c8648e9c --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-GCC-11.2.0.eb @@ -0,0 +1,21 @@ +name = 'Boost' +version = '1.55.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] +checksums = ['19c4305cd6669f2216260258802a7abc73c1624758294b2cad209d45cc13a767'] + +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.11'), +] + +configopts = '--without-libraries=python' + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Bowtie/Bowtie-1.3.1-GCC-12.2.0.eb b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.3.1-GCC-12.2.0.eb new file mode 100644 index 000000000000..202b84a29536 --- /dev/null +++ b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.3.1-GCC-12.2.0.eb @@ -0,0 +1,30 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: Artistic v2.0 +# +# Notes:: +## + +name = 'Bowtie' +version = '1.3.1' + +homepage = 'http://bowtie-bio.sourceforge.net/index.shtml' +description = """Bowtie is an ultrafast, memory-efficient short read aligner. + It aligns short DNA sequences (reads) to the human genome.""" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} +toolchainopts = {'pic': True, 'cstd': 'gnu++98'} + +source_urls = ['https://sourceforge.net/projects/bowtie-bio/files/bowtie/%(version)s/'] +sources = ['%(namelower)s-%(version)s-src.zip'] +checksums = ['e23517aa53846ef828172be911750cd05748522117efcbbe5a36f3241fb40761'] + +dependencies = [ + ('tbb', '2021.9.0'), + ('zlib', '1.2.12'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bowtie/Bowtie-1.3.1-GCC-12.3.0.eb b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.3.1-GCC-12.3.0.eb new file mode 100644 index 000000000000..9617ba2e3435 --- /dev/null +++ b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.3.1-GCC-12.3.0.eb @@ -0,0 +1,30 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: Artistic v2.0 +# +# Notes:: +## + +name = 'Bowtie' +version = '1.3.1' + +homepage = 'http://bowtie-bio.sourceforge.net/index.shtml' +description = """Bowtie is an ultrafast, memory-efficient short read aligner. + It aligns short DNA sequences (reads) to the human genome.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} +toolchainopts = {'pic': True, 'cstd': 'gnu++98'} + +source_urls = ['https://sourceforge.net/projects/bowtie-bio/files/bowtie/%(version)s/'] +sources = ['%(namelower)s-%(version)s-src.zip'] +checksums = ['e23517aa53846ef828172be911750cd05748522117efcbbe5a36f3241fb40761'] + +dependencies = [ + ('tbb', '2021.11.0'), + ('zlib', '1.2.13'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb index 22f38cbf5f96..9e505b4df5e4 100644 --- a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb @@ -21,7 +21,6 @@ builddependencies = [ dependencies = [ ('Brotli', '1.0.9'), - ('Highway', '0.12.2'), ] # skip use of third_party directory, since we provide Brotli via a proper dependency diff --git a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.3.0.eb index 301194a32a4d..0661abf0609f 100644 --- a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.3.0.eb @@ -22,7 +22,6 @@ builddependencies = [ dependencies = [ ('Brotli', '1.0.9'), - ('Highway', '0.12.2'), ] # skip use of third_party directory, since we provide Brotli via a proper dependency diff --git a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-11.3.0.eb index 7522f1025e33..57bba400bde0 100644 --- a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-11.3.0.eb @@ -22,7 +22,6 @@ builddependencies = [ dependencies = [ ('Brotli', '1.0.9'), - ('Highway', '1.0.3'), ] # skip use of third_party directory, since we provide Brotli via a proper dependency diff --git a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-12.2.0.eb index cc914cae6cd4..df29a7bda206 100644 --- a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-12.2.0.eb @@ -22,7 +22,6 @@ builddependencies = [ dependencies = [ ('Brotli', '1.0.9'), - ('Highway', '1.0.3'), ] # skip use of third_party directory, since we provide Brotli via a proper dependency diff --git a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-12.3.0.eb index 22917f651e9a..42e15bb43561 100644 --- a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-12.3.0.eb @@ -22,7 +22,6 @@ builddependencies = [ dependencies = [ ('Brotli', '1.0.9'), - ('Highway', '1.0.4'), ] # skip use of third_party directory, since we provide Brotli via a proper dependency diff --git a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..6481ba231cd3 --- /dev/null +++ b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-13.2.0.eb @@ -0,0 +1,53 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +# update: Thomas Hoffmann (EMBL) +easyblock = 'CMakeMake' + +name = 'Brunsli' +version = '0.1' + +homepage = 'https://github.com/google/brunsli/' +description = """Brunsli is a lossless JPEG repacking library.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://github.com/google/brunsli/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['62762dc740f9fcc9706449c078f12c2a366416486d2882be50a9f201f99ac0bc'] + +builddependencies = [ + ('CMake', '3.27.6'), + ('binutils', '2.40'), +] + +dependencies = [ + ('Brotli', '1.1.0'), +] + +# skip use of third_party directory, since we provide Brotli via a proper dependency +preconfigopts = "sed -i 's/add_subdirectory(third_party)//g' ../brunsli-%(version)s/CMakeLists.txt && " +preconfigopts += "sed -i 's/\\(brotli...\\)-static/\\1/g' ../brunsli-%(version)s/brunsli.cmake && " + +configopts = '-DCMAKE_CXX_FLAGS="$CXXFLAGS -lbrotlienc -lbrotlidec -lbrotlicommon" ' + +# make sure that libraries end up in /lib (not lib64) +configopts += "-DCMAKE_INSTALL_LIBDIR=lib " + +buildopts = "BROTLI_DIR=$EBROOTBROTLI BROTLI_INCLUDE=$EBROOTBROTLI/include" + +# also install dbrunsli binary and missing libraries +postinstallcmds = [ + "mkdir %(installdir)s/bin", + "cp dbrunsli %(installdir)s/bin/", + "cp libbrunsli*.a %(installdir)s/lib/", + "cp libbrunsli*.%s %%(installdir)s/lib/" % SHLIB_EXT, +] + +sanity_check_paths = { + 'files': ['bin/dbrunsli'], + 'dirs': ['include/brunsli', 'lib'], +} + +sanity_check_commands = ['dbrunsli 2>&1 | grep Usage'] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..3afc7fffd752 --- /dev/null +++ b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-13.3.0.eb @@ -0,0 +1,53 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +# update: Thomas Hoffmann (EMBL) +easyblock = 'CMakeMake' + +name = 'Brunsli' +version = '0.1' + +homepage = 'https://github.com/google/brunsli/' +description = """Brunsli is a lossless JPEG repacking library.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/google/brunsli/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['62762dc740f9fcc9706449c078f12c2a366416486d2882be50a9f201f99ac0bc'] + +builddependencies = [ + ('CMake', '3.29.3'), + ('binutils', '2.42'), +] + +dependencies = [ + ('Brotli', '1.1.0'), +] + +# skip use of third_party directory, since we provide Brotli via a proper dependency +preconfigopts = "sed -i 's/add_subdirectory(third_party)//g' ../brunsli-%(version)s/CMakeLists.txt && " +preconfigopts += "sed -i 's/\\(brotli...\\)-static/\\1/g' ../brunsli-%(version)s/brunsli.cmake && " + +configopts = '-DCMAKE_CXX_FLAGS="$CXXFLAGS -lbrotlienc -lbrotlidec -lbrotlicommon" ' + +# make sure that libraries end up in /lib (not lib64) +configopts += "-DCMAKE_INSTALL_LIBDIR=lib " + +buildopts = "BROTLI_DIR=$EBROOTBROTLI BROTLI_INCLUDE=$EBROOTBROTLI/include" + +# also install dbrunsli binary and missing libraries +postinstallcmds = [ + "mkdir %(installdir)s/bin", + "cp dbrunsli %(installdir)s/bin/", + "cp libbrunsli*.a %(installdir)s/lib/", + "cp libbrunsli*.%s %%(installdir)s/lib/" % SHLIB_EXT, +] + +sanity_check_paths = { + 'files': ['bin/dbrunsli'], + 'dirs': ['include/brunsli', 'lib'], +} + +sanity_check_commands = ['dbrunsli 2>&1 | grep Usage'] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/b/bayesian-optimization/bayesian-optimization-1.5.1-foss-2023a.eb b/easybuild/easyconfigs/b/bayesian-optimization/bayesian-optimization-1.5.1-foss-2023a.eb new file mode 100644 index 000000000000..8215f2c822a4 --- /dev/null +++ b/easybuild/easyconfigs/b/bayesian-optimization/bayesian-optimization-1.5.1-foss-2023a.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonBundle' + +name = 'bayesian-optimization' +version = '1.5.1' + +homepage = 'https://bayesian-optimization.github.io/BayesianOptimization/index.html' +description = "Pure Python implementation of bayesian global optimization with gaussian processes." + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('scikit-learn', '1.3.1'), + ('SciPy-bundle', '2023.07'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('colorama', '0.4.6', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['4f1d9991f5acc0ca119f9d443620b77f9d6b33703e51011c16baf57afb285fc6'], + }), + ('bayesian_optimization', version, { + 'source_tmpl': SOURCE_PY3_WHL, + 'modulename': 'bayes_opt', + 'checksums': ['098946c933d6039073b7ccb0c9f1b4c73ac6e39350043b02e5243b08583c4c5c'], + }), +] + +sanity_check_commands = ["python -c 'from bayes_opt import BayesianOptimization'"] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/b/bcl-convert/bcl-convert-4.2.7-2el7.x86_64.eb b/easybuild/easyconfigs/b/bcl-convert/bcl-convert-4.2.7-2el7.x86_64.eb new file mode 100644 index 000000000000..dfed34de9423 --- /dev/null +++ b/easybuild/easyconfigs/b/bcl-convert/bcl-convert-4.2.7-2el7.x86_64.eb @@ -0,0 +1,26 @@ +easyblock = 'Rpm' + +name = 'bcl-convert' +version = '4.2.7-2' +versionsuffix = 'el7.x86_64' + +homepage = 'https://support.illumina.com/sequencing/sequencing_software/bcl-convert.html' +description = """The Illumina BCL Convert v4.0 is a standalone local software app that converts the + Binary Base Call (BCL) files produced by Illumina sequencing systems to FASTQ files.""" + +toolchain = SYSTEM + +builddependencies = [('rpmrebuild', '2.18')] + +source_urls = ['https://webdata.illumina.com/downloads/software/bcl-convert/'] +sources = ['bcl-convert-%(version)s.%(versionsuffix)s.rpm'] +checksums = ['ea508d763dc27d30d1a34f6a38d8da31ea67797d7b4971e8c10677bc48539565'] + +sanity_check_paths = { + 'files': ['usr/bin/bcl-convert'], + 'dirs': [], +} + +sanity_check_commands = ["bcl-convert --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-4.0.1-GCC-12.3.0-CUDA-12.1.1.eb b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-4.0.1-GCC-12.3.0-CUDA-12.1.1.eb new file mode 100644 index 000000000000..2c2bbf6705ba --- /dev/null +++ b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-4.0.1-GCC-12.3.0-CUDA-12.1.1.eb @@ -0,0 +1,35 @@ +easyblock = 'CMakeMake' + +name = 'beagle-lib' +version = '4.0.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/beagle-dev/beagle-lib' +description = """beagle-lib is a high-performance library that can perform the core calculations at the heart of most + Bayesian and Maximum Likelihood phylogenetics packages.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/beagle-dev/beagle-lib/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['9d258cd9bedd86d7c28b91587acd1132f4e01d4f095c657ad4dc93bd83d4f120'] + +dependencies = [ + ('Java', '11', '', SYSTEM), + ('CUDA', '12.1.1', '', SYSTEM), +] + +builddependencies = [ + ('CMake', '3.26.3'), + ('pkgconf', '1.9.5'), +] + +configopts = '-DBUILD_CUDA=ON ' + +sanity_check_paths = { + 'files': ["include/libhmsbeagle-1/libhmsbeagle/%s" % x for x in ["beagle.h", "platform.h"]] + + ["lib/libhmsbeagle%s.%s" % (x, SHLIB_EXT) for x in ["-cpu", "-cpu-sse", "-jni", ""]], + 'dirs': [] +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.42-GCCcore-14.2.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.42-GCCcore-14.2.0.eb new file mode 100644 index 000000000000..94b762d78033 --- /dev/null +++ b/easybuild/easyconfigs/b/binutils/binutils-2.42-GCCcore-14.2.0.eb @@ -0,0 +1,31 @@ +name = 'binutils' +version = '2.42' + +homepage = 'https://directory.fsf.org/project/binutils/' +description = "binutils: GNU binary utilities" + +toolchain = {'name': 'GCCcore', 'version': '14.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['5d2a6c1d49686a557869caae08b6c2e83699775efd27505e01b2f4db1a024ffc'] + +builddependencies = [ + ('flex', '2.6.4'), + ('Bison', '3.8.2'), + # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils + ('binutils', version, '', SYSTEM) +] + +dependencies = [ + # zlib is a runtime dep to avoid that it gets embedded in libbfd.so, + # see https://github.com/easybuilders/easybuild-easyblocks/issues/1350 + ('zlib', '1.3.1'), +] + +# avoid build failure when makeinfo command is not available +# see https://sourceware.org/bugzilla/show_bug.cgi?id=15345 +buildopts = 'MAKEINFO=true' +installopts = buildopts + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/biom-format/biom-format-2.1.16-foss-2023b.eb b/easybuild/easyconfigs/b/biom-format/biom-format-2.1.16-foss-2023b.eb new file mode 100644 index 000000000000..91d9cecbd994 --- /dev/null +++ b/easybuild/easyconfigs/b/biom-format/biom-format-2.1.16-foss-2023b.eb @@ -0,0 +1,49 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: Revised BSD +# +# Notes:: updated by Kenneth Hoste (HPC-UGent) for foss/2021b +## +# Updated: Petr Král (INUITS) +# Updated: Lara Peeters (Ghent University) + +easyblock = 'PythonPackage' + +name = 'biom-format' +version = '2.1.16' + +homepage = 'https://biom-format.org' +description = """ +The BIOM file format (canonically pronounced biome) is designed to be + a general-use format for representing biological sample by observation + contingency tables. BIOM is a recognized standard for the Earth Microbiome + Project and is a Genomics Standards Consortium supported project. +""" + +toolchain = {'name': 'foss', 'version': '2023b'} +toolchainopts = {'usempi': True} + +sources = [SOURCE_TAR_GZ] +checksums = ['47f88d57a94ecaa4d06f3578ca394e78db6d12e46ab0886634743181e67dcfc9'] + +dependencies = [ + ('Python', '3.11.5'), + ('SciPy-bundle', '2023.11'), + ('h5py', '3.11.0'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +sanity_check_paths = { + 'files': ['bin/biom'], + 'dirs': ['lib'], +} + +options = {'modulename': 'biom'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/bitsandbytes/bitsandbytes-0.43.3-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/b/bitsandbytes/bitsandbytes-0.43.3-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 000000000000..8127a86c558a --- /dev/null +++ b/easybuild/easyconfigs/b/bitsandbytes/bitsandbytes-0.43.3-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,49 @@ +easyblock = 'CMakeMake' + +name = 'bitsandbytes' +version = '0.43.3' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://huggingface.co/docs/bitsandbytes/main/en/index' +description = "bitsandbytes enables accessible large language models via k-bit quantization for PyTorch." +github_account = 'bitsandbytes-foundation' + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['7a468bc977da19c176cc578954bfd7a3c64182f387a6849e9f0a38d5cba1b4df'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('pkgconf', '1.9.5'), +] + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('Python', '3.11.3'), + ('PyTorch', '2.1.2', versionsuffix), + ('SciPy-bundle', '2023.07'), +] + +configopts = '-DCOMPUTE_BACKEND=cuda' +skipsteps = ['install'] + +postinstallcmds = [ + 'pip install --prefix=%(installdir)s --no-deps --ignore-installed --no-index --no-build-isolation %(start_dir)s', +] + +sanity_check_paths = { + 'files': ['lib/python%%(pyshortver)s/site-packages/bitsandbytes/libbitsandbytes_cuda121.%s' % SHLIB_EXT], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "python -c 'import bitsandbytes'", +] + +modextrapaths = { + 'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/b/bitsandbytes/bitsandbytes-0.43.3-foss-2023a.eb b/easybuild/easyconfigs/b/bitsandbytes/bitsandbytes-0.43.3-foss-2023a.eb new file mode 100644 index 000000000000..8b360bb263b5 --- /dev/null +++ b/easybuild/easyconfigs/b/bitsandbytes/bitsandbytes-0.43.3-foss-2023a.eb @@ -0,0 +1,46 @@ +easyblock = 'CMakeMake' + +name = 'bitsandbytes' +version = '0.43.3' + +homepage = 'https://huggingface.co/docs/bitsandbytes/main/en/index' +description = "bitsandbytes enables accessible large language models via k-bit quantization for PyTorch." +github_account = 'bitsandbytes-foundation' + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['7a468bc977da19c176cc578954bfd7a3c64182f387a6849e9f0a38d5cba1b4df'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('pkgconf', '1.9.5'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('PyTorch', '2.1.2'), + ('SciPy-bundle', '2023.07'), +] + +skipsteps = ['install'] + +postinstallcmds = [ + 'pip install --prefix=%(installdir)s --no-deps --ignore-installed --no-index --no-build-isolation %(start_dir)s', +] + +sanity_check_paths = { + 'files': ['lib/python%%(pyshortver)s/site-packages/bitsandbytes/libbitsandbytes_cpu.%s' % SHLIB_EXT], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "python -c 'import bitsandbytes'", +] + +modextrapaths = { + 'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/b/bliss/bliss-0.77-GCC-13.2.0.eb b/easybuild/easyconfigs/b/bliss/bliss-0.77-GCC-13.2.0.eb new file mode 100644 index 000000000000..ec9a99bc3067 --- /dev/null +++ b/easybuild/easyconfigs/b/bliss/bliss-0.77-GCC-13.2.0.eb @@ -0,0 +1,41 @@ +easyblock = 'CMakeMake' + +name = 'bliss' +version = '0.77' + +homepage = 'https://users.aalto.fi/~tjunttil/bliss/' +description = """Bliss is an open-source tool for computing canonical labelings and automorphism groups of graphs.""" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +source_urls = ['https://users.aalto.fi/~tjunttil/bliss/downloads/'] +sources = [SOURCE_ZIP] +patches = ['bliss-0.77_install_fix.patch'] +checksums = [ + {'bliss-0.77.zip': 'acc8b98034f30fad24c897f365abd866c13d9f1bb207e398d0caf136875972a4'}, + {'bliss-0.77_install_fix.patch': '1550b6c7f8208f56093c0b6bf0d2e3df42afab81cd69eb70303515c9923e9513'}, +] + +builddependencies = [ + ('CMake', '3.27.6'), +] + +dependencies = [ + ('GMP', '6.3.0'), +] + +configopts = "-DUSE_GMP=ON " + +sanity_check_paths = { + 'files': [ + 'bin/bliss', + 'lib/libbliss.%s' % SHLIB_EXT, + ], + 'dirs': [ + 'include/%(name)s', + ], +} + +sanity_check_commands = ["bliss -help"] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/b/bliss/bliss-0.77_install_fix.patch b/easybuild/easyconfigs/b/bliss/bliss-0.77_install_fix.patch new file mode 100644 index 000000000000..faea2ad4dafa --- /dev/null +++ b/easybuild/easyconfigs/b/bliss/bliss-0.77_install_fix.patch @@ -0,0 +1,33 @@ +Adds install commands to CMakeLists.txt +Source: https://gitlab.archlinux.org/archlinux/packaging/packages/bliss/-/blob/0.77-3/make-install.patch +diff -u CMakeLists.txt.orig CMakeLists.txt +--- CMakeLists.txt.orig 2021-02-18 11:59:34.000000000 +0100 ++++ CMakeLists.txt 2024-08-15 15:04:21.293765655 +0200 +@@ -62,3 +62,27 @@ + target_link_libraries(bliss-executable ${GMP_LIBRARIES}) + endif(USE_GMP) + set_target_properties(bliss-executable PROPERTIES OUTPUT_NAME bliss) ++ ++include(GNUInstallDirs) ++ ++set( ++ BLISS_HEADERS ++ src/bliss_C.h ++ src/uintseqhash.hh ++ src/abstractgraph.hh ++ src/stats.hh ++ src/digraph.hh ++ src/defs.hh ++ src/heap.hh ++ src/graph.hh ++ src/partition.hh ++ src/kqueue.hh ++ src/utils.hh ++ src/orbit.hh ++ src/timer.hh ++ src/bignum.hh ++) ++ ++install(TARGETS bliss-executable RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}) ++install(TARGETS bliss LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}) ++install(FILES ${BLISS_HEADERS} DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/bliss) diff --git a/easybuild/easyconfigs/b/byacc/byacc-2.0.20240109-GCCcore-13.3.0.eb b/easybuild/easyconfigs/b/byacc/byacc-2.0.20240109-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..fa57e4306e6f --- /dev/null +++ b/easybuild/easyconfigs/b/byacc/byacc-2.0.20240109-GCCcore-13.3.0.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'byacc' +version = '2.0.20240109' + +homepage = 'http://invisible-island.net/byacc/byacc.html' +description = """Berkeley Yacc (byacc) is generally conceded to be the best yacc variant available. + In contrast to bison, it is written to avoid dependencies upon a particular compiler. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://invisible-island.net/archives/byacc/'] +sources = ['byacc-%s.tgz' % version.split('.')[2]] +checksums = ['f2897779017189f1a94757705ef6f6e15dc9208ef079eea7f28abec577e08446'] + +builddependencies = [('binutils', '2.42')] + +sanity_check_paths = { + 'files': ["bin/yacc"], + 'dirs': [] +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCC-12.3.0.eb b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCC-12.3.0.eb new file mode 100644 index 000000000000..bd59609605cb --- /dev/null +++ b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCC-12.3.0.eb @@ -0,0 +1,41 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# changed toolchain and Perl version +# Updated by: Thomas Eylenbosch(Gluo N.V.), Pavel Tománek (Inuits) + +easyblock = 'MakeCp' + +name = 'CD-HIT' +version = '4.8.1' + +homepage = 'http://weizhongli-lab.org/cd-hit/' +description = """ CD-HIT is a very widely used program for clustering and + comparing protein or nucleotide sequences.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/weizhongli/cdhit/releases/download/V%(version)s/'] +sources = ['%(namelower)s-v%(version)s-2019-0228.tar.gz'] +checksums = ['26172dba3040d1ae5c73ff0ac6c3be8c8e60cc49fc7379e434cdf9cb1e7415de'] + +dependencies = [ + ('Perl', '5.36.1'), + ('zlib', '1.2.13'), +] + +buildopts = ' CC="$CXX" CCFLAGS="$CPPFLAGS $CXXFLAGS"' + +local_list_of_executables = ['cd-hit', 'cd-hit-est', 'cd-hit-2d', 'cd-hit-est-2d', 'cd-hit-div', 'cd-hit-454'] + +files_to_copy = [(local_list_of_executables, 'bin'), (['*.pl'], 'bin'), 'README', 'doc', 'license.txt'] + +fix_perl_shebang_for = ['bin/*.pl'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_list_of_executables], + 'dirs': [], +} + +sanity_check_commands = ["cd-hit -h | grep 'CD-HIT version %(version)s'"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/CDO/CDO-2.3.0-iimpi-2022a.eb b/easybuild/easyconfigs/c/CDO/CDO-2.3.0-iimpi-2022a.eb new file mode 100644 index 000000000000..58cf406d1642 --- /dev/null +++ b/easybuild/easyconfigs/c/CDO/CDO-2.3.0-iimpi-2022a.eb @@ -0,0 +1,58 @@ +# updated to version 2.0.6, based on the previous 2.0.5 version +# J. Sassmannshausen (Imperial College London, UK) +# Alex Domingo (Vrije Universiteit Brussel, BE) +# Maxim Masterov (SURF, NL) + +easyblock = 'ConfigureMake' + +name = 'CDO' +version = '2.3.0' + +homepage = 'https://code.zmaw.de/projects/cdo' +description = """CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.""" + +toolchain = {'name': 'iimpi', 'version': '2022a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://code.mpimet.mpg.de/attachments/download/29019/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['10c878227baf718a6917837527d4426c2d0022cfac4457c65155b9c57f091f6b'] + +builddependencies = [ + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('cURL', '7.83.0'), + ('ecCodes', '2.27.0'), + ('FFTW', '3.3.10'), + ('HDF5', '1.12.2'), + ('libxml2', '2.9.13'), + ('netCDF', '4.9.0'), + ('PROJ', '9.0.0'), + ('Szip', '2.1.1'), + ('UDUNITS', '2.2.28'), + ('util-linux', '2.38'), +] + +# Build libcdi +configopts = "--enable-cdi-lib " + +# Use dependencies from EasyBuild +configopts += "--with-curl=$EBROOTCURL --with-eccodes=$EBROOTECCODES --with-fftw3 --with-hdf5=$EBROOTHDF5 " +configopts += "--with-netcdf=$EBROOTNETCDF --with-proj=$EBROOTPROJ --with-szlib=$EBROOTSZIP " +configopts += "--with-udunits2=$EBROOTUDUNITS --with-util-linux-uuid=$EBROOTUTILMINLINUX " + +# Make sure that right Fortran compiler is used, also on non-x86_64 architectures +configopts += 'CPPFLAGS="$CPPFLAGS -DgFortran" ' + +buildopts = "V=1" + +sanity_check_paths = { + 'files': ['bin/cdo', 'lib/libcdi.a', 'lib/libcdi.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +sanity_check_commands = ["cdo --version 2>&1 | grep 'CDI library version : %(version)s'"] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/c/CESM-deps/CESM-deps-2-foss-2023a.eb b/easybuild/easyconfigs/c/CESM-deps/CESM-deps-2-foss-2023a.eb new file mode 100644 index 000000000000..1144c2b34cc1 --- /dev/null +++ b/easybuild/easyconfigs/c/CESM-deps/CESM-deps-2-foss-2023a.eb @@ -0,0 +1,51 @@ +easyblock = 'Bundle' + +name = 'CESM-deps' +version = '2' + +homepage = 'https://www.cesm.ucar.edu/models/cesm2/' +description = """CESM is a fully-coupled, community, global climate model that +provides state-of-the-art computer simulations of the Earth's past, present, +and future climate states.""" + +# The following environment is suitable for CESM >= 2.2.2 and CTSM >= 5.2.0 +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('CMake', '3.26.3'), + ('Python', '3.11.3'), + ('lxml', '4.9.2'), + ('Perl', '5.36.1'), + ('XML-LibXML', '2.0209'), + ('ESMF', '8.6.0'), + ('netCDF', '4.9.2'), + ('netCDF-Fortran', '4.6.1'), + ('netCDF-C++4', '4.3.1'), + ('PnetCDF', '1.12.3'), + ('git', '2.41.0', '-nodocs'), + ('git-lfs', '3.5.1', '', SYSTEM), +] + +components = [ + # install extra configuration tools and files for VSC clusters + ('cesm-config', '1.7.0', { + 'easyblock': 'Tarball', + 'source_urls': ['https://github.com/vub-hpc/%(name)s/archive'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'checksums': ['c5aeb50595ca4d342a5024d593c2549acf16e72dadc5f39d9a7915d3dc8f3c13'], + 'start_dir': '%(name)s-%(version)s', + }), +] + +sanity_check_paths = { + 'files': ['bin/update-cesm-machines', 'scripts/case.pbs', 'scripts/case.slurm'], + 'dirs': ['machines', 'irods'], +} + +usage = """Environment to build and run CESM v2 simulations + 1. Download a release of CESM v2: `git clone -b release-cesm2.2.2 https://github.com/ESCOMP/cesm.git cesm-2.2.2` + 2. Add external programs for CESM: `cd cesm-2.2.2; ./manage_externals/checkout_externals` + 3. Update config files: `update-cesm-machines cime/config/cesm/machines/ $EBROOTCESMMINDEPS/machines/` + 4. Create case: `cd cime/scripts && ./create_newcase --machine ...`""" + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-4.4.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-4.4.1-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..eaa1b0866aca --- /dev/null +++ b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-4.4.1-GCCcore-13.3.0.eb @@ -0,0 +1,43 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'ConfigureMake' + +name = 'CFITSIO' +version = '4.4.1' + +homepage = 'https://heasarc.gsfc.nasa.gov/fitsio/' +description = """CFITSIO is a library of C and Fortran subroutines for reading and writing data files in +FITS (Flexible Image Transport System) data format.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c/'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['%(name)s-3.48_install_test_data.patch'] +checksums = [ + {'cfitsio-4.4.1.tar.gz': '66a1dc3f21800f9eeabd9eac577b91fcdd9aabba678fbba3b8527319110d1d25'}, + {'CFITSIO-3.48_install_test_data.patch': 'dbf16f857f133468fc1e6a793c6e89fca66d54796593e03606f2722a2a980c0c'}, +] + +builddependencies = [ + ('binutils', '2.42'), +] +# curl for HTTPs support +dependencies = [ + ('cURL', '8.7.1'), +] + +# make would create just static libcfitsio.a. +# Let's create dynamic lib and testprog too. +buildopts = "&& make shared && make testprog" + + +sanity_check_paths = { + 'files': ['lib/libcfitsio.a', 'lib/libcfitsio.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +sanity_check_commands = ['cd %(installdir)s/share && testprog'] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-5.6.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/c/CGAL/CGAL-5.6.1-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..01aa21c63113 --- /dev/null +++ b/easybuild/easyconfigs/c/CGAL/CGAL-5.6.1-GCCcore-13.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'CMakeMake' +name = 'CGAL' +version = '5.6.1' + +homepage = 'https://www.cgal.org/' +description = """The goal of the CGAL Open Source Project is to provide easy access to efficient + and reliable geometric algorithms in the form of a C++ library.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'strict': True} + +source_urls = ['https://github.com/CGAL/cgal/releases/download/v%(version)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['cdb15e7ee31e0663589d3107a79988a37b7b1719df3d24f2058545d1bcdd5837'] + +builddependencies = [ + ('CMake', '3.29.3'), + ('binutils', '2.42'), +] + +sanity_check_paths = { + 'files': ['include/CGAL/Simple_cartesian.h'], + 'dirs': ['include/CGAL', 'lib/cmake/CGAL'], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/c/CLANS/CLANS-2.0.8-foss-2023a.eb b/easybuild/easyconfigs/c/CLANS/CLANS-2.0.8-foss-2023a.eb new file mode 100644 index 000000000000..e1ce2f2a9e1b --- /dev/null +++ b/easybuild/easyconfigs/c/CLANS/CLANS-2.0.8-foss-2023a.eb @@ -0,0 +1,38 @@ +easyblock = "PythonBundle" + +name = 'CLANS' +version = '2.0.8' + +homepage = 'https://github.com/inbalpaz/CLANS' +description = """ +CLANS 2.0 is a Python-based program for clustering sequences in the 2D or 3D space, based on +their sequence similarities. CLANS visualizes the dynamic clustering process and enables the +user to interactively control it and explore the cluster map in various ways. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('numba', '0.58.1'), + ('VisPy', '0.12.2'), + ('Biopython', '1.83'), + ('Pillow', '10.0.0'), + ('PyQt5', '5.15.10'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'source_urls': ['https://github.com/inbalpaz/CLANS/archive/refs/tags/'], + 'sources': ['%(version)s.tar.gz'], + 'checksums': ['7b856ec3b13c420dbe30169e8cdd7d6899acb79042ca66920eafd05adf4d2815'], + }), +] + +sanity_check_commands = ['python -m clans -h'] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/c/CORSIKA/CORSIKA-77550-foss-2023a.eb b/easybuild/easyconfigs/c/CORSIKA/CORSIKA-77550-foss-2023a.eb new file mode 100644 index 000000000000..c6f619d9d750 --- /dev/null +++ b/easybuild/easyconfigs/c/CORSIKA/CORSIKA-77550-foss-2023a.eb @@ -0,0 +1,49 @@ +easyblock = "ConfigureMake" + +name = 'CORSIKA' +version = '77550' + +homepage = "https://www.iap.kit.edu/corsika" +description = """CORSIKA (COsmic Ray SImulations for KAscade) is a program for detailed +simulation of extensive air showers initiated by high energy cosmic ray +particles. Protons, light nuclei up to iron, photons, and many other particles +may be treated as primaries.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'usempi': True} + +download_instructions = "Sources have to be requested to the developers" +sources = [SOURCELOWER_TAR_GZ] +patches = ['%(name)s-%(version)s_fix_include.patch'] +checksums = [ + {'corsika-77550.tar.gz': 'fed74c144e22deb5a7c1d2dc1f04f0100eb2732cb48665a3da49ce471a3775ee'}, + {'CORSIKA-77550_fix_include.patch': 'e858fc4c1fa33d31d050b2fca50e130c23b2d3e4b81b851af34dc3f39e9c709e'}, +] + +dependencies = [ + ("ROOT", "6.30.06"), +] + +# custom coconut script does not recognize -j +parallel = False + +# execute ./coconut manually with your own options and extract configure command from top of config.log +_mpi_opts = "--enable-PARALLEL --with-mpirunner-lib=src/parallel --enable-PARALLELIB " +configopts = "CORDETECTOR=HORIZONTAL CORTIMELIB=TIMEAUTO CORHEMODEL=QGSJETII CORLEMODEL=URQMD " +configopts += "--enable-UPWARD --enable-SLANT --enable-THIN --enable-COREAS " +configopts += _mpi_opts + +build_cmd = "./coconut" +buildopts = "--batch " + _mpi_opts + +install_cmd = ' && '.join([ + 'mkdir -p %(installdir)s/bin', + 'cp %(builddir)s/%(namelower)s-%(version)s/run/* %(installdir)s/bin/', +]) + +sanity_check_paths = { + 'files': ['bin/mpi_corsika77550Linux_QGSII_urqmd_thin_coreas_parallel_runner'], + 'dirs': [], +} + +moduleclass = "phys" diff --git a/easybuild/easyconfigs/c/CORSIKA/CORSIKA-77550_fix_include.patch b/easybuild/easyconfigs/c/CORSIKA/CORSIKA-77550_fix_include.patch new file mode 100644 index 000000000000..e7bc3863fae5 --- /dev/null +++ b/easybuild/easyconfigs/c/CORSIKA/CORSIKA-77550_fix_include.patch @@ -0,0 +1,22 @@ +Move include out of function to avoid error: +/usr/include/sys/stat.h:453:1: error: nested function ‘stat’ declared ‘extern’ +Author: Samuel Moors (Vrije Universiteit Brussel) +diff -Nur corsika-77550.orig/src/parallel/mpi_runner.c corsika-77550/src/parallel/mpi_runner.c +--- corsika-77550.orig/src/parallel/mpi_runner.c 2024-04-18 18:30:39.000000000 +0200 ++++ corsika-77550/src/parallel/mpi_runner.c 2024-08-09 16:15:39.969688000 +0200 +@@ -99,6 +99,7 @@ + #include + #include + #include "config.h" ++#include + + /////////////////////initializing parameters/////////////////// + //the number of data type block in the MPI message +@@ -1023,7 +1024,6 @@ + strcpy(str2, strtmp); + } + strcpy(statdir,str2); +- #include + struct stat sb; + if (stat(statdir, &sb) == 0 && S_ISDIR(sb.st_mode)) + { diff --git a/easybuild/easyconfigs/c/COSTA/COSTA-2.2.2-foss-2023a.eb b/easybuild/easyconfigs/c/COSTA/COSTA-2.2.2-foss-2023a.eb new file mode 100644 index 000000000000..0f347ce481e3 --- /dev/null +++ b/easybuild/easyconfigs/c/COSTA/COSTA-2.2.2-foss-2023a.eb @@ -0,0 +1,27 @@ +easyblock = 'CMakeMake' + +name = 'COSTA' +version = '2.2.2' + +homepage = 'https://github.com/eth-cscs/COSTA' +description = """OSTA is a communication-optimal, highly-optimised algorithm for data redistribution +accross multiple processors, using MPI and OpenMP and offering the possibility +to transpose and scale some or all data.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/eth-cscs/COSTA/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['e87bc37aad14ac0c5922237be5d5390145c9ac6aef0350ed17d86cb2d994e67c'] + +builddependencies = [ + ('CMake', '3.26.3'), +] + +sanity_check_paths = { + 'files': ['lib/libcosta.a'], + 'dirs': ['include/costa'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-2023.1-foss-2023a.eb b/easybuild/easyconfigs/c/CP2K/CP2K-2023.1-foss-2023a.eb index d16e202463a5..d9ace4b896b7 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-2023.1-foss-2023a.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-2023.1-foss-2023a.eb @@ -25,11 +25,16 @@ builddependencies = [ dependencies = [ ('Libint', '2.7.2', '-lmax-6-cp2k'), ('libxc', '6.2.2'), - ('libxsmm', '1.17'), ('libvori', '220621'), ('FFTW', '3.3.10'), ('PLUMED', '2.9.0'), ] +if ARCH == 'x86_64': + # LIBXSMM is not supported supported on ARM with GCC 12.2.0 and 12.3.0 + # see https://www.cp2k.org/dev:compiler_support + dependencies += [ + ('libxsmm', '1.17'), + ] type = 'psmp' diff --git a/easybuild/easyconfigs/c/CSBDeep/CSBDeep-0.7.4-foss-2023a.eb b/easybuild/easyconfigs/c/CSBDeep/CSBDeep-0.7.4-foss-2023a.eb new file mode 100644 index 000000000000..3b3b0f376502 --- /dev/null +++ b/easybuild/easyconfigs/c/CSBDeep/CSBDeep-0.7.4-foss-2023a.eb @@ -0,0 +1,37 @@ +# This easyconfig was created by the BEAR Software team at the University of Birmingham. +# Update: Petr Král (INUITS) +easyblock = 'PythonBundle' + +name = 'CSBDeep' +version = '0.7.4' + +homepage = "https://csbdeep.bioimagecomputing.com/" +description = """CSBDeep is a toolbox for Content-aware Image Restoration (CARE).""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('TensorFlow', '2.13.0'), + ('matplotlib', '3.7.2'), + ('tqdm', '4.66.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('tifffile', '2024.6.18', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['67299c0445fc47463bbc71f3cb4676da2ab0242b0c6c6542a0680801b4b97d8a'], + }), + ('%(namelower)s', version, { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['155d61827439373dc9c2a730a1ef621f7e373fea16599d583e0a70f1e48bd6db'], + }), +] + +sanity_check_commands = ['care_predict'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.3-GCC-10.3.0-CUDA-11.3.1.eb b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.3-GCC-10.3.0-CUDA-11.3.1.eb index b71d2bfad4d6..ad7b6aba80b6 100644 --- a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.3-GCC-10.3.0-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.3-GCC-10.3.0-CUDA-11.3.1.eb @@ -11,7 +11,11 @@ toolchain = {'name': 'GCC', 'version': '10.3.0'} source_urls = ['https://github.com/NVIDIA/cuda-samples/archive/'] sources = ['v%(version)s.tar.gz'] -checksums = ['2bee5f7c89347259aaab75aa6df6e10375059bdbbaf04cc7936f5db7d54fa3ac'] +patches = ['cuda-samples-11.3_multiple-sms.patch'] +checksums = [ + {'v11.3.tar.gz': '2bee5f7c89347259aaab75aa6df6e10375059bdbbaf04cc7936f5db7d54fa3ac'}, + {'cuda-samples-11.3_multiple-sms.patch': 'b31613f4160456f0d0abf82999c7fb7eee781f0efadc8b9bbb5a02ef0f37e21d'}, +] dependencies = [ ('CUDA', '11.3.1', '', SYSTEM), @@ -32,7 +36,7 @@ local_filters += "Samples/simpleVulkan/Makefile " local_filters += "Samples/simpleVulkanMMAP/Makefile " local_filters += "Samples/streamOrderedAllocationIPC/Makefile " local_filters += "Samples/vulkanImageCUDA/Makefile" -buildopts = "HOST_COMPILER=g++ FILTER_OUT='%s'" % local_filters +buildopts = "HOST_COMPILER=g++ SMS='%%(cuda_cc_space_sep_no_period)s' FILTER_OUT='%s'" % local_filters files_to_copy = [ (['bin/%s/linux/release/*' % ARCH], 'bin'), diff --git a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.6-GCC-11.3.0-CUDA-11.7.0.eb b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.6-GCC-11.3.0-CUDA-11.7.0.eb index d4240930bd18..ea78eae4061f 100644 --- a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.6-GCC-11.3.0-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.6-GCC-11.3.0-CUDA-11.7.0.eb @@ -11,7 +11,11 @@ toolchain = {'name': 'GCC', 'version': '11.3.0'} source_urls = ['https://github.com/NVIDIA/cuda-samples/archive/'] sources = ['v%(version)s.tar.gz'] -checksums = ['75b858bcf9e534eaa0f129c418e661b83872d743de218df8a5278cc429f9ea98'] +patches = ['cuda-samples-11.6_multiple-sms.patch'] +checksums = [ + {'v11.6.tar.gz': '75b858bcf9e534eaa0f129c418e661b83872d743de218df8a5278cc429f9ea98'}, + {'cuda-samples-11.6_multiple-sms.patch': '8849e4882d797d155d6ebb71377fa1409205361776ade8da699452a4ecb94a0a'}, +] dependencies = [ ('CUDA', '11.7.0', '', SYSTEM), @@ -33,7 +37,7 @@ local_filters += "Samples/simpleVulkanMMAP/Makefile " local_filters += "Samples/streamOrderedAllocationIPC/Makefile " local_filters += "Samples/vulkanImageCUDA/Makefile" -buildopts = "HOST_COMPILER=g++ FILTER_OUT='%s'" % local_filters +buildopts = "HOST_COMPILER=g++ SMS='%%(cuda_cc_space_sep_no_period)s' FILTER_OUT='%s'" % local_filters files_to_copy = [ (['bin/%s/linux/release/*' % ARCH], 'bin'), diff --git a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.8-GCC-11.3.0-CUDA-11.7.0.eb b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.8-GCC-11.3.0-CUDA-11.7.0.eb new file mode 100644 index 000000000000..be16c76f3be6 --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.8-GCC-11.3.0-CUDA-11.7.0.eb @@ -0,0 +1,59 @@ +easyblock = 'MakeCp' + +name = 'CUDA-Samples' +version = '11.8' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/NVIDIA/cuda-samples' +description = "Samples for CUDA Developers which demonstrates features in CUDA Toolkit" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://github.com/NVIDIA/cuda-samples/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['cuda-samples-11.6_multiple-sms.patch'] +checksums = [ + {'v11.8.tar.gz': '1bc02c0ca42a323f3c7a05b5682eae703681a91e95b135bfe81f848b2d6a2c51'}, + {'cuda-samples-11.6_multiple-sms.patch': '8849e4882d797d155d6ebb71377fa1409205361776ade8da699452a4ecb94a0a'}, +] + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), +] + +# Get rid of pre-built Windows DLLs and only build deviceQuery for now. +prebuildopts = "rm -r bin/win64 && " + +# Filter out samples that require extensive dependencies. +local_filters = "Samples/2_Concepts_and_Techniques/EGLStream_CUDA_Interop/Makefile " +local_filters += "Samples/4_CUDA_Libraries/boxFilterNPP/Makefile " +local_filters += "Samples/4_CUDA_Libraries/cannyEdgeDetectorNPP/Makefile " +local_filters += "Samples/4_CUDA_Libraries/cudaNvSci/Makefile " +local_filters += "Samples/4_CUDA_Libraries/cudaNvSciNvMedia/Makefile " +local_filters += "Samples/5_Domain_Specific/simpleGL/Makefile " +local_filters += "Samples/3_CUDA_Features/warpAggregatedAtomicsCG/Makefile " +local_filters += "Samples/5_Domain_Specific/simpleVulkan/Makefile " +local_filters += "Samples/5_Domain_Specific/simpleVulkanMMAP/Makefile " +local_filters += "Samples/2_Concepts_and_Techniques/streamOrderedAllocationIPC/Makefile " +local_filters += "Samples/5_Domain_Specific/vulkanImageCUDA/Makefile " +local_filters += "Samples/6_Performance/LargeKernelParameter/Makefile " + +buildopts = "HOST_COMPILER=g++ SMS='%%(cuda_cc_space_sep_no_period)s' FILTER_OUT='%s'" % local_filters + +files_to_copy = [ + (['bin/%s/linux/release/*' % ARCH], 'bin'), + 'LICENSE', +] + +local_binaries = ['deviceQuery', 'matrixMul', 'bandwidthTest', 'cudaOpenMP'] + +# Only paths are used for sanity checks. +# Commands may fail due to missing compatibility libraries that might be needed +# to be able to use this specific CUDA version in combination with the available +# NVIDIA drivers. +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_binaries], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.1-GCC-12.3.0-CUDA-12.1.1.eb b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.1-GCC-12.3.0-CUDA-12.1.1.eb index 3e7ffe79da06..5a886ca74d4c 100644 --- a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.1-GCC-12.3.0-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.1-GCC-12.3.0-CUDA-12.1.1.eb @@ -11,7 +11,11 @@ toolchain = {'name': 'GCC', 'version': '12.3.0'} source_urls = ['https://github.com/NVIDIA/cuda-samples/archive/'] sources = ['v%(version)s.tar.gz'] -checksums = ['f758160645b366d79c2638d8dfd389f01029b8d179ab0c11726b9ef58aecebd9'] +patches = ['cuda-samples-11.6_multiple-sms.patch'] +checksums = [ + {'v12.1.tar.gz': 'f758160645b366d79c2638d8dfd389f01029b8d179ab0c11726b9ef58aecebd9'}, + {'cuda-samples-11.6_multiple-sms.patch': '8849e4882d797d155d6ebb71377fa1409205361776ade8da699452a4ecb94a0a'}, +] dependencies = [ ('CUDA', '12.1.1', '', SYSTEM), @@ -58,7 +62,7 @@ if ARCH == 'aarch64': local_filters += "Samples/3_CUDA_Features/cdpQuadtree/Makefile " local_filters += "Samples/3_CUDA_Features/cdpAdvancedQuicksort/Makefile " -buildopts = "HOST_COMPILER=g++ FILTER_OUT='%s'" % local_filters +buildopts = "HOST_COMPILER=g++ SMS='%%(cuda_cc_space_sep_no_period)s' FILTER_OUT='%s'" % local_filters # Remove libraries in the bin dir after a successful 'make' buildopts += " && rm bin/*/linux/release/lib*.so.*" diff --git a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.2-GCC-11.3.0-CUDA-12.2.0.eb b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.2-GCC-11.3.0-CUDA-12.2.0.eb new file mode 100644 index 000000000000..89e1c6fc87b3 --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.2-GCC-11.3.0-CUDA-12.2.0.eb @@ -0,0 +1,63 @@ +easyblock = 'MakeCp' + +name = 'CUDA-Samples' +version = '12.2' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/NVIDIA/cuda-samples' +description = "Samples for CUDA Developers which demonstrates features in CUDA Toolkit" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://github.com/NVIDIA/cuda-samples/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['cuda-samples-11.6_multiple-sms.patch'] +checksums = [ + {'v12.2.tar.gz': '1823cfe28e97a9230107aa72b231f78952c0f178b71a920f036d360518480bdc'}, + {'cuda-samples-11.6_multiple-sms.patch': '8849e4882d797d155d6ebb71377fa1409205361776ade8da699452a4ecb94a0a'}, +] + +builddependencies = [ + ('CMake', '3.24.3'), +] + +dependencies = [ + ('CUDA', '12.2.0', '', SYSTEM), +] + +# Get rid of pre-built Windows DLLs and only build deviceQuery for now. +prebuildopts = "rm -r bin/win64 && " + +# Filter out samples that require extensive dependencies. +local_filters = "Samples/2_Concepts_and_Techniques/EGLStream_CUDA_Interop/Makefile " +local_filters += "Samples/4_CUDA_Libraries/boxFilterNPP/Makefile " +local_filters += "Samples/4_CUDA_Libraries/cannyEdgeDetectorNPP/Makefile " +local_filters += "Samples/4_CUDA_Libraries/cudaNvSci/Makefile " +local_filters += "Samples/4_CUDA_Libraries/cudaNvSciNvMedia/Makefile " +local_filters += "Samples/5_Domain_Specific/simpleGL/Makefile " +local_filters += "Samples/3_CUDA_Features/warpAggregatedAtomicsCG/Makefile " +local_filters += "Samples/5_Domain_Specific/simpleVulkan/Makefile " +local_filters += "Samples/5_Domain_Specific/simpleVulkanMMAP/Makefile " +local_filters += "Samples/2_Concepts_and_Techniques/streamOrderedAllocationIPC/Makefile " +local_filters += "Samples/5_Domain_Specific/vulkanImageCUDA/Makefile " +local_filters += "Samples/6_Performance/LargeKernelParameter/Makefile " + +buildopts = "HOST_COMPILER=g++ SMS='%%(cuda_cc_space_sep_no_period)s' FILTER_OUT='%s'" % local_filters + +files_to_copy = [ + (['bin/%s/linux/release/*' % ARCH], 'bin'), + 'LICENSE', +] + +local_binaries = ['deviceQuery', 'matrixMul', 'bandwidthTest', 'cudaOpenMP'] + +# Only paths are used for sanity checks. +# Commands may fail due to missing compatibility libraries that might be needed +# to be able to use this specific CUDA version in combination with the available +# NVIDIA drivers. +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_binaries], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/c/CUDA-Samples/cuda-samples-11.3_multiple-sms.patch b/easybuild/easyconfigs/c/CUDA-Samples/cuda-samples-11.3_multiple-sms.patch new file mode 100644 index 000000000000..b6613f6a3c4e --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA-Samples/cuda-samples-11.3_multiple-sms.patch @@ -0,0 +1,31 @@ +# Fixes "nvcc fatal: Option '--ptx (-ptx)' is not allowed when compiling for multiple GPU architectures" +# fatal compilation issue when building for multiple SM architectures +# More info, see https://github.com/NVIDIA/cuda-samples/issues/289 + +# Author: Caspar van Leeuwen + +diff -Nru cuda-samples-11.3.orig/Samples/memMapIPCDrv/Makefile cuda-samples-11.3/Samples/memMapIPCDrv/Makefile +--- cuda-samples-11.3.orig/Samples/memMapIPCDrv/Makefile 2024-07-29 13:17:10.330743000 +0200 ++++ cuda-samples-11.3/Samples/memMapIPCDrv/Makefile 2024-07-29 13:19:13.158507504 +0200 +@@ -321,6 +321,12 @@ + ifneq ($(HIGHEST_SM),) + GENCODE_FLAGS += -gencode arch=compute_$(HIGHEST_SM),code=compute_$(HIGHEST_SM) + endif ++ ++# Generate the explicit PTX file for the lowest SM architecture in $(SMS), so it works on all SMS listed there ++LOWEST_SM := $(firstword $(sort $(SMS))) ++ifneq ($(LOWEST_SM),) ++GENCODE_FLAGS_LOWEST_SM += -gencode arch=compute_$(LOWEST_SM),code=compute_$(LOWEST_SM) ++endif + endif + + ifeq ($(TARGET_OS),darwin) +@@ -401,7 +407,7 @@ + endif + + $(PTX_FILE): memMapIpc_kernel.cu +- $(EXEC) $(NVCC) $(INCLUDES) $(ALL_CCFLAGS) $(GENCODE_FLAGS) -o $@ -ptx $< ++ $(EXEC) $(NVCC) $(INCLUDES) $(ALL_CCFLAGS) $(GENCODE_FLAGS_LOWEST_SM) -o $@ -ptx $< + $(EXEC) mkdir -p data + $(EXEC) cp -f $@ ./data + $(EXEC) mkdir -p ../../bin/$(TARGET_ARCH)/$(TARGET_OS)/$(BUILD_TYPE) diff --git a/easybuild/easyconfigs/c/CUDA-Samples/cuda-samples-11.6_multiple-sms.patch b/easybuild/easyconfigs/c/CUDA-Samples/cuda-samples-11.6_multiple-sms.patch new file mode 100644 index 000000000000..8c4e36f7e74f --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA-Samples/cuda-samples-11.6_multiple-sms.patch @@ -0,0 +1,56 @@ +# Fixes "nvcc fatal: Option '--ptx (-ptx)' is not allowed when compiling for multiple GPU architectures" +# fatal compilation issue when building for multiple SM architectures +# More info, see https://github.com/NVIDIA/cuda-samples/issues/289 + +# Author: Caspar van Leeuwen + +diff -Nru cuda-samples-12.2.orig/Samples/3_CUDA_Features/memMapIPCDrv/Makefile cuda-samples-12.2/Samples/3_CUDA_Features/memMapIPCDrv/Makefile +--- cuda-samples-12.2.orig/Samples/3_CUDA_Features/memMapIPCDrv/Makefile 2024-07-29 12:14:28.538848000 +0200 ++++ cuda-samples-12.2/Samples/3_CUDA_Features/memMapIPCDrv/Makefile 2024-07-29 13:02:45.134261829 +0200 +@@ -313,6 +313,12 @@ + ifneq ($(HIGHEST_SM),) + GENCODE_FLAGS += -gencode arch=compute_$(HIGHEST_SM),code=compute_$(HIGHEST_SM) + endif ++ ++# Generate the explicit PTX file for the lowest SM architecture in $(SMS), so it works on all SMS listed there ++LOWEST_SM := $(firstword $(sort $(SMS))) ++ifneq ($(LOWEST_SM),) ++GENCODE_FLAGS_LOWEST_SM += -gencode arch=compute_$(LOWEST_SM),code=compute_$(LOWEST_SM) ++endif + endif + + ifeq ($(TARGET_OS),darwin) +@@ -394,7 +400,7 @@ + endif + + $(PTX_FILE): memMapIpc_kernel.cu +- $(EXEC) $(NVCC) $(INCLUDES) $(ALL_CCFLAGS) $(GENCODE_FLAGS) -o $@ -ptx $< ++ $(EXEC) $(NVCC) $(INCLUDES) $(ALL_CCFLAGS) $(GENCODE_FLAGS_LOWEST_SM) -o $@ -ptx $< + $(EXEC) mkdir -p data + $(EXEC) cp -f $@ ./data + $(EXEC) mkdir -p ../../../bin/$(TARGET_ARCH)/$(TARGET_OS)/$(BUILD_TYPE) +diff -Nru cuda-samples-12.2.orig/Samples/3_CUDA_Features/ptxjit/Makefile cuda-samples-12.2/Samples/3_CUDA_Features/ptxjit/Makefile +--- cuda-samples-12.2.orig/Samples/3_CUDA_Features/ptxjit/Makefile 2024-07-29 12:14:28.546771000 +0200 ++++ cuda-samples-12.2/Samples/3_CUDA_Features/ptxjit/Makefile 2024-07-29 13:02:38.741961008 +0200 +@@ -307,6 +307,12 @@ + ifneq ($(HIGHEST_SM),) + GENCODE_FLAGS += -gencode arch=compute_$(HIGHEST_SM),code=compute_$(HIGHEST_SM) + endif ++ ++# Generate the explicit PTX file for the lowest SM architecture in $(SMS), so it works on all SMS listed there ++LOWEST_SM := $(firstword $(sort $(SMS))) ++ifneq ($(LOWEST_SM),) ++GENCODE_FLAGS_LOWEST_SM += -gencode arch=compute_$(LOWEST_SM),code=compute_$(LOWEST_SM) ++endif + endif + + ifeq ($(TARGET_OS),darwin) +@@ -390,7 +396,7 @@ + endif + + $(PTX_FILE): ptxjit_kernel.cu +- $(EXEC) $(NVCC) $(INCLUDES) $(ALL_CCFLAGS) $(GENCODE_FLAGS) -o $@ -ptx $< ++ $(EXEC) $(NVCC) $(INCLUDES) $(ALL_CCFLAGS) $(GENCODE_FLAGS_LOWEST_SM) -o $@ -ptx $< + $(EXEC) mkdir -p data + $(EXEC) cp -f $@ ./data + $(EXEC) mkdir -p ../../../bin/$(TARGET_ARCH)/$(TARGET_OS)/$(BUILD_TYPE) diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-12.5.0.eb b/easybuild/easyconfigs/c/CUDA/CUDA-12.5.0.eb new file mode 100644 index 000000000000..0a81b7bd4c1d --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA/CUDA-12.5.0.eb @@ -0,0 +1,24 @@ +name = 'CUDA' +version = '12.5.0' +local_nv_version = '555.42.02' + +homepage = 'https://developer.nvidia.com/cuda-toolkit' +description = """CUDA (formerly Compute Unified Device Architecture) is a parallel + computing platform and programming model created by NVIDIA and implemented by the + graphics processing units (GPUs) that they produce. CUDA gives developers access + to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.""" + +toolchain = SYSTEM + +source_urls = ['https://developer.download.nvidia.com/compute/cuda/%(version)s/local_installers/'] +sources = ['cuda_%%(version)s_%s_linux%%(cudaarch)s.run' % local_nv_version] +checksums = [{ + 'cuda_%%(version)s_%s_linux.run' % local_nv_version: + '90fcc7df48226434065ff12a4372136b40b9a4cbf0c8602bb763b745f22b7a99', + 'cuda_%%(version)s_%s_linux_ppc64le.run' % local_nv_version: + '33f39ad7bc624d5c8e59938990358cec80b9966431e34d1ab2d6115d78a3f264', + 'cuda_%%(version)s_%s_linux_sbsa.run' % local_nv_version: + 'e7b864c9ae27cef77cafc78614ec33cbb0a27606af9375deffa09c4269a07f04' +}] + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-12.6.0.eb b/easybuild/easyconfigs/c/CUDA/CUDA-12.6.0.eb new file mode 100644 index 000000000000..24c7b5f5c908 --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA/CUDA-12.6.0.eb @@ -0,0 +1,22 @@ +name = 'CUDA' +version = '12.6.0' +local_nv_version = '560.28.03' + +homepage = 'https://developer.nvidia.com/cuda-toolkit' +description = """CUDA (formerly Compute Unified Device Architecture) is a parallel + computing platform and programming model created by NVIDIA and implemented by the + graphics processing units (GPUs) that they produce. CUDA gives developers access + to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.""" + +toolchain = SYSTEM + +source_urls = ['https://developer.download.nvidia.com/compute/cuda/%(version)s/local_installers/'] +sources = ['cuda_%%(version)s_%s_linux%%(cudaarch)s.run' % local_nv_version] +checksums = [{ + 'cuda_%%(version)s_%s_linux.run' % local_nv_version: + '31ab04394e69b14dd8656e2b44c2877db1a0e898dff8a7546a4c628438101b94', + 'cuda_%%(version)s_%s_linux_sbsa.run' % local_nv_version: + '398db7baca17d51ad5035c606714c96380c965fd1742478c743bc6bbb1d8f63c' +}] + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/c/CUDD/CUDD-3.0.0-GCC-13.2.0.eb b/easybuild/easyconfigs/c/CUDD/CUDD-3.0.0-GCC-13.2.0.eb new file mode 100644 index 000000000000..c1f83cad0995 --- /dev/null +++ b/easybuild/easyconfigs/c/CUDD/CUDD-3.0.0-GCC-13.2.0.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'CUDD' +version = '3.0.0' + +homepage = 'https://github.com/ivmai/cudd' +description = """The CUDD package is a package written in C for the manipulation of + decision diagrams. It supports binary decision diagrams (BDDs), algebraic decision + diagrams (ADDs), and Zero-Suppressed BDDs (ZDDs).""" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +source_urls = ['https://github.com/ivmai/cudd/archive/refs/tags'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['5fe145041c594689e6e7cf4cd623d5f2b7c36261708be8c9a72aed72cf67acce'] + +sanity_check_paths = { + 'files': ['include/cudd.h', 'lib/libcudd.a'], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/c/CUTLASS/CUTLASS-3.4.0-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/c/CUTLASS/CUTLASS-3.4.0-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 000000000000..3322e6b4b56c --- /dev/null +++ b/easybuild/easyconfigs/c/CUTLASS/CUTLASS-3.4.0-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,49 @@ +easyblock = 'CMakeMake' + +name = 'CUTLASS' +version = '3.4.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/NVIDIA/cutlass' +description = """CUTLASS is a collection of CUDA C++ template +abstractions for implementing high-performance matrix-matrix +multiplication (GEMM) and related computations at all levels and scales +within CUDA. It incorporates strategies for hierarchical decomposition +and data movement similar to those used to implement cuBLAS and cuDNN. +CUTLASS decomposes these "moving parts" into reusable, modular software +components abstracted by C++ template classes. Primitives for different +levels of a conceptual parallelization hierarchy can be specialized and +tuned via custom tiling sizes, data types, and other algorithmic policy. +The resulting flexibility simplifies their use as building blocks within +custom kernels and applications.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +github_account = 'NVIDIA' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['49f4b854acc2a520126ceefe4f701cfe8c2b039045873e311b1f10a8ca5d5de1'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('Python', '3.11.3'), +] + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('cuDNN', '8.9.2.26', versionsuffix, SYSTEM), +] + +_copts = [ + '-DCUTLASS_NVCC_ARCHS="%(cuda_cc_cmake)s"', + '-DCUTLASS_ENABLE_CUBLAS=1', + '-DCUTLASS_ENABLE_CUDNN=1', +] +configopts = ' '.join(_copts) + +sanity_check_paths = { + 'files': ['include/cutlass/cutlass.h', 'lib/libcutlass.%s' % SHLIB_EXT], + 'dirs': ['lib/cmake'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/c/Catch2/Catch2-2.13.10-GCCcore-13.3.0.eb b/easybuild/easyconfigs/c/Catch2/Catch2-2.13.10-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..00abfac39c8e --- /dev/null +++ b/easybuild/easyconfigs/c/Catch2/Catch2-2.13.10-GCCcore-13.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'CMakeMake' + +name = 'Catch2' +version = '2.13.10' + +homepage = 'https://github.com/catchorg/Catch2' +description = """A modern, C++-native, header-only, + test framework for unit-tests, TDD and BDD + - using C++11, C++14, C++17 and later +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/catchorg/Catch2/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['d54a712b7b1d7708bc7a819a8e6e47b2fde9536f487b89ccbca295072a7d9943'] + +builddependencies = [ + ('binutils', '2.42'), # to make CMake compiler health check pass on old systems + ('CMake', '3.29.3'), +] + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['include/catch2/catch.hpp'], + 'dirs': ['lib/cmake'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/c/CellOracle/CellOracle-0.18.0-foss-2023a.eb b/easybuild/easyconfigs/c/CellOracle/CellOracle-0.18.0-foss-2023a.eb new file mode 100644 index 000000000000..d6eb8f4ceade --- /dev/null +++ b/easybuild/easyconfigs/c/CellOracle/CellOracle-0.18.0-foss-2023a.eb @@ -0,0 +1,66 @@ +easyblock = 'PythonBundle' + +name = 'CellOracle' +version = '0.18.0' + +homepage = 'https://github.com/morris-lab/CellOracle' +description = """CellOracle is a Python library for in silico gene perturbation analyses using single-cell omics data +and Gene Regulatory Network models.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('R', '4.3.2'), + ('SciPy-bundle', '2023.07'), + ('Python-bundle-PyPI', '2023.06'), + ('numba', '0.58.1'), + ('matplotlib', '3.7.2'), + ('Seaborn', '0.13.2'), + ('scikit-learn', '1.3.1'), + ('h5py', '3.9.0'), + ('velocyto', '0.17.17'), + ('umap-learn', '0.5.5'), + ('Arrow', '14.0.1'), + ('tqdm', '4.66.1'), + ('python-igraph', '0.11.4'), + ('IPython', '8.14.0'), + ('scanpy', '1.9.8'), + ('GOATOOLS', '1.4.5'), + ('genomepy', '0.16.1'), + ('GimmeMotifs', '0.17.2'), + ('anndata', '0.10.5.post1'), + ('python-louvain', '0.16'), + ('jupyter-contrib-nbextensions', '0.7.0'), + ('Qtconsole', '5.5.1'), +] + +use_pip = True + +# remove louvain from requirements, since CellOracle doesn't actually use it at all +local_preinstallopts = "sed -i '/louvain/d' requirements.txt && " +# drop strict version requirement for matplotlib dependency +local_preinstallopts += "sed -i 's/matplotlib.*/matplotlib/g' requirements.txt && " +# drop strict version requirement for pandas dependency +local_preinstallopts += "sed -i 's/pandas.*/pandas/g' requirements.txt && " + + +exts_list = [ + ('jupyter_console', '6.6.3', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['309d33409fcc92ffdad25f0bcdf9a4a9daa61b6f341177570fdac03de5352485'], + }), + ('jupyter', '1.0.0', { + 'checksums': ['d9dc4b3318f310e34c82951ea5d6683f67bed7def4b259fafbfe4f1beb1d8e5f'], + }), + ('celloracle', version, { + 'preinstallopts': local_preinstallopts, + 'checksums': ['a73bbdae36289748051e073409d853489a233bda90f50ab5031131b92dda2133'], + }), +] + +sanity_check_commands = ["python -c 'import celloracle; celloracle.check_python_requirements()'"] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/Clang/Clang-18.1.8-GCCcore-13.3.0.eb b/easybuild/easyconfigs/c/Clang/Clang-18.1.8-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..8b096078c890 --- /dev/null +++ b/easybuild/easyconfigs/c/Clang/Clang-18.1.8-GCCcore-13.3.0.eb @@ -0,0 +1,55 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2013-2015 Dmitri Gribenko, Ward Poelmans +# Authors:: Dmitri Gribenko +# Authors:: Ward Poelmans +# License:: GPLv2 or later, MIT, three-clause BSD. +# $Id$ +## + +name = 'Clang' +version = '18.1.8' + +homepage = 'https://clang.llvm.org/' +description = """C, C++, Objective-C compiler, based on LLVM. Does not + include C++ standard library -- use libstdc++ from GCC.""" + +# Clang also depends on libstdc++ during runtime, but this dependency is +# already specified as the toolchain. +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ["https://github.com/llvm/llvm-project/releases/download/llvmorg-%(version)s"] +sources = [ + 'llvm-project-%(version)s.src.tar.xz', +] +checksums = ['0b58557a6d32ceee97c8d533a59b9212d87e0fc4d2833924eb6c611247db2f2a'] + +builddependencies = [ + ('CMake', '3.29.3'), + ('Perl', '5.38.2'), + # Including Python bindings would require this as a runtime dep + # and SWIG as an additional build dep + ('Python', '3.12.3'), +] +dependencies = [ + # since Clang is a compiler, binutils is a runtime dependency too + ('binutils', '2.42'), + ('hwloc', '2.10.0'), + ('libxml2', '2.12.7'), + ('ncurses', '6.5'), + ('GMP', '6.3.0'), + ('Z3', '4.13.0'), +] + +# If True, Flang does not currently support building with LLVM exceptions enabled. +enable_rtti = False + +assertions = True +python_bindings = False +skip_all_tests = True + +llvm_runtimes = ['libunwind', 'libcxx', 'libcxxabi'] +llvm_projects = ['polly', 'lld', 'lldb', 'clang-tools-extra', 'flang'] + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/c/ConcurrentVersionsSystem/ConcurrentVersionsSystem-1.11.23-GCCcore-13.3.0.eb b/easybuild/easyconfigs/c/ConcurrentVersionsSystem/ConcurrentVersionsSystem-1.11.23-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..b43a426454f4 --- /dev/null +++ b/easybuild/easyconfigs/c/ConcurrentVersionsSystem/ConcurrentVersionsSystem-1.11.23-GCCcore-13.3.0.eb @@ -0,0 +1,45 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +## + +easyblock = 'ConfigureMake' + +name = 'ConcurrentVersionsSystem' +version = '1.11.23' + +homepage = 'https://savannah.nongnu.org/projects/cvs' +description = """CVS is a version control system, an important component of +Source Configuration Management (SCM). +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [' https://ftp.gnu.org/non-gnu/cvs/source/stable/%(version)s/'] +sources = ['cvs-%(version)s.tar.bz2'] +patches = [ + 'CVS-1.11.23-zlib-1.patch', + 'CVS-1.11.23-getline.patch', +] +checksums = [ + '400f51b59d85116e79b844f2d5dbbad4759442a789b401a94aa5052c3d7a4aa9', # cvs-1.11.23.tar.bz2 + # CVS-1.11.23-zlib-1.patch + '3c0ee6509c4622778c093316437a5b047c51820e11cee3ed3a405c2a590a9ff4', + # CVS-1.11.23-getline.patch + '6a1aa65acfbb41b7639adc70248d908981f172c2529bb52d84359713f9541874', +] + +builddependencies = [ + ('binutils', '2.42') +] + +dependencies = [ + ('zlib', '1.3.1') +] + +sanity_check_paths = { + 'files': ['bin/cvs', 'bin/cvsbug', 'bin/rcs2log'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/Coreutils/Coreutils-9.5-GCCcore-13.3.0.eb b/easybuild/easyconfigs/c/Coreutils/Coreutils-9.5-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..60e5009dc91d --- /dev/null +++ b/easybuild/easyconfigs/c/Coreutils/Coreutils-9.5-GCCcore-13.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = "Coreutils" +version = "9.5" + +homepage = 'https://www.gnu.org/software/coreutils/' +description = """The GNU Core Utilities are the basic file, shell and text +manipulation utilities of the GNU operating system. These are +the core utilities which are expected to exist on every +operating system. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +checksums = ['cd328edeac92f6a665de9f323c93b712af1858bc2e0d88f3f7100469470a1b8a'] + +builddependencies = [('binutils', '2.42')] + +sanity_check_paths = { + 'files': ['bin/sort', 'bin/echo', 'bin/du', 'bin/date', 'bin/true'], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/Critic2/Critic2-1.2-foss-2023a.eb b/easybuild/easyconfigs/c/Critic2/Critic2-1.2-foss-2023a.eb new file mode 100644 index 000000000000..9d1605b73667 --- /dev/null +++ b/easybuild/easyconfigs/c/Critic2/Critic2-1.2-foss-2023a.eb @@ -0,0 +1,37 @@ +easyblock = 'CMakeMake' + +name = 'Critic2' +version = '1.2' + +homepage = 'https://aoterodelaroza.github.io/critic2/' +description = """Critic2 is a program for the analysis of quantum mechanical +calculation results in molecules and periodic solids.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'extra_fflags': '-ffree-line-length-none'} + +source_urls = ['https://github.com/aoterodelaroza/critic2/archive/refs/tags/'] +sources = ['%(version)s.tar.gz'] +checksums = ['b59ecffd83405dbcc4b5d157d4a94bf2756916f72e83e09a94d277d54d0f2225'] + +configopts = '-DLIBCINT_INCLUDE_DIRS=$EBROOTLIBCINT/include/ ' +configopts += '-DLIBCINT_LIBRARY=$EBROOTLIBCINT/lib64/libcint.so ' + +builddependencies = [ + ('CMake', '3.26.3'), +] + +dependencies = [ + ('libxc', '6.2.2'), + ('libcint', '5.4.0'), + ('libreadline', '8.2'), +] + +sanity_check_paths = { + 'files': ["bin/critic2"], + 'dirs': ["bin"], +} + +sanity_check_commands = ['critic2 -h'] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/CubeLib/CubeLib-4.8.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/c/CubeLib/CubeLib-4.8.2-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..6b2414be4467 --- /dev/null +++ b/easybuild/easyconfigs/c/CubeLib/CubeLib-4.8.2-GCCcore-13.3.0.eb @@ -0,0 +1,52 @@ +# Copyright 2019-2024 Juelich Supercomputing Centre, Germany +# Copyright 2023-2024 TU Dresden, Germany +# Authors:: Markus Geimer +# Alexander Grund +# Jan André Reuter +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ + +easyblock = 'EB_Score_minus_P' + +name = 'CubeLib' +version = '4.8.2' + +homepage = 'https://www.scalasca.org/software/cube-4.x/download.html' +description = """ + Cube, which is used as performance report explorer for Scalasca and Score-P, + is a generic tool for displaying a multi-dimensional performance space + consisting of the dimensions (i) performance metric, (ii) call path, and + (iii) system resource. Each dimension can be represented as a tree, where + non-leaf nodes of the tree can be collapsed or expanded to achieve the + desired level of granularity. + + This module provides the Cube general purpose C++ library component and + command-line tools. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['d6fdef57b1bc9594f1450ba46cf08f431dd0d4ae595c47e2f3454e17e4ae74f4'] + +builddependencies = [ + # use same binutils version that was used when building GCCcore + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), +] +dependencies = [ + ('zlib', '1.3.1'), +] + +configopts = '--enable-shared' + +sanity_check_paths = { + 'files': ['bin/cubelib-config', + 'lib/libcube4.a', 'lib/libcube4.%s' % SHLIB_EXT], + 'dirs': ['include/cubelib'], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.8.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.8.2-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..e030f21ba6c6 --- /dev/null +++ b/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.8.2-GCCcore-13.3.0.eb @@ -0,0 +1,52 @@ +# Copyright:: Copyright 2019-2024 Juelich Supercomputing Centre, Germany +# Copyright 2023-2024 TU Dresden, Germany +# Authors:: Markus Geimer +# Alexander Grund +# Jan André Reuter +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ + +easyblock = 'EB_Score_minus_P' + +name = 'CubeWriter' +version = '4.8.2' + +homepage = 'https://www.scalasca.org/software/cube-4.x/download.html' +description = """ + Cube, which is used as performance report explorer for Scalasca and Score-P, + is a generic tool for displaying a multi-dimensional performance space + consisting of the dimensions (i) performance metric, (ii) call path, and + (iii) system resource. Each dimension can be represented as a tree, where + non-leaf nodes of the tree can be collapsed or expanded to achieve the + desired level of granularity. + + This module provides the Cube high-performance C writer library component. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] +sources = ['cubew-%(version)s.tar.gz'] +checksums = ['4f3bcf0622c2429b8972b5eb3f14d79ec89b8161e3c1cc5862ceda417d7975d2'] + +builddependencies = [ + # use same binutils version that was used when building GCCcore + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), +] + +dependencies = [ + ('zlib', '1.3.1'), +] + +configopts = '--enable-shared' + +sanity_check_paths = { + 'files': ['bin/cubew-config', + 'lib/libcube4w.a', 'lib/libcube4w.%s' % SHLIB_EXT], + 'dirs': ['include/cubew'], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/c/Cython/Cython-3.0.10-GCCcore-13.3.0.eb b/easybuild/easyconfigs/c/Cython/Cython-3.0.10-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..c9e419d570ad --- /dev/null +++ b/easybuild/easyconfigs/c/Cython/Cython-3.0.10-GCCcore-13.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonPackage' + +name = 'Cython' +version = '3.0.10' + +homepage = 'https://cython.org/' +description = """ +Cython is an optimising static compiler for both the Python programming +language and the extended Cython programming language (based on Pyrex). +""" +docurls = [ + 'https://cython.org/#documentation', + 'https://github.com/cython/cython', +] + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['dcc96739331fb854dcf503f94607576cfe8488066c61ca50dfd55836f132de99'] + +builddependencies = [ + ('binutils', '2.42'), +] + +dependencies = [ + ('Python', '3.12.3'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/cygdb', 'bin/cython', 'bin/cythonize'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["cython --version"] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.18.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/c/cairo/cairo-1.18.0-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..2622f0101263 --- /dev/null +++ b/easybuild/easyconfigs/c/cairo/cairo-1.18.0-GCCcore-13.3.0.eb @@ -0,0 +1,51 @@ +easyblock = 'MesonNinja' + + +name = 'cairo' +version = '1.18.0' + +homepage = 'https://cairographics.org' +description = """Cairo is a 2D graphics library with support for multiple output devices. + Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers, + PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [ + 'https://cairographics.org/releases/', + 'https://cairographics.org/snapshots/' +] +sources = [SOURCE_TAR_XZ] +checksums = ['243a0736b978a33dee29f9cca7521733b78a65b5418206fef7bd1c3d4cf10b64'] + +builddependencies = [ + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), + ('Ninja', '1.12.1'), + ('Meson', '1.4.0'), +] +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.3.1'), + ('libpng', '1.6.43'), + ('freetype', '2.13.2'), + ('pixman', '0.43.4'), + ('expat', '2.6.2'), + ('GLib', '2.80.4'), + ('X11', '20240607'), +] + +configopts = "--default-library=both" # static and shared library + +sanity_check_paths = { + 'files': ['bin/cairo-trace', 'lib/cairo/libcairo-trace.%s' % SHLIB_EXT, 'lib/cairo/libcairo-trace.a', + 'lib/libcairo.a', 'lib/libcairo-gobject.a', 'lib/libcairo-script-interpreter.a', + 'lib/libcairo.%s' % SHLIB_EXT, 'lib/libcairo-gobject.%s' % SHLIB_EXT, + 'lib/libcairo-script-interpreter.%s' % SHLIB_EXT] + + ['include/cairo/cairo%s.h' % x for x in ['', '-deprecated', '-features', '-ft', '-gobject', '-pdf', '-ps', + '-script', '-script-interpreter', '-svg', '-version', '-xcb', + '-xlib', '-xlib-xrender']], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/c/cairomm/cairomm-1.16.2-GCC-12.3.0.eb b/easybuild/easyconfigs/c/cairomm/cairomm-1.16.2-GCC-12.3.0.eb new file mode 100644 index 000000000000..286c56e1bbb2 --- /dev/null +++ b/easybuild/easyconfigs/c/cairomm/cairomm-1.16.2-GCC-12.3.0.eb @@ -0,0 +1,39 @@ +# Updated to MesonNinja as the autogen.sh complained. +# Author: J. Sassmannshausen (Imperial College London) + +easyblock = 'MesonNinja' + +name = 'cairomm' +version = '1.16.2' + +homepage = 'http://cairographics.org' +description = "The Cairomm package provides a C++ interface to Cairo." + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['http://cairographics.org/releases/'] +sources = [SOURCE_TAR_XZ] +checksums = ['6a63bf98a97dda2b0f55e34d1b5f3fb909ef8b70f9b8d382cb1ff3978e7dc13f'] + +builddependencies = [ + ('Meson', '1.1.1'), + ('Ninja', '1.11.1'), + ('Doxygen', '1.9.7'), + ('M4', '1.4.19'), +] + +dependencies = [ + ('cairo', '1.17.8'), + ('libsigc++', '3.6.0'), + ('mm-common', '1.0.6'), + ('Boost', '1.82.0'), +] + +runtest = 'ninja test' + +sanity_check_paths = { + 'files': ['lib/libcairomm-1.16.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb b/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb index 9a0eeba16281..1556b0f9dad2 100644 --- a/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb @@ -45,12 +45,6 @@ preinstallopts = "sed -i 's/theano/Theano-PyMC/g' setup.py && " use_pip = True -exts_default_options = { - 'download_dep_fail': True, - 'sanity_pip_check': True, - 'use_pip': True, -} - exts_list = [ ('opt-einsum', '3.3.0', { 'source_tmpl': 'opt_einsum-%(version)s.tar.gz', diff --git a/easybuild/easyconfigs/c/cfgrib/cfgrib-0.9.14.0-foss-2023a.eb b/easybuild/easyconfigs/c/cfgrib/cfgrib-0.9.14.0-foss-2023a.eb new file mode 100644 index 000000000000..b6b2b66159c1 --- /dev/null +++ b/easybuild/easyconfigs/c/cfgrib/cfgrib-0.9.14.0-foss-2023a.eb @@ -0,0 +1,41 @@ +easyblock = "PythonBundle" + +name = 'cfgrib' +version = '0.9.14.0' + +homepage = 'https://github.com/ecmwf/cfgrib/' +description = """ +A Python interface to map GRIB files to the NetCDF Common Data Model following the CF +Convention using ecCodes. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('poetry', '1.7.1'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('ecCodes', '2.31.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('findlibs', '0.0.5', { + 'checksums': ['7a801571e999d0ee83f9b92cbb598c21f861ee26ca9dba74cea8958ba4335e7e'], + }), + ('eccodes', '1.7.1', { + 'checksums': ['d3c7e9bab779d35b624cfd7b3331de111602cba6a6f6368efcc12407f30b2697'], + }), + (name, version, { + 'checksums': ['2b9a1e6bd47397e585f878ffd8aaac5969f6c9a448da767c700917b89c275bb2'], + }), +] + +sanity_check_commands = ['python -m cfgrib selfcheck'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/chewBBACA/chewBBACA-3.3.9-foss-2022b.eb b/easybuild/easyconfigs/c/chewBBACA/chewBBACA-3.3.9-foss-2022b.eb new file mode 100644 index 000000000000..b9964db690ac --- /dev/null +++ b/easybuild/easyconfigs/c/chewBBACA/chewBBACA-3.3.9-foss-2022b.eb @@ -0,0 +1,66 @@ +easyblock = 'PythonBundle' + +name = 'chewBBACA' +version = '3.3.9' + +homepage = 'https://github.com/B-UMMI/chewBBACA' +description = """chewBBACA is a software suite for the creation and evaluation of core genome and whole genome +MultiLocus Sequence Typing (cg/wgMLST) schemas and results. The "BBACA" stands for "BSR-Based Allele Calling Algorithm". +BSR stands for BLAST Score Ratio as proposed by Rasko DA et al. The "chew" part adds extra coolness to the name and +could be thought of as "Comprehensive and Highly Efficient Workflow".""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + # Cython 3 is required, see https://github.com/althonos/pyrodigal/issues/40 + # Cython included with Python-bundle-PyPI (0.29.35) is too old + ('Cython', '3.0.8'), + ('Biopython', '1.81'), + ('plotly.py', '5.13.1'), + ('BLAST+', '2.14.0'), + ('prodigal', '2.6.3'), + ('MAFFT', '7.505', '-with-extensions'), + ('FastTree', '2.1.11'), + ('archspec', '0.2.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('pyrodigal', '3.5.1', { + 'checksums': ['20af59a6d968c88910b99d5f647bb7dd22d49e440ead95fe715cdd2c49f36e9f'], + }), + ('isodate', '0.6.1', { + 'checksums': ['48c5881de7e8b0a0d648cb024c8062dc84e7b840ed81e864c7614fd3c127bde9'], + }), + ('rdflib', '7.0.0', { + 'checksums': ['9995eb8569428059b8c1affd26b25eac510d64f5043d9ce8c84e0d0036e995ae'], + }), + ('SPARQLWrapper', '2.0.0', { + 'modulename': 'SPARQLWrapper', + 'checksums': ['3fed3ebcc77617a4a74d2644b86fd88e0f32e7f7003ac7b2b334c026201731f1'], + }), + (name, version, { + 'modulename': 'CHEWBBACA', + # relax numpy version requirement + 'preinstallopts': "sed -i 's/numpy~=1.24.3/numpy~=1.24.2/g' pyproject.toml && ", + 'runtest': "python setup.py test", + 'sources': ['%(namelower)s-%(version)s.tar.gz'], + 'checksums': ['4bf0792b8cdd1783b50340ac713748ef2a351209cacb50ad4c9e2fe2e7fba772'], + }), +] + +sanity_check_paths = { + 'files': ['bin/chewBBACA.py', 'bin/chewie'], + 'dirs': [], +} + +sanity_check_commands = [ + 'chewBBACA.py --help', + 'chewie --help', +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/code-server/code-server-4.90.2.eb b/easybuild/easyconfigs/c/code-server/code-server-4.90.2.eb new file mode 100644 index 000000000000..d85b34c752cb --- /dev/null +++ b/easybuild/easyconfigs/c/code-server/code-server-4.90.2.eb @@ -0,0 +1,20 @@ +name = 'code-server' +version = '4.90.2' + +homepage = 'https://github.com/coder/code-server' +description = """Run VS Code on any machine anywhere and access it in the browser.""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/coder/code-server/releases/download/v%(version)s/'] +sources = ['code-server-%(version)s-linux-%(mapped_arch)s.tar.gz'] +checksums = [ + { + 'code-server-%(version)s-linux-amd64.tar.gz': + 'c66b57759e41c66c28577eaefa4cce106f7b5ad5fb3ab394baea5eaa5b604cce', + 'code-server-%(version)s-linux-arm64.tar.gz': + '12e51e3575069c438aa4dee93bddfc221e7850192a7745b84fc77b420cedf205', + } +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/colorize/colorize-0.7.7-GCC-12.3.0.eb b/easybuild/easyconfigs/c/colorize/colorize-0.7.7-GCC-12.3.0.eb new file mode 100644 index 000000000000..35921013c3e2 --- /dev/null +++ b/easybuild/easyconfigs/c/colorize/colorize-0.7.7-GCC-12.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'RubyGem' + +name = 'colorize' +version = '0.7.7' + +homepage = 'https://github.com/fazibear/colorize' +description = """Ruby gem for colorizing text using ANSI escape sequences. +Extends String class or add a ColorizedString with methods to set the text color, background color and text effects.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://rubygems.org/downloads/'] +sources = ['%(name)s-%(version)s.gem'] +checksums = ['d6ab95a5fcdea3c36c3327d38c1e79e2950ee1788506d8489ae35db330937a99'] + +gem_file = '%(name)s-%(version)s.gem' + +dependencies = [ + ('Ruby', '3.3.0'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['gems/%(namelower)s-%(version)s'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/c/connected-components-3d/connected-components-3d-3.14.1-foss-2023a.eb b/easybuild/easyconfigs/c/connected-components-3d/connected-components-3d-3.14.1-foss-2023a.eb new file mode 100644 index 000000000000..5a366beb6d0e --- /dev/null +++ b/easybuild/easyconfigs/c/connected-components-3d/connected-components-3d-3.14.1-foss-2023a.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'connected-components-3d' +version = '3.14.1' + +homepage = 'https://github.com/seung-lab/connected-components-3d/' +description = """cc3d is an implementation of connected components in three dimensions using a 26, 18, + or 6-connected neighborhood in 3D or 4 and 8-connected in 2D.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['fdc4099508b734b266a42ee12534ee42e29467c28506b137e8c1edc8c7513c92'] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +options = {'modulename': 'cc3d'} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/c/cooler/cooler-0.10.2-foss-2023a.eb b/easybuild/easyconfigs/c/cooler/cooler-0.10.2-foss-2023a.eb new file mode 100644 index 000000000000..57091228de31 --- /dev/null +++ b/easybuild/easyconfigs/c/cooler/cooler-0.10.2-foss-2023a.eb @@ -0,0 +1,49 @@ +easyblock = 'PythonBundle' + +name = 'cooler' +version = '0.10.2' + +homepage = 'https://open2c.github.io/cooler' +description = """Cooler is a support library for a storage format, also called cooler, used to store + genomic interaction data of any size, such as Hi-C contact matrices.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('hatchling', '1.18.0'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('h5py', '3.9.0'), + ('PyYAML', '6.0'), + ('pyfaidx', '0.8.1.1'), +] + +use_pip = True + +exts_list = [ + ('asciitree', '0.3.3', { + 'checksums': ['4aa4b9b649f85e3fcb343363d97564aa1fb62e249677f2e18a96765145cc0f6e'], + }), + ('toolz', '0.12.0', { + 'checksums': ['88c570861c440ee3f2f6037c4654613228ff40c93a6c25e0eba70d17282c6194'], + }), + ('cytoolz', '0.12.3', { + 'checksums': ['4503dc59f4ced53a54643272c61dc305d1dbbfbd7d6bdf296948de9f34c3a282'], + }), + ('dill', '0.3.8', { + 'checksums': ['3ebe3c479ad625c4553aca177444d89b486b1d84982eeacded644afc0cf797ca'], + }), + ('multiprocess', '0.70.16', { + 'checksums': ['161af703d4652a0e1410be6abccecde4a7ddffd19341be0a7011b94aeb171ac1'], + }), + (name, version, { + 'checksums': ['3780a2e69b2ec89882dfc2775de5d9b54ccb79569dc5f042b4851599388112dc'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/coxeter/coxeter-20180226-GCCcore-13.2.0.eb b/easybuild/easyconfigs/c/coxeter/coxeter-20180226-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..247bb5ac24dc --- /dev/null +++ b/easybuild/easyconfigs/c/coxeter/coxeter-20180226-GCCcore-13.2.0.eb @@ -0,0 +1,45 @@ +easyblock = 'ConfigureMake' + +name = 'coxeter' +version = '20180226' +local_commit = '7b5a1f0' + +homepage = 'https://github.com/tscrim/coxeter' +description = """A library for the study of combinatorial aspects of Coxeter group theory""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://github.com/tscrim/coxeter/archive/%s/' % local_commit] +sources = [SOURCE_TAR_GZ] +patches = [ + 'coxeter-20180226_makefile.patch', + ('coxeter-20180226_sage_interface.patch', 0), +] +checksums = [ + {'coxeter-20180226.tar.gz': '5e0668c40b29c03c438a6ebc0f49f13aaf155b4bcbff56303a753390e6fce3aa'}, + {'coxeter-20180226_makefile.patch': '229ed201e41bae0ae7b22aa21d5007127aeb52fd158543dd5fff2e89797e211f'}, + {'coxeter-20180226_sage_interface.patch': '18ba75e51a944ffccb7fa440b823f68a0aad9066e8edcdd2b52bac6b43404bd3'}, +] + +builddependencies = [('binutils', '2.40')] + +skipsteps = ['configure'] + +buildopts = 'CC="$CC" CFLAGS="$CFLAGS"' +preinstallopts = 'mkdir -p "%(installdir)s/bin" "%(installdir)s/lib" && ' +installopts = 'SAGE_LOCAL="%(installdir)s"' + +sanity_check_paths = { + 'files': [ + 'bin/%(name)s', + 'lib/lib%%(name)s3.%s' % SHLIB_EXT, + ], + 'dirs': [ + 'include/%(name)s', + 'share/%(name)s', + ] +} + +sanity_check_commands = ['echo "qq" | coxeter'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/c/coxeter/coxeter-20180226_makefile.patch b/easybuild/easyconfigs/c/coxeter/coxeter-20180226_makefile.patch new file mode 100644 index 000000000000..d00d68606895 --- /dev/null +++ b/easybuild/easyconfigs/c/coxeter/coxeter-20180226_makefile.patch @@ -0,0 +1,101 @@ +Allows installation of files needed for Sagemath +Source: https://gitlab.archlinux.org/archlinux/packaging/packages/coxeter/-/blob/main/coxeter-makefile.patch +diff -u makefile.orig makefile +--- makefile.orig 2018-02-26 13:57:36.000000000 +0100 ++++ makefile 2024-08-16 14:15:51.889503570 +0200 +@@ -12,6 +12,7 @@ + gflags = -c $(includedirs) -g + + cflags = $(gflags) # the default setting ++cflags = -c $(includedirs) $(CPPFLAGS) $(CXXFLAGS) -fPIC + + ifdef optimize + NDEBUG = true +@@ -22,18 +23,74 @@ + cflags = $(pflags) + endif + +-cc = g++ ++EXENAME = coxeter ++LIBNAME = coxeter3 ++ifeq ($(UNAME),Darwin) ++ EXEEXT = ++ LIBPREFIX = lib ++ LIBEXT = .dylib ++ LIBDIR = lib ++ LINKFLAGS = -dynamiclib -Wl,-headerpad_max_install_names,-undefined,dynamic_lookup,-compatibility_version,3.0,-current_version,3.0,-install_name,$(SAGE_LOCAL)/lib/$(LIBPREFIX)$(LIBNAME)$(LIBEXT) ++ LINKLIBS = ++else ++ifeq ($(UNAME),CYGWIN) ++ EXEEXT = .exe ++ LIBPREFIX = cyg ++ LIBEXT = .dll ++ LIBDIR = bin ++ IMPLIB = lib$(LIBNAME).dll.a ++ LINKFLAGS = -shared -Wl,--out-implib=$(IMPLIB) -Wl,--export-all-symbols ++ LINKLIBS = -lc ++else ++ EXEEXT = ++ LIBPREFIX = lib ++ LIBEXT = .so ++ LIBDIR = lib ++ LINKFLAGS = $(LDFLAGS) -shared -Wl,-soname,libcoxeter3.so ++ LINKLIBS = -lc ++endif ++endif ++LIBRARY = $(LIBPREFIX)$(LIBNAME)$(LIBEXT) + +-all: coxeter #clean ++all: coxeter executable + + coxeter: $(objects) +- $(cc) -o coxeter $(objects) ++ $(CXX) $(LINKFLAGS) -o $(LIBRARY) $(objects) $(LINKLIBS) ++ ++executable: $(objects) ++ $(CXX) $(LDFLAGS) -o $(EXENAME)$(EXEEXT) $(objects) ++ ++DATADIR="$$SAGE_LOCAL/share/coxeter/" ++INCLUDEDIR="$$SAGE_LOCAL/include/coxeter/" ++LIBRARYDIR="$$SAGE_LOCAL/$(LIBDIR)" ++ ++install: coxeter executable ++ cp $(EXENAME)$(EXEEXT) "$$SAGE_LOCAL/bin/" ++ cp $(LIBRARY) $(LIBRARYDIR) ++ if [ $(UNAME) = "CYGWIN" ]; then \ ++ cp $(IMPLIB) "$$SAGE_LOCAL/lib/"; \ ++ fi ++ ++ mkdir -p $(DATADIR) ++ cp -r coxeter_matrices headers messages $(DATADIR) ++ mkdir -p $(INCLUDEDIR) ++ cp -r *.h *.hpp $(INCLUDEDIR) ++ ++check: coxeter executable ++ $(EXENAME)$(EXEEXT) < test.input > test.output ++ ++ if ! diff test.output.expected test.output > /dev/null; then \ ++ echo >&2 "Error testing coxeter on test.input:"; \ ++ diff test.output.expected test.output; \ ++ exit 1; \ ++ fi ++ rm -f test.output + + clean: + rm -f $(objects) + + %.o:%.cpp +- $(cc) $(cflags) $*.cpp ++ $(CXX) $(cflags) $*.cpp + + # dependencies --- these were generated automatically by make depend on my + # system; they are explicitly copied for portability. Only local dependencies +@@ -43,7 +100,7 @@ + # contents of tmp in lieu of the dependencies listed here. + + %.d:%.cpp +- @$(cc) -MM $*.cpp ++ @$(CXX) -MM $*.cpp + depend: $(dependencies) + + affine.o: affine.cpp affine.h globals.h coxgroup.h coxtypes.h io.h list.h \ diff --git a/easybuild/easyconfigs/c/coxeter/coxeter-20180226_sage_interface.patch b/easybuild/easyconfigs/c/coxeter/coxeter-20180226_sage_interface.patch new file mode 100644 index 000000000000..2b4cd427ca92 --- /dev/null +++ b/easybuild/easyconfigs/c/coxeter/coxeter-20180226_sage_interface.patch @@ -0,0 +1,89 @@ +Adds sage interface. See https://github.com/tscrim/coxeter/pull/14 +Source: https://gitlab.archlinux.org/archlinux/packaging/packages/coxeter/-/blob/git.20180226-4/coxeter-sage.patch +diff -u /dev/null sage.h +--- /dev/null 2024-08-27 08:29:37.672016778 +0200 ++++ sage.h 2024-08-27 12:17:23.716096310 +0200 +@@ -0,0 +1,23 @@ ++/* ++ Coxeter version 3.0 Copyright (C) 2009 Mike Hansen ++ See file main.cpp for full copyright notice ++*/ ++ ++#ifndef SAGE_H /* guard against multiple inclusions */ ++#define SAGE_H ++ ++#include "globals.h" ++#include "coxgroup.h" ++#include "coxtypes.h" ++#include "schubert.h" ++#include "list.h" ++ ++namespace sage { ++ using namespace coxeter; ++ using namespace coxtypes; ++ using namespace list; ++ ++ void interval(List& result, CoxGroup& W, const CoxWord& g, const CoxWord& h); ++} ++ ++#endif +diff -u /dev/null sage.cpp +--- /dev/null 2024-08-27 08:29:37.672016778 +0200 ++++ sage.cpp 2024-08-27 12:17:23.716096310 +0200 +@@ -0,0 +1,56 @@ ++/* ++ Coxeter version 3.0 Copyright (C) 2009 Mike Hansen ++ See file main.cpp for full copyright notice ++*/ ++ ++#include "sage.h" ++ ++namespace sage { ++ ++ void interval(List& list, CoxGroup& W, const CoxWord& g, const CoxWord& h) ++ ++ /* ++ Returns a list of the elements in the Bruhat interval between g and h. ++ Note that this assumes that g and h are in order. ++ */ ++ { ++ if (not W.inOrder(g,h)) { ++ return; ++ } ++ ++ W.extendContext(h); ++ ++ CoxNbr x = W.contextNumber(g); ++ CoxNbr y = W.contextNumber(h); ++ ++ BitMap b(W.contextSize()); ++ W.extractClosure(b,y); ++ ++ BitMap::ReverseIterator b_rend = b.rend(); ++ List res(0); ++ ++ for (BitMap::ReverseIterator i = b.rbegin(); i != b_rend; ++i) ++ if (not W.inOrder(x,*i)) { ++ BitMap bi(W.contextSize()); ++ W.extractClosure(bi,*i); ++ CoxNbr z = *i; // andnot will invalidate iterator ++ b.andnot(bi); ++ b.setBit(z); // otherwise the decrement will not be correct ++ } else ++ res.append(*i); ++ ++ schubert::NFCompare nfc(W.schubert(),W.ordering()); ++ Permutation a(res.size()); ++ sortI(res,nfc,a); ++ ++ list.setSize(0); ++ for (size_t j = 0; j < res.size(); ++j) { ++ CoxWord w(0); ++ W.schubert().append(w, res[a[j]]); ++ list.append(w); ++ } ++ ++ return; ++ } ++ ++} diff --git a/easybuild/easyconfigs/c/cppy/cppy-1.2.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/c/cppy/cppy-1.2.1-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..3043857d9254 --- /dev/null +++ b/easybuild/easyconfigs/c/cppy/cppy-1.2.1-GCCcore-13.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'cppy' +version = '1.2.1' + +homepage = "https://github.com/nucleic/cppy" +description = """A small C++ header library which makes it easier to write +Python extension modules. The primary feature is a PyObject smart pointer +which automatically handles reference counting and provides convenience +methods for performing common object operations.""" + + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [('binutils', '2.42')] + +dependencies = [ + ('Python', '3.12.3'), +] + +sources = ['%(name)s-%(version)s.tar.gz'] +patches = ['cppy-1.2.1-manual_version.patch'] +checksums = [ + {'cppy-1.2.1.tar.gz': '83b43bf17b1085ac15c5debdb42154f138b928234b21447358981f69d0d6fe1b'}, + {'cppy-1.2.1-manual_version.patch': '048aa0a86fd2e99c6896443b07ec83eaa369724297f639ef74c65c404b8f288f'}, +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/crb-blast/crb-blast-0.6.9-GCC-12.3.0.eb b/easybuild/easyconfigs/c/crb-blast/crb-blast-0.6.9-GCC-12.3.0.eb new file mode 100644 index 000000000000..c9e4de852a54 --- /dev/null +++ b/easybuild/easyconfigs/c/crb-blast/crb-blast-0.6.9-GCC-12.3.0.eb @@ -0,0 +1,58 @@ +easyblock = 'Bundle' + +name = 'crb-blast' +version = '0.6.9' + +homepage = 'https://github.com/cboursnell/crb-blast' +description = """Conditional Reciprocal Best BLAST - high confidence ortholog assignment.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +dependencies = [ + ('Ruby', '3.3.0'), +] + +exts_default_options = { + 'source_urls': ['https://rubygems.org/downloads/'], + 'source_tmpl': '%(name)s-%(version)s.gem', +} + +exts_defaultclass = 'RubyGem' + +exts_list = [ + ('facade', '1.2.1', { + 'checksums': ['0764de5519088227675a2a67da23322500c3c507b89486d91296e031d87d036e'], + }), + ('pathname2', '1.8.4', { + 'checksums': ['1711264f3f7c1b380f96e1f0383b135d9703488f7b1acf66346a176efc257b7a'], + }), + ('fixwhich', '1.0.2', { + 'checksums': ['c6a8f796a7eb60ffbc29f0d2af85461761a36c2864d25e445ff18bfbd1657078'], + }), + ('bindeps', '1.2.1', { + 'checksums': ['3c11d75aa722bed67246852bb430a182361a128910d384b664b91f3e65bc34b5'], + }), + ('bio', '1.6.0.pre.20181210', { + 'checksums': ['c4114aeb99b012f90660b92ead4ca88c1578fd58252ed3ec46eb45dc4a2c6cc9'], + }), + ('threach', '0.2.0', { + 'checksums': ['432cbf3569bf9b09e26f93d0959fd6fb911c71e790e8a4cc4d1110e139a2ffca'], + }), + ('trollop', '2.9.10', { + 'checksums': ['ceca2d91f349163d6ee3e792d356d4ded7472e6da31ac6dcc5956d1b03607bf7'], + }), + (name, version, { + 'checksums': ['69c346e7d83efe9b9a383a39b57e7cce186a82b7074f275b14906f8f05678e3e'], + }), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['gems/%(namelower)s-%(version)s'], +} + +sanity_check_commands = ["%(namelower)s --help"] + +modextrapaths = {'GEM_PATH': ['']} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/crypt4gh/crypt4gh-1.7-GCC-12.3.0.eb b/easybuild/easyconfigs/c/crypt4gh/crypt4gh-1.7-GCC-12.3.0.eb new file mode 100644 index 000000000000..c52d7b3d83df --- /dev/null +++ b/easybuild/easyconfigs/c/crypt4gh/crypt4gh-1.7-GCC-12.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonBundle' + +name = 'crypt4gh' +version = '1.7' + +homepage = 'https://github.com/EGA-archive/crypt4gh' +description = """crypt4gh is a Python tool to encrypt, decrypt or re-encrypt files, +according to the GA4GH encryption file format.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('PyYAML', '6.0'), + ('cryptography', '41.0.1'), + ('bcrypt', '4.0.1'), +] + +use_pip = True + +exts_list = [ + (name, version, { + 'checksums': ['1569bc4ff9b689c8852e3892ac3f6fea4b31948ca0b1e5bc28d0d2f80def2a28'], + }), +] + +sanity_pip_check = True + +sanity_check_commands = ['crypt4gh -h'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/cryptography/cryptography-42.0.8-GCCcore-13.3.0.eb b/easybuild/easyconfigs/c/cryptography/cryptography-42.0.8-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..be6bff8c4784 --- /dev/null +++ b/easybuild/easyconfigs/c/cryptography/cryptography-42.0.8-GCCcore-13.3.0.eb @@ -0,0 +1,131 @@ +easyblock = 'CargoPythonPackage' + +name = 'cryptography' +version = '42.0.8' + +homepage = 'https://github.com/pyca/cryptography' +description = "cryptography is a package designed to expose cryptographic primitives and recipes to Python developers." + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +builddependencies = [ + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), + ('Rust', '1.78.0'), # required for cryptography + ('hatchling', '1.24.2'), + ('setuptools-rust', '1.9.0'), +] + +dependencies = [ + ('Python', '3.12.3'), + ('cffi', '1.16.0'), +] +crates = [ + ('asn1', '0.15.5'), + ('asn1_derive', '0.15.5'), + ('autocfg', '1.1.0'), + ('base64', '0.21.7'), + ('bitflags', '1.3.2'), + ('bitflags', '2.4.2'), + ('cc', '1.0.83'), + ('cfg-if', '1.0.0'), + ('foreign-types', '0.3.2'), + ('foreign-types-shared', '0.1.1'), + ('heck', '0.4.1'), + ('indoc', '2.0.4'), + ('libc', '0.2.152'), + ('lock_api', '0.4.11'), + ('memoffset', '0.9.0'), + ('once_cell', '1.19.0'), + ('openssl', '0.10.64'), + ('openssl-macros', '0.1.1'), + ('openssl-sys', '0.9.102'), + ('parking_lot', '0.12.1'), + ('parking_lot_core', '0.9.9'), + ('pem', '3.0.3'), + ('pkg-config', '0.3.29'), + ('portable-atomic', '1.6.0'), + ('proc-macro2', '1.0.78'), + ('pyo3', '0.20.3'), + ('pyo3-build-config', '0.20.3'), + ('pyo3-ffi', '0.20.3'), + ('pyo3-macros', '0.20.3'), + ('pyo3-macros-backend', '0.20.3'), + ('quote', '1.0.35'), + ('redox_syscall', '0.4.1'), + ('scopeguard', '1.2.0'), + ('self_cell', '1.0.3'), + ('smallvec', '1.13.1'), + ('syn', '2.0.48'), + ('target-lexicon', '0.12.13'), + ('unicode-ident', '1.0.12'), + ('unindent', '0.2.3'), + ('vcpkg', '0.2.15'), + ('windows-targets', '0.48.5'), + ('windows_aarch64_gnullvm', '0.48.5'), + ('windows_aarch64_msvc', '0.48.5'), + ('windows_i686_gnu', '0.48.5'), + ('windows_i686_msvc', '0.48.5'), + ('windows_x86_64_gnu', '0.48.5'), + ('windows_x86_64_gnullvm', '0.48.5'), + ('windows_x86_64_msvc', '0.48.5'), +] +sources = [SOURCE_TAR_GZ] +checksums = [ + {'cryptography-42.0.8.tar.gz': '8d09d05439ce7baa8e9e95b07ec5b6c886f548deb7e0f69ef25f64b3bce842f2'}, + {'asn1-0.15.5.tar.gz': 'ae3ecbce89a22627b5e8e6e11d69715617138290289e385cde773b1fe50befdb'}, + {'asn1_derive-0.15.5.tar.gz': '861af988fac460ac69a09f41e6217a8fb9178797b76fcc9478444be6a59be19c'}, + {'autocfg-1.1.0.tar.gz': 'd468802bab17cbc0cc575e9b053f41e72aa36bfa6b7f55e3529ffa43161b97fa'}, + {'base64-0.21.7.tar.gz': '9d297deb1925b89f2ccc13d7635fa0714f12c87adce1c75356b39ca9b7178567'}, + {'bitflags-1.3.2.tar.gz': 'bef38d45163c2f1dde094a7dfd33ccf595c92905c8f8f4fdc18d06fb1037718a'}, + {'bitflags-2.4.2.tar.gz': 'ed570934406eb16438a4e976b1b4500774099c13b8cb96eec99f620f05090ddf'}, + {'cc-1.0.83.tar.gz': 'f1174fb0b6ec23863f8b971027804a42614e347eafb0a95bf0b12cdae21fc4d0'}, + {'cfg-if-1.0.0.tar.gz': 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{'pyo3-ffi-0.20.3.tar.gz': '62b42531d03e08d4ef1f6e85a2ed422eb678b8cd62b762e53891c05faf0d4afa'}, + {'pyo3-macros-0.20.3.tar.gz': '7305c720fa01b8055ec95e484a6eca7a83c841267f0dd5280f0c8b8551d2c158'}, + {'pyo3-macros-backend-0.20.3.tar.gz': '7c7e9b68bb9c3149c5b0cade5d07f953d6d125eb4337723c4ccdb665f1f96185'}, + {'quote-1.0.35.tar.gz': '291ec9ab5efd934aaf503a6466c5d5251535d108ee747472c3977cc5acc868ef'}, + {'redox_syscall-0.4.1.tar.gz': '4722d768eff46b75989dd134e5c353f0d6296e5aaa3132e776cbdb56be7731aa'}, + {'scopeguard-1.2.0.tar.gz': '94143f37725109f92c262ed2cf5e59bce7498c01bcc1502d7b9afe439a4e9f49'}, + {'self_cell-1.0.3.tar.gz': '58bf37232d3bb9a2c4e641ca2a11d83b5062066f88df7fed36c28772046d65ba'}, + {'smallvec-1.13.1.tar.gz': 'e6ecd384b10a64542d77071bd64bd7b231f4ed5940fba55e98c3de13824cf3d7'}, + {'syn-2.0.48.tar.gz': '0f3531638e407dfc0814761abb7c00a5b54992b849452a0646b7f65c9f770f3f'}, + {'target-lexicon-0.12.13.tar.gz': '69758bda2e78f098e4ccb393021a0963bb3442eac05f135c30f61b7370bbafae'}, + {'unicode-ident-1.0.12.tar.gz': '3354b9ac3fae1ff6755cb6db53683adb661634f67557942dea4facebec0fee4b'}, + {'unindent-0.2.3.tar.gz': 'c7de7d73e1754487cb58364ee906a499937a0dfabd86bcb980fa99ec8c8fa2ce'}, + {'vcpkg-0.2.15.tar.gz': 'accd4ea62f7bb7a82fe23066fb0957d48ef677f6eeb8215f372f52e48bb32426'}, + {'windows-targets-0.48.5.tar.gz': '9a2fa6e2155d7247be68c096456083145c183cbbbc2764150dda45a87197940c'}, + {'windows_aarch64_gnullvm-0.48.5.tar.gz': '2b38e32f0abccf9987a4e3079dfb67dcd799fb61361e53e2882c3cbaf0d905d8'}, + {'windows_aarch64_msvc-0.48.5.tar.gz': 'dc35310971f3b2dbbf3f0690a219f40e2d9afcf64f9ab7cc1be722937c26b4bc'}, + {'windows_i686_gnu-0.48.5.tar.gz': 'a75915e7def60c94dcef72200b9a8e58e5091744960da64ec734a6c6e9b3743e'}, + {'windows_i686_msvc-0.48.5.tar.gz': '8f55c233f70c4b27f66c523580f78f1004e8b5a8b659e05a4eb49d4166cca406'}, + {'windows_x86_64_gnu-0.48.5.tar.gz': '53d40abd2583d23e4718fddf1ebec84dbff8381c07cae67ff7768bbf19c6718e'}, + {'windows_x86_64_gnullvm-0.48.5.tar.gz': '0b7b52767868a23d5bab768e390dc5f5c55825b6d30b86c844ff2dc7414044cc'}, + {'windows_x86_64_msvc-0.48.5.tar.gz': 'ed94fce61571a4006852b7389a063ab983c02eb1bb37b47f8272ce92d06d9538'}, +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-4.9-GCCcore-12.3.0.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-4.9-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..1f54c552c2e0 --- /dev/null +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-4.9-GCCcore-12.3.0.eb @@ -0,0 +1,60 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel +# Modified by: Adam Huffman, Jonas Demeulemeester +# The Francis Crick Institute +# Modified by: Albert Bogdanowicz +# Institute of Biochemistry and Biophysics PAS +# Modified by: Jasper Grimm +# University of York + +easyblock = 'PythonBundle' + +name = 'cutadapt' +version = '4.9' + +homepage = 'https://opensource.scilifelab.se/projects/cutadapt/' +description = """Cutadapt finds and removes adapter sequences, primers, poly-A tails and + other types of unwanted sequence from your high-throughput sequencing reads.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('Cython', '3.0.8'), # required for dnaio +] + +dependencies = [ + ('pigz', '2.8'), + ('Python', '3.11.3'), + ('python-isal', '1.1.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + # note: newer xopen versions require newer python-isal + ('xopen', '1.7.0', { + 'checksums': ['901f9c8298e95ed74767a4bd76d9f4cf71d8de27b8cf296ac3e7bc1c11520d9f'], + }), + ('dnaio', '1.2.1', { + 'checksums': ['4786dc63614b9f3011463d9ea9d981723dd38d1091a415a557f71d8c74400f38'], + }), + (name, version, { + 'checksums': ['da3b45775b07334d2e2580a7b154d19ea7e872f0da813bb1ac2a4da712bfc223'], + }), +] + +sanity_check_paths = { + 'files': ['bin/cutadapt'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "cutadapt --help", + "cutadapt --version", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/cyvcf2/cyvcf2-0.31.1-gfbf-2023a.eb b/easybuild/easyconfigs/c/cyvcf2/cyvcf2-0.31.1-gfbf-2023a.eb new file mode 100644 index 000000000000..6604fb2a1af3 --- /dev/null +++ b/easybuild/easyconfigs/c/cyvcf2/cyvcf2-0.31.1-gfbf-2023a.eb @@ -0,0 +1,45 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 +easyblock = 'PythonBundle' + +name = 'cyvcf2' +version = '0.31.1' + +homepage = 'https://github.com/brentp/cyvcf2' +description = "cyvcf2 is a cython wrapper around htslib built for fast parsing of Variant Call Format (VCF) files." + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('HTSlib', '1.18'), +] + +fix_python_shebang_for = ['bin/*'] + +use_pip = True + +exts_list = [ + ('humanfriendly', '10.0', { + 'checksums': ['6b0b831ce8f15f7300721aa49829fc4e83921a9a301cc7f606be6686a2288ddc'], + }), + ('coloredlogs', '15.0.1', { + 'checksums': ['7c991aa71a4577af2f82600d8f8f3a89f936baeaf9b50a9c197da014e5bf16b0'], + }), + (name, version, { + 'preinstallopts': 'CYVCF2_HTSLIB_MODE=EXTERNAL', + 'checksums': ['00bd0e09a3719d29fbc02bc8a40a690ac2c475e91744648750907d1816558fc5'], + }), +] + +sanity_check_paths = { + 'files': ['bin/cyvcf2'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["cyvcf2 --help"] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-13.3.0.eb b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..640228278059 --- /dev/null +++ b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-13.3.0.eb @@ -0,0 +1,33 @@ +name = 'DB' +version = '18.1.40' + +homepage = 'https://www.oracle.com/technetwork/products/berkeleydb' + +description = """Berkeley DB enables the development of custom data management + solutions, without the overhead traditionally associated with such custom + projects.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +# use http to allow auto-downloading... +source_urls = ['http://download.oracle.com/berkeley-db/'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['%(name)s-%(version)s_fix_doc_install.patch'] +checksums = [ + '0cecb2ef0c67b166de93732769abdeba0555086d51de1090df325e18ee8da9c8', # db-18.1.40.tar.gz + '441f48568156f72f02a8662998d293cc7edad687604b4f8af722f21c6db2a52d', # DB-18.1.40_fix_doc_install.patch +] + +builddependencies = [('binutils', '2.42')] + +dependencies = [('OpenSSL', '3', '', SYSTEM)] + +sanity_check_paths = { + 'files': ['bin/db_%s' % x for x in ['archive', 'checkpoint', 'convert', 'deadlock', 'dump', 'hotbackup', + 'load', 'log_verify', 'printlog', 'recover', 'replicate', 'stat', + 'tuner', 'upgrade', 'verify']] + + ['include/db.h', 'lib/libdb.a', 'lib/libdb.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/d/DB_File/DB_File-1.859-GCCcore-13.3.0.eb b/easybuild/easyconfigs/d/DB_File/DB_File-1.859-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..e7120c9c13e0 --- /dev/null +++ b/easybuild/easyconfigs/d/DB_File/DB_File-1.859-GCCcore-13.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'PerlModule' + +name = 'DB_File' +version = '1.859' + +homepage = 'https://perldoc.perl.org/DB_File.html' +description = """Perl5 access to Berkeley DB version 1.x.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://www.cpan.org/modules/by-module/DB_File/PMQS'] +sources = [SOURCE_TAR_GZ] +checksums = ['5674e0d2cd0b060c4d1253670ea022c64d842a55257f9eb8edb19c0f53e2565c'] + +builddependencies = [ + ('binutils', '2.42'), +] + +dependencies = [ + ('Perl', '5.38.2'), + ('DB', '18.1.40'), +] + +preconfigopts = 'env DB_FILE_INCLUDE="$EBROOTDB/include" DB_FILE_LIB="$EBROOTDB/lib" ' + +sanity_check_paths = { + 'files': ['lib/perl5/site_perl/%(perlver)s/%(arch)s-linux-thread-multi/DB_File.pm'], + 'dirs': [], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/d/DBus/DBus-1.15.8-GCCcore-13.3.0.eb b/easybuild/easyconfigs/d/DBus/DBus-1.15.8-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..ca182becfcdf --- /dev/null +++ b/easybuild/easyconfigs/d/DBus/DBus-1.15.8-GCCcore-13.3.0.eb @@ -0,0 +1,45 @@ +easyblock = 'CMakeMake' + +name = 'DBus' +version = '1.15.8' + +homepage = 'https://dbus.freedesktop.org/' + +description = """ + D-Bus is a message bus system, a simple way for applications to talk + to one another. In addition to interprocess communication, D-Bus helps + coordinate process lifecycle; it makes it simple and reliable to code + a "single instance" application or daemon, and to launch applications + and daemons on demand when their services are needed. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://dbus.freedesktop.org/releases/dbus'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['84fc597e6ec82f05dc18a7d12c17046f95bad7be99fc03c15bc254c4701ed204'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), + ('pkgconf', '2.2.0'), +] + +dependencies = [ + ('expat', '2.6.2'), +] + +configopts = '-DENABLE_SYSTEMD=OFF ' +# disable documentation +configopts += '-DDBUS_ENABLE_XML_DOCS=OFF -DDBUS_ENABLE_QTHELP_DOCS=OFF -DDBUS_ENABLE_DOXYGEN_DOCS=OFF ' + +sanity_check_paths = { + 'files': ['bin/dbus-%s' % x for x in + ['cleanup-sockets', 'daemon', 'launch', 'monitor', + 'run-session', 'send', 'uuidgen']] + + ['lib/libdbus-1.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/d/DETONATE/DETONATE-1.11-GCC-12.3.0.eb b/easybuild/easyconfigs/d/DETONATE/DETONATE-1.11-GCC-12.3.0.eb index c1457cc041cd..24a8b13835c3 100644 --- a/easybuild/easyconfigs/d/DETONATE/DETONATE-1.11-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/d/DETONATE/DETONATE-1.11-GCC-12.3.0.eb @@ -33,6 +33,7 @@ builddependencies = [ ] dependencies = [ + ('Perl', '5.36.1'), ('Boost', '1.82.0'), ('sparsehash', '2.0.4'), ('BamTools', '2.5.2'), @@ -45,16 +46,20 @@ buildopts = 'CXX="$CXX" CXXFLAGS="$CXXFLAGS -fopenmp" && cd ../rsem-eval && make runtest = 'test' -files_to_copy = [(['ref-eval', 'ref-eval-estimate-true-assembly', '../rsem-eval/rsem-*'], 'bin')] +files_to_copy = [ + (['ref-eval', 'ref-eval-estimate-true-assembly', '../rsem-eval/rsem-*', '../rsem-eval/*.pm'], 'bin'), +] sanity_check_paths = { 'files': ['bin/%s' % x for x in ['ref-eval', 'ref-eval-estimate-true-assembly', 'rsem-build-read-index', 'rsem-eval-calculate-score', 'rsem-eval-estimate-transcript-length-distribution', 'rsem-eval-run-em', 'rsem-extract-reference-transcripts', - 'rsem-parse-alignments', 'rsem-plot-model', 'rsem-preref', 'rsem-sam-validator', - 'rsem-scan-for-paired-end-reads', 'rsem-simulate-reads', + 'rsem-parse-alignments', 'rsem_perl_utils.pm', 'rsem-plot-model', 'rsem-preref', + 'rsem-sam-validator', 'rsem-scan-for-paired-end-reads', 'rsem-simulate-reads', 'rsem-synthesis-reference-transcripts']], 'dirs': [], } +sanity_check_commands = [r"rsem-eval-calculate-score --help 2>&1 | grep 'rsem-eval-calculate-score \[options\]'"] + moduleclass = 'bio' diff --git a/easybuild/easyconfigs/d/DL_POLY_4/DL_POLY_4-5.1.0-foss-2023a.eb b/easybuild/easyconfigs/d/DL_POLY_4/DL_POLY_4-5.1.0-foss-2023a.eb new file mode 100644 index 000000000000..1d47dce62d0c --- /dev/null +++ b/easybuild/easyconfigs/d/DL_POLY_4/DL_POLY_4-5.1.0-foss-2023a.eb @@ -0,0 +1,24 @@ +easyblock = 'CMakeMake' + +name = "DL_POLY_4" +version = "5.1.0" + +homepage = "https://www.scd.stfc.ac.uk/Pages/DL_POLY.aspx" +description = "DL_POLY is a general purpose classical molecular dynamics (MD) simulation software" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://gitlab.com/ccp5/dl-poly/-/archive/%(version)s/'] +sources = ['dl_poly_%(version)s.tar.bz2'] +checksums = ['da5364986cd71e047e080753f6ca75135bf19bd5607770b839dea3734c2fdfaa'] + +builddependencies = [('CMake', '3.26.3')] + +sanity_check_paths = { + 'files': ['bin/DLPOLY.Z'], + 'dirs': [] +} + +sanity_check_commands = ['DLPOLY.Z -h'] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/d/DL_POLY_Classic_GUI/DL_POLY_Classic_GUI-1.10.eb b/easybuild/easyconfigs/d/DL_POLY_Classic_GUI/DL_POLY_Classic_GUI-1.10.eb new file mode 100644 index 000000000000..84de0bbf36a2 --- /dev/null +++ b/easybuild/easyconfigs/d/DL_POLY_Classic_GUI/DL_POLY_Classic_GUI-1.10.eb @@ -0,0 +1,34 @@ +easyblock = 'JAR' + +name = 'DL_POLY_Classic_GUI' +version = '1.10' + +homepage = 'https://gitlab.com/DL_POLY_Classic/dl_poly' +description = """ +The DL_POLY Graphical User Interface (or GUI) is a program written in the +Java language and is intended for use with the DL_POLY molecular +simulation program. +This is the GUI for DL_POLY Classic, it can also be used for DL_POLY_4. +""" + +toolchain = SYSTEM + +source_urls = ['https://gitlab.com/DL_POLY_Classic/dl_poly/-/raw/RELEASE-%(version_major)s-%(version_minor)s/java/'] +sources = ['GUI.jar'] +checksums = ['8d3a5ed75d5ee8eb2e4403d8ed9355cd214c7e5b7afc8161c89a50edbc0a481d'] + +dependencies = [ + ('Java', '17', '', SYSTEM), +] + + +sanity_check_paths = { + 'files': ['GUI.jar'], + 'dirs': [''], +} + +modloadmsg = """ +To execute this Graphical User Interface run: java GUI +""" + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/d/DMTCP/DMTCP-3.0.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/d/DMTCP/DMTCP-3.0.0-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..0474c5e8f889 --- /dev/null +++ b/easybuild/easyconfigs/d/DMTCP/DMTCP-3.0.0-GCCcore-12.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'DMTCP' +version = '3.0.0' + +homepage = 'http://dmtcp.sourceforge.net/index.html' +description = """DMTCP is a tool to transparently checkpoint the state of multiple +simultaneous applications, including multi-threaded and distributed applications. +It operates directly on the user binary executable, without any Linux kernel modules +or other kernel modifications.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/dmtcp/dmtcp/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['2c7e95e1dbc55db33433bfee48a65f274298e98f246a36ab6dad1e0694750d37'] + +builddependencies = [('binutils', '2.39')] + +sanity_check_paths = { + 'files': ['bin/dmtcp_command', 'bin/dmtcp_discover_rm', 'bin/dmtcp_nocheckpoint', 'bin/dmtcp_srun_helper', + 'bin/dmtcp_sshd', 'bin/dmtcp_coordinator', 'bin/dmtcp_launch', 'bin/dmtcp_restart', 'bin/dmtcp_ssh'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/d/DMTCP/DMTCP-3.0.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/d/DMTCP/DMTCP-3.0.0-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..9947d4f758d7 --- /dev/null +++ b/easybuild/easyconfigs/d/DMTCP/DMTCP-3.0.0-GCCcore-12.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'DMTCP' +version = '3.0.0' + +homepage = 'http://dmtcp.sourceforge.net/index.html' +description = """DMTCP is a tool to transparently checkpoint the state of multiple +simultaneous applications, including multi-threaded and distributed applications. +It operates directly on the user binary executable, without any Linux kernel modules +or other kernel modifications.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/dmtcp/dmtcp/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['2c7e95e1dbc55db33433bfee48a65f274298e98f246a36ab6dad1e0694750d37'] + +builddependencies = [('binutils', '2.40')] + +sanity_check_paths = { + 'files': ['bin/dmtcp_command', 'bin/dmtcp_discover_rm', 'bin/dmtcp_nocheckpoint', 'bin/dmtcp_srun_helper', + 'bin/dmtcp_sshd', 'bin/dmtcp_coordinator', 'bin/dmtcp_launch', 'bin/dmtcp_restart', 'bin/dmtcp_ssh'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/d/DMTCP/DMTCP-3.0.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/d/DMTCP/DMTCP-3.0.0-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..9721668c2084 --- /dev/null +++ b/easybuild/easyconfigs/d/DMTCP/DMTCP-3.0.0-GCCcore-13.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'DMTCP' +version = '3.0.0' + +homepage = 'http://dmtcp.sourceforge.net/index.html' +description = """DMTCP is a tool to transparently checkpoint the state of multiple +simultaneous applications, including multi-threaded and distributed applications. +It operates directly on the user binary executable, without any Linux kernel modules +or other kernel modifications.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://github.com/dmtcp/dmtcp/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['2c7e95e1dbc55db33433bfee48a65f274298e98f246a36ab6dad1e0694750d37'] + +builddependencies = [('binutils', '2.40')] + +sanity_check_paths = { + 'files': ['bin/dmtcp_command', 'bin/dmtcp_discover_rm', 'bin/dmtcp_nocheckpoint', 'bin/dmtcp_srun_helper', + 'bin/dmtcp_sshd', 'bin/dmtcp_coordinator', 'bin/dmtcp_launch', 'bin/dmtcp_restart', 'bin/dmtcp_ssh'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/d/dblatex/dblatex-0.3.12-foss-2023a.eb b/easybuild/easyconfigs/d/dblatex/dblatex-0.3.12-foss-2023a.eb new file mode 100644 index 000000000000..db41d0c240fb --- /dev/null +++ b/easybuild/easyconfigs/d/dblatex/dblatex-0.3.12-foss-2023a.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'dblatex' +version = '0.3.12' + +homepage = 'https://dblatex.sourceforge.net/' +description = """dblatex is a program that transforms your SGML/XML DocBook documents to DVI, + PostScript or PDF by translating them into pure LaTeX as a first process. + MathML 2.0 markups are supported, too. It started as a clone of DB2LaTeX.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://master.dl.sourceforge.net/project/dblatex/dblatex/dblatex-%(version)s/'] +sources = ['%(name)s3-%(version)s.tar.bz2'] +checksums = ['16e82786272ed1806a079d37914d7ba7a594db792dc4cc34c1c3737dbd4da079'] + +dependencies = [ + ('Python', '3.11.3'), + ('libxslt', '1.1.38'), + ('texlive', '20230313'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +options = {'modulename': 'dbtexmf.dblatex'} + +postinstallcmds = ["cp -r %(builddir)s/%(name)s3-%(version)s/scripts %(installdir)s/bin"] + +sanity_check_commands = ['dblatex --help'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 000000000000..f04774b1b550 --- /dev/null +++ b/easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,83 @@ +easyblock = 'PythonBundle' + +name = 'dictys' +version = '1.1.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/pinellolab/dictys' +description = "Context specific and dynamic gene regulatory network reconstruction and analysis." + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [('poetry', '1.5.1')] +dependencies = [ + ('Python', '3.11.3'), + ('CUDA', '12.1.1', '', SYSTEM), + ('PyTorch-bundle', '2.1.2', versionsuffix), + ('pybedtools', '0.9.1'), + ('SAMtools', '1.18'), + ('MACS2', '2.2.9.1'), + ('FFmpeg', '6.0'), + ('matplotlib', '3.7.2'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('networkx', '3.1'), + ('h5py', '3.9.0'), + ('pyro-ppl', '1.9.0', versionsuffix), + ('adjustText', '0.7.3'), + ('Pysam', '0.22.0'), + ('paramiko', '3.2.0'), + ('Jupyter-bundle', '20230823'), + ('Qtconsole', '5.5.1'), + ('junos-eznc', '2.7.1'), +] + +# regenerate WellingtonC.c to works with python 3.11 + unpin matplotlib version +local_pyDNase_preinstallopts = ( + "cd pyDNase/footprinting && rm WellingtonC.c && cythonize -i WellingtonC.pyx && cd .. && cd .. && " + "sed -i 's/matplotlib < 2.0.0/matplotlib/' setup.py && " +) + +exts_list = [ + ('jupyter_console', '6.6.3', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['309d33409fcc92ffdad25f0bcdf9a4a9daa61b6f341177570fdac03de5352485'], + }), + ('jupyter', '1.0.0', { + 'checksums': ['d9dc4b3318f310e34c82951ea5d6683f67bed7def4b259fafbfe4f1beb1d8e5f'], + }), + ('args', '0.1.0', { + 'checksums': ['a785b8d837625e9b61c39108532d95b85274acd679693b71ebb5156848fcf814'], + }), + ('clint', '0.5.1', { + 'checksums': ['05224c32b1075563d0b16d0015faaf9da43aa214e4a2140e51f08789e7a4c5aa'], + }), + ('pynetbox', '7.4.0', { + 'checksums': ['fd0b1f197b3880048408ff5ed84422dd599bcd9389e32cb06a09b9b0d55c1636'], + }), + ('absl-py', '1.4.0', { + 'modulename': 'absl', + 'checksums': ['d2c244d01048ba476e7c080bd2c6df5e141d211de80223460d5b3b8a2a58433d'], + }), + ('aerleon', '1.9.0', { + 'checksums': ['850cd621dda750263db313d4473302b48b82adaaa9220e6fd0677cb7900f95f6'], + }), + ('homer', '0.7.0', { + 'checksums': ['efaf9b3948f6aecdf88cc87c0296a18aed77c152489a7f85c571965fb16f9e57'], + }), + ('pyDNase', '0.3.0', { + 'preinstallopts': local_pyDNase_preinstallopts, + 'modulename': 'pyDNase', + 'checksums': ['dba03cadca37929a1cc41545e962136f29efc41f8e3c6de042c51c47ee04d558'], + }), + (name, version, { + 'checksums': ['59610a8c57e9fc525ec5d13b69efc8b513c78a85a595e0e2b0138da62a035978'], + }), +] + +use_pip = True +sanity_pip_check = True + +sanity_check_commands = ["dictys --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a.eb b/easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a.eb new file mode 100644 index 000000000000..0b97a82cfde1 --- /dev/null +++ b/easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a.eb @@ -0,0 +1,81 @@ +easyblock = 'PythonBundle' + +name = 'dictys' +version = '1.1.0' + +homepage = 'https://github.com/pinellolab/dictys' +description = "Context specific and dynamic gene regulatory network reconstruction and analysis." + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [('poetry', '1.5.1')] +dependencies = [ + ('Python', '3.11.3'), + ('PyTorch-bundle', '2.1.2'), + ('pybedtools', '0.9.1'), + ('SAMtools', '1.18'), + ('MACS2', '2.2.9.1'), + ('FFmpeg', '6.0'), + ('matplotlib', '3.7.2'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('networkx', '3.1'), + ('h5py', '3.9.0'), + ('pyro-ppl', '1.9.0'), + ('adjustText', '0.7.3'), + ('Pysam', '0.22.0'), + ('paramiko', '3.2.0'), + ('Jupyter-bundle', '20230823'), + ('Qtconsole', '5.5.1'), + ('junos-eznc', '2.7.1'), +] + +# regenerate WellingtonC.c to works with python 3.11 + unpin matplotlib version +local_pyDNase_preinstallopts = ( + "cd pyDNase/footprinting && rm WellingtonC.c && cythonize -i WellingtonC.pyx && cd .. && cd .. && " + "sed -i 's/matplotlib < 2.0.0/matplotlib/' setup.py && " +) + +exts_list = [ + ('jupyter_console', '6.6.3', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['309d33409fcc92ffdad25f0bcdf9a4a9daa61b6f341177570fdac03de5352485'], + }), + ('jupyter', '1.0.0', { + 'checksums': ['d9dc4b3318f310e34c82951ea5d6683f67bed7def4b259fafbfe4f1beb1d8e5f'], + }), + ('args', '0.1.0', { + 'checksums': ['a785b8d837625e9b61c39108532d95b85274acd679693b71ebb5156848fcf814'], + }), + ('clint', '0.5.1', { + 'checksums': ['05224c32b1075563d0b16d0015faaf9da43aa214e4a2140e51f08789e7a4c5aa'], + }), + ('pynetbox', '7.4.0', { + 'checksums': ['fd0b1f197b3880048408ff5ed84422dd599bcd9389e32cb06a09b9b0d55c1636'], + }), + ('absl-py', '1.4.0', { + 'modulename': 'absl', + 'checksums': ['d2c244d01048ba476e7c080bd2c6df5e141d211de80223460d5b3b8a2a58433d'], + }), + ('aerleon', '1.9.0', { + 'checksums': ['850cd621dda750263db313d4473302b48b82adaaa9220e6fd0677cb7900f95f6'], + }), + ('homer', '0.7.0', { + 'checksums': ['efaf9b3948f6aecdf88cc87c0296a18aed77c152489a7f85c571965fb16f9e57'], + }), + ('pyDNase', '0.3.0', { + 'preinstallopts': local_pyDNase_preinstallopts, + 'modulename': 'pyDNase', + 'checksums': ['dba03cadca37929a1cc41545e962136f29efc41f8e3c6de042c51c47ee04d558'], + }), + (name, version, { + 'checksums': ['59610a8c57e9fc525ec5d13b69efc8b513c78a85a595e0e2b0138da62a035978'], + }), +] + +use_pip = True +sanity_pip_check = True + +sanity_check_commands = ["dictys --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/d/dorado/dorado-0.6.1-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/d/dorado/dorado-0.6.1-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 000000000000..e292bfcc18b3 --- /dev/null +++ b/easybuild/easyconfigs/d/dorado/dorado-0.6.1-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,80 @@ +easyblock = 'CMakeMake' + +name = 'dorado' +version = '0.6.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/nanoporetech/dorado' +description = """Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/nanoporetech/dorado/archive/'] +sources = [{ + 'git_config': { + 'url': 'https://github.com/nanoporetech', + 'repo_name': name, + 'tag': 'v%(version)s', + 'recursive': True, + }, + 'filename': SOURCE_TAR_GZ, +}] +patches = ['dorado-0.6.1_include-fstream.patch'] +checksums = [ + None, + 'a7692a2d67422d808b3b81f3a297b7b89299ab0091e5d01f0b8a9aee9b942377', +] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), +] + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('OpenSSL', '1.1', '', SYSTEM), + ('PyTorch', '2.1.2', '-CUDA-%(cudaver)s'), + ('HDF5', '1.14.0'), + ('zstd', '1.5.5'), + ('HTSlib', '1.18'), + ('kineto', '0.4.0'), + ('libaec', '1.0.6'), +] + +# don't link to OpenSSL static libraries +# fix for CMake Error "missing: OPENSSL_CRYPTO_LIBRARY" (if only shared OpenSSL libraries are available) +preconfigopts = "sed -i '/OPENSSL_USE_STATIC_LIBS TRUE/d' ../dorado/cmake/OpenSSL.cmake && " +preconfigopts += "export OPENSSL_ROOT_DIR=$EBROOTOPENSSL && " +# link in the ssl and crypto libs, to fix: +# undefined reference to symbol 'SSL_get_peer_certificate@@OPENSSL_1_1_0' +preconfigopts += "sed -i 's/OpenSSL::SSL/ssl\\n crypto/g' ../dorado/dorado/utils/CMakeLists.txt && " + +# don't use vendored HTSlib, use provided HTSlib dependency +preconfigopts += "rm -r ../dorado/dorado/3rdparty/htslib/ && " +preconfigopts += "sed -i '/add_dependencies.*htslib_project/d' ../dorado/CMakeLists.txt && " +preconfigopts += "sed -i '/add_dependencies.*htslib_project/d' ../dorado/dorado/utils/CMakeLists.txt && " +preconfigopts += "sed -i '/Htslib.cmake/d' ../dorado/CMakeLists.txt && " +# link with -lhts, not -lhtslib +preconfigopts += "sed -i 's/htslib/hts/g' ../dorado/CMakeLists.txt && " +preconfigopts += "sed -i 's/htslib/hts/g' ../dorado/dorado/utils/CMakeLists.txt && " + +# disable treating warnings like errors by stripping out -Werror +# cfr. https://github.com/nanoporetech/dorado/issues/779 +preconfigopts += "sed -i 's/-Werror//g' ../dorado/cmake/Warnings.cmake && " + +configopts = "-DDORADO_INSTALL_PATH=%(installdir)s " +configopts += "-DCUDA_TOOLKIT_ROOT_DIR=$EBROOTCUDA -DCMAKE_CUDA_COMPILER=$EBROOTCUDA/bin/nvcc " +configopts += "-DDORADO_LIBTORCH_DIR=$EBROOTPYTORCH/lib " +# add -pthread flag (in addition to -lpthread) to avoid linking error: +# in function `_GLOBAL__sub_I_mutex.cc': mutex.cc:(.text.startup+0x17): undefined reference to `pthread_atfork' +configopts += '-DCMAKE_C_FLAGS="$CFLAGS -pthread" ' + +sanity_check_paths = { + 'files': ['bin/dorado'], + 'dirs': [], +} + +sanity_check_commands = ["dorado basecaller --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/d/dorado/dorado-0.6.1_include-fstream.patch b/easybuild/easyconfigs/d/dorado/dorado-0.6.1_include-fstream.patch new file mode 100644 index 000000000000..c1165f3fe5c8 --- /dev/null +++ b/easybuild/easyconfigs/d/dorado/dorado-0.6.1_include-fstream.patch @@ -0,0 +1,27 @@ +add missing include to fix compiler errors like: + + error: variable std::ofstream summary_out has initializer but incomplete type + +see also https://github.com/nanoporetech/dorado/pull/780 + +author: Kenneth Hoste (HPC-UGent) +--- dorado/dorado/cli/duplex.cpp.orig 2024-04-30 17:59:15.483935823 +0200 ++++ dorado/dorado/cli/duplex.cpp 2024-04-30 17:59:34.658694274 +0200 +@@ -39,6 +39,7 @@ + #include + #include + #include ++#include + #include + #include + #include +--- dorado/dorado/cli/demux.cpp.orig 2024-04-30 18:13:40.327122548 +0200 ++++ dorado/dorado/cli/demux.cpp 2024-04-30 18:15:37.576760942 +0200 +@@ -17,6 +17,7 @@ + #include + + #include ++#include + #include + #include + #include diff --git a/easybuild/easyconfigs/d/dorado/dorado-0.7.3-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/d/dorado/dorado-0.7.3-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 000000000000..0e32e9616ca5 --- /dev/null +++ b/easybuild/easyconfigs/d/dorado/dorado-0.7.3-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,89 @@ +easyblock = 'CMakeMake' + +name = 'dorado' +version = '0.7.3' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/nanoporetech/dorado' +description = """Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/nanoporetech/dorado/archive/'] +sources = [{ + 'git_config': { + 'url': 'https://github.com/nanoporetech', + 'repo_name': name, + 'tag': 'v%(version)s', + 'recursive': True, + }, + 'filename': SOURCE_TAR_GZ, +}] +patches = [ + '%(name)s-%(version)s_include-fstream.patch', + '%(name)s-%(version)s_dont_install_external_libraries.patch', +] + +checksums = [ + None, + 'a32cbd34185bcc5ae3d552a072e396825aa7184187cd11c70a4380618387a530', + '2a250d606c0ae17f47d99981309fa204a1394ddd81851a1d530dcd0aea2306ac', +] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), +] + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('OpenSSL', '1.1', '', SYSTEM), + ('PyTorch', '2.1.2', '-CUDA-%(cudaver)s'), + ('HDF5', '1.14.0'), + ('zstd', '1.5.5'), + ('HTSlib', '1.18'), + ('kineto', '0.4.0'), + ('libaec', '1.0.6'), +] + +# don't link to OpenSSL static libraries +# fix for CMake Error "missing: OPENSSL_CRYPTO_LIBRARY" (if only shared OpenSSL libraries are available) +preconfigopts = "sed -i '/OPENSSL_USE_STATIC_LIBS TRUE/d' ../dorado/cmake/OpenSSL.cmake && " +# link in the ssl and crypto libs, to fix: +# undefined reference to symbol 'SSL_get_peer_certificate@@OPENSSL_1_1_0' +preconfigopts += "sed -i 's/OpenSSL::SSL/ssl\\n crypto/g' ../dorado/dorado/utils/CMakeLists.txt && " + +# don't use vendored HTSlib, use provided HTSlib dependency +preconfigopts += "rm -r ../dorado/dorado/3rdparty/htslib/ && " +preconfigopts += "sed -i '/add_dependencies.*htslib_project/d' ../dorado/CMakeLists.txt && " +preconfigopts += "sed -i '/add_dependencies.*htslib_project/d' ../dorado/dorado/utils/CMakeLists.txt && " +preconfigopts += "sed -i '/Htslib.cmake/d' ../dorado/CMakeLists.txt && " +# link with -lhts, not -lhtslib +preconfigopts += "sed -i 's/htslib/hts/g' ../dorado/CMakeLists.txt && " +preconfigopts += "sed -i 's/htslib/hts/g' ../dorado/dorado/utils/CMakeLists.txt && " + +# disable treating warnings like errors by stripping out -Werror +# cfr. https://github.com/nanoporetech/dorado/issues/779 +preconfigopts += "sed -i 's/-Werror//g' ../dorado/cmake/Warnings.cmake && " + +_copts = [ + "-DCUDA_TOOLKIT_ROOT_DIR=$EBROOTCUDA", + "-DCMAKE_CUDA_COMPILER=$EBROOTCUDA/bin/nvcc", + '-DOPENSSL_ROOT_DIR=$EBROOTOPENSSL', + "-DDORADO_LIBTORCH_DIR=$EBROOTPYTORCH/lib", + # add -pthread flag (in addition to -lpthread) to avoid linking error: + # in function `_GLOBAL__sub_I_mutex.cc': mutex.cc:(.text.startup+0x17): undefined reference to `pthread_atfork' + '-DCMAKE_C_FLAGS="$CFLAGS -pthread"', +] + +configopts = ' '.join(_copts) + +sanity_check_paths = { + 'files': ['bin/dorado'], + 'dirs': [], +} + +sanity_check_commands = ["dorado basecaller --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/d/dorado/dorado-0.7.3_dont_install_external_libraries.patch b/easybuild/easyconfigs/d/dorado/dorado-0.7.3_dont_install_external_libraries.patch new file mode 100644 index 000000000000..67bd9efee781 --- /dev/null +++ b/easybuild/easyconfigs/d/dorado/dorado-0.7.3_dont_install_external_libraries.patch @@ -0,0 +1,54 @@ +Don't install external libraries in Dorado's lib directory. + +Åke Sandgren, 2024-09-02 +diff --git a/CMakeLists.txt b/CMakeLists.txt +index a84c7524..0791dda8 100755 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -431,7 +431,7 @@ if(CMAKE_SYSTEM_NAME STREQUAL "Linux") + else() + # bundle the libraries from the cuda toolkit + file(GLOB NATIVE_CUDA_LIBS "${CUDAToolkit_TARGET_DIR}/targets/${CMAKE_SYSTEM_PROCESSOR}-linux/lib/${LIB}") +- install(FILES ${NATIVE_CUDA_LIBS} DESTINATION lib COMPONENT redist_libs) ++ #install(FILES ${NATIVE_CUDA_LIBS} DESTINATION lib COMPONENT redist_libs) + endif() + endforeach() + +@@ -444,14 +444,14 @@ if(CMAKE_SYSTEM_NAME STREQUAL "Linux") + RESOLVE_SYMLINKS("${DEBUG_LIBRARIES}" NEW_HDF_DEBUG_LIBRARIES) + foreach(HDF_LIB IN LISTS NEW_HDF_DEBUG_LIBRARIES) + if(${HDF_LIB} MATCHES "hdf5") +- install(FILES ${HDF_LIB} DESTINATION lib COMPONENT redist_libs CONFIGURATIONS Debug) ++ #install(FILES ${HDF_LIB} DESTINATION lib COMPONENT redist_libs CONFIGURATIONS Debug) + endif() + endforeach() + FILTER_LIST("${HDF5_C_LIBRARIES}" RELEASE_LIBRARIES optimized debug ${SHARED_LIB_EXT}) + RESOLVE_SYMLINKS("${RELEASE_LIBRARIES}" NEW_HDF_RELEASE_LIBRARIES) + foreach(HDF_LIB IN LISTS NEW_HDF_RELEASE_LIBRARIES) + if(${HDF_LIB} MATCHES "hdf5") +- install(FILES ${HDF_LIB} DESTINATION lib COMPONENT redist_libs CONFIGURATIONS Release ReleaseWithDebInfo) ++ #install(FILES ${HDF_LIB} DESTINATION lib COMPONENT redist_libs CONFIGURATIONS Release ReleaseWithDebInfo) + endif() + endforeach() + endif() +@@ -459,17 +459,17 @@ if(CMAKE_SYSTEM_NAME STREQUAL "Linux") + find_library(SZ_DLL sz REQUIRED) + get_filename_component(SZ_DLL_PATH ${SZ_DLL} DIRECTORY) + file(GLOB SZ_DLLS "${SZ_DLL_PATH}/libsz.so*") +- install(FILES ${SZ_DLLS} DESTINATION lib COMPONENT redist_libs) ++ #install(FILES ${SZ_DLLS} DESTINATION lib COMPONENT redist_libs) + + find_library(AEC_DLL aec REQUIRED) + get_filename_component(AEC_DLL_PATH ${AEC_DLL} DIRECTORY) + file(GLOB AEC_DLLS "${AEC_DLL_PATH}/libaec.so*") +- install(FILES ${AEC_DLLS} DESTINATION lib COMPONENT redist_libs) ++ #install(FILES ${AEC_DLLS} DESTINATION lib COMPONENT redist_libs) + + # If zstd has been dynamically linked, add the .so to the package + get_filename_component(ZSTD_LIBRARY_PATH ${ZSTD_LIBRARY_RELEASE} DIRECTORY) + file(GLOB ZSTD_DLLS "${ZSTD_LIBRARY_PATH}/*zstd.so*") +- install(FILES ${ZSTD_DLLS} DESTINATION lib COMPONENT redist_libs) ++ #install(FILES ${ZSTD_DLLS} DESTINATION lib COMPONENT redist_libs) + + elseif(WIN32) + file(GLOB TORCH_DLLS "${TORCH_LIB}/lib/*.dll") diff --git a/easybuild/easyconfigs/d/dorado/dorado-0.7.3_include-fstream.patch b/easybuild/easyconfigs/d/dorado/dorado-0.7.3_include-fstream.patch new file mode 100644 index 000000000000..bf8d2346e5d7 --- /dev/null +++ b/easybuild/easyconfigs/d/dorado/dorado-0.7.3_include-fstream.patch @@ -0,0 +1,27 @@ +add missing include to fix compiler errors like: + + error: variable std::ofstream summary_out has initializer but incomplete type + +see also https://github.com/nanoporetech/dorado/pull/780 + +author: Kenneth Hoste (HPC-UGent) +--- dorado/dorado/cli/duplex.cpp.orig 2024-04-30 17:59:15.483935823 +0200 ++++ dorado/dorado/cli/duplex.cpp 2024-04-30 17:59:34.658694274 +0200 +@@ -39,6 +39,7 @@ + #include + #include + #include ++#include + #include + #include + #include +--- dorado/dorado/cli/demux.cpp.orig 2024-04-30 18:13:40.327122548 +0200 ++++ dorado/dorado/cli/demux.cpp 2024-04-30 18:15:37.576760942 +0200 +@@ -17,6 +17,7 @@ + #include + + #include ++#include + #include + #include + #include \ No newline at end of file diff --git a/easybuild/easyconfigs/d/dtcmp/dtcmp-1.1.5-gompi-2024a.eb b/easybuild/easyconfigs/d/dtcmp/dtcmp-1.1.5-gompi-2024a.eb new file mode 100644 index 000000000000..5143b629849a --- /dev/null +++ b/easybuild/easyconfigs/d/dtcmp/dtcmp-1.1.5-gompi-2024a.eb @@ -0,0 +1,39 @@ +# +# Author: Robert Mijakovic +# +easyblock = 'ConfigureMake' + +name = 'dtcmp' +version = '1.1.5' + +homepage = 'https://github.com/LLNL/dtcmp' +description = """The Datatype Comparison (DTCMP) Library provides pre-defined and user-defined +comparison operations to compare the values of two items which can be arbitrary MPI datatypes. +Using these comparison operations, the library provides various routines for manipulating data, +which may be distributed over the processes of an MPI communicator.""" + +toolchain = {'name': 'gompi', 'version': '2024a'} + +github_account = 'LLNL' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['5c3d672fcf1be81e9afb65ef3f860a7dfe0f1bd79360ac63848acfe4d44439c9'] + +builddependencies = [ + ('Autotools', '20231222'), + ('pkgconf', '2.2.0'), +] + +dependencies = [ + ('lwgrp', '1.0.6'), +] + +preconfigopts = './autogen.sh && ' +configopts = '--with-lwgrp=$EBROOTLWGRP' + +sanity_check_paths = { + 'files': ['include/%(name)s.h', 'lib/lib%%(name)s.%s' % SHLIB_EXT, 'share/%(name)s/README.md'], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/d/duplex-tools/duplex-tools-0.3.3-foss-2023a.eb b/easybuild/easyconfigs/d/duplex-tools/duplex-tools-0.3.3-foss-2023a.eb new file mode 100644 index 000000000000..fb67d050e02c --- /dev/null +++ b/easybuild/easyconfigs/d/duplex-tools/duplex-tools-0.3.3-foss-2023a.eb @@ -0,0 +1,68 @@ +# Author: Jasper Grimm (UoY) +# Updated: Petr Král, Pavel Tománek (INUITS) +easyblock = 'PythonBundle' + +name = 'duplex-tools' +version = '0.3.3' + +homepage = 'https://github.com/nanoporetech/duplex-tools' +description = """ +Duplex Tools contains a set of utilities for dealing with Duplex sequencing data. Tools are provided + to identify and prepare duplex pairs for basecalling by Dorado (recommended) and Guppy, and for + recovering simplex basecalls from incorrectly concatenated pairs. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +_minimap2_ver = '2.26' +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('matplotlib', '3.7.2'), + ('edlib', '1.3.9'), + ('minimap2', _minimap2_ver), + ('python-parasail', '1.3.4'), + ('Pysam', '0.22.0'), + ('tqdm', '4.66.1'), + ('Arrow', '14.0.1'), + ('h5py', '3.9.0'), + ('pod5-file-format', '0.3.10'), + ('parasail', '2.6.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('mappy', _minimap2_ver, { + 'checksums': ['e53fbe9a3ea8762a64b8103f4f779c9fb16d418eaa0a731f45cebc83867a9b71'], + }), + ('natsort', '8.4.0', { + 'checksums': ['45312c4a0e5507593da193dedd04abb1469253b601ecaf63445ad80f0a1ea581'], + }), + ('pyfastx', '2.0.1', { + # PYPI source tarball is incomplete, causes ImportErrors + # see https://github.com/lmdu/pyfastx/issues/60 + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'source_urls': ['https://github.com/lmdu/%(name)s/archive'], + 'checksums': ['93aff63ce88bc5cfe7152d8dcb3f2164356bcd8f95a68fb20af107e59a7f9b55'], + }), + (name, version, { + 'sources': [{'download_filename': 'duplex_tools-%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'checksums': ['883e0a6610d14328a640b6a31eaef90592d2967cda68db0547a4d99924281300'], + }), +] + +_bins = ['dorado_stereo.sh', 'duplex_tools', 'minimap2.py', 'natsort', 'pyfastx'] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in _bins], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + 'dorado_stereo.sh -h', + 'duplex_tools --help', + 'pyfastx --help', +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/e/EGA-QuickView/EGA-QuickView-20240620-GCC-12.3.0.eb b/easybuild/easyconfigs/e/EGA-QuickView/EGA-QuickView-20240620-GCC-12.3.0.eb new file mode 100644 index 000000000000..24e7302367a7 --- /dev/null +++ b/easybuild/easyconfigs/e/EGA-QuickView/EGA-QuickView-20240620-GCC-12.3.0.eb @@ -0,0 +1,43 @@ +easyblock = 'ConfigureMake' + +name = 'EGA-QuickView' +version = '20240620' +local_commit = 'fe2034d' + +homepage = 'https://github.com/EGA-archive/ega-quickview' +description = """EGA-QuickView is a FUSE file system to access EGA files remotely.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +github_account = 'EGA-archive' +source_urls = [GITHUB_SOURCE] +sources = [{ + 'download_filename': '%s.tar.gz' % local_commit, + 'filename': '%(name)s-%(version)s.tar.gz', +}] +checksums = ['90836e42009736a8e20a2569918638f3cb2b53574265ca4f4bed7abd81a5e887'] + +builddependencies = [ + ('make', '4.4.1'), + ('Autotools', '20220317'), + ('pkgconf', '1.9.5'), +] + +dependencies = [ + ('libsodium', '1.0.18'), + ('FUSE', '3.16.2'), + ('GLib', '2.77.1'), +] + +preconfigopts = "autoreconf -i && " +# fix Makefile to create /bin in installdir +preinstallopts = "sed -i 's/install: $(TARGET)/install: $(TARGET) $(bindir)/' Makefile && " + +sanity_check_paths = { + 'files': ['bin/ega-qv'], + 'dirs': [], +} + +sanity_check_commands = ['ega-qv -h'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/e/EMMAX/EMMAX-20100310-foss-2023a.eb b/easybuild/easyconfigs/e/EMMAX/EMMAX-20100310-foss-2023a.eb new file mode 100644 index 000000000000..c68628823fb5 --- /dev/null +++ b/easybuild/easyconfigs/e/EMMAX/EMMAX-20100310-foss-2023a.eb @@ -0,0 +1,40 @@ +easyblock = 'MakeCp' + +name = 'EMMAX' +# version is based on datestamp of files in emmax-beta-src.tar.gz +# (last checked on 13 Aug 2024) +version = '20100310' + +homepage = 'https://csg.sph.umich.edu//kang/emmax' +description = """EMMAX is a statistical test for large scale human or model organism + association mapping accounting for the sample structure""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://csg.sph.umich.edu//kang/emmax/download/'] +sources = [{'download_filename': 'emmax-beta-src.tar.gz', 'filename': SOURCE_TAR_GZ}] +patches = ['EMMAX-20100310_fix-build.patch'] +checksums = [ + {'EMMAX-20100310.tar.gz': '79670917a0ac74ff1899fb27361e2e07b0f3a7911a9d9c6e0c18cf066b8987ea'}, + {'EMMAX-20100310_fix-build.patch': 'fae62d1f9f7bd4b94c81cdeb01d5134cc2825bcab050ddbfa89ce232eca8497e'}, +] + +dependencies = [ + ('zlib', '1.2.13'), +] + +buildopts = 'CC="$CC $CFLAGS" CLIBS="-lflexiblas -lm -lz"' + +files_to_copy = [(['emmax', 'emmax-kin'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/emmax', 'bin/emmax-kin'], + 'dirs': [], +} + +sanity_check_commands = [ + "emmax 2>&1 | grep '^Usage: emmax'", + "emmax-kin 2>&1 | grep '^Usage: emmax_IBS_kin'", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/e/EMMAX/EMMAX-20100310_fix-build.patch b/easybuild/easyconfigs/e/EMMAX/EMMAX-20100310_fix-build.patch new file mode 100644 index 000000000000..c2827ab10a98 --- /dev/null +++ b/easybuild/easyconfigs/e/EMMAX/EMMAX-20100310_fix-build.patch @@ -0,0 +1,88 @@ +fix build with recent compiler & BLAS/LAPACK library +author: Kenneth Hoste (HPC-UGent) + +--- emmax-beta-src/emmax.c.orig 2024-08-13 16:28:41.536119000 +0200 ++++ emmax-beta-src/emmax.c 2024-08-13 16:54:06.856501202 +0200 +@@ -7,7 +7,8 @@ + #include + #include + #include +-#include ++#include ++#include + #include + //#include "lapack_wrapper.h" + +@@ -1621,15 +1622,13 @@ + double *W, + double *WORK, int LWORK, int *IWORK, int LIWORK) + { +- extern void dsyevd_ (char *JOBZp, char *UPLOp, int *Np, +- double *A, int *LDAp, +- double *W, +- double *WORK, int *LWORKp, int *IWORK, int *LIWORKp, +- int *INFOp); + int INFO; +- dsyevd_ (&JOBZ, &UPLO, &N, A, &LDA, ++ int32_t N32 = N; ++ int32_t LDA32 = LDA; ++ int32_t LWORK32 = LWORK; ++ dsyevd_ (&JOBZ, &UPLO, &N32, A, &LDA32, + W, +- WORK, &LWORK, IWORK, &LIWORK, &INFO); ++ WORK, &LWORK32, IWORK, &LIWORK, &INFO, 1, 1); + + return INFO; + } +@@ -1640,16 +1639,11 @@ + double *W, double *Z, int LDZ, int *ISUPPZ, + double *WORK, int LWORK, int *IWORK, int LIWORK) + { +- extern void dsyevr_ (char *JOBZp, char *RANGEp, char *UPLOp, int *Np, +- double *A, int *LDAp, double *VLp, double *VUp, +- int *ILp, int *IUp, double *ABSTOLp, int *Mp, +- double *W, double *Z, int *LDZp, int *ISUPPZ, +- double *WORK, int *LWORKp, int *IWORK, int *LIWORKp, +- int *INFOp); + int INFO; +- dsyevr_ (&JOBZ, &RANGE, &UPLO, &N, A, &LDA, &VL, &VU, +- &IL, &IU, &ABSTOL, M, W, Z, &LDZ, ISUPPZ, +- WORK, &LWORK, IWORK, &LIWORK, &INFO); ++ int32_t N32 = N, LDA32 = LDA, IL32 = IL, IU32 = IU, LDZ32 = LDZ, LWORK32 = LWORK, LIWORK32 = LIWORK; ++ dsyevr_ (&JOBZ, &RANGE, &UPLO, &N32, A, &LDA32, &VL, &VU, ++ &IL32, &IU32, &ABSTOL, M, W, Z, &LDZ32, ISUPPZ, ++ WORK, &LWORK32, IWORK, &LIWORK32, &INFO, 1, 1, 1); + + return INFO; + } +@@ -1739,16 +1733,27 @@ + } + + /* Turn Y into its LU form, store pivot matrix */ +- info = clapack_dgetrf (CblasColMajor, n, n, Y, n, ipiv); ++ dgetrf_(&n, &n, Y, &n, ipiv, &info); + + /* Don't bother continuing when illegal argument (info<0) or singularity (info>0) occurs */ +- if (info!=0) return info; ++ if (info != 0) { ++ free(ipiv); ++ return info; ++ } + + /* Feed this to the lapack inversion routine. */ +- info = clapack_dgetri (CblasColMajor, n, Y, n, ipiv); ++ int lwork = n * n; ++ double *work = malloc(lwork * sizeof(double)); ++ if (work == NULL) { ++ printf("malloc failed for work array in matrix_invert\n"); ++ free(ipiv); ++ return 2; ++ } ++ dgetri_(&n, Y, &n, ipiv, work, &lwork, &info); + + /* Cleanup and exit */ + free(ipiv); ++ free(work); + return info; + } + diff --git a/easybuild/easyconfigs/e/ESIpy/ESIpy-20240709-foss-2022a.eb b/easybuild/easyconfigs/e/ESIpy/ESIpy-20240709-foss-2022a.eb new file mode 100644 index 000000000000..8b8af45bccf5 --- /dev/null +++ b/easybuild/easyconfigs/e/ESIpy/ESIpy-20240709-foss-2022a.eb @@ -0,0 +1,40 @@ +easyblock = 'Tarball' + +name = 'ESIpy' +version = '20240709' +_commit = '206f863' + +homepage = 'https://github.com/jgrebol/ESIpy' +description = """Program aimed at the calculation of population analysis and aromaticity +indicators from different Hilbert space partitions.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = [ + { + 'source_urls': ['https://github.com/jgrebol/ESIpy/archive'], + 'download_filename': '%s.tar.gz' % _commit, + 'filename': SOURCE_TAR_GZ, + }, +] +checksums = ['7f963f47558b26f545c8963b2191a78b5b2522347d78ee96f0462dccaa0b4f86'] + +dependencies = [ + ('Python', '3.10.4'), + ('PySCF', '2.1.1'), +] + +sanity_check_paths = { + 'files': ['esi.py'], + 'dirs': ['utils', 'examples'], +} + +sanity_check_commands = [ + "python -c 'import esi'", +] + +modextrapaths = { + 'PYTHONPATH': '', +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/e/ESMF/ESMF-8.6.0-foss-2023a.eb b/easybuild/easyconfigs/e/ESMF/ESMF-8.6.0-foss-2023a.eb new file mode 100644 index 000000000000..356f3864756d --- /dev/null +++ b/easybuild/easyconfigs/e/ESMF/ESMF-8.6.0-foss-2023a.eb @@ -0,0 +1,37 @@ +name = 'ESMF' +version = '8.6.0' + +homepage = 'https://www.earthsystemcog.org/projects/esmf/' +description = """The Earth System Modeling Framework (ESMF) is a suite of software tools for developing + high-performance, multi-component Earth science modeling applications.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'usempi': True, 'openmp': True, 'cstd': 'c++11', 'pic': True} + +source_urls = ['https://github.com/esmf-org/esmf/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['ESMF-6.1.1_libopts.patch'] +checksums = [ + 'ed057eaddb158a3cce2afc0712b49353b7038b45b29aee86180f381457c0ebe7', # v8.6.0.tar.gz + '3851627f07c32a7da55d99072d619942bd3a1d9dd002e1557716158e7aacdaf4', # ESMF-6.1.1_libopts.patch +] + +builddependencies = [('CMake', '3.26.3')] + +dependencies = [ + ('netCDF', '4.9.2'), + ('netCDF-Fortran', '4.6.1'), + ('netCDF-C++4', '4.3.1'), + ('libarchive', '3.6.2'), +] + +# disable errors from GCC 10 on mismatches between actual and dummy argument lists (GCC 9 behaviour) +prebuildopts = 'ESMF_F90COMPILEOPTS="${ESMF_F90COMPILEOPTS} -fallow-argument-mismatch"' + +buildopts = 'ESMF_NETCDF_INCLUDE=$EBROOTNETCDFMINFORTRAN/include ' +buildopts += 'ESMF_NETCDF_LIBS="`nc-config --libs` `nf-config --flibs` `ncxx4-config --libs`"' + +# too parallel causes the build to become really slow +maxparallel = 8 + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/e/ESMF/ESMF-8.6.1-foss-2023b.eb b/easybuild/easyconfigs/e/ESMF/ESMF-8.6.1-foss-2023b.eb new file mode 100644 index 000000000000..d8471ef09d1b --- /dev/null +++ b/easybuild/easyconfigs/e/ESMF/ESMF-8.6.1-foss-2023b.eb @@ -0,0 +1,37 @@ +name = 'ESMF' +version = '8.6.1' + +homepage = 'https://www.earthsystemcog.org/projects/esmf/' +description = """The Earth System Modeling Framework (ESMF) is a suite of software tools for developing + high-performance, multi-component Earth science modeling applications.""" + +toolchain = {'name': 'foss', 'version': '2023b'} +toolchainopts = {'usempi': True, 'openmp': True, 'cstd': 'c++11', 'pic': True} + +source_urls = ['https://github.com/esmf-org/esmf/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['ESMF-6.1.1_libopts.patch'] +checksums = [ + {'v8.6.1.tar.gz': 'dc270dcba1c0b317f5c9c6a32ab334cb79468dda283d1e395d98ed2a22866364'}, + {'ESMF-6.1.1_libopts.patch': '3851627f07c32a7da55d99072d619942bd3a1d9dd002e1557716158e7aacdaf4'}, +] + +builddependencies = [('CMake', '3.27.6')] + +dependencies = [ + ('netCDF', '4.9.2'), + ('netCDF-Fortran', '4.6.1'), + ('netCDF-C++4', '4.3.1'), + ('libarchive', '3.7.2'), +] + +# disable errors from GCC 10 on mismatches between actual and dummy argument lists (GCC 9 behaviour) +prebuildopts = 'ESMF_F90COMPILEOPTS="${ESMF_F90COMPILEOPTS} -fallow-argument-mismatch"' + +buildopts = 'ESMF_NETCDF_INCLUDE=$EBROOTNETCDFMINFORTRAN/include ' +buildopts += 'ESMF_NETCDF_LIBS="`nc-config --libs` `nf-config --flibs` `ncxx4-config --libs`"' + +# too parallel causes the build to become really slow +maxparallel = 8 + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.2-foss-2023b.eb b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.2-foss-2023b.eb new file mode 100644 index 000000000000..950f31dba266 --- /dev/null +++ b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.2-foss-2023b.eb @@ -0,0 +1,55 @@ +easyblock = 'CMakeMake' + +name = 'ESPResSo' +version = '4.2.2' + +homepage = 'https://espressomd.org/wordpress' +description = """A software package for performing and analyzing scientific Molecular Dynamics simulations.""" + +source_urls = ['https://github.com/espressomd/espresso/releases/download/%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['2bc02f91632b0030f1203759768bd718bd8a0005f72696980b12331b4bfa0d76'] + +toolchain = {'name': 'foss', 'version': '2023b'} +toolchainopts = {'usempi': True, 'pic': True} + +builddependencies = [('CMake', '3.27.6')] + +dependencies = [ + ('Python', '3.11.5'), + ('SciPy-bundle', '2023.11'), + ('Boost.MPI', '1.83.0'), + ('HDF5', '1.14.3'), + ('Mesa', '23.1.9'), + ('GSL', '2.7'), + ('IPython', '8.17.2'), + ('Pint', '0.24'), +] + +configopts = ' -DCMAKE_SKIP_RPATH=OFF -DWITH_TESTS=ON -DWITH_CUDA=OFF' +# make sure the right Python is used (note: -DPython3_EXECUTABLE or -DPython_EXECUTABLE does not work!) +configopts += ' -DPYTHON_EXECUTABLE=$EBROOTPYTHON/bin/python ' + +runtest = 'check_unit_tests && make check_python' + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +_binaries = ['ipypresso', 'pypresso'] +_libs = [ + 'Espresso_config', 'Espresso_core', 'Espresso_script_interface', 'Espresso_shapes', + '_init', 'analyze', 'code_info', 'electrokinetics', 'galilei', + 'integrate', 'interactions', 'lb', 'particle_data', 'polymer', 'profiler', + 'script_interface', 'system', 'thermostat', 'utils', 'version', +] + +_lib_path = 'lib/python%(pyshortver)s/site-packages/espressomd' + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in _binaries] + + [_lib_path + '/%s.' % x + SHLIB_EXT for x in _libs], + 'dirs': ['bin', 'lib'] +} + +sanity_check_commands = ['pypresso -h', 'ipypresso -h'] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.9.2.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.9.2.eb new file mode 100644 index 000000000000..cb476c53d7f5 --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.9.2.eb @@ -0,0 +1,56 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = '4.9.2' + +homepage = 'https://easybuilders.github.io/easybuild' +description = """EasyBuild is a software build and installation framework + written in Python that allows you to install software in a structured, + repeatable and robust way.""" + +toolchain = SYSTEM + +source_urls = [ + # easybuild-framework + 'https://files.pythonhosted.org/packages/cc/1f/676fc9e29c68e9c39c6dadf150ab4e5bf4907de4b9afd2bc6e0afd24ab7c/', + # easybuild-easyblocks + 'https://files.pythonhosted.org/packages/5d/85/e8593ceeb00c61253204e74d2a8360076ce016f42d83d33841f8e7de57a1/', + # easybuild-easyconfigs + 'https://files.pythonhosted.org/packages/99/b2/d899b4310bc54a10e0fb46995a2abc333857db16d116f22a53b0313d13d7/', +] +# note: subdirectory for each unpacked source tarball is renamed because custom easyblock in older EasyBuild version +# that is used for installing EasyBuild with EasyBuild expects subdirectories with '-' rather than '_'; +# see also https://github.com/easybuilders/easybuild-easyblocks/pull/3358 +sources = [ + { + 'filename': 'easybuild_framework-%(version)s.tar.gz', + 'extract_cmd': "tar xfvz %s && mv easybuild_framework-%(version)s easybuild-framework-%(version)s", + }, + { + 'filename': 'easybuild_easyblocks-%(version)s.tar.gz', + 'extract_cmd': "tar xfvz %s && mv easybuild_easyblocks-%(version)s easybuild-easyblocks-%(version)s", + }, + { + 'filename': 'easybuild_easyconfigs-%(version)s.tar.gz', + 'extract_cmd': "tar xfvz %s && mv easybuild_easyconfigs-%(version)s easybuild-easyconfigs-%(version)s", + }, +] +checksums = [ + {'easybuild_framework-4.9.2.tar.gz': 'cc6e0fe7bab2a96d424656ed70bf33e3b083eef5ceaa5d5fed88aa7b91dd3d63'}, + {'easybuild_easyblocks-4.9.2.tar.gz': '48202a89995a3d0a19228a35e409228bb6aa190ec7d7a7560e449303954953df'}, + {'easybuild_easyconfigs-4.9.2.tar.gz': '52d6f6378fc331cda8a94ff196d5bd6bb74c8029c973ee6a92763c256571eec7'}, +] + +# order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) +# EasyBuild is a (set of) Python packages, so it depends on Python +# usually, we want to use the system Python, so no actual Python dependency is listed +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +local_pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) + +sanity_check_paths = { + 'files': ['bin/eb'], + 'dirs': ['lib/python%s/site-packages' % local_pyshortver], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/e/EvidentialGene/EvidentialGene-2023.07.15-gompi-2023a.eb b/easybuild/easyconfigs/e/EvidentialGene/EvidentialGene-2023.07.15-gompi-2023a.eb new file mode 100644 index 000000000000..c4ae0c4e12dc --- /dev/null +++ b/easybuild/easyconfigs/e/EvidentialGene/EvidentialGene-2023.07.15-gompi-2023a.eb @@ -0,0 +1,40 @@ +easyblock = "PackedBinary" + +name = "EvidentialGene" +version = '2023.07.15' +local_month = ['', 'jan', 'feb', 'mar', 'apr', 'may', 'jun', 'jul', 'aug', 'sep', 'oct', 'nov', 'dec'] +local_dlver = version.split('.')[0][-2:] + local_month[int(version.split('.')[1])] + version.split('.')[2] + +homepage = 'http://arthropods.eugenes.org/EvidentialGene/' +description = """EvidentialGene is a genome informatics project for + "Evidence Directed Gene Construction for Eukaryotes", + for constructing high quality, accurate gene sets for + animals and plants (any eukaryotes), being developed by + Don Gilbert at Indiana University, gilbertd at indiana edu.""" + +toolchain = {'name': 'gompi', 'version': '2023a'} + +source_urls = [ + 'http://arthropods.eugenes.org/EvidentialGene/other/evigene_old/', + 'http://arthropods.eugenes.org/EvidentialGene/other/evigene_old/evigene_older/', +] +sources = ['evigene%s.tar' % local_dlver] +checksums = ['8fe8e5c21ac3f8b7134d8e26593fe66647eb8b7ba2c1cd1c158fc811769b9539'] + +dependencies = [ + ('Perl', '5.36.1'), + ('Exonerate', '2.4.0'), + ('CD-HIT', '4.8.1'), + ('BLAST+', '2.14.1'), +] + +fix_perl_shebang_for = ['scripts/*.pl', 'scripts/*/*.pl', 'scripts/*/*/*.pl'] + +sanity_check_paths = { + 'files': [], + 'dirs': ['scripts/'], +} + +modextravars = {'evigene': '%(installdir)s'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-GCC-12.3.0.eb b/easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-GCC-12.3.0.eb new file mode 100644 index 000000000000..4e57e85a280e --- /dev/null +++ b/easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-GCC-12.3.0.eb @@ -0,0 +1,47 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# foss-2016b modified by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'Exonerate' +version = '2.4.0' + +homepage = 'https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate' +# also https://github.com/nathanweeks/exonerate +description = """ Exonerate is a generic tool for pairwise sequence comparison. + It allows you to align sequences using a many alignment models, using either + exhaustive dynamic programming, or a variety of heuristics. """ + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://ftp.ebi.ac.uk/pub/software/vertebrategenomics/%(namelower)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f849261dc7c97ef1f15f222e955b0d3daf994ec13c9db7766f1ac7e77baa4042'] + +builddependencies = [ + ('pkgconf', '1.9.5'), +] +dependencies = [ + ('GLib', '2.77.1'), +] + +# parallel build fails +parallel = 1 + +runtest = 'check' + +_bins = ['exonerate', 'fastaclip', 'fastacomposition', 'fastafetch', 'fastaoverlap', 'ipcress'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in _bins], + 'dirs': ['share'], +} + +sanity_check_commands = ['%s -h | grep "from exonerate version %%(version)s"' % x for x in _bins] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-debug_add_event.patch b/easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-debug_add_event.patch new file mode 100644 index 000000000000..bd5c925f69f6 --- /dev/null +++ b/easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-debug_add_event.patch @@ -0,0 +1,12 @@ +diff -Nru extrae-4.2.0.orig/src/tracer/hwc/papi_hwc.c extrae-4.2.0/src/tracer/hwc/papi_hwc.c +--- extrae-4.2.0.orig/src/tracer/hwc/papi_hwc.c 2024-07-01 16:12:04.562957639 +0200 ++++ extrae-4.2.0/src/tracer/hwc/papi_hwc.c 2024-07-02 17:21:19.783586061 +0200 +@@ -615,7 +615,7 @@ + char EventName[PAPI_MAX_STR_LEN]; + + PAPI_event_code_to_name (HWC_sets[i].counters[j], EventName); +- fprintf (stderr, PACKAGE_NAME": Error! Hardware counter %s (0x%08x) cannot be added in set %d (task %d, thread %d)\n", EventName, HWC_sets[i].counters[j], i+1, TASKID, threadid); ++ fprintf (stderr, PACKAGE_NAME": Error! Hardware counter %s (0x%08x) cannot be added in set %d (task %d, thread %d) because of %d\n", EventName, HWC_sets[i].counters[j], i+1, TASKID, threadid, rc); + HWC_sets[i].counters[j] = NO_COUNTER; + /* break; */ + } diff --git a/easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-detect_binutils.patch b/easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-detect_binutils.patch new file mode 100644 index 000000000000..ae5847ad80e0 --- /dev/null +++ b/easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-detect_binutils.patch @@ -0,0 +1,42 @@ +diff -Nru extrae-4.2.0.orig/config/macros.m4 extrae-4.2.0/config/macros.m4 +--- extrae-4.2.0.orig/config/macros.m4 2024-07-01 16:12:03.689962036 +0200 ++++ extrae-4.2.0/config/macros.m4 2024-07-01 16:13:05.811649165 +0200 +@@ -779,6 +779,8 @@ + elif test -r "${binutils_home_dir}/lib/libbfd.a" -a \ + "${binutils_require_shared}" = "no" ; then + BFD_LIBSDIR="${binutils_home_dir}/lib" ++ elif test -r "${binutils_home_dir}/libbfd.so" ; then ++ BFD_LIBSDIR="${binutils_home_dir}" + else + dnl Try something more automatic using find command + libbfd_lib="" +@@ -814,6 +816,8 @@ + LIBERTY_LIBSDIR="${binutils_home_dir}/lib" + elif test -r "${binutils_home_dir}/lib/libiberty.a" ; then + LIBERTY_LIBSDIR="${binutils_home_dir}/lib" ++ elif test -r "${binutils_home_dir}/libiberty.a" ; then ++ LIBERTY_LIBSDIR="${binutils_home_dir}" + else + dnl Try something more automatic using find command + libiberty_lib="" +diff -Nru extrae-4.2.0.orig/configure extrae-4.2.0/configure +--- extrae-4.2.0.orig/configure 2024-07-01 16:12:03.308963954 +0200 ++++ extrae-4.2.0/configure 2024-07-01 16:17:00.458465744 +0200 +@@ -35074,6 +35074,8 @@ + elif test -r "${binutils_home_dir}/lib/libbfd.a" -a \ + "${binutils_require_shared}" = "no" ; then + BFD_LIBSDIR="${binutils_home_dir}/lib" ++ elif test -r "${binutils_home_dir}/libbfd.so" ; then ++ BFD_LIBSDIR="${binutils_home_dir}" + else + libbfd_lib="" + +@@ -35108,6 +35110,8 @@ + LIBERTY_LIBSDIR="${binutils_home_dir}/lib" + elif test -r "${binutils_home_dir}/lib/libiberty.a" ; then + LIBERTY_LIBSDIR="${binutils_home_dir}/lib" ++ elif test -r "${binutils_home_dir}/libiberty.a" ; then ++ LIBERTY_LIBSDIR="${binutils_home_dir}" + else + libiberty_lib="" + diff --git a/easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-fix-hw-counters-checks.patch b/easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-fix-hw-counters-checks.patch new file mode 100644 index 000000000000..2d588694b4c4 --- /dev/null +++ b/easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-fix-hw-counters-checks.patch @@ -0,0 +1,137 @@ +diff -Nru extrae-4.2.0.orig/tests/functional/hw-counters/check_Extrae_PAPI_TOT_CYC.sh extrae-4.2.0/tests/functional/hw-counters/check_Extrae_PAPI_TOT_CYC.sh +--- extrae-4.2.0.orig/tests/functional/hw-counters/check_Extrae_PAPI_TOT_CYC.sh 2024-07-01 16:12:03.454963219 +0200 ++++ extrae-4.2.0/tests/functional/hw-counters/check_Extrae_PAPI_TOT_CYC.sh 2024-07-03 16:51:00.533542188 +0200 +@@ -10,7 +10,29 @@ + EXTRAE_CONFIG_FILE=extrae-PAPI_TOT_CYC.xml ./check_Extrae_counters_xml + ../../../src/merger/mpi2prv -f TRACE.mpits -o ${TRACE}.prv + +-# Check ++# Check PAPI availability ++if ! command -v papi_avail &> /dev/null ++then ++ echo "papi_avail could not be found" ++ exit 0 ++fi ++ ++# Check COUNTER availability ++PAPI_TOT_CYC_available=`papi_avail | grep PAPI_TOT_CYC | awk '{print $3}'` ++if [[ "$PAPI_TOT_CYC_available" == No ]] ++then ++ echo "PAPI_TOT_CYC is not available" ++ exit 0 ++fi ++ ++# Check that HW counters are accessible ++ACCESS_LEVEL=`sysctl kernel.perf_event_paranoid |awk '{print $3}'` ++if [ $ACCESS_LEVEL \> 1 ] ++then ++ echo "perf_event_paranoid configuration does not allow access to HW counters" ++ exit 0 ++fi ++ + CheckEntryInPCF ${TRACE}.pcf PAPI_TOT_CYC + + rm -fr TRACE* set-0 ${TRACE}.??? +diff -Nru extrae-4.2.0.orig/tests/functional/hw-counters/check_Extrae_PAPI_TOT_INS_CYC.sh extrae-4.2.0/tests/functional/hw-counters/check_Extrae_PAPI_TOT_INS_CYC.sh +--- extrae-4.2.0.orig/tests/functional/hw-counters/check_Extrae_PAPI_TOT_INS_CYC.sh 2024-07-01 16:12:03.448963249 +0200 ++++ extrae-4.2.0/tests/functional/hw-counters/check_Extrae_PAPI_TOT_INS_CYC.sh 2024-07-03 16:52:55.509932826 +0200 +@@ -10,7 +10,30 @@ + EXTRAE_CONFIG_FILE=extrae-PAPI_TOT_INS_CYC.xml ./check_Extrae_counters_xml + ../../../src/merger/mpi2prv -f TRACE.mpits -o ${TRACE}.prv + +-# Check ++# Check PAPI availability ++if ! command -v papi_avail &> /dev/null ++then ++ echo "papi_avail could not be found" ++ exit 0 ++fi ++ ++# Check COUNTER availability ++PAPI_TOT_CYC_available=`papi_avail | grep PAPI_TOT_CYC | awk '{print $3}'` ++if [[ "$PAPI_TOT_CYC_available" == No ]] ++then ++ echo "PAPI_TOT_CYC is not available" ++ exit 0 ++fi ++ ++# Check counters accessibility level ++ACCESS_LEVEL=`sysctl kernel.perf_event_paranoid |awk '{print $3}'` ++if [ $ACCESS_LEVEL \> 1 ] ++then ++ echo "perf_event_paranoid configuration does not allow access to HW counters" ++ exit 0 ++fi ++ ++ + CheckEntryInPCF ${TRACE}.pcf PAPI_TOT_INS + CheckEntryInPCF ${TRACE}.pcf PAPI_TOT_CYC + +diff -Nru extrae-4.2.0.orig/tests/functional/hw-counters/check_Extrae_PAPI_TOT_INS.sh extrae-4.2.0/tests/functional/hw-counters/check_Extrae_PAPI_TOT_INS.sh +--- extrae-4.2.0.orig/tests/functional/hw-counters/check_Extrae_PAPI_TOT_INS.sh 2024-07-01 16:12:03.455963214 +0200 ++++ extrae-4.2.0/tests/functional/hw-counters/check_Extrae_PAPI_TOT_INS.sh 2024-07-03 16:54:17.878497036 +0200 +@@ -10,7 +10,29 @@ + EXTRAE_CONFIG_FILE=extrae-PAPI_TOT_INS.xml ./check_Extrae_counters_xml + ../../../src/merger/mpi2prv -f TRACE.mpits -o ${TRACE}.prv + +-# Check ++# Check PAPI availability ++if ! command -v papi_avail &> /dev/null ++then ++ echo "papi_avail could not be found" ++ exit 0 ++fi ++ ++# Check COUNTERS availability ++PAPI_TOT_INS_available=`papi_avail | grep PAPI_TOT_INS | awk '{print $3}'` ++if [[ "$PAPI_TOT_INS_available" == No ]] ++then ++ echo "PAPI_TOT_INS is not available" ++ exit 0 ++fi ++ ++# Check COUNTERS accessibility level ++ACCESS_LEVEL=`sysctl kernel.perf_event_paranoid |awk '{print $3}'` ++if [ $ACCESS_LEVEL \> 1 ] ++then ++ echo "perf_event_paranoid configuration does not allow access to HW counters" ++ exit 0 ++fi ++ + CheckEntryInPCF ${TRACE}.pcf PAPI_TOT_INS + + rm -fr TRACE* set-0 ${TRACE}.??? +diff -Nru extrae-4.2.0.orig/tests/functional/xml/check_Extrae_xml_envvar_counters.sh extrae-4.2.0/tests/functional/xml/check_Extrae_xml_envvar_counters.sh +--- extrae-4.2.0.orig/tests/functional/xml/check_Extrae_xml_envvar_counters.sh 2024-07-01 16:12:03.484963068 +0200 ++++ extrae-4.2.0/tests/functional/xml/check_Extrae_xml_envvar_counters.sh 2024-07-03 16:56:41.975736132 +0200 +@@ -10,7 +10,29 @@ + COUNTERS=PAPI_TOT_INS EXTRAE_CONFIG_FILE=extrae_envvar_counters.xml ./check_Extrae_xml + ../../../src/merger/mpi2prv -f TRACE.mpits -o ${TRACE}.prv + +-# Check ++# Check PAPI availability ++if ! command -v papi_avail &> /dev/null ++then ++ echo "papi_avail could not be found" ++ exit 0 ++fi ++ ++# Check COUNTER availability ++PAPI_TOT_INS_available=`papi_avail | grep PAPI_TOT_INS | awk '{print $3}'` ++if [[ "$PAPI_TOT_INS_available" == No ]] ++then ++ echo "PAPI_TOT_INS is not available" ++ exit 0 ++fi ++ ++# Check COUNTERS accessibility level ++ACCESS_LEVEL=`sysctl kernel.perf_event_paranoid |awk '{print $3}'` ++if [ $ACCESS_LEVEL \> 1 ] ++then ++ echo "perf_event_paranoid configuration does not allow access to HW counters" ++ exit 0 ++fi ++ + CheckEntryInPCF ${TRACE}.pcf PAPI_TOT_INS + + rm -fr TRACE* set-0 ${TRACE}.??? diff --git a/easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-gompi-2023b.eb b/easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-gompi-2023b.eb new file mode 100644 index 000000000000..4fca4663aca1 --- /dev/null +++ b/easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-gompi-2023b.eb @@ -0,0 +1,54 @@ +name = 'Extrae' +version = '4.2.0' + +homepage = 'https://tools.bsc.es/extrae' +description = """Extrae is the package devoted to generate Paraver trace-files for a post-mortem analysis. +Extrae is a tool that uses different interposition mechanisms to inject probes into the target application +so as to gather information regarding the application performance.""" + +toolchain = {'name': 'gompi', 'version': '2023b'} + +toolchainopts = {'usempi': True} + +source_urls = ['https://ftp.tools.bsc.es/%(namelower)s'] + +sources = ['%(namelower)s-%(version)s-src.tar.bz2'] + +patches = [ + 'Extrae-4.2.0-detect_binutils.patch', + 'Extrae-4.2.0-fix-hw-counters-checks.patch', + 'Extrae-4.2.0-debug_add_event.patch', +] + +checksums = [ + # extrae-4.2.0-src.tar.bz2 + '7b83a1ed008440bbc1bda88297d2d0e9256780db1cf8401b3c12718451f8919a', + '1c7bf9d97405c5c2f9dba3604faf141c1563c70958e942822aab521eb7ea0c9e', # Extrae-4.2.0-detect_binutils.patch + '147d897a5a9ba6ebb1b5de32c964b2cd73534f31a540125a94fd37f2ceb1edfe', # Extrae-4.2.0-fix-hw-counters-checks.patch + '9c3541b16f1acf6ff56ab44a24d44c2ec91f9415be217c39f9c0a32e2093ccca', # Extrae-4.2.0-debug_add_event.patch +] + +builddependencies = [ + ('Automake', '1.16.5'), +] + +dependencies = [ + ('zlib', '1.2.13'), + ('Boost', '1.83.0'), + ('libxml2', '2.11.5'), + ('libdwarf', '0.9.2'), + ('PAPI', '7.1.0'), +] + +# libunwind causes segv errors on aarch64 +if ARCH != 'aarch64': + dependencies.append( + ('libunwind', '1.6.2'), + ) + +# Disable dynamic memory instrumentation for this release, has been seen to sometimes cause MPI test failures +configopts = '--disable-instrument-dynamic-memory' + +runtest = 'check' + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/e/ecBuild/ecBuild-3.8.5-GCCcore-13.3.0.eb b/easybuild/easyconfigs/e/ecBuild/ecBuild-3.8.5-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..97c3992ce77f --- /dev/null +++ b/easybuild/easyconfigs/e/ecBuild/ecBuild-3.8.5-GCCcore-13.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'Tarball' + +name = 'ecBuild' +version = '3.8.5' + +homepage = 'https://ecbuild.readthedocs.io/' + +description = """ +A CMake-based build system, consisting of a collection of CMake macros and +functions that ease the managing of software build systems """ + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +github_account = 'ecmwf' +sources = [ + { + 'source_urls': [GITHUB_SOURCE], + 'filename': '%(version)s.tar.gz', + 'extract_cmd': 'tar -xzf %s --strip-components=1', + }, +] +checksums = ['aa0c44cab0fffec4c0b3542e91ebcc736b3d41b68a068d30c023ec0df5f93425'] + +builddependencies = [('binutils', '2.42')] + +buildininstalldir = True + +skipsteps = ['install'] + +sanity_check_paths = { + 'files': ['bin/ecbuild', 'cmake/ecbuild-config.cmake'], + 'dirs': ['bin', 'lib', 'share', 'cmake'], +} + +sanity_check_commands = ['ecbuild --help'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/e/ecCodes/ecCodes-2.27.0-iimpi-2022a.eb b/easybuild/easyconfigs/e/ecCodes/ecCodes-2.27.0-iimpi-2022a.eb new file mode 100644 index 000000000000..33fddc6886ae --- /dev/null +++ b/easybuild/easyconfigs/e/ecCodes/ecCodes-2.27.0-iimpi-2022a.eb @@ -0,0 +1,47 @@ +easyblock = 'CMakeMake' + +name = 'ecCodes' +version = '2.27.0' + +homepage = 'https://software.ecmwf.int/wiki/display/ECC/ecCodes+Home' +description = """ecCodes is a package developed by ECMWF which provides an application programming interface and + a set of tools for decoding and encoding messages in the following formats: WMO FM-92 GRIB edition 1 and edition 2, + WMO FM-94 BUFR edition 3 and edition 4, WMO GTS abbreviated header (only decoding).""" + +toolchain = {'name': 'iimpi', 'version': '2022a'} +toolchainopts = {'usempi': False} + +source_urls = ['https://confluence.ecmwf.int/download/attachments/45757960/'] +sources = ['eccodes-%(version)s-Source.tar.gz'] +checksums = ['ede5b3ffd503967a5eac89100e8ead5e16a881b7585d02f033584ed0c4269c99'] + +builddependencies = [('CMake', '3.23.1')] + +dependencies = [ + ('netCDF', '4.9.0'), + ('JasPer', '2.0.33'), + ('libjpeg-turbo', '2.1.3'), + ('libpng', '1.6.37'), + ('zlib', '1.2.12'), + ('libaec', '1.0.6'), +] + +# Python bindings are provided by a separate package 'eccodes-python' +configopts = "-DENABLE_NETCDF=ON -DENABLE_PNG=ON -DENABLE_PYTHON=OFF " +configopts += "-DENABLE_JPG=ON -DENABLE_JPG_LIBJASPER=ON " +configopts += "-DENABLE_ECCODES_THREADS=ON" # multi-threading with pthreads + +local_exes = ['%s_%s' % (a, b) + for a in ['bufr', 'grib', 'gts', 'metar'] + for b in ['compare', 'copy', 'dump', 'filter', 'get', 'ls']] +local_exes += ['codes_%s' % c for c in ['count', 'info', 'split_file']] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_exes] + + ['lib/libeccodes_f90.%s' % SHLIB_EXT, 'lib/libeccodes.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +sanity_check_commands = ['%s -V' % x for x in local_exes if not x.startswith('codes_')] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/e/einops/einops-0.7.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/e/einops/einops-0.7.0-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..7af581e455f5 --- /dev/null +++ b/easybuild/easyconfigs/e/einops/einops-0.7.0-GCCcore-12.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'einops' +version = '0.7.0' + +homepage = 'https://einops.rocks/' +description = """ +Flexible and powerful tensor operations for readable and reliable code. +Supports numpy, pytorch, tensorflow, jax, and others.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['b2b04ad6081a3b227080c9bf5e3ace7160357ff03043cd66cc5b2319eb7031d1'] + +builddependencies = [ + ('binutils', '2.39'), +] + +dependencies = [ + ('Python', '3.10.8'), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/e/elfutils/elfutils-0.191-GCCcore-13.3.0.eb b/easybuild/easyconfigs/e/elfutils/elfutils-0.191-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..e5eb4ef3c7d5 --- /dev/null +++ b/easybuild/easyconfigs/e/elfutils/elfutils-0.191-GCCcore-13.3.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'elfutils' +version = '0.191' + +homepage = 'https://elfutils.org/' + +description = """ + The elfutils project provides libraries and tools for ELF files + and DWARF data. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://sourceware.org/elfutils/ftp/%(version)s/'] +sources = [SOURCE_TAR_BZ2] +checksums = ['df76db71366d1d708365fc7a6c60ca48398f14367eb2b8954efc8897147ad871'] + +builddependencies = [ + ('M4', '1.4.19'), + ('pkgconf', '2.2.0'), +] + +dependencies = [ + ('binutils', '2.42'), + ('bzip2', '1.0.8'), + ('libarchive', '3.7.4'), + ('XZ', '5.4.5'), + ('zstd', '1.5.6'), +] + +configopts = "--disable-debuginfod --disable-libdebuginfod" + +sanity_check_paths = { + 'files': ['bin/eu-elfcmp', 'include/dwarf.h', 'lib/libelf.%s' % SHLIB_EXT], + 'dirs': [] +} + +sanity_check_commands = ["eu-elfcmp --help"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/e/empanada-dl/empanada-dl-0.1.7-foss-2023a.eb b/easybuild/easyconfigs/e/empanada-dl/empanada-dl-0.1.7-foss-2023a.eb new file mode 100644 index 000000000000..168c3e3c751c --- /dev/null +++ b/easybuild/easyconfigs/e/empanada-dl/empanada-dl-0.1.7-foss-2023a.eb @@ -0,0 +1,43 @@ +easyblock = 'PythonBundle' + +name = 'empanada-dl' +version = '0.1.7' + +homepage = 'https://empanada.readthedocs.io/' +description = "Tool for panoptic segmentation of organelles in 2D and 3D electron microscopy (EM) images." + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('numba', '0.58.1'), + ('OpenCV', '4.8.1', '-contrib'), + ('PyYAML', '6.0'), + ('zarr', '2.17.1'), + ('torchvision', '0.16.0'), + ('Albumentations', '1.4.0'), + ('dask', '2023.9.2'), + ('connected-components-3d', '3.14.1'), + ('matplotlib', '3.7.2'), + ('imagecodecs', '2024.1.1'), +] + +use_pip = True + +exts_list = [ + ('cztile', '0.1.2', { + 'checksums': ['3e42c4a93fd7b2df985b42e66dc3c585b3ebd9c1167e9f7e7d5c34c57697b929'], + }), + (name, version, { + # fix requirements - numpy version and opencv-python>=4.5.3 - pip is not aware of cv2 in OpenCV from EB + 'preinstallopts': "sed -i 's/numpy==1.22/numpy>=1.22/g' setup.cfg && sed -i '34d' setup.cfg && ", + 'modulename': 'empanada', + 'checksums': ['4289e69842242203be77cdb656a12fb2be4ed83816969b24a0b4eab1d67c3b91'], + }), +] + +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/e/empanada-napari/empanada-napari-1.1.0-foss-2023a.eb b/easybuild/easyconfigs/e/empanada-napari/empanada-napari-1.1.0-foss-2023a.eb new file mode 100644 index 000000000000..e429617f7180 --- /dev/null +++ b/easybuild/easyconfigs/e/empanada-napari/empanada-napari-1.1.0-foss-2023a.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonBundle' + +name = 'empanada-napari' +version = '1.1.0' + +homepage = 'https://empanada.readthedocs.io/' +description = "Panoptic segmentation algorithms for 2D and 3D electron microscopy in napari." + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('napari', '0.4.18'), + ('MLflow', '2.10.2'), + ('openpyxl', '3.1.2'), + ('SimpleITK', '2.3.1'), + ('imagecodecs', '2024.1.1'), + ('Albumentations', '1.4.0'), + ('connected-components-3d', '3.14.1'), + ('empanada-dl', '0.1.7'), +] + +exts_list = [ + ('ImageHash', '4.3.1', { + 'checksums': ['7038d1b7f9e0585beb3dd8c0a956f02b95a346c0b5f24a9e8cc03ebadaf0aa70'], + }), + (name, version, { + 'preinstallopts': "sed -i 's/numpy==1.22/numpy>=1.22/g' setup.cfg && ", + 'checksums': ['f4890cb6f20689933e28903dd7d43238aeae32afb53fa225bdf41d4bdcfc2c71'], + }), +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/e/expecttest/expecttest-0.2.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/e/expecttest/expecttest-0.2.1-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..a70bf3973ca2 --- /dev/null +++ b/easybuild/easyconfigs/e/expecttest/expecttest-0.2.1-GCCcore-13.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'expecttest' +version = '0.2.1' + +homepage = 'https://github.com/ezyang/expecttest' +description = """This library implements expect tests (also known as "golden" tests). Expect tests are a method of + writing tests where instead of hard-coding the expected output of a test, you run the test to get the output, and + the test framework automatically populates the expected output. If the output of the test changes, you can rerun + the test with the environment variable EXPECTTEST_ACCEPT=1 to automatically update the expected output.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['e52b1cf8a6f84506e6962a0bbdd248ea442124d826e849f263ec1c322ebb73f5'] + +builddependencies = [ + ('binutils', '2.42'), + ('poetry', '1.8.3'), +] +dependencies = [ + ('Python', '3.12.3'), +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-gmpich-2024.06.eb b/easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-gmpich-2024.06.eb new file mode 100644 index 000000000000..4b79e9e7c278 --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-gmpich-2024.06.eb @@ -0,0 +1,19 @@ +name = 'FFTW.MPI' +version = '3.3.10' + +homepage = 'https://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) +in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'gmpich', 'version': '2024.06'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = ['fftw-%(version)s.tar.gz'] +checksums = ['56c932549852cddcfafdab3820b0200c7742675be92179e59e6215b340e26467'] + +dependencies = [('FFTW', '3.3.10')] + +runtest = 'check' + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-gompi-2024a.eb b/easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-gompi-2024a.eb new file mode 100644 index 000000000000..2ed420c412f0 --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-gompi-2024a.eb @@ -0,0 +1,19 @@ +name = 'FFTW.MPI' +version = '3.3.10' + +homepage = 'https://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) +in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'gompi', 'version': '2024a'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = ['fftw-%(version)s.tar.gz'] +checksums = ['56c932549852cddcfafdab3820b0200c7742675be92179e59e6215b340e26467'] + +dependencies = [('FFTW', '3.3.10')] + +runtest = 'check' + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-7.0.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-7.0.2-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..246a8306b76f --- /dev/null +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-7.0.2-GCCcore-13.3.0.eb @@ -0,0 +1,45 @@ +easyblock = 'ConfigureMake' + +name = 'FFmpeg' +version = '7.0.2' + +homepage = 'https://www.ffmpeg.org/' +description = "A complete, cross-platform solution to record, convert and stream audio and video." + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://%(namelower)s.org/releases/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['1ed250407ea8f955cca2f1139da3229fbc13032a0802e4b744be195865ff1541'] + +builddependencies = [ + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), + ('ffnvcodec', '12.2.72.0', '', SYSTEM), # optional nvenc/dec support +] +dependencies = [ + ('NASM', '2.16.03'), + ('zlib', '1.3.1'), + ('bzip2', '1.0.8'), + ('x264', '20240513'), + ('LAME', '3.100'), + ('x265', '3.6'), + ('X11', '20240607'), + ('freetype', '2.13.2'), + ('fontconfig', '2.15.0'), + ('FriBidi', '1.0.15'), + ('SDL2', '2.30.6'), +] + +configopts = '--enable-pic --enable-shared --enable-gpl --enable-version3 --enable-nonfree --cc="$CC" --cxx="$CXX" ' +configopts += '--enable-libx264 --enable-libx265 --enable-libmp3lame --enable-libfreetype --enable-fontconfig ' +configopts += '--enable-libfribidi --enable-sdl2 --disable-htmlpages' + +sanity_check_paths = { + 'files': ['bin/ff%s' % x for x in ['mpeg', 'probe', 'play']] + + ['lib/lib%s.%s' % (x, y) for x in ['avdevice', 'avfilter', 'avformat', 'avcodec', 'postproc', + 'swresample', 'swscale', 'avutil'] for y in [SHLIB_EXT, 'a']], + 'dirs': ['include'] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/FLAC/FLAC-1.4.3-GCCcore-13.2.0.eb b/easybuild/easyconfigs/f/FLAC/FLAC-1.4.3-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..a0abaac6ca9f --- /dev/null +++ b/easybuild/easyconfigs/f/FLAC/FLAC-1.4.3-GCCcore-13.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'FLAC' +version = '1.4.3' + +homepage = 'https://xiph.org/flac/' +description = """FLAC stands for Free Lossless Audio Codec, an audio format similar to MP3, but lossless, meaning +that audio is compressed in FLAC without any loss in quality.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://ftp.osuosl.org/pub/xiph/releases/flac/'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['6c58e69cd22348f441b861092b825e591d0b822e106de6eb0ee4d05d27205b70'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [('libogg', '1.3.5')] + +configopts = '--enable-static --enable-shared' + +sanity_check_paths = { + 'files': ['bin/flac', 'lib/libFLAC.a', 'lib/libFLAC++.a', + 'lib/libFLAC.%s' % SHLIB_EXT, 'lib/libFLAC++.%s' % SHLIB_EXT], + 'dirs': ['include/FLAC', 'include/FLAC++'], +} + +sanity_check_commands = ["flac --help"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/FLAC/FLAC-1.4.3-GCCcore-13.3.0.eb b/easybuild/easyconfigs/f/FLAC/FLAC-1.4.3-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..f767483f7cde --- /dev/null +++ b/easybuild/easyconfigs/f/FLAC/FLAC-1.4.3-GCCcore-13.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'FLAC' +version = '1.4.3' + +homepage = 'https://xiph.org/flac/' +description = """FLAC stands for Free Lossless Audio Codec, an audio format similar to MP3, but lossless, meaning +that audio is compressed in FLAC without any loss in quality.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://ftp.osuosl.org/pub/xiph/releases/flac/'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['6c58e69cd22348f441b861092b825e591d0b822e106de6eb0ee4d05d27205b70'] + +builddependencies = [('binutils', '2.42')] + +dependencies = [('libogg', '1.3.5')] + +configopts = '--enable-static --enable-shared' + +sanity_check_paths = { + 'files': ['bin/flac', 'lib/libFLAC.a', 'lib/libFLAC++.a', + 'lib/libFLAC.%s' % SHLIB_EXT, 'lib/libFLAC++.%s' % SHLIB_EXT], + 'dirs': ['include/FLAC', 'include/FLAC++'], +} + +sanity_check_commands = ["flac --help"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-GCCcore-11.3.0.eb index 856159422b14..f82d2647cebd 100644 --- a/easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-GCCcore-11.3.0.eb @@ -18,13 +18,15 @@ builddependencies = [ ('binutils', '2.38'), ] -# -Dutils=True only works as root -configopts = '-Dutils=False' +# avoid that root permissions are required when installing utils (like fusermount) +configopts = "-Dinitscriptdir=%(installdir)s/etc/init.d -Dudevrulesdir=%(installdir)s/udev/rules.d -Duseroot=false" sanity_check_paths = { - 'files': ['lib64/libfuse%%(version_major)s.%s' % SHLIB_EXT, - 'lib64/pkgconfig/fuse%(version_major)s.pc'], - 'dirs': ['include/fuse%(version_major)s'], + 'files': ['bin/fusermount3', 'etc/fuse.conf', 'lib/libfuse%%(version_major)s.%s' % SHLIB_EXT, + 'lib/pkgconfig/fuse%(version_major)s.pc'], + 'dirs': ['include/fuse%(version_major)s', 'share/man'], } +sanity_check_commands = ["fusermount3 -h | grep '^fusermount3'"] + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-GCCcore-12.2.0.eb index 1be427492064..b16a0debad63 100644 --- a/easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-GCCcore-12.2.0.eb @@ -18,13 +18,15 @@ builddependencies = [ ('binutils', '2.39') ] -# -Dutils=True only works as root -configopts = '-Dutils=False' +# avoid that root permissions are required when installing utils (like fusermount) +configopts = "-Dinitscriptdir=%(installdir)s/etc/init.d -Dudevrulesdir=%(installdir)s/udev/rules.d -Duseroot=false" sanity_check_paths = { - 'files': ['lib64/libfuse%%(version_major)s.%s' % SHLIB_EXT, - 'lib64/pkgconfig/fuse%(version_major)s.pc'], - 'dirs': ['include/fuse%(version_major)s'], + 'files': ['bin/fusermount3', 'etc/fuse.conf', 'lib/libfuse%%(version_major)s.%s' % SHLIB_EXT, + 'lib/pkgconfig/fuse%(version_major)s.pc'], + 'dirs': ['include/fuse%(version_major)s', 'share/man'], } +sanity_check_commands = ["fusermount3 -h | grep '^fusermount3'"] + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/FUSE/FUSE-3.16.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/f/FUSE/FUSE-3.16.2-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..341358950aa3 --- /dev/null +++ b/easybuild/easyconfigs/f/FUSE/FUSE-3.16.2-GCCcore-12.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'MesonNinja' + +name = 'FUSE' +version = '3.16.2' + +homepage = 'https://github.com/libfuse/libfuse' +description = "The reference implementation of the Linux FUSE (Filesystem in Userspace) interface" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/libfuse/libfuse/archive/'] +sources = ['fuse-%(version)s.tar.gz'] +checksums = ['1bc306be1a1f4f6c8965fbdd79c9ccca021fdc4b277d501483a711cbd7dbcd6c'] + +builddependencies = [ + ('Meson', '1.1.1'), + ('Ninja', '1.11.1'), + ('binutils', '2.40'), +] + +# avoid that root permissions are required when installing utils (like fusermount) +configopts = "-Dinitscriptdir=%(installdir)s/etc/init.d -Dudevrulesdir=%(installdir)s/udev/rules.d -Duseroot=false" + +sanity_check_paths = { + 'files': ['bin/fusermount3', 'etc/fuse.conf', 'lib/libfuse%%(version_major)s.%s' % SHLIB_EXT, + 'lib/pkgconfig/fuse%(version_major)s.pc'], + 'dirs': ['include/fuse%(version_major)s', 'share/man'], +} + +sanity_check_commands = ["fusermount3 -h | grep '^fusermount3'"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-12.2.0.eb b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..abb4f2931280 --- /dev/null +++ b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-12.2.0.eb @@ -0,0 +1,42 @@ +# Updated from previous config +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'CmdCp' + +name = 'FastTree' +version = '2.1.11' + +homepage = 'http://www.microbesonline.org/fasttree/' +description = """FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide + or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of + time and memory. """ + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'openmp': True} + +# HTTPS cert error: +# hostname 'www.microbesonline.org' doesn't match either of 'genomics.lbl.gov', 'mojave.qb3.berkeley.edu', ... +source_urls = ['http://www.microbesonline.org/fasttree/'] +sources = [{'filename': '%(name)s-%(version)s.c', 'extract_cmd': 'cp %s FastTree.c'}] +checksums = ['9026ae550307374be92913d3098f8d44187d30bea07902b9dcbfb123eaa2050f'] + +builddependencies = [('binutils', '2.39')] + +cmds_map = [('%(name)s-%(version)s.c', '$CC -DOPENMP $CFLAGS $LIBS %%(source)s -o %(name)s')] + +files_to_copy = [(['FastTree'], 'bin')] + +# as FastTree is built with OpenMP, the correct binary is FastTreeMP +# the FastTree binary should normally be built without OpenMP, but let’s keep it as is for backward compatibility +# see http://www.microbesonline.org/fasttree/#OpenMP +postinstallcmds = ['cd %(installdir)s/bin && ln -s FastTree FastTreeMP'] + +sanity_check_paths = { + 'files': ['bin/FastTree'], + 'dirs': [], +} + +sanity_check_commands = ['FastTree 2>&1 | grep "FastTree Version %(version)s"'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/Filtlong/Filtlong-0.2.1-GCC-12.3.0.eb b/easybuild/easyconfigs/f/Filtlong/Filtlong-0.2.1-GCC-12.3.0.eb new file mode 100644 index 000000000000..25bf2c570f0b --- /dev/null +++ b/easybuild/easyconfigs/f/Filtlong/Filtlong-0.2.1-GCC-12.3.0.eb @@ -0,0 +1,39 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'MakeCp' + +name = 'Filtlong' +version = '0.2.1' + +homepage = 'https://github.com/rrwick/Filtlong' +description = """Filtlong is a tool for filtering long reads by quality. It can take a set + of long reads and produce a smaller, better subset. It uses both read length (longer is better) + and read identity (higher is better) when choosing which reads pass the filter""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/rrwick/Filtlong/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['e6f47675e87f98cf2481a60bef5cad38396f1e4db653a5c1673139f37770273a'] + +unpack_options = '--strip-components=1' + +parallel = 1 + +dependencies = [ + ('zlib', '1.2.13'), +] + +files_to_copy = ["*"] + +sanity_check_paths = { + 'files': ['bin/filtlong'], + 'dirs': [] +} + +sanity_check_commands = ["filtlong --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/Flask/Flask-3.0.3-GCCcore-13.3.0.eb b/easybuild/easyconfigs/f/Flask/Flask-3.0.3-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..46b9452f48b0 --- /dev/null +++ b/easybuild/easyconfigs/f/Flask/Flask-3.0.3-GCCcore-13.3.0.eb @@ -0,0 +1,65 @@ +easyblock = 'PythonBundle' + +name = 'Flask' +version = '3.0.3' + +homepage = 'https://flask.palletsprojects.com/' +description = """ +Flask is a lightweight WSGI web application framework. It is designed to make +getting started quick and easy, with the ability to scale up to complex +applications. +This module includes the Flask extensions: Flask-Cors""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('binutils', '2.42'), +] +dependencies = [ + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('itsdangerous', '2.2.0', { + 'checksums': ['e0050c0b7da1eea53ffaf149c0cfbb5c6e2e2b69c4bef22c81fa6eb73e5f6173'], + }), + ('werkzeug', '3.0.4', { + 'checksums': ['34f2371506b250df4d4f84bfe7b0921e4762525762bbd936614909fe25cd7306'], + }), + ('asgiref', '3.7.2', { + 'checksums': ['9e0ce3aa93a819ba5b45120216b23878cf6e8525eb3848653452b4192b92afed'], + }), + ('blinker', '1.8.2', { + 'checksums': ['8f77b09d3bf7c795e969e9486f39c2c5e9c39d4ee07424be2bc594ece9642d83'], + }), + ('flask', version, { + 'checksums': ['ceb27b0af3823ea2737928a4d99d125a06175b8512c445cbd9a9ce200ef76842'], + }), + ('msgspec', '0.18.6', { + 'checksums': ['a59fc3b4fcdb972d09138cb516dbde600c99d07c38fd9372a6ef500d2d031b4e'], + }), + ('Flask-Cors', '5.0.0', { + 'sources': ['flask_cors-%(version)s.tar.gz'], + 'checksums': ['5aadb4b950c4e93745034594d9f3ea6591f734bb3662e16e255ffbf5e89c88ef'], + }), + ('cachelib', '0.13.0', { + 'checksums': ['209d8996e3c57595bee274ff97116d1d73c4980b2fd9a34c7846cd07fd2e1a48'], + }), + ('Flask-Session', '0.8.0', { + 'sources': ['flask_session-%(version)s.tar.gz'], + 'checksums': ['20e045eb01103694e70be4a49f3a80dbb1b57296a22dc6f44bbf3f83ef0742ff'], + }), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['%(namelower)s --version'] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/Flax/Flax-0.8.4-gfbf-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/f/Flax/Flax-0.8.4-gfbf-2023a-CUDA-12.1.1.eb new file mode 100644 index 000000000000..4aeb0c7d8153 --- /dev/null +++ b/easybuild/easyconfigs/f/Flax/Flax-0.8.4-gfbf-2023a-CUDA-12.1.1.eb @@ -0,0 +1,44 @@ +easyblock = 'PythonBundle' + +name = 'Flax' +version = '0.8.4' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://flax.readthedocs.io' +description = """Flax is a high-performance neural network library and ecosystem for JAX that is +designed for flexibility: Try new forms of training by forking an example and +by modifying the training loop, not by adding features to a framework.""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('jax', '0.4.25', versionsuffix), + ('Optax', '0.2.2', versionsuffix), + ('protobuf-python', '4.24.0'), + ('PyYAML', '6.0'), +] + +use_pip = True + +exts_list = [ + ('nest_asyncio', '1.6.0', { + 'checksums': ['6f172d5449aca15afd6c646851f4e31e02c598d553a667e38cafa997cfec55fe'], + }), + ('orbax_checkpoint', '0.5.15', { + 'modulename': 'orbax.checkpoint', + 'checksums': ['15195e8d1b381b56f23a62a25599a3644f5d08655fa64f60bb1b938b8ffe7ef3'], + }), + ('tensorstore', '0.1.60', { + 'checksums': ['88da8f1978982101b8dbb144fd29ee362e4e8c97fc595c4992d555f80ce62a79'], + }), + ('flax', '0.8.4', { + 'checksums': ['968683f850198e1aa5eb2d9d1e20bead880ef7423c14f042db9d60848cb1c90b'], + }), +] + +sanity_pip_check = True + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/f/Flax/Flax-0.8.4-gfbf-2023a.eb b/easybuild/easyconfigs/f/Flax/Flax-0.8.4-gfbf-2023a.eb new file mode 100644 index 000000000000..dedc08531c39 --- /dev/null +++ b/easybuild/easyconfigs/f/Flax/Flax-0.8.4-gfbf-2023a.eb @@ -0,0 +1,42 @@ +easyblock = 'PythonBundle' + +name = 'Flax' +version = '0.8.4' + +homepage = 'https://flax.readthedocs.io' +description = """Flax is a high-performance neural network library and ecosystem for JAX that is +designed for flexibility: Try new forms of training by forking an example and +by modifying the training loop, not by adding features to a framework.""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('jax', '0.4.25'), + ('Optax', '0.2.2'), + ('protobuf-python', '4.24.0'), + ('PyYAML', '6.0'), +] + +use_pip = True + +exts_list = [ + ('nest_asyncio', '1.6.0', { + 'checksums': ['6f172d5449aca15afd6c646851f4e31e02c598d553a667e38cafa997cfec55fe'], + }), + ('orbax_checkpoint', '0.5.15', { + 'modulename': 'orbax.checkpoint', + 'checksums': ['15195e8d1b381b56f23a62a25599a3644f5d08655fa64f60bb1b938b8ffe7ef3'], + }), + ('tensorstore', '0.1.60', { + 'checksums': ['88da8f1978982101b8dbb144fd29ee362e4e8c97fc595c4992d555f80ce62a79'], + }), + ('flax', '0.8.4', { + 'checksums': ['968683f850198e1aa5eb2d9d1e20bead880ef7423c14f042db9d60848cb1c90b'], + }), +] + +sanity_pip_check = True + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/f/Flye/Flye-2.9.4-GCC-13.2.0.eb b/easybuild/easyconfigs/f/Flye/Flye-2.9.4-GCC-13.2.0.eb new file mode 100644 index 000000000000..c11373f69a1b --- /dev/null +++ b/easybuild/easyconfigs/f/Flye/Flye-2.9.4-GCC-13.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'Flye' +version = '2.9.4' + +homepage = 'https://github.com/fenderglass/Flye' +description = """Flye is a de novo assembler for long and noisy reads, such as those produced by PacBio + and Oxford Nanopore Technologies.""" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +source_urls = ['https://github.com/fenderglass/Flye/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['197a2dfe39fc324a39d8e1901af4f539609159c4a64a578ec8e60f73f5ea4696'] + +dependencies = [('Python', '3.11.5')] + +download_dep_fail = True +use_pip = True + +if ARCH == "aarch64": + preinstallopts = 'export arm_neon=1 && export aarch64=1 && ' + +sanity_check_paths = { + 'files': ['bin/flye'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['%(namelower)s --help'] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/FragGeneScan/FragGeneScan-1.31-GCCcore-12.3.0.eb b/easybuild/easyconfigs/f/FragGeneScan/FragGeneScan-1.31-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..8466e596a3d9 --- /dev/null +++ b/easybuild/easyconfigs/f/FragGeneScan/FragGeneScan-1.31-GCCcore-12.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'MakeCp' + +name = 'FragGeneScan' +version = '1.31' + +homepage = 'https://omics.informatics.indiana.edu/FragGeneScan/' +description = "FragGeneScan is an application for finding (fragmented) genes in short reads." + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(name)s%(version)s.tar.gz'] +checksums = ['cd3212d0f148218eb3b17d24fcd1fc897fb9fee9b2c902682edde29f895f426c'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [('Perl', '5.36.1')] + +fix_perl_shebang_for = ['*.pl'] + +prebuildopts = "make clean && " +buildopts = 'CC="$CC" CFLAG="$CFLAGS" fgs && chmod -R go+rx *.pl train example' + +files_to_copy = ['FragGeneScan', 'run_FragGeneScan.pl', 'example', 'train'] + +modextrapaths = {'PATH': ['']} + +sanity_check_paths = { + 'files': ['FragGeneScan', 'run_FragGeneScan.pl'], + 'dirs': ['example', 'train'], +} + +sanity_check_commands = [ + "run_FragGeneScan.pl help", + "run_FragGeneScan.pl -genome=./example/NC_000913.fna -out=./example/NC_000913-fgs -complete=1 -train=complete", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.15-GCCcore-13.3.0.eb b/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.15-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..a31f21a37dd4 --- /dev/null +++ b/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.15-GCCcore-13.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'FriBidi' +version = '1.0.15' + +homepage = 'https://github.com/fribidi/fribidi' + +description = """ + The Free Implementation of the Unicode Bidirectional Algorithm. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/fribidi/fribidi/releases/download/v%(version)s'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['0bbc7ff633bfa208ae32d7e369cf5a7d20d5d2557a0b067c9aa98bcbf9967587'] + +builddependencies = [ + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), + ('Autotools', '20231222'), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s', 'include/%(namelower)s/%(namelower)s.h', + 'lib/lib%%(namelower)s.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/fastahack/fastahack-1.0.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/f/fastahack/fastahack-1.0.0-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..2d430c8a5f21 --- /dev/null +++ b/easybuild/easyconfigs/f/fastahack/fastahack-1.0.0-GCCcore-12.2.0.eb @@ -0,0 +1,36 @@ +# Updated: Denis Kristak (INUITS) +# Updated: Petr Král (INUITS) + +easyblock = 'ConfigureMake' + +name = 'fastahack' +version = '1.0.0' + +homepage = 'https://github.com/ekg/fastahack' +description = """Utilities for indexing and sequence extraction from FASTA files.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +github_account = 'ekg' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_build-libs.patch'] +checksums = [ + 'cc1c04729b0c8ba3647cbb7e15e2b490ce701d73773f30f5892d68c36a1dceae', # v1.0.0.tar.gz + '7f804486c6bafd9b1572cb5f86ff28dbebb4d6da551bde1091d6ff8f82748bf4', # fastahack-1.0.0_build-libs.patch +] + +builddependencies = [('binutils', '2.39')] + +skipsteps = ['configure'] + +installopts = 'PREFIX=%(installdir)s ' + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'lib/libfastahack.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ['%(name)s --help'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/fastfilters/fastfilters-0.3-foss-2023a.eb b/easybuild/easyconfigs/f/fastfilters/fastfilters-0.3-foss-2023a.eb new file mode 100644 index 000000000000..a9d67a037980 --- /dev/null +++ b/easybuild/easyconfigs/f/fastfilters/fastfilters-0.3-foss-2023a.eb @@ -0,0 +1,46 @@ +easyblock = 'CMakeMake' + +name = 'fastfilters' +version = '0.3' + +homepage = 'https://github.com/ilastik/fastfilters/' +description = """Fast gaussian and derivative convolutional filters.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'optarch': False} + +sources = [{ + 'filename': 'v%(version)s.tar.gz', + 'git_config': { + 'url': 'https://github.com/ilastik', + 'repo_name': 'fastfilters', + 'tag': 'v%(version)s', + 'recursive': True, + 'keep_git_dir': True, + } +}] +checksums = [None] + +builddependencies = [ + ('CMake', '3.26.3'), +] +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('pybind11', '2.11.1'), +] + +configopts = '-DFF_INSTALL_DIR="%(installdir)s/lib/python%(pyshortver)s/site-packages/" ' +configopts += '-DPYTHON_EXECUTABLE="$EBROOTPYTHON/bin/python"' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib', 'include'], +} + +sanity_check_commands = ["python -c 'import fastfilters'"] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/fastp/fastp-0.23.4-GCC-13.2.0.eb b/easybuild/easyconfigs/f/fastp/fastp-0.23.4-GCC-13.2.0.eb new file mode 100644 index 000000000000..49b2a29c4f91 --- /dev/null +++ b/easybuild/easyconfigs/f/fastp/fastp-0.23.4-GCC-13.2.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'fastp' +version = '0.23.4' + +homepage = 'https://github.com/OpenGene/fastp' +description = """A tool designed to provide fast all-in-one preprocessing for FastQ files. + This tool is developed in C++ with multithreading supported to afford high performance.""" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +github_account = 'OpenGene' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['4fad6db156e769d46071add8a778a13a5cb5186bc1e1a5f9b1ffd499d84d72b5'] + +dependencies = [ + ('zlib', '1.2.13'), + ('libdeflate', '1.19'), + ('ISA-L', '2.31.0'), +] + +skipsteps = ['configure'] + +buildopts = ' CXX=${CXX}' + +preinstallopts = 'mkdir -p %(installdir)s/bin && ' + +installopts = 'PREFIX=%(installdir)s' + +sanity_check_paths = { + 'files': ['bin/fastp'], + 'dirs': [], +} + +sanity_check_commands = [('fastp', '--help')] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/ffnvcodec/ffnvcodec-12.2.72.0.eb b/easybuild/easyconfigs/f/ffnvcodec/ffnvcodec-12.2.72.0.eb new file mode 100644 index 000000000000..cc4461c3a8bd --- /dev/null +++ b/easybuild/easyconfigs/f/ffnvcodec/ffnvcodec-12.2.72.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'ffnvcodec' +version = '12.2.72.0' + +homepage = 'https://git.videolan.org/?p=ffmpeg/nv-codec-headers.git' + +description = """FFmpeg nvidia headers. Adds support for nvenc and nvdec. Requires Nvidia GPU and drivers to be present +(picked up dynamically).""" + +toolchain = SYSTEM + +sources = [{ + 'git_config': { + 'url': 'https://git.videolan.org/git/ffmpeg/', + 'repo_name': 'nv-codec-headers', + 'tag': 'n%(version)s', + }, + 'filename': SOURCE_TAR_GZ, +}] +checksums = [None] + +skipsteps = ['configure'] + +preinstallopts = 'sed -i "s|PREFIX =.*|PREFIX ?= %(installdir)s|" Makefile && ' + +sanity_check_paths = { + 'files': ['include/ffnvcodec/nvEncodeAPI.h', 'lib/pkgconfig/ffnvcodec.pc'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/file/file-5.43-GCCcore-13.2.0.eb b/easybuild/easyconfigs/f/file/file-5.43-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..dcd8b7cbfa0b --- /dev/null +++ b/easybuild/easyconfigs/f/file/file-5.43-GCCcore-13.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'file' +version = '5.43' + +homepage = 'https://www.darwinsys.com/file/' +description = """The file command is 'a file type guesser', that is, a command-line tool + that tells you in words what kind of data a file contains.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['ftp://ftp.astron.com/pub/file/'] +sources = [SOURCE_TAR_GZ] +checksums = ['8c8015e91ae0e8d0321d94c78239892ef9dbc70c4ade0008c0e95894abfb1991'] + +builddependencies = [ + ('Autotools', '20220317'), + ('binutils', '2.40'), +] + +preconfigopts = "autoreconf -f -i && " + +sanity_check_paths = { + 'files': ['bin/file', 'include/magic.h', 'lib/libmagic.%s' % SHLIB_EXT], + 'dirs': ['share'] +} + +sanity_check_commands = ['%(name)s --help'] + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/f/filevercmp/filevercmp-20191210-GCCcore-12.2.0.eb b/easybuild/easyconfigs/f/filevercmp/filevercmp-20191210-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..f9acad2dfe36 --- /dev/null +++ b/easybuild/easyconfigs/f/filevercmp/filevercmp-20191210-GCCcore-12.2.0.eb @@ -0,0 +1,37 @@ +# Updated: Denis Kristak (INUITS) +# Updated: Petr Král (INUITS) + +easyblock = 'ConfigureMake' + +name = 'filevercmp' +version = '20191210' +local_commit = 'df20dcc' + +homepage = 'https://github.com/ekg/filevercmp' +description = """filevercmp function as in sort --version-sort.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +github_account = 'ekg' +source_urls = [GITHUB_SOURCE] +sources = ['%s.tar.gz' % local_commit] +patches = ['%(name)s-%(version)s_build-libs.patch'] +checksums = [ + '89835829a7829f7a25783b2cf9d482f1e3c794703343c9214c15c66a8c7f4aae', # df20dcc.tar.gz + '051438f76dd04219abfb283f61101c04d748407031e180b7ae3841344416ec4f', # filevercmp-20191210_build-libs.patch +] + +builddependencies = [('binutils', '2.39')] + +skipsteps = ['configure'] + +installopts = 'DESTDIR="" PREFIX=%(installdir)s ' + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'lib/libfilevercmp.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ['%(name)s abca bcac'] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/fish/fish-3.7.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/f/fish/fish-3.7.1-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..0c7e084ac23a --- /dev/null +++ b/easybuild/easyconfigs/f/fish/fish-3.7.1-GCCcore-13.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'CMakeMake' + +name = 'fish' + +version = '3.7.1' + +homepage = 'https://fishshell.com/' +description = """ +fish is a smart and user-friendly command line shell for Linux, macOS, and the rest of the family. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/fish-shell/fish-shell/releases/download/%(version)s/'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['614c9f5643cd0799df391395fa6bbc3649427bb839722ce3b114d3bbc1a3b250'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3') +] + +dependencies = [ + ('ncurses', '6.5'), +] + +configopts = '-DBUILD_DOCS=off ' + +sanity_check_paths = { + 'files': ['bin/fish'], + 'dirs': [], +} + +sanity_check_commands = ['fish --version'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/flash-attention/flash-attention-2.6.3-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/f/flash-attention/flash-attention-2.6.3-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 000000000000..754eef2c70ed --- /dev/null +++ b/easybuild/easyconfigs/f/flash-attention/flash-attention-2.6.3-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,41 @@ +easyblock = 'PythonBundle' + +name = 'flash-attention' +version = '2.6.3' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/Dao-AILab/flash-attention' +description = """Fast and memory-efficient exact attention.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [('Ninja', '1.11.1')] +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('CUDA', '12.1.1', '', SYSTEM), + ('PyTorch-bundle', '2.1.2', versionsuffix), + ('einops', '0.7.0'), + ('CUTLASS', '3.4.0', versionsuffix), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + (name, version, { + 'modulename': 'flash_attn', + # solves Invalid cross-device link error + # https://github.com/Dao-AILab/flash-attention/issues/875 + 'preinstallopts': "sed -i 's/os.rename/shutil.move/' setup.py && ", + 'source_urls': ['https://github.com/Dao-AILab/flash-attention/archive/'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['136e149165d4c8c67273d16daa957b5cd5e6fc629061ffd39fa5a25224454d6c'], + }), +] + +sanity_check_commands = [ + "python -c 'from flash_attn import flash_attn_qkvpacked_func, flash_attn_func'", +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/flatbuffers-python/flatbuffers-python-24.3.25-GCCcore-13.3.0.eb b/easybuild/easyconfigs/f/flatbuffers-python/flatbuffers-python-24.3.25-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..6e3bd3159653 --- /dev/null +++ b/easybuild/easyconfigs/f/flatbuffers-python/flatbuffers-python-24.3.25-GCCcore-13.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'flatbuffers-python' +version = '24.3.25' + +homepage = 'https://github.com/google/flatbuffers/' +description = """Python Flatbuffers runtime library.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://pypi.python.org/packages/source/f/flatbuffers'] +sources = [{'download_filename': 'flatbuffers-%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['de2ec5b203f21441716617f38443e0a8ebf3d25bf0d9c0bb0ce68fa00ad546a4'] + +dependencies = [ + ('binutils', '2.42'), + ('Python', '3.12.3'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +preinstallopts = 'VERSION=%(version)s ' +options = {'modulename': 'flatbuffers'} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/f/flatbuffers/flatbuffers-24.3.25-GCCcore-13.3.0.eb b/easybuild/easyconfigs/f/flatbuffers/flatbuffers-24.3.25-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..42c0b9a28f18 --- /dev/null +++ b/easybuild/easyconfigs/f/flatbuffers/flatbuffers-24.3.25-GCCcore-13.3.0.eb @@ -0,0 +1,33 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'CMakeNinja' + +name = 'flatbuffers' +version = '24.3.25' + +homepage = 'https://github.com/google/flatbuffers/' +description = """FlatBuffers: Memory Efficient Serialization Library""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/google/flatbuffers/archive/v%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['4157c5cacdb59737c5d627e47ac26b140e9ee28b1102f812b36068aab728c1ed'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), + ('Ninja', '1.12.1'), + ('Python', '3.12.3'), +] + +configopts = '-DFLATBUFFERS_ENABLE_PCH=ON ' + +sanity_check_paths = { + 'files': ['include/flatbuffers/flatbuffers.h', 'bin/flatc', 'lib/libflatbuffers.a'], + 'dirs': ['lib/cmake'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-14.2.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-14.2.0.eb new file mode 100644 index 000000000000..d91f13aa5d0d --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-14.2.0.eb @@ -0,0 +1,34 @@ +name = 'flex' +version = '2.6.4' + +homepage = 'https://github.com/westes/flex' + +description = """ + Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns + in text. +""" + +toolchain = {'name': 'GCCcore', 'version': '14.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/westes/flex/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e87aae032bf07c26f85ac0ed3250998c37621d95f8bd748b31f15b33c45ee995'] + +builddependencies = [ + ('Bison', '3.8.2'), + ('help2man', '1.49.3'), + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.42', '', SYSTEM), +] + +dependencies = [ + ('M4', '1.4.19'), +] + +# glibc 2.26 requires _GNU_SOURCE defined to expose reallocarray in the correct +# header, see https://github.com/westes/flex/issues/241 +preconfigopts = 'export CPPFLAGS="$CPPFLAGS -D_GNU_SOURCE" && ' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flit/flit-3.9.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/f/flit/flit-3.9.0-GCCcore-12.3.0.eb index 15b9ad83d78f..a19ba3242508 100644 --- a/easybuild/easyconfigs/f/flit/flit-3.9.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/f/flit/flit-3.9.0-GCCcore-12.3.0.eb @@ -17,11 +17,8 @@ dependencies = [ ('Python', '3.11.3'), ] -exts_default_options = { - 'download_dep_fail': True, - 'sanity_pip_check': True, - 'use_pip': True, -} +sanity_pip_check = True +use_pip = True exts_list = [ ('idna', '3.4', { diff --git a/easybuild/easyconfigs/f/flit/flit-3.9.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/f/flit/flit-3.9.0-GCCcore-13.2.0.eb index 79b1a625e7ee..9ef1de6c8b75 100644 --- a/easybuild/easyconfigs/f/flit/flit-3.9.0-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/f/flit/flit-3.9.0-GCCcore-13.2.0.eb @@ -18,11 +18,8 @@ dependencies = [ ('Python', '3.11.5'), ] -exts_default_options = { - 'download_dep_fail': True, - 'sanity_pip_check': True, - 'use_pip': True, -} +sanity_pip_check = True +use_pip = True exts_list = [ ('idna', '3.4', { diff --git a/easybuild/easyconfigs/f/flit/flit-3.9.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/f/flit/flit-3.9.0-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..650b15edaa57 --- /dev/null +++ b/easybuild/easyconfigs/f/flit/flit-3.9.0-GCCcore-13.3.0.eb @@ -0,0 +1,72 @@ +easyblock = 'PythonBundle' + +name = 'flit' +version = '3.9.0' + +homepage = 'https://github.com/pypa/flit' +description = "A simple packaging tool for simple packages." + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +builddependencies = [ + ('binutils', '2.42'), + ('hatchling', '1.24.2'), +] + +dependencies = [ + ('Python', '3.12.3'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('idna', '3.7', { + 'checksums': ['028ff3aadf0609c1fd278d8ea3089299412a7a8b9bd005dd08b9f8285bcb5cfc'], + }), + ('certifi', '2024.6.2', { + 'checksums': ['3cd43f1c6fa7dedc5899d69d3ad0398fd018ad1a17fba83ddaf78aa46c747516'], + }), + ('urllib3', '2.2.1', { + 'checksums': ['d0570876c61ab9e520d776c38acbbb5b05a776d3f9ff98a5c8fd5162a444cf19'], + }), + ('charset-normalizer', '3.3.2', { + 'checksums': ['f30c3cb33b24454a82faecaf01b19c18562b1e89558fb6c56de4d9118a032fd5'], + }), + ('packaging', '24.1', { + 'checksums': ['026ed72c8ed3fcce5bf8950572258698927fd1dbda10a5e981cdf0ac37f4f002'], + }), + ('setuptools-scm', '8.1.0', { + 'sources': ['setuptools_scm-%(version)s.tar.gz'], + 'checksums': ['42dea1b65771cba93b7a515d65a65d8246e560768a66b9106a592c8e7f26c8a7'], + }), + ('typing-extensions', '4.12.2', { + 'sources': ['typing_extensions-%(version)s.tar.gz'], + 'checksums': ['1a7ead55c7e559dd4dee8856e3a88b41225abfe1ce8df57b7c13915fe121ffb8'], + }), + ('flit-scm', '1.7.0', { + 'sources': ['flit_scm-%(version)s.tar.gz'], + 'checksums': ['961bd6fb24f31bba75333c234145fff88e6de0a90fc0f7e5e7c79deca69f6bb2'], + }), + ('requests', '2.32.3', { + 'checksums': ['55365417734eb18255590a9ff9eb97e9e1da868d4ccd6402399eaf68af20a760'], + }), + ('docutils', '0.21.2', { + 'checksums': ['3a6b18732edf182daa3cd12775bbb338cf5691468f91eeeb109deff6ebfa986f'], + }), + ('tomli-w', '1.0.0', { + 'sources': ['tomli_w-%(version)s.tar.gz'], + 'checksums': ['f463434305e0336248cac9c2dc8076b707d8a12d019dd349f5c1e382dd1ae1b9'], + }), + (name, version, { + 'checksums': ['d75edf5eb324da20d53570a6a6f87f51e606eee8384925cd66a90611140844c7'], + }), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/fmt/fmt-10.2.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/f/fmt/fmt-10.2.1-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..45cfe72e73f3 --- /dev/null +++ b/easybuild/easyconfigs/f/fmt/fmt-10.2.1-GCCcore-13.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'CMakeMake' + +name = 'fmt' +version = '10.2.1' + +homepage = 'http://fmtlib.net/' +description = "fmt (formerly cppformat) is an open-source formatting library." + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/fmtlib/fmt/releases/download/%(version)s/'] +sources = ['fmt-%(version)s.zip'] +checksums = ['312151a2d13c8327f5c9c586ac6cf7cddc1658e8f53edae0ec56509c8fa516c9'] + + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.27.6'), +] + +sanity_check_paths = { + 'files': ['lib/libfmt.a'], + 'dirs': ['include/fmt', 'lib/cmake'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..8453a35a6951 --- /dev/null +++ b/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-11.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'fonttools' +version = '4.53.1' + +homepage = 'https://python-markdown.github.io/' +description = """ +fontTools is a library for manipulating fonts, written in Python. +The project includes the TTX tool, that can convert TrueType and OpenType fonts to and from an XML text format, +which is also called TTX. +It supports TrueType, OpenType, AFM and to an extent Type 1 and some Mac-specific formats.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e128778a8e9bc11159ce5447f76766cefbd876f44bd79aff030287254e4752c4'] + +builddependencies = [('binutils', '2.38')] +dependencies = [('Python', '3.10.4')] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +options = {'modulename': 'fontTools'} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..cfaada6dee85 --- /dev/null +++ b/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-12.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'fonttools' +version = '4.53.1' + +homepage = 'https://python-markdown.github.io/' +description = """ +fontTools is a library for manipulating fonts, written in Python. +The project includes the TTX tool, that can convert TrueType and OpenType fonts to and from an XML text format, +which is also called TTX. +It supports TrueType, OpenType, AFM and to an extent Type 1 and some Mac-specific formats.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e128778a8e9bc11159ce5447f76766cefbd876f44bd79aff030287254e4752c4'] + +builddependencies = [('binutils', '2.39')] +dependencies = [('Python', '3.10.8')] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +options = {'modulename': 'fontTools'} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..bf71a8f341f1 --- /dev/null +++ b/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-12.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'fonttools' +version = '4.53.1' + +homepage = 'https://python-markdown.github.io/' +description = """ +fontTools is a library for manipulating fonts, written in Python. +The project includes the TTX tool, that can convert TrueType and OpenType fonts to and from an XML text format, +which is also called TTX. +It supports TrueType, OpenType, AFM and to an extent Type 1 and some Mac-specific formats.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e128778a8e9bc11159ce5447f76766cefbd876f44bd79aff030287254e4752c4'] + +builddependencies = [('binutils', '2.40')] +dependencies = [('Python', '3.11.3')] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +options = {'modulename': 'fontTools'} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..0e8a62e088b9 --- /dev/null +++ b/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-13.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'fonttools' +version = '4.53.1' + +homepage = 'https://python-markdown.github.io/' +description = """ +fontTools is a library for manipulating fonts, written in Python. +The project includes the TTX tool, that can convert TrueType and OpenType fonts to and from an XML text format, +which is also called TTX. +It supports TrueType, OpenType, AFM and to an extent Type 1 and some Mac-specific formats.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e128778a8e9bc11159ce5447f76766cefbd876f44bd79aff030287254e4752c4'] + +builddependencies = [('binutils', '2.40')] +dependencies = [('Python', '3.11.5')] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +options = {'modulename': 'fontTools'} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..ed395cfd0ee5 --- /dev/null +++ b/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-13.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'fonttools' +version = '4.53.1' + +homepage = 'https://python-markdown.github.io/' +description = """ +fontTools is a library for manipulating fonts, written in Python. +The project includes the TTX tool, that can convert TrueType and OpenType fonts to and from an XML text format, +which is also called TTX. +It supports TrueType, OpenType, AFM and to an extent Type 1 and some Mac-specific formats.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e128778a8e9bc11159ce5447f76766cefbd876f44bd79aff030287254e4752c4'] + +builddependencies = [('binutils', '2.42')] +dependencies = [('Python', '3.12.3')] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +options = {'modulename': 'fontTools'} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/f/foss/foss-2024a.eb b/easybuild/easyconfigs/f/foss/foss-2024a.eb new file mode 100644 index 000000000000..7e9a4ba51129 --- /dev/null +++ b/easybuild/easyconfigs/f/foss/foss-2024a.eb @@ -0,0 +1,28 @@ +easyblock = 'Toolchain' + +name = 'foss' +version = '2024a' + +homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#foss-toolchain' +description = """GNU Compiler Collection (GCC) based compiler toolchain, including + OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" + +toolchain = SYSTEM + +local_gccver = '13.3.0' + +# toolchain used to build foss dependencies +local_comp_mpi_tc = ('gompi', version) + +# we need GCC and OpenMPI as explicit dependencies instead of gompi toolchain +# because of toolchain preparation functions +dependencies = [ + ('GCC', local_gccver), + ('OpenMPI', '5.0.3', '', ('GCC', local_gccver)), + ('FlexiBLAS', '3.4.4', '', ('GCC', local_gccver)), + ('FFTW', '3.3.10', '', ('GCC', local_gccver)), + ('FFTW.MPI', '3.3.10', '', local_comp_mpi_tc), + ('ScaLAPACK', '2.2.0', '-fb', local_comp_mpi_tc), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/f/fplll/fplll-5.4.5-GCCcore-13.2.0.eb b/easybuild/easyconfigs/f/fplll/fplll-5.4.5-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..5184f1f3c1ee --- /dev/null +++ b/easybuild/easyconfigs/f/fplll/fplll-5.4.5-GCCcore-13.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'fplll' +version = '5.4.5' + +homepage = 'https://github.com/fplll/fplll' +description = """fplll contains implementations of several lattice algorithms. + The implementation relies on floating-point orthogonalization, and the 1982 paper from +Lenstra, Lenstra Jr. and Lovasz (LLL) is central to the code, hence the name.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://github.com/fplll/fplll/releases/download/%(version)s'] +sources = [SOURCE_TAR_GZ] +checksums = ['76d3778f0326597ed7505bab19493a9bf6b73a5c5ca614e8fb82f42105c57d00'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('MPFR', '4.2.1'), +] + +sanity_check_paths = { + 'files': ['bin/fplll', 'lib/libfplll.%s' % SHLIB_EXT, 'include/fplll.h'], + 'dirs': ['share'] +} + +sanity_check_commands = ["fplll --help"] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/f/fpylll/fpylll-0.6.1-foss-2023b.eb b/easybuild/easyconfigs/f/fpylll/fpylll-0.6.1-foss-2023b.eb new file mode 100644 index 000000000000..5361252deb7d --- /dev/null +++ b/easybuild/easyconfigs/f/fpylll/fpylll-0.6.1-foss-2023b.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'fpylll' +version = '0.6.1' + +homepage = 'https://pypi.org/project/fpylll' +description = "A Python wrapper for fplll." + +# can be moved down to gfbf in more recent toolchain versions +toolchain = {'name': 'foss', 'version': '2023b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['dfd9529a26c50993a2a716177debd7994312219070574cad31b35b4f0c040a19'] + +dependencies = [ + ('Python', '3.11.5'), + ('SciPy-bundle', '2023.11'), + ('cysignals', '1.11.4'), + ('fplll', '5.4.5'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/f/fsm-lite/fsm-lite-1.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/f/fsm-lite/fsm-lite-1.0-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..65a1167d998f --- /dev/null +++ b/easybuild/easyconfigs/f/fsm-lite/fsm-lite-1.0-GCCcore-12.2.0.eb @@ -0,0 +1,36 @@ +# This easyconfig was created by the BEAR Software team at the University of Birmingham. +easyblock = "MakeCp" + +name = 'fsm-lite' +version = '1.0' + +homepage = "https://github.com/nvalimak/fsm-lite" +description = """A singe-core implemetation of frequency-based substring mining.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/nvalimak/%(name)s/archive/'] +sources = ['v%(version)s-stable.tar.gz'] +checksums = ['f781a9fbab5265bd09b3b5b7e1cba904582ec201c3d30baed36e28a03de3ac61'] + +builddependencies = [ + ('CMake', '3.24.3'), + ('binutils', '2.39'), +] + +dependencies = [ + ('sdsl-lite', '2.0.3'), +] + +prebuildopts = "sed -i '1s/.*/SDSL_INSTALL_PREFIX=${EBROOTSDSLMINLITE}/' Makefile && make depend &&" + +files_to_copy = [(['fsm-lite'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/fsm-lite'], + 'dirs': [], +} + +sanity_check_commands = ["fsm-lite --help 2>&1 | grep usage"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/fsom/fsom-20151117-GCCcore-12.2.0.eb b/easybuild/easyconfigs/f/fsom/fsom-20151117-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..b9de5b70eff1 --- /dev/null +++ b/easybuild/easyconfigs/f/fsom/fsom-20151117-GCCcore-12.2.0.eb @@ -0,0 +1,43 @@ +# Updated: Denis Kristak (INUITS) +# Updated: Petr Král (INUITS) + +easyblock = 'ConfigureMake' + +name = 'fsom' +version = '20151117' +local_commit = '56695e1' + +homepage = 'https://github.com/ekg/fsom' +description = """A tiny C library for managing SOM (Self-Organizing Maps) neural networks.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +github_account = 'ekg' + +source_urls = [GITHUB_SOURCE] +sources = ['%s.tar.gz' % local_commit] + +patches = [ + '%(name)s-%(version)s_build-libs.patch', + '%(name)s-20141119_fix-abs-overload.patch' +] + +checksums = [ + '1ba3360985be781bb9f79d974705c86e7bb0719cb83638955e113b5dd83ec8dd', # 56695e1.tar.gz + 'd4e19b2db054cc5d3153ceba88ad2b11e5143e3a3c243103ce1e6994a83c43fe', # fsom-20151117_build-libs.patch + '54dd6ae76033535fe1b0231142d8bd41a815950dc3fd269dc321f698d4973639', # fsom-20141119_fix-abs-overload.patch +] + +builddependencies = [('binutils', '2.39')] + +skipsteps = ['configure'] + +installopts = 'PREFIX=%(installdir)s ' + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'lib/libfsom.%s' % SHLIB_EXT], + 'dirs': [], +} +sanity_check_commands = ["%(name)s --help"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/GCC/GCC-14.2.0.eb b/easybuild/easyconfigs/g/GCC/GCC-14.2.0.eb new file mode 100644 index 000000000000..7126db6c52d0 --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-14.2.0.eb @@ -0,0 +1,22 @@ +easyblock = 'Bundle' + +name = 'GCC' +version = '14.2.0' + +homepage = 'https://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, + as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = SYSTEM + +dependencies = [ + ('GCCcore', version), + # binutils built on top of GCCcore, which was built on top of binutils (built with system toolchain) + ('binutils', '2.42', '', ('GCCcore', version)), +] + +altroot = 'GCCcore' +altversion = 'GCCcore' + +# this bundle serves as a compiler-only toolchain, so it should be marked as compiler (important for HMNS) +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-14.2.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-14.2.0.eb new file mode 100644 index 000000000000..438a848145f2 --- /dev/null +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-14.2.0.eb @@ -0,0 +1,63 @@ +easyblock = 'EB_GCC' + +name = 'GCCcore' +version = '14.2.0' + +homepage = 'https://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, + as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = SYSTEM + +source_urls = [ + 'https://ftpmirror.gnu.org/gnu/gcc/gcc-%(version)s', # GCC auto-resolving HTTP mirror + 'https://sourceware.org/pub/gcc/releases/gcc-%(version)s', # fallback URL for GCC + 'https://ftpmirror.gnu.org/gnu/gmp', # idem for GMP + 'https://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR + 'https://ftpmirror.gnu.org/gnu/mpc', # idem for MPC + 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies + 'https://gcc.gnu.org/pub/gcc/infrastructure/', # HTTPS mirror for GCC dependencies + 'https://libisl.sourceforge.io/', # fallback URL for isl + 'https://sourceware.org/pub/newlib/', # for newlib + 'https://github.com/MentorEmbedded/nvptx-tools/archive', # for nvptx-tools +] +sources = [ + 'gcc-%(version)s.tar.gz', + 'gmp-6.3.0.tar.bz2', + 'mpfr-4.2.1.tar.bz2', + 'mpc-1.3.1.tar.gz', + 'isl-0.26.tar.bz2', + 'newlib-4.4.0.20231231.tar.gz', + {'download_filename': '3136cf9.tar.gz', 'filename': 'nvptx-tools-20240801.tar.gz'}, +] +patches = [ + 'GCCcore-6.2.0-fix-find-isl.patch', + 'GCCcore-9.3.0_gmp-c99.patch', +] +checksums = [ + {'gcc-14.2.0.tar.gz': '7d376d445f93126dc545e2c0086d0f647c3094aae081cdb78f42ce2bc25e7293'}, + {'gmp-6.3.0.tar.bz2': 'ac28211a7cfb609bae2e2c8d6058d66c8fe96434f740cf6fe2e47b000d1c20cb'}, + {'mpfr-4.2.1.tar.bz2': 'b9df93635b20e4089c29623b19420c4ac848a1b29df1cfd59f26cab0d2666aa0'}, + {'mpc-1.3.1.tar.gz': 'ab642492f5cf882b74aa0cb730cd410a81edcdbec895183ce930e706c1c759b8'}, + {'isl-0.26.tar.bz2': '5eac8664e9d67be6bd0bee5085d6840b8baf738c06814df47eaf4166d9776436'}, + {'newlib-4.4.0.20231231.tar.gz': '0c166a39e1bf0951dfafcd68949fe0e4b6d3658081d6282f39aeefc6310f2f13'}, + {'nvptx-tools-20240801.tar.gz': 'a1106bf11b66d12e67194d8aa37196bb96996b614f44b3d3bc1b5854eefec03c'}, + {'GCCcore-6.2.0-fix-find-isl.patch': '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68'}, + {'GCCcore-9.3.0_gmp-c99.patch': '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e'}, +] + +builddependencies = [ + ('M4', '1.4.19'), + ('binutils', '2.42'), +] + +languages = ['c', 'c++', 'fortran'] + +withisl = True +withnvptx = True + +# Perl is only required when building with NVPTX support +if withnvptx: + osdependencies = ['perl'] + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.6.2-foss-2022b.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.6.2-foss-2022b.eb index c293d01731d8..576d90e74d64 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-3.6.2-foss-2022b.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.6.2-foss-2022b.eb @@ -61,9 +61,9 @@ dependencies = [ # common configopts for static, shared library builds _base_configopts = ' '.join([ '-DGDAL_USE_INTERNAL_LIBS=OFF', - '-DArrow_DIR=$EBROOTARROW', '-DGEOTIFF_INCLUDE_DIR=$EBROOTLIBGEOTIFF/include', '-DPython_ROOT=$EBROOTPYTHON', + '-DGDAL_USE_MYSQL=OFF', ]) # iterative build for both static and shared libraries diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.7.1-foss-2023a.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.7.1-foss-2023a.eb index 92bfe549e746..88e35cd4db44 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-3.7.1-foss-2023a.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.7.1-foss-2023a.eb @@ -61,7 +61,7 @@ dependencies = [ ] # iterative build for both static and shared libraries -local_configopts_common = "-DGDAL_USE_INTERNAL_LIBS=OFF -DArrow_DIR=$EBROOTARROW " +local_configopts_common = "-DGDAL_USE_INTERNAL_LIBS=OFF -DGDAL_USE_MYSQL=OFF " local_configopts_common += "-DGEOTIFF_INCLUDE_DIR=$EBROOTLIBGEOTIFF/include -DPython_ROOT=$EBROOTPYTHON " configopts = [ diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.9.0-foss-2023b.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.9.0-foss-2023b.eb new file mode 100644 index 000000000000..212994575169 --- /dev/null +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.9.0-foss-2023b.eb @@ -0,0 +1,81 @@ +easyblock = 'CMakeMake' + +name = 'GDAL' +version = '3.9.0' + +homepage = 'https://www.gdal.org' +description = """GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style + Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model + to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for + data translation and processing.""" + +toolchain = {'name': 'foss', 'version': '2023b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://download.osgeo.org/%(namelower)s/%(version)s/'] +sources = [SOURCELOWER_TAR_XZ] +patches = ['%(name)s-3.6.2_fix-python-CC-CXX.patch'] +checksums = [ + {'gdal-3.9.0.tar.xz': '577f80e9d14ff7c90b6bfbc34201652b4546700c01543efb4f4c3050e0b3fda2'}, + {'GDAL-3.6.2_fix-python-CC-CXX.patch': '859b874b0c8ff7626a76d51f008bf05b7f89a35b325bdd1d126d2364154acc63'}, +] + +builddependencies = [ + ('CMake', '3.27.6'), + ('pkgconf', '2.0.3'), + ('Bison', '3.8.2'), +] +dependencies = [ + ('Python', '3.11.5'), + ('netCDF', '4.9.2'), + ('expat', '2.5.0'), + ('GEOS', '3.12.1'), + ('SQLite', '3.43.1'), + ('libarchive', '3.7.2'), + ('libxml2', '2.11.5'), + ('libpng', '1.6.40'), + ('libjpeg-turbo', '3.0.1'), + ('LibTIFF', '4.6.0'), + ('zlib', '1.2.13'), + ('cURL', '8.3.0'), + ('PCRE', '8.45'), + ('PROJ', '9.3.1'), + ('libgeotiff', '1.7.3'), + ('SciPy-bundle', '2023.11'), + ('HDF5', '1.14.3'), + ('HDF', '4.2.16-2'), + ('Armadillo', '12.8.0'), + ('CFITSIO', '4.3.1'), + ('zstd', '1.5.5'), + ('giflib', '5.2.1'), + ('json-c', '0.17'), + ('Xerces-C++', '3.2.5'), + ('PCRE2', '10.42'), + ('OpenEXR', '3.2.0'), + ('Brunsli', '0.1'), + ('Qhull', '2020.2'), + ('LERC', '4.0.0'), + ('OpenJPEG', '2.5.0'), + ('SWIG', '4.1.1'), +] + +# iterative build for both static and shared libraries +local_configopts_common = "-DGDAL_USE_INTERNAL_LIBS=OFF -DGDAL_USE_MYSQL=OFF " +local_configopts_common += "-DGEOTIFF_INCLUDE_DIR=$EBROOTLIBGEOTIFF/include -DPython_ROOT=$EBROOTPYTHON " + +configopts = [ + local_configopts_common + "-DBUILD_SHARED_LIBS=OFF", + local_configopts_common +] + + +sanity_check_paths = { + 'files': ['lib/libgdal.a', 'lib/libgdal.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["python -c 'import osgeo.%(namelower)s'"] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/g/GDMA/GDMA-2.3.3_20230603-GCC-12.3.0.eb b/easybuild/easyconfigs/g/GDMA/GDMA-2.3.3_20230603-GCC-12.3.0.eb new file mode 100644 index 000000000000..d22b6d746896 --- /dev/null +++ b/easybuild/easyconfigs/g/GDMA/GDMA-2.3.3_20230603-GCC-12.3.0.eb @@ -0,0 +1,42 @@ +easyblock = 'ConfigureMake' + +name = 'GDMA' +version = '2.3.3_20230603' +_commit = '6b8e81ec' + +homepage = 'https://gitlab.com/anthonyjs/gdma' +description = """ +The GDMA program carries out Distributed Multipole Analysis of wavefunctions +calculated by the Gaussian system of programs or the Psi4 package, using the +formatted checkpoint files that they can produce. The result is a set of +multipole moments at sites defined by the user (usually at the positions of the +atomic nuclei) which, given an accurate wavefunction, provide an accurate +description of the electrostatic field of the molecule.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +sources = [{ + 'source_urls': ['https://gitlab.com/anthonyjs/gdma/-/archive/'], + 'download_filename': '%s.tar.gz' % _commit, + 'filename': SOURCE_TAR_GZ, +}] +checksums = ['cc008932ae8768e6cbd444337a998e02b2100c123492c260d6020590e76bec1e'] + +parallel = 1 + +skipsteps = ['configure'] + +# avoid using git to obtain the commit: not a cloned repo +prebuildopts = """sed -i "/^log =/,/^commit =/c commit = '%s'" src/version.py && """ % _commit + +preinstallopts = 'mkdir -p %(installdir)s/bin && ' +installopts = 'INSTALL_DIR=%(installdir)s/bin' + +sanity_check_paths = { + 'files': ['bin/gdma'], + 'dirs': [], +} + +sanity_check_commands = ['echo|gdma'] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/g/GEOS/GEOS-3.12.1-GCC-13.2.0.eb b/easybuild/easyconfigs/g/GEOS/GEOS-3.12.1-GCC-13.2.0.eb new file mode 100644 index 000000000000..8dc235ab95ce --- /dev/null +++ b/easybuild/easyconfigs/g/GEOS/GEOS-3.12.1-GCC-13.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'CMakeMake' + +name = 'GEOS' +version = '3.12.1' + +homepage = 'https://trac.osgeo.org/geos' +description = """GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS)""" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://download.osgeo.org/geos/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['d6ea7e492224b51193e8244fe3ec17c4d44d0777f3c32ca4fb171140549a0d03'] + +builddependencies = [('CMake', '3.27.6')] + +# Build static and shared libraries +configopts = ['', '-DBUILD_SHARED_LIBS=OFF'] + +sanity_check_paths = { + 'files': ['bin/geos-config', 'lib/libgeos.%s' % SHLIB_EXT, 'lib/libgeos.a', 'include/geos.h'], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/g/GHC/GHC-9.10.1-x86_64.eb b/easybuild/easyconfigs/g/GHC/GHC-9.10.1-x86_64.eb new file mode 100644 index 000000000000..2074b920ebd8 --- /dev/null +++ b/easybuild/easyconfigs/g/GHC/GHC-9.10.1-x86_64.eb @@ -0,0 +1,82 @@ +# This is a binary install that requires a './configure' and 'make install' steps for GHC. +# We pull the centos7 binary tarball as is the one built against oldest system libs, +# making it upwards compatible with newer distros. +# +# To get a functional 'ghc' binary on the SYSTEM toolchain we need +# gmp headers and ncurses libtinfo.so.5, to avoid requiring extra OS deps for them +# we include them in this bundle. +# Binaries obtained with ghc do not require them, so it should be possible to use this bundle +# just as builddep among different toolchains. +# +# For details, see the PR discussion: +# https://github.com/easybuilders/easybuild-easyconfigs/pull/11310 + +easyblock = 'Bundle' + +name = 'GHC' +version = '9.10.1' +versionsuffix = '-x86_64' + +homepage = 'https://haskell.org/ghc/' +description = """The Glorious/Glasgow Haskell Compiler""" + +toolchain = SYSTEM + +builddependencies = [ + ('binutils', '2.42'), + ('M4', '1.4.19'), +] + +default_easyblock = 'ConfigureMake' + +local_distro_tarball = 'centos7' + +components = [ + ('GMP', '6.3.0', { + 'source_urls': [GNU_SOURCE], + 'sources': [SOURCELOWER_TAR_BZ2], + 'checksums': ['ac28211a7cfb609bae2e2c8d6058d66c8fe96434f740cf6fe2e47b000d1c20cb'], + 'configopts': ' --enable-cxx', + 'start_dir': '%(namelower)s-%(version)s', + }), + ('ncurses', '5.9', { + 'source_urls': [GNU_SOURCE], + 'sources': [SOURCE_TAR_GZ], + 'patches': [ + 'ncurses-%(version)s_configure_darwin.patch', + 'ncurses-%(version)s_fix-missing-const.patch', + ], + 'checksums': [ + '9046298fb440324c9d4135ecea7879ffed8546dd1b58e59430ea07a4633f563b', + '8c471fc2b1961a6e6e5981b7f7b3512e7fe58fcb04461aa4520157d4c1159998', + '027f7bd5876b761b48db624ddbdd106fa1c535dfb2752ef5a0eddeb2a8896cfd', + ], + 'preconfigopts': "export CPPFLAGS='-P -std=c++14' && ", + 'configopts': ' --with-shared --enable-overwrite --with-termlib=tinfo', + 'start_dir': '%(namelower)s-%(version)s', + }), + (name, version, { + 'source_urls': ['https://downloads.haskell.org/~ghc/%(version)s/'], + 'sources': ['%%(namelower)s-%%(version)s-x86_64-%s-linux.tar.xz' % local_distro_tarball], + 'checksums': ['fab143f10f845629cb1b373309b5680667cbaab298cf49827e383ee8a9ddf683'], + # ghc-8.6.5-x86_64-centos7-linux.tar.xz + 'skipsteps': ['build'], + 'preinstallopts': 'LD_LIBRARY_PATH="%(installdir)s/lib:$LD_LIBRARY_PATH" ', + 'start_dir': '%(namelower)s-%(version)s-x86_64-unknown-linux', + }), +] + +local_ncurses_libs = ["form", "menu", "ncurses", "panel", "tinfo"] + +sanity_check_paths = { + 'files': ['lib/lib%s.%s' % (x, y) for x in ['gmp', 'gmpxx'] for y in [SHLIB_EXT, 'a']] + + ['include/gmp.h', 'include/gmpxx.h'] + + ['lib/lib%s%s.a' % (x, y) for x in local_ncurses_libs for y in ['', '_g']] + + ['lib/lib%s.%s' % (x, y) for x in local_ncurses_libs for y in [SHLIB_EXT]] + + ['bin/ghc', 'bin/ghci', 'bin/ghc-pkg', 'bin/runghc', 'bin/runhaskell'], + 'dirs': ['bin', 'lib', 'share', 'include'], +} + +sanity_check_commands = ['ghc --version'] + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GI-DocGen/GI-DocGen-2023.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/GI-DocGen/GI-DocGen-2023.3-GCCcore-12.3.0.eb index d098c3c3cbc0..4fae7c08b542 100644 --- a/easybuild/easyconfigs/g/GI-DocGen/GI-DocGen-2023.3-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/g/GI-DocGen/GI-DocGen-2023.3-GCCcore-12.3.0.eb @@ -21,11 +21,8 @@ dependencies = [ ('Python-bundle-PyPI', '2023.06'), ] -exts_default_options = { - 'download_dep_fail': True, - 'sanity_pip_check': True, - 'use_pip': True, -} +sanity_pip_check = True +use_pip = True exts_list = [ ('Markdown', '3.5.2', { diff --git a/easybuild/easyconfigs/g/GLM/GLM-1.0.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/GLM/GLM-1.0.1-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..e57a89d030a9 --- /dev/null +++ b/easybuild/easyconfigs/g/GLM/GLM-1.0.1-GCCcore-13.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'CMakeMake' + +name = 'GLM' +version = '1.0.1' + +homepage = 'https://github.com/g-truc/glm' +description = """ +OpenGL Mathematics (GLM) is a header only C++ mathematics library for graphics +software based on the OpenGL Shading Language (GLSL) specifications.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/g-truc/glm/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['9f3174561fd26904b23f0db5e560971cbf9b3cbda0b280f04d5c379d03bf234c'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['include/glm/gtc', 'include/glm/gtx'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.80.4-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/GLib/GLib-2.80.4-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..f95eacd4a7b8 --- /dev/null +++ b/easybuild/easyconfigs/g/GLib/GLib-2.80.4-GCCcore-13.3.0.eb @@ -0,0 +1,53 @@ +easyblock = 'MesonNinja' + +name = 'GLib' +version = '2.80.4' + +homepage = 'https://www.gtk.org/' +description = """GLib is one of the base libraries of the GTK+ project""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['24e029c5dfc9b44e4573697adf33078a9827c48938555004b3b9096fa4ea034f'] + +builddependencies = [ + # Python is required for building against GLib, at least when + # gdbus-codegen or one of the other python scripts are used. + # Since Meson 0.50 and later are Python >=3.5 only we can't build + # Python specific versions of GLib that uses Python 2.x + # thus Python should not be a runtime dependency for GLib. + # Packages that use GLib should either have an explicit + # (build)dependency on Python or it will use the system version + # EasyBuild itself uses. + ('Python', '3.12.3'), + ('Meson', '1.4.0'), + ('Ninja', '1.12.1'), + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), +] + +dependencies = [ + ('libffi', '3.4.5'), + ('gettext', '0.22.5'), + ('libxml2', '2.12.7'), + ('PCRE2', '10.43'), + ('util-linux', '2.40'), +] + +# avoid using hardcoded path to Python binary in build step +preconfigopts = "export PYTHON=python && " + +configopts = "--buildtype=release --default-library=both " + +fix_python_shebang_for = ['bin/*'] + +sanity_check_paths = { + 'files': ['lib/libglib-%(version_major)s.0.a', 'lib/libglib-%%(version_major)s.0.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include'], +} + + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GLibmm/GLibmm-2.72.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/GLibmm/GLibmm-2.72.1-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..728b2ec6a200 --- /dev/null +++ b/easybuild/easyconfigs/g/GLibmm/GLibmm-2.72.1-GCCcore-11.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'MesonNinja' + +name = 'GLibmm' +version = '2.72.1' + +homepage = 'https://www.gtk.org/' +description = """C++ bindings for Glib""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://ftp.gnome.org/pub/gnome/sources/glibmm/%(version_major_minor)s/'] +sources = ['%(namelower)s-%(version)s.tar.xz'] +checksums = ['2a7649a28ab5dc53ac4dabb76c9f61599fbc628923ab6a7dd74bf675d9155cd8'] + +builddependencies = [ + ('binutils', '2.38'), + ('pkgconf', '1.8.0'), + ('Meson', '0.62.1'), + ('Ninja', '1.10.2'), +] + +dependencies = [ + ('GLib', '2.72.1'), + ('libsigc++', '3.4.0'), +] + +sanity_check_paths = { + 'files': ['lib/libglibmm-2.68.%s' % SHLIB_EXT, 'lib/libgiomm-2.68.%s' % SHLIB_EXT, + 'include/glibmm-2.68/glibmm.h', 'include/giomm-2.68/giomm.h'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GLibmm/GLibmm-2.75.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/GLibmm/GLibmm-2.75.0-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..ba2c86f40575 --- /dev/null +++ b/easybuild/easyconfigs/g/GLibmm/GLibmm-2.75.0-GCCcore-12.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'MesonNinja' + +name = 'GLibmm' +version = '2.75.0' + +homepage = 'https://www.gtk.org/' +description = """C++ bindings for Glib""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://ftp.gnome.org/pub/gnome/sources/glibmm/%(version_major_minor)s/'] +sources = ['%(namelower)s-%(version)s.tar.xz'] +checksums = ['60bb12e66488aa8ce41f0eb2f3612f89f5ddc887e3e4d45498524bf60b266b3d'] + +builddependencies = [ + ('binutils', '2.39'), + ('pkgconf', '1.9.3'), + ('Meson', '0.64.0'), + ('Ninja', '1.11.1'), +] + +dependencies = [ + ('GLib', '2.75.0'), + ('libsigc++', '3.6.0'), +] + +sanity_check_paths = { + 'files': ['lib/libglibmm-2.68.%s' % SHLIB_EXT, 'lib/libgiomm-2.68.%s' % SHLIB_EXT, + 'include/glibmm-2.68/glibmm.h', 'include/giomm-2.68/giomm.h'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GLibmm/GLibmm-2.77.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/GLibmm/GLibmm-2.77.0-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..768bdcbb2ed1 --- /dev/null +++ b/easybuild/easyconfigs/g/GLibmm/GLibmm-2.77.0-GCCcore-12.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'MesonNinja' + +name = 'GLibmm' +version = '2.77.0' + +homepage = 'https://www.gtk.org/' +description = """C++ bindings for Glib""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://ftp.gnome.org/pub/gnome/sources/glibmm/%(version_major_minor)s/'] +sources = ['%(namelower)s-%(version)s.tar.xz'] +checksums = ['7cb34684e7ac6dfbf83492a52dff3f919e2fff63eb7810613bf71eb272d5450e'] + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '1.9.5'), + ('Meson', '1.1.1'), + ('Ninja', '1.11.1'), +] + +dependencies = [ + ('GLib', '2.77.1'), + ('libsigc++', '3.6.0'), +] + +sanity_check_paths = { + 'files': ['lib/libglibmm-2.68.%s' % SHLIB_EXT, 'lib/libgiomm-2.68.%s' % SHLIB_EXT, + 'include/glibmm-2.68/glibmm.h', 'include/giomm-2.68/giomm.h'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GLibmm/GLibmm-2.78.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/g/GLibmm/GLibmm-2.78.1-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..1cfbeec1c858 --- /dev/null +++ b/easybuild/easyconfigs/g/GLibmm/GLibmm-2.78.1-GCCcore-13.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'MesonNinja' + +name = 'GLibmm' +version = '2.78.1' + +homepage = 'https://www.gtk.org/' +description = """C++ bindings for Glib""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://ftp.gnome.org/pub/gnome/sources/glibmm/%(version_major_minor)s/'] +sources = ['%(namelower)s-%(version)s.tar.xz'] +checksums = ['f473f2975d26c3409e112ed11ed36406fb3843fa975df575c22d4cb843085f61'] + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '2.0.3'), + ('Meson', '1.2.3'), + ('Ninja', '1.11.1'), +] + +dependencies = [ + ('GLib', '2.78.1'), + ('libsigc++', '3.6.0'), +] + +sanity_check_paths = { + 'files': ['lib/libglibmm-2.68.%s' % SHLIB_EXT, 'lib/libgiomm-2.68.%s' % SHLIB_EXT, + 'include/glibmm-2.68/glibmm.h', 'include/giomm-2.68/giomm.h'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GOATOOLS/GOATOOLS-1.4.5-foss-2022b.eb b/easybuild/easyconfigs/g/GOATOOLS/GOATOOLS-1.4.5-foss-2022b.eb new file mode 100644 index 000000000000..46728a39e63b --- /dev/null +++ b/easybuild/easyconfigs/g/GOATOOLS/GOATOOLS-1.4.5-foss-2022b.eb @@ -0,0 +1,73 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +# Update: Pavel Tománek (Inuits) +easyblock = 'PythonPackage' + +name = 'GOATOOLS' +version = '1.4.5' + +homepage = 'https://github.com/tanghaibao/goatools' +description = "A Python library for Gene Ontology analyses" + +toolchain = {'name': 'foss', 'version': '2022b'} + +# must download sources via git to preserve .git directory, +# since setuptools-scm is used to determine version +sources = [{ + 'git_config': { + 'url': 'https://github.com/tanghaibao', + 'repo_name': 'goatools', + 'tag': 'v%(version)s', + 'keep_git_dir': True, + }, + 'filename': SOURCE_TAR_GZ, +}] +checksums = [None] + +builddependencies = [('cURL', '7.86.0')] + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('XlsxWriter', '3.1.2'), + ('statsmodels', '0.14.0'), + ('pydot', '2.0.0'), + ('openpyxl', '3.1.2'), +] + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'download_dep_fail': True, + 'use_pip': True, + 'sanity_pip_check': True, +} + +exts_list = [ + ('ftpretty', '0.4.0', { + 'checksums': ['61233b9212f2cceec96ee2c972738fa31cae7248e92d0874c99c04ee739bb5a9'], + }), +] + +download_dep_fail = True +use_pip = True + +postinstallcmds = ["cp -a %(builddir)s/goatools/data/ %(installdir)s/"] + +sanity_check_paths = { + 'files': ['bin/find_enrichment.py'], + 'dirs': ['data', 'lib/python%(pyshortver)s/site-packages'], +} + +# example test run, see https://github.com/tanghaibao/goatools/blob/master/run.sh +sanity_check_commands = [ + "mkdir -p %(builddir)s", + "cd %(builddir)s && curl -OL http://geneontology.org/ontology/go-basic.obo", + "cd %(builddir)s && curl -OL http://www.geneontology.org/ontology/subsets/goslim_generic.obo", + "cd %(builddir)s && cp -a %(installdir)s/data .", + "cd %(builddir)s && find_enrichment.py --pval=0.05 --indent data/study data/population data/association", +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-24.6.0-foss-2023a-ASE-3.23.0.eb b/easybuild/easyconfigs/g/GPAW/GPAW-24.6.0-foss-2023a-ASE-3.23.0.eb new file mode 100644 index 000000000000..62db4b694404 --- /dev/null +++ b/easybuild/easyconfigs/g/GPAW/GPAW-24.6.0-foss-2023a-ASE-3.23.0.eb @@ -0,0 +1,52 @@ +easyblock = "PythonPackage" + +name = 'GPAW' +version = '24.6.0' +_aseversion = '3.23.0' +versionsuffix = '-ASE-' + _aseversion + +homepage = 'https://wiki.fysik.dtu.dk/gpaw/' +description = """GPAW is a density-functional theory (DFT) Python code based on the projector-augmented wave (PAW) + method and the atomic simulation environment (ASE). It uses real-space uniform grids and multigrid methods or + atom-centered basis-functions.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'usempi': True, 'openmp': False} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + ('GPAW-20.1.0-Add-Easybuild-configuration-files.patch', 1), +] +checksums = [ + {'gpaw-24.6.0.tar.gz': 'fb48ef0db48c0e321ce5967126a47900bba20c7efb420d6e7b5459983bd8f6f6'}, + {'GPAW-20.1.0-Add-Easybuild-configuration-files.patch': + '2b337399479bf018a86156ed073dd7a78ec8c0df1f28b015f9284c6bf9fa5f15'}, +] + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('ASE', _aseversion), + ('libxc', '6.2.2'), + ('libvdwxc', '0.4.0'), + ('ELPA', '2023.05.001'), + ('PyYAML', '6.0'), + ('GPAW-setups', '24.1.0', '', SYSTEM), +] + +prebuildopts = 'GPAW_CONFIG=doc/platforms/Linux/EasyBuild/config_foss.py' +preinstallopts = prebuildopts + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/gpaw%s' % x for x in ['', '-analyse-basis', '-basis', '-plot-parallel-timings', + '-runscript', '-setup', '-upfplot']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-24.6.0-intel-2023a-ASE-3.23.0.eb b/easybuild/easyconfigs/g/GPAW/GPAW-24.6.0-intel-2023a-ASE-3.23.0.eb new file mode 100644 index 000000000000..dc4091af2d3d --- /dev/null +++ b/easybuild/easyconfigs/g/GPAW/GPAW-24.6.0-intel-2023a-ASE-3.23.0.eb @@ -0,0 +1,51 @@ +easyblock = "PythonPackage" + +name = 'GPAW' +version = '24.6.0' +_aseversion = '3.23.0' +versionsuffix = '-ASE-' + _aseversion + +homepage = 'https://wiki.fysik.dtu.dk/gpaw/' +description = """GPAW is a density-functional theory (DFT) Python code based on the projector-augmented wave (PAW) + method and the atomic simulation environment (ASE). It uses real-space uniform grids and multigrid methods or + atom-centered basis-functions.""" + +toolchain = {'name': 'intel', 'version': '2023a'} +toolchainopts = {'usempi': True, 'openmp': False} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + ('GPAW-20.1.0-Add-Easybuild-configuration-files.patch', 1), +] +checksums = [ + {'gpaw-24.6.0.tar.gz': 'fb48ef0db48c0e321ce5967126a47900bba20c7efb420d6e7b5459983bd8f6f6'}, + {'GPAW-20.1.0-Add-Easybuild-configuration-files.patch': + '2b337399479bf018a86156ed073dd7a78ec8c0df1f28b015f9284c6bf9fa5f15'}, +] + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('ASE', _aseversion), + ('libxc', '6.2.2'), + ('ELPA', '2023.05.001'), + ('PyYAML', '6.0'), + ('GPAW-setups', '24.1.0', '', SYSTEM), +] + +prebuildopts = 'GPAW_CONFIG=doc/platforms/Linux/EasyBuild/config_intel.py' +preinstallopts = prebuildopts + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/gpaw%s' % x for x in ['', '-analyse-basis', '-basis', '-plot-parallel-timings', + '-runscript', '-setup', '-upfplot']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/g/GPflow/GPflow-2.9.2-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/g/GPflow/GPflow-2.9.2-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 000000000000..8838542f89ba --- /dev/null +++ b/easybuild/easyconfigs/g/GPflow/GPflow-2.9.2-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,49 @@ +easyblock = 'PythonBundle' + +name = 'GPflow' +version = '2.9.2' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://gpflow.github.io' +description = """GPflow is a package for building Gaussian process models in Python. It +implements modern Gaussian process inference for composable kernels and +likelihoods.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('Python', '3.10.4'), + ('TensorFlow', '2.11.0', versionsuffix), + ('tensorflow-probability', '0.19.0', versionsuffix), +] + +use_pip = True + +exts_list = [ + ('Deprecated', '1.2.14', { + 'checksums': ['e5323eb936458dccc2582dc6f9c322c852a775a27065ff2b0c4970b9d53d01b3'], + }), + ('dropstackframe', '0.1.0', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['d619c7f87d144660f4569d447648830932f7920d570fd14f0dec552c81a0eb22'], + }), + ('lark', '1.1.9', { + 'checksums': ['15fa5236490824c2c4aba0e22d2d6d823575dcaf4cdd1848e34b6ad836240fba'], + }), + ('check_shapes', '1.1.1', { + 'checksums': ['b699fcb1e60bb17e2c97007e444b89eeeea2a9102ff11d61fb52454af5348403'], + }), + ('multipledispatch', '1.0.0', { + 'checksums': ['5c839915465c68206c3e9c473357908216c28383b425361e5d144594bf85a7e0'], + }), + ('gpflow', version, { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/GPflow/GPflow/archive/'], + 'checksums': ['a32914c2b581b1dd2ac9a6f40352adb5f6f2c32f53028382e542014dd829553e'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/GPflow/GPflow-2.9.2-foss-2022a.eb b/easybuild/easyconfigs/g/GPflow/GPflow-2.9.2-foss-2022a.eb new file mode 100644 index 000000000000..b94a4e3bc292 --- /dev/null +++ b/easybuild/easyconfigs/g/GPflow/GPflow-2.9.2-foss-2022a.eb @@ -0,0 +1,47 @@ +easyblock = 'PythonBundle' + +name = 'GPflow' +version = '2.9.2' + +homepage = 'https://gpflow.github.io' +description = """GPflow is a package for building Gaussian process models in Python. It +implements modern Gaussian process inference for composable kernels and +likelihoods.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('TensorFlow', '2.11.0'), + ('tensorflow-probability', '0.19.0'), +] + +use_pip = True + +exts_list = [ + ('Deprecated', '1.2.14', { + 'checksums': ['e5323eb936458dccc2582dc6f9c322c852a775a27065ff2b0c4970b9d53d01b3'], + }), + ('dropstackframe', '0.1.0', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['d619c7f87d144660f4569d447648830932f7920d570fd14f0dec552c81a0eb22'], + }), + ('lark', '1.1.9', { + 'checksums': ['15fa5236490824c2c4aba0e22d2d6d823575dcaf4cdd1848e34b6ad836240fba'], + }), + ('check_shapes', '1.1.1', { + 'checksums': ['b699fcb1e60bb17e2c97007e444b89eeeea2a9102ff11d61fb52454af5348403'], + }), + ('multipledispatch', '1.0.0', { + 'checksums': ['5c839915465c68206c3e9c473357908216c28383b425361e5d144594bf85a7e0'], + }), + ('gpflow', version, { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/GPflow/GPflow/archive/'], + 'checksums': ['a32914c2b581b1dd2ac9a6f40352adb5f6f2c32f53028382e542014dd829553e'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/GPflow/GPflow-2.9.2-foss-2023a.eb b/easybuild/easyconfigs/g/GPflow/GPflow-2.9.2-foss-2023a.eb new file mode 100644 index 000000000000..a2a0f0a5adcc --- /dev/null +++ b/easybuild/easyconfigs/g/GPflow/GPflow-2.9.2-foss-2023a.eb @@ -0,0 +1,51 @@ +easyblock = 'PythonBundle' + +name = 'GPflow' +version = '2.9.2' + +homepage = 'https://gpflow.github.io' +description = """GPflow is a package for building Gaussian process models in Python. It +implements modern Gaussian process inference for composable kernels and +likelihoods.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('poetry', '1.7.1'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('TensorFlow', '2.13.0'), + ('tensorflow-probability', '0.20.0'), +] + +use_pip = True + +exts_list = [ + ('Deprecated', '1.2.14', { + 'checksums': ['e5323eb936458dccc2582dc6f9c322c852a775a27065ff2b0c4970b9d53d01b3'], + }), + ('dropstackframe', '0.1.0', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['d619c7f87d144660f4569d447648830932f7920d570fd14f0dec552c81a0eb22'], + }), + ('lark', '1.1.9', { + 'checksums': ['15fa5236490824c2c4aba0e22d2d6d823575dcaf4cdd1848e34b6ad836240fba'], + }), + ('check_shapes', '1.1.1', { + 'checksums': ['b699fcb1e60bb17e2c97007e444b89eeeea2a9102ff11d61fb52454af5348403'], + }), + ('multipledispatch', '1.0.0', { + 'checksums': ['5c839915465c68206c3e9c473357908216c28383b425361e5d144594bf85a7e0'], + }), + ('gpflow', version, { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/GPflow/GPflow/archive/'], + 'checksums': ['a32914c2b581b1dd2ac9a6f40352adb5f6f2c32f53028382e542014dd829553e'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/GPyOpt/GPyOpt-1.2.6-foss-2023a.eb b/easybuild/easyconfigs/g/GPyOpt/GPyOpt-1.2.6-foss-2023a.eb new file mode 100644 index 000000000000..ca08a08a88c7 --- /dev/null +++ b/easybuild/easyconfigs/g/GPyOpt/GPyOpt-1.2.6-foss-2023a.eb @@ -0,0 +1,63 @@ +easyblock = 'PythonBundle' + +name = 'GPyOpt' +version = '1.2.6' + +homepage = 'https://sheffieldml.github.io/GPyOpt' +description = "GPyOpt is a Python open-source library for Bayesian Optimization" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('matplotlib', '3.7.2'), +] + +use_pip = True + +exts_list = [ + ('paramz', '0.9.6', { + 'sources': ['%(name)s-%(version)s-py3-none-any.whl'], + 'checksums': ['4916be6f77f457316bcac8460be9c226026aed81fe7be302b32c0ba74e2ac6dd'], + }), + ('GPy', '1.13.2', { + 'modulename': 'GPy', + 'checksums': ['a38256b4dda536a5b5e6134a3924b42d454e987ee801fb6fc8b55a922da27920'], + }), + ('python-dateutil', '2.9.0.post0', { + 'modulename': 'dateutil', + 'checksums': ['37dd54208da7e1cd875388217d5e00ebd4179249f90fb72437e91a35459a0ad3'], + }), + ('pyDOE', '0.3.8', { + 'modulename': '%(name)s', + 'sources': ['%(name)s-%(version)s.zip'], + 'checksums': ['cbd6f14ae26d3c9f736013205f53ea1191add4567033c3ee77b7dd356566c4b6'], + }), + ('sobol-seq', '0.2.0', { + 'sources': ['sobol_seq-%(version)s.tar.gz'], + 'checksums': ['e16e701bd7b03ec6ce65b3a64c9205799f6a2d00c2054dd8c4ff4343f3981172'], + }), + ('emcee', '2.2.1', { + 'checksums': ['b83551e342b37311897906b3b8acf32979f4c5542e0a25786ada862d26241172'], + }), + (name, version, { + 'modulename': 'GPyOpt', + 'checksums': ['e714daa035bb529a6db23c53665a762a4ab3456b9329c19ad3b03983f94c9b2a'], + }), +] + +local_GPy_file = '%(installdir)s/lib/python%(pyshortver)s/site-packages/GPy/plotting/matplot_dep/plot_definitions.py' + +# Fix GPy with matplotlib>=3.4.0 +# see issue 953 and fix from https://github.com/SheffieldML/GPy/pull/960 +postinstallcmds = [ + 'sed -i ' + '''-e 's|ax._process_unit_info(xdata=X, ydata=y1)|ax._process_unit_info([("x", X), ("y", y1)], convert=False)|' ''' + '''-e 's|ax._process_unit_info(ydata=y2)|ax._process_unit_info([("y", y2)], convert=False)|' %s''' % local_GPy_file, +] + + +sanity_pip_check = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.3-foss-2023a-PLUMED-2.9.0.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.3-foss-2023a-PLUMED-2.9.0.eb new file mode 100644 index 000000000000..943aa4ac8393 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.3-foss-2023a-PLUMED-2.9.0.eb @@ -0,0 +1,100 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2016 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, +# Ghent University / The Francis Crick Institute +# Authors:: +# * Wiktor Jurkowski +# * Fotis Georgatos +# * George Tsouloupas +# * Kenneth Hoste +# * Adam Huffman +# * Ake Sandgren +# * J. Sassmannshausen +# * Dugan Witherick +# * Christoph Siegert +# License:: MIT/GPL + +name = 'GROMACS' +version = '2023.3' +_plumedver = '2.9.0' +versionsuffix = '-PLUMED-%s' % _plumedver + +homepage = 'https://www.gromacs.org' +description = """ +GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the +Newtonian equations of motion for systems with hundreds to millions of +particles. + +This is a CPU only build, containing both MPI and threadMPI binaries +for both single and double precision. + +It also contains the gmxapi extension for the single precision MPI build +next to PLUMED.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = [ + 'https://ftp.gromacs.org/pub/gromacs/', + 'ftp://ftp.gromacs.org/pub/gromacs/', +] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch', + 'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch', + '%(name)s-%(version)s_skip_test_for_plumed.patch', +] +checksums = [ + {'gromacs-2023.3.tar.gz': '4ec8f8d0c7af76b13f8fd16db8e2c120e749de439ae9554d9f653f812d78d1cb'}, + {'GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch': + '7f41bda16c9c2837624265dda4be252f655d1288ddc4486b1a2422af30d5d199'}, + {'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch': + '6df844bb3bbc51180446a3595c61a4ef195e5f975533a04cef76841aa763aec1'}, + {'GROMACS-2023.3_skip_test_for_plumed.patch': + '6c541ee74f71f6a63950134d9d0e3afb176a2e25e76e017b4d1986a59163c083'}, +] + +builddependencies = [ + ('CMake', '3.26.3'), + ('scikit-build', '0.17.6'), + ('Doxygen', '1.9.7'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('networkx', '3.1'), + ('mpi4py', '3.1.4'), + ('PLUMED', _plumedver), +] + + +configopts = '-DCMAKE_CXX_FLAGS="$CXXFLAGS -fpermissive" ' + +# PLUMED 2.9.0 is compatible with GROMACS 2023; 2023.3 seems to work fine too +ignore_plumed_version_check = True + +exts_defaultclass = 'PythonPackage' + +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'use_pip': True, + 'download_dep_fail': True, + 'sanity_pip_check': True, +} + +exts_list = [ + ('gmxapi', '0.4.2', { + 'preinstallopts': 'export CMAKE_ARGS="-Dgmxapi_ROOT=%(installdir)s ' + + '-C %(installdir)s/share/cmake/gromacs_mpi/gromacs-hints_mpi.cmake" && ', + 'source_tmpl': 'gromacs-2023.3.tar.gz', + 'start_dir': 'python_packaging/gmxapi', + 'checksums': ['4ec8f8d0c7af76b13f8fd16db8e2c120e749de439ae9554d9f653f812d78d1cb'], + }), +] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GTS/GTS-0.7.6-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/GTS/GTS-0.7.6-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..dd36868a20d5 --- /dev/null +++ b/easybuild/easyconfigs/g/GTS/GTS-0.7.6-GCCcore-13.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'GTS' +version = '0.7.6' + +homepage = 'http://gts.sourceforge.net/' +description = """GTS stands for the GNU Triangulated Surface Library. +It is an Open Source Free Software Library intended to provide a set of useful +functions to deal with 3D surfaces meshed with interconnected triangles.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['059c3e13e3e3b796d775ec9f96abdce8f2b3b5144df8514eda0cc12e13e8b81e'] + +builddependencies = [ + ('pkgconf', '2.2.0'), + ('binutils', '2.42'), +] +dependencies = [ + ('GLib', '2.80.4'), +] + +sanity_check_paths = { + 'files': ['lib/libgts.%s' % SHLIB_EXT, 'bin/gts2oogl', 'bin/gtscheck'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GeoDict/GeoDict-2024.SP2-gmpich-2024.06.eb b/easybuild/easyconfigs/g/GeoDict/GeoDict-2024.SP2-gmpich-2024.06.eb new file mode 100644 index 000000000000..42186eafddb1 --- /dev/null +++ b/easybuild/easyconfigs/g/GeoDict/GeoDict-2024.SP2-gmpich-2024.06.eb @@ -0,0 +1,41 @@ +easyblock = 'Tarball' + +name = 'GeoDict' +version = '2024.SP2' + +homepage = 'https://www.math2market.com/geodict-software/geodict-applications.html' +description = """ +The innovative and easy-to-use material simulator GeoDict is the most complete software +solution for multi-scale 3D image processing, modeling of materials, visualization, material +property characterization, simulation-based material development, and optimization of +processes. +""" + +toolchain = {'name': 'gmpich', 'version': '2024.06'} + +source_urls = [ + 'https://www.gddownload.de/Releases' +] +sources = [ + '%(name)s2024-3-4-Linux-x86_64-ServicePack2.tar.gz', + '%(name)s2024-3-4-Linux-x86_64-ServicePack2-Tools.tar.gz' +] +checksums = [ + {'GeoDict2024-3-4-Linux-x86_64-ServicePack2.tar.gz': + '049401063d892eac65696d7d1ed8d4b915c9a81bb13e325cc0657c60ce8aeb28'}, + {'GeoDict2024-3-4-Linux-x86_64-ServicePack2-Tools.tar.gz': + '1b50fb840e8e78c225c748d73eaca60faedd822de33f20c716b1e98b15492eac'}, +] + +dependencies = [ + ('X11', '20230603'), +] + +modextrapaths = {'PATH': '.'} + +sanity_check_paths = { + 'files': ['geodict2024'], + 'dirs': ['Python', 'Tools'], +} + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/g/GetOrganelle/GetOrganelle-1.7.7.1-foss-2023a.eb b/easybuild/easyconfigs/g/GetOrganelle/GetOrganelle-1.7.7.1-foss-2023a.eb new file mode 100644 index 000000000000..4c6746689d9c --- /dev/null +++ b/easybuild/easyconfigs/g/GetOrganelle/GetOrganelle-1.7.7.1-foss-2023a.eb @@ -0,0 +1,43 @@ +easyblock = 'PythonPackage' + +name = 'GetOrganelle' +version = '1.7.7.1' + +homepage = 'https://github.com/Kinggerm/GetOrganelle' +description = """This toolkit assemblies organelle genome from genomic skimming data.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/Kinggerm/GetOrganelle/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['cf8e14766de43967182be839de20c9d1709b60fae38a0b3d175742dfad7a5d44'] + +dependencies = [ + ('Python', '3.11.3'), + ('Bandage', '0.9.0'), + ('SciPy-bundle', '2023.07'), + ('sympy', '1.12'), + ('SPAdes', '3.15.4'), + ('Bowtie2', '2.5.1'), + ('BLAST+', '2.14.1'), + ('Perl', '5.36.1'), + ('matplotlib', '3.7.2') +] + +download_dep_fail = True +use_pip = True + +options = {'modulename': False} + +fix_python_shebang_for = ['bin/*.py'] + +sanity_pip_check = True + +sanity_check_commands = ["get_organelle_from_reads.py -h"] + +sanity_check_paths = { + 'files': ['bin/check_annotations.py', 'bin/get_organelle_from_reads.py', 'bin/slim_graph.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GimmeMotifs/GimmeMotifs-0.17.2-foss-2023a.eb b/easybuild/easyconfigs/g/GimmeMotifs/GimmeMotifs-0.17.2-foss-2023a.eb new file mode 100644 index 000000000000..64b42485b8fa --- /dev/null +++ b/easybuild/easyconfigs/g/GimmeMotifs/GimmeMotifs-0.17.2-foss-2023a.eb @@ -0,0 +1,81 @@ +easyblock = 'PythonBundle' + +name = 'GimmeMotifs' +version = '0.17.2' + +homepage = 'https://github.com/vanheeringen-lab/gimmemotifs' +description = "Suite of motif tools, including a motif prediction pipeline for ChIP-seq experiments" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [('poetry', '1.5.1')] +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('matplotlib', '3.7.2'), + ('pybedtools', '0.9.1'), + ('Pysam', '0.22.0'), + ('scikit-learn', '1.3.1'), + ('Seaborn', '0.13.2'), + ('statsmodels', '0.14.1'), + ('tqdm', '4.66.1'), + ('genomepy', '0.16.1'), + ('qnorm', '0.8.1'), + ('Arrow', '14.0.1'), # provides pyarrow, required by feather-format + ('HTSeq', '2.0.7'), # required by biofluff + ('pyBigWig', '0.3.22'), # required by biofluff +] + +use_pip = True + +exts_list = [ + ('palettable', '3.3.3', { + 'checksums': ['094dd7d9a5fc1cca4854773e5c1fc6a315b33bd5b3a8f47064928facaf0490a8'], + }), + ('biofluff', '3.0.4', { + 'modulename': 'fluff', + # remove pyBigWig dependency - pip_check fails with "import pybigwig" + 'preinstallopts': "sed -i '/pyBigWig/d' setup.py && ", + 'checksums': ['ef7b0a54103a830f197f21aa3d1ade8bdcddf613b437ea38c95260bb45324d6b'], + }), + ('diskcache', '5.6.3', { + 'checksums': ['2c3a3fa2743d8535d832ec61c2054a1641f41775aa7c556758a109941e33e4fc'], + }), + ('feather-format', '0.4.1', { + 'modulename': 'feather', + 'checksums': ['45f67e3745d394d4f160ca6d636bbfd4f8b68d01199dc1649b6e487d3e878903'], + }), + ('iteround', '1.0.4', { + 'source_urls': ['https://github.com/cgdeboer/iteround/archive/'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['445e4f0c793ae558e4db3cdee7e23d77459b9c586e8021667aa60c14ba7ff45f'], + }), + ('logomaker', '0.8', { + 'checksums': ['d8c7501a7d6d7961cd68e5a44e939000ebf1b0c4197a0c9198351e1d681d3f6d'], + }), + ('loguru', '0.7.2', { + 'checksums': ['e671a53522515f34fd406340ee968cb9ecafbc4b36c679da03c18fd8d0bd51ac'], + }), + ('xxhash', '3.4.1', { + 'checksums': ['0379d6cf1ff987cd421609a264ce025e74f346e3e145dd106c0cc2e3ec3f99a9'], + }), + ('xdg', '6.0.0', { + 'checksums': ['24278094f2d45e846d1eb28a2ebb92d7b67fc0cab5249ee3ce88c95f649a1c92'], + }), + ('gimmemotifs', version, { + 'preinstallopts': """sed -i '/"configparser"/d' setup.py && """, + 'checksums': ['fbf70997abce6a75451c10b96994f8dbc03152b01df5cf30bf4397c98a9b54d2'], + }), +] + +sanity_check_paths = { + 'files': ['bin/gimme'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["gimme --help"] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/gubbins/gubbins-2.4.0.eb b/easybuild/easyconfigs/g/Gubbins/Gubbins-2.4.0.eb similarity index 98% rename from easybuild/easyconfigs/g/gubbins/gubbins-2.4.0.eb rename to easybuild/easyconfigs/g/Gubbins/Gubbins-2.4.0.eb index c209965f2eb4..7b9bbd1be454 100644 --- a/easybuild/easyconfigs/g/gubbins/gubbins-2.4.0.eb +++ b/easybuild/easyconfigs/g/Gubbins/Gubbins-2.4.0.eb @@ -10,7 +10,7 @@ easyblock = 'Conda' -name = 'gubbins' +name = 'Gubbins' version = '2.4.0' homepage = 'https://sanger-pathogens.github.io/gubbins' diff --git a/easybuild/easyconfigs/g/Gubbins/Gubbins-3.3.5-foss-2022b.eb b/easybuild/easyconfigs/g/Gubbins/Gubbins-3.3.5-foss-2022b.eb new file mode 100644 index 000000000000..57a08aeb182a --- /dev/null +++ b/easybuild/easyconfigs/g/Gubbins/Gubbins-3.3.5-foss-2022b.eb @@ -0,0 +1,65 @@ +# This easyconfig was created by the BEAR Software team at the University of Birmingham. +easyblock = 'ConfigureMake' + +name = 'Gubbins' +version = '3.3.5' + +homepage = "https://nickjcroucher.github.io/gubbins/" +description = """Gubbins (Genealogies Unbiased By recomBinations In Nucleotide Sequences) is an algorithm that + iteratively identifies loci containing elevated densities of base substitutions, which are marked as recombinations, + while concurrently constructing a phylogeny based on the putative point mutations outside of these regions. + Simulations demonstrate the algorithm generates highly accurate reconstructions under realistic models of short-term + bacterial evolution, and can be run in only a few hours on alignments of hundreds of bacterial genome sequences.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +source_urls = ['https://github.com/nickjcroucher/gubbins/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['4ee363f82708bdda0c00d1c6c334cf20127bd852ee488619f61140771a279774'] + +builddependencies = [ + ('Autotools', '20220317'), + ('Autoconf-archive', '2023.02.20'), + ('pkgconf', '1.9.3'), + ('Check', '0.15.2'), + ('subunit', '1.4.3'), +] + +dependencies = [ + ('Python', '3.10.8'), + ('Biopython', '1.81'), + ('DendroPy', '4.5.2'), + ('numba', '0.58.1'), + ('SciPy-bundle', '2023.02'), + ('FastTree', '2.1.11'), + ('IQ-TREE', '2.2.2.6'), + ('rapidNJ', '2.3.3'), + ('RAxML', '8.2.12', '-avx2'), + ('RAxML-NG', '1.2.0'), + ('SKA2', '0.3.7'), + ('dill', '0.3.7'), + ('multiprocess', '0.70.15'), +] + +preconfigopts = "autoreconf -i && " +# runtest = 'check' # runs the Python tests and this causes package to be installed into the Python install +postinstallcmds = [ + """sed -i 's/self.executable = "iqtree"/self.executable = "iqtree2"/' python/gubbins/treebuilders.py""", + "cd python && python -m pip install --prefix %(installdir)s --no-build-isolation . " +] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['bin/gubbins', 'lib/libgubbins.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = [ + "gubbins --help", + "run_gubbins.py --version", + 'python -c "import gubbins"', + 'python -m pip check', +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/Guile/Guile-2.0.14-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/Guile/Guile-2.0.14-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..06a1dc6a05a2 --- /dev/null +++ b/easybuild/easyconfigs/g/Guile/Guile-2.0.14-GCCcore-13.3.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'Guile' +version = '2.0.14' + +homepage = 'http://www.gnu.org/software/guile' +description = """Guile is the GNU Ubiquitous Intelligent Language for Extensions, the official extension language for +the GNU operating system. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['8aeb2f353881282fe01694cce76bb72f7ffdd296a12c7a1a39255c27b0dfe5f1'] + +builddependencies = [ + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), +] + +dependencies = [ + ('gc', '8.2.6'), + ('GMP', '6.3.0'), + ('libffi', '3.4.5'), + ('libunistring', '1.2'), + ('libtool', '2.4.7'), + ('libreadline', '8.2'), + ('XZ', '5.4.5'), +] + +configopts = " --enable-error-on-warning=no" + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["guile", 'guile-config', 'guile-snarf', 'guile-tools']] + + ["lib/libguile-%(version_major_minor)s.a", + "include/guile/%(version_major_minor)s/libguile.h"], + 'dirs': [] +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/g/Guile/Guile-3.0.10-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/Guile/Guile-3.0.10-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..46917679856c --- /dev/null +++ b/easybuild/easyconfigs/g/Guile/Guile-3.0.10-GCCcore-13.3.0.eb @@ -0,0 +1,46 @@ +easyblock = 'ConfigureMake' + +name = 'Guile' +version = '3.0.10' + +homepage = 'https://www.gnu.org/software/guile/' + +description = """ + Guile is a programming language, designed to help programmers create flexible + applications that can be extended by users or other programmers with plug-ins, + modules, or scripts. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['2dbdbc97598b2faf31013564efb48e4fed44131d28e996c26abe8a5b23b56c2a'] + +builddependencies = [ + ('Autotools', '20231222'), + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), +] + +dependencies = [ + ('gc', '8.2.6'), + ('GMP', '6.3.0'), + ('libffi', '3.4.5'), + ('libunistring', '1.2'), +] + +postinstallcmds = ["cd %(installdir)s/bin && ln -s guile guile%(version_major)s"] + +sanity_check_paths = { + 'files': ['bin/guild', 'bin/guile', 'bin/guile-config', + 'bin/guile-snarf', 'bin/guile-tools', + 'include/guile/%(version_major_minor)s/libguile.h', + 'lib/libguile-%(version_major_minor)s.a', + 'lib/libguile-%%(version_major_minor)s.%s' % SHLIB_EXT], + 'dirs': ['include/guile/%(version_major_minor)s/libguile', + 'lib/guile/%(version_major_minor)s/ccache'], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/g/Gurobi/Gurobi-11.0.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/Gurobi/Gurobi-11.0.2-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..0e8c4d8115e7 --- /dev/null +++ b/easybuild/easyconfigs/g/Gurobi/Gurobi-11.0.2-GCCcore-12.3.0.eb @@ -0,0 +1,63 @@ +name = 'Gurobi' +version = '11.0.2' + +homepage = 'https://www.gurobi.com' +description = """The Gurobi Optimizer is a state-of-the-art solver for mathematical programming. +The solvers in the Gurobi Optimizer were designed from the ground up to exploit modern +architectures and multi-core processors, using the most advanced implementations of the +latest algorithms.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://packages.gurobi.com/%(version_major_minor)s/'] +local_archs = {'aarch64': 'armlinux64', 'x86_64': 'linux64'} +sources = ['gurobi%%(version)s_%s.tar.gz' % local_archs[ARCH]] +patches = ['Gurobi-11.0.0_use-eb-python-gurobi-shell.patch'] +checksums = [ + {'gurobi11.0.2_linux64.tar.gz': 'f43ac8a3edb987b9a0a61452acd9d8dbe9eb37368c6da7ce36e5247cb2a1a368', + 'gurobi11.0.2_armlinux64.tar.gz': '311b38a89717e26f3f829479ef8e6776674b2711c427a90b84ac9978acd19ff2'}, + {'Gurobi-11.0.0_use-eb-python-gurobi-shell.patch': + '566473a3ba4e35b0e74595368f9f4133fc4a3c97cca84154c4b938645786e663'}, +] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('Python', '3.11.3'), +] + +exts_defaultclass = 'PythonPackage' + +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'download_dep_fail': True, + 'use_pip': True, +} + +exts_list = [ + ('gurobipy', version, { + 'sources': ['gurobipy-%(version)s-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_%(arch)s.whl'], + 'checksums': [{ + 'gurobipy-%(version)s-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_aarch64.whl': + '871e818026c8f288d7440fcd4b842becdf1006f43495fc4f6e3ec6d9b8ba3d7a', + 'gurobipy-%(version)s-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl': + '86265b7a9a8f3e531c1bbee6e61c1e7d0b68264e976795b4cf7aec68b9e66eb8', + }], + }), +] + +# remove bundled Python interpreter in favour of the dependency in EB +postinstallcmds = ['rm %(installdir)s/bin/python*'] + +# license is mandatory for installation +# use EB_GUROBI_LICENSE_FILE environment variable, or +# uncomment and modify the following variable: +# license_file = '/path/to/my-license-file' + +modloadmsg = """Gurobi shell based on Python %(pyver)s can be launched with command `gurobi.sh` +Gurobi Python Interface can be loaded in Python %(pyver)s with 'import gurobipy' +""" + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/g/Gymnasium/Gymnasium-0.29.1-foss-2023a.eb b/easybuild/easyconfigs/g/Gymnasium/Gymnasium-0.29.1-foss-2023a.eb new file mode 100644 index 000000000000..e389e3ef7d75 --- /dev/null +++ b/easybuild/easyconfigs/g/Gymnasium/Gymnasium-0.29.1-foss-2023a.eb @@ -0,0 +1,52 @@ +easyblock = 'PythonBundle' + +name = 'Gymnasium' +version = '0.29.1' + +homepage = 'https://gymnasium.farama.org/' +description = """ +Gymnasium is an open source Python library for developing and comparing reinforcement learning +algorithms by providing a standard API to communicate between learning algorithms and +environments, as well as a standard set of environments compliant with that API. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('CMake', '3.26.3'), + ('SWIG', '4.1.1'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('OpenCV', '4.8.1', '-contrib'), + ('pygame', '2.5.2'), + ('MuJoCo', '3.1.4'), +] + +use_pip = True + +exts_list = [ + ('cloudpickle', '3.0.0', { + 'checksums': ['996d9a482c6fb4f33c1a35335cf8afd065d2a56e973270364840712d9131a882'], + }), + ('Farama-Notifications', '0.0.4', { + 'checksums': ['13fceff2d14314cf80703c8266462ebf3733c7d165336eee998fc58e545efd18'], + }), + ('box2d-py', '2.3.8', { + 'modulename': 'Box2D', + 'checksums': ['bdacfbbc56079bb317548efe49d3d5a86646885cc27f4a2ee97e4b2960921ab7'], + }), + ('gymnasium', version, { + 'use_pip_extras': 'all', + 'checksums': ['1a532752efcb7590478b1cc7aa04f608eb7a2fdad5570cd217b66b6a35274bb1'], + }), +] + +local_envs = ['box2d', 'classic_control', 'mujoco', 'toy_text'] +sanity_check_commands = ["python -c 'import gymnasium.envs.%s'" % e for e in local_envs] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/g2lib/g2lib-3.2.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/g/g2lib/g2lib-3.2.0-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..04674a29ff76 --- /dev/null +++ b/easybuild/easyconfigs/g/g2lib/g2lib-3.2.0-GCCcore-13.2.0.eb @@ -0,0 +1,32 @@ +name = 'g2lib' +version = '3.2.0' + +homepage = 'https://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/' +description = """Library contains GRIB2 encoder/decoder and search/indexing routines.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = [homepage] +sources = ['%(name)s-%(version)s.tar'] +patches = [ + '%(name)s-%(version)s_makefile.patch', +] +checksums = [ + '9d3866de32e13e80798bfb08dbbea9223f32cec3fce3c57b6838e76f27d5a1d3', # g2lib-3.2.0.tar + 'e434394a6ec8bd68dbd57e3fdb44c47372b07380e362ed955bb038b78dd81812', # g2lib-3.2.0_makefile.patch +] + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('JasPer', '4.0.0'), + ('libpng', '1.6.40'), +] + +buildopts = 'CFLAGS="$CFLAGS -DLINUXG95 -D__64BIT__" FC=$FC CC=$CC ' +buildopts += 'FFLAGS="$FFLAGS -fno-range-check -fallow-invalid-boz -fallow-argument-mismatch -I."' + +# parallel build tends to fail +parallel = 1 + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/g/gap/gap-4.13.0-foss-2023b.eb b/easybuild/easyconfigs/g/gap/gap-4.13.0-foss-2023b.eb new file mode 100644 index 000000000000..248ab5ded0aa --- /dev/null +++ b/easybuild/easyconfigs/g/gap/gap-4.13.0-foss-2023b.eb @@ -0,0 +1,55 @@ +easyblock = 'ConfigureMake' + +name = 'gap' +version = '4.13.0' + +homepage = 'https://www.gap-system.org' +description = """GAP is a system for computational discrete algebra, +with particular emphasis on Computational Group Theory.""" + +toolchain = {'name': 'foss', 'version': '2023b'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.gap-system.org/pub/gap/gap-%(version_major_minor)s/tar.gz/'] +sources = [SOURCE_TAR_GZ] +checksums = ['cc76ecbe33d6719450a593e613fb87e9e4247faa876f632dd0f97c398f92265d'] + +unpack_options = '--strip-components=1' + +builddependencies = [ + ('Perl', '5.38.0'), # needed to install NormalizInterface +] + +dependencies = [ + ('GMP', '6.3.0'), + ('libreadline', '8.2'), + ('zlib', '1.2.13'), + ('4ti2', '1.6.10'), # needed by 4ti2Interface, HeLP + ('cddlib', '0.94m'), # needed by CddInterface + ('cURL', '8.3.0'), # needed by curlInterface + ('lrslib', '7.2'), # needed by HeLP + ('ncurses', '6.4'), # needed by Browse + ('Normaliz', '3.10.3'), # needed by NormalizInterface, HeLP + ('Singular', '4.4.0'), # needed by singular + ('ZeroMQ', '4.3.5'), # needed by ZeroMQInterface +] + +# install target is incomplete and hardcodes the build path +buildininstalldir = True + +# Disable bundled script to download and build Normaliz +prebuildopts = "sed -i 's|./build-normaliz.sh|continue # build-normaliz.sh|' bin/BuildPackages.sh && " +# BuildPackages.sh tries to build any GAP packages that require compilation +# If one fails due to missing dependencies, it's skipped automatically +buildopts = ' && cd pkg && ../bin/BuildPackages.sh' + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['gap', 'gac']] + + ['include/gap/%s.h' % h for h in ['gap', 'system', 'version']] + + ['lib/libgap.%s' % SHLIB_EXT], + 'dirs': ['share/gap'] +} + +sanity_check_commands = ["gap tst/testinstall.g"] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/g/gawk/gawk-5.3.0-GCC-12.3.0.eb b/easybuild/easyconfigs/g/gawk/gawk-5.3.0-GCC-12.3.0.eb new file mode 100644 index 000000000000..8c63821d169a --- /dev/null +++ b/easybuild/easyconfigs/g/gawk/gawk-5.3.0-GCC-12.3.0.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'gawk' +version = '5.3.0' + +homepage = 'https://www.gnu.org/software/gawk' +description = """The awk utility interprets a special-purpose programming language that makes it possible to handle +simple data-reformatting jobs with just a few lines of code.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['378f8864ec21cfceaa048f7e1869ac9b4597b449087caf1eb55e440d30273336'] + +sanity_check_paths = { + 'files': ['bin/gawk'], + 'dirs': [], +} + +sanity_check_commands = ["gawk --help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/gc/gc-8.2.6-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/gc/gc-8.2.6-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..3a120e6a4e95 --- /dev/null +++ b/easybuild/easyconfigs/g/gc/gc-8.2.6-GCCcore-13.3.0.eb @@ -0,0 +1,42 @@ +easyblock = 'ConfigureMake' + +name = 'gc' +version = '8.2.6' +local_libatomic_version = '7.8.2' + +homepage = 'https://hboehm.info/gc/' +description = """The Boehm-Demers-Weiser conservative garbage collector can be used as a +garbage collecting replacement for C malloc or C++ new. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [ + 'https://github.com/ivmai/bdwgc/releases/download/v%(version)s/', # preferred for gc-%(version)s.tar.gz + 'https://hboehm.info/gc/gc_source/', # alternate for gc-%(version)s.tar.gz + 'https://github.com/ivmai/libatomic_ops/releases/download/v%s/' % local_libatomic_version, +] +sources = [ + SOURCE_TAR_GZ, + 'libatomic_ops-%s.tar.gz' % local_libatomic_version, +] +checksums = [ + {'gc-8.2.6.tar.gz': 'b9183fe49d4c44c7327992f626f8eaa1d8b14de140f243edb1c9dcff7719a7fc'}, + {'libatomic_ops-7.8.2.tar.gz': 'd305207fe207f2b3fb5cb4c019da12b44ce3fcbc593dfd5080d867b1a2419b51'}, +] + +builddependencies = [ + ('binutils', '2.42'), +] + +preconfigopts = 'ln -s %(builddir)s/libatomic_ops*/ libatomic_ops && ' + +configopts = "--enable-static" + +sanity_check_paths = { + 'files': ['include/gc.h', 'lib/libcord.a', 'lib/libcord.%s' % SHLIB_EXT, + 'lib/libgc.a', 'lib/libgc.%s' % SHLIB_EXT], + 'dirs': ['include/gc', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/genomepy/genomepy-0.16.1-foss-2023a.eb b/easybuild/easyconfigs/g/genomepy/genomepy-0.16.1-foss-2023a.eb new file mode 100644 index 000000000000..345af8fe3251 --- /dev/null +++ b/easybuild/easyconfigs/g/genomepy/genomepy-0.16.1-foss-2023a.eb @@ -0,0 +1,56 @@ +easyblock = 'PythonBundle' + +name = 'genomepy' +version = '0.16.1' + +homepage = 'https://github.com/vanheeringen-lab/genomepy' +description = "genomepy is designed to provide a simple and straightforward way to download and use genomic data" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [('hatchling', '1.18.0')] +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('tqdm', '4.66.1'), + ('Biopython', '1.83'), + ('mygene', '3.2.2'), + ('pyfaidx', '0.8.1.1'), + ('PyYAML', '6.0'), + ('protobuf-python', '4.24.0'), +] + +use_pip = True + +exts_list = [ + ('diskcache', '5.6.3', { + 'checksums': ['2c3a3fa2743d8535d832ec61c2054a1641f41775aa7c556758a109941e33e4fc'], + }), + ('loguru', '0.7.2', { + 'checksums': ['e671a53522515f34fd406340ee968cb9ecafbc4b36c679da03c18fd8d0bd51ac'], + }), + ('mysql-connector-python', '8.4.0', { + 'modulename': 'mysql.connector', + 'sources': ['mysql_connector_python-%(version)s-py2.py3-none-any.whl'], + 'checksums': ['35939c4ff28f395a5550bae67bafa4d1658ea72ea3206f457fff64a0fbec17e4'], + }), + ('norns', '0.1.6', { + 'preinstallopts': "sed -i '/nose/d' setup.py && ", + 'checksums': ['1f3c6ccbe79b2cb3076f66a352cd76462593adbabe9ebb262f879a9d0a6634e4'], + }), + (name, version, { + 'checksums': ['22e81827acfdb4d9e6adda1f8e4cfafbb97f1c1788348e86b930c9daa51088c5'], + }), +] + +sanity_check_paths = { + 'files': ['bin/genomepy'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["genomepy --help"] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/gensim/gensim-4.3.2-foss-2023a.eb b/easybuild/easyconfigs/g/gensim/gensim-4.3.2-foss-2023a.eb new file mode 100644 index 000000000000..cb315af1a31a --- /dev/null +++ b/easybuild/easyconfigs/g/gensim/gensim-4.3.2-foss-2023a.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonBundle' + +name = 'gensim' +version = '4.3.2' + +homepage = 'https://radimrehurek.com/gensim' +description = """Gensim is a Python library for topic modelling, document indexing and similarity retrieval with + large corpora.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('wrapt', '1.15.0'), +] + +use_pip = True + +exts_list = [ + ('smart_open', '7.0.4', { + 'checksums': ['62b65852bdd1d1d516839fcb1f6bc50cd0f16e05b4ec44b52f43d38bcb838524'], + }), + (name, version, { + 'checksums': ['99ac6af6ffd40682e70155ed9f92ecbf4384d59fb50af120d343ea5ee1b308ab'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/gfbf/gfbf-2024a.eb b/easybuild/easyconfigs/g/gfbf/gfbf-2024a.eb new file mode 100644 index 000000000000..51b74722cb57 --- /dev/null +++ b/easybuild/easyconfigs/g/gfbf/gfbf-2024a.eb @@ -0,0 +1,20 @@ +easyblock = 'Toolchain' + +name = 'gfbf' +version = '2024a' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, including + FlexiBLAS (BLAS and LAPACK support) and (serial) FFTW.""" + +toolchain = SYSTEM + +local_gccver = '13.3.0' + +dependencies = [ + ('GCC', local_gccver), + ('FlexiBLAS', '3.4.4', '', ('GCC', local_gccver)), + ('FFTW', '3.3.10', '', ('GCC', local_gccver)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/gffutils/gffutils-0.13-foss-2023a.eb b/easybuild/easyconfigs/g/gffutils/gffutils-0.13-foss-2023a.eb new file mode 100644 index 000000000000..2b52f3965bcc --- /dev/null +++ b/easybuild/easyconfigs/g/gffutils/gffutils-0.13-foss-2023a.eb @@ -0,0 +1,47 @@ +easyblock = 'PythonBundle' + +name = 'gffutils' +version = '0.13' + +homepage = 'https://github.com/daler/gffutils' +description = """Gffutils is a Python package for working with and manipulating + the GFF and GTF format files typically used for genomic annotations.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('pyfaidx', '0.8.1.1'), + ('Biopython', '1.83'), + ('pybedtools', '0.9.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('six', '1.16.0', { + 'checksums': ['1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926'], + }), + ('argh', '0.31.3', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['2edac856ff50126f6e47d884751328c9f466bacbbb6cbfdac322053d94705494'], + }), + ('argcomplete', '3.5.0', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['d4bcf3ff544f51e16e54228a7ac7f486ed70ebf2ecfe49a63a91171c76bf029b'], + }), + ('simplejson', '3.19.3', { + 'checksums': ['8e086896c36210ab6050f2f9f095a5f1e03c83fa0e7f296d6cba425411364680'], + }), + (name, version, { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['58e7bb579796fff70e728380ef2d8ffd4a3bc895e53e6529855a0cf87ba6a77a'], + }), +] + +sanity_check_commands = [ + "python -c 'from gffutils import helpers'" +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/gflags/gflags-2.2.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/gflags/gflags-2.2.2-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..de0ad50b22c2 --- /dev/null +++ b/easybuild/easyconfigs/g/gflags/gflags-2.2.2-GCCcore-13.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'CMakeMake' + +name = 'gflags' +version = '2.2.2' + +homepage = 'https://github.com/gflags/gflags' +description = """ +The gflags package contains a C++ library that implements commandline flags +processing. It includes built-in support for standard types such as string +and the ability to define flags in the source file in which they are used. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/gflags/gflags/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['34af2f15cf7367513b352bdcd2493ab14ce43692d2dcd9dfc499492966c64dcf'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] + +configopts = '-DBUILD_SHARED_LIBS=ON -DBUILD_STATIC_LIBS=ON' + +sanity_check_paths = { + 'files': ['bin/gflags_completions.sh'] + + ['lib/%s' % x for x in ['libgflags.%s' % SHLIB_EXT, 'libgflags_nothreads.%s' % SHLIB_EXT, + 'libgflags.a', 'libgflags_nothreads.a']] + + ['include/gflags/gflags_completions.h'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/gh/gh-2.52.0.eb b/easybuild/easyconfigs/g/gh/gh-2.52.0.eb new file mode 100644 index 000000000000..53a5bb57d66c --- /dev/null +++ b/easybuild/easyconfigs/g/gh/gh-2.52.0.eb @@ -0,0 +1,28 @@ +easyblock = 'GoPackage' + +name = 'gh' +version = '2.52.0' + +homepage = 'https://github.com/cli/' +description = "GitHub’s official command line tool" + +toolchain = SYSTEM + +source_urls = ['https://github.com/cli/cli/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['41de39d0f1bcacb454d9b8a46e5b97ff8b8e803cd26d284e553e45bf025325d9'] + +builddependencies = [ + ('Go', '1.22.1') +] + +installopts = './cmd/%(name)s' + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [] +} + +sanity_check_commands = ['%(name)s --version'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/giflib/giflib-5.2.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/giflib/giflib-5.2.1-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..66ef70d59ce2 --- /dev/null +++ b/easybuild/easyconfigs/g/giflib/giflib-5.2.1-GCCcore-13.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'giflib' +version = '5.2.1' + +homepage = 'http://giflib.sourceforge.net/' +description = """giflib is a library for reading and writing gif images. +It is API and ABI compatible with libungif which was in wide use while +the LZW compression algorithm was patented.""" + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['31da5562f44c5f15d63340a09a4fd62b48c45620cd302f77a6d9acf0077879bd'] + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [('binutils', '2.42')] + +skipsteps = ['configure'] + +installopts = 'PREFIX=%(installdir)s' + +sanity_check_paths = { + 'files': ['bin/giftool'], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/git-annex/git-annex-10.20240731-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/git-annex/git-annex-10.20240731-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..89c70af2f45d --- /dev/null +++ b/easybuild/easyconfigs/g/git-annex/git-annex-10.20240731-GCCcore-13.3.0.eb @@ -0,0 +1,48 @@ +easyblock = 'MakeCp' + +name = 'git-annex' +version = '10.20240731' + +homepage = 'https://git-annex.branchable.com' +description = """git-annex allows managing large files with git, without storing the file contents in git. It can sync, +backup, and archive your data, offline and online. Checksums and encryption keep your data safe and secure. Bring the +power and distributed nature of git to bear on your large files with git-annex.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('binutils', '2.42') +] + +dependencies = [ + ('GHC', '9.10.1', '-x86_64', SYSTEM), + ('Stack', '3.1.1', '-x86_64', SYSTEM), + ('git', '2.45.1'), +] + +sources = [{ + 'git_config': {'url': 'git://git-annex.branchable.com', + 'repo_name': '%(name)s', + 'tag': '%(version)s', + 'clone_into': '%(name)s-%(version)s', + }, + 'filename': '%(name)s-%(version)s.tar.gz', +}] + +checksums = [None] + +prebuildopts = "stack setup && stack build && " +buildopts = "install-bins BUILDER=stack PREFIX=%(builddir)s" + +files_to_copy = [ + (['git-annex', 'git-annex-shell'], 'bin'), +] + +sanity_check_paths = { + 'files': ['bin/git-annex', 'bin/git-annex-shell'], + 'dirs': [], +} + +sanity_check_commands = ['git-annex version'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/gmpflf/gmpflf-2024.06.eb b/easybuild/easyconfigs/g/gmpflf/gmpflf-2024.06.eb new file mode 100644 index 000000000000..bd4f74361b7e --- /dev/null +++ b/easybuild/easyconfigs/g/gmpflf/gmpflf-2024.06.eb @@ -0,0 +1,27 @@ +easyblock = 'Toolchain' + +name = 'gmpflf' +version = '2024.06' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, including + MPICH for MPI support, FlexiBLAS (OpenBLAS and LAPACK), FFTW and ScaLAPACK.""" + +toolchain = SYSTEM + +local_gccver = '12.3.0' + +# toolchain used to build gmpflf dependencies +local_comp_mpi_tc = ('gmpich', version) + +# we need GCC and MPICH as explicit dependencies instead of gompi toolchain +# because of toolchain preparation functions +dependencies = [ + ('GCC', local_gccver), + ('MPICH', '4.2.1', '', ('GCC', local_gccver)), + ('FlexiBLAS', '3.3.1', '', ('GCC', local_gccver)), + ('FFTW', '3.3.10', '', ('GCC', local_gccver)), + ('FFTW.MPI', '3.3.10', '', local_comp_mpi_tc), + ('ScaLAPACK', '2.2.0', '-fb', local_comp_mpi_tc), +] +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/gmpich/gmpich-2024.06.eb b/easybuild/easyconfigs/g/gmpich/gmpich-2024.06.eb new file mode 100644 index 000000000000..14afd408f3d7 --- /dev/null +++ b/easybuild/easyconfigs/g/gmpich/gmpich-2024.06.eb @@ -0,0 +1,20 @@ +easyblock = 'Toolchain' + +name = 'gmpich' +version = '2024.06' + + +homepage = '(none)' +description = """gcc and GFortran based compiler toolchain, + including MPICH for MPI support.""" + +toolchain = SYSTEM + +local_gccver = '12.3.0' + +dependencies = [ + ('GCC', local_gccver), + ('MPICH', '4.2.1', '', ('GCC', local_gccver)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/gmpy2/gmpy2-2.2.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/gmpy2/gmpy2-2.2.0-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..45d90e26d6a6 --- /dev/null +++ b/easybuild/easyconfigs/g/gmpy2/gmpy2-2.2.0-GCCcore-13.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'gmpy2' +version = '2.2.0' + +homepage = 'https://github.com/aleaxit/gmpy' +description = "GMP/MPIR, MPFR, and MPC interface to Python 2.6+ and 3.x" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['e19e62dfeb1e4a57079f0bf51c51dec30633d9fe9e89cb9a083e05e4823afa70'] + +builddependencies = [ + ('binutils', '2.42') +] + +dependencies = [ + ('Python', '3.12.3'), + ('GMP', '6.3.0'), + ('MPFR', '4.2.1'), + ('MPC', '1.3.1'), +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/g/gompi/gompi-2024a.eb b/easybuild/easyconfigs/g/gompi/gompi-2024a.eb new file mode 100644 index 000000000000..c49f4050ff8a --- /dev/null +++ b/easybuild/easyconfigs/g/gompi/gompi-2024a.eb @@ -0,0 +1,20 @@ +easyblock = 'Toolchain' + +name = 'gompi' +version = '2024a' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, + including OpenMPI for MPI support.""" + +toolchain = SYSTEM + +local_gccver = '13.3.0' + +# compiler toolchain dependencies +dependencies = [ + ('GCC', local_gccver), # includes both GCC and binutils + ('OpenMPI', '5.0.3', '', ('GCC', local_gccver)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/googletest/googletest-1.15.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/googletest/googletest-1.15.2-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..16b74bdae1b3 --- /dev/null +++ b/easybuild/easyconfigs/g/googletest/googletest-1.15.2-GCCcore-13.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'googletest' +version = '1.15.2' + +homepage = 'https://github.com/google/googletest' +description = "Google's framework for writing C++ tests on a variety of platforms" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/google/googletest/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['7b42b4d6ed48810c5362c265a17faebe90dc2373c885e5216439d37927f02926'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] +# build twice, once for static, once for shared libraries +configopts = ['', ' -DBUILD_SHARED_LIBS=ON '] + +sanity_check_paths = { + 'files': ['lib/lib%s.%s' % (local_lib, local_ext) for local_lib in ['gmock', 'gmock_main', 'gtest', 'gtest_main'] + for local_ext in ['a', SHLIB_EXT]], + 'dirs': ['include/gmock', 'include/gtest'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/graph-tool/graph-tool-2.59-foss-2023a.eb b/easybuild/easyconfigs/g/graph-tool/graph-tool-2.59-foss-2023a.eb new file mode 100644 index 000000000000..307e764d139c --- /dev/null +++ b/easybuild/easyconfigs/g/graph-tool/graph-tool-2.59-foss-2023a.eb @@ -0,0 +1,62 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) +# Update: Pavel Tománek (Inuits) + +easyblock = 'ConfigureMake' + +name = 'graph-tool' +version = '2.59' + +homepage = 'https://graph-tool.skewed.de/' +description = """Graph-tool is an efficient Python module for manipulation and + statistical analysis of graphs (a.k.a. networks). Contrary to + most other python modules with similar functionality, the core + data structures and algorithms are implemented in C++, making + extensive use of template metaprogramming, based heavily on + the Boost Graph Library. This confers it a level of + performance that is comparable (both in memory usage and + computation time) to that of a pure C/C++ library.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'cstd': 'c++17', 'openmp': True} + +source_urls = ['https://downloads.skewed.de/%(name)s/'] +sources = [SOURCE_TAR_BZ2] +checksums = ['cde479c0a7254b72f6e795d03b0273b0a7d81611a6a3364ba649c2c85c99acae'] + +builddependencies = [ + ('gawk', '5.3.0'), + ('pkgconf', '1.9.5'), + ('expat', '2.5.0'), + ('CGAL', '5.6'), + ('GMP', '6.2.1'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('Boost.Python', '1.82.0'), + ('sparsehash', '2.0.4'), + ('matplotlib', '3.7.2'), + ('PyCairo', '1.25.0'), + ('cairomm', '1.16.2'), + ('PyGObject', '3.46.0'), + ('GTK3', '3.24.37'), +] + +configopts = '--enable-openmp --with-cgal=$EBROOTCGAL --with-boost=$EBROOTBOOST ' +configopts += '--with-boost-python=boost_python311 ' +configopts += '--with-python-module-path=%(installdir)s/lib/python%(pyshortver)s/site-packages ' + + +sanity_check_paths = { + 'files': ['lib/python%(pyshortver)s/site-packages/graph_tool/all.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/graph_tool/include', 'share'], +} + +sanity_check_commands = [ + "python -c 'from graph_tool.all import Graph, BlockState'", + "python -c 'import graph_tool.inference'", +] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/g/graphite2/graphite2-1.3.14-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/graphite2/graphite2-1.3.14-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..7e199ecf26b0 --- /dev/null +++ b/easybuild/easyconfigs/g/graphite2/graphite2-1.3.14-GCCcore-13.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'CMakeMake' + +name = 'graphite2' +version = '1.3.14' + +homepage = 'https://scripts.sil.org/cms/scripts/page.php?site_id=projects&item_id=graphite_home' +description = """Graphite is a "smart font" system developed specifically to + handle the complexities of lesser-known languages of the world.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/silnrsi/graphite/archive/'] +sources = ['%(version)s.zip'] +checksums = ['36e15981af3bf7a3ca3daf53295c8ffde04cf7d163e3474e4d0836e2728b4149'] + +builddependencies = [ + ('CMake', '3.29.3'), + ('binutils', '2.42'), +] + +sanity_check_paths = { + 'files': ['bin/gr2fonttest'] + + ['lib/lib%%(name)s.%s' % x for x in [SHLIB_EXT, 'la']], + 'dirs': ['include/%(name)s', 'share'] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/groff/groff-1.23.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/groff/groff-1.23.0-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..000049dbdda4 --- /dev/null +++ b/easybuild/easyconfigs/g/groff/groff-1.23.0-GCCcore-13.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'groff' +version = '1.23.0' + +homepage = 'https://www.gnu.org/software/groff' +description = """Groff (GNU troff) is a typesetting system that reads plain text mixed with formatting commands + and produces formatted output.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://ftp.gnu.org/gnu/groff'] +sources = [SOURCE_TAR_GZ] +checksums = ['6b9757f592b7518b4902eb6af7e54570bdccba37a871fddb2d30ae3863511c13'] + +builddependencies = [ + ('binutils', '2.42'), + ('M4', '1.4.19'), +] + +sanity_check_paths = { + 'files': ['bin/groff', 'bin/nroff', 'bin/troff'], + 'dirs': ['lib/groff', 'share'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/grpcio/grpcio-1.57.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/grpcio/grpcio-1.57.0-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..27e974c5de03 --- /dev/null +++ b/easybuild/easyconfigs/g/grpcio/grpcio-1.57.0-GCCcore-12.2.0.eb @@ -0,0 +1,54 @@ +easyblock = 'PythonBundle' + +name = 'grpcio' +version = '1.57.0' + +homepage = 'https://grpc.io/' +description = """gRPC is a modern, open source, high-performance remote procedure call (RPC) +framework that can run anywhere. gRPC enables client and server applications to +communicate transparently, and simplifies the building of connected systems.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +use_pip = True +sanity_pip_check = True + +builddependencies = [ + ('binutils', '2.39'), + ('OpenSSL', '1.1', '', SYSTEM), + ('RE2', '2023-03-01'), +] + +dependencies = [ + ('Python', '3.10.8'), + ('protobuf-python', '4.23.0'), + ('Abseil', '20230125.2'), +] + +exts_list = [ + (name, version, { + 'modulename': 'grpc', + 'preinstallopts': ( + # patch hardcoded /usr paths to prefix them with alternate sysroot path (if defined) + "sed -i 's@/usr@%(sysroot)s/usr@g' setup.py && " + "export GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS=%(parallel)s && " + # Required to avoid building with non-default C++ standard but keep other flags, + # see https://github.com/grpc/grpc/issues/34256 + 'export GRPC_PYTHON_CFLAGS="-fvisibility=hidden -fno-wrapv -fno-exceptions" &&' + "GRPC_PYTHON_BUILD_SYSTEM_OPENSSL=True " + "GRPC_PYTHON_BUILD_SYSTEM_ZLIB=True " + "GRPC_PYTHON_BUILD_SYSTEM_RE2=True " + "GRPC_PYTHON_BUILD_SYSTEM_ABSL=True " + ), + 'patches': ['grpcio-1.57.0_use-ebroot.patch'], + 'checksums': [ + {'grpcio-1.57.0.tar.gz': + '4b089f7ad1eb00a104078bab8015b0ed0ebcb3b589e527ab009c53893fd4e613'}, + {'grpcio-1.57.0_use-ebroot.patch': + '5faf822cd817b723ae9361e43656d0ecc7b3333a166bbab2df80b43ae588e510'}, + ], + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/gtk-doc/gtk-doc-1.34.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/gtk-doc/gtk-doc-1.34.0-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..dd18263d557e --- /dev/null +++ b/easybuild/easyconfigs/g/gtk-doc/gtk-doc-1.34.0-GCCcore-12.3.0.eb @@ -0,0 +1,51 @@ +easyblock = 'MesonNinja' + +name = 'gtk-doc' +version = '1.34.0' + +homepage = 'https://gitlab.gnome.org/GNOME/gtk-doc' +description = """Documentation tool for public library API""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://gitlab.gnome.org/GNOME/gtk-doc/-/archive/%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['e1d544fa70ae60014a241b674c9d989f4ad6a96554652ebf73bbe94b4da1aa35'] + +builddependencies = [ + ('binutils', '2.40'), + ('yelp-tools', '42.1'), + ('Ninja', '1.11.1'), + ('Meson', '1.1.1'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('Pygments', '2.18.0'), + ('GLib', '2.77.1'), +] + +sanity_check_paths = { + 'files': [ + 'bin/gtkdoc-depscan', + 'bin/gtkdoc-fixxref', + 'bin/gtkdoc-check', + 'bin/gtkdocize', + 'bin/gtkdoc-mkdb', + 'bin/gtkdoc-mkhtml', + 'bin/gtkdoc-mkhtml2', + 'bin/gtkdoc-mkman', + 'bin/gtkdoc-mkpdf', + 'bin/gtkdoc-rebase', + 'bin/gtkdoc-scan', + 'bin/gtkdoc-scangobj', + ], + 'dirs': [ + 'lib/cmake/GtkDoc', + 'share/%(name)s', + ], +} + +sanity_check_commands = ['gtkdoc-depscan'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HDBSCAN/HDBSCAN-0.8.38.post1-foss-2023a.eb b/easybuild/easyconfigs/h/HDBSCAN/HDBSCAN-0.8.38.post1-foss-2023a.eb new file mode 100644 index 000000000000..b260708eab8c --- /dev/null +++ b/easybuild/easyconfigs/h/HDBSCAN/HDBSCAN-0.8.38.post1-foss-2023a.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'HDBSCAN' +version = '0.8.38.post1' + +homepage = 'http://hdbscan.readthedocs.io/en/latest/' +description = """The hdbscan library is a suite of tools to use unsupervised learning to find clusters, or dense + regions, of a dataset. The primary algorithm is HDBSCAN* as proposed by Campello, Moulavi, and Sander. The library + provides a high performance implementation of this algorithm, along with tools for analysing the resulting + clustering.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['5fbdba2ffb5a99a8b52fa2915658ced6bed59f4d0d5f40b1c673646c928aac0b'] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('scikit-learn', '1.3.1'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.11-intel-2016a.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.11-intel-2016a.eb index e115932f8eef..3e25fa941333 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.11-intel-2016a.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.11-intel-2016a.eb @@ -3,15 +3,16 @@ easyblock = 'ConfigureMake' name = 'HDF' version = '4.2.11' -homepage = 'http://www.hdfgroup.org/products/hdf4/' +homepage = 'http://support.hdfgroup.org/products/hdf4/' description = """HDF (also known as HDF4) is a library and multi-object file format for storing and managing data between machines.""" toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'pic': True} +source_urls = ['http://support.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] +checksums = ['c3f7753b2fb9b27d09eced4d2164605f111f270c9a60b37a578f7de02de86d24'] builddependencies = [ ('flex', '2.6.0'), diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.12-intel-2017a.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.12-intel-2017a.eb index 36b03f185363..5fade2d22484 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.12-intel-2017a.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.12-intel-2017a.eb @@ -3,15 +3,16 @@ easyblock = 'ConfigureMake' name = 'HDF' version = '4.2.12' -homepage = 'http://www.hdfgroup.org/products/hdf4/' +homepage = 'http://support.hdfgroup.org/products/hdf4/' description = """HDF (also known as HDF4) is a library and multi-object file format for storing and managing data between machines.""" toolchain = {'name': 'intel', 'version': '2017a'} toolchainopts = {'pic': True} +source_urls = ['http://support.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] +checksums = ['dd419c55e85d1a0e13f3ea5ed35d00710033ccb16c85df088eb7925d486e040c'] builddependencies = [ ('flex', '2.6.3'), diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.13-GCCcore-6.4.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.13-GCCcore-6.4.0.eb index f1b4395af488..39dc55079351 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.13-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.13-GCCcore-6.4.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'HDF' version = '4.2.13' -homepage = 'http://www.hdfgroup.org/products/hdf4/' +homepage = 'http://support.hdfgroup.org/products/hdf4/' description = """ HDF (also known as HDF4) is a library and multi-object file format for @@ -14,7 +14,7 @@ toolchain = {'name': 'GCCcore', 'version': '6.4.0'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] +source_urls = ['http://support.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] checksums = ['be9813c1dc3712c2df977d4960e1f13f20f447dfa8c3ce53331d610c1f470483'] builddependencies = [ diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.13-intel-2017a-no-netcdf.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.13-intel-2017a-no-netcdf.eb index 84bff2749e91..74e44dbfc263 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.13-intel-2017a-no-netcdf.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.13-intel-2017a-no-netcdf.eb @@ -4,7 +4,7 @@ name = 'HDF' version = '4.2.13' versionsuffix = '-no-netcdf' -homepage = 'http://www.hdfgroup.org/products/hdf4/' +homepage = 'http://support.hdfgroup.org/products/hdf4/' description = """HDF (also known as HDF4) is a library and multi-object file format for storing and managing data between machines. This version suppresses the netcdf api, that gives issues with some applications""" @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2017a'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] +source_urls = ['http://support.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] checksums = ['be9813c1dc3712c2df977d4960e1f13f20f447dfa8c3ce53331d610c1f470483'] builddependencies = [ diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-6.4.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-6.4.0.eb index 1f31e675f7ad..56e705f36a21 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-6.4.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'HDF' version = '4.2.14' -homepage = 'http://www.hdfgroup.org/products/hdf4/' +homepage = 'http://support.hdfgroup.org/products/hdf4/' description = """ HDF (also known as HDF4) is a library and multi-object file format for @@ -13,7 +13,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '6.4.0'} toolchainopts = {'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] +source_urls = ['http://support.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['2d383e87c8a0ca6a5352adbd1d5546e6cc43dc21ff7d90f93efa644d85c0b14a'] diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-7.3.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-7.3.0.eb index 204d917a1790..51b65acec93d 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-7.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'HDF' version = '4.2.14' -homepage = 'https://www.hdfgroup.org/products/hdf4/' +homepage = 'https://support.hdfgroup.org/products/hdf4/' description = """ HDF (also known as HDF4) is a library and multi-object file format for @@ -13,7 +13,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '7.3.0'} toolchainopts = {'pic': True} -source_urls = ['https://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] +source_urls = ['https://support.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['2d383e87c8a0ca6a5352adbd1d5546e6cc43dc21ff7d90f93efa644d85c0b14a'] diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-8.2.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-8.2.0.eb index bf3fff366f27..a78efd6cee28 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-8.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'HDF' version = '4.2.14' -homepage = 'https://www.hdfgroup.org/products/hdf4/' +homepage = 'https://support.hdfgroup.org/products/hdf4/' description = """ HDF (also known as HDF4) is a library and multi-object file format for @@ -13,7 +13,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '8.2.0'} toolchainopts = {'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] +source_urls = ['http://support.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['2d383e87c8a0ca6a5352adbd1d5546e6cc43dc21ff7d90f93efa644d85c0b14a'] diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-8.3.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-8.3.0.eb index ff08dc71e807..fdee3ff0383f 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-8.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'HDF' version = '4.2.14' -homepage = 'https://www.hdfgroup.org/products/hdf4/' +homepage = 'https://support.hdfgroup.org/products/hdf4/' description = """ HDF (also known as HDF4) is a library and multi-object file format for @@ -13,7 +13,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '8.3.0'} toolchainopts = {'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] +source_urls = ['http://support.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['2d383e87c8a0ca6a5352adbd1d5546e6cc43dc21ff7d90f93efa644d85c0b14a'] diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-10.2.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-10.2.0.eb index bdb2cb878ee9..91e084fc238a 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-10.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'HDF' version = '4.2.15' -homepage = 'https://www.hdfgroup.org/products/hdf4/' +homepage = 'https://support.hdfgroup.org/products/hdf4/' description = """ HDF (also known as HDF4) is a library and multi-object file format for @@ -13,7 +13,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} toolchainopts = {'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] +source_urls = ['http://support.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] sources = [SOURCELOWER_TAR_GZ] patches = ['HDF-4.2.15_fix-aarch64.patch'] checksums = [ diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-10.3.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-10.3.0.eb index 869a6a796a26..7fff3f348bba 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-10.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'HDF' version = '4.2.15' -homepage = 'https://www.hdfgroup.org/products/hdf4/' +homepage = 'https://support.hdfgroup.org/products/hdf4/' description = """ HDF (also known as HDF4) is a library and multi-object file format for @@ -13,7 +13,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '10.3.0'} toolchainopts = {'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] +source_urls = ['http://support.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] sources = [SOURCELOWER_TAR_GZ] patches = ['HDF-4.2.15_fix-aarch64.patch'] checksums = [ diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-11.2.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-11.2.0.eb index fc36bb04673d..7acaaafc09d1 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-11.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'HDF' version = '4.2.15' -homepage = 'https://www.hdfgroup.org/products/hdf4/' +homepage = 'https://support.hdfgroup.org/products/hdf4/' description = """ HDF (also known as HDF4) is a library and multi-object file format for @@ -13,7 +13,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '11.2.0'} toolchainopts = {'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] +source_urls = ['http://support.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] sources = [SOURCELOWER_TAR_GZ] patches = ['HDF-4.2.15_fix-aarch64.patch'] checksums = [ diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-11.3.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-11.3.0.eb index 682e5e20b6ca..4af8d2741646 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-11.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'HDF' version = '4.2.15' -homepage = 'https://www.hdfgroup.org/products/hdf4/' +homepage = 'https://support.hdfgroup.org/products/hdf4/' description = """ HDF (also known as HDF4) is a library and multi-object file format for @@ -13,7 +13,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '11.3.0'} toolchainopts = {'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] +source_urls = ['http://support.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] sources = [SOURCELOWER_TAR_GZ] patches = ['HDF-4.2.15_fix-aarch64.patch'] checksums = [ diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-12.2.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-12.2.0.eb index f0286cd30bdc..abab2d962f58 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-12.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'HDF' version = '4.2.15' -homepage = 'https://www.hdfgroup.org/products/hdf4/' +homepage = 'https://support.hdfgroup.org/products/hdf4/' description = """ HDF (also known as HDF4) is a library and multi-object file format for @@ -13,7 +13,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '12.2.0'} toolchainopts = {'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] +source_urls = ['http://support.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] sources = [SOURCELOWER_TAR_GZ] patches = ['HDF-4.2.15_fix-aarch64.patch'] checksums = [ diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-9.3.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-9.3.0.eb index fd6e66939775..7e6b5eefbe82 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-9.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'HDF' version = '4.2.15' -homepage = 'https://www.hdfgroup.org/products/hdf4/' +homepage = 'https://support.hdfgroup.org/products/hdf4/' description = """ HDF (also known as HDF4) is a library and multi-object file format for @@ -13,7 +13,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '9.3.0'} toolchainopts = {'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] +source_urls = ['http://support.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] sources = [SOURCELOWER_TAR_GZ] patches = ['HDF-4.2.15_fix-aarch64.patch'] checksums = [ diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.16-2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.16-2-GCCcore-12.3.0.eb index 453ca292d426..175aaba4731e 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.16-2-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.16-2-GCCcore-12.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'HDF' version = '4.2.16-2' -homepage = 'https://www.hdfgroup.org/products/hdf4/' +homepage = 'https://support.hdfgroup.org/products/hdf4/' description = """ HDF (also known as HDF4) is a library and multi-object file format for storing and managing data between machines. @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} toolchainopts = {'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/%(name)s/releases/%(name)s%(version)s/src/'] +source_urls = ['http://support.hdfgroup.org/ftp/%(name)s/releases/%(name)s%(version)s/src/'] sources = [SOURCELOWER_TAR_GZ] checksums = [ diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.16-2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.16-2-GCCcore-13.2.0.eb index 6f54f50d4887..f2c20e888b94 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.16-2-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.16-2-GCCcore-13.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'HDF' version = '4.2.16-2' -homepage = 'https://www.hdfgroup.org/products/hdf4/' +homepage = 'https://support.hdfgroup.org/products/hdf4/' description = """ HDF (also known as HDF4) is a library and multi-object file format for storing and managing data between machines. @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '13.2.0'} toolchainopts = {'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/%(name)s/releases/%(name)s%(version)s/src/'] +source_urls = ['http://support.hdfgroup.org/ftp/%(name)s/releases/%(name)s%(version)s/src/'] sources = [SOURCELOWER_TAR_GZ] checksums = [ diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.16-GCCcore-12.3.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.16-GCCcore-12.3.0.eb index d24dbfac77e9..fd9d8d3d4ea5 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.16-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.16-GCCcore-12.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'HDF' version = '4.2.16' -homepage = 'https://www.hdfgroup.org/products/hdf4/' +homepage = 'https://support.hdfgroup.org/products/hdf4/' description = """ HDF (also known as HDF4) is a library and multi-object file format for @@ -13,7 +13,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} toolchainopts = {'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] +source_urls = ['http://support.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['2bd48dcefb5ab4829fba27dca6fad20b842d495dfd64944b2412b2b0968bf167'] diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.14.3-gompi-2023b.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.14.3-gompi-2023b.eb index f2aab3663a35..5cb05f4a4a19 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.14.3-gompi-2023b.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.14.3-gompi-2023b.eb @@ -12,7 +12,11 @@ toolchainopts = {'pic': True, 'usempi': True} source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['09cdb287aa7a89148c1638dd20891fdbae08102cf433ef128fd345338aa237c7'] +patches = ['HDF5-1.14.3_suppress_fp_exceptions.patch'] +checksums = [ + {'hdf5-1.14.3.tar.gz': '09cdb287aa7a89148c1638dd20891fdbae08102cf433ef128fd345338aa237c7'}, + {'HDF5-1.14.3_suppress_fp_exceptions.patch': 'bf33e579c93a16043c54b266321bbe95e4a8797f7fe6d096a13ce905ed2ffde7'}, +] # replace src include path with installation dir for $H5BLD_CPPFLAGS _regex = 's, -I[^[:space:]]+H5FDsubfiling , -I%(installdir)s/include ,g' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.14.3-iimpi-2023b.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.14.3-iimpi-2023b.eb index 77fa0c12ab96..e180d8619eed 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.14.3-iimpi-2023b.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.14.3-iimpi-2023b.eb @@ -12,7 +12,11 @@ toolchainopts = {'pic': True, 'usempi': True} source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['09cdb287aa7a89148c1638dd20891fdbae08102cf433ef128fd345338aa237c7'] +patches = ['HDF5-1.14.3_suppress_fp_exceptions.patch'] +checksums = [ + {'hdf5-1.14.3.tar.gz': '09cdb287aa7a89148c1638dd20891fdbae08102cf433ef128fd345338aa237c7'}, + {'HDF5-1.14.3_suppress_fp_exceptions.patch': 'bf33e579c93a16043c54b266321bbe95e4a8797f7fe6d096a13ce905ed2ffde7'}, +] # replace src include path with installation dir for $H5BLD_CPPFLAGS _regex = 's, -I[^[:space:]]+H5FDsubfiling , -I%(installdir)s/include ,g' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.14.3_suppress_fp_exceptions.patch b/easybuild/easyconfigs/h/HDF5/HDF5-1.14.3_suppress_fp_exceptions.patch new file mode 100644 index 000000000000..420125db46d3 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.14.3_suppress_fp_exceptions.patch @@ -0,0 +1,223 @@ +See: https://github.com/HDFGroup/hdf5/commit/e0d095ebf020706ec7d7c82e6674b18f1a0a2d5b + +Created using +git checkout hdf5-1_14_3 +git cherry-pick e0d095ebf020706ec7d7c82e6674b18f1a0a2d5b + +commit 7c58dd64db0a6c04dea46dee1c7effbe8103ae82 +Author: Dana Robinson <43805+derobins@users.noreply.github.com> +Date: Tue Nov 7 08:13:30 2023 -0800 + + Disable FP exceptions in H5T init code (#3837) + + The H5T floating-point datatype initialization code can raise exceptions when handling signaling NaNs. This change disables FE_INVALID exceptions during initialization. + + Also removes the -ieee=full change for NAG Fortran as that shouldn't be necessary anymore. + + Fixes #3831 + +diff --git a/config/linux-gnulibc1 b/config/linux-gnulibc1 +index 328f8d3cec..079f08d96c 100644 +--- a/config/linux-gnulibc1 ++++ b/config/linux-gnulibc1 +@@ -173,10 +173,7 @@ case $FC_BASENAME in + nagfor) + + F9XSUFFIXFLAG="" +- # NOTE: The default is -ieee=stop, which will cause problems +- # when the H5T module performs floating-point type +- # introspection +- AM_FCFLAGS="$AM_FCFLAGS -ieee=full" ++ AM_FCFLAGS="$AM_FCFLAGS" + FSEARCH_DIRS="" + + # Production +diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt +index 200576332b..7de2a56974 100644 +--- a/release_docs/RELEASE.txt ++++ b/release_docs/RELEASE.txt +@@ -250,6 +250,29 @@ Bug Fixes since HDF5-1.14.2 release + =================================== + Library + ------- ++ - Suppressed floating-point exceptions in H5T init code ++ ++ The floating-point datatype initialization code in H5Tinit_float.c ++ could raise FE_INVALID exceptions while munging bits and performing ++ comparisons that might involve NaN. This was not a problem when the ++ initialization code was executed in H5detect at compile time (prior ++ to 1.14.3), but now that the code is executed at library startup ++ (1.14.3+), these exceptions can be caught by user code, as is the ++ default in the NAG Fortran compiler. ++ ++ Starting in 1.14.4, we now suppress floating-point exceptions while ++ initializing the floating-point types and clear FE_INVALID before ++ restoring the original environment. ++ ++ Fixes GitHub #3831 ++ ++ - Fixed a file handle leak in the core VFD ++ ++ When opening a file with the core VFD and a file image, if the file ++ already exists, the file check would leak the POSIX file handle. ++ ++ Fixes GitHub issue #635 ++ + - Fixed some issues with chunk index metadata not getting read + collectively when collective metadata reads are enabled + +@@ -619,12 +642,6 @@ Known Problems + this release with link errors. As a result, Windows binaries for this release + will not include Fortran. The problem will be addressed in HDF5 1.14.4. + +- IEEE standard arithmetic enables software to raise exceptions such as overflow, +- division by zero, and other illegal operations without interrupting or halting +- the program flow. The HDF5 C library intentionally performs these exceptions. +- Therefore, the "-ieee=full" nagfor switch is necessary when compiling a program +- to avoid stopping on an exception. +- + CMake files do not behave correctly with paths containing spaces. + Do not use spaces in paths because the required escaping for handling spaces + results in very complex and fragile build files. +diff --git a/src/H5Tinit_float.c b/src/H5Tinit_float.c +index 3b9e127fe4..3213f00fec 100644 +--- a/src/H5Tinit_float.c ++++ b/src/H5Tinit_float.c +@@ -51,19 +51,23 @@ + * Function: DETECT_F + * + * Purpose: This macro takes a floating point type like `double' and +- * a base name like `natd' and detects byte order, mantissa +- * location, exponent location, sign bit location, presence or +- * absence of implicit mantissa bit, and exponent bias and +- * initializes a detected_t structure with those properties. ++ * and detects byte order, mantissa location, exponent location, ++ * sign bit location, presence or absence of implicit mantissa ++ * bit, and exponent bias and initializes a detected_t structure ++ * with those properties. ++ * ++ * Note that these operations can raise floating-point ++ * exceptions and building with some compiler options ++ * (especially Fortran) can cause problems. + *------------------------------------------------------------------------- + */ +-#define DETECT_F(TYPE, VAR, INFO) \ ++#define DETECT_F(TYPE, INFO) \ + do { \ +- TYPE _v1, _v2, _v3; \ +- unsigned char _buf1[sizeof(TYPE)], _buf3[sizeof(TYPE)]; \ +- unsigned char _pad_mask[sizeof(TYPE)]; \ +- unsigned char _byte_mask; \ +- int _i, _j, _last = (-1); \ ++ TYPE _v1, _v2, _v3; \ ++ uint8_t _buf1[sizeof(TYPE)], _buf3[sizeof(TYPE)]; \ ++ uint8_t _pad_mask[sizeof(TYPE)]; \ ++ uint8_t _byte_mask; \ ++ int _i, _j, _last = -1; \ + \ + memset(&INFO, 0, sizeof(INFO)); \ + INFO.size = sizeof(TYPE); \ +@@ -81,7 +85,7 @@ + _v1 = (TYPE)4.0L; \ + H5MM_memcpy(_buf1, (const void *)&_v1, sizeof(TYPE)); \ + for (_i = 0; _i < (int)sizeof(TYPE); _i++) \ +- for (_byte_mask = (unsigned char)1; _byte_mask; _byte_mask = (unsigned char)(_byte_mask << 1)) { \ ++ for (_byte_mask = (uint8_t)1; _byte_mask; _byte_mask = (uint8_t)(_byte_mask << 1)) { \ + _buf1[_i] ^= _byte_mask; \ + H5MM_memcpy((void *)&_v2, (const void *)_buf1, sizeof(TYPE)); \ + H5_GCC_CLANG_DIAG_OFF("float-equal") \ +@@ -118,7 +122,7 @@ + _v1 = (TYPE)1.0L; \ + _v2 = (TYPE)-1.0L; \ + if (H5T__bit_cmp(sizeof(TYPE), INFO.perm, &_v1, &_v2, _pad_mask, &(INFO.sign)) < 0) \ +- HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "failed to detect byte order"); \ ++ HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "failed to determine sign bit"); \ + \ + /* Mantissa */ \ + INFO.mpos = 0; \ +@@ -126,12 +130,11 @@ + _v1 = (TYPE)1.0L; \ + _v2 = (TYPE)1.5L; \ + if (H5T__bit_cmp(sizeof(TYPE), INFO.perm, &_v1, &_v2, _pad_mask, &(INFO.msize)) < 0) \ +- HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "failed to detect byte order"); \ ++ HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "failed to determine mantissa"); \ + INFO.msize += 1 + (unsigned)(INFO.imp ? 0 : 1) - INFO.mpos; \ + \ + /* Exponent */ \ +- INFO.epos = INFO.mpos + INFO.msize; \ +- \ ++ INFO.epos = INFO.mpos + INFO.msize; \ + INFO.esize = INFO.sign - INFO.epos; \ + \ + _v1 = (TYPE)1.0L; \ +@@ -456,17 +459,24 @@ H5T__set_precision(H5T_fpoint_det_t *d) + herr_t H5_NO_UBSAN + H5T__init_native_float_types(void) + { ++ fenv_t saved_fenv; + H5T_fpoint_det_t det; + H5T_t *dt = NULL; + herr_t ret_value = SUCCEED; + + FUNC_ENTER_PACKAGE + ++ /* Turn off floating-point exceptions while initializing to avoid ++ * tripping over signaling NaNs while looking at "don't care" bits. ++ */ ++ if (feholdexcept(&saved_fenv) != 0) ++ HSYS_GOTO_ERROR(H5E_DATATYPE, H5E_CANTSET, FAIL, "can't save floating-point environment"); ++ + /* H5T_NATIVE_FLOAT */ + + /* Get the type's characteristics */ + memset(&det, 0, sizeof(H5T_fpoint_det_t)); +- DETECT_F(float, FLOAT, det); ++ DETECT_F(float, det); + + /* Allocate and fill type structure */ + if (NULL == (dt = H5T__alloc())) +@@ -497,7 +507,7 @@ H5T__init_native_float_types(void) + + /* Get the type's characteristics */ + memset(&det, 0, sizeof(H5T_fpoint_det_t)); +- DETECT_F(double, DOUBLE, det); ++ DETECT_F(double, det); + + /* Allocate and fill type structure */ + if (NULL == (dt = H5T__alloc())) +@@ -528,7 +538,7 @@ H5T__init_native_float_types(void) + + /* Get the type's characteristics */ + memset(&det, 0, sizeof(H5T_fpoint_det_t)); +- DETECT_F(long double, LDOUBLE, det); ++ DETECT_F(long double, det); + + /* Allocate and fill type structure */ + if (NULL == (dt = H5T__alloc())) +@@ -561,6 +571,14 @@ H5T__init_native_float_types(void) + H5T_native_order_g = det.order; + + done: ++ /* Clear any FE_INVALID exceptions from NaN handling */ ++ if (feclearexcept(FE_INVALID) != 0) ++ HSYS_GOTO_ERROR(H5E_DATATYPE, H5E_CANTSET, FAIL, "can't clear floating-point exceptions"); ++ ++ /* Restore the original environment */ ++ if (feupdateenv(&saved_fenv) != 0) ++ HSYS_GOTO_ERROR(H5E_DATATYPE, H5E_CANTSET, FAIL, "can't restore floating-point environment"); ++ + if (ret_value < 0) { + if (dt != NULL) { + dt->shared = H5FL_FREE(H5T_shared_t, dt->shared); +diff --git a/src/H5private.h b/src/H5private.h +index 14a0ac3225..3aaa0d5245 100644 +--- a/src/H5private.h ++++ b/src/H5private.h +@@ -26,6 +26,7 @@ + #include + #include + #include ++#include + #include + #include + #include diff --git a/easybuild/easyconfigs/h/HERRO/HERRO-0.1.0_20240808-foss-2023a.eb b/easybuild/easyconfigs/h/HERRO/HERRO-0.1.0_20240808-foss-2023a.eb new file mode 100644 index 000000000000..a4057965c49b --- /dev/null +++ b/easybuild/easyconfigs/h/HERRO/HERRO-0.1.0_20240808-foss-2023a.eb @@ -0,0 +1,382 @@ +easyblock = 'Cargo' + +name = 'HERRO' +version = '0.1.0_20240808' +local_commit = 'deccc46' + +homepage = 'https://github.com/lbcb-sci/herro' +description = """ +HERRO is a highly-accurate, haplotype-aware, deep-learning tool for error correction of Nanopore R10.4.1 or +R9.4.1 reads (read length of >= 10 kbps is recommended). +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/lbcb-sci/herro/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] + +builddependencies = [ + ('Rust', '1.75.0'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('bzip2', '1.0.8'), + ('libffi', '3.4.4'), + ('libnsl', '2.0.1'), + ('SQLite', '3.42.0'), + ('util-linux', '2.39'), + ('zlib', '1.2.13'), + ('ncurses', '6.4'), + ('libreadline', '8.2'), + ('SeqKit', '2.3.1', '', SYSTEM), + ('Tk', '8.6.13'), + ('XZ', '5.4.2'), + ('matplotlib', '3.7.2'), + ('edlib', '1.3.9'), + ('h5py', '3.9.0'), + ('duplex-tools', '0.3.3'), + ('PyTorch', '2.1.2'), + ('Pillow', '10.0.0'), + ('zstd', '1.5.5'), + ('parasail', '2.6.2'), +] + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'download_dep_fail': True, + 'use_pip': True, + 'sanity_pip_check': True, + 'preinstallopts': '', + 'installopts': '', +} + +exts_list = [ + ('zstandard', '0.22.0', { + 'checksums': ['8226a33c542bcb54cd6bd0a366067b610b41713b64c9abec1bc4533d69f51e70'], + }), + ('Porechop', '20240119', { + 'modulename': 'porechop', + 'source_urls': ['https://github.com/dehui333/Porechop/archive/'], + 'sources': [{'download_filename': 'd2e77c6.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'checksums': ['6e5ff3a780fc2855b0101b4a6102437d9a0fc201e40ffabc44c0c67d7c9ad621'], + }), +] + +# use tch version 0.14.0 - compatible with PyTorch 2.1 +local_torch_opts = "sed -i 's/tch = \"0.13.0\"/tch = \"0.14.0\"/' Cargo.toml && " +local_torch_opts += 'export LIBTORCH_BYPASS_VERSION_CHECK=1 && export LIBTORCH_USE_PYTORCH=1 && ' +local_torch_opts += 'export LIBTORCH=$EBROOTPYTORCH/lib && RUSTFLAGS="-Ctarget-cpu=native"' +prebuildopts = pretestopts = preinstallopts = local_torch_opts + +# copy scripts to /bin to be easier to run scripts for users +postinstallcmds = [ + 'cp -a %(start_dir)s/scripts/* %(installdir)s/bin', + 'rm %(installdir)s/bin/herro-env.yml', + "chmod a+rx %(installdir)s/bin/*.sh", + "chmod a-x %(installdir)s/bin/*.py", +] + +_bins = [ + 'herro', + 'porechop', + 'no_split.sh', + 'postprocess_corrected.sh', + 'create_batched_alignments.sh', + 'porechop_with_split.sh', + 'preprocess.sh', + 'batch.py', + 'create_clusters.py', +] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in _bins], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["herro --help"] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +modloadmsg = """ +To run scripts from /scripts directory just run .sh +Do not run it as scripts/.sh +For example - run preprocess.sh as: + $ preprocess.sh +""" + +crates = [ + ('adler2', '2.0.0'), + ('aes', '0.8.4'), + ('anstream', '0.6.15'), + ('anstyle', '1.0.8'), + ('anstyle-parse', '0.2.5'), + ('anstyle-query', '1.1.1'), + ('anstyle-wincon', '3.0.4'), + ('anyhow', '1.0.86'), + ('approx', '0.5.1'), + ('autocfg', '1.3.0'), + ('base64ct', '1.6.0'), + ('block-buffer', '0.10.4'), + ('buffer-redux', '1.0.2'), + ('bytecount', '0.6.8'), + ('byteorder', '1.5.0'), + ('bzip2', '0.4.4'), + ('bzip2-sys', '0.1.11+1.0.8'), + ('cc', '1.1.13'), + ('cfg-if', '1.0.0'), + ('cipher', '0.4.4'), + ('clap', '4.4.18'), + ('clap_builder', '4.4.18'), + ('clap_derive', '4.4.7'), + ('clap_lex', '0.6.0'), + ('colorchoice', '1.0.2'), + ('console', '0.15.8'), + ('constant_time_eq', '0.1.5'), + ('cpufeatures', '0.2.13'), + ('crc32fast', '1.4.2'), + ('crossbeam-channel', '0.5.13'), + ('crossbeam-utils', '0.8.20'), + ('crunchy', '0.2.2'), + ('crypto-common', '0.1.6'), + ('deranged', '0.3.11'), + ('digest', '0.10.7'), + ('either', '1.13.0'), + ('encode_unicode', '0.3.6'), + ('flate2', '1.0.32'), + ('generic-array', '0.14.7'), + ('getrandom', '0.2.15'), + ('glob', '0.3.1'), + ('half', '2.4.1'), + ('heck', '0.4.1'), + ('hmac', '0.12.1'), + 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'54a3ab4db68cea366acc5c897c7b4d4d1b8994a9cd6e6f841f8964566a419059'}, + {'zstd-sys-2.0.13+zstd.1.5.6.tar.gz': '38ff0f21cfee8f97d94cef41359e0c89aa6113028ab0291aa8ca0038995a95aa'}, +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HOMER/HOMER-4.11.1-foss-2022b.eb b/easybuild/easyconfigs/h/HOMER/HOMER-4.11.1-foss-2022b.eb new file mode 100644 index 000000000000..0131cad97711 --- /dev/null +++ b/easybuild/easyconfigs/h/HOMER/HOMER-4.11.1-foss-2022b.eb @@ -0,0 +1,57 @@ +easyblock = 'Binary' + +name = 'HOMER' +version = '4.11.1' + +homepage = 'http://homer.ucsd.edu/homer/' +description = """HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and +next-gen sequencing analysis. It is a collection of command line programs for unix-style operating systems written +in Perl and C++. HOMER was primarily written as a de novo motif discovery algorithm and is well suited for finding +8-20 bp motifs in large scale genomics data. HOMER contains many useful tools for analyzing ChIP-Seq, GRO-Seq, +RNA-Seq, DNase-Seq, Hi-C and numerous other types of functional genomics sequencing data sets.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +source_urls = ['http://homer.ucsd.edu/homer/data/software'] +sources = ['homer.v%(version)s.zip'] +checksums = ['80d1cd00616729894017b24a36a2ef81f9cde8bd364e875aead1e0cfb500c82b'] + +extract_sources = True + +builddependencies = [ + ('wget', '1.21.4'), + ('Zip', '3.0'), + ('UnZip', '6.0'), +] + +dependencies = [ + ('Perl', '5.36.0'), + ('weblogo', '2.8.2'), + ('SAMtools', '1.17'), + ('Kent_tools', '461'), + ('R', '4.2.2'), + ('R-bundle-Bioconductor', '3.16', '-R-4.2.2') +] + +buildininstalldir = True +skipsteps = ['install'] + +# This installs the entire suite, to install only base Homer package run : +# cd %(installdir)s; perl ./configureHomer.pl -install homer +postinstallcmds = ['perl ./configureHomer.pl -install -all -keepScript'] + +sanity_check_paths = { + 'dirs': ['bin', 'data', 'motifs', 'update'], + 'files': [ + 'bin/homer', + 'bin/getGenomeTilingPeaks', + 'config.txt', + 'DoughnutDocumentation.pdf', + 'data/accession/homologene.data', + 'motifs/hnf1b.motif', + ], +} + +sanity_check_commands = ["%(namelower)s --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.3-foss-2024a.eb b/easybuild/easyconfigs/h/HPL/HPL-2.3-foss-2024a.eb new file mode 100644 index 000000000000..8a70a42bb412 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.3-foss-2024a.eb @@ -0,0 +1,21 @@ +name = 'HPL' +version = '2.3' + +homepage = 'https://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'foss', 'version': '2024a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://www.netlib.org/benchmark/%(namelower)s'] +sources = [SOURCELOWER_TAR_GZ] +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] +checksums = [ + '32c5c17d22330e6f2337b681aded51637fb6008d3f0eb7c277b163fadd612830', # hpl-2.3.tar.gz + '2a5bf9c4f328049828ddecec7ba3f05a9e25d236f4212747c53bd22fea80c5e6', # HPL_parallel-make.patch +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.3-gmpflf-2024.06.eb b/easybuild/easyconfigs/h/HPL/HPL-2.3-gmpflf-2024.06.eb new file mode 100644 index 000000000000..a6a7fb49164b --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.3-gmpflf-2024.06.eb @@ -0,0 +1,21 @@ +name = 'HPL' +version = '2.3' + +homepage = 'https://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'gmpflf', 'version': '2024.06'} +toolchainopts = {'usempi': True} + +source_urls = ['https://www.netlib.org/benchmark/%(namelower)s'] +sources = [SOURCELOWER_TAR_GZ] +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] +checksums = [ + '32c5c17d22330e6f2337b681aded51637fb6008d3f0eb7c277b163fadd612830', # hpl-2.3.tar.gz + '2a5bf9c4f328049828ddecec7ba3f05a9e25d236f4212747c53bd22fea80c5e6', # HPL_parallel-make.patch +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2024a.eb b/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2024a.eb new file mode 100644 index 000000000000..5544839d1772 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2024a.eb @@ -0,0 +1,21 @@ +name = 'HPL' +version = '2.3' + +homepage = 'https://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'intel', 'version': '2024a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://www.netlib.org/benchmark/%(namelower)s'] +sources = [SOURCELOWER_TAR_GZ] +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] +checksums = [ + '32c5c17d22330e6f2337b681aded51637fb6008d3f0eb7c277b163fadd612830', # hpl-2.3.tar.gz + '2a5bf9c4f328049828ddecec7ba3f05a9e25d236f4212747c53bd22fea80c5e6', # HPL_parallel-make.patch +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HTSeq/HTSeq-2.0.7-foss-2023a.eb b/easybuild/easyconfigs/h/HTSeq/HTSeq-2.0.7-foss-2023a.eb new file mode 100644 index 000000000000..60ffab860b4e --- /dev/null +++ b/easybuild/easyconfigs/h/HTSeq/HTSeq-2.0.7-foss-2023a.eb @@ -0,0 +1,43 @@ +# Updated to PythonBundle and latest version from Pypi +# Author: J. Sassmannshausen (Imperial College London/UK) +# Update: P.Tománek (Inuits) + +easyblock = 'PythonBundle' + +name = 'HTSeq' +version = '2.0.7' + +homepage = 'https://github.com/simon-anders/htseq' +description = """HTSeq is a Python library to facilitate processing and analysis + of data from high-throughput sequencing (HTS) experiments.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [('SWIG', '4.1.1')] + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('Pysam', '0.22.0'), + ('SciPy-bundle', '2023.07'), + ('matplotlib', '3.7.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('htseq', version, { + 'modulename': 'HTSeq', + 'checksums': ['c1490cede77fb04c8f3a9efeb44d41399cd466a6082180529e63c1dade203fdd'], + }), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s-count', 'bin/%(namelower)s-qa'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s/scripts'], +} + +sanity_check_commands = ['%(namelower)s-count --help'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HiCMatrix/HiCMatrix-17.2-foss-2023a.eb b/easybuild/easyconfigs/h/HiCMatrix/HiCMatrix-17.2-foss-2023a.eb new file mode 100644 index 000000000000..474b8906ff54 --- /dev/null +++ b/easybuild/easyconfigs/h/HiCMatrix/HiCMatrix-17.2-foss-2023a.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonBundle' + +name = 'HiCMatrix' +version = '17.2' + +homepage = 'https://github.com/deeptools/HiCMatrix' +description = "This library implements the central class of HiCExplorer to manage Hi-C interaction matrices." + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('PyTables', '3.8.0'), + ('cooler', '0.10.2'), +] + +use_pip = True + +exts_list = [ + ('intervaltree', '3.1.0', { + 'checksums': ['902b1b88936918f9b2a19e0e5eb7ccb430ae45cde4f39ea4b36932920d33952d'], + }), + (name, version, { + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/deeptools/HiCMatrix/archive/'], + 'checksums': ['a2428676b5aad014e7b1653e3effe94f7ea8a68cc78be83e4b67f2255f6b4fbb'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/Highway/Highway-1.0.4-GCCcore-12.3.0.eb b/easybuild/easyconfigs/h/Highway/Highway-1.0.4-GCCcore-12.3.0.eb index a05239847d3c..993087b828c4 100644 --- a/easybuild/easyconfigs/h/Highway/Highway-1.0.4-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/h/Highway/Highway-1.0.4-GCCcore-12.3.0.eb @@ -12,7 +12,13 @@ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} source_urls = ['https://github.com/google/highway/archive/refs/tags/'] sources = ['%(version)s.tar.gz'] -checksums = ['faccd343935c9e98afd1016e9d20e0b8b89d908508d1af958496f8c2d3004ac2'] +patches = ['Highway-1.0.4-zen4-fix-TruncateTo-bug.patch'] + +checksums = [ + {'1.0.4.tar.gz': 'faccd343935c9e98afd1016e9d20e0b8b89d908508d1af958496f8c2d3004ac2'}, + {'Highway-1.0.4-zen4-fix-TruncateTo-bug.patch': + 'e571413c290076a729dbb1df105a4bfa106099238d1b438e74a9dfc9557eb4a2'}, +] builddependencies = [ ('binutils', '2.40'), diff --git a/easybuild/easyconfigs/h/Highway/Highway-1.0.4-zen4-fix-TruncateTo-bug.patch b/easybuild/easyconfigs/h/Highway/Highway-1.0.4-zen4-fix-TruncateTo-bug.patch new file mode 100644 index 000000000000..f489a6bd15fc --- /dev/null +++ b/easybuild/easyconfigs/h/Highway/Highway-1.0.4-zen4-fix-TruncateTo-bug.patch @@ -0,0 +1,59 @@ +A single test failed when building on AMD Genoa a.k.a Zen4 with the error message +reported in https://github.com/google/highway/issues/1913 + +Building v1.0.5 passed all tests. Hence, this patch uses some of the changes made +in v1.0.5 to let the single failing test succeed. + +Looking at the PRs added by v1.0.5 a promising candidate was identified +(https://github.com/google/highway/pull/1276) and all changed files in the PR +were "studied in detail" (assessed if the changes could be related to the failing +test on Zen4). Luckily, the four changes provided in the patch below were +found to resolve the issue. It was also tested if a subset of these four changes +would resolve the issue, but this did not succeed. + +Author: Thomas Roeblitz (University of Bergen) + +diff --git a/hwy/ops/x86_256-inl.h b/hwy/ops/x86_256-inl.h +index 4e2e83e8..2fbf99c7 100644 +--- a/hwy/ops/x86_256-inl.h ++++ b/hwy/ops/x86_256-inl.h +@@ -4185,7 +4185,7 @@ HWY_INLINE Vec128 LookupAndConcatHalves(Vec256 v) { + #if HWY_TARGET <= HWY_AVX3_DL + alignas(32) static constexpr uint32_t kMap[8] = { + LO, HI, 0x10101010 + LO, 0x10101010 + HI, 0, 0, 0, 0}; +- const auto result = _mm256_permutexvar_epi8(v.raw, Load(d32, kMap).raw); ++ const auto result = _mm256_permutexvar_epi8(Load(d32, kMap).raw, v.raw); + #else + alignas(32) static constexpr uint32_t kMap[8] = {LO, HI, ~0u, ~0u, + ~0u, ~0u, LO, HI}; +@@ -4208,7 +4208,7 @@ HWY_INLINE Vec128 LookupAndConcatQuarters(Vec256 v) { + #if HWY_TARGET <= HWY_AVX3_DL + alignas(32) static constexpr uint16_t kMap[16] = { + LO, HI, 0x1010 + LO, 0x1010 + HI, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}; +- const auto result = _mm256_permutexvar_epi8(v.raw, Load(d16, kMap).raw); ++ const auto result = _mm256_permutexvar_epi8(Load(d16, kMap).raw, v.raw); + return LowerHalf(Vec128{_mm256_castsi256_si128(result)}); + #else + constexpr uint16_t ff = static_cast(~0u); +@@ -4229,7 +4229,7 @@ HWY_API Vec32 TruncateTo(D /* tag */, Vec256 v) { + #if HWY_TARGET <= HWY_AVX3_DL + alignas(32) static constexpr uint32_t kMap[8] = {0x18100800u, 0, 0, 0, + 0, 0, 0, 0}; +- const auto result = _mm256_permutexvar_epi8(v.raw, Load(d32, kMap).raw); ++ const auto result = _mm256_permutexvar_epi8(Load(d32, kMap).raw, v.raw); + return LowerHalf(LowerHalf(LowerHalf(Vec256{result}))); + #else + alignas(32) static constexpr uint32_t kMap[8] = {0xFFFF0800u, ~0u, ~0u, ~0u, +diff --git a/hwy/ops/x86_512-inl.h b/hwy/ops/x86_512-inl.h +index 167922d8..83f2ee67 100644 +--- a/hwy/ops/x86_512-inl.h ++++ b/hwy/ops/x86_512-inl.h +@@ -3497,7 +3497,7 @@ HWY_API Vec128 TruncateTo(D /* tag */, const Vec512 v) { + alignas(16) static constexpr uint8_t k8From32[16] = { + 0, 4, 8, 12, 16, 20, 24, 28, 32, 36, 40, 44, 48, 52, 56, 60}; + const Vec512 bytes{ +- _mm512_permutexvar_epi32(LoadDup128(d8, k8From32).raw, v.raw)}; ++ _mm512_permutexvar_epi8(LoadDup128(d8, k8From32).raw, v.raw)}; + #else + const Full512 d32; + // In each 128 bit block, gather the lower byte of 4 uint32_t lanes into the diff --git a/easybuild/easyconfigs/h/Highway/Highway-1.2.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/h/Highway/Highway-1.2.0-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..27739befe526 --- /dev/null +++ b/easybuild/easyconfigs/h/Highway/Highway-1.2.0-GCCcore-13.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'CMakeMake' + +name = 'Highway' +version = '1.2.0' + +homepage = 'https://github.com/google/highway' + +description = """Highway is a C++ library for SIMD (Single Instruction, Multiple Data), i.e. applying the same +operation to 'lanes'.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/google/highway/archive/refs/tags/'] +sources = ['%(version)s.tar.gz'] +checksums = ['7e0be78b8318e8bdbf6fa545d2ecb4c90f947df03f7aadc42c1967f019e63343'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), + ('googletest', '1.15.2'), +] + +configopts = "-DHWY_SYSTEM_GTEST=ON" + +runtest = "test" + +sanity_check_paths = { + 'files': ['lib/libhwy.a'], + 'dirs': ['include/hwy'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/h/Hypre/Hypre-2.31.0-foss-2023b.eb b/easybuild/easyconfigs/h/Hypre/Hypre-2.31.0-foss-2023b.eb new file mode 100644 index 000000000000..62d72e357a8d --- /dev/null +++ b/easybuild/easyconfigs/h/Hypre/Hypre-2.31.0-foss-2023b.eb @@ -0,0 +1,18 @@ +name = 'Hypre' +version = '2.31.0' + +homepage = 'https://computation.llnl.gov/projects/hypre-scalable-linear-solvers-multigrid-methods' +description = """Hypre is a library for solving large, sparse linear systems of equations on massively + parallel computers. The problems of interest arise in the simulation codes being developed at LLNL + and elsewhere to study physical phenomena in the defense, environmental, energy, and biological sciences.""" + +toolchain = {'name': 'foss', 'version': '2023b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/hypre-space/hypre/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['9a7916e2ac6615399de5010eb39c604417bb3ea3109ac90e199c5c63b0cb4334'] + +start_dir = 'src' + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.3-foss-2018b.eb b/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.3-foss-2018b.eb index 0b79b7cfc94b..605d20f196f3 100644 --- a/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.3-foss-2018b.eb +++ b/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.3-foss-2018b.eb @@ -3,13 +3,13 @@ easyblock = 'ConfigureMake' name = 'h4toh5' version = '2.2.3' -homepage = 'http://www.hdfgroup.org/h4toh5/' +homepage = "https://docs.hdfgroup.org/archive/support/products/hdf5_tools/h4toh5/index.html" description = """The h4toh5 software consists of the h4toh5 and h5toh4 command-line utilities, as well as a conversion library for converting between individual HDF4 and HDF5 objects.""" toolchain = {'name': 'foss', 'version': '2018b'} -source_urls = ['http://www.hdfgroup.org/ftp/HDF5/tools/%s/src' % name] +source_urls = ['http://support.hdfgroup.org/ftp/HDF5/tools/%s/src' % name] sources = ['h4h5tools-%(version)s.tar.gz'] checksums = ['ba167d9e5ec1f9014a95e3f5d0621f814caa6e83508e235ce60cfd315e3a9d3f'] diff --git a/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.3-gompi-2019b.eb b/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.3-gompi-2019b.eb index 81636ad6de34..079d5eb7de16 100644 --- a/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.3-gompi-2019b.eb +++ b/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.3-gompi-2019b.eb @@ -3,13 +3,13 @@ easyblock = 'ConfigureMake' name = 'h4toh5' version = '2.2.3' -homepage = 'http://www.hdfgroup.org/h4toh5/' +homepage = "https://docs.hdfgroup.org/archive/support/products/hdf5_tools/h4toh5/index.html" description = """The h4toh5 software consists of the h4toh5 and h5toh4 command-line utilities, as well as a conversion library for converting between individual HDF4 and HDF5 objects.""" toolchain = {'name': 'gompi', 'version': '2019b'} -source_urls = ['http://www.hdfgroup.org/ftp/HDF5/tools/%s/src' % name] +source_urls = ['http://support.hdfgroup.org/ftp/HDF5/tools/%s/src' % name] sources = ['h4h5tools-%(version)s%(versionsuffix)s.tar.gz'] checksums = ['ba167d9e5ec1f9014a95e3f5d0621f814caa6e83508e235ce60cfd315e3a9d3f'] diff --git a/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.3-gompi-2020b.eb b/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.3-gompi-2020b.eb index 8e8e8c7f705f..50fe19e455a8 100644 --- a/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.3-gompi-2020b.eb +++ b/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.3-gompi-2020b.eb @@ -3,13 +3,13 @@ easyblock = 'ConfigureMake' name = 'h4toh5' version = '2.2.3' -homepage = 'http://www.hdfgroup.org/h4toh5/' +homepage = "https://docs.hdfgroup.org/archive/support/products/hdf5_tools/h4toh5/index.html" description = """The h4toh5 software consists of the h4toh5 and h5toh4 command-line utilities, as well as a conversion library for converting between individual HDF4 and HDF5 objects.""" toolchain = {'name': 'gompi', 'version': '2020b'} -source_urls = ['http://www.hdfgroup.org/ftp/HDF5/tools/%s/src' % name] +source_urls = ['http://support.hdfgroup.org/ftp/HDF5/tools/%s/src' % name] sources = ['h4h5tools-%(version)s%(versionsuffix)s.tar.gz'] checksums = ['ba167d9e5ec1f9014a95e3f5d0621f814caa6e83508e235ce60cfd315e3a9d3f'] diff --git a/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.5-gompi-2022a.eb b/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.5-gompi-2022a.eb index 1a825bc8ed86..28d67776a1b0 100644 --- a/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.5-gompi-2022a.eb +++ b/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.5-gompi-2022a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'h4toh5' version = '2.2.5' -homepage = 'http://www.hdfgroup.org/h4toh5/' +homepage = "https://docs.hdfgroup.org/archive/support/products/hdf5_tools/h4toh5/index.html" description = """The h4toh5 software consists of the h4toh5 and h5toh4 command-line utilities, as well as a conversion library for converting between individual HDF4 and HDF5 objects.""" diff --git a/easybuild/easyconfigs/h/hatchling/hatchling-1.24.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/h/hatchling/hatchling-1.24.2-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..d936671cca96 --- /dev/null +++ b/easybuild/easyconfigs/h/hatchling/hatchling-1.24.2-GCCcore-13.3.0.eb @@ -0,0 +1,59 @@ +easyblock = 'PythonBundle' + +name = 'hatchling' +version = '1.24.2' + +homepage = 'https://hatch.pypa.io' +description = """Extensible, standards compliant build backend used by Hatch, +a modern, extensible Python project manager.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('binutils', '2.42'), +] + +dependencies = [ + ('Python', '3.12.3'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('pathspec', '0.12.1', { + 'checksums': ['a482d51503a1ab33b1c67a6c3813a26953dbdc71c31dacaef9a838c4e29f5712'], + }), + ('pluggy', '1.5.0', { + 'checksums': ['2cffa88e94fdc978c4c574f15f9e59b7f4201d439195c3715ca9e2486f1d0cf1'], + }), + ('editables', '0.5', { + 'checksums': ['309627d9b5c4adc0e668d8c6fa7bac1ba7c8c5d415c2d27f60f081f8e80d1de2'], + }), + ('trove-classifiers', '2024.5.22', { + 'sources': ['trove_classifiers-%(version)s-py3-none-any.whl'], + 'checksums': ['c43ade18704823e4afa3d9db7083294bc4708a5e02afbcefacd0e9d03a7a24ef'], + }), + (name, version, { + 'checksums': ['41ddc27cdb25db9ef7b68bef075f829c84cb349aa1bff8240797d012510547b0'], + }), + ('hatch-vcs', '0.4.0', { + 'sources': ['hatch_vcs-%(version)s.tar.gz'], + 'checksums': ['093810748fe01db0d451fabcf2c1ac2688caefd232d4ede967090b1c1b07d9f7'], + }), + ('hatch-fancy-pypi-readme', '24.1.0', { + 'sources': ['hatch_fancy_pypi_readme-%(version)s.tar.gz'], + 'checksums': ['44dd239f1a779b9dcf8ebc9401a611fd7f7e3e14578dcf22c265dfaf7c1514b8'], + }), + ('hatch-requirements-txt', '0.4.1', { + 'source_tmpl': 'hatch_requirements_txt-%(version)s.tar.gz', + 'checksums': ['2c686e5758fd05bb55fa7d0c198fdd481f8d3aaa3c693260f5c0d74ce3547d20'], + }), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.49.3-GCCcore-14.2.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.49.3-GCCcore-14.2.0.eb new file mode 100644 index 000000000000..2161ee0b1af0 --- /dev/null +++ b/easybuild/easyconfigs/h/help2man/help2man-1.49.3-GCCcore-14.2.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'help2man' +version = '1.49.3' + +homepage = 'https://www.gnu.org/software/help2man/' +description = """help2man produces simple manual pages from the '--help' and '--version' output of other commands.""" + +toolchain = {'name': 'GCCcore', 'version': '14.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_XZ] +checksums = ['4d7e4fdef2eca6afe07a2682151cea78781e0a4e8f9622142d9f70c083a2fd4f'] + +builddependencies = [ + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.42', '', SYSTEM), +] + +sanity_check_paths = { + 'files': ['bin/help2man'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/hiredis/hiredis-1.2.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/h/hiredis/hiredis-1.2.0-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..bc3a5a1c7156 --- /dev/null +++ b/easybuild/easyconfigs/h/hiredis/hiredis-1.2.0-GCCcore-13.3.0.eb @@ -0,0 +1,41 @@ +# Author: Alexander Grund (TU Dresden) +# Based on EC by J. Sassmannshausen (Imperial College London) + +easyblock = 'CMakeMake' + +name = 'hiredis' +version = '1.2.0' + +homepage = 'https://github.com/redis/hiredis' +description = """Hiredis is a minimalistic C client library for the Redis database. + +It is minimalistic because it just adds minimal support for the protocol, +but at the same time it uses a high level printf-alike API in order to +make it much higher level than otherwise suggested by its minimal code base +and the lack of explicit bindings for every Redis command.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +github_account = 'redis' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['82ad632d31ee05da13b537c124f819eb88e18851d9cb0c30ae0552084811588c'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] + +dependencies = [ + ('OpenSSL', '3', '', SYSTEM), +] + +configopts = ['-DBUILD_SHARED_LIBS=ON', '-DBUILD_SHARED_LIBS=OFF'] + +sanity_check_paths = { + 'files': ['lib/libhiredis.a', 'lib/libhiredis.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/histolab/histolab-0.6.0-foss-2022a.eb b/easybuild/easyconfigs/h/histolab/histolab-0.6.0-foss-2022a.eb new file mode 100644 index 000000000000..a7dc410e6f04 --- /dev/null +++ b/easybuild/easyconfigs/h/histolab/histolab-0.6.0-foss-2022a.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonBundle' + +name = 'histolab' +version = '0.6.0' + +homepage = 'https://github.com/histolab/histolab' +description = """Library for Digital Pathology Image Processing.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +builddependencies = [('poetry', '1.2.2')] +dependencies = [ + ('Python', '3.10.4'), + ('Pillow', '9.1.1'), + ('scikit-image', '0.19.3'), + ('SciPy-bundle', '2022.05'), + ('openslide-python', '1.2.0'), +] + +use_pip = True + +exts_list = [ + # requires importlib-metadata = ">=4.12,<7.0" + ('importlib_metadata', '6.11.0', { + 'checksums': ['1231cf92d825c9e03cfc4da076a16de6422c863558229ea0b22b675657463443'], + }), + ('certifi', '2024.6.2', { + 'checksums': ['3cd43f1c6fa7dedc5899d69d3ad0398fd018ad1a17fba83ddaf78aa46c747516'], + }), + (name, version, { + 'checksums': ['fcb8cf70fdf32a58e2980905d657ea53a541503a436e8303f0cb0da6e9f2e20f'], + }), +] + +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/h/histolab/histolab-0.7.0-foss-2023a.eb b/easybuild/easyconfigs/h/histolab/histolab-0.7.0-foss-2023a.eb new file mode 100644 index 000000000000..3aa69b74e7b7 --- /dev/null +++ b/easybuild/easyconfigs/h/histolab/histolab-0.7.0-foss-2023a.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonBundle' + +name = 'histolab' +version = '0.7.0' + +homepage = 'https://github.com/histolab/histolab' +description = """Library for Digital Pathology Image Processing.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [('poetry', '1.5.1')] +dependencies = [ + ('Python', '3.11.3'), + ('Pillow', '10.0.0'), + ('scikit-image', '0.22.0'), + ('SciPy-bundle', '2023.07'), + ('openslide-python', '1.3.1'), +] + +use_pip = True + +local_preinstallopts = """sed -i 's/scikit-image = ">=0.19.0,<0.19.4"/scikit-image = ">=0.19.0"/' pyproject.toml && """ +local_preinstallopts += """sed -i 's/numpy = ">=1.23.2,<=1.24.4"/numpy = ">=1.23.2"/' pyproject.toml && """ +local_preinstallopts += """sed -i 's/scipy = ">=1.5.0,<1.10.1"/scipy = ">=1.5.0"/' pyproject.toml && """ + +exts_list = [ + ('certifi', '2024.6.2', { + 'checksums': ['3cd43f1c6fa7dedc5899d69d3ad0398fd018ad1a17fba83ddaf78aa46c747516'], + }), + (name, version, { + 'preinstallopts': local_preinstallopts, + 'checksums': ['c0f6a6d0381f0ca056f524e3b8217b0a8304ea79a0cdc88f76a39b1bf7531031'], + }), +] + +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/h/hypothesis/hypothesis-6.103.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/h/hypothesis/hypothesis-6.103.1-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..e9bb1d78543c --- /dev/null +++ b/easybuild/easyconfigs/h/hypothesis/hypothesis-6.103.1-GCCcore-13.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'hypothesis' +version = '6.103.1' + +homepage = "https://github.com/HypothesisWorks/hypothesis" +description = """Hypothesis is an advanced testing library for Python. It lets you write tests which are parametrized + by a source of examples, and then generates simple and comprehensible examples that make your tests fail. This lets + you find more bugs in your code with less work.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['d299d5c21d6408eab3be670c94c974f3acf0b511c61fe81804b09091e393ee1f'] + +builddependencies = [ + ('binutils', '2.42'), +] + +dependencies = [ + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), # required for attrs, sortedcontainers +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/IEntropy/IEntropy-2024.06.12-foss-2023a-R-4.3.2.eb b/easybuild/easyconfigs/i/IEntropy/IEntropy-2024.06.12-foss-2023a-R-4.3.2.eb new file mode 100644 index 000000000000..ee26df679bff --- /dev/null +++ b/easybuild/easyconfigs/i/IEntropy/IEntropy-2024.06.12-foss-2023a-R-4.3.2.eb @@ -0,0 +1,36 @@ +easyblock = 'RPackage' + +name = 'IEntropy' +version = '2024.06.12' +local_commit = '3cd58ab' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/LinLi-0909/IEntropy' +description = """Here, by deriving entropy decomposition formula, we proposed a feature selection method, +intrinsic entropy (IE) model, to identify the informative genes for accurately clustering analysis.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/LinLi-0909/IEntropy/archive/'] +sources = [{ + "download_filename": "%s.tar.gz" % local_commit, + "filename": "%(name)s-%(version)s.tar.gz" +}] +checksums = ['7449340df7218c790dcdff5dbb14ba7d613bd9bdfb0a440296a561bbb742f9c1'] + +dependencies = [ + ('R', '4.3.2'), + ('R-bundle-Bioconductor', '3.18', '-R-%(rver)s'), +] + +unpack_sources = True +start_dir = 'IEntropy' + +sanity_check_paths = { + 'files': [], + 'dirs': ['%(name)s'], +} + +sanity_check_commands = ['Rscript -e "library(IEntropy)"'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/i/IGV/IGV-2.17.4-Java-17.eb b/easybuild/easyconfigs/i/IGV/IGV-2.17.4-Java-17.eb new file mode 100644 index 000000000000..35e427d0ad07 --- /dev/null +++ b/easybuild/easyconfigs/i/IGV/IGV-2.17.4-Java-17.eb @@ -0,0 +1,34 @@ +# EasyBuild easyconfig +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# Modified by Adam Huffman +# Big Data Institute, University of Oxford + +easyblock = 'Tarball' + +name = 'IGV' +version = '2.17.4' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://www.broadinstitute.org/software/igv/' +description = """This package contains command line utilities for + preprocessing, computing feature count density (coverage), sorting, and + indexing data files.""" + +toolchain = SYSTEM + +source_urls = ['http://data.broadinstitute.org/igv/projects/downloads/%(version_major)s.%(version_minor)s'] +sources = ['%(name)s_%(version)s.zip'] +checksums = ['6a36ae64fa3b74182db654a93f6254256305a8afa6b878f381b5d04fc1e8eaa5'] + +dependencies = [('Java', '17', '', SYSTEM)] + +sanity_check_paths = { + 'files': ['%(namelower)s.sh', 'lib/%(namelower)s.jar'], + 'dirs': [], +} + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/i/IMAGE/IMAGE-1.1-foss-2022b.eb b/easybuild/easyconfigs/i/IMAGE/IMAGE-1.1-foss-2022b.eb new file mode 100644 index 000000000000..3b7413af016d --- /dev/null +++ b/easybuild/easyconfigs/i/IMAGE/IMAGE-1.1-foss-2022b.eb @@ -0,0 +1,57 @@ +easyblock = 'Tarball' + +name = 'IMAGE' +version = '1.1' + +homepage = 'https://github.com/JesperGrud/IMAGE' +description = """IMAGE (Motif Activity and Gene Expression changes of transcription factors) is software for +integrated analysis of motif activity and gene expression changes of transcription factors. IMAGE makes prediction +of causal transcription factors based on transcriptome profiling and genome-wide maps of enhancer activity.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +source_urls = ['https://github.com/JesperGrud/IMAGE/archive/refs/tags'] +sources = ['v%(version)s.tar.gz'] +checksums = ['e286cd5e7eb5aaaf9e103a9651ece39ff4ce260c463facdf1758b6d72a285062'] + +dependencies = [ + ('Perl', '5.36.0'), + ('HOMER', '4.11.1'), + ('R', '4.2.2'), + ('R-bundle-Bioconductor', '3.16', '-R-4.2.2'), +] + +postinstallcmds = [ + 'mkdir %(installdir)s/bin', + 'mv %(installdir)s/IMAGE.pl %(installdir)s/bin/', + 'chmod +x %(installdir)s/bin/IMAGE.pl', + ( + 'sed -i "s|my \\$TMPDIR = \\$INSTALLDIR . \\$TMP;|my \\$TMPDIR = \\$TMP;|g" ' + '%(installdir)s/bin/IMAGE.pl' + ), + ( + 'sed -i "s|my \\$UTILDIR = \\$INSTALLDIR . \\$UTIL;|my \\$UTILDIR = \'%(installdir)s\' . \\$UTIL;|g" ' + '%(installdir)s/bin/IMAGE.pl' + ), +] + +fix_perl_shebang_for = ['bin/*.pl'] + +sanity_check_paths = { + 'dirs': ['bin', 'utils', 'tmp'], + 'files': [ + 'utils/Collection.motif', + 'utils/extractSequence', + 'utils/Genename_Motif.txt', + 'utils/Parallel.sh', + 'utils/Regression.R', + 'utils/SplitMotifLibrary.sh', + 'bin/IMAGE.pl', + ] +} + +sanity_check_commands = [ + "IMAGE.pl", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/i/IML/IML-1.0.5-gfbf-2023b.eb b/easybuild/easyconfigs/i/IML/IML-1.0.5-gfbf-2023b.eb index d91714897486..29698d8351f9 100644 --- a/easybuild/easyconfigs/i/IML/IML-1.0.5-gfbf-2023b.eb +++ b/easybuild/easyconfigs/i/IML/IML-1.0.5-gfbf-2023b.eb @@ -8,6 +8,7 @@ description = """IML is a free library of C source code which implements algorit exact solutions to dense systems of linear equations over the integers.""" toolchain = {'name': 'gfbf', 'version': '2023b'} +toolchainopts = {'pic': True} source_urls = ['http://www.cs.uwaterloo.ca/~astorjoh'] sources = [SOURCELOWER_TAR_BZ2] diff --git a/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.3.5-gompi-2023a.eb b/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.3.5-gompi-2023a.eb new file mode 100644 index 000000000000..ca4c707da699 --- /dev/null +++ b/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.3.5-gompi-2023a.eb @@ -0,0 +1,55 @@ +# Updated to v2.1.3 by +# R.QIAO +# DeepThought, Flinders University + +easyblock = 'CMakeMake' + +name = 'IQ-TREE' +version = '2.3.5' + +# HTTPS is not working +homepage = 'http://www.iqtree.org/' +description = """Efficient phylogenomic software by maximum likelihood""" + +toolchain = {'name': 'gompi', 'version': '2023a'} +# Including 'usempi' will take precedence and override IQTREE_FLAGS and produces only 'iqtree-mpi' binary + +source_urls = ['https://github.com/iqtree/iqtree2/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'IQ-TREE-2.3.5_use_EB_LSD2.patch', +] +checksums = [ + {'v2.3.5.tar.gz': '8e323e0b7c46e97901d3500f11e810703e0e5d25848188047eca9602d03fa6b1'}, + {'IQ-TREE-2.3.5_use_EB_LSD2.patch': 'b4578b01f06ae52b94b332622c0f6630497cd29cb61010f58f7c5018c2c32a5f'}, +] + +builddependencies = [ + ('CMake', '3.26.3'), + ('Eigen', '3.4.0'), +] +dependencies = [ + ('zlib', '1.2.13'), + ('Boost', '1.82.0'), + ('LSD2', '2.4.1'), +] + +local_conf_opts = ' -DUSE_LSD2=ON ' +configopts = [ + '-DIQTREE_FLAGS=omp' + local_conf_opts, + '-DIQTREE_FLAGS=mpi -DCMAKE_C_COMPILER="$MPICC" -DCMAKE_CXX_COMPILER="$MPICXX"' + local_conf_opts, +] + +sanity_check_paths = { + 'files': ['bin/iqtree2', 'bin/iqtree2-mpi'], + 'dirs': [], +} + +sanity_check_commands = [ + "iqtree2 --help", + "mkdir -p $TMPDIR/{test-omp,test-mpi}", + "cd $TMPDIR/test-omp && cp -a %(installdir)s/example.phy . && iqtree2 -s example.phy -redo", + "cd $TMPDIR/test-mpi && cp -a %(installdir)s/example.phy . && mpirun -np 1 iqtree2-mpi -s example.phy -redo", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.3.5_use_EB_LSD2.patch b/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.3.5_use_EB_LSD2.patch new file mode 100644 index 000000000000..b567f096fa93 --- /dev/null +++ b/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.3.5_use_EB_LSD2.patch @@ -0,0 +1,36 @@ +diff -ruN iqtree2-2.3.5/CMakeLists.txt iqtree2-2.3.5-orig/CMakeLists.txt +--- iqtree2-2.3.5/CMakeLists.txt 2024-06-26 04:33:33.000000000 +0000 ++++ iqtree2-2.3.5-orig/CMakeLists.txt 2024-07-03 08:23:41.030462539 +0000 +@@ -758,10 +758,6 @@ + add_subdirectory(terracetphast) + endif() + +-if (USE_LSD2) +- add_subdirectory(lsd2) +-endif() +- + add_library(kernelsse tree/phylokernelsse.cpp) + + if (NOT BINARY32 AND NOT IQTREE_FLAGS MATCHES "novx") +@@ -820,9 +816,6 @@ + if (USE_TERRAPHAST) + set_target_properties(terracetphast terraphast PROPERTIES COMPILE_FLAGS "${SSE_FLAGS}") + endif() +- if (USE_LSD2) +- set_target_properties(lsd2 PROPERTIES COMPILE_FLAGS "${SSE_FLAGS}") +- endif() + if (USE_BOOSTER) + set_target_properties(booster PROPERTIES COMPILE_FLAGS "${SSE_FLAGS}") + endif() +diff -ruN iqtree2-2.3.5/main/timetree.cpp iqtree2-2.3.5-orig/main/timetree.cpp +--- iqtree2-2.3.5/main/timetree.cpp 2024-06-26 04:33:33.000000000 +0000 ++++ iqtree2-2.3.5-orig/main/timetree.cpp 2024-07-03 08:24:32.438606710 +0000 +@@ -8,7 +8,7 @@ + #include "timetree.h" + + #ifdef USE_LSD2 +-#include "lsd2/src/lsd.h" ++#include "lsd.h" + #endif + + /** map from taxon name to date */ diff --git a/easybuild/easyconfigs/i/ITK/ITK-5.3.0-foss-2022b.eb b/easybuild/easyconfigs/i/ITK/ITK-5.3.0-foss-2022b.eb new file mode 100644 index 000000000000..9ba65978898b --- /dev/null +++ b/easybuild/easyconfigs/i/ITK/ITK-5.3.0-foss-2022b.eb @@ -0,0 +1,78 @@ +# Contributors: +# Fenglai Liu (fenglai@accre.vanderbilt.edu) - Vanderbilt University +# Alex Domingo (alex.domingo.toro@vub.be) - Vrije Universiteit Brussel (VUB) +# Denis Kristak, Pavel Tománek (INUITS) +# +easyblock = 'CMakeMake' + +name = 'ITK' +version = '5.3.0' + +homepage = 'https://itk.org' +description = """Insight Segmentation and Registration Toolkit (ITK) provides + an extensive suite of software tools for registering and segmenting + multidimensional imaging data.""" + +toolchain = {'name': 'foss', 'version': '2022b'} +toolchainopts = {'pic': True, 'cstd': 'c++11'} + +github_account = 'InsightSoftwareConsortium' +source_urls = [GITHUB_SOURCE] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +patches = [ + 'ITK-5.3.0_vtk-include.patch', + 'ITK-5.3.0_fix-compatibility-swig-4-1.patch', +] +checksums = [ + {'ITK-5.3.0.tar.gz': '64e7e8094a5023c8f68ee042459d6319581fadb35e2fe90a4ae230ce36369db1'}, + {'ITK-5.3.0_vtk-include.patch': '138ebd2e0e7f9001aba5f4a7e8145ffcf0093913d50f109ecff447773fd52a48'}, + {'ITK-5.3.0_fix-compatibility-swig-4-1.patch': '0138878d96e90d6bfdc81fd4f2b5ec413d61c1de666a16842b417c2686ebf506'}, +] + +builddependencies = [ + ('CMake', '3.24.3'), + ('Bison', '3.8.2'), + ('Eigen', '3.4.0'), + ('SWIG', '4.1.1'), + ('Perl', '5.36.0'), +] +dependencies = [ + ('Python', '3.10.8'), + ('double-conversion', '3.2.1'), + ('expat', '2.4.9'), + ('HDF5', '1.14.0'), + ('libjpeg-turbo', '2.1.4'), + ('libpng', '1.6.38'), + ('LibTIFF', '4.4.0'), + ('VTK', '9.2.6'), + ('zlib', '1.2.12'), +] + +# Features +configopts = '-DBUILD_SHARED_LIBS=ON -DBUILD_TESTING=OFF ' +configopts += '-DModule_ITKReview=ON -DModule_ITKVtkGlue=ON -DModule_SimpleITKFilters=ON ' +# Enable Python bindings +configopts += '-DITK_WRAP_PYTHON:BOOL=ON -DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python ' +configopts += '-DSWIG_EXECUTABLE=$EBROOTSWIG/bin/swig -DSWIG_DIR=$EBROOTSWIG ' +configopts += '-DPY_SITE_PACKAGES_PATH=%(installdir)s/lib/python%(pyshortver)s/site-packages ' +# Dependencies from EB +local_sys_deps = ['DOUBLECONVERSION', 'EIGEN', 'EXPAT', 'FFTW', 'HDF5', 'JPEG', 'PNG', 'SWIG', 'TIFF', 'ZLIB'] +local_sys_cmake = ['-DITK_USE_SYSTEM_%s=ON' % d for d in local_sys_deps] +configopts += ' '.join(local_sys_cmake) + +prebuildopts = "LC_ALL=C " + +local_lib_names = ['ITKCommon', 'ITKIOHDF5', 'ITKIOJPEG', 'ITKIOPNG', 'ITKIOTIFF', + 'ITKReview', 'ITKVTK', 'ITKVtkGlue', 'itkSimpleITKFilters'] + +sanity_check_paths = { + 'files': ['bin/itkTestDriver'] + + ['lib/lib%s-%%(version_major)s.%%(version_minor)s.%s' % (l, SHLIB_EXT) for l in local_lib_names], + 'dirs': ['include/ITK-%(version_major)s.%(version_minor)s', 'lib/python%(pyshortver)s/site-packages', 'share'], +} + +sanity_check_commands = ["python -c 'import itk'"] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/i/ITK/ITK-5.3.0_vtk-include.patch b/easybuild/easyconfigs/i/ITK/ITK-5.3.0_vtk-include.patch new file mode 100644 index 000000000000..f77306c9f8e2 --- /dev/null +++ b/easybuild/easyconfigs/i/ITK/ITK-5.3.0_vtk-include.patch @@ -0,0 +1,13 @@ +Manually add the include directory of VTK +dirty fix for issue https://github.com/InsightSoftwareConsortium/ITK/issues/4375 +author: Alex Domingo (Vrije Universiteit Brussel) +--- Wrapping/CMakeLists.txt.orig 2023-12-21 13:41:44.845008000 +0100 ++++ Wrapping/CMakeLists.txt 2023-12-21 13:42:14.794328946 +0100 +@@ -112,6 +112,7 @@ + ############################################################################### + # Configure specific wrapper modules + ############################################################################### ++include_directories("$ENV{EBROOTVTK}/include/vtk-9.2/") + + unset(WRAP_ITK_MODULES CACHE) + \ No newline at end of file diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-37-GCCcore-11.3.0.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-37-GCCcore-11.3.0.eb index efff91588b05..6a78cb9c5a94 100644 --- a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-37-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-37-GCCcore-11.3.0.eb @@ -30,14 +30,18 @@ builddependencies = [ ('pkgconf', '1.8.0'), ] +preconfigopts = 'PKG_CONFIG=$EBROOTPKGCONF/bin/pkgconf' configopts = "--with-gslib --with-x" sanity_check_paths = { - 'files': [], - 'dirs': ['bin', 'etc/%(name)s-%(version_major)s', - 'include/%(name)s-%(version_major)s', 'lib', 'share'], + 'files': ['bin/magick'], + 'dirs': ['etc/%(name)s-%(version_major)s', 'include/%(name)s-%(version_major)s', 'lib', 'share'], } +sanity_check_commands = [ + 'magick --help', +] + modextravars = {'MAGICK_HOME': '%(installdir)s'} moduleclass = 'vis' diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-4-GCCcore-11.2.0.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-4-GCCcore-11.2.0.eb index c3033c0d0804..7d03b87d1d8c 100644 --- a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-4-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-4-GCCcore-11.2.0.eb @@ -30,14 +30,18 @@ builddependencies = [ ('pkg-config', '0.29.2'), ] +preconfigopts = 'PKG_CONFIG=$EBROOTPKGCONF/bin/pkgconf' configopts = "--with-gslib --with-x" sanity_check_paths = { - 'files': [], - 'dirs': ['bin', 'etc/%(name)s-%(version_major)s', - 'include/%(name)s-%(version_major)s', 'lib', 'share'], + 'files': ['bin/magick'], + 'dirs': ['etc/%(name)s-%(version_major)s', 'include/%(name)s-%(version_major)s', 'lib', 'share'], } +sanity_check_commands = [ + 'magick --help', +] + modextravars = {'MAGICK_HOME': '%(installdir)s'} moduleclass = 'vis' diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-53-GCCcore-12.2.0.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-53-GCCcore-12.2.0.eb index 1ddf40ec50a6..e758d987dfa6 100644 --- a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-53-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-53-GCCcore-12.2.0.eb @@ -30,14 +30,18 @@ builddependencies = [ ('pkgconf', '1.9.3'), ] +preconfigopts = 'PKG_CONFIG=$EBROOTPKGCONF/bin/pkgconf' configopts = "--with-gslib --with-x" sanity_check_paths = { - 'files': [], - 'dirs': ['bin', 'etc/%(name)s-%(version_major)s', - 'include/%(name)s-%(version_major)s', 'lib', 'share'], + 'files': ['bin/magick'], + 'dirs': ['etc/%(name)s-%(version_major)s', 'include/%(name)s-%(version_major)s', 'lib', 'share'], } +sanity_check_commands = [ + 'magick --help', +] + modextravars = {'MAGICK_HOME': '%(installdir)s'} moduleclass = 'vis' diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.1-15-GCCcore-12.3.0.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.1-15-GCCcore-12.3.0.eb index 9504c2276809..4fe1068022b9 100644 --- a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.1-15-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.1-15-GCCcore-12.3.0.eb @@ -29,14 +29,18 @@ dependencies = [ ('FriBidi', '1.0.12'), ] +preconfigopts = 'PKG_CONFIG=$EBROOTPKGCONF/bin/pkgconf' configopts = "--with-gslib --with-x" - sanity_check_paths = { - 'files': [], - 'dirs': ['bin', 'etc/%(name)s-%(version_major)s', 'include/%(name)s-%(version_major)s', 'lib', 'share'], + 'files': ['bin/magick'], + 'dirs': ['etc/%(name)s-%(version_major)s', 'include/%(name)s-%(version_major)s', 'lib', 'share'], } +sanity_check_commands = [ + 'magick --help', +] + modextravars = {'MAGICK_HOME': '%(installdir)s'} moduleclass = 'vis' diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.1-34-GCCcore-13.2.0.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.1-34-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..2ccdcb32a55f --- /dev/null +++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.1-34-GCCcore-13.2.0.eb @@ -0,0 +1,46 @@ +easyblock = 'ConfigureMake' + +name = 'ImageMagick' +version = '7.1.1-34' + +homepage = 'https://www.imagemagick.org/' +description = "ImageMagick is a software suite to create, edit, compose, or convert bitmap images" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://github.com/%(name)s/%(name)s/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['19f4303774b56be182c576b266c34bc824fcaef1d1d243192344d015adb0ec28'] + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '2.0.3'), +] +dependencies = [ + ('bzip2', '1.0.8'), + ('X11', '20231019'), + ('Ghostscript', '10.02.1'), + ('JasPer', '4.0.0'), + ('libjpeg-turbo', '3.0.1'), + ('LibTIFF', '4.6.0'), + ('LittleCMS', '2.15'), + ('Pango', '1.51.0'), + ('pixman', '0.42.2'), + ('FriBidi', '1.0.13'), +] + +preconfigopts = 'PKG_CONFIG=$EBROOTPKGCONF/bin/pkgconf' +configopts = "--with-gslib --with-x" + +sanity_check_paths = { + 'files': ['bin/magick'], + 'dirs': ['etc/%(name)s-%(version_major)s', 'include/%(name)s-%(version_major)s', 'lib', 'share'], +} + +sanity_check_commands = [ + 'magick --help', +] + +modextravars = {'MAGICK_HOME': '%(installdir)s'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/i/Imath/Imath-3.1.11-GCCcore-13.3.0.eb b/easybuild/easyconfigs/i/Imath/Imath-3.1.11-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..05efb6d6c628 --- /dev/null +++ b/easybuild/easyconfigs/i/Imath/Imath-3.1.11-GCCcore-13.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'Imath' +version = '3.1.11' + +homepage = 'https://imath.readthedocs.io/en/latest/' +description = """ +Imath is a C++ and python library of 2D and 3D vector, matrix, and math operations for computer graphics +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/AcademySoftwareFoundation/%(namelower)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['9057849585e49b8b85abe7cc1e76e22963b01bfdc3b6d83eac90c499cd760063'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] + +sanity_check_paths = { + 'files': ['lib/libImath.%s' % SHLIB_EXT], + 'dirs': ['include/Imath'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/i/Inspector/Inspector-2019_update5.eb b/easybuild/easyconfigs/i/Inspector/Inspector-2019_update5.eb index b27635916caf..179e26005de3 100644 --- a/easybuild/easyconfigs/i/Inspector/Inspector-2019_update5.eb +++ b/easybuild/easyconfigs/i/Inspector/Inspector-2019_update5.eb @@ -7,7 +7,7 @@ description = """Intel Inspector XE is an easy to use memory error checker and t toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15827/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15827/'] sources = ['inspector_%(version)s.tar.gz'] checksums = ['676fd0b25a56fba63495c048abf485b08583cbb01eb0cf6e1174ee7b352af6d5'] diff --git a/easybuild/easyconfigs/i/Inspector/Inspector-2021.4.0.eb b/easybuild/easyconfigs/i/Inspector/Inspector-2021.4.0.eb index 11b56c0bc1c3..494b031a5e18 100644 --- a/easybuild/easyconfigs/i/Inspector/Inspector-2021.4.0.eb +++ b/easybuild/easyconfigs/i/Inspector/Inspector-2021.4.0.eb @@ -10,7 +10,7 @@ description = """Intel Inspector is a dynamic memory and threading error toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18239/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18239/'] sources = ['l_inspector_oneapi_p_%(version)s.266_offline.sh'] checksums = ['c8210cbcd0e07cc75e773249a5e4a02cf34894ec80a213939f3a20e6c5705274'] diff --git a/easybuild/easyconfigs/i/Inspector/Inspector-2022.0.0.eb b/easybuild/easyconfigs/i/Inspector/Inspector-2022.0.0.eb index 430cc62b2d43..22f082dd1f43 100644 --- a/easybuild/easyconfigs/i/Inspector/Inspector-2022.0.0.eb +++ b/easybuild/easyconfigs/i/Inspector/Inspector-2022.0.0.eb @@ -10,7 +10,7 @@ description = """Intel Inspector is a dynamic memory and threading error toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18363/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18363/'] sources = ['l_inspector_oneapi_p_%(version)s.56_offline.sh'] checksums = ['79a0eb2ae3f1de1e3456076685680c468702922469c3fda3e074718fb0bea741'] diff --git a/easybuild/easyconfigs/i/Inspector/Inspector-2022.1.0.eb b/easybuild/easyconfigs/i/Inspector/Inspector-2022.1.0.eb index a7772259cc87..33515e7a8e5a 100644 --- a/easybuild/easyconfigs/i/Inspector/Inspector-2022.1.0.eb +++ b/easybuild/easyconfigs/i/Inspector/Inspector-2022.1.0.eb @@ -10,7 +10,7 @@ description = """Intel Inspector is a dynamic memory and threading error toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18712/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18712/'] sources = ['l_inspector_oneapi_p_%(version)s.123_offline.sh'] checksums = ['8551180aa30be3abea11308fb11ea9a296f0e056ab07d9254585448a0b23333e'] diff --git a/easybuild/easyconfigs/i/IntelClusterChecker/IntelClusterChecker-2021.5.0.eb b/easybuild/easyconfigs/i/IntelClusterChecker/IntelClusterChecker-2021.5.0.eb index 55107c33e8a3..c0357dea2d0a 100644 --- a/easybuild/easyconfigs/i/IntelClusterChecker/IntelClusterChecker-2021.5.0.eb +++ b/easybuild/easyconfigs/i/IntelClusterChecker/IntelClusterChecker-2021.5.0.eb @@ -13,7 +13,7 @@ can be identified and practical resolutions provided. toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18359/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18359/'] sources = ['l_clck_p_%(version)s.560_offline.sh'] checksums = ['2b661eff4a87607fd29e21fe29883873c0a7216d7d0a99557dc48b6eae9adeb0'] diff --git a/easybuild/easyconfigs/i/IntelPython/IntelPython-2.7.15-2019.2.066.eb b/easybuild/easyconfigs/i/IntelPython/IntelPython-2.7.15-2019.2.066.eb index c46f42bb81b9..48ab0a8f8368 100644 --- a/easybuild/easyconfigs/i/IntelPython/IntelPython-2.7.15-2019.2.066.eb +++ b/easybuild/easyconfigs/i/IntelPython/IntelPython-2.7.15-2019.2.066.eb @@ -15,7 +15,7 @@ description = """ Accelerating Python* performance on modern architectures from Intel. """ -source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15115/'] +source_urls = ['http://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15115/'] sources = ['l_pythoni%s_p_%s.tar.gz' % (local_pysver, local_relver)] checksums = ['dd0b73db5d0d79c3cdf779d10092eae32780d720b74ed8fde2a2c46e23143de1'] diff --git a/easybuild/easyconfigs/i/IntelPython/IntelPython-3.6.8-2019.2.066.eb b/easybuild/easyconfigs/i/IntelPython/IntelPython-3.6.8-2019.2.066.eb index fd51e3b2082b..d0c2dc13c679 100644 --- a/easybuild/easyconfigs/i/IntelPython/IntelPython-3.6.8-2019.2.066.eb +++ b/easybuild/easyconfigs/i/IntelPython/IntelPython-3.6.8-2019.2.066.eb @@ -15,7 +15,7 @@ description = """ Accelerating Python* performance on modern architectures from Intel. """ -source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15115/'] +source_urls = ['http://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15115/'] sources = ['l_pythoni%s_p_%s.tar.gz' % (local_pysver, local_relver)] checksums = ['804883fc1413ee72b0ae421a8ac82ab158fc01c8b4631a44a9d2ef1a19324751'] diff --git a/easybuild/easyconfigs/i/IsoQuant/IsoQuant-3.5.0-foss-2023a.eb b/easybuild/easyconfigs/i/IsoQuant/IsoQuant-3.5.0-foss-2023a.eb new file mode 100644 index 000000000000..41248bcbf731 --- /dev/null +++ b/easybuild/easyconfigs/i/IsoQuant/IsoQuant-3.5.0-foss-2023a.eb @@ -0,0 +1,45 @@ +easyblock = 'Tarball' + +name = 'IsoQuant' +version = '3.5.0' + +homepage = 'https://github.com/ablab/IsoQuant' +description = """IsoQuant is a tool for the genome-based analysis of long RNA reads, + such as PacBio or Oxford Nanopores. IsoQuant allows to reconstruct and quantify + transcript models with high precision and decent recall. If the reference annotation is given, + IsoQuant also assigns reads to the annotated isoforms based on their intron and exon structure. + IsoQuant further performs annotated gene, isoform, exon and intron quantification. + If reads are grouped (e.g. according to cell type), counts are reported according to the provided grouping.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/ablab/%(name)s/archive/'] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}] +checksums = ['8cbba80b5eb0ed85fe0b519693157eb97820bc1d79ff44435736bf799af85c1f'] + +dependencies = [ + ('Python', '3.11.3'), + ('gffutils', '0.13'), + ('Biopython', '1.83'), + ('SciPy-bundle', '2023.07'), + ('pybedtools', '0.9.1'), + ('Pysam', '0.22.0'), + ('pyfaidx', '0.8.1.1'), + ('minimap2', '2.26'), + ('SAMtools', '1.18'), + ('PyYAML', '6.0'), +] + +modextrapaths = { + 'PATH': '', + 'PYTHONPATH': '', +} + +sanity_check_paths = { + 'files': ['isoquant.py'], + 'dirs': [], +} + +sanity_check_commands = ["mkdir -p %(builddir)s && cd %(builddir)s && isoquant.py --test"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/i/icc/icc-2018.1.163-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/icc/icc-2018.1.163-GCC-6.4.0-2.28.eb index ca49a084587d..f6eb99cebdca 100644 --- a/easybuild/easyconfigs/i/icc/icc-2018.1.163-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/icc/icc-2018.1.163-GCC-6.4.0-2.28.eb @@ -8,7 +8,7 @@ description = "Intel C and C++ compilers" toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12382/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/12382/'] sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_cpp.tgz'] checksums = ['ddbfdf88eed095817650ec0a226ef3b9c07c41c855d258e80eaade5173fedb6e'] diff --git a/easybuild/easyconfigs/i/icc/icc-2018.3.222-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/i/icc/icc-2018.3.222-GCC-7.3.0-2.30.eb index 9b3a071f0057..c04b1a099097 100644 --- a/easybuild/easyconfigs/i/icc/icc-2018.3.222-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/i/icc/icc-2018.3.222-GCC-7.3.0-2.30.eb @@ -8,7 +8,7 @@ description = "Intel C and C++ compilers" toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13003/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13003/'] sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_cpp.tgz'] checksums = ['d8b7e6633faa2e0b7d4eebf3260cb3a200b951cb2cf7b5db957c5ae71508d34b'] diff --git a/easybuild/easyconfigs/i/icc/icc-2018.5.274-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/i/icc/icc-2018.5.274-GCC-7.3.0-2.30.eb index 3918ba3f3f12..f2d6c096878f 100644 --- a/easybuild/easyconfigs/i/icc/icc-2018.5.274-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/i/icc/icc-2018.5.274-GCC-7.3.0-2.30.eb @@ -8,7 +8,7 @@ description = "Intel C and C++ compilers" toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13723/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13723/'] # released as "2018 update 4" despite internal version number if 2018.5.274, so can't use %(version_minor)s template sources = ['parallel_studio_xe_%(version_major)s_update4_composer_edition_for_cpp.tgz'] checksums = ['3850ab2a01fe8888af8fed65b7d24e0ddf45a84efe9635ff0f118c38dfc4544b'] diff --git a/easybuild/easyconfigs/i/icc/icc-2019.0.117-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/i/icc/icc-2019.0.117-GCC-8.2.0-2.31.1.eb index b78d2e8e11c4..5cf05e6a5598 100644 --- a/easybuild/easyconfigs/i/icc/icc-2019.0.117-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/i/icc/icc-2019.0.117-GCC-8.2.0-2.31.1.eb @@ -8,7 +8,7 @@ description = "Intel C and C++ compilers" toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13582/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13582/'] sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_cpp.tgz'] checksums = ['17932a54a76d04432de16e6db15a6ed80fa80ed20193f3b717fd391f623e23e1'] diff --git a/easybuild/easyconfigs/i/icc/icc-2019.1.144-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/i/icc/icc-2019.1.144-GCC-8.2.0-2.31.1.eb index 7b37d3169dc8..f2341a844c37 100644 --- a/easybuild/easyconfigs/i/icc/icc-2019.1.144-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/i/icc/icc-2019.1.144-GCC-8.2.0-2.31.1.eb @@ -8,7 +8,7 @@ description = "Intel C and C++ compilers" toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/14865/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/14865/'] sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_cpp.tgz'] checksums = ['4a156bbeac9bd8d67e74b33ad6f3ae02d4c24c8444365465db6dc50d3e891946'] diff --git a/easybuild/easyconfigs/i/icc/icc-2019.2.187-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/i/icc/icc-2019.2.187-GCC-8.2.0-2.31.1.eb index f192fd17472a..9f9b71a21dfe 100644 --- a/easybuild/easyconfigs/i/icc/icc-2019.2.187-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/i/icc/icc-2019.2.187-GCC-8.2.0-2.31.1.eb @@ -8,7 +8,7 @@ description = "Intel C and C++ compilers" toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15093/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15093/'] sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_cpp.tgz'] checksums = ['fc434a2e005af223f43d258c16f004134def726a8d2a225e830af85d553bee55'] diff --git a/easybuild/easyconfigs/i/icc/icc-2019.3.199-GCC-8.3.0-2.32.eb b/easybuild/easyconfigs/i/icc/icc-2019.3.199-GCC-8.3.0-2.32.eb index 65821a417db9..2d194db100a3 100644 --- a/easybuild/easyconfigs/i/icc/icc-2019.3.199-GCC-8.3.0-2.32.eb +++ b/easybuild/easyconfigs/i/icc/icc-2019.3.199-GCC-8.3.0-2.32.eb @@ -8,7 +8,7 @@ description = "Intel C and C++ compilers" toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15273/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15273/'] sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_cpp.tgz'] checksums = ['969985e83ebf7bfe3c3ac3b771a7d16ba9b5dfbda84e7c2a60ef25fb827b58ae'] diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2019.4.243.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2019.4.243.eb index 5cefbfc2dee8..85453f372516 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2019.4.243.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2019.4.243.eb @@ -8,7 +8,7 @@ description = "Intel C, C++ & Fortran compilers" toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15537/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15537/'] sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition.tgz'] patches = ['iccifort-%(version)s_no_mpi_rt_dependency.patch'] checksums = [ diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2019.5.281.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2019.5.281.eb index c080762f21da..b4eb6588ec7d 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2019.5.281.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2019.5.281.eb @@ -8,7 +8,7 @@ description = "Intel C, C++ & Fortran compilers" toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15813/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15813/'] sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition.tgz'] patches = ['iccifort-%(version)s_no_mpi_rt_dependency.patch'] checksums = [ diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2020.0.166-GCC-9.2.0.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2020.0.166-GCC-9.2.0.eb index a8f9c94588f4..a21e15527d5b 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2020.0.166-GCC-9.2.0.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2020.0.166-GCC-9.2.0.eb @@ -8,7 +8,7 @@ description = "Intel C, C++ & Fortran compilers" toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16229/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16229/'] sources = ['parallel_studio_xe_%(version_major)s_composer_edition.tgz'] patches = ['iccifort-%(version)s_no_mpi_rt_dependency.patch'] checksums = [ diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2020.0.166.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2020.0.166.eb index 70593480c690..4ad42c13a31e 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2020.0.166.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2020.0.166.eb @@ -8,7 +8,7 @@ description = "Intel C, C++ & Fortran compilers" toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16229/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16229/'] sources = ['parallel_studio_xe_%(version_major)s_composer_edition.tgz'] patches = ['iccifort-%(version)s_no_mpi_rt_dependency.patch'] checksums = [ diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2020.1.217.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2020.1.217.eb index 89d42319787a..98e64dff9187 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2020.1.217.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2020.1.217.eb @@ -8,7 +8,7 @@ description = "Intel C, C++ & Fortran compilers" toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16530/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16530/'] sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition.tgz'] patches = ['iccifort-%(version)s_no_mpi_rt_dependency.patch'] checksums = [ diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2020.4.304.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2020.4.304.eb index fbd8bc1719bd..056539c7f760 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2020.4.304.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2020.4.304.eb @@ -8,7 +8,7 @@ description = "Intel C, C++ & Fortran compilers" toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/17117/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/17117/'] sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition.tgz'] patches = ['iccifort-%(version)s_no_mpi_rt_dependency.patch'] checksums = [ diff --git a/easybuild/easyconfigs/i/ifort/ifort-2018.1.163-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/ifort/ifort-2018.1.163-GCC-6.4.0-2.28.eb index 66cf55bd0c01..2ce7d5ee7f13 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2018.1.163-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2018.1.163-GCC-6.4.0-2.28.eb @@ -8,7 +8,7 @@ description = "Intel Fortran compiler" toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12383/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/12383/'] sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_fortran.tgz'] patches = ['ifort_%(version)s_no_mpi_mic_dependency.patch'] checksums = [ diff --git a/easybuild/easyconfigs/i/ifort/ifort-2018.3.222-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/i/ifort/ifort-2018.3.222-GCC-7.3.0-2.30.eb index 8572f079dca8..3bdc51210af2 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2018.3.222-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2018.3.222-GCC-7.3.0-2.30.eb @@ -8,7 +8,7 @@ description = "Intel Fortran compiler" toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13004/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13004/'] sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_fortran.tgz'] patches = ['ifort_%(version)s_no_mpi_mic_dependency.patch'] checksums = [ diff --git a/easybuild/easyconfigs/i/ifort/ifort-2018.5.274-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/i/ifort/ifort-2018.5.274-GCC-7.3.0-2.30.eb index 7668ec767495..3f9f1de0c453 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2018.5.274-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2018.5.274-GCC-7.3.0-2.30.eb @@ -8,7 +8,7 @@ description = "Intel Fortran compiler" toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13724/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13724/'] # released as "2018 update 4" despite internal version number if 2018.5.274, so can't use %(version_minor)s template sources = ['parallel_studio_xe_%(version_major)s_update4_composer_edition_for_fortran.tgz'] patches = ['ifort-%(version)s_no_mpi_mic_dependency.patch'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2019.0.117-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/i/ifort/ifort-2019.0.117-GCC-8.2.0-2.31.1.eb index 3457239087db..453cf476095a 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2019.0.117-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2019.0.117-GCC-8.2.0-2.31.1.eb @@ -8,7 +8,7 @@ description = "Intel Fortran compiler" toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13583/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13583/'] sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_fortran.tgz'] patches = ['ifort-%(version)s_no_mpi_mic_dependency.patch'] checksums = [ diff --git a/easybuild/easyconfigs/i/ifort/ifort-2019.1.144-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/i/ifort/ifort-2019.1.144-GCC-8.2.0-2.31.1.eb index c47117b085bb..c6c03d9340fa 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2019.1.144-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2019.1.144-GCC-8.2.0-2.31.1.eb @@ -8,7 +8,7 @@ description = "Intel Fortran compiler" toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/14866/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/14866/'] sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_fortran.tgz'] patches = ['ifort-%(version)s_no_mpi_mic_dependency.patch'] checksums = [ diff --git a/easybuild/easyconfigs/i/ifort/ifort-2019.2.187-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/i/ifort/ifort-2019.2.187-GCC-8.2.0-2.31.1.eb index 924762c6de22..5a043c03822e 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2019.2.187-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2019.2.187-GCC-8.2.0-2.31.1.eb @@ -8,7 +8,7 @@ description = "Intel Fortran compiler" toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15094/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15094/'] sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_fortran.tgz'] patches = ['ifort-%(version)s_no_mpi_mic_dependency.patch'] checksums = [ diff --git a/easybuild/easyconfigs/i/ifort/ifort-2019.3.199-GCC-8.3.0-2.32.eb b/easybuild/easyconfigs/i/ifort/ifort-2019.3.199-GCC-8.3.0-2.32.eb index b8eb911adc2e..b996c679995d 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2019.3.199-GCC-8.3.0-2.32.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2019.3.199-GCC-8.3.0-2.32.eb @@ -8,7 +8,7 @@ description = "Intel Fortran compiler" toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15274/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15274/'] sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_fortran.tgz'] patches = ['ifort-%(version)s_no_mpi_mic_dependency.patch'] checksums = [ diff --git a/easybuild/easyconfigs/i/igraph/igraph-0.10.12-foss-2023b.eb b/easybuild/easyconfigs/i/igraph/igraph-0.10.12-foss-2023b.eb new file mode 100644 index 000000000000..6e5f77cd3c82 --- /dev/null +++ b/easybuild/easyconfigs/i/igraph/igraph-0.10.12-foss-2023b.eb @@ -0,0 +1,42 @@ +# Author: Denis Krišťák (INUITS) +# Modified: Jasper Grimm (UoY) +# Update: Pavel Tománek (INUITS) +# Update: Petr Král (INUITS) + +easyblock = 'CMakeMake' + +name = 'igraph' +version = '0.10.12' + +homepage = 'https://igraph.org' +description = """igraph is a collection of network analysis tools with the emphasis on +efficiency, portability and ease of use. igraph is open source and free. igraph can be +programmed in R, Python and C/C++.""" + +toolchain = {'name': 'foss', 'version': '2023b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/igraph/igraph/releases/download/%(version)s'] +sources = [SOURCE_TAR_GZ] +checksums = ['b011f7f9f38a3e59924cc9ff652e6d33105fa03fcaf3792f47d752626a0a4625'] + +builddependencies = [ + ('CMake', '3.27.6'), +] + +dependencies = [ + ('GLPK', '5.0'), + ('libxml2', '2.11.5'), + ('zlib', '1.2.13'), + ('arpack-ng', '3.9.0'), +] + +# Build static and shared libraries +configopts = ["-DBUILD_SHARED_LIBS=OFF", "-DBUILD_SHARED_LIBS=ON"] + +sanity_check_paths = { + 'files': ['include/igraph/igraph.h'] + ['lib/libigraph.%s' % x for x in ['a', SHLIB_EXT]], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2024a.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2024a.eb new file mode 100644 index 000000000000..d6150133621c --- /dev/null +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2024a.eb @@ -0,0 +1,18 @@ +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild +easyblock = 'Toolchain' + +name = 'iimpi' +version = '2024a' + +homepage = 'https://software.intel.com/parallel-studio-xe' +description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" + +toolchain = SYSTEM + +local_comp_ver = '2024.2.0' +dependencies = [ + ('intel-compilers', local_comp_ver), + ('impi', '2021.13.0', '', ('intel-compilers', local_comp_ver)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/ilastik-napari/ilastik-napari-0.2.4-foss-2023a.eb b/easybuild/easyconfigs/i/ilastik-napari/ilastik-napari-0.2.4-foss-2023a.eb new file mode 100644 index 000000000000..64e20f93f388 --- /dev/null +++ b/easybuild/easyconfigs/i/ilastik-napari/ilastik-napari-0.2.4-foss-2023a.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonBundle' + +name = 'ilastik-napari' +version = '0.2.4' + +homepage = 'https://github.com/ilastik/ilastik-napari/' +description = "Napari plugin for interactive pixel classification." + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('napari', '0.4.18'), + ('QtPy', '2.4.1'), + ('scikit-learn', '1.3.1'), + ('numba', '0.58.1'), + ('fastfilters', '0.3'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('sparse', '0.15.4', { + 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'checksums': ['76ec76fee2aee82a84eb97155dd530a9644e3b1fdea2406bc4b454698b36d938'], + }), + (name, version, { + 'source_tmpl': 'ilastik_napari-%(version)s.tar.gz', + 'modulename': 'ilastik', + 'checksums': ['8e971a70389f9257eaca7561637301f996f316fdff2cb223c5828d162970bec4'], + }), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/i/imageio/imageio-2.34.1-gfbf-2023b.eb b/easybuild/easyconfigs/i/imageio/imageio-2.34.1-gfbf-2023b.eb new file mode 100644 index 000000000000..8f602262f3de --- /dev/null +++ b/easybuild/easyconfigs/i/imageio/imageio-2.34.1-gfbf-2023b.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'imageio' +version = '2.34.1' + +homepage = 'https://imageio.github.io' +description = """Imageio is a Python library that provides an easy interface to read and write a wide range of + image data, including animated images, video, volumetric data, and scientific formats.""" + +toolchain = {'name': 'gfbf', 'version': '2023b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['f13eb76e4922f936ac4a7fec77ce8a783e63b93543d4ea3e40793a6cabd9ac7d'] + +dependencies = [ + ('Python', '3.11.5'), + ('matplotlib', '3.8.2'), + ('Pillow', '10.2.0'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.12.3-gfbf-2023a.eb b/easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.12.3-gfbf-2023a.eb new file mode 100644 index 000000000000..4881e78a0e71 --- /dev/null +++ b/easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.12.3-gfbf-2023a.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonBundle' + +name = 'imbalanced-learn' +version = '0.12.3' + +homepage = 'https://github.com/scikit-learn-contrib/imbalanced-learn' +description = """imbalanced-learn is a Python package offering a number of re-sampling techniques commonly used in + datasets showing strong between-class imbalance.""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('scikit-learn', '1.3.1'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + (name, version, { + 'modulename': 'imblearn', + 'checksums': ['5b00796a01419e9102bd425e27c319d58d1f6cf2dfa751e02ed7f4edf67c3c1b'], + }), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2024.2.0-iimpi-2024a.eb b/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2024.2.0-iimpi-2024a.eb new file mode 100644 index 000000000000..b26ab65f4521 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2024.2.0-iimpi-2024a.eb @@ -0,0 +1,11 @@ +name = 'imkl-FFTW' +version = '2024.2.0' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/onemkl.html' +description = "FFTW interfaces using Intel oneAPI Math Kernel Library" + +toolchain = {'name': 'iimpi', 'version': '2024a'} + +dependencies = [('imkl', version, '', SYSTEM)] + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-2018.1.163-iccifort-2018.1.163-GCC-6.4.0-2.28-serial.eb b/easybuild/easyconfigs/i/imkl/imkl-2018.1.163-iccifort-2018.1.163-GCC-6.4.0-2.28-serial.eb index 65486c1a5222..1af220dba70e 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2018.1.163-iccifort-2018.1.163-GCC-6.4.0-2.28-serial.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2018.1.163-iccifort-2018.1.163-GCC-6.4.0-2.28-serial.eb @@ -12,7 +12,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iccifort', 'version': '2018.1.163-GCC-6.4.0-2.28'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12384/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/12384/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['f6dc263fc6f3c350979740a13de1b1e8745d9ba0d0f067ece503483b9189c2ca'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2018.1.163-iimpi-2018a.eb b/easybuild/easyconfigs/i/imkl/imkl-2018.1.163-iimpi-2018a.eb index 770acb76d877..a90fc9aaaac1 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2018.1.163-iimpi-2018a.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2018.1.163-iimpi-2018a.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpi', 'version': '2018a'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12384/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/12384/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['f6dc263fc6f3c350979740a13de1b1e8745d9ba0d0f067ece503483b9189c2ca'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-gimpi-2018b.eb b/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-gimpi-2018b.eb index f340d755ee22..c873144967bb 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-gimpi-2018b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-gimpi-2018b.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'gimpi', 'version': '2018b'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13005/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13005/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['108d59c0927e58ce8c314db6c2b48ee331c3798f7102725f425d6884eb6ed241'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-gompi-2018b.eb b/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-gompi-2018b.eb index 6ead35efc9ae..89a3f33d184c 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-gompi-2018b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-gompi-2018b.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'gompi', 'version': '2018b'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13005/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13005/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['108d59c0927e58ce8c314db6c2b48ee331c3798f7102725f425d6884eb6ed241'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-iimpi-2018b.eb b/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-iimpi-2018b.eb index 7f53145d6a31..450dc0082e29 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-iimpi-2018b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-iimpi-2018b.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpi', 'version': '2018b'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13005/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13005/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['108d59c0927e58ce8c314db6c2b48ee331c3798f7102725f425d6884eb6ed241'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-iompi-2018b.eb b/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-iompi-2018b.eb index aeabee4d300a..0fcf2f60e8e8 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-iompi-2018b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-iompi-2018b.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iompi', 'version': '2018b'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13005/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13005/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['108d59c0927e58ce8c314db6c2b48ee331c3798f7102725f425d6884eb6ed241'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2018.4.274-iimpi-2018.04.eb b/easybuild/easyconfigs/i/imkl/imkl-2018.4.274-iimpi-2018.04.eb index 02dba60737e7..7d2dc1809af7 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2018.4.274-iimpi-2018.04.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2018.4.274-iimpi-2018.04.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpi', 'version': '2018.04'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13725/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13725/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['18eb3cde3e6a61a88f25afff25df762a560013f650aaf363f7d3d516a0d04881'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2019.0.117-iimpi-2019.00.eb b/easybuild/easyconfigs/i/imkl/imkl-2019.0.117-iimpi-2019.00.eb index a382ae20ac72..d222e9cd3b31 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2019.0.117-iimpi-2019.00.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2019.0.117-iimpi-2019.00.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpi', 'version': '2019.00'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13575/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13575/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['4e1fe2c705cfc47050064c0d6c4dee1a8c6740ac1c4f64dde9c7511c4989c7ad'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-gompi-2019a.eb b/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-gompi-2019a.eb index aa6a03a69295..ae7e676174ec 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-gompi-2019a.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-gompi-2019a.eb @@ -9,7 +9,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'gompi', 'version': '2019a'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/14895/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/14895/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['5205a460a9c685f7a442868367389b2d0c25e1455346bc6a37c5b8ff90a20fbb'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpi-2019.01.eb b/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpi-2019.01.eb index e63cc1a26955..15e03750772e 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpi-2019.01.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpi-2019.01.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpi', 'version': '2019.01'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/14895/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/14895/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['5205a460a9c685f7a442868367389b2d0c25e1455346bc6a37c5b8ff90a20fbb'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpi-2019a.eb b/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpi-2019a.eb index 782473ec9fa7..dcd07853ae8e 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpi-2019a.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpi-2019a.eb @@ -9,7 +9,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpi', 'version': '2019a'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/14895/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/14895/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['5205a460a9c685f7a442868367389b2d0c25e1455346bc6a37c5b8ff90a20fbb'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpic-2019a.eb b/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpic-2019a.eb index b8fb1ebef4cc..af64b61bfd72 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpic-2019a.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpic-2019a.eb @@ -9,7 +9,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpic', 'version': '2019a'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/14895/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/14895/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['5205a460a9c685f7a442868367389b2d0c25e1455346bc6a37c5b8ff90a20fbb'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iompi-2019.01.eb b/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iompi-2019.01.eb index 3a5e6baedc41..e7a42454f04e 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iompi-2019.01.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iompi-2019.01.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iompi', 'version': '2019.01'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/14895/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/14895/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['5205a460a9c685f7a442868367389b2d0c25e1455346bc6a37c5b8ff90a20fbb'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2019.2.187-iimpi-2019.02.eb b/easybuild/easyconfigs/i/imkl/imkl-2019.2.187-iimpi-2019.02.eb index 645ffaf31a7c..8cd693cc5ec4 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2019.2.187-iimpi-2019.02.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2019.2.187-iimpi-2019.02.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpi', 'version': '2019.02'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15095/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15095/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['2bf004e6b5adb4f956993d6c20ea6ce289bb630314dd501db7f2dd5b9978ed1d'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2019.3.199-iimpi-2019.03.eb b/easybuild/easyconfigs/i/imkl/imkl-2019.3.199-iimpi-2019.03.eb index 2c06461ab97d..8685b03cc912 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2019.3.199-iimpi-2019.03.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2019.3.199-iimpi-2019.03.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpi', 'version': '2019.03'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15275/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15275/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['06de2b54f4812e7c39a118536259c942029fe1d6d8918ad9df558a83c4162b8f'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-gompi-2019b.eb b/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-gompi-2019b.eb index 3c2759d15391..940151b46dc9 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-gompi-2019b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-gompi-2019b.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'gompi', 'version': '2019b'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15816/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15816/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['9995ea4469b05360d509c9705e9309dc983c0a10edc2ae3a5384bc837326737e'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-gompic-2019b.eb b/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-gompic-2019b.eb index 3421505968ce..91ca97f6bc6a 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-gompic-2019b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-gompic-2019b.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'gompic', 'version': '2019b'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15816/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15816/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['9995ea4469b05360d509c9705e9309dc983c0a10edc2ae3a5384bc837326737e'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-iimpi-2019b.eb b/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-iimpi-2019b.eb index d95d740ea28c..61489356fe3e 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-iimpi-2019b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-iimpi-2019b.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpi', 'version': '2019b'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15816/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15816/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['9995ea4469b05360d509c9705e9309dc983c0a10edc2ae3a5384bc837326737e'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-iimpic-2019b.eb b/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-iimpic-2019b.eb index 62cf27a52511..b1e88a55dd3d 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-iimpic-2019b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-iimpic-2019b.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpic', 'version': '2019b'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15816/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15816/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['9995ea4469b05360d509c9705e9309dc983c0a10edc2ae3a5384bc837326737e'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-iompi-2019b.eb b/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-iompi-2019b.eb index 906ad9525cd5..8e7d6fa5ec26 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-iompi-2019b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-iompi-2019b.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iompi', 'version': '2019b'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15816/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15816/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['9995ea4469b05360d509c9705e9309dc983c0a10edc2ae3a5384bc837326737e'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.0.166-iimpi-2020.00.eb b/easybuild/easyconfigs/i/imkl/imkl-2020.0.166-iimpi-2020.00.eb index 610ba0040094..d27b6e673461 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2020.0.166-iimpi-2020.00.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2020.0.166-iimpi-2020.00.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpi', 'version': '2020.00'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16232/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16232/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['f6d92deb3ff10b11ba3df26b2c62bb4f0f7ae43e21905a91d553e58f0f5a8ae0'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-gompi-2020a.eb b/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-gompi-2020a.eb index dcb4894a2a4a..d662fdae1719 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-gompi-2020a.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-gompi-2020a.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'gompi', 'version': '2020a'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16533/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16533/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['082a4be30bf4f6998e4d6e3da815a77560a5e66a68e254d161ab96f07086066d'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iimpi-2020.06-impi-18.5.eb b/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iimpi-2020.06-impi-18.5.eb index 89aac0e15478..a683875dd816 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iimpi-2020.06-impi-18.5.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iimpi-2020.06-impi-18.5.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpi', 'version': '2020.06-impi-18.5'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16533/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16533/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['082a4be30bf4f6998e4d6e3da815a77560a5e66a68e254d161ab96f07086066d'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iimpi-2020a.eb b/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iimpi-2020a.eb index 3111a3509b06..aef431b9b6d7 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iimpi-2020a.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iimpi-2020a.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpi', 'version': '2020a'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16533/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16533/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['082a4be30bf4f6998e4d6e3da815a77560a5e66a68e254d161ab96f07086066d'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iimpic-2020a.eb b/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iimpic-2020a.eb index 3475dab254ac..dbfbc3564558 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iimpic-2020a.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iimpic-2020a.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpic', 'version': '2020a'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16533/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16533/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['082a4be30bf4f6998e4d6e3da815a77560a5e66a68e254d161ab96f07086066d'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iompi-2020a.eb b/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iompi-2020a.eb index 3eca90fc0a24..1f80ac1e253f 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iompi-2020a.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iompi-2020a.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iompi', 'version': '2020a'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16533/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16533/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['082a4be30bf4f6998e4d6e3da815a77560a5e66a68e254d161ab96f07086066d'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-NVHPC-21.2.eb b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-NVHPC-21.2.eb index 75ac380269e6..71a9f0f37b98 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-NVHPC-21.2.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-NVHPC-21.2.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'NVHPC', 'version': '21.2'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16917/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16917/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['2314d46536974dbd08f2a4e4f9e9a155dc7e79e2798c74e7ddfaad00a5917ea5'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-gompi-2020b.eb b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-gompi-2020b.eb index 541c3c12aea2..1526523c7888 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-gompi-2020b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-gompi-2020b.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'gompi', 'version': '2020b'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16917/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16917/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['2314d46536974dbd08f2a4e4f9e9a155dc7e79e2798c74e7ddfaad00a5917ea5'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-gompic-2020b.eb b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-gompic-2020b.eb index e07323d8ee38..570499af77df 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-gompic-2020b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-gompic-2020b.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'gompic', 'version': '2020b'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16917/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16917/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['2314d46536974dbd08f2a4e4f9e9a155dc7e79e2798c74e7ddfaad00a5917ea5'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iimpi-2020b.eb b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iimpi-2020b.eb index e1f7dd0c3fdc..15ccb6b8c779 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iimpi-2020b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iimpi-2020b.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpi', 'version': '2020b'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16917/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16917/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['2314d46536974dbd08f2a4e4f9e9a155dc7e79e2798c74e7ddfaad00a5917ea5'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iimpic-2020b.eb b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iimpic-2020b.eb index a350ab4a6ed4..73aac3a85e76 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iimpic-2020b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iimpic-2020b.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpic', 'version': '2020b'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16917/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16917/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['2314d46536974dbd08f2a4e4f9e9a155dc7e79e2798c74e7ddfaad00a5917ea5'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iompi-2020b.eb b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iompi-2020b.eb index 89d0c991d88a..68e2a157d3dd 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iompi-2020b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iompi-2020b.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iompi', 'version': '2020b'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16917/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16917/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['2314d46536974dbd08f2a4e4f9e9a155dc7e79e2798c74e7ddfaad00a5917ea5'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2021.1.1-iimpi-2020.12.eb b/easybuild/easyconfigs/i/imkl/imkl-2021.1.1-iimpi-2020.12.eb index 737f7462d7d7..363e95f7dc9b 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2021.1.1-iimpi-2020.12.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2021.1.1-iimpi-2020.12.eb @@ -7,7 +7,7 @@ description = "Intel oneAPI Math Kernel Library" toolchain = {'name': 'iimpi', 'version': '2020.12'} # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17402/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/17402/'] sources = ['l_onemkl_p_%(version)s.52_offline.sh'] checksums = ['818b6bd9a6c116f4578cda3151da0612ec9c3ce8b2c8a64730d625ce5b13cc0c'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2021.2.0-gompi-2021a.eb b/easybuild/easyconfigs/i/imkl/imkl-2021.2.0-gompi-2021a.eb index ff7c13049ead..77a41fb58ed7 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2021.2.0-gompi-2021a.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2021.2.0-gompi-2021a.eb @@ -7,7 +7,7 @@ description = "Intel oneAPI Math Kernel Library" toolchain = {'name': 'gompi', 'version': '2021a'} # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/17757/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/17757/'] sources = ['l_onemkl_p_%(version)s.296_offline.sh'] checksums = ['816e9df26ff331d6c0751b86ed5f7d243f9f172e76f14e83b32bf4d1d619dbae'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2021.2.0-iimpi-2021a.eb b/easybuild/easyconfigs/i/imkl/imkl-2021.2.0-iimpi-2021a.eb index aa8f14f2250c..741b626f55c6 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2021.2.0-iimpi-2021a.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2021.2.0-iimpi-2021a.eb @@ -7,7 +7,7 @@ description = "Intel oneAPI Math Kernel Library" toolchain = {'name': 'iimpi', 'version': '2021a'} # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/17757/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/17757/'] sources = ['l_onemkl_p_%(version)s.296_offline.sh'] checksums = ['816e9df26ff331d6c0751b86ed5f7d243f9f172e76f14e83b32bf4d1d619dbae'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2021.2.0-iompi-2021a.eb b/easybuild/easyconfigs/i/imkl/imkl-2021.2.0-iompi-2021a.eb index 60282631f052..2bb82fd33809 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2021.2.0-iompi-2021a.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2021.2.0-iompi-2021a.eb @@ -7,7 +7,7 @@ description = "Intel oneAPI Math Kernel Library" toolchain = {'name': 'iompi', 'version': '2021a'} # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/17757/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/17757/'] sources = ['l_onemkl_p_%(version)s.296_offline.sh'] checksums = ['816e9df26ff331d6c0751b86ed5f7d243f9f172e76f14e83b32bf4d1d619dbae'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2021.3.0-gompi-2021a.eb b/easybuild/easyconfigs/i/imkl/imkl-2021.3.0-gompi-2021a.eb index 07a876f213e2..a4746816d23f 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2021.3.0-gompi-2021a.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2021.3.0-gompi-2021a.eb @@ -10,7 +10,7 @@ description = "Intel oneAPI Math Kernel Library" toolchain = {'name': 'gompi', 'version': '2021a'} # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17901'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/17901'] sources = ['l_onemkl_p_%(version)s.520_offline.sh'] checksums = ['a06e1cdbfd8becc63440b473b153659885f25a6e3c4dcb2907ad9cd0c3ad59ce'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2021.4.0-iompi-2021b.eb b/easybuild/easyconfigs/i/imkl/imkl-2021.4.0-iompi-2021b.eb old mode 100755 new mode 100644 index a6e0651ef645..4f45be5badc2 --- a/easybuild/easyconfigs/i/imkl/imkl-2021.4.0-iompi-2021b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2021.4.0-iompi-2021b.eb @@ -7,7 +7,7 @@ description = "Intel oneAPI Math Kernel Library" toolchain = {'name': 'iompi', 'version': '2021b'} # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18222/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18222/'] sources = ['l_onemkl_p_%(version)s.640_offline.sh'] checksums = ['9ad546f05a421b4f439e8557fd0f2d83d5e299b0d9bd84bdd86be6feba0c3915'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2021.4.0.eb b/easybuild/easyconfigs/i/imkl/imkl-2021.4.0.eb index f3e3040b1ee3..bacd9ba46071 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2021.4.0.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2021.4.0.eb @@ -7,7 +7,7 @@ description = "Intel oneAPI Math Kernel Library" toolchain = SYSTEM # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18222/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18222/'] sources = ['l_onemkl_p_%(version)s.640_offline.sh'] checksums = ['9ad546f05a421b4f439e8557fd0f2d83d5e299b0d9bd84bdd86be6feba0c3915'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2022.0.1.eb b/easybuild/easyconfigs/i/imkl/imkl-2022.0.1.eb index 67a5563ac0b9..c348328e0e41 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2022.0.1.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2022.0.1.eb @@ -7,7 +7,7 @@ description = "Intel oneAPI Math Kernel Library" toolchain = SYSTEM # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18444/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18444/'] sources = ['l_onemkl_p_%(version)s.117_offline.sh'] checksums = ['22afafbe2f3762eca052ac21ec40b845ff2f3646077295c88c2f37f80a0cc160'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2022.1.0-gompi-2022a.eb b/easybuild/easyconfigs/i/imkl/imkl-2022.1.0-gompi-2022a.eb index 2eb923c837ed..955038d0fc18 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2022.1.0-gompi-2022a.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2022.1.0-gompi-2022a.eb @@ -10,7 +10,7 @@ description = "Intel oneAPI Math Kernel Library" toolchain = {'name': 'gompi', 'version': '2022a'} # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18721/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18721/'] sources = ['l_onemkl_p_%(version)s.223_offline.sh'] checksums = ['4b325a3c4c56e52f4ce6c8fbb55d7684adc16425000afc860464c0f29ea4563e'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2022.1.0.eb b/easybuild/easyconfigs/i/imkl/imkl-2022.1.0.eb index c34d533cf35b..b06534438590 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2022.1.0.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2022.1.0.eb @@ -7,7 +7,7 @@ description = "Intel oneAPI Math Kernel Library" toolchain = SYSTEM # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18721/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18721/'] sources = ['l_onemkl_p_%(version)s.223_offline.sh'] checksums = ['4b325a3c4c56e52f4ce6c8fbb55d7684adc16425000afc860464c0f29ea4563e'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2022.2.0.eb b/easybuild/easyconfigs/i/imkl/imkl-2022.2.0.eb index 82776023871b..a3c46807fc64 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2022.2.0.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2022.2.0.eb @@ -7,7 +7,7 @@ description = "Intel oneAPI Math Kernel Library" toolchain = SYSTEM # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18898/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18898/'] sources = ['l_onemkl_p_%(version)s.8748_offline.sh'] checksums = ['07d7caedd4b9f025c6fd439a0d2c2f279b18ecbbb63cadb864f6c63c1ed942db'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2022.2.1.eb b/easybuild/easyconfigs/i/imkl/imkl-2022.2.1.eb index 3daf55958a30..f2a7a15068ee 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2022.2.1.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2022.2.1.eb @@ -7,7 +7,7 @@ description = "Intel oneAPI Math Kernel Library" toolchain = SYSTEM # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/19038/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/19038/'] sources = ['l_onemkl_p_%(version)s.16993_offline.sh'] checksums = ['eedd4b795720de776b1fc5f542ae0fac37ec235cdb567f7c2ee3182e73e3e59d'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2023.0.0.eb b/easybuild/easyconfigs/i/imkl/imkl-2023.0.0.eb index 4e6e5afb3444..f29032bc3dd3 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2023.0.0.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2023.0.0.eb @@ -7,7 +7,7 @@ description = "Intel oneAPI Math Kernel Library" toolchain = SYSTEM # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/19138/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/19138/'] sources = ['l_onemkl_p_%(version)s.25398_offline.sh'] checksums = ['0d61188e91a57bdb575782eb47a05ae99ea8eebefee6b2dfe20c6708e16e9927'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2023.1.0-gompi-2023a.eb b/easybuild/easyconfigs/i/imkl/imkl-2023.1.0-gompi-2023a.eb index 5e4f3cb8b1d5..17ed1c0a2aa4 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2023.1.0-gompi-2023a.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2023.1.0-gompi-2023a.eb @@ -10,7 +10,7 @@ description = "Intel oneAPI Math Kernel Library" toolchain = {'name': 'gompi', 'version': '2023a'} # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18721/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/cd17b7fe-500e-4305-a89b-bd5b42bfd9f8/'] sources = ['l_onemkl_p_%(version)s.46342_offline.sh'] checksums = ['cc28c94cab23c185520b93c5a04f3979d8da6b4c90cee8c0681dd89819d76167'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2024.2.0.eb b/easybuild/easyconfigs/i/imkl/imkl-2024.2.0.eb new file mode 100644 index 000000000000..30331a8a80a1 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-2024.2.0.eb @@ -0,0 +1,18 @@ +name = 'imkl' +version = '2024.2.0' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/onemkl.html' +description = "Intel oneAPI Math Kernel Library" + +toolchain = SYSTEM + +# see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/cdff21a5-6ac7-4b41-a7ec-351b5f9ce8fd'] +sources = ['l_onemkl_p_%(version)s.664_offline.sh'] +checksums = ['f1f46f5352c197a9840e08fc191a879dad79ebf742fe782e386ba8006f262f7a'] + +interfaces = False + +installopts = "--download-cache=%(builddir)s/cache --download-dir=%(builddir)s/download --log-dir=%(builddir)s/log" + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/impi/impi-2018.1.163-iccifort-2018.1.163-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/impi/impi-2018.1.163-iccifort-2018.1.163-GCC-6.4.0-2.28.eb index 21ad001e53c8..a0341a987d6d 100644 --- a/easybuild/easyconfigs/i/impi/impi-2018.1.163-iccifort-2018.1.163-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/impi/impi-2018.1.163-iccifort-2018.1.163-GCC-6.4.0-2.28.eb @@ -8,7 +8,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifort', 'version': '2018.1.163-GCC-6.4.0-2.28'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12405/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/12405/'] sources = ['l_mpi_%(version)s.tgz'] checksums = ['130b11571c3f71af00a722fa8641db5a1552ac343d770a8304216d8f5d00e75c'] diff --git a/easybuild/easyconfigs/i/impi/impi-2018.3.222-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/i/impi/impi-2018.3.222-GCC-7.3.0-2.30.eb index e39879ac218b..60f2eed4dd9c 100644 --- a/easybuild/easyconfigs/i/impi/impi-2018.3.222-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/i/impi/impi-2018.3.222-GCC-7.3.0-2.30.eb @@ -8,7 +8,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'GCC', 'version': '7.3.0-2.30'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13063/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13063/'] sources = ['l_mpi_%(version)s.tgz'] checksums = ['5021d14b344fc794e89f146e4d53d70184d7048610895d7a6a1e8ac0cf258999'] diff --git a/easybuild/easyconfigs/i/impi/impi-2018.3.222-iccifort-2018.3.222-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/i/impi/impi-2018.3.222-iccifort-2018.3.222-GCC-7.3.0-2.30.eb index f4e9e1a638f1..0fc63f042f87 100644 --- a/easybuild/easyconfigs/i/impi/impi-2018.3.222-iccifort-2018.3.222-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/i/impi/impi-2018.3.222-iccifort-2018.3.222-GCC-7.3.0-2.30.eb @@ -8,7 +8,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifort', 'version': '2018.3.222-GCC-7.3.0-2.30'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13063/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13063/'] sources = ['l_mpi_%(version)s.tgz'] checksums = ['5021d14b344fc794e89f146e4d53d70184d7048610895d7a6a1e8ac0cf258999'] diff --git a/easybuild/easyconfigs/i/impi/impi-2018.4.274-iccifort-2018.5.274-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/i/impi/impi-2018.4.274-iccifort-2018.5.274-GCC-7.3.0-2.30.eb index 060befc0a5a5..75004db76a81 100644 --- a/easybuild/easyconfigs/i/impi/impi-2018.4.274-iccifort-2018.5.274-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/i/impi/impi-2018.4.274-iccifort-2018.5.274-GCC-7.3.0-2.30.eb @@ -8,7 +8,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifort', 'version': '2018.5.274-GCC-7.3.0-2.30'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13651/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13651/'] sources = ['l_mpi_%(version)s.tgz'] checksums = ['a1114b3eb4149c2f108964b83cad02150d619e50032059d119ac4ffc9d5dd8e0'] diff --git a/easybuild/easyconfigs/i/impi/impi-2018.4.274-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/i/impi/impi-2018.4.274-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb index e6c3602e1e38..d4574181af95 100644 --- a/easybuild/easyconfigs/i/impi/impi-2018.4.274-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/i/impi/impi-2018.4.274-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb @@ -6,7 +6,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifort', 'version': '2019.1.144-GCC-8.2.0-2.31.1'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13651/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13651/'] sources = ['l_mpi_%(version)s.tgz'] checksums = ['a1114b3eb4149c2f108964b83cad02150d619e50032059d119ac4ffc9d5dd8e0'] diff --git a/easybuild/easyconfigs/i/impi/impi-2018.4.274-iccifortcuda-2019a.eb b/easybuild/easyconfigs/i/impi/impi-2018.4.274-iccifortcuda-2019a.eb index 137bf491a274..c28ff1e7e55f 100644 --- a/easybuild/easyconfigs/i/impi/impi-2018.4.274-iccifortcuda-2019a.eb +++ b/easybuild/easyconfigs/i/impi/impi-2018.4.274-iccifortcuda-2019a.eb @@ -6,7 +6,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifortcuda', 'version': '2019a'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13651/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13651/'] sources = ['l_mpi_%(version)s.tgz'] checksums = ['a1114b3eb4149c2f108964b83cad02150d619e50032059d119ac4ffc9d5dd8e0'] diff --git a/easybuild/easyconfigs/i/impi/impi-2018.5.288-iccifort-2019.5.281.eb b/easybuild/easyconfigs/i/impi/impi-2018.5.288-iccifort-2019.5.281.eb index 8f89b212fa40..4cb68a33fc8a 100644 --- a/easybuild/easyconfigs/i/impi/impi-2018.5.288-iccifort-2019.5.281.eb +++ b/easybuild/easyconfigs/i/impi/impi-2018.5.288-iccifort-2019.5.281.eb @@ -8,7 +8,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifort', 'version': '2019.5.281'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15614/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15614/'] sources = ['l_mpi_%(version)s.tgz'] checksums = ['3198257c19e82cd327d739b10120933e0547da8cddf8a8005677717326236796'] diff --git a/easybuild/easyconfigs/i/impi/impi-2018.5.288-iccifort-2020.1.217.eb b/easybuild/easyconfigs/i/impi/impi-2018.5.288-iccifort-2020.1.217.eb index 4c7b3a6b0df9..e27d2ec5b552 100644 --- a/easybuild/easyconfigs/i/impi/impi-2018.5.288-iccifort-2020.1.217.eb +++ b/easybuild/easyconfigs/i/impi/impi-2018.5.288-iccifort-2020.1.217.eb @@ -8,7 +8,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifort', 'version': '2020.1.217'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15614/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15614/'] sources = ['l_mpi_%(version)s.tgz'] checksums = ['3198257c19e82cd327d739b10120933e0547da8cddf8a8005677717326236796'] diff --git a/easybuild/easyconfigs/i/impi/impi-2018.5.288-iccifortcuda-2019b.eb b/easybuild/easyconfigs/i/impi/impi-2018.5.288-iccifortcuda-2019b.eb index 02e2ace82513..2f959f48e46b 100644 --- a/easybuild/easyconfigs/i/impi/impi-2018.5.288-iccifortcuda-2019b.eb +++ b/easybuild/easyconfigs/i/impi/impi-2018.5.288-iccifortcuda-2019b.eb @@ -8,7 +8,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifortcuda', 'version': '2019b'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15614/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15614/'] sources = ['l_mpi_%(version)s.tgz'] checksums = ['3198257c19e82cd327d739b10120933e0547da8cddf8a8005677717326236796'] diff --git a/easybuild/easyconfigs/i/impi/impi-2019.0.117-iccifort-2019.0.117-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/i/impi/impi-2019.0.117-iccifort-2019.0.117-GCC-8.2.0-2.31.1.eb index 2f60b4227038..77755c776205 100644 --- a/easybuild/easyconfigs/i/impi/impi-2019.0.117-iccifort-2019.0.117-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/i/impi/impi-2019.0.117-iccifort-2019.0.117-GCC-8.2.0-2.31.1.eb @@ -8,7 +8,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifort', 'version': '2019.0.117-GCC-8.2.0-2.31.1'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13584/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13584/'] sources = ['l_mpi_%(version)s.tgz'] checksums = ['dfb403f49c1af61b337aa952b71289c7548c3a79c32c57865eab0ea0f0e1bc08'] diff --git a/easybuild/easyconfigs/i/impi/impi-2019.1.144-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/i/impi/impi-2019.1.144-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb index 8e2ed0b39808..6a222b3ed18e 100644 --- a/easybuild/easyconfigs/i/impi/impi-2019.1.144-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/i/impi/impi-2019.1.144-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb @@ -8,7 +8,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifort', 'version': '2019.1.144-GCC-8.2.0-2.31.1'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/14879/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/14879/'] sources = ['l_mpi_%(version)s.tgz'] checksums = ['dac86a5db6b86503313742b17535856a432955604f7103cb4549a9bfc256c3cd'] diff --git a/easybuild/easyconfigs/i/impi/impi-2019.12.320-iccifort-2020.4.304.eb b/easybuild/easyconfigs/i/impi/impi-2019.12.320-iccifort-2020.4.304.eb index a5ba5409ff06..2bf8b19fb293 100644 --- a/easybuild/easyconfigs/i/impi/impi-2019.12.320-iccifort-2020.4.304.eb +++ b/easybuild/easyconfigs/i/impi/impi-2019.12.320-iccifort-2020.4.304.eb @@ -8,7 +8,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifort', 'version': '2020.4.304'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/17836/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/17836/'] sources = ['l_mpi_%(version)s.tgz'] checksums = ['8108fbf2353a9f1926036bb67647b65c0e4933a3eb66e1dc933960e5b055f320'] diff --git a/easybuild/easyconfigs/i/impi/impi-2019.2.187-iccifort-2019.2.187-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/i/impi/impi-2019.2.187-iccifort-2019.2.187-GCC-8.2.0-2.31.1.eb index 7cdc6aca4295..5f75ad2ec682 100644 --- a/easybuild/easyconfigs/i/impi/impi-2019.2.187-iccifort-2019.2.187-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/i/impi/impi-2019.2.187-iccifort-2019.2.187-GCC-8.2.0-2.31.1.eb @@ -8,7 +8,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifort', 'version': '2019.2.187-GCC-8.2.0-2.31.1'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15040/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15040/'] sources = ['l_mpi_%(version)s.tgz'] checksums = ['6a3305933b5ef9e3f7de969e394c91620f3fa4bb815a4f439577739d04778b20'] diff --git a/easybuild/easyconfigs/i/impi/impi-2019.3.199-iccifort-2019.3.199-GCC-8.3.0-2.32.eb b/easybuild/easyconfigs/i/impi/impi-2019.3.199-iccifort-2019.3.199-GCC-8.3.0-2.32.eb index c0b1f565c0a6..cb1ec1f179c4 100644 --- a/easybuild/easyconfigs/i/impi/impi-2019.3.199-iccifort-2019.3.199-GCC-8.3.0-2.32.eb +++ b/easybuild/easyconfigs/i/impi/impi-2019.3.199-iccifort-2019.3.199-GCC-8.3.0-2.32.eb @@ -8,7 +8,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifort', 'version': '2019.3.199-GCC-8.3.0-2.32'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15260/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15260/'] sources = ['l_mpi_%(version)s.tgz'] checksums = ['5304346c863f64de797250eeb14f51c5cfc8212ff20813b124f20e7666286990'] diff --git a/easybuild/easyconfigs/i/impi/impi-2019.6.166-iccifort-2020.0.166-GCC-9.2.0.eb b/easybuild/easyconfigs/i/impi/impi-2019.6.166-iccifort-2020.0.166-GCC-9.2.0.eb index e19a15d6e333..49f0fa7a8d72 100644 --- a/easybuild/easyconfigs/i/impi/impi-2019.6.166-iccifort-2020.0.166-GCC-9.2.0.eb +++ b/easybuild/easyconfigs/i/impi/impi-2019.6.166-iccifort-2020.0.166-GCC-9.2.0.eb @@ -8,7 +8,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifort', 'version': '2020.0.166-GCC-9.2.0'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16120/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16120/'] sources = ['l_mpi_%(version)s.tgz'] checksums = ['119be69f1117c93a9e5e9b8b4643918e55d2a55a78ad9567f77d16cdaf18cd6e'] diff --git a/easybuild/easyconfigs/i/impi/impi-2019.7.217-iccifort-2020.1.217.eb b/easybuild/easyconfigs/i/impi/impi-2019.7.217-iccifort-2020.1.217.eb index d0ad0188c0de..07f8323810ce 100644 --- a/easybuild/easyconfigs/i/impi/impi-2019.7.217-iccifort-2020.1.217.eb +++ b/easybuild/easyconfigs/i/impi/impi-2019.7.217-iccifort-2020.1.217.eb @@ -8,7 +8,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifort', 'version': '2020.1.217'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16546/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16546/'] sources = ['l_mpi_%(version)s.tgz'] checksums = ['90383b0023f84ac003a55d8bb29dbcf0c639f43a25a2d8d8698a16e770ac9c07'] diff --git a/easybuild/easyconfigs/i/impi/impi-2019.7.217-iccifortcuda-2020a.eb b/easybuild/easyconfigs/i/impi/impi-2019.7.217-iccifortcuda-2020a.eb index 557e0a8eab1e..8a5646c25c19 100644 --- a/easybuild/easyconfigs/i/impi/impi-2019.7.217-iccifortcuda-2020a.eb +++ b/easybuild/easyconfigs/i/impi/impi-2019.7.217-iccifortcuda-2020a.eb @@ -8,7 +8,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifortcuda', 'version': '2020a'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16546/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16546/'] sources = ['l_mpi_%(version)s.tgz'] checksums = ['90383b0023f84ac003a55d8bb29dbcf0c639f43a25a2d8d8698a16e770ac9c07'] diff --git a/easybuild/easyconfigs/i/impi/impi-2019.9.304-iccifort-2020.4.304.eb b/easybuild/easyconfigs/i/impi/impi-2019.9.304-iccifort-2020.4.304.eb index d4a9ef76ae4a..d723d12dc1c2 100644 --- a/easybuild/easyconfigs/i/impi/impi-2019.9.304-iccifort-2020.4.304.eb +++ b/easybuild/easyconfigs/i/impi/impi-2019.9.304-iccifort-2020.4.304.eb @@ -8,7 +8,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifort', 'version': '2020.4.304'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/17263/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/17263/'] sources = ['l_mpi_%(version)s.tgz'] checksums = ['618a5dc2de54306645e6428c5eb7d267b54b11b5a83dfbcad7d0f9e0d90bb2e7'] diff --git a/easybuild/easyconfigs/i/impi/impi-2019.9.304-iccifortcuda-2020b.eb b/easybuild/easyconfigs/i/impi/impi-2019.9.304-iccifortcuda-2020b.eb index 3305cf60a8df..7082d103ec8d 100644 --- a/easybuild/easyconfigs/i/impi/impi-2019.9.304-iccifortcuda-2020b.eb +++ b/easybuild/easyconfigs/i/impi/impi-2019.9.304-iccifortcuda-2020b.eb @@ -8,7 +8,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifortcuda', 'version': '2020b'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/17263/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/17263/'] sources = ['l_mpi_%(version)s.tgz'] checksums = ['618a5dc2de54306645e6428c5eb7d267b54b11b5a83dfbcad7d0f9e0d90bb2e7'] diff --git a/easybuild/easyconfigs/i/impi/impi-2021.1.1-intel-compilers-2021.1.2.eb b/easybuild/easyconfigs/i/impi/impi-2021.1.1-intel-compilers-2021.1.2.eb index 1a0fbe3b0357..d8a92d6db7ea 100644 --- a/easybuild/easyconfigs/i/impi/impi-2021.1.1-intel-compilers-2021.1.2.eb +++ b/easybuild/easyconfigs/i/impi/impi-2021.1.1-intel-compilers-2021.1.2.eb @@ -7,7 +7,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'intel-compilers', 'version': '2021.1.2'} # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17397/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/17397/'] sources = ['l_mpi_oneapi_p_%(version)s.76_offline.sh'] checksums = ['8b7693a156c6fc6269637bef586a8fd3ea6610cac2aae4e7f48c1fbb601625fe'] diff --git a/easybuild/easyconfigs/i/impi/impi-2021.13.0-intel-compilers-2024.2.0.eb b/easybuild/easyconfigs/i/impi/impi-2021.13.0-intel-compilers-2024.2.0.eb new file mode 100644 index 000000000000..2e99bc6c0d8a --- /dev/null +++ b/easybuild/easyconfigs/i/impi/impi-2021.13.0-intel-compilers-2024.2.0.eb @@ -0,0 +1,16 @@ +name = 'impi' +version = '2021.13.0' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/mpi-library.html' +description = "Intel MPI Library, compatible with MPICH ABI" + +toolchain = {'name': 'intel-compilers', 'version': '2024.2.0'} + +# see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/9f84e1e8-11b2-4bd1-8512-3e3343585956'] +sources = ['l_mpi_oneapi_p_%(version)s.719_offline.sh'] +checksums = ['5e23cf495c919e17032577e3059438f632297ee63f2cdb906a2547298823cc64'] + +dependencies = [('UCX', '1.16.0')] + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-2021.2.0-intel-compilers-2021.2.0.eb b/easybuild/easyconfigs/i/impi/impi-2021.2.0-intel-compilers-2021.2.0.eb index 345fd82fc3dc..ecd3c9521f14 100644 --- a/easybuild/easyconfigs/i/impi/impi-2021.2.0-intel-compilers-2021.2.0.eb +++ b/easybuild/easyconfigs/i/impi/impi-2021.2.0-intel-compilers-2021.2.0.eb @@ -7,7 +7,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'intel-compilers', 'version': '2021.2.0'} # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17729/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/17729/'] sources = ['l_mpi_oneapi_p_%(version)s.215_offline.sh'] checksums = ['d0d4cdd11edaff2e7285e38f537defccff38e37a3067c02f4af43a3629ad4aa3'] diff --git a/easybuild/easyconfigs/i/impi/impi-2021.3.0-intel-compilers-2021.3.0.eb b/easybuild/easyconfigs/i/impi/impi-2021.3.0-intel-compilers-2021.3.0.eb index 8a7368219261..1507acd54130 100644 --- a/easybuild/easyconfigs/i/impi/impi-2021.3.0-intel-compilers-2021.3.0.eb +++ b/easybuild/easyconfigs/i/impi/impi-2021.3.0-intel-compilers-2021.3.0.eb @@ -10,7 +10,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'intel-compilers', 'version': '2021.3.0'} # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17947'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/17947'] sources = ['l_mpi_oneapi_p_%(version)s.294_offline.sh'] checksums = ['04c48f864ee4c723b1b4ca62f2bea8c04d5d7e3de19171fd62b17868bc79bc36'] diff --git a/easybuild/easyconfigs/i/impi/impi-2021.4.0-intel-compilers-2021.4.0.eb b/easybuild/easyconfigs/i/impi/impi-2021.4.0-intel-compilers-2021.4.0.eb index a0c8a98edd87..24180258119c 100644 --- a/easybuild/easyconfigs/i/impi/impi-2021.4.0-intel-compilers-2021.4.0.eb +++ b/easybuild/easyconfigs/i/impi/impi-2021.4.0-intel-compilers-2021.4.0.eb @@ -7,7 +7,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'intel-compilers', 'version': '2021.4.0'} # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18186/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18186/'] sources = ['l_mpi_oneapi_p_%(version)s.441_offline.sh'] checksums = ['cc4b7072c61d0bd02b1c431b22d2ea3b84b967b59d2e587e77a9e7b2c24f2a29'] diff --git a/easybuild/easyconfigs/i/impi/impi-2021.5.0-intel-compilers-2022.0.1.eb b/easybuild/easyconfigs/i/impi/impi-2021.5.0-intel-compilers-2022.0.1.eb index bee008101999..ea941c35ab22 100644 --- a/easybuild/easyconfigs/i/impi/impi-2021.5.0-intel-compilers-2022.0.1.eb +++ b/easybuild/easyconfigs/i/impi/impi-2021.5.0-intel-compilers-2022.0.1.eb @@ -7,7 +7,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'intel-compilers', 'version': '2022.0.1'} # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18370/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18370/'] sources = ['l_mpi_oneapi_p_%(version)s.495_offline.sh'] checksums = ['3aae53fe77f7c6aac7a32b299c25d6ca9a00ba4e2d512a26edd90811e59e7471'] diff --git a/easybuild/easyconfigs/i/impi/impi-2021.6.0-intel-compilers-2022.1.0.eb b/easybuild/easyconfigs/i/impi/impi-2021.6.0-intel-compilers-2022.1.0.eb index b1d328caa627..288c103cd032 100644 --- a/easybuild/easyconfigs/i/impi/impi-2021.6.0-intel-compilers-2022.1.0.eb +++ b/easybuild/easyconfigs/i/impi/impi-2021.6.0-intel-compilers-2022.1.0.eb @@ -7,7 +7,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'intel-compilers', 'version': '2022.1.0'} # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18714/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18714/'] sources = ['l_mpi_oneapi_p_%(version)s.602_offline.sh'] checksums = ['e85db63788c434d43c1378e5e2bf7927a75d11aee8e6b78ee0d933da920977a6'] diff --git a/easybuild/easyconfigs/i/impi/impi-2021.7.0-intel-compilers-2022.2.0.eb b/easybuild/easyconfigs/i/impi/impi-2021.7.0-intel-compilers-2022.2.0.eb index 8f400fabac49..2df8a69062f2 100644 --- a/easybuild/easyconfigs/i/impi/impi-2021.7.0-intel-compilers-2022.2.0.eb +++ b/easybuild/easyconfigs/i/impi/impi-2021.7.0-intel-compilers-2022.2.0.eb @@ -7,7 +7,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'intel-compilers', 'version': '2022.2.0'} # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18926/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18926/'] sources = ['l_mpi_oneapi_p_%(version)s.8711_offline.sh'] checksums = ['4eb1e1487b67b98857bc9b7b37bcac4998e0aa6d1b892b2c87b003bf84fb38e9'] diff --git a/easybuild/easyconfigs/i/impi/impi-2021.7.1-intel-compilers-2022.2.1.eb b/easybuild/easyconfigs/i/impi/impi-2021.7.1-intel-compilers-2022.2.1.eb index 68aeb9beb636..aa2976fafaf7 100644 --- a/easybuild/easyconfigs/i/impi/impi-2021.7.1-intel-compilers-2022.2.1.eb +++ b/easybuild/easyconfigs/i/impi/impi-2021.7.1-intel-compilers-2022.2.1.eb @@ -7,7 +7,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'intel-compilers', 'version': '2022.2.1'} # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/19010/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/19010/'] sources = ['l_mpi_oneapi_p_%(version)s.16815_offline.sh'] checksums = ['90e7804f2367d457cd4cbf7aa29f1c5676287aa9b34f93e7c9a19e4b8583fff7'] diff --git a/easybuild/easyconfigs/i/impi/impi-2021.8.0-intel-compilers-2023.0.0.eb b/easybuild/easyconfigs/i/impi/impi-2021.8.0-intel-compilers-2023.0.0.eb index 86153bb28f51..89dce35e1f20 100644 --- a/easybuild/easyconfigs/i/impi/impi-2021.8.0-intel-compilers-2023.0.0.eb +++ b/easybuild/easyconfigs/i/impi/impi-2021.8.0-intel-compilers-2023.0.0.eb @@ -7,7 +7,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'intel-compilers', 'version': '2023.0.0'} # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/19131/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/19131/'] sources = ['l_mpi_oneapi_p_%(version)s.25329_offline.sh'] checksums = ['0fcb1171fc42fd4b2d863ae474c0b0f656b0fa1fdc1df435aa851ccd6d1eaaf7'] diff --git a/easybuild/easyconfigs/i/inferCNV/inferCNV-1.21.0-foss-2023a-R-4.3.2.eb b/easybuild/easyconfigs/i/inferCNV/inferCNV-1.21.0-foss-2023a-R-4.3.2.eb new file mode 100644 index 000000000000..7404bfe1502c --- /dev/null +++ b/easybuild/easyconfigs/i/inferCNV/inferCNV-1.21.0-foss-2023a-R-4.3.2.eb @@ -0,0 +1,59 @@ +easyblock = 'Bundle' + +name = 'inferCNV' +version = '1.21.0' +versionsuffix = '-R-%(rver)s' +local_biocver = '3.18' +local_commit = '124eec089e5d9ab5a2a2352461d03db6cdcf0ea0' +github_account = 'broadinstitute' + +homepage = 'https://github.com/broadinstitute/inferCNV/wiki' +description = """InferCNV is used to explore tumor single cell RNA-Seq data to identify evidence + for somatic large-scale chromosomal copy number alterations, such as gains or + deletions of entire chromosomes or large segments of chromosomes.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('R', '4.3.2'), + ('R-bundle-Bioconductor', local_biocver, '-R-%(rver)s'), + ('rjags', '4-15', '-R-%(rver)s'), +] + +exts_default_options = { + 'source_urls': [ + 'https://bioconductor.org/packages/release/bioc/src/contrib/', # current version of packages + 'https://bioconductor.org/packages/%s/bioc/src/contrib/' % local_biocver, + 'https://bioconductor.org/packages/%s/bioc/src/contrib/Archive/%%(name)s' % local_biocver, + 'https://bioconductor.org/packages/%s/data/annotation/src/contrib/' % local_biocver, + 'https://bioconductor.org/packages/%s/data/experiment/src/contrib/' % local_biocver, + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz' +} + +exts_defaultclass = 'RPackage' + +exts_list = [ + ('phyclust', '0.1-34', { + 'checksums': ['d2047030e9f24c5dc8bbb378867fbcb8e71d1f1c2ab77e9285f79f670568f5f3'], + }), + (name, version, { + 'modulename': '%(namelower)s', + 'source_urls': ['https://github.com/%(github_account)s/%(name)s/archive'], + 'sources': [{'download_filename': '%s.tar.gz' % local_commit, 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['c8886c0a7c292e28a5fb0acaab3ae00eb2b3906aa0a1d146d5931819a37daefb'], + }), +] + +modextrapaths = {'R_LIBS_SITE': ''} + +sanity_check_paths = { + 'files': [], + 'dirs': ['infercnv'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.1.2.eb b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.1.2.eb index 820a237e44d8..67a5c1f57012 100644 --- a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.1.2.eb +++ b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.1.2.eb @@ -9,11 +9,11 @@ toolchain = SYSTEM # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html sources = [ { - 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17513/'], + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/17513/'], 'filename': 'l_dpcpp-cpp-compiler_p_%(version)s.63_offline.sh', }, { - 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17508/'], + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/17508/'], 'filename': 'l_fortran-compiler_p_%(version)s.62_offline.sh', }, ] diff --git a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.2.0.eb b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.2.0.eb index 4fe1af0da995..e4986d623f0d 100644 --- a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.2.0.eb +++ b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.2.0.eb @@ -9,11 +9,11 @@ toolchain = SYSTEM # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html sources = [ { - 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17749/'], + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/17749/'], 'filename': 'l_dpcpp-cpp-compiler_p_%(version)s.118_offline.sh', }, { - 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17756/'], + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/17756/'], 'filename': 'l_fortran-compiler_p_%(version)s.136_offline.sh', }, ] diff --git a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.3.0.eb b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.3.0.eb index efcc5a7498b3..cececeebef0a 100644 --- a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.3.0.eb +++ b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.3.0.eb @@ -12,11 +12,11 @@ toolchain = SYSTEM # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html sources = [ { - 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17928/'], + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/17928/'], 'filename': 'l_dpcpp-cpp-compiler_p_%(version)s.3168_offline.sh', }, { - 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17959/'], + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/17959/'], 'filename': 'l_fortran-compiler_p_%(version)s.3168_offline.sh', }, ] diff --git a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.4.0.eb b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.4.0.eb index b12d0b8bb3c7..977bf5ced0ef 100644 --- a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.4.0.eb +++ b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.4.0.eb @@ -9,11 +9,11 @@ toolchain = SYSTEM # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html sources = [ { - 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18209/'], + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18209/'], 'filename': 'l_dpcpp-cpp-compiler_p_%(version)s.3201_offline.sh', }, { - 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18210/'], + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18210/'], 'filename': 'l_fortran-compiler_p_%(version)s.3224_offline.sh', }, ] diff --git a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.0.1.eb b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.0.1.eb index 56c8e9b5da4d..967197cdfd74 100644 --- a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.0.1.eb +++ b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.0.1.eb @@ -9,11 +9,11 @@ toolchain = SYSTEM # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html sources = [ { - 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18435/'], + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18435/'], 'filename': 'l_dpcpp-cpp-compiler_p_%(version)s.71_offline.sh', }, { - 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18436/'], + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18436/'], 'filename': 'l_fortran-compiler_p_%(version)s.70_offline.sh', }, ] diff --git a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.0.2.eb b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.0.2.eb index b54023cfe84a..011509935b00 100644 --- a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.0.2.eb +++ b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.0.2.eb @@ -9,11 +9,11 @@ toolchain = SYSTEM # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html sources = [ { - 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18478/'], + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18478/'], 'filename': 'l_dpcpp-cpp-compiler_p_%(version)s.84_offline.sh', }, { - 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18481/'], + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18481/'], 'filename': 'l_fortran-compiler_p_%(version)s.83_offline.sh', }, ] diff --git a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.1.0.eb b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.1.0.eb index f25617230acb..92ac06db4923 100644 --- a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.1.0.eb +++ b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.1.0.eb @@ -9,11 +9,11 @@ toolchain = SYSTEM # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html sources = [ { - 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18717/'], + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18717/'], 'filename': 'l_dpcpp-cpp-compiler_p_%(version)s.137_offline.sh', }, { - 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18703/'], + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18703/'], 'filename': 'l_fortran-compiler_p_%(version)s.134_offline.sh', }, ] diff --git a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.2.0.eb b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.2.0.eb index 17262278b137..8c1390dae954 100644 --- a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.2.0.eb +++ b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.2.0.eb @@ -9,11 +9,11 @@ toolchain = SYSTEM # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html sources = [ { - 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18849/'], + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18849/'], 'filename': 'l_dpcpp-cpp-compiler_p_%(version)s.8772_offline.sh', }, { - 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18909/'], + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18909/'], 'filename': 'l_fortran-compiler_p_%(version)s.8773_offline.sh', }, ] diff --git a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.2.1.eb b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.2.1.eb index a6ae81701053..e67292301d5c 100644 --- a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.2.1.eb +++ b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.2.1.eb @@ -9,11 +9,11 @@ toolchain = SYSTEM # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html sources = [ { - 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/19030/'], + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/19030/'], 'filename': 'l_dpcpp-cpp-compiler_p_%(version)s.16991_offline.sh', }, { - 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18998/'], + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18998/'], 'filename': 'l_fortran-compiler_p_%(version)s.16992_offline.sh', }, ] diff --git a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2023.0.0.eb b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2023.0.0.eb index 8d97d1ec3e5e..f1e9b21f0096 100644 --- a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2023.0.0.eb +++ b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2023.0.0.eb @@ -9,11 +9,11 @@ toolchain = SYSTEM # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html sources = [ { - 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/19123/'], + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/19123/'], 'filename': 'l_dpcpp-cpp-compiler_p_%(version)s.25393_offline.sh', }, { - 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/19105/'], + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/19105/'], 'filename': 'l_fortran-compiler_p_%(version)s.25394_offline.sh', }, ] diff --git a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2024.2.0.eb b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2024.2.0.eb new file mode 100644 index 000000000000..90e271fe60a1 --- /dev/null +++ b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2024.2.0.eb @@ -0,0 +1,37 @@ +name = 'intel-compilers' +version = '2024.2.0' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/hpc-toolkit.html' +description = "Intel C, C++ & Fortran compilers (classic and oneAPI)" + +toolchain = SYSTEM + +# see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html +sources = [ + { + 'source_urls': [ + 'https://registrationcenter-download.intel.com/akdlm/IRC_NAS/6780ac84-6256-4b59-a647-330eb65f32b6/' + ], + 'filename': 'l_dpcpp-cpp-compiler_p_%(version)s.495_offline.sh', + }, + { + 'source_urls': [ + 'https://registrationcenter-download.intel.com/akdlm/IRC_NAS/801143de-6c01-4181-9911-57e00fe40181/' + ], + 'filename': 'l_fortran-compiler_p_%(version)s.426_offline.sh', + }, +] +checksums = [ + {'l_dpcpp-cpp-compiler_p_2024.2.0.495_offline.sh': + '9463aa979314d2acc51472d414ffcee032e9869ca85ac6ff4c71d39500e5173d'}, + {'l_fortran-compiler_p_2024.2.0.426_offline.sh': + 'fd19a302662b2f86f76fc115ef53a69f16488080278dba4c573cc705f3a52ffa'}, +] + +local_gccver = '13.3.0' +dependencies = [ + ('GCCcore', local_gccver), + ('binutils', '2.42', '', ('GCCcore', local_gccver)), +] + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/intel/intel-2024a.eb b/easybuild/easyconfigs/i/intel/intel-2024a.eb new file mode 100644 index 000000000000..7b08707e0fc8 --- /dev/null +++ b/easybuild/easyconfigs/i/intel/intel-2024a.eb @@ -0,0 +1,22 @@ +easyblock = 'Toolchain' + +name = 'intel' +version = '2024a' + +homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#intel-toolchain' +description = "Compiler toolchain including Intel compilers, Intel MPI and Intel Math Kernel Library (MKL)." + +toolchain = SYSTEM + +local_comp_ver = '2024.2.0' +local_gccver = '13.3.0' +dependencies = [ + ('GCCcore', local_gccver), + ('binutils', '2.42', '', ('GCCcore', local_gccver)), + ('intel-compilers', local_comp_ver), + ('impi', '2021.13.0', '', ('intel-compilers', local_comp_ver)), + ('imkl', '2024.2.0', '', SYSTEM), + ('imkl-FFTW', '2024.2.0', '', ('iimpi', version)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/intervaltree/intervaltree-0.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/i/intervaltree/intervaltree-0.1-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..06f61418ed78 --- /dev/null +++ b/easybuild/easyconfigs/i/intervaltree/intervaltree-0.1-GCCcore-12.2.0.eb @@ -0,0 +1,38 @@ +# Updated: Denis Kristak (INUITS) +# Updated: Petr Král (INUITS) + +easyblock = 'ConfigureMake' + +name = 'intervaltree' +version = '0.1' + +homepage = 'https://github.com/ekg/intervaltree' +description = """An interval tree can be used to efficiently find a set of numeric intervals + overlapping or containing another interval. This library provides a basic implementation of an + interval tree using C++ templates, allowing the insertion of arbitrary types into the tree. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +github_account = 'ekg' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_fix-numeric_limits.patch'] +checksums = [ + '7ba41f164a98bdcd570f1416fde1634b23d3b0d885b11ccebeec76f58810c307', # v0.1.tar.gz + '1d69caf35af86c0a55000e1bde3f9a0f19dd63d1d2b6bd48e4e5fecbb1aaa6b0', # intervaltree-0.1_fix-numeric_limits.patch +] + +builddependencies = [('binutils', '2.39')] + +skipsteps = ['configure'] + +preinstallopts = 'DESTDIR="" PREFIX=%(installdir)s' + +sanity_check_paths = { + 'files': ['bin/interval_tree_test', 'include/intervaltree/IntervalTree.h'], + 'dirs': [], +} +sanity_check_commands = ["interval_tree_test"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/i/intltool/intltool-0.51.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/i/intltool/intltool-0.51.0-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..e5797e51b02b --- /dev/null +++ b/easybuild/easyconfigs/i/intltool/intltool-0.51.0-GCCcore-13.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'intltool' +version = '0.51.0' + +homepage = 'https://freedesktop.org/wiki/Software/intltool/' +description = """intltool is a set of tools to centralize translation of + many different file formats using GNU gettext-compatible PO files.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://launchpad.net/intltool/trunk/%(version)s/+download/'] +sources = [SOURCE_TAR_GZ] +patches = ['intltool-%(version)s_fix-Perl-compat.patch'] +checksums = [ + '67c74d94196b153b774ab9f89b2fa6c6ba79352407037c8c14d5aeb334e959cd', # intltool-0.51.0.tar.gz + 'e839f7228b2b92301831bca88ed0bc7bce5dbf862568f1644642988204903db6', # intltool-0.51.0_fix-Perl-compat.patch +] + +builddependencies = [ + ('binutils', '2.42'), +] + +dependencies = [ + ('Perl-bundle-CPAN', '5.38.2'), +] + +fix_perl_shebang_for = ['bin/intltool-*'] + +sanity_check_paths = { + 'files': ['bin/intltool%s' % x for x in ['-extract', '-merge', '-prepare', '-update', 'ize']], + 'dirs': [] +} + +sanity_check_commands = ["intltool-merge --help"] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/i/itac/itac-2021.2.0.eb b/easybuild/easyconfigs/i/itac/itac-2021.2.0.eb index 3deaaa9e7116..ea2cfcb26506 100644 --- a/easybuild/easyconfigs/i/itac/itac-2021.2.0.eb +++ b/easybuild/easyconfigs/i/itac/itac-2021.2.0.eb @@ -11,7 +11,7 @@ description = """The Intel Trace Collector is a low-overhead tracing library tha toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17686/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/17686/'] sources = ['l_itac_oneapi_p_%(version)s.152_offline.sh'] checksums = ['dca9d1cb2b77c43496009e191916e0d37c2e6606c228e37c11091778d038dd90'] diff --git a/easybuild/easyconfigs/i/itac/itac-2021.5.0.eb b/easybuild/easyconfigs/i/itac/itac-2021.5.0.eb index f9d10379c85c..ea05e25db95b 100644 --- a/easybuild/easyconfigs/i/itac/itac-2021.5.0.eb +++ b/easybuild/easyconfigs/i/itac/itac-2021.5.0.eb @@ -11,7 +11,7 @@ description = """The Intel Trace Collector is a low-overhead tracing library tha toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18367/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18367/'] sources = ['l_itac_oneapi_p_%(version)s.370_offline.sh'] checksums = ['c2b31298d8b4069a62d9352873c7f6e17ce240ad7293f9bacdc6de3794675b58'] diff --git a/easybuild/easyconfigs/i/itac/itac-2021.6.0.eb b/easybuild/easyconfigs/i/itac/itac-2021.6.0.eb index 22e6230e15b4..0f35b870046c 100644 --- a/easybuild/easyconfigs/i/itac/itac-2021.6.0.eb +++ b/easybuild/easyconfigs/i/itac/itac-2021.6.0.eb @@ -11,7 +11,7 @@ description = """The Intel Trace Collector is a low-overhead tracing library tha toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18694/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18694/'] sources = ['l_itac_oneapi_p_%(version)s.434_offline.sh'] checksums = ['1ecc2735da960041b051e377cadb9f6ab2f44e8aa44d0f642529a56a3cbba436'] diff --git a/easybuild/easyconfigs/j/JsonCpp/JsonCpp-1.9.5-GCCcore-13.2.0.eb b/easybuild/easyconfigs/j/JsonCpp/JsonCpp-1.9.5-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..dd5dda233d2d --- /dev/null +++ b/easybuild/easyconfigs/j/JsonCpp/JsonCpp-1.9.5-GCCcore-13.2.0.eb @@ -0,0 +1,29 @@ +easyblock = "CMakeNinja" + +name = 'JsonCpp' +version = '1.9.5' + +homepage = 'https://open-source-parsers.github.io/jsoncpp-docs/doxygen/index.html' +description = """ JsonCpp is a C++ library that allows manipulating JSON values, + including serialization and deserialization to and from strings. It can also preserve existing comment in + unserialization/serialization steps, making it a convenient format to store user input files. """ + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://github.com/open-source-parsers/jsoncpp/archive'] +sources = ['%(version)s.tar.gz'] +checksums = ['f409856e5920c18d0c2fb85276e24ee607d2a09b5e7d5f0a371368903c275da2'] + +builddependencies = [ + ('CMake', '3.27.6'), + ('Ninja', '1.11.1'), + ('pkgconf', '2.0.3'), + ('binutils', '2.40'), +] + +sanity_check_paths = { + 'files': ['include/json/json.h', 'lib/libjsoncpp.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/j/JsonCpp/JsonCpp-1.9.5-GCCcore-13.3.0.eb b/easybuild/easyconfigs/j/JsonCpp/JsonCpp-1.9.5-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..b1d3f620566d --- /dev/null +++ b/easybuild/easyconfigs/j/JsonCpp/JsonCpp-1.9.5-GCCcore-13.3.0.eb @@ -0,0 +1,29 @@ +easyblock = "CMakeNinja" + +name = 'JsonCpp' +version = '1.9.5' + +homepage = 'https://open-source-parsers.github.io/jsoncpp-docs/doxygen/index.html' +description = """ JsonCpp is a C++ library that allows manipulating JSON values, + including serialization and deserialization to and from strings. It can also preserve existing comment in + unserialization/serialization steps, making it a convenient format to store user input files. """ + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/open-source-parsers/jsoncpp/archive'] +sources = ['%(version)s.tar.gz'] +checksums = ['f409856e5920c18d0c2fb85276e24ee607d2a09b5e7d5f0a371368903c275da2'] + +builddependencies = [ + ('CMake', '3.29.3'), + ('Ninja', '1.12.1'), + ('pkgconf', '2.2.0'), + ('binutils', '2.42'), +] + +sanity_check_paths = { + 'files': ['include/json/json.h', 'lib/libjsoncpp.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/j/Judy/Judy-1.0.5-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/Judy/Judy-1.0.5-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..183e8e08ea45 --- /dev/null +++ b/easybuild/easyconfigs/j/Judy/Judy-1.0.5-GCCcore-12.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'Judy' +version = '1.0.5' + +homepage = 'http://judy.sourceforge.net/' +description = "A C library that implements a dynamic array." + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['http://downloads.sourceforge.net/judy'] +sources = ['%(name)s-%(version)s.tar.gz'] +patches = ['Judy-1.0.5_parallel-make.patch'] # fix Make dependencies, so parallel build also works + +builddependencies = [ + ('Autotools', '20220317'), + ('binutils', '2.40'), +] +checksums = [ + 'd2704089f85fdb6f2cd7e77be21170ced4b4375c03ef1ad4cf1075bd414a63eb', # Judy-1.0.5.tar.gz + '14c2eba71088f3db9625dc4605c6d7183d72412d75ef6c9fd9b95186165cf009', # Judy-1.0.5_parallel-make.patch +] + +preconfigopts = "sed -i 's/AM_CONFIG_HEADER/AC_CONFIG_HEADERS/g' configure.ac && " +preconfigopts += "autoreconf -i && " + +configopts = '--enable-shared --enable-static' + +sanity_check_paths = { + 'files': ["include/%(name)s.h", "lib/lib%(name)s.a", "lib/lib%(name)s.la", "lib/lib%%(name)s.%s" % SHLIB_EXT], + 'dirs': ["share/man"] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.10.0-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.10.0-linux-x86_64.eb index 6671e1cd4ff5..6081619a3312 100644 --- a/easybuild/easyconfigs/j/Julia/Julia-1.10.0-linux-x86_64.eb +++ b/easybuild/easyconfigs/j/Julia/Julia-1.10.0-linux-x86_64.eb @@ -11,21 +11,20 @@ toolchain = SYSTEM source_urls = ['https://julialang-s3.julialang.org/bin/linux/x64/%(version_major_minor)s/'] sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz'] -checksums = ['a7298207f72f2b27b2ab1ce392a6ea37afbd1fbee0f1f8d190b054dcaba878fe'] +patches = [('julia.wrapper', 'bin/')] +checksums = [ + {'julia-1.10.0-linux-x86_64.tar.gz': 'a7298207f72f2b27b2ab1ce392a6ea37afbd1fbee0f1f8d190b054dcaba878fe'}, + {'julia.wrapper': 'd10aeaff53cca9875f7b0ce9218eae3bd21870b654e26c4c52aa8bfcc9da702d'}, +] + +# install wrapper with linking safeguards for Julia libraries +postinstallcmds = ["cd %(installdir)s/bin && mv julia julia.bin && mv julia.wrapper julia"] sanity_check_paths = { - 'files': ['bin/julia', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], - 'dirs': ['bin', 'etc', 'include', 'lib', 'share'] + 'files': ['bin/julia', 'bin/julia.bin', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], + 'dirs': ['bin', 'etc', 'include', 'lib', 'lib/julia', 'share'] } sanity_check_commands = ['julia --help'] -modextrapaths_append = { - # Use default DEPOT_PATH where first entry is user's depot. - # JULIA_DEPOT_PATH must be set to be able to load other JuliaPackage modules and have - # those installations appended to DEPOT_PATH without disabling any of the default paths. - # Appending ':' to make sure we don't override the user's custom JULIA_DEPOT_PATH if set. - 'JULIA_DEPOT_PATH': ':', -} - moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.10.4-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.10.4-linux-x86_64.eb new file mode 100644 index 000000000000..767a23c33a46 --- /dev/null +++ b/easybuild/easyconfigs/j/Julia/Julia-1.10.4-linux-x86_64.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# Updated by: Dugan Witherick, University of Warwick +# Robert Mijakovic +# Wahid Mainassara + +easyblock = 'Tarball' + +name = 'Julia' +version = '1.10.4' +versionsuffix = '-linux-x86_64' + +homepage = 'https://julialang.org' +description = "Julia is a high-level, high-performance dynamic programming language for numerical computing" + +toolchain = SYSTEM + +source_urls = ['https://julialang-s3.julialang.org/bin/linux/x64/%(version_major_minor)s/'] +sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz'] +patches = [('julia.wrapper', 'bin/')] +checksums = [ + {'julia-1.10.4-linux-x86_64.tar.gz': '079f61757c3b5b40d2ade052b3cc4816f50f7ef6df668825772562b3746adff1'}, + {'julia.wrapper': 'd10aeaff53cca9875f7b0ce9218eae3bd21870b654e26c4c52aa8bfcc9da702d'}, +] + +# install wrapper with linking safeguards for Julia libraries +postinstallcmds = ["cd %(installdir)s/bin && mv julia julia.bin && mv julia.wrapper julia"] + +sanity_check_paths = { + 'files': ['bin/julia', 'bin/julia.bin', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], + 'dirs': ['bin', 'etc', 'include', 'lib', 'lib/julia', 'share'] +} +sanity_check_commands = ['julia --help'] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.6.0-linux-aarch64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.6.0-linux-aarch64.eb index 225d86de75a2..17abf7d929c7 100644 --- a/easybuild/easyconfigs/j/Julia/Julia-1.6.0-linux-aarch64.eb +++ b/easybuild/easyconfigs/j/Julia/Julia-1.6.0-linux-aarch64.eb @@ -15,20 +15,20 @@ toolchain = SYSTEM source_urls = ['https://julialang-s3.julialang.org/bin/linux/aarch64/%(version_major_minor)s/'] sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz'] -checksums = ['0f496972d26cea88151204d03e6bd87702aa1ff983de3b1e4f320c48ef67325f'] +patches = [('julia.wrapper', 'bin/')] +checksums = [ + {'julia-1.6.0-linux-aarch64.tar.gz': '0f496972d26cea88151204d03e6bd87702aa1ff983de3b1e4f320c48ef67325f'}, + {'julia.wrapper': 'd10aeaff53cca9875f7b0ce9218eae3bd21870b654e26c4c52aa8bfcc9da702d'}, +] + +# install wrapper with linking safeguards for Julia libraries +postinstallcmds = ["cd %(installdir)s/bin && mv julia julia.bin && mv julia.wrapper julia"] sanity_check_paths = { - 'files': ['bin/julia', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], - 'dirs': ['bin', 'etc', 'include', 'lib', 'share'] + 'files': ['bin/julia', 'bin/julia.bin', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], + 'dirs': ['bin', 'etc', 'include', 'lib', 'lib/julia', 'share'] } sanity_check_commands = ['julia --help'] -modextravars = { - # Use default DEPOT_PATH where first entry is user's depot - # JULIA_DEPOT_PATH must be set to be able to load other JuliaPackage modules and have - # those installations appended to DEPOT_PATH without disabling any of the default paths - 'JULIA_DEPOT_PATH': ':', -} - moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.6.5-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.6.5-linux-x86_64.eb index 45b365aa65d4..dd9ad4890db4 100644 --- a/easybuild/easyconfigs/j/Julia/Julia-1.6.5-linux-x86_64.eb +++ b/easybuild/easyconfigs/j/Julia/Julia-1.6.5-linux-x86_64.eb @@ -19,20 +19,20 @@ toolchain = SYSTEM source_urls = ['https://julialang-s3.julialang.org/bin/linux/x64/%(version_major_minor)s/'] sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz'] -checksums = ['b8fe23ee547254a2fe14be587284ed77c78c06c2d8e9aad5febce0d21cab8e2c'] +patches = [('julia.wrapper', 'bin/')] +checksums = [ + {'julia-1.6.5-linux-x86_64.tar.gz': 'b8fe23ee547254a2fe14be587284ed77c78c06c2d8e9aad5febce0d21cab8e2c'}, + {'julia.wrapper': 'd10aeaff53cca9875f7b0ce9218eae3bd21870b654e26c4c52aa8bfcc9da702d'}, +] + +# install wrapper with linking safeguards for Julia libraries +postinstallcmds = ["cd %(installdir)s/bin && mv julia julia.bin && mv julia.wrapper julia"] sanity_check_paths = { - 'files': ['bin/julia', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], - 'dirs': ['bin', 'etc', 'include', 'lib', 'share'] + 'files': ['bin/julia', 'bin/julia.bin', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], + 'dirs': ['bin', 'etc', 'include', 'lib', 'lib/julia', 'share'] } sanity_check_commands = ['julia --help'] -modextravars = { - # Use default DEPOT_PATH where first entry is user's depot - # JULIA_DEPOT_PATH must be set to be able to load other JuliaPackage modules and have - # those installations appended to DEPOT_PATH without disabling any of the default paths - 'JULIA_DEPOT_PATH': ':', -} - moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.6.6-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.6.6-linux-x86_64.eb index 48c2259422eb..03bdc16da5a8 100644 --- a/easybuild/easyconfigs/j/Julia/Julia-1.6.6-linux-x86_64.eb +++ b/easybuild/easyconfigs/j/Julia/Julia-1.6.6-linux-x86_64.eb @@ -19,20 +19,19 @@ toolchain = SYSTEM source_urls = ['https://julialang-s3.julialang.org/bin/linux/x64/%(version_major_minor)s/'] sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz'] -checksums = ['c25ff71a4242207ab2681a0fcc5df50014e9d99f814e77cacbc5027e20514945'] +patches = [('julia.wrapper', 'bin/')] +checksums = [ + {'julia-1.6.6-linux-x86_64.tar.gz': 'c25ff71a4242207ab2681a0fcc5df50014e9d99f814e77cacbc5027e20514945'}, + {'julia.wrapper': 'd10aeaff53cca9875f7b0ce9218eae3bd21870b654e26c4c52aa8bfcc9da702d'}, +] + +# install wrapper with linking safeguards for Julia libraries +postinstallcmds = ["cd %(installdir)s/bin && mv julia julia.bin && mv julia.wrapper julia"] sanity_check_paths = { - 'files': ['bin/julia', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], - 'dirs': ['bin', 'etc', 'include', 'lib', 'share'] + 'files': ['bin/julia', 'bin/julia.bin', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], + 'dirs': ['bin', 'etc', 'include', 'lib', 'lib/julia', 'share'] } - sanity_check_commands = ['julia --help'] -modextravars = { - # Use default DEPOT_PATH where first entry is user's depot - # JULIA_DEPOT_PATH must be set to be able to load other JuliaPackage modules and have - # those installations appended to DEPOT_PATH without disabling any of the default paths - 'JULIA_DEPOT_PATH': ':', -} - moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.6.7-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.6.7-linux-x86_64.eb index f5d1446913f2..7046809d33df 100644 --- a/easybuild/easyconfigs/j/Julia/Julia-1.6.7-linux-x86_64.eb +++ b/easybuild/easyconfigs/j/Julia/Julia-1.6.7-linux-x86_64.eb @@ -19,20 +19,19 @@ toolchain = SYSTEM source_urls = ['https://julialang-s3.julialang.org/bin/linux/x64/%(version_major_minor)s/'] sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz'] -checksums = ['6c4522d595e4cbcd00157ac458a72f8aec01757053d2073f99daa39e442b2a36'] +patches = [('julia.wrapper', 'bin/')] +checksums = [ + {'julia-1.6.7-linux-x86_64.tar.gz': '6c4522d595e4cbcd00157ac458a72f8aec01757053d2073f99daa39e442b2a36'}, + {'julia.wrapper': 'd10aeaff53cca9875f7b0ce9218eae3bd21870b654e26c4c52aa8bfcc9da702d'}, +] + +# install wrapper with linking safeguards for Julia libraries +postinstallcmds = ["cd %(installdir)s/bin && mv julia julia.bin && mv julia.wrapper julia"] sanity_check_paths = { - 'files': ['bin/julia', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], - 'dirs': ['bin', 'etc', 'include', 'lib', 'share'] + 'files': ['bin/julia', 'bin/julia.bin', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], + 'dirs': ['bin', 'etc', 'include', 'lib', 'lib/julia', 'share'] } - sanity_check_commands = ['julia --help'] -modextravars = { - # Use default DEPOT_PATH where first entry is user's depot - # JULIA_DEPOT_PATH must be set to be able to load other JuliaPackage modules and have - # those installations appended to DEPOT_PATH without disabling any of the default paths - 'JULIA_DEPOT_PATH': ':', -} - moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.7.0-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.7.0-linux-x86_64.eb index ecc3020f4c0d..39df361aa993 100644 --- a/easybuild/easyconfigs/j/Julia/Julia-1.7.0-linux-x86_64.eb +++ b/easybuild/easyconfigs/j/Julia/Julia-1.7.0-linux-x86_64.eb @@ -19,20 +19,19 @@ toolchain = SYSTEM source_urls = ['https://julialang-s3.julialang.org/bin/linux/x64/%(version_major_minor)s/'] sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz'] -checksums = ['7299f3a638aec5e0b9e14eaf0e6221c4fe27189aa0b38ac5a36f03f0dc4c0d40'] +patches = [('julia.wrapper', 'bin/')] +checksums = [ + {'julia-1.7.0-linux-x86_64.tar.gz': '7299f3a638aec5e0b9e14eaf0e6221c4fe27189aa0b38ac5a36f03f0dc4c0d40'}, + {'julia.wrapper': 'd10aeaff53cca9875f7b0ce9218eae3bd21870b654e26c4c52aa8bfcc9da702d'}, +] + +# install wrapper with linking safeguards for Julia libraries +postinstallcmds = ["cd %(installdir)s/bin && mv julia julia.bin && mv julia.wrapper julia"] sanity_check_paths = { - 'files': ['bin/julia', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], - 'dirs': ['bin', 'etc', 'include', 'lib', 'share'] + 'files': ['bin/julia', 'bin/julia.bin', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], + 'dirs': ['bin', 'etc', 'include', 'lib', 'lib/julia', 'share'] } - sanity_check_commands = ['julia --help'] -modextravars = { - # Use default DEPOT_PATH where first entry is user's depot - # JULIA_DEPOT_PATH must be set to be able to load other JuliaPackage modules and have - # those installations appended to DEPOT_PATH without disabling any of the default paths - 'JULIA_DEPOT_PATH': ':', -} - moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.7.1-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.7.1-linux-x86_64.eb index b8b0a744c041..87f911a7da04 100644 --- a/easybuild/easyconfigs/j/Julia/Julia-1.7.1-linux-x86_64.eb +++ b/easybuild/easyconfigs/j/Julia/Julia-1.7.1-linux-x86_64.eb @@ -19,20 +19,19 @@ toolchain = SYSTEM source_urls = ['https://julialang-s3.julialang.org/bin/linux/x64/%(version_major_minor)s/'] sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz'] -checksums = ['44658e9c7b45e2b9b5b59239d190cca42de05c175ea86bc346c294a8fe8d9f11'] +patches = [('julia.wrapper', 'bin/')] +checksums = [ + {'julia-1.7.1-linux-x86_64.tar.gz': '44658e9c7b45e2b9b5b59239d190cca42de05c175ea86bc346c294a8fe8d9f11'}, + {'julia.wrapper': 'd10aeaff53cca9875f7b0ce9218eae3bd21870b654e26c4c52aa8bfcc9da702d'}, +] + +# install wrapper with linking safeguards for Julia libraries +postinstallcmds = ["cd %(installdir)s/bin && mv julia julia.bin && mv julia.wrapper julia"] sanity_check_paths = { - 'files': ['bin/julia', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], - 'dirs': ['bin', 'etc', 'include', 'lib', 'share'] + 'files': ['bin/julia', 'bin/julia.bin', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], + 'dirs': ['bin', 'etc', 'include', 'lib', 'lib/julia', 'share'] } - sanity_check_commands = ['julia --help'] -modextravars = { - # Use default DEPOT_PATH where first entry is user's depot - # JULIA_DEPOT_PATH must be set to be able to load other JuliaPackage modules and have - # those installations appended to DEPOT_PATH without disabling any of the default paths - 'JULIA_DEPOT_PATH': ':', -} - moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.7.2-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.7.2-linux-x86_64.eb index e88e509e0985..5e48ff39fbe2 100644 --- a/easybuild/easyconfigs/j/Julia/Julia-1.7.2-linux-x86_64.eb +++ b/easybuild/easyconfigs/j/Julia/Julia-1.7.2-linux-x86_64.eb @@ -19,20 +19,19 @@ toolchain = SYSTEM source_urls = ['https://julialang-s3.julialang.org/bin/linux/x64/%(version_major_minor)s/'] sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz'] -checksums = ['a75244724f3b2de0e7249c861fbf64078257c16fb4203be78f1cf4dd5973ba95'] +patches = [('julia.wrapper', 'bin/')] +checksums = [ + {'julia-1.7.2-linux-x86_64.tar.gz': 'a75244724f3b2de0e7249c861fbf64078257c16fb4203be78f1cf4dd5973ba95'}, + {'julia.wrapper': 'd10aeaff53cca9875f7b0ce9218eae3bd21870b654e26c4c52aa8bfcc9da702d'}, +] + +# install wrapper with linking safeguards for Julia libraries +postinstallcmds = ["cd %(installdir)s/bin && mv julia julia.bin && mv julia.wrapper julia"] sanity_check_paths = { - 'files': ['bin/julia', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], - 'dirs': ['bin', 'etc', 'include', 'lib', 'share'] + 'files': ['bin/julia', 'bin/julia.bin', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], + 'dirs': ['bin', 'etc', 'include', 'lib', 'lib/julia', 'share'] } - sanity_check_commands = ['julia --help'] -modextravars = { - # Use default DEPOT_PATH where first entry is user's depot - # JULIA_DEPOT_PATH must be set to be able to load other JuliaPackage modules and have - # those installations appended to DEPOT_PATH without disabling any of the default paths - 'JULIA_DEPOT_PATH': ':', -} - moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.7.3-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.7.3-linux-x86_64.eb index dac9088825ad..0f1649345d9e 100644 --- a/easybuild/easyconfigs/j/Julia/Julia-1.7.3-linux-x86_64.eb +++ b/easybuild/easyconfigs/j/Julia/Julia-1.7.3-linux-x86_64.eb @@ -19,20 +19,19 @@ toolchain = SYSTEM source_urls = ['https://julialang-s3.julialang.org/bin/linux/x64/%(version_major_minor)s/'] sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz'] -checksums = ['9b2f4fa12d92b4dcc5d11dc66fb118c47681a76d3df8da064cc97573f2f5c739'] +patches = [('julia.wrapper', 'bin/')] +checksums = [ + {'julia-1.7.3-linux-x86_64.tar.gz': '9b2f4fa12d92b4dcc5d11dc66fb118c47681a76d3df8da064cc97573f2f5c739'}, + {'julia.wrapper': 'd10aeaff53cca9875f7b0ce9218eae3bd21870b654e26c4c52aa8bfcc9da702d'}, +] + +# install wrapper with linking safeguards for Julia libraries +postinstallcmds = ["cd %(installdir)s/bin && mv julia julia.bin && mv julia.wrapper julia"] sanity_check_paths = { - 'files': ['bin/julia', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], - 'dirs': ['bin', 'etc', 'include', 'lib', 'share'] + 'files': ['bin/julia', 'bin/julia.bin', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], + 'dirs': ['bin', 'etc', 'include', 'lib', 'lib/julia', 'share'] } - sanity_check_commands = ['julia --help'] -modextravars = { - # Use default DEPOT_PATH where first entry is user's depot - # JULIA_DEPOT_PATH must be set to be able to load other JuliaPackage modules and have - # those installations appended to DEPOT_PATH without disabling any of the default paths - 'JULIA_DEPOT_PATH': ':', -} - moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.8.0-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.8.0-linux-x86_64.eb index c7f6214e4a81..701b6bcbde70 100644 --- a/easybuild/easyconfigs/j/Julia/Julia-1.8.0-linux-x86_64.eb +++ b/easybuild/easyconfigs/j/Julia/Julia-1.8.0-linux-x86_64.eb @@ -19,20 +19,19 @@ toolchain = SYSTEM source_urls = ['https://julialang-s3.julialang.org/bin/linux/x64/%(version_major_minor)s/'] sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz'] -checksums = ['e80d732ccb7f79e000d798cb8b656dc3641ab59516d6e4e52e16765017892a00'] +patches = [('julia.wrapper', 'bin/')] +checksums = [ + {'julia-1.8.0-linux-x86_64.tar.gz': 'e80d732ccb7f79e000d798cb8b656dc3641ab59516d6e4e52e16765017892a00'}, + {'julia.wrapper': 'd10aeaff53cca9875f7b0ce9218eae3bd21870b654e26c4c52aa8bfcc9da702d'}, +] + +# install wrapper with linking safeguards for Julia libraries +postinstallcmds = ["cd %(installdir)s/bin && mv julia julia.bin && mv julia.wrapper julia"] sanity_check_paths = { - 'files': ['bin/julia', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], - 'dirs': ['bin', 'etc', 'include', 'lib', 'share'] + 'files': ['bin/julia', 'bin/julia.bin', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], + 'dirs': ['bin', 'etc', 'include', 'lib', 'lib/julia', 'share'] } - sanity_check_commands = ['julia --help'] -modextravars = { - # Use default DEPOT_PATH where first entry is user's depot - # JULIA_DEPOT_PATH must be set to be able to load other JuliaPackage modules and have - # those installations appended to DEPOT_PATH without disabling any of the default paths - 'JULIA_DEPOT_PATH': ':', -} - moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.8.2-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.8.2-linux-x86_64.eb index 37b817f557e4..c85c5bdc291c 100644 --- a/easybuild/easyconfigs/j/Julia/Julia-1.8.2-linux-x86_64.eb +++ b/easybuild/easyconfigs/j/Julia/Julia-1.8.2-linux-x86_64.eb @@ -19,20 +19,19 @@ toolchain = SYSTEM source_urls = ['https://julialang-s3.julialang.org/bin/linux/x64/%(version_major_minor)s/'] sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz'] -checksums = ['671cf3a450b63a717e1eedd7f69087e3856f015b2e146cb54928f19a3c05e796'] +patches = [('julia.wrapper', 'bin/')] +checksums = [ + {'julia-1.8.2-linux-x86_64.tar.gz': '671cf3a450b63a717e1eedd7f69087e3856f015b2e146cb54928f19a3c05e796'}, + {'julia.wrapper': 'd10aeaff53cca9875f7b0ce9218eae3bd21870b654e26c4c52aa8bfcc9da702d'}, +] + +# install wrapper with linking safeguards for Julia libraries +postinstallcmds = ["cd %(installdir)s/bin && mv julia julia.bin && mv julia.wrapper julia"] sanity_check_paths = { - 'files': ['bin/julia', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], - 'dirs': ['bin', 'etc', 'include', 'lib', 'share'] + 'files': ['bin/julia', 'bin/julia.bin', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], + 'dirs': ['bin', 'etc', 'include', 'lib', 'lib/julia', 'share'] } - sanity_check_commands = ['julia --help'] -modextravars = { - # Use default DEPOT_PATH where first entry is user's depot - # JULIA_DEPOT_PATH must be set to be able to load other JuliaPackage modules and have - # those installations appended to DEPOT_PATH without disabling any of the default paths - 'JULIA_DEPOT_PATH': ':', -} - moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.8.5-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.8.5-linux-x86_64.eb index 1d5fa47c96c8..6e60397495dc 100644 --- a/easybuild/easyconfigs/j/Julia/Julia-1.8.5-linux-x86_64.eb +++ b/easybuild/easyconfigs/j/Julia/Julia-1.8.5-linux-x86_64.eb @@ -19,20 +19,19 @@ toolchain = SYSTEM source_urls = ['https://julialang-s3.julialang.org/bin/linux/x64/%(version_major_minor)s/'] sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz'] -checksums = ['e71a24816e8fe9d5f4807664cbbb42738f5aa9fe05397d35c81d4c5d649b9d05'] +patches = [('julia.wrapper', 'bin/')] +checksums = [ + {'julia-1.8.5-linux-x86_64.tar.gz': 'e71a24816e8fe9d5f4807664cbbb42738f5aa9fe05397d35c81d4c5d649b9d05'}, + {'julia.wrapper': 'd10aeaff53cca9875f7b0ce9218eae3bd21870b654e26c4c52aa8bfcc9da702d'}, +] + +postinstallcmds = ["cd %(installdir)s/bin && mv julia julia.bin && mv julia.wrapper julia"] sanity_check_paths = { - 'files': ['bin/julia', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], - 'dirs': ['bin', 'etc', 'include', 'lib', 'share'] + 'files': ['bin/julia', 'bin/julia.bin', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], + 'dirs': ['bin', 'etc', 'include', 'lib', 'lib/julia', 'share'] } sanity_check_commands = ['julia --help'] -modextravars = { - # Use default DEPOT_PATH where first entry is user's depot - # JULIA_DEPOT_PATH must be set to be able to load other JuliaPackage modules and have - # those installations appended to DEPOT_PATH without disabling any of the default paths - 'JULIA_DEPOT_PATH': ':', -} - moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.9.0-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.9.0-linux-x86_64.eb index 2ee4230cbb9c..2e89fb8640b8 100644 --- a/easybuild/easyconfigs/j/Julia/Julia-1.9.0-linux-x86_64.eb +++ b/easybuild/easyconfigs/j/Julia/Julia-1.9.0-linux-x86_64.eb @@ -19,20 +19,19 @@ toolchain = SYSTEM source_urls = ['https://julialang-s3.julialang.org/bin/linux/x64/%(version_major_minor)s/'] sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz'] -checksums = ['00c614466ef9809c2eb23480e38d196a2c577fff2730c4f83d135b913d473359'] +patches = [('julia.wrapper', 'bin/')] +checksums = [ + {'julia-1.9.0-linux-x86_64.tar.gz': '00c614466ef9809c2eb23480e38d196a2c577fff2730c4f83d135b913d473359'}, + {'julia.wrapper': 'd10aeaff53cca9875f7b0ce9218eae3bd21870b654e26c4c52aa8bfcc9da702d'}, +] + +# install wrapper with linking safeguards for Julia libraries +postinstallcmds = ["cd %(installdir)s/bin && mv julia julia.bin && mv julia.wrapper julia"] sanity_check_paths = { - 'files': ['bin/julia', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], - 'dirs': ['bin', 'etc', 'include', 'lib', 'share'] + 'files': ['bin/julia', 'bin/julia.bin', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], + 'dirs': ['bin', 'etc', 'include', 'lib', 'lib/julia', 'share'] } - sanity_check_commands = ['julia --help'] -modextravars = { - # Use default DEPOT_PATH where first entry is user's depot - # JULIA_DEPOT_PATH must be set to be able to load other JuliaPackage modules and have - # those installations appended to DEPOT_PATH without disabling any of the default paths - 'JULIA_DEPOT_PATH': ':', -} - moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.9.2-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.9.2-linux-x86_64.eb index a0d92b7aacb9..fef2c5a347c7 100644 --- a/easybuild/easyconfigs/j/Julia/Julia-1.9.2-linux-x86_64.eb +++ b/easybuild/easyconfigs/j/Julia/Julia-1.9.2-linux-x86_64.eb @@ -19,20 +19,19 @@ toolchain = SYSTEM source_urls = ['https://julialang-s3.julialang.org/bin/linux/x64/%(version_major_minor)s/'] sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz'] -checksums = ['4c2d799f442d7fe718827b19da2bacb72ea041b9ce55f24eee7b1313f57c4383'] +patches = [('julia.wrapper', 'bin/')] +checksums = [ + {'julia-1.9.2-linux-x86_64.tar.gz': '4c2d799f442d7fe718827b19da2bacb72ea041b9ce55f24eee7b1313f57c4383'}, + {'julia.wrapper': 'd10aeaff53cca9875f7b0ce9218eae3bd21870b654e26c4c52aa8bfcc9da702d'}, +] + +postinstallcmds = ["cd %(installdir)s/bin && mv julia julia.bin && mv julia.wrapper julia"] sanity_check_paths = { - 'files': ['bin/julia', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], - 'dirs': ['bin', 'etc', 'include', 'lib', 'share'] + 'files': ['bin/julia', 'bin/julia.bin', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], + 'dirs': ['bin', 'etc', 'include', 'lib', 'lib/julia', 'share'] } sanity_check_commands = ['julia --help'] -modextravars = { - # Use default DEPOT_PATH where first entry is user's depot - # JULIA_DEPOT_PATH must be set to be able to load other JuliaPackage modules and have - # those installations appended to DEPOT_PATH without disabling any of the default paths - 'JULIA_DEPOT_PATH': ':', -} - moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.9.3-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.9.3-linux-x86_64.eb index 7b207dc635c7..1d0f85d9874c 100644 --- a/easybuild/easyconfigs/j/Julia/Julia-1.9.3-linux-x86_64.eb +++ b/easybuild/easyconfigs/j/Julia/Julia-1.9.3-linux-x86_64.eb @@ -19,20 +19,19 @@ toolchain = SYSTEM source_urls = ['https://julialang-s3.julialang.org/bin/linux/x64/%(version_major_minor)s/'] sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz'] -checksums = ['d76670cc9ba3e0fd4c1545dd3d00269c0694976a1176312795ebce1692d323d1'] +patches = [('julia.wrapper', 'bin/')] +checksums = [ + {'julia-1.9.3-linux-x86_64.tar.gz': 'd76670cc9ba3e0fd4c1545dd3d00269c0694976a1176312795ebce1692d323d1'}, + {'julia.wrapper': 'd10aeaff53cca9875f7b0ce9218eae3bd21870b654e26c4c52aa8bfcc9da702d'}, +] + +# install wrapper with linking safeguards for Julia libraries +postinstallcmds = ["cd %(installdir)s/bin && mv julia julia.bin && mv julia.wrapper julia"] sanity_check_paths = { - 'files': ['bin/julia', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], - 'dirs': ['bin', 'etc', 'include', 'lib', 'share'] + 'files': ['bin/julia', 'bin/julia.bin', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], + 'dirs': ['bin', 'etc', 'include', 'lib', 'lib/julia', 'share'] } - sanity_check_commands = ['julia --help'] -modextravars = { - # Use default DEPOT_PATH where first entry is user's depot - # JULIA_DEPOT_PATH must be set to be able to load other JuliaPackage modules and have - # those installations appended to DEPOT_PATH without disabling any of the default paths - 'JULIA_DEPOT_PATH': ':', -} - moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Julia/julia.wrapper b/easybuild/easyconfigs/j/Julia/julia.wrapper new file mode 100755 index 000000000000..613b8a831f16 --- /dev/null +++ b/easybuild/easyconfigs/j/Julia/julia.wrapper @@ -0,0 +1,2 @@ +#!/bin/sh +LD_LIBRARY_PATH="$EBROOTJULIA/lib:$EBROOTJULIA/lib/julia:$LD_LIBRARY_PATH" julia.bin "$@" diff --git a/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a-CUDA-12.1.1.eb new file mode 100644 index 000000000000..75355c6c842f --- /dev/null +++ b/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a-CUDA-12.1.1.eb @@ -0,0 +1,135 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +# Updated by: Alex Domingo (Vrije Universiteit Brussel) +# Updated by: Pavel Tománek (INUITS) +# Updated by: Thomas Hoffmann (EMBL Heidelberg) +easyblock = 'PythonBundle' + +name = 'jax' +version = '0.4.25' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://jax.readthedocs.io/' +description = """Composable transformations of Python+NumPy programs: +differentiate, vectorize, JIT to GPU/TPU, and more""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} +cuda_compute_capabilities = ["5.0", "6.0", "6.1", "7.0", "7.5", "8.0", "8.6", "9.0"] + +builddependencies = [ + ('Bazel', '6.3.1'), + ('pytest-xdist', '3.3.1'), + ('git', '2.41.0', '-nodocs'), # bazel uses git to fetch repositories + ('matplotlib', '3.7.2'), # required for tests/lobpcg_test.py + ('poetry', '1.5.1'), + ('pybind11', '2.11.1'), +] + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('cuDNN', '8.9.2.26', versionsuffix, SYSTEM), + ('NCCL', '2.18.3', versionsuffix), + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('absl-py', '2.1.0'), + ('flatbuffers-python', '23.5.26'), + ('ml_dtypes', '0.3.2'), + ('zlib', '1.2.13'), +] + +# downloading xla and other tarballs to avoid that Bazel downloads it during the build +local_extract_cmd = 'mkdir -p %(builddir)s/archives && cp %s %(builddir)s/archives' +# note: following commits *must* be the exact same onces used upstream +# XLA_COMMIT from jax-jaxlib: third_party/xla/workspace.bzl +local_xla_commit = '4ccfe33c71665ddcbca5b127fefe8baa3ed632d4' +# TFRT_COMMIT from xla: third_party/tsl/third_party/tf_runtime/workspace.bzl +local_tfrt_commit = '0aeefb1660d7e37964b2bb71b1f518096bda9a25' + +# Use sources downloaded by EasyBuild +_jaxlib_buildopts = '--bazel_options="--distdir=%(builddir)s/archives" ' +# Use dependencies from EasyBuild +_jaxlib_buildopts += '--bazel_options="--action_env=TF_SYSTEM_LIBS=pybind11" ' +_jaxlib_buildopts += '--bazel_options="--action_env=CPATH=$EBROOTPYBIND11/include" ' +# Avoid warning (treated as error) in upb/table.c +_jaxlib_buildopts += '--bazel_options="--copt=-Wno-maybe-uninitialized" ' + +components = [ + ('jaxlib', version, { + 'sources': [ + { + 'source_urls': ['https://github.com/google/jax/archive/'], + 'filename': '%(name)s-v%(version)s.tar.gz', + }, + { + 'source_urls': ['https://github.com/openxla/xla/archive'], + 'download_filename': '%s.tar.gz' % local_xla_commit, + 'filename': 'xla-%s.tar.gz' % local_xla_commit[:8], + 'extract_cmd': local_extract_cmd, + }, + { + 'source_urls': ['https://github.com/tensorflow/runtime/archive'], + 'download_filename': '%s.tar.gz' % local_tfrt_commit, + 'filename': 'tf_runtime-%s.tar.gz' % local_tfrt_commit[:8], + 'extract_cmd': local_extract_cmd, + }, + ], + 'patches': ['jax-0.4.25_fix-pybind11-systemlib.patch'], + 'checksums': [ + {'jaxlib-v0.4.25.tar.gz': + 'fc1197c401924942eb14185a61688d0c476e3e81ff71f9dc95e620b57c06eec8'}, + {'xla-4ccfe33c.tar.gz': + '8a59b9af7d0850059d7043f7043c780066d61538f3af536e8a10d3d717f35089'}, + {'tf_runtime-0aeefb16.tar.gz': + 'a3df827d7896774cb1d80bf4e1c79ab05c268f29bd4d3db1fb5a4b9c2079d8e3'}, + {'jax-0.4.25_fix-pybind11-systemlib.patch': + 'daad5b726d1a138431b05eb60ecf4c89c7b5148eb939721800bdf43d804ca033'}, + ], + 'start_dir': 'jax-jaxlib-v%(version)s', + 'buildopts': _jaxlib_buildopts + }), +] + +# Some tests require an isolated run: +local_isolated_tests = [ + 'tests/host_callback_test.py::HostCallbackTapTest::test_tap_scan_custom_jvp', + 'tests/host_callback_test.py::HostCallbackTapTest::test_tap_transforms_doc', + 'tests/lax_scipy_special_functions_test.py::LaxScipySpcialFunctionsTest' + + '::testScipySpecialFun_gammainc_s_2x1x4_float32_float32', +] +# deliberately not testing in parallel, as that results in (additional) failing tests; +# use XLA_PYTHON_CLIENT_ALLOCATOR=platform to allocate and deallocate GPU memory during testing, +# see https://github.com/google/jax/issues/7323 and +# https://github.com/google/jax/blob/main/docs/gpu_memory_allocation.rst; +# use CUDA_VISIBLE_DEVICES=0 to avoid failing tests on systems with multiple GPUs; +# use NVIDIA_TF32_OVERRIDE=0 to avoid loosing numerical precision by disabling TF32 Tensor Cores; +local_test_exports = [ + "NVIDIA_TF32_OVERRIDE=0", + "CUDA_VISIBLE_DEVICES=0", + "XLA_PYTHON_CLIENT_ALLOCATOR=platform", + "JAX_ENABLE_X64=true", +] +local_test = ''.join(['export %s;' % x for x in local_test_exports]) +# run all tests at once except for local_isolated_tests: +local_test += "pytest -vv tests %s && " % ' '.join(['--deselect %s' % x for x in local_isolated_tests]) +# run remaining local_isolated_tests separately: +local_test += ' && '.join(['pytest -vv %s' % x for x in local_isolated_tests]) + +use_pip = True + +exts_list = [ + (name, version, { + 'source_tmpl': '%(name)s-v%(version)s.tar.gz', + 'source_urls': ['https://github.com/google/jax/archive/'], + 'patches': ['jax-0.4.25_fix_env_test_no_log_spam.patch'], + 'checksums': [ + {'jax-v0.4.25.tar.gz': '8b30af49688c0c13b82c6f5ce992727c00b5fc6d04a4c6962012f4246fa664eb'}, + {'jax-0.4.25_fix_env_test_no_log_spam.patch': + 'a18b5f147569d9ad41025124333a0f04fd0d0e0f9e4309658d7f6b9b838e2e2a'}, + ], + 'runtest': local_test, + }), +] + +sanity_pip_check = True + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a.eb b/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a.eb new file mode 100644 index 000000000000..a4a86382ad64 --- /dev/null +++ b/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a.eb @@ -0,0 +1,109 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +# Updated by: Alex Domingo (Vrije Universiteit Brussel) +# Updated by: Pavel Tománek (INUITS) +# Updated by: Thomas Hoffmann (EMBL Heidelberg) +easyblock = 'PythonBundle' + +name = 'jax' +version = '0.4.25' + +homepage = 'https://jax.readthedocs.io/' +description = """Composable transformations of Python+NumPy programs: +differentiate, vectorize, JIT to GPU/TPU, and more""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +builddependencies = [ + ('Bazel', '6.3.1'), + ('pytest-xdist', '3.3.1'), + ('git', '2.41.0', '-nodocs'), # bazel uses git to fetch repositories + ('matplotlib', '3.7.2'), # required for tests/lobpcg_test.py + ('poetry', '1.5.1'), + ('pybind11', '2.11.1'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('absl-py', '2.1.0'), + ('flatbuffers-python', '23.5.26'), + ('ml_dtypes', '0.3.2'), + ('zlib', '1.2.13'), +] + +# downloading xla and other tarballs to avoid that Bazel downloads it during the build +local_extract_cmd = 'mkdir -p %(builddir)s/archives && cp %s %(builddir)s/archives' +# note: following commits *must* be the exact same onces used upstream +# XLA_COMMIT from jax-jaxlib: third_party/xla/workspace.bzl +local_xla_commit = '4ccfe33c71665ddcbca5b127fefe8baa3ed632d4' +# TFRT_COMMIT from xla: third_party/tsl/third_party/tf_runtime/workspace.bzl +local_tfrt_commit = '0aeefb1660d7e37964b2bb71b1f518096bda9a25' + +# Use sources downloaded by EasyBuild +_jaxlib_buildopts = '--bazel_options="--distdir=%(builddir)s/archives" ' +# Use dependencies from EasyBuild +_jaxlib_buildopts += '--bazel_options="--action_env=TF_SYSTEM_LIBS=pybind11" ' +_jaxlib_buildopts += '--bazel_options="--action_env=CPATH=$EBROOTPYBIND11/include" ' +# Avoid warning (treated as error) in upb/table.c +_jaxlib_buildopts += '--bazel_options="--copt=-Wno-maybe-uninitialized" ' + +components = [ + ('jaxlib', version, { + 'sources': [ + { + 'source_urls': ['https://github.com/google/jax/archive/'], + 'filename': '%(name)s-v%(version)s.tar.gz', + }, + { + 'source_urls': ['https://github.com/openxla/xla/archive'], + 'download_filename': '%s.tar.gz' % local_xla_commit, + 'filename': 'xla-%s.tar.gz' % local_xla_commit[:8], + 'extract_cmd': local_extract_cmd, + }, + { + 'source_urls': ['https://github.com/tensorflow/runtime/archive'], + 'download_filename': '%s.tar.gz' % local_tfrt_commit, + 'filename': 'tf_runtime-%s.tar.gz' % local_tfrt_commit[:8], + 'extract_cmd': local_extract_cmd, + }, + ], + 'patches': ['jax-0.4.25_fix-pybind11-systemlib.patch'], + 'checksums': [ + {'jaxlib-v0.4.25.tar.gz': + 'fc1197c401924942eb14185a61688d0c476e3e81ff71f9dc95e620b57c06eec8'}, + {'xla-4ccfe33c.tar.gz': + '8a59b9af7d0850059d7043f7043c780066d61538f3af536e8a10d3d717f35089'}, + {'tf_runtime-0aeefb16.tar.gz': + 'a3df827d7896774cb1d80bf4e1c79ab05c268f29bd4d3db1fb5a4b9c2079d8e3'}, + {'jax-0.4.25_fix-pybind11-systemlib.patch': + 'daad5b726d1a138431b05eb60ecf4c89c7b5148eb939721800bdf43d804ca033'}, + ], + 'start_dir': 'jax-jaxlib-v%(version)s', + 'buildopts': _jaxlib_buildopts + }), +] + +use_pip = True + +exts_list = [ + (name, version, { + 'sources': [ + { + 'source_urls': ['https://github.com/google/jax/archive/'], + 'filename': '%(name)s-v%(version)s.tar.gz', + }, + ], + 'patches': ['jax-0.4.25_fix_env_test_no_log_spam.patch'], + 'checksums': [ + {'jax-v0.4.25.tar.gz': '8b30af49688c0c13b82c6f5ce992727c00b5fc6d04a4c6962012f4246fa664eb'}, + {'jax-0.4.25_fix_env_test_no_log_spam.patch': + 'a18b5f147569d9ad41025124333a0f04fd0d0e0f9e4309658d7f6b9b838e2e2a'}, + ], + 'runtest': "pytest -n %(parallel)s tests", + }), +] + +sanity_pip_check = True + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/j/jax/jax-0.4.25_fix-pybind11-systemlib.patch b/easybuild/easyconfigs/j/jax/jax-0.4.25_fix-pybind11-systemlib.patch new file mode 100644 index 000000000000..c404ee6917fb --- /dev/null +++ b/easybuild/easyconfigs/j/jax/jax-0.4.25_fix-pybind11-systemlib.patch @@ -0,0 +1,38 @@ +Add missing value for System Pybind11 Bazel config + +Author: Alexander Grund (TU Dresden) + +diff --git a/third_party/xla/fix-pybind11-systemlib.patch b/third_party/xla/fix-pybind11-systemlib.patch +new file mode 100644 +index 000000000..68bd2063d +--- /dev/null ++++ b/third_party/xla/fix-pybind11-systemlib.patch +@@ -0,0 +1,13 @@ ++--- xla-orig/third_party/tsl/third_party/systemlibs/pybind11.BUILD +++++ xla-4ccfe33c71665ddcbca5b127fefe8baa3ed632d4/third_party/tsl/third_party/systemlibs/pybind11.BUILD ++@@ -6,3 +6,10 @@ ++ "@tsl//third_party/python_runtime:headers", ++ ], ++ ) +++ +++# Needed by pybind11_bazel. +++config_setting( +++ name = "osx", +++ constraint_values = ["@platforms//os:osx"], +++) +++ +diff --git a/third_party/xla/workspace.bzl b/third_party/xla/workspace.bzl +index ebc8d9838..125e1c173 100644 +--- a/third_party/xla/workspace.bzl ++++ b/third_party/xla/workspace.bzl +@@ -29,6 +29,9 @@ def repo(): + sha256 = XLA_SHA256, + strip_prefix = "xla-{commit}".format(commit = XLA_COMMIT), + urls = tf_mirror_urls("https://github.com/openxla/xla/archive/{commit}.tar.gz".format(commit = XLA_COMMIT)), ++ patch_file = [ ++ "//third_party/xla:fix-pybind11-systemlib.patch", ++ ], + ) + + # For development, one often wants to make changes to the TF repository as well + diff --git a/easybuild/easyconfigs/j/jax/jax-0.4.25_fix_env_test_no_log_spam.patch b/easybuild/easyconfigs/j/jax/jax-0.4.25_fix_env_test_no_log_spam.patch new file mode 100644 index 000000000000..ad9196084373 --- /dev/null +++ b/easybuild/easyconfigs/j/jax/jax-0.4.25_fix_env_test_no_log_spam.patch @@ -0,0 +1,18 @@ +# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2024/03 +# avoid overriding LD_LIBRARY_PATH, which would lead to test error: error while loading shared libraries: libpython3.11.so.1.0: cannot open shared object file: No such file or directory' +diff -ru jax-jax-v0.4.25/tests/logging_test.py jax-jax-v0.4.25_fix_env_test_no_log_spam/tests/logging_test.py +--- jax-jax-v0.4.25/tests/logging_test.py 2024-02-24 19:25:17.000000000 +0100 ++++ jax-jax-v0.4.25_fix_env_test_no_log_spam/tests/logging_test.py 2024-03-15 12:00:34.133022613 +0100 +@@ -72,8 +72,11 @@ + python = sys.executable + assert "python" in python + # Make sure C++ logging is at default level for the test process. ++ import os ++ tmp_env=os.environ.copy() ++ tmp_env['TF_CPP_MIN_LOG_LEVEL']='1' + proc = subprocess.run([python, "-c", program], capture_output=True, +- env={"TF_CPP_MIN_LOG_LEVEL": "1"}) ++ env=tmp_env) + + lines = proc.stdout.split(b"\n") + lines.extend(proc.stderr.split(b"\n")) diff --git a/easybuild/easyconfigs/j/jemalloc/jemalloc-5.3.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/j/jemalloc/jemalloc-5.3.0-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..023c3001dd3a --- /dev/null +++ b/easybuild/easyconfigs/j/jemalloc/jemalloc-5.3.0-GCCcore-13.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'jemalloc' +version = '5.3.0' + +homepage = 'http://jemalloc.net' +description = """jemalloc is a general purpose malloc(3) implementation that emphasizes fragmentation avoidance and + scalable concurrency support.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/jemalloc/jemalloc/archive'] +sources = ['%(version)s.tar.gz'] +checksums = ['ef6f74fd45e95ee4ef7f9e19ebe5b075ca6b7fbe0140612b2a161abafb7ee179'] + +builddependencies = [ + ('Autotools', '20231222'), + ('binutils', '2.42'), +] + +# From version 5.2.1 (or maybe earlier) it does no longer build, +# nor try to install, documentation if xsltproc is missing. +# So we can use normal installation. +preconfigopts = "./autogen.sh && " +configopts = "--with-version=%(version)s-0-g0000 " # build with version info + +sanity_check_paths = { + 'files': ['bin/jeprof', 'lib/libjemalloc.a', 'lib/libjemalloc_pic.a', 'lib/libjemalloc.%s' % SHLIB_EXT, + 'include/jemalloc/jemalloc.h'], + 'dirs': [], +} + +# jemalloc can be used via $LD_PRELOAD, but we don't enable this by +# default, you need to opt-in to it +# modextrapaths = {'LD_PRELOAD': ['lib/libjemalloc.%s' % SHLIB_EXT]} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/j/json-c/json-c-0.17-GCCcore-13.3.0.eb b/easybuild/easyconfigs/j/json-c/json-c-0.17-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..87642888aa18 --- /dev/null +++ b/easybuild/easyconfigs/j/json-c/json-c-0.17-GCCcore-13.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'CMakeMake' + +name = 'json-c' +version = '0.17' +local_suff = '-20230812' + +homepage = 'https://github.com/json-c/json-c' +description = """JSON-C implements a reference counting object model that allows you to easily construct JSON objects + in C, output them as JSON formatted strings and parse JSON formatted strings back into the C representation of JSON +objects.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/json-c/json-c/archive/'] +sources = ['json-c-%%(version)s%s.tar.gz' % local_suff] +checksums = ['024d302a3aadcbf9f78735320a6d5aedf8b77876c8ac8bbb95081ca55054c7eb'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] + +# disable using Valgrind during the tests to avoid failures caused by using an OS Valgrind +pretestopts = 'USE_VALGRIND=0 ' +runtest = 'test' + +sanity_check_paths = { + 'files': ['lib/libjson-c.a', 'lib/libjson-c.%s' % SHLIB_EXT, 'lib/pkgconfig/json-c.pc'], + 'dirs': ['include/json-c'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/j/json-fortran/json-fortran-8.5.2-GCC-13.2.0.eb b/easybuild/easyconfigs/j/json-fortran/json-fortran-8.5.2-GCC-13.2.0.eb new file mode 100644 index 000000000000..da205b23c097 --- /dev/null +++ b/easybuild/easyconfigs/j/json-fortran/json-fortran-8.5.2-GCC-13.2.0.eb @@ -0,0 +1,32 @@ +# J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'CMakeMake' + +name = 'json-fortran' +version = '8.5.2' + +homepage = 'https://github.com/jacobwilliams/json-fortran' +description = "JSON-Fortran: A Modern Fortran JSON API" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +source_urls = ['https://github.com/jacobwilliams/json-fortran/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['ba7243ab28d4d06c5d0baef27dab0041cee0f050dea9ec3a854a03f4e3e9667a'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.27.6'), +] + +configopts = '-DUSE_GNU_INSTALL_CONVENTION=TRUE' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libjsonfortran.a', 'lib/libjsonfortran.%s' % SHLIB_EXT, + 'include/json_module.mod', 'include/json_parameters.mod'], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/j/json-fortran/json-fortran-8.5.2-intel-compilers-2023.2.1.eb b/easybuild/easyconfigs/j/json-fortran/json-fortran-8.5.2-intel-compilers-2023.2.1.eb new file mode 100644 index 000000000000..50d89ee34e23 --- /dev/null +++ b/easybuild/easyconfigs/j/json-fortran/json-fortran-8.5.2-intel-compilers-2023.2.1.eb @@ -0,0 +1,32 @@ +# J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'CMakeMake' + +name = 'json-fortran' +version = '8.5.2' + +homepage = 'https://github.com/jacobwilliams/json-fortran' +description = "JSON-Fortran: A Modern Fortran JSON API" + +toolchain = {'name': 'intel-compilers', 'version': '2023.2.1'} + +source_urls = ['https://github.com/jacobwilliams/json-fortran/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['ba7243ab28d4d06c5d0baef27dab0041cee0f050dea9ec3a854a03f4e3e9667a'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.27.6'), +] + +configopts = '-DUSE_GNU_INSTALL_CONVENTION=TRUE' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libjsonfortran.a', 'lib/libjsonfortran.%s' % SHLIB_EXT, + 'include/json_module.mod', 'include/json_parameters.mod'], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/j/junos-eznc/junos-eznc-2.7.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/junos-eznc/junos-eznc-2.7.1-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..ceaec648de37 --- /dev/null +++ b/easybuild/easyconfigs/j/junos-eznc/junos-eznc-2.7.1-GCCcore-12.3.0.eb @@ -0,0 +1,54 @@ +easyblock = 'PythonBundle' + +name = 'junos-eznc' +version = '2.7.1' + +homepage = 'https://github.com/Juniper/py-junos-eznc' +description = "Python library for Junos automation." + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [('binutils', '2.40')] +dependencies = [ + ('Python', '3.11.3'), + ('lxml', '4.9.2'), + ('PyYAML', '6.0'), + ('Python-bundle-PyPI', '2023.06'), + ('bcrypt', '4.0.1'), +] + +exts_list = [ + ('yamlordereddictloader', '0.4.2', { + 'checksums': ['36af2f6210fcff5da4fc4c12e1d815f973dceb41044e795e1f06115d634bca13'], + }), + ('transitions', '0.9.2', { + 'checksums': ['2f8490dbdbd419366cef1516032ab06d07ccb5839ef54905e842a472692d4204'], + }), + ('scp', '0.15.0', { + 'checksums': ['f1b22e9932123ccf17eebf19e0953c6e9148f589f93d91b872941a696305c83f'], + }), + ('pyserial', '3.5', { + 'modulename': 'serial', + 'checksums': ['3c77e014170dfffbd816e6ffc205e9842efb10be9f58ec16d3e8675b4925cddb'], + }), + ('ncclient', '0.6.15', { + 'checksums': ['6757cb41bc9160dfe47f22f5de8cf2f1adf22f27463fb50453cc415ab96773d8'], + }), + ('paramiko', '3.4.0', { + # Juniper fork of paramiko - compatible with junos-eznc + 'source_urls': ['https://github.com/Juniper/paramiko/archive/'], + 'sources': [{'download_filename': 'v%(version)s-JNPR.tar.gz', 'filename': '%(name)s-%(version)s-JNPR.tar.gz'}], + 'checksums': ['6b3b62e18a2b693169eaa50a7cdd2ab5637fc423205ce85e109cb37722f9eeda'], + }), + (name, version, { + 'modulename': 'jnpr.junos', + # delete 'os.system("pip install git+https://github.com/Juniper/paramiko.git@v3.4.0-JNPR")' from setup.py + 'preinstallopts': "sed -i '/pip install/d' setup.py && ", + 'checksums': ['371f0298bf03e0cb4c017c43f6f4122263584eda0d690d0112e93f13daae41ac'], + }), +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/jupyter-collaboration/jupyter-collaboration-2.1.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/j/jupyter-collaboration/jupyter-collaboration-2.1.1-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..1755481085ec --- /dev/null +++ b/easybuild/easyconfigs/j/jupyter-collaboration/jupyter-collaboration-2.1.1-GCCcore-13.2.0.eb @@ -0,0 +1,55 @@ +easyblock = 'PythonBundle' + +name = 'jupyter-collaboration' +version = "2.1.1" + +homepage = 'https://github.com/jupyterlab/jupyter-collaboration' +description = """JupyterLab Real-Time Collaboration is a Jupyter Server Extension and JupyterLab +extensions providing support for Y documents and adding collaboration UI +elements in JupyterLab.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('hatch-jupyter-builder', '0.9.1'), + ('maturin', '1.3.1'), +] +dependencies = [ + ('Python', '3.11.5'), + ('JupyterLab', '4.2.0'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('sqlite_anyio', '0.2.0', { + 'checksums': ['9ecbcddf105e5862f7975a9827b684a19a987aad46f10699eadb22ea33bbd060'], + }), + ('pycrdt', '0.8.27', { + 'checksums': ['a486a967ab82d92e51211757d888367b9d1882cfd4db6199485a8fd3d2271dce'], + }), + ('pycrdt_websocket', '0.13.4', { + 'checksums': ['dce8259345ac14e08e9cf124cd1d66ea1b9d17ab1af79e63f50a611fb676421c'], + }), + ('jupyter_ydoc', '2.0.1', { + 'checksums': ['716dda8cb8af881fec2fbc88aea3fb0d3bb24bbeb80a99a8aff2e01d089d5b0d'], + }), + ('jupyter_server_fileid', '0.9.2', { + 'checksums': ['ffb11460ca5f8567644f6120b25613fca8e3f3048b38d14c6e3fe1902f314a9b'], + }), + ('jupyter_collaboration', version, { + 'checksums': ['4f50c25c6d81126c16deaf92d2bd78a39b2fcb86690dce696b4006b740d71c1f'], + }), +] + +sanity_check_paths = { + 'files': ['bin/jupyter-fileid'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/', 'etc/jupyter', 'share/jupyter'], +} + +# Add the notebook extension to the search path for jupyter notebooks +modextrapaths = {'EB_ENV_JUPYTER_ROOT': ''} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/jupyter-vscode-proxy/jupyter-vscode-proxy-0.6-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/jupyter-vscode-proxy/jupyter-vscode-proxy-0.6-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..1f8a364ba257 --- /dev/null +++ b/easybuild/easyconfigs/j/jupyter-vscode-proxy/jupyter-vscode-proxy-0.6-GCCcore-12.3.0.eb @@ -0,0 +1,32 @@ +easyblock = "PythonBundle" + +name = 'jupyter-vscode-proxy' +version = '0.6' + +homepage = 'https://github.com/betatim/vscode-binder' +description = "VS Code extension for Jupyter" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('jupyter-server-proxy', '4.0.0'), + ('code-server', '4.90.2', '', SYSTEM), +] + +use_pip = True + +exts_list = [ + ('jupyter_vscode_proxy', version, { + 'sources': ['%(name)s-%(version)s-py3-none-any.whl'], + 'checksums': ['c72037d1234f0cd489ecb0ab40ec8b150fc9cd7006b4d9c7036200e76689da78'], + }), +] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/k/Kaleido/Kaleido-0.2.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/k/Kaleido/Kaleido-0.2.1-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..231466bb169e --- /dev/null +++ b/easybuild/easyconfigs/k/Kaleido/Kaleido-0.2.1-GCCcore-12.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonBundle' + +name = 'Kaleido' +version = '0.2.1' + +homepage = 'https://github.com/plotly/Kaleido' +description = "Fast static image export for web-based visualization libraries with zero dependencies" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [('Python', '3.11.3')] + +if ARCH == 'x86_64': + local_source_tmpl = '%(namelower)s-%(version)s-py2.py3-none-manylinux1_%(arch)s.whl' +elif ARCH == 'aarch64': + local_source_tmpl = '%(namelower)s-%(version)s-py2.py3-none-manylinux2014_%(arch)s.whl' + +exts_list = [ + (name, version, { + 'source_tmpl': local_source_tmpl, + 'checksums': ['aa21cf1bf1c78f8fa50a9f7d45e1003c387bd3d6fe0a767cfbbf344b95bdc3a8'], + }), +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/k/Kent_tools/Kent_tools-461-GCC-12.2.0.eb b/easybuild/easyconfigs/k/Kent_tools/Kent_tools-461-GCC-12.2.0.eb new file mode 100644 index 000000000000..9679801e25f9 --- /dev/null +++ b/easybuild/easyconfigs/k/Kent_tools/Kent_tools-461-GCC-12.2.0.eb @@ -0,0 +1,44 @@ +easyblock = 'MakeCp' + +name = 'Kent_tools' +version = '461' + +homepage = 'https://genome.cse.ucsc.edu/' +description = """Kent utilities: collection of tools used by the UCSC genome browser.""" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} +source_urls = [ + 'https://hgdownload.cse.ucsc.edu/admin/exe/', + 'https://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/', +] +sources = ['userApps.v%(version)s.src.tgz'] +checksums = [ + {'userApps.v461.src.tgz': 'ff350f030906bea2cdfa5c57d713568123e17c1a5c0ce578d2d9633ca1b742bc'}, +] + +dependencies = [ + ('MariaDB', '10.11.2'), + ('libpng', '1.6.38'), + ('zlib', '1.2.12'), + ('util-linux', '2.38.1'), + ('OpenSSL', '1.1', '', SYSTEM), + ('freetype', '2.12.1'), +] + +prebuildopts = 'sed -i "s/rsync -a /cp -a /" %(builddir)s/userApps/kent/src/parasol/makefile && ' + +buildopts = 'CC="$CC" COPT="$CFLAGS -fcommon" PNGLIB="-L$EBROOTLIBPNG/lib -lpng" ZLIB="-L$EBROOTZLIB/lib -lz" ' +buildopts += 'SSL_DIR="$EBROOTOPENSSL" SSLDIR="$EBROOTOPENSSL" MYSQLLIBS="-L$EBROOTMARIADB/lib -lmariadb -lstdc++" ' + +local_binaries = ['blat', 'bedPartition', 'getRna', 'liftOver', 'mafGene', 'splitFile', 'twoBitToFa'] + +files_to_copy = [(['bin/*'], 'bin'), 'licenseBlat.txt', 'licenseUcscGenomeBrowser.txt'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_binaries], + 'dirs': [], +} + +sanity_check_commands = ["%s 2>&1 | grep '^usage:'" % x for x in local_binaries] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/k/Kent_tools/Kent_tools-468-GCC-12.3.0.eb b/easybuild/easyconfigs/k/Kent_tools/Kent_tools-468-GCC-12.3.0.eb new file mode 100644 index 000000000000..e4fd527e908c --- /dev/null +++ b/easybuild/easyconfigs/k/Kent_tools/Kent_tools-468-GCC-12.3.0.eb @@ -0,0 +1,42 @@ +easyblock = 'MakeCp' + +name = 'Kent_tools' +version = '468' + +homepage = 'https://genome.cse.ucsc.edu/' +description = """Kent utilities: collection of tools used by the UCSC genome browser.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} +source_urls = [ + 'https://hgdownload.cse.ucsc.edu/admin/exe/', + 'https://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/', +] +sources = ['userApps.v%(version)s.src.tgz'] +checksums = ['f57b49be7e4eeb0719ac9414ca8878f93916fc3eb8dd408c8f7e076a999d1ca8'] + +dependencies = [ + ('MariaDB', '11.6.0'), + ('libpng', '1.6.39'), + ('zlib', '1.2.13'), + ('util-linux', '2.39'), + ('OpenSSL', '1.1', '', SYSTEM), + ('freetype', '2.13.0'), +] + +prebuildopts = 'sed -i "s/rsync -a /cp -a /" %(builddir)s/userApps/kent/src/parasol/makefile && ' + +buildopts = 'CC="$CC" COPT="$CFLAGS -fcommon" PNGLIB="-L$EBROOTLIBPNG/lib -lpng" ZLIB="-L$EBROOTZLIB/lib -lz" ' +buildopts += 'SSL_DIR="$EBROOTOPENSSL" SSLDIR="$EBROOTOPENSSL" MYSQLLIBS="-L$EBROOTMARIADB/lib -lmariadb -lstdc++" ' + +local_binaries = ['blat', 'bedPartition', 'getRna', 'liftOver', 'mafGene', 'splitFile', 'twoBitToFa'] + +files_to_copy = [(['bin/*'], 'bin'), 'licenseBlat.txt', 'licenseUcscGenomeBrowser.txt'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_binaries], + 'dirs': [], +} + +sanity_check_commands = ["%s 2>&1 | grep '^usage:'" % x for x in local_binaries] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/k/kineto/kineto-0.4.0-GCC-12.3.0.eb b/easybuild/easyconfigs/k/kineto/kineto-0.4.0-GCC-12.3.0.eb new file mode 100644 index 000000000000..4dd6b4afdf1e --- /dev/null +++ b/easybuild/easyconfigs/k/kineto/kineto-0.4.0-GCC-12.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'CMakeMake' + +name = 'kineto' +version = '0.4.0' + +homepage = 'https://github.com/pytorch/kineto' +description = "A CPU+GPU Profiling library that provides access to timeline traces and hardware performance counters" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/pytorch/kineto/archive/'] +sources = [{ + 'git_config': { + 'url': 'https://github.com/pytorch', + 'repo_name': name, + 'tag': 'v%(version)s', + 'recursive': True, + }, + 'filename': SOURCE_TAR_GZ, +}] +checksums = [None] + +builddependencies = [ + ('CMake', '3.26.3'), + ('Python', '3.11.3'), +] + +start_dir = 'libkineto' + +sanity_check_paths = { + 'files': ['lib/libkineto.a'], + 'dirs': ['include/kineto'], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-11.2.0.eb index 1bb5846fed47..9e8668e6a501 100644 --- a/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-11.2.0.eb @@ -25,9 +25,6 @@ dependencies = [('ncurses', '6.2')] preconfigopts = "autoconf && " -# configure is broken: add workaround to find libncurses... -configure_cmd_prefix = "FRONTEND_LDADD='-L${EBROOTNCURSES}/lib' " - sanity_check_paths = { 'files': ['bin/lame', 'include/lame/lame.h', 'lib/libmp3lame.%s' % SHLIB_EXT], 'dirs': [], diff --git a/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-11.3.0.eb index f067051ffe7e..5efdefb761f6 100644 --- a/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-11.3.0.eb @@ -25,9 +25,6 @@ dependencies = [('ncurses', '6.3')] preconfigopts = "autoconf && " -# configure is broken: add workaround to find libncurses... -configure_cmd_prefix = "FRONTEND_LDADD='-L${EBROOTNCURSES}/lib' " - sanity_check_paths = { 'files': ['bin/lame', 'include/lame/lame.h', 'lib/libmp3lame.%s' % SHLIB_EXT], 'dirs': [], diff --git a/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-12.2.0.eb index 4008e0b34555..7d4bae408d59 100644 --- a/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-12.2.0.eb @@ -25,9 +25,6 @@ dependencies = [('ncurses', '6.3')] preconfigopts = "autoconf && " -# configure is broken: add workaround to find libncurses... -configure_cmd_prefix = "FRONTEND_LDADD='-L${EBROOTNCURSES}/lib' " - sanity_check_paths = { 'files': ['bin/lame', 'include/lame/lame.h', 'lib/libmp3lame.%s' % SHLIB_EXT], 'dirs': [], diff --git a/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-12.3.0.eb index 4573d76f9472..a4c7dbd42780 100644 --- a/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-12.3.0.eb @@ -25,9 +25,6 @@ dependencies = [('ncurses', '6.4')] preconfigopts = "autoconf && " -# configure is broken: add workaround to find libncurses... -configure_cmd_prefix = "FRONTEND_LDADD='-L${EBROOTNCURSES}/lib' " - sanity_check_paths = { 'files': ['bin/lame', 'include/lame/lame.h', 'lib/libmp3lame.%s' % SHLIB_EXT], 'dirs': [], diff --git a/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-13.2.0.eb index 7b163dff6997..1bffb9a1939b 100644 --- a/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-13.2.0.eb @@ -25,9 +25,6 @@ dependencies = [('ncurses', '6.4')] preconfigopts = "autoconf && " -# configure is broken: add workaround to find libncurses... -configure_cmd_prefix = "FRONTEND_LDADD='-L${EBROOTNCURSES}/lib' " - sanity_check_paths = { 'files': ['bin/lame', 'include/lame/lame.h', 'lib/libmp3lame.%s' % SHLIB_EXT], 'dirs': [], diff --git a/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..1fa3ca78fd97 --- /dev/null +++ b/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-13.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'LAME' +version = '3.100' + +homepage = 'http://lame.sourceforge.net/' +description = """LAME is a high quality MPEG Audio Layer III (MP3) encoder licensed under the LGPL.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://sourceforge.net/projects/lame/files/lame/%(version_major_minor)s/'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['LAME-3.99.5_check-tgetent.patch'] +checksums = [ + 'ddfe36cab873794038ae2c1210557ad34857a4b6bdc515785d1da9e175b1da1e', # lame-3.100.tar.gz + '8bfb6a73f2db1511baf90fbd7174f11043ec4b592a4917edc30ccfb53bf37256', # LAME-3.99.5_check-tgetent.patch +] + +builddependencies = [ + ('binutils', '2.42'), + ('Autotools', '20231222'), +] + +dependencies = [('ncurses', '6.5')] + +preconfigopts = "autoconf && " + +# configure is broken: add workaround to find libncurses... +preconfigopts += "FRONTEND_LDADD='-L${EBROOTNCURSES}/lib' " + +sanity_check_paths = { + 'files': ['bin/lame', 'include/lame/lame.h', 'lib/libmp3lame.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-18.1.8-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/LLVM/LLVM-18.1.8-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..a0c29eba130a --- /dev/null +++ b/easybuild/easyconfigs/l/LLVM/LLVM-18.1.8-GCCcore-13.3.0.eb @@ -0,0 +1,48 @@ +name = 'LLVM' +version = '18.1.8' + +homepage = "https://llvm.org/" +description = """The LLVM Core libraries provide a modern source- and target-independent + optimizer, along with code generation support for many popular CPUs + (as well as some less common ones!) These libraries are built around a well + specified code representation known as the LLVM intermediate representation + ("LLVM IR"). The LLVM Core libraries are well documented, and it is + particularly easy to invent your own language (or port an existing compiler) + to use LLVM as an optimizer and code generator.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'cstd': 'gnu++11', 'pic': True} + +source_urls = ['https://github.com/llvm/llvm-project/releases/download/llvmorg-%(version)s/'] +sources = [ + 'llvm-%(version)s.src.tar.xz', + 'cmake-%(version)s.src.tar.xz', + 'third-party-%(version)s.src.tar.xz', +] +checksums = [ + {'llvm-18.1.8.src.tar.xz': 'f68cf90f369bc7d0158ba70d860b0cb34dbc163d6ff0ebc6cfa5e515b9b2e28d'}, + {'cmake-18.1.8.src.tar.xz': '59badef592dd34893cd319d42b323aaa990b452d05c7180ff20f23ab1b41e837'}, + {'third-party-18.1.8.src.tar.xz': 'b76b810f3d3dc5d08e83c4236cb6e395aa9bd5e3ea861e8c319b216d093db074'}, +] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), + ('Python', '3.12.3'), +] + +dependencies = [ + ('ncurses', '6.5'), + ('zlib', '1.3.1'), +] + +build_shared_libs = True + +sanity_check_paths = { + 'files': ['bin/llvm-ar', 'bin/FileCheck'], + 'dirs': ['include/llvm', 'include/llvm-c'], +} + +sanity_check_commands = ["llvm-ar --help"] + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/l/LMDB/LMDB-0.9.31-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/LMDB/LMDB-0.9.31-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..a10be56a891d --- /dev/null +++ b/easybuild/easyconfigs/l/LMDB/LMDB-0.9.31-GCCcore-13.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'MakeCp' + +name = 'LMDB' +version = '0.9.31' + +homepage = 'https://symas.com/lmdb' +description = """LMDB is a fast, memory-efficient database. With memory-mapped files, it has the read performance + of a pure in-memory database while retaining the persistence of standard disk-based databases.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/LMDB/lmdb/archive/'] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['dd70a8c67807b3b8532b3e987b0a4e998962ecc28643e1af5ec77696b081c9b0'] + +builddependencies = [('binutils', '2.42')] + +buildopts = 'CC="$CC" OPT="$CFLAGS"' + +runtest = 'test' + +local_binaries = ['mdb_copy', 'mdb_dump', 'mdb_load', 'mdb_stat'] + +files_to_copy = [ + (['lmdb.h', 'midl.h'], 'include'), + (local_binaries, 'bin'), + (['liblmdb.a', 'liblmdb.%s' % SHLIB_EXT], 'lib'), +] + +sanity_check_paths = { + 'files': ['bin/mdb_copy', 'bin/mdb_dump', 'bin/mdb_load', 'bin/mdb_stat', 'include/lmdb.h', + 'include/midl.h', 'lib/liblmdb.a', 'lib/liblmdb.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ["%s -V" % x for x in local_binaries] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/LRBinner/LRBinner-0.1-foss-2023a.eb b/easybuild/easyconfigs/l/LRBinner/LRBinner-0.1-foss-2023a.eb new file mode 100644 index 000000000000..143e59d35c5e --- /dev/null +++ b/easybuild/easyconfigs/l/LRBinner/LRBinner-0.1-foss-2023a.eb @@ -0,0 +1,44 @@ +easyblock = 'PythonBundle' + +name = 'LRBinner' +version = '0.1' + +homepage = 'https://github.com/anuradhawick/LRBinner' +description = "LRBinner is a long-read binning tool published in WABI 2021 proceedings and AMB. " + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('HMMER', '3.4'), + ('Seaborn', '0.13.2'), + ('h5py', '3.9.0'), + ('PyTorch', '2.1.2'), + ('tqdm', '4.66.1'), + ('Biopython', '1.83'), + ('scikit-learn', '1.3.1'), + ('FragGeneScan', '1.31'), + ('HDBSCAN', '0.8.38.post1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('tabulate', '0.9.0', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['024ca478df22e9340661486f85298cff5f6dcdba14f3813e8830015b9ed1948f'], + }), + (name, version, { + 'modulename': 'mbcclr_utils', + 'preinstallopts': "sed -i 's/pytorch/torch/g' setup.py && ", + 'source_urls': ['https://github.com/anuradhawick/LRBinner/archive/'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['2d77dde8ab1272c432b20eb18a352326c622e929261562ef6d680c6638cc4bd1'], + }), +] + +sanity_check_commands = ['LRBinner --help'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/LZO/LZO-2.10-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/LZO/LZO-2.10-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..4d8ccd20b1f5 --- /dev/null +++ b/easybuild/easyconfigs/l/LZO/LZO-2.10-GCCcore-13.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'LZO' +version = '2.10' + +homepage = 'https://www.oberhumer.com/opensource/lzo/' +description = "Portable lossless data compression library" + +source_urls = [homepage + 'download/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c0f892943208266f9b6543b3ae308fab6284c5c90e627931446fb49b4221a072'] + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +builddependencies = [('binutils', '2.42')] + +configopts = '--enable-shared' + +runtest = 'test' + +sanity_check_paths = { + 'files': ['lib/liblzo2.a', 'lib/liblzo2.%s' % SHLIB_EXT], + 'dirs': ['include'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.16-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.16-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..121d33200a22 --- /dev/null +++ b/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.16-GCCcore-13.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'LittleCMS' +version = '2.16' + +homepage = 'https://www.littlecms.com/' +description = """ Little CMS intends to be an OPEN SOURCE small-footprint color management engine, + with special focus on accuracy and performance. """ + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://sourceforge.net/projects/lcms/files/lcms/%s/' % '.'.join(version.split('.')[:2])] +sources = ['lcms2-%(version)s.tar.gz'] +checksums = ['d873d34ad8b9b4cea010631f1a6228d2087475e4dc5e763eb81acc23d9d45a51'] + +builddependencies = [('binutils', '2.42')] + +dependencies = [('libjpeg-turbo', '3.0.1')] + +sanity_check_paths = { + 'files': ['bin/jpgicc', 'bin/linkicc', 'bin/psicc', 'bin/transicc', 'include/lcms2.h', 'include/lcms2_plugin.h', + 'lib/liblcms2.a', 'lib/liblcms2.%s' % SHLIB_EXT, 'lib/pkgconfig/lcms2.pc'], + 'dirs': ['share/man'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/langchain-anthropic/langchain-anthropic-0.1.15-foss-2023a.eb b/easybuild/easyconfigs/l/langchain-anthropic/langchain-anthropic-0.1.15-foss-2023a.eb index 1bb545a30d32..6031932aa6cc 100644 --- a/easybuild/easyconfigs/l/langchain-anthropic/langchain-anthropic-0.1.15-foss-2023a.eb +++ b/easybuild/easyconfigs/l/langchain-anthropic/langchain-anthropic-0.1.15-foss-2023a.eb @@ -11,7 +11,6 @@ This package contains the LangChain integration for Anthropic's generative model toolchain = {'name': 'foss', 'version': '2023a'} builddependencies = [ - ('maturin', '1.1.0'), ('poetry', '1.5.1'), ] diff --git a/easybuild/easyconfigs/l/langchain-mistralai/langchain-mistralai-0.1.8-foss-2023a.eb b/easybuild/easyconfigs/l/langchain-mistralai/langchain-mistralai-0.1.8-foss-2023a.eb new file mode 100644 index 000000000000..78fc26dda3fb --- /dev/null +++ b/easybuild/easyconfigs/l/langchain-mistralai/langchain-mistralai-0.1.8-foss-2023a.eb @@ -0,0 +1,59 @@ +easyblock = 'PythonBundle' + +name = 'langchain-mistralai' +version = '0.1.8' + +homepage = 'https://github.com/langchain-ai/langchain' +description = """ +This package contains the LangChain integrations for MistralAI through their mistralai SDK. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('poetry', '1.5.1'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('LangChain', '0.2.1'), + ('tokenizers', '0.15.2'), + ('jiter', '0.4.1'), +] + +exts_list = [ + ('langchain-core', '0.2.3', { + 'sources': ['langchain_core-%(version)s.tar.gz'], + 'checksums': ['fbc75a64b9c0b7655d96ca57a707df1e6c09efc1539c36adbd73260612549810'], + }), + ('anyio', '4.4.0', { + 'checksums': ['5aadc6a1bbb7cdb0bede386cac5e2940f5e2ff3aa20277e991cf028e0585ce94'], + }), + ('h11', '0.14.0', { + 'checksums': ['8f19fbbe99e72420ff35c00b27a34cb9937e902a8b810e2c88300c6f0a3b699d'], + }), + ('httpcore', '1.0.5', { + 'checksums': ['34a38e2f9291467ee3b44e89dd52615370e152954ba21721378a87b2960f7a61'], + }), + ('httpx', '0.25.2', { + 'checksums': ['8b8fcaa0c8ea7b05edd69a094e63a2094c4efcb48129fb757361bc423c0ad9e8'], + }), + ('httpx-sse', '0.4.0', { + 'checksums': ['1e81a3a3070ce322add1d3529ed42eb5f70817f45ed6ec915ab753f961139721'], + }), + ('sniffio', '1.3.1', { + 'checksums': ['f4324edc670a0f49750a81b895f35c3adb843cca46f0530f79fc1babb23789dc'], + }), + ('mistralai', '0.4.0', { + 'checksums': ['1f21f02dec1fd6fefe12ca100d5937fd62542c11008c193d16df6f4a2d8554da'], + }), + (name, version, { + 'sources': ['langchain_mistralai-%(version)s.tar.gz'], + 'checksums': ['dc328f7aedfd9e88eeb79de5692dfc3907793b82ef59f0d6722d19c1c8bfcdc2'], + }), +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/l/langchain-openai/langchain-openai-0.1.8-foss-2023a.eb b/easybuild/easyconfigs/l/langchain-openai/langchain-openai-0.1.8-foss-2023a.eb new file mode 100644 index 000000000000..e46f2e43b4ca --- /dev/null +++ b/easybuild/easyconfigs/l/langchain-openai/langchain-openai-0.1.8-foss-2023a.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonBundle' + +name = 'langchain-openai' +version = '0.1.8' + +homepage = 'https://github.com/langchain-ai/langchain' +description = """ +This package contains the LangChain integrations for OpenAI through their openai SDK. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('poetry', '1.5.1'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('LangChain', '0.2.1'), + ('tiktoken', '0.7.0'), # needs tiktoken >= 0.7.0 + ('openai-python', '1.30.5'), +] + +exts_list = [ + (name, version, { + 'sources': ['langchain_openai-%(version)s.tar.gz'], + 'checksums': ['a11fcce15def7917c44232abda6baaa63dfc79fe44be1531eea650d39a44cd95'], + }), +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/l/libcircle/libcircle-0.3-gompi-2024a.eb b/easybuild/easyconfigs/l/libcircle/libcircle-0.3-gompi-2024a.eb new file mode 100644 index 000000000000..1ea2630b3271 --- /dev/null +++ b/easybuild/easyconfigs/l/libcircle/libcircle-0.3-gompi-2024a.eb @@ -0,0 +1,38 @@ +## +# Authors: +# * Petar Forai +# * Robert Mijakovic +## +easyblock = 'ConfigureMake' + +name = 'libcircle' +version = '0.3' + +homepage = 'https://github.com/hpc/libcircle/' + +description = """ + An API to provide an efficient distributed queue on a cluster. libcircle is an + API for distributing embarrassingly parallel workloads using self-stabilization. +""" + +toolchain = {'name': 'gompi', 'version': '2024a'} +toolchainopts = {'usempi': True, 'pic': True} + +github_account = 'hpc' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['fd8bc6e4dcc6fdec9d2a3d1c78a4060948ae4f11f0b278792610d6c05d53e14c'] + +builddependencies = [ + ('Autotools', '20231222'), + ('pkgconf', '2.2.0'), +] + +preconfigopts = './autogen.sh && ' + +sanity_check_paths = { + 'files': ['include/%(name)s.h', 'lib/%(name)s.a', 'lib/%%(name)s.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libdap/libdap-3.20.11-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libdap/libdap-3.20.11-GCCcore-11.3.0.eb index 237260a43f78..063ce985f475 100644 --- a/easybuild/easyconfigs/l/libdap/libdap-3.20.11-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/l/libdap/libdap-3.20.11-GCCcore-11.3.0.eb @@ -9,14 +9,15 @@ description = """A C++ SDK which contains an implementation of DAP 2.0 and toolchain = {'name': 'GCCcore', 'version': '11.3.0'} -source_urls = ['https://www.opendap.org/pub/source/'] -sources = [SOURCE_TAR_GZ] -checksums = ['850debf6ee6991350bf31051308093bee35ddd2121e4002be7e130a319de1415'] +source_urls = ['https://github.com/OPENDAP/libdap4/archive/refs/tags/'] +sources = ['%(version)s.tar.gz'] +checksums = ['319e9771d037b6c796f04e6a96bb27db1706bc5931ca149c78347c623a747771'] builddependencies = [ ('binutils', '2.38'), ('Bison', '3.8.2'), ('flex', '2.6.4'), + ('Autotools', '20220317'), ] dependencies = [ @@ -27,6 +28,7 @@ dependencies = [ ('util-linux', '2.38'), ] +preconfigopts = "autoreconf -fi && " configopts = 'TIRPC_LIBS="-ltirpc"' sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/libdap/libdap-3.20.11-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libdap/libdap-3.20.11-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..a6dbd52797f5 --- /dev/null +++ b/easybuild/easyconfigs/l/libdap/libdap-3.20.11-GCCcore-12.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'libdap' +version = '3.20.11' + +homepage = 'https://www.opendap.org/software/libdap' +description = """A C++ SDK which contains an implementation of DAP 2.0 and + DAP4.0. This includes both Client- and Server-side support classes.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/OPENDAP/libdap4/archive/refs/tags/'] +sources = ['%(version)s.tar.gz'] +checksums = ['319e9771d037b6c796f04e6a96bb27db1706bc5931ca149c78347c623a747771'] + +builddependencies = [ + ('binutils', '2.40'), + ('Bison', '3.8.2'), + ('flex', '2.6.4'), + ('Autotools', '20220317'), +] + +dependencies = [ + ('cURL', '8.0.1'), + ('libxml2', '2.11.4'), + ('libtirpc', '1.3.3'), + ('PCRE', '8.45'), + ('util-linux', '2.39'), +] + +preconfigopts = "autoreconf -fi && " +configopts = 'TIRPC_LIBS="-ltirpc"' + + +sanity_check_paths = { + 'files': ['bin/getdap', 'bin/getdap4', 'bin/dap-config', 'lib/libdap.a', 'lib/libdap.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libdap/libdap-3.20.7-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libdap/libdap-3.20.7-GCCcore-10.3.0.eb index e2bb8f718abb..c1cb33551f72 100644 --- a/easybuild/easyconfigs/l/libdap/libdap-3.20.7-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/l/libdap/libdap-3.20.7-GCCcore-10.3.0.eb @@ -9,14 +9,15 @@ description = """A C++ SDK which contains an implementation of DAP 2.0 and toolchain = {'name': 'GCCcore', 'version': '10.3.0'} -source_urls = ['https://www.opendap.org/pub/source/'] -sources = [SOURCE_TAR_GZ] -checksums = ['6856813d0b29e70a36e8a53e9cf20ad680d21d615952263e9c6586704539e78c'] +source_urls = ['https://github.com/OPENDAP/libdap4/archive/refs/tags/'] +sources = ['%(version)s.tar.gz'] +checksums = ['f6e907ea7a9f878965a3af2a858423450dde389d851fc67a33b0096b8b9b6085'] builddependencies = [ ('binutils', '2.36.1'), ('Bison', '3.7.6'), ('flex', '2.6.4'), + ('Autotools', '20210128'), ] dependencies = [ @@ -27,6 +28,7 @@ dependencies = [ ('util-linux', '2.36'), ] +preconfigopts = "autoreconf -fi && " configopts = 'TIRPC_LIBS="-ltirpc"' sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/libdap/libdap-3.20.8-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libdap/libdap-3.20.8-GCCcore-11.2.0.eb index b48c3f1b6bc9..1172b66d8f25 100644 --- a/easybuild/easyconfigs/l/libdap/libdap-3.20.8-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/l/libdap/libdap-3.20.8-GCCcore-11.2.0.eb @@ -9,14 +9,15 @@ description = """A C++ SDK which contains an implementation of DAP 2.0 and toolchain = {'name': 'GCCcore', 'version': '11.2.0'} -source_urls = ['https://www.opendap.org/pub/source/'] -sources = [SOURCE_TAR_GZ] -checksums = ['65eb5c8f693cf74d58eece5eaa2e7c3c65f368926b1bffab0cf5b207757b94eb'] +source_urls = ['https://github.com/OPENDAP/libdap4/archive/refs/tags/'] +sources = ['%(version)s.tar.gz'] +checksums = ['e59b48f48bb37b36dcf9618043881e1d4150abd9b2ea3fa7474647c4ad622ccc'] builddependencies = [ ('binutils', '2.37'), ('Bison', '3.7.6'), ('flex', '2.6.4'), + ('Autotools', '20210726'), ] dependencies = [ @@ -27,6 +28,7 @@ dependencies = [ ('util-linux', '2.37'), ] +preconfigopts = "autoreconf -fi && " configopts = 'TIRPC_LIBS="-ltirpc"' sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.122-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.122-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..beff58c433a8 --- /dev/null +++ b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.122-GCCcore-13.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'MesonNinja' + +name = 'libdrm' +version = '2.4.122' + +homepage = 'https://dri.freedesktop.org' +description = """Direct Rendering Manager runtime library.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://dri.freedesktop.org/libdrm/'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['d9f5079b777dffca9300ccc56b10a93588cdfbc9dde2fae111940dfb6292f251'] + +builddependencies = [ + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), + ('Meson', '1.4.0'), + ('Ninja', '1.12.1'), +] +dependencies = [('X11', '20240607')] + +# installing manpages requires an extra build dependency (docbook xsl) +configopts = '-Dman-pages=disabled' + +sanity_check_paths = { + 'files': ['lib/libdrm.%s' % SHLIB_EXT, 'include/libdrm/drm.h'], + 'dirs': ['include', 'lib'], +} + + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libdwarf/libdwarf-0.10.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libdwarf/libdwarf-0.10.1-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..95a46c43114f --- /dev/null +++ b/easybuild/easyconfigs/l/libdwarf/libdwarf-0.10.1-GCCcore-13.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libdwarf' +version = '0.10.1' + +homepage = 'https://www.prevanders.net/dwarf.html' +description = """The DWARF Debugging Information Format is of interest to programmers working on compilers +and debuggers (and anyone interested in reading or writing DWARF information))""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/davea42/libdwarf-code/releases/download/v%(version)s'] +sources = [SOURCE_TAR_XZ] +checksums = ['b511a2dc78b98786064889deaa2c1bc48a0c70115c187900dd838474ded1cc19'] + +builddependencies = [ + ('binutils', '2.42'), +] +dependencies = [ + ('elfutils', '0.191'), +] + +configopts = "--enable-shared " + +sanity_check_paths = { + 'files': ['bin/dwarfdump', 'lib/libdwarf.a', 'lib/libdwarf.%s' % SHLIB_EXT], + 'dirs': ['include'] +} + +sanity_check_commands = ['dwarfdump --help'] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libedit/libedit-20240517-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libedit/libedit-20240517-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..098fd8b7bde6 --- /dev/null +++ b/easybuild/easyconfigs/l/libedit/libedit-20240517-GCCcore-13.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libedit' +version = '20240517' + +homepage = 'https://thrysoee.dk/editline/' +description = """ +This BSD-style licensed command line editor library provides generic line editing, +history, and tokenization functions, similar to those found in GNU Readline. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://thrysoee.dk/editline/'] +sources = ['%(namelower)s-%(version)s-3.1.tar.gz'] +checksums = ['3a489097bb4115495f3bd85ae782852b7097c556d9500088d74b6fa38dbd12ff'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [('ncurses', '6.4')] + +sanity_check_paths = { + 'files': ['include/editline/readline.h', 'lib/libedit.%s' % SHLIB_EXT, 'lib/libedit.a'], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libgeotiff/libgeotiff-1.7.3-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libgeotiff/libgeotiff-1.7.3-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..ce66887030e7 --- /dev/null +++ b/easybuild/easyconfigs/l/libgeotiff/libgeotiff-1.7.3-GCCcore-13.2.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'libgeotiff' +version = '1.7.3' + +homepage = 'https://directory.fsf.org/wiki/Libgeotiff' +description = """Library for reading and writing coordinate system information from/to GeoTIFF files""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://download.osgeo.org/geotiff/libgeotiff'] +sources = [SOURCE_TAR_GZ] +checksums = ['ba23a3a35980ed3de916e125c739251f8e3266be07540200125a307d7cf5a704'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('PROJ', '9.3.1'), + ('libjpeg-turbo', '3.0.1'), + ('zlib', '1.2.13'), + ('SQLite', '3.43.1'), + ('LibTIFF', '4.6.0'), + ('cURL', '8.3.0'), +] + +configopts = ' --with-libtiff=$EBROOTLIBTIFF --with-proj=$EBROOTPROJ --with-zlib=$EBROOTZLIB' +configopts += ' --with-jpeg=$EBROOTLIBJPEGMINTURBO' + +sanity_check_paths = { + 'files': ['bin/listgeo', 'lib/libgeotiff.a', 'lib/libgeotiff.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libgit2/libgit2-1.8.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libgit2/libgit2-1.8.1-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..07da30e2a80e --- /dev/null +++ b/easybuild/easyconfigs/l/libgit2/libgit2-1.8.1-GCCcore-13.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'CMakeMake' + +name = 'libgit2' +version = '1.8.1' + +homepage = 'https://libgit2.org/' +description = """libgit2 is a portable, pure C implementation of the Git core methods provided as a re-entrant +linkable library with a solid API, allowing you to write native speed custom Git applications in any language +which supports C bindings.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [GITHUB_SOURCE] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['8c1eaf0cf07cba0e9021920bfba9502140220786ed5d8a8ec6c7ad9174522f8e'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), + ('pkgconf', '2.2.0'), +] +dependencies = [ + ('PCRE2', '10.43'), + ('OpenSSL', '3', '', SYSTEM), +] + +configopts = '-DREGEX_BACKEND=pcre2' + +sanity_check_paths = { + 'files': ['include/git2.h', 'lib64/%%(name)s.%s' % SHLIB_EXT, 'lib64/pkgconfig/%(name)s.pc'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libglvnd/libglvnd-1.7.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libglvnd/libglvnd-1.7.0-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..c6a03d1b419e --- /dev/null +++ b/easybuild/easyconfigs/l/libglvnd/libglvnd-1.7.0-GCCcore-13.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'MesonNinja' + +name = 'libglvnd' +version = '1.7.0' + +homepage = 'https://gitlab.freedesktop.org/glvnd/libglvnd' +description = "libglvnd is a vendor-neutral dispatch layer for arbitrating OpenGL API calls between multiple vendors." + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://gitlab.freedesktop.org/glvnd/libglvnd/-/archive/v%(version)s/'] +sources = ['libglvnd-v%(version)s.tar.gz'] +checksums = ['2b6e15b06aafb4c0b6e2348124808cbd9b291c647299eaaba2e3202f51ff2f3d'] + +builddependencies = [ + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), + ('Meson', '1.4.0'), + ('Ninja', '1.12.1'), +] + +dependencies = [('X11', '20240607')] + +# Let EGL find system-installed vendor files in /etc/glvnd/egl_vendor.d etc. +allow_prepend_abs_path = True +modextrapaths = {"__EGL_VENDOR_LIBRARY_DIRS": "/etc/glvnd/egl_vendor.d:/usr/share/glvnd/egl_vendor.d"} + +sanity_check_paths = { + 'files': ['lib/lib%s.%s' % (x, SHLIB_EXT) for x in ['EGL', 'GL', 'GLX', 'OpenGL']], + 'dirs': ['include/%s' % x for x in ['EGL', 'GL', 'GLES', 'GLES2', 'GLES3', 'glvnd', 'KHR']] + ['lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libidn2/libidn2-2.3.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libidn2/libidn2-2.3.4-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..b9ddb22009e0 --- /dev/null +++ b/easybuild/easyconfigs/l/libidn2/libidn2-2.3.4-GCCcore-12.2.0.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libidn2' +version = '2.3.4' + +homepage = 'http://www.gnu.org/software/%(name)s' +description = """Libidn2 implements the revised algorithm for internationalized domain names called IDNA2008/TR46.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://ftp.gnu.org/gnu/libidn/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['93caba72b4e051d1f8d4f5a076ab63c99b77faee019b72b9783b267986dbb45f'] + +builddependencies = [('binutils', '2.39')] + +sanity_check_paths = { + 'files': ['bin/idn2', 'lib/libidn2.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +sanity_check_commands = ["idn2 --help"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libmatheval/003-guile2.0.patch b/easybuild/easyconfigs/l/libmatheval/003-guile2.0.patch new file mode 100644 index 000000000000..3f592cadb0de --- /dev/null +++ b/easybuild/easyconfigs/l/libmatheval/003-guile2.0.patch @@ -0,0 +1,402 @@ +Description: Increase precision of floating point tests + guile-2.0 has increased the precision of the floating point maths returns, + so the test suite needs to allow for the correct values to be returned + with higher precision. Thanks to Dave Pigott + Also adapt the configure script to build against guile-2.0 - patch from + Hilo Bengen . + . + libmatheval (1.1.11+dfsg-1.1) unstable; urgency=low + . + * Non-maintainer upload. + * Migrate to guile-2.0 - patch from Hilo Bengen, + extended to support higher precision of return values + by guile-2.0. (Closes: #746013) +Author: Neil Williams +Bug-Debian: https://bugs.debian.org/746013 + +--- + +--- libmatheval-1.1.11+dfsg.orig/configure.in ++++ libmatheval-1.1.11+dfsg/configure.in +@@ -60,10 +60,11 @@ dnl Checks for library functions. + AC_CHECK_FUNCS([bzero memset], [break]) + + dnl Additional Guile feature checks. ++CFLAGS="$CFLAGS $GUILE_CFLAGS" + AC_CHECK_TYPE([scm_t_bits], [AC_DEFINE([HAVE_SCM_T_BITS], [1], [Define to 1 if you have the `scm_t_bits' type.])], [], [#include ]) +-AC_CHECK_LIB([guile], [scm_c_define_gsubr], [AC_DEFINE([HAVE_SCM_C_DEFINE_GSUBR], [1], [Define to 1 if you have the `scm_c_define_gsubr' function.])], [], [$GUILE_LDFLAGS]) +-AC_CHECK_LIB([guile], [scm_make_gsubr], [AC_DEFINE([HAVE_SCM_MAKE_GSUBR], [1], [Define to 1 if you have the `scm_make_gsubr' function.])], [], [$GUILE_LDFLAGS]) +-AC_CHECK_LIB([guile], [scm_num2dbl], [AC_DEFINE([HAVE_SCM_NUM2DBL], [1], [Define to 1 if you have the `scm_num2dbl' function.])], [], [$GUILE_LDFLAGS]) ++AC_CHECK_LIB([guile-2.0], [scm_c_define_gsubr], [AC_DEFINE([HAVE_SCM_C_DEFINE_GSUBR], [1], [Define to 1 if you have the `scm_c_define_gsubr' function.])], [], [$GUILE_LDFLAGS]) ++AC_CHECK_LIB([guile-2.0], [scm_make_gsubr], [AC_DEFINE([HAVE_SCM_MAKE_GSUBR], [1], [Define to 1 if you have the `scm_make_gsubr' function.])], [], [$GUILE_LDFLAGS]) ++AC_CHECK_LIB([guile-2.0], [scm_num2dbl], [AC_DEFINE([HAVE_SCM_NUM2DBL], [1], [Define to 1 if you have the `scm_num2dbl' function.])], [], [$GUILE_LDFLAGS]) + + AC_CONFIG_FILES([Makefile doc/Makefile lib/Makefile]) + AC_OUTPUT(libmatheval.pc) +--- libmatheval-1.1.11+dfsg.orig/tests/basics.at ++++ libmatheval-1.1.11+dfsg/tests/basics.at +@@ -62,7 +62,7 @@ AT_DATA([basics.scm], + (display (evaluator-evaluate-x f 0)) + ]]) + +-AT_CHECK([matheval.sh basics.scm], [ignore], [10.0], [ignore]) ++AT_CHECK([matheval.sh basics.scm], [ignore], [10.000000000000002], [ignore]) + + AT_DATA([basics.scm], + [[ +@@ -70,7 +70,7 @@ AT_DATA([basics.scm], + (display (evaluator-evaluate-x f 0.7)) + ]]) + +-AT_CHECK([matheval.sh basics.scm], [ignore], [0.220966666722528], [ignore]) ++AT_CHECK([matheval.sh basics.scm], [ignore], [0.22096666672252796], [ignore]) + + AT_DATA([basics.scm], + [[ +@@ -78,7 +78,7 @@ AT_DATA([basics.scm], + (display (evaluator-evaluate-x-y f 0.4 -0.7)) + ]]) + +-AT_CHECK([matheval.sh basics.scm], [ignore], [-1.14962406520749], [ignore]) ++AT_CHECK([matheval.sh basics.scm], [ignore], [-1.1496240652074883], [ignore]) + + AT_DATA([basics.scm], + [[ +@@ -86,7 +86,7 @@ AT_DATA([basics.scm], + (display (evaluator-evaluate-x-y-z f 11.2 0.41 -0.66)) + ]]) + +-AT_CHECK([matheval.sh basics.scm], [ignore], [3.99876152571934], [ignore]) ++AT_CHECK([matheval.sh basics.scm], [ignore], [3.9987615257193383], [ignore]) + + AT_DATA([basics.scm], + [[ +--- libmatheval-1.1.11+dfsg.orig/tests/constants.at ++++ libmatheval-1.1.11+dfsg/tests/constants.at +@@ -29,7 +29,7 @@ AT_DATA([constant.scm], + (display (evaluator-evaluate-x f 0)) + ]]) + +-AT_CHECK([matheval.sh constant.scm], [ignore], [2.71828182845905], [ignore]) ++AT_CHECK([matheval.sh constant.scm], [ignore], [2.718281828459045], [ignore]) + + AT_DATA([constant.scm], + [[ +@@ -37,7 +37,7 @@ AT_DATA([constant.scm], + (display (evaluator-evaluate-x f 0)) + ]]) + +-AT_CHECK([matheval.sh constant.scm], [ignore], [1.44269504088896], [ignore]) ++AT_CHECK([matheval.sh constant.scm], [ignore], [1.4426950408889634], [ignore]) + + AT_DATA([constant.scm], + [[ +@@ -45,7 +45,7 @@ AT_DATA([constant.scm], + (display (evaluator-evaluate-x f 0)) + ]]) + +-AT_CHECK([matheval.sh constant.scm], [ignore], [0.434294481903252], [ignore]) ++AT_CHECK([matheval.sh constant.scm], [ignore], [0.4342944819032518], [ignore]) + + AT_DATA([constant.scm], + [[ +@@ -53,7 +53,7 @@ AT_DATA([constant.scm], + (display (evaluator-evaluate-x f 0)) + ]]) + +-AT_CHECK([matheval.sh constant.scm], [ignore], [0.693147180559945], [ignore]) ++AT_CHECK([matheval.sh constant.scm], [ignore], [0.6931471805599453], [ignore]) + + AT_DATA([constant.scm], + [[ +@@ -61,7 +61,7 @@ AT_DATA([constant.scm], + (display (evaluator-evaluate-x f 0)) + ]]) + +-AT_CHECK([matheval.sh constant.scm], [ignore], [2.30258509299405], [ignore]) ++AT_CHECK([matheval.sh constant.scm], [ignore], [2.302585092994046], [ignore]) + + AT_DATA([constant.scm], + [[ +@@ -69,7 +69,7 @@ AT_DATA([constant.scm], + (display (evaluator-evaluate-x f 0)) + ]]) + +-AT_CHECK([matheval.sh constant.scm], [ignore], [3.14159265358979], [ignore]) ++AT_CHECK([matheval.sh constant.scm], [ignore], [3.141592653589793], [ignore]) + + AT_DATA([constant.scm], + [[ +@@ -77,7 +77,7 @@ AT_DATA([constant.scm], + (display (evaluator-evaluate-x f 0)) + ]]) + +-AT_CHECK([matheval.sh constant.scm], [ignore], [1.5707963267949], [ignore]) ++AT_CHECK([matheval.sh constant.scm], [ignore], [1.5707963267948966], [ignore]) + + AT_DATA([constant.scm], + [[ +@@ -85,7 +85,7 @@ AT_DATA([constant.scm], + (display (evaluator-evaluate-x f 0)) + ]]) + +-AT_CHECK([matheval.sh constant.scm], [ignore], [0.785398163397448], [ignore]) ++AT_CHECK([matheval.sh constant.scm], [ignore], [0.7853981633974483], [ignore]) + + AT_DATA([constant.scm], + [[ +@@ -93,7 +93,7 @@ AT_DATA([constant.scm], + (display (evaluator-evaluate-x f 0)) + ]]) + +-AT_CHECK([matheval.sh constant.scm], [ignore], [0.318309886183791], [ignore]) ++AT_CHECK([matheval.sh constant.scm], [ignore], [0.3183098861837907], [ignore]) + + AT_DATA([constant.scm], + [[ +@@ -101,7 +101,7 @@ AT_DATA([constant.scm], + (display (evaluator-evaluate-x f 0)) + ]]) + +-AT_CHECK([matheval.sh constant.scm], [ignore], [0.636619772367581], [ignore]) ++AT_CHECK([matheval.sh constant.scm], [ignore], [0.6366197723675814], [ignore]) + + AT_DATA([constant.scm], + [[ +@@ -109,7 +109,7 @@ AT_DATA([constant.scm], + (display (evaluator-evaluate-x f 0)) + ]]) + +-AT_CHECK([matheval.sh constant.scm], [ignore], [1.12837916709551], [ignore]) ++AT_CHECK([matheval.sh constant.scm], [ignore], [1.1283791670955126], [ignore]) + + AT_DATA([constant.scm], + [[ +@@ -117,7 +117,7 @@ AT_DATA([constant.scm], + (display (evaluator-evaluate-x f 0)) + ]]) + +-AT_CHECK([matheval.sh constant.scm], [ignore], [1.4142135623731], [ignore]) ++AT_CHECK([matheval.sh constant.scm], [ignore], [1.4142135623730951], [ignore]) + + AT_DATA([constant.scm], + [[ +@@ -125,7 +125,7 @@ AT_DATA([constant.scm], + (display (evaluator-evaluate-x f 0)) + ]]) + +-AT_CHECK([matheval.sh constant.scm], [ignore], [0.707106781186548], [ignore]) ++AT_CHECK([matheval.sh constant.scm], [ignore], [0.7071067811865476], [ignore]) + + AT_DATA([constant.scm], + [[ +@@ -133,7 +133,7 @@ AT_DATA([constant.scm], + (display (evaluator-evaluate-x f 0)) + ]]) + +-AT_CHECK([matheval.sh constant.scm], [ignore], [10.0], [ignore]) ++AT_CHECK([matheval.sh constant.scm], [ignore], [10.000000000000002], [ignore]) + + AT_DATA([constant.scm], + [[ +--- libmatheval-1.1.11+dfsg.orig/tests/functions.at ++++ libmatheval-1.1.11+dfsg/tests/functions.at +@@ -29,7 +29,7 @@ AT_DATA([function.scm], + (display (evaluator-evaluate-x f 1)) + ]]) + +-AT_CHECK([matheval.sh function.scm], [ignore], [2.71828182845905], [ignore]) ++AT_CHECK([matheval.sh function.scm], [ignore], [2.718281828459045], [ignore]) + + AT_DATA([function.scm], + [[ +@@ -80,7 +80,7 @@ AT_DATA([function.scm], + (display (evaluator-evaluate-x f 1)) + ]]) + +-AT_CHECK([matheval.sh function.scm], [ignore], [0.841470984807897], [ignore]) ++AT_CHECK([matheval.sh function.scm], [ignore], [0.8414709848078965], [ignore]) + + AT_DATA([function.scm], + [[ +@@ -97,7 +97,7 @@ AT_DATA([function.scm], + (display (evaluator-evaluate-x f 1)) + ]]) + +-AT_CHECK([matheval.sh function.scm], [ignore], [0.54030230586814], [ignore]) ++AT_CHECK([matheval.sh function.scm], [ignore], [0.5403023058681398], [ignore]) + + AT_DATA([function.scm], + [[ +@@ -114,7 +114,7 @@ AT_DATA([function.scm], + (display (evaluator-evaluate-x f 1)) + ]]) + +-AT_CHECK([matheval.sh function.scm], [ignore], [1.5574077246549], [ignore]) ++AT_CHECK([matheval.sh function.scm], [ignore], [1.5574077246549023], [ignore]) + + AT_DATA([function.scm], + [[ +@@ -131,7 +131,7 @@ AT_DATA([function.scm], + (display (evaluator-evaluate-x f 1)) + ]]) + +-AT_CHECK([matheval.sh function.scm], [ignore], [0.642092615934331], [ignore]) ++AT_CHECK([matheval.sh function.scm], [ignore], [0.6420926159343306], [ignore]) + + AT_DATA([function.scm], + [[ +@@ -148,7 +148,7 @@ AT_DATA([function.scm], + (display (evaluator-evaluate-x f 1)) + ]]) + +-AT_CHECK([matheval.sh function.scm], [ignore], [1.85081571768093], [ignore]) ++AT_CHECK([matheval.sh function.scm], [ignore], [1.8508157176809255], [ignore]) + + AT_DATA([function.scm], + [[ +@@ -165,7 +165,7 @@ AT_DATA([function.scm], + (display (evaluator-evaluate-x f 1)) + ]]) + +-AT_CHECK([matheval.sh function.scm], [ignore], [1.18839510577812], [ignore]) ++AT_CHECK([matheval.sh function.scm], [ignore], [1.1883951057781212], [ignore]) + + AT_DATA([function.scm], + [[ +@@ -182,7 +182,7 @@ AT_DATA([function.scm], + (display (evaluator-evaluate-x f 1)) + ]]) + +-AT_CHECK([matheval.sh function.scm], [ignore], [1.5707963267949], [ignore]) ++AT_CHECK([matheval.sh function.scm], [ignore], [1.5707963267948966], [ignore]) + + AT_DATA([function.scm], + [[ +@@ -216,7 +216,7 @@ AT_DATA([function.scm], + (display (evaluator-evaluate-x f 1)) + ]]) + +-AT_CHECK([matheval.sh function.scm], [ignore], [0.785398163397448], [ignore]) ++AT_CHECK([matheval.sh function.scm], [ignore], [0.7853981633974483], [ignore]) + + AT_DATA([function.scm], + [[ +@@ -233,7 +233,7 @@ AT_DATA([function.scm], + (display (evaluator-evaluate-x f 1)) + ]]) + +-AT_CHECK([matheval.sh function.scm], [ignore], [0.785398163397448], [ignore]) ++AT_CHECK([matheval.sh function.scm], [ignore], [0.7853981633974483], [ignore]) + + AT_DATA([function.scm], + [[ +@@ -267,7 +267,7 @@ AT_DATA([function.scm], + (display (evaluator-evaluate-x f 1)) + ]]) + +-AT_CHECK([matheval.sh function.scm], [ignore], [1.5707963267949], [ignore]) ++AT_CHECK([matheval.sh function.scm], [ignore], [1.5707963267948966], [ignore]) + + AT_DATA([function.scm], + [[ +@@ -284,7 +284,7 @@ AT_DATA([function.scm], + (display (evaluator-evaluate-x f 1)) + ]]) + +-AT_CHECK([matheval.sh function.scm], [ignore], [1.1752011936438], [ignore]) ++AT_CHECK([matheval.sh function.scm], [ignore], [1.1752011936438014], [ignore]) + + AT_DATA([function.scm], + [[ +@@ -301,7 +301,7 @@ AT_DATA([function.scm], + (display (evaluator-evaluate-x f 1)) + ]]) + +-AT_CHECK([matheval.sh function.scm], [ignore], [1.54308063481524], [ignore]) ++AT_CHECK([matheval.sh function.scm], [ignore], [1.5430806348152437], [ignore]) + + AT_DATA([function.scm], + [[ +@@ -318,7 +318,7 @@ AT_DATA([function.scm], + (display (evaluator-evaluate-x f 1)) + ]]) + +-AT_CHECK([matheval.sh function.scm], [ignore], [0.761594155955765], [ignore]) ++AT_CHECK([matheval.sh function.scm], [ignore], [0.7615941559557649], [ignore]) + + AT_DATA([function.scm], + [[ +@@ -335,7 +335,7 @@ AT_DATA([function.scm], + (display (evaluator-evaluate-x f 1)) + ]]) + +-AT_CHECK([matheval.sh function.scm], [ignore], [1.31303528549933], [ignore]) ++AT_CHECK([matheval.sh function.scm], [ignore], [1.3130352854993315], [ignore]) + + AT_DATA([function.scm], + [[ +@@ -352,7 +352,7 @@ AT_DATA([function.scm], + (display (evaluator-evaluate-x f 1)) + ]]) + +-AT_CHECK([matheval.sh function.scm], [ignore], [0.648054273663885], [ignore]) ++AT_CHECK([matheval.sh function.scm], [ignore], [0.6480542736638855], [ignore]) + + AT_DATA([function.scm], + [[ +@@ -368,7 +368,7 @@ AT_DATA([function.scm], + (display (evaluator-evaluate-x f 1)) + ]]) + +-AT_CHECK([matheval.sh function.scm], [ignore], [0.850918128239322], [ignore]) ++AT_CHECK([matheval.sh function.scm], [ignore], [0.8509181282393216], [ignore]) + + AT_DATA([function.scm], + [[ +@@ -385,7 +385,7 @@ AT_DATA([function.scm], + (display (evaluator-evaluate-x f 1)) + ]]) + +-AT_CHECK([matheval.sh function.scm], [ignore], [0.881373587019543], [ignore]) ++AT_CHECK([matheval.sh function.scm], [ignore], [0.8813735870195429], [ignore]) + + AT_DATA([function.scm], + [[ +@@ -419,7 +419,7 @@ AT_DATA([function.scm], + (display (evaluator-evaluate-x f 0.5)) + ]]) + +-AT_CHECK([matheval.sh function.scm], [ignore], [0.549306144334055], [ignore]) ++AT_CHECK([matheval.sh function.scm], [ignore], [0.5493061443340549], [ignore]) + + AT_DATA([function.scm], + [[ +@@ -436,7 +436,7 @@ AT_DATA([function.scm], + (display (evaluator-evaluate-x f 2)) + ]]) + +-AT_CHECK([matheval.sh function.scm], [ignore], [0.549306144334055], [ignore]) ++AT_CHECK([matheval.sh function.scm], [ignore], [0.5493061443340549], [ignore]) + + AT_DATA([function.scm], + [[ +@@ -470,7 +470,7 @@ AT_DATA([function.scm], + (display (evaluator-evaluate-x f 1)) + ]]) + +-AT_CHECK([matheval.sh function.scm], [ignore], [0.881373587019543], [ignore]) ++AT_CHECK([matheval.sh function.scm], [ignore], [0.8813735870195429], [ignore]) + + AT_DATA([function.scm], + [[ +--- libmatheval-1.1.11+dfsg.orig/tests/numbers.at ++++ libmatheval-1.1.11+dfsg/tests/numbers.at +@@ -53,6 +53,6 @@ AT_DATA([number.scm], + (display (evaluator-evaluate-x f 0)) + ]]) + +-AT_CHECK([matheval.sh number.scm], [ignore], [0.644394014977254], [ignore]) ++AT_CHECK([matheval.sh number.scm], [ignore], [0.6443940149772542], [ignore]) + + AT_CLEANUP diff --git a/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..b8bf07966b16 --- /dev/null +++ b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-GCCcore-13.3.0.eb @@ -0,0 +1,45 @@ +easyblock = 'ConfigureMake' + +name = 'libmatheval' +version = '1.1.11' # still the latest version available on the ftp mirror + +homepage = 'https://www.gnu.org/software/libmatheval/' +description = """GNU libmatheval is a library (callable from C and Fortran) to parse + and evaluate symbolic expressions input as text. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + '003-guile2.0.patch', + 'libmatheval-1.1.11_fix-matheval-test.patch' +] +checksums = [ + {'libmatheval-1.1.11.tar.gz': '474852d6715ddc3b6969e28de5e1a5fbaff9e8ece6aebb9dc1cc63e9e88e89ab'}, + {'003-guile2.0.patch': 'd0ad39d54800153cbaa26c01448f040d405f09e9fd57e1357eab170a274a9b5c'}, + {'libmatheval-1.1.11_fix-matheval-test.patch': '2888ee1ba32bb864b655e53e13b06eafc23b598faed80b90585d41c98e2ae073'}, +] + +builddependencies = [ + ('binutils', '2.42'), + ('flex', '2.6.4'), + ('Bison', '3.8.2'), + ('byacc', '2.0.20240109'), + # guile 2.2.X, 3.0.7 removed scm_num2dbl (among others), which are needed for libmatheval (at least for 1.1.11) + ('Guile', '2.0.14') +] + +configopts = '--with-pic ' + +# fix for guile-config being broken because shebang line contains full path to bin/guile +configopts += 'GUILE_CONFIG="$EBROOTGUILE/bin/guile -e main -s $EBROOTGUILE/bin/guile-config"' + +sanity_check_paths = { + 'files': ['lib/libmatheval.a', 'include/matheval.h'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libogg/libogg-1.3.5-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libogg/libogg-1.3.5-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..a2f347826969 --- /dev/null +++ b/easybuild/easyconfigs/l/libogg/libogg-1.3.5-GCCcore-13.2.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libogg' +version = '1.3.5' + +homepage = 'https://xiph.org/ogg/' +description = """Ogg is a multimedia container format, and the native file and stream format for the Xiph.org +multimedia codecs.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://ftp.osuosl.org/pub/xiph/releases/ogg/'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['c4d91be36fc8e54deae7575241e03f4211eb102afb3fc0775fbbc1b740016705'] + +builddependencies = [('binutils', '2.40')] + +configopts = '--enable-static --enable-shared' + +sanity_check_paths = { + 'files': ['lib/libogg.a', 'lib/libogg.%s' % SHLIB_EXT], + 'dirs': ['include/ogg'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libogg/libogg-1.3.5-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libogg/libogg-1.3.5-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..810ddbe1169e --- /dev/null +++ b/easybuild/easyconfigs/l/libogg/libogg-1.3.5-GCCcore-13.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libogg' +version = '1.3.5' + +homepage = 'https://xiph.org/ogg/' +description = """Ogg is a multimedia container format, and the native file and stream format for the Xiph.org +multimedia codecs.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://ftp.osuosl.org/pub/xiph/releases/ogg/'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['c4d91be36fc8e54deae7575241e03f4211eb102afb3fc0775fbbc1b740016705'] + +builddependencies = [('binutils', '2.42')] + +configopts = '--enable-static --enable-shared' + +sanity_check_paths = { + 'files': ['lib/libogg.a', 'lib/libogg.%s' % SHLIB_EXT], + 'dirs': ['include/ogg'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libopus/libopus-1.5.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libopus/libopus-1.5.2-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..7d0630bb477e --- /dev/null +++ b/easybuild/easyconfigs/l/libopus/libopus-1.5.2-GCCcore-13.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'libopus' +version = '1.5.2' + +homepage = 'https://www.opus-codec.org/' +description = """Opus is a totally open, royalty-free, highly versatile audio codec. Opus is unmatched for interactive + speech and music transmission over the Internet, but is also intended for storage and streaming applications. It is + standardized by the Internet Engineering Task Force (IETF) as RFC 6716 which incorporated technology from Skype’s + SILK codec and Xiph.Org’s CELT codec.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://downloads.xiph.org/releases/opus/'] +sources = ['opus-%(version)s.tar.gz'] +checksums = ['65c1d2f78b9f2fb20082c38cbe47c951ad5839345876e46941612ee87f9a7ce1'] + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '2.0.3'), +] + +configopts = '--enable-static --enable-shared' + +sanity_check_paths = { + 'files': ['lib/libopus.a', 'lib/libopus.%s' % SHLIB_EXT], + 'dirs': ['include/opus'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libopus/libopus-1.5.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libopus/libopus-1.5.2-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..c09615c86f87 --- /dev/null +++ b/easybuild/easyconfigs/l/libopus/libopus-1.5.2-GCCcore-13.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'libopus' +version = '1.5.2' + +homepage = 'https://www.opus-codec.org/' +description = """Opus is a totally open, royalty-free, highly versatile audio codec. Opus is unmatched for interactive + speech and music transmission over the Internet, but is also intended for storage and streaming applications. It is + standardized by the Internet Engineering Task Force (IETF) as RFC 6716 which incorporated technology from Skype’s + SILK codec and Xiph.Org’s CELT codec.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://downloads.xiph.org/releases/opus/'] +sources = ['opus-%(version)s.tar.gz'] +checksums = ['65c1d2f78b9f2fb20082c38cbe47c951ad5839345876e46941612ee87f9a7ce1'] + +builddependencies = [ + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), +] + +configopts = '--enable-static --enable-shared' + +sanity_check_paths = { + 'files': ['lib/libopus.a', 'lib/libopus.%s' % SHLIB_EXT], + 'dirs': ['include/opus'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libsigc++/libsigc++-3.6.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libsigc++/libsigc++-3.6.0-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..8657a57fde1b --- /dev/null +++ b/easybuild/easyconfigs/l/libsigc++/libsigc++-3.6.0-GCCcore-12.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'CMakeMake' + +name = 'libsigc++' +version = '3.6.0' + +homepage = 'https://libsigcplusplus.github.io/libsigcplusplus/' +description = """The libsigc++ package implements a typesafe callback system +for standard C++.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['c3d23b37dfd6e39f2e09f091b77b1541fbfa17c4f0b6bf5c89baef7229080e17'] + +builddependencies = [ + ('binutils', '2.39'), + ('libxslt', '1.1.37'), + ('mm-common', '1.0.6'), + ('CMake', '3.24.3'), +] + +test_cmd = 'ctest' +runtest = '-j' + +sanity_check_paths = { + 'files': ['lib/libsigc-%%(version_major)s.0.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libsigc++/libsigc++-3.6.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libsigc++/libsigc++-3.6.0-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..4f452cbc432e --- /dev/null +++ b/easybuild/easyconfigs/l/libsigc++/libsigc++-3.6.0-GCCcore-12.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'CMakeMake' + +name = 'libsigc++' +version = '3.6.0' + +homepage = 'https://libsigcplusplus.github.io/libsigcplusplus/' +description = """The libsigc++ package implements a typesafe callback system +for standard C++.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['c3d23b37dfd6e39f2e09f091b77b1541fbfa17c4f0b6bf5c89baef7229080e17'] + +builddependencies = [ + ('binutils', '2.40'), + ('libxslt', '1.1.38'), + ('mm-common', '1.0.6'), + ('CMake', '3.26.3'), +] + +test_cmd = 'ctest' +runtest = '-j' + +sanity_check_paths = { + 'files': ['lib/libsigc-%%(version_major)s.0.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libsigc++/libsigc++-3.6.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libsigc++/libsigc++-3.6.0-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..e64e49e0f741 --- /dev/null +++ b/easybuild/easyconfigs/l/libsigc++/libsigc++-3.6.0-GCCcore-13.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'CMakeMake' + +name = 'libsigc++' +version = '3.6.0' + +homepage = 'https://libsigcplusplus.github.io/libsigcplusplus/' +description = """The libsigc++ package implements a typesafe callback system +for standard C++.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['c3d23b37dfd6e39f2e09f091b77b1541fbfa17c4f0b6bf5c89baef7229080e17'] + +builddependencies = [ + ('binutils', '2.40'), + ('libxslt', '1.1.38'), + ('mm-common', '1.0.6'), + ('CMake', '3.27.6'), +] + +test_cmd = 'ctest' +runtest = '-j' + +sanity_check_paths = { + 'files': ['lib/libsigc-%%(version_major)s.0.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libsndfile/libsndfile-1.2.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libsndfile/libsndfile-1.2.2-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..66345e011054 --- /dev/null +++ b/easybuild/easyconfigs/l/libsndfile/libsndfile-1.2.2-GCCcore-13.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'CMakeMake' + +name = 'libsndfile' +version = '1.2.2' + +homepage = 'http://www.mega-nerd.com/libsndfile' +description = """Libsndfile is a C library for reading and writing files containing sampled sound + (such as MS Windows WAV and the Apple/SGI AIFF format) through one standard library interface.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://github.com/%(name)s/%(name)s/releases/download/%(version)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['3799ca9924d3125038880367bf1468e53a1b7e3686a934f098b7e1d286cdb80e'] + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '2.0.3'), + ('CMake', '3.27.6'), +] +dependencies = [ + ('FLAC', '1.4.3'), + ('libvorbis', '1.3.7'), + ('libopus', '1.5.2'), + ('LAME', '3.100'), +] + +configopts = [ + '', + '-DBUILD_SHARED_LIBS=ON', +] + + +sanity_check_paths = { + 'files': ['include/sndfile.h', 'include/sndfile.hh', 'lib/%(name)s.a', 'lib/%(name)s.so'], + 'dirs': ['bin'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libsndfile/libsndfile-1.2.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libsndfile/libsndfile-1.2.2-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..e60ad09d1a1a --- /dev/null +++ b/easybuild/easyconfigs/l/libsndfile/libsndfile-1.2.2-GCCcore-13.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'CMakeMake' + +name = 'libsndfile' +version = '1.2.2' + +homepage = 'http://www.mega-nerd.com/libsndfile' +description = """Libsndfile is a C library for reading and writing files containing sampled sound + (such as MS Windows WAV and the Apple/SGI AIFF format) through one standard library interface.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/%(name)s/%(name)s/releases/download/%(version)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['3799ca9924d3125038880367bf1468e53a1b7e3686a934f098b7e1d286cdb80e'] + +builddependencies = [ + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), + ('CMake', '3.29.3'), +] +dependencies = [ + ('FLAC', '1.4.3'), + ('libvorbis', '1.3.7'), + ('libopus', '1.5.2'), + ('LAME', '3.100'), +] + +configopts = [ + '', + '-DBUILD_SHARED_LIBS=ON', +] + + +sanity_check_paths = { + 'files': ['include/sndfile.h', 'include/sndfile.hh', 'lib/%(name)s.a', 'lib/%(name)s.so'], + 'dirs': ['bin'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.20-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.20-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..e98d28304a85 --- /dev/null +++ b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.20-GCCcore-13.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libsodium' +version = '1.0.20' + +homepage = 'https://doc.libsodium.org/' +description = """ + Sodium is a modern, easy-to-use software library for encryption, decryption, + signatures, password hashing and more. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'https://download.%(name)s.org/%(name)s/releases/', + 'https://download.%(name)s.org/%(name)s/releases/old/', + 'https://download.%(name)s.org/%(name)s/releases/old/unsupported/', +] +sources = [SOURCE_TAR_GZ] +checksums = ['ebb65ef6ca439333c2bb41a0c1990587288da07f6c7fd07cb3a18cc18d30ce19'] + +builddependencies = [ + ('binutils', '2.42'), +] + + +sanity_check_paths = { + 'files': ['include/sodium.h', 'lib/%%(name)s.%s' % SHLIB_EXT, 'lib/%(name)s.a'], + 'dirs': ['include/sodium', 'lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libspatialindex/libspatialindex-2.0.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libspatialindex/libspatialindex-2.0.0-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..1752b337b051 --- /dev/null +++ b/easybuild/easyconfigs/l/libspatialindex/libspatialindex-2.0.0-GCCcore-13.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'CMakeMake' + +name = 'libspatialindex' +version = '2.0.0' + +homepage = 'https://libspatialindex.org' +description = "C++ implementation of R*-tree, an MVR-tree and a TPR-tree with C API" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/%(name)s/%(name)s/releases/download/%(version)s/'] +sources = ['spatialindex-src-%(version)s.tar.gz'] +checksums = ['f1d5a369681fa6ac3301a54db412ccf3180fc17163ebc3252f32c752f77345de'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] + +sanity_check_paths = { + 'files': ['lib/%s.%s' % (name, SHLIB_EXT)], + 'dirs': ['include/spatialindex'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libunistring/libunistring-1.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libunistring/libunistring-1.2-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..7fa2f46eb1f9 --- /dev/null +++ b/easybuild/easyconfigs/l/libunistring/libunistring-1.2-GCCcore-13.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'libunistring' +version = '1.2' + +homepage = 'https://www.gnu.org/software/libunistring/' + +description = """This library provides functions for manipulating Unicode strings and for + manipulating C strings according to the Unicode standard.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['632bd65ed74a881ca8a0309a1001c428bd1cbd5cd7ddbf8cedcd2e65f4dcdc44'] + +builddependencies = [ + ('binutils', '2.42'), +] + +dependencies = [ + ('libiconv', '1.17'), +] + +parallel = 1 + +sanity_check_paths = { + 'files': ['lib/libunistring.a', 'lib/libunistring.%s' % SHLIB_EXT] + + ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', + 'stdio', 'str', 'types', 'wbrk', 'width']], + 'dirs': ['include/unistring'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.8.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.8.1-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..777376a73aef --- /dev/null +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.8.1-GCCcore-13.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libunwind' +version = '1.8.1' + +homepage = 'https://www.nongnu.org/libunwind/' +description = """The primary goal of libunwind is to define a portable and efficient C programming interface + (API) to determine the call-chain of a program. The API additionally provides the means to manipulate the + preserved (callee-saved) state of each call-frame and to resume execution at any point in the call-chain + (non-local goto). The API supports both local (same-process) and remote (across-process) operation. + As such, the API is useful in a number of applications""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/libunwind/libunwind/releases/download/v%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['ddf0e32dd5fafe5283198d37e4bf9decf7ba1770b6e7e006c33e6df79e6a6157'] + +builddependencies = [('binutils', '2.42')] + +dependencies = [ + ('XZ', '5.4.5'), +] + +preconfigopts = 'export LIBS="$LIBS -llzma" && export CFLAGS="$CFLAGS -fno-common" && ' + +sanity_check_paths = { + 'files': ['include/libunwind.h', 'lib/libunwind.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libvorbis/libvorbis-1.3.7-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libvorbis/libvorbis-1.3.7-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..50a45ea05a1e --- /dev/null +++ b/easybuild/easyconfigs/l/libvorbis/libvorbis-1.3.7-GCCcore-13.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'libvorbis' +version = '1.3.7' + +homepage = 'https://xiph.org/vorbis/' +description = """Ogg Vorbis is a fully open, non-proprietary, patent-and-royalty-free, general-purpose compressed +audio format""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://ftp.osuosl.org/pub/xiph/releases/vorbis/'] +sources = [SOURCE_TAR_XZ] +checksums = ['b33cc4934322bcbf6efcbacf49e3ca01aadbea4114ec9589d1b1e9d20f72954b'] + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '2.0.3'), +] + +dependencies = [('libogg', '1.3.5')] + +configopts = '--enable-static --enable-shared' + +sanity_check_paths = { + 'files': ['lib/libvorbis.a', 'lib/libvorbis.%s' % SHLIB_EXT], + 'dirs': ['include/vorbis'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libvorbis/libvorbis-1.3.7-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libvorbis/libvorbis-1.3.7-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..7e32c5c3a99f --- /dev/null +++ b/easybuild/easyconfigs/l/libvorbis/libvorbis-1.3.7-GCCcore-13.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'libvorbis' +version = '1.3.7' + +homepage = 'https://xiph.org/vorbis/' +description = """Ogg Vorbis is a fully open, non-proprietary, patent-and-royalty-free, general-purpose compressed +audio format""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://ftp.osuosl.org/pub/xiph/releases/vorbis/'] +sources = [SOURCE_TAR_XZ] +checksums = ['b33cc4934322bcbf6efcbacf49e3ca01aadbea4114ec9589d1b1e9d20f72954b'] + +builddependencies = [ + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), +] + +dependencies = [('libogg', '1.3.5')] + +configopts = '--enable-static --enable-shared' + +sanity_check_paths = { + 'files': ['lib/libvorbis.a', 'lib/libvorbis.%s' % SHLIB_EXT], + 'dirs': ['include/vorbis'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libwebp/libwebp-1.4.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libwebp/libwebp-1.4.0-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..70084689c611 --- /dev/null +++ b/easybuild/easyconfigs/l/libwebp/libwebp-1.4.0-GCCcore-13.3.0.eb @@ -0,0 +1,45 @@ +easyblock = 'ConfigureMake' + +name = 'libwebp' +version = '1.4.0' + +homepage = 'https://developers.google.com/speed/webp/' +description = """WebP is a modern image format that provides superior +lossless and lossy compression for images on the web. Using WebP, +webmasters and web developers can create smaller, richer images that +make the web faster.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://storage.googleapis.com/downloads.webmproject.org/releases/webp'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['61f873ec69e3be1b99535634340d5bde750b2e4447caa1db9f61be3fd49ab1e5'] + +builddependencies = [ + ('binutils', '2.42'), +] +dependencies = [ + ('libjpeg-turbo', '3.0.1'), + ('libpng', '1.6.43'), + ('LibTIFF', '4.6.0'), + ('giflib', '5.2.1'), +] + +configopts = '--enable-libwebpmux' + +local_headers, local_libs = ( + ['decode.h', 'demux.h', 'encode.h', 'mux.h', 'mux_types.h', 'types.h'], + ['webp', 'webpdemux', 'webpmux'] +) + +sanity_check_paths = { + 'files': ( + ['include/webp/%s' % h for h in local_headers] + + ['lib/lib%s.a' % s for s in local_libs] + + ['lib/lib%s.%s' % (s, SHLIB_EXT) for s in local_libs] + ), + 'dirs': ['lib/'] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.42-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.42-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..a38c53ef8416 --- /dev/null +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.42-GCCcore-13.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'libxslt' +version = '1.1.42' + +homepage = 'http://xmlsoft.org/' +description = """Libxslt is the XSLT C library developed for the GNOME project + (but usable outside of the Gnome platform).""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://download.gnome.org/sources/libxslt/%(version_major_minor)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['85ca62cac0d41fc77d3f6033da9df6fd73d20ea2fc18b0a3609ffb4110e1baeb'] + +builddependencies = [ + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), +] + +dependencies = [ + ('zlib', '1.3.1'), + ('libxml2', '2.12.7'), +] + +# Make sure it doesn't pick up OS installed libgcrypt or Python +# enable building static libs +configopts = '--with-crypto=no --with-python=no --enable-static=yes ' + +sanity_check_paths = { + 'files': ['bin/xsltproc', 'include/libxslt/xslt.h', 'lib/%%(name)s.%s' % SHLIB_EXT, 'lib/%(name)s.a', + 'lib/libexslt.%s' % SHLIB_EXT, 'lib/libexslt.a'], + 'dirs': ['include/libxslt', 'include/libexslt'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libzip/libzip-1.10.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libzip/libzip-1.10.1-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..99551efad574 --- /dev/null +++ b/easybuild/easyconfigs/l/libzip/libzip-1.10.1-GCCcore-13.2.0.eb @@ -0,0 +1,44 @@ +easyblock = 'CMakeMake' + +name = 'libzip' +version = '1.10.1' + +homepage = 'https://libzip.org/' +description = "libzip is a C library for reading, creating, and modifying zip archives." + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://github.com/nih-at/libzip/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['d56d857d1c3ad4a7f3a4c01a51c6a6e5530e35ab93503f62276e8ba2b306186a'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.27.6'), +] + +dependencies = [ + ('OpenSSL', '1.1', '', SYSTEM), + ('zlib', '1.2.13'), + ('bzip2', '1.0.8'), + ('XZ', '5.4.4'), + ('zstd', '1.5.5'), +] + +sanity_check_paths = { + 'files': [ + 'bin/zipcmp', + 'bin/zipmerge', + 'bin/ziptool', + 'lib64/libzip.%s' % SHLIB_EXT, + ], + 'dirs': ['include', 'lib/pkgconfig'], +} + +sanity_check_commands = [ + "zipcmp -h", + "zipmerge -h", + "ziptool -h" +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/longread_umi/longread_umi-0.3.2-foss-2023a.eb b/easybuild/easyconfigs/l/longread_umi/longread_umi-0.3.2-foss-2023a.eb new file mode 100644 index 000000000000..ce954f2edaea --- /dev/null +++ b/easybuild/easyconfigs/l/longread_umi/longread_umi-0.3.2-foss-2023a.eb @@ -0,0 +1,82 @@ +easyblock = 'Bundle' + +name = 'longread_umi' +version = '0.3.2' + +homepage = 'https://github.com/SorenKarst/longread_umi' +description = "A collection of scripts for processing longread UMI data." +github_account = 'SorenKarst' + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('cutadapt', '4.9'), + ('BCFtools', '1.18'), + ('BWA', '0.7.17'), + ('Filtlong', '0.2.1'), + ('gawk', '5.3.0'), + ('medaka', '1.11.3'), + ('minimap2', '2.26'), + ('parallel', '20230722'), + ('Pysam', '0.22.0'), + ('Racon', '1.5.0'), + ('SAMtools', '1.18'), + ('seqtk', '1.4'), + ('VSEARCH', '2.25.0'), +] + +components = [ + (name, version, { + 'easyblock': 'Tarball', + 'source_urls': [GITHUB_LOWER_SOURCE], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'checksums': ['62b8e156c00c0ec10fa8eae1cde5430922462f167fc537417ce0b47cd50a20cb'], + 'start_dir': '%(name)s-%(version)s', + }), + # PythonPackage executes Bundle-level postinstallcmds for some reason, + # which rely on both components being installed, so Porechop is installed second + ('Porechop', '0.2.4', { + 'easyblock': 'PythonPackage', + 'source_urls': ['https://github.com/rrwick/Porechop/archive'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'checksums': ['44b499157d933be43f702cec198d1d693dcb9276e3c545669be63c2612493299'], + 'start_dir': '%(name)s-%(version)s', + 'use_pip': True, + 'download_dep_fail': True, + 'sanity_pip_check': True, + }), +] + +# Adapt the built-in tool check but make it fail on error, replace usearch with vsearch and use our version +local_deps_patch = ( + "sed -i " + "-e '2s;^;set -e ;' " + "-e 's/USEARCH=usearch/USEARCH=vsearch/' " + "-e 's;$(git --git-dir ${LONGREAD_UMI_PATH}/.git describe --tag);%(version)s;' " + "%(installdir)s/scripts/dependencies.sh" +) + +postinstallcmds = [ + 'find %(installdir)s -name "*.sh" -exec chmod +x {} \\;', + 'ln -s %(installdir)s/longread_umi.sh %(installdir)s/bin/longread_umi', + # Part of the installation process; longread uses porechop with custom adapters + 'cp %(installdir)s/scripts/adapters.py %(installdir)s/lib/python%(pyshortver)s/site-packages/porechop/', + local_deps_patch, +] + +sanity_check_paths = { + 'files': ['bin/longread_umi'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} +sanity_check_commands = [ + 'longread_umi -h | grep qc_pipeline', + 'longread_umi nanopore_pipeline -h | grep rrna_operon', + 'source %(installdir)s/scripts/dependencies.sh && longread_umi_version_dump', +] + +modextrapaths = { + 'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/l/lrcalc/lrcalc-2.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/lrcalc/lrcalc-2.1-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..aa14572bef64 --- /dev/null +++ b/easybuild/easyconfigs/l/lrcalc/lrcalc-2.1-GCCcore-13.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'lrcalc' +version = '2.1' + +homepage = 'https://sites.math.rutgers.edu/~asbuch/lrcalc/' +description = """The Littlewood-Richardson Calculator is a program + designed to compute Littlewood-Richardson coefficients.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://math.rutgers.edu/~asbuch/lrcalc/'] +sources = [SOURCE_TAR_GZ] +checksums = ['996ac00e6ea8321ef09b34478f5379f613933c3254aeba624b6419b8afa5df57'] + +builddependencies = [ + ('binutils', '2.40'), +] + +sanity_check_paths = { + 'files': [ + 'bin/lrcalc', + 'lib/liblrcalc.%s' % SHLIB_EXT, + 'include/lrcalc/ivector.h', + ], + 'dirs': [] +} + +sanity_check_commands = ["lrcalc 2>&1 | grep '^Usage:'"] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/l/lwgrp/lwgrp-1.0.6-gompi-2024a.eb b/easybuild/easyconfigs/l/lwgrp/lwgrp-1.0.6-gompi-2024a.eb new file mode 100644 index 000000000000..c36ee58b2733 --- /dev/null +++ b/easybuild/easyconfigs/l/lwgrp/lwgrp-1.0.6-gompi-2024a.eb @@ -0,0 +1,36 @@ +# +# Author: Robert Mijakovic +# +easyblock = 'ConfigureMake' + +name = 'lwgrp' +version = '1.0.6' + +homepage = 'https://github.com/LLNL/lwgrp' +description = """The light-weight group library defines data structures and collective operations to +group MPI processes as an ordered set. Such groups are useful as substitutes for MPI communicators +when the overhead of communicator creation is too costly. For example, certain sorting algorithms +recursively divide processes into subgroups as the sort algorithm progresses. These groups may be +different with each invocation, so that it is inefficient to create and destroy communicators during +the sort routine.""" + +toolchain = {'name': 'gompi', 'version': '2024a'} + +github_account = 'LLNL' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['108e622441028b7f88223244c9117d5de18a91fd7c246bfa48802b5c585557d0'] + +builddependencies = [ + ('Autotools', '20231222'), + ('pkgconf', '2.2.0'), +] + +preconfigopts = './autogen.sh && ' + +sanity_check_paths = { + 'files': ['include/%(name)s.h', 'lib/lib%%(name)s.%s' % SHLIB_EXT], + 'dirs': ['share/%(name)s'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/lxml/lxml-5.3.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/lxml/lxml-5.3.0-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..0af2dcbed3f6 --- /dev/null +++ b/easybuild/easyconfigs/l/lxml/lxml-5.3.0-GCCcore-13.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'lxml' +version = '5.3.0' + +homepage = 'https://lxml.de/' +description = """The lxml XML toolkit is a Pythonic binding for the C libraries libxml2 and libxslt.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['4e109ca30d1edec1ac60cdbe341905dc3b8f55b16855e03a54aaf59e51ec8c6f'] + +builddependencies = [ + ('binutils', '2.42'), +] + +dependencies = [ + ('Python', '3.12.3'), + ('libxml2', '2.12.7'), + ('libxslt', '1.1.42'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-14.2.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-14.2.0.eb new file mode 100644 index 000000000000..c5c3ad83f3a7 --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-14.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.19' + +homepage = 'https://www.gnu.org/software/m4/m4.html' +description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible + although it has some extensions (for example, handling more than 9 positional parameters to macros). + GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" + +toolchain = {'name': 'GCCcore', 'version': '14.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3be4a26d825ffdfda52a56fc43246456989a3630093cced3fbddf4771ee58a70'] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.42', '', SYSTEM)] + +# '-fgnu89-inline' is required to avoid linking errors with older glibc's, +# see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 +configopts = "--enable-c++ CPPFLAGS=-fgnu89-inline" + +sanity_check_paths = { + 'files': ['bin/m4'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/MAGIC/MAGIC-3.0.0-foss-2023a.eb b/easybuild/easyconfigs/m/MAGIC/MAGIC-3.0.0-foss-2023a.eb new file mode 100644 index 000000000000..9e22b652a23a --- /dev/null +++ b/easybuild/easyconfigs/m/MAGIC/MAGIC-3.0.0-foss-2023a.eb @@ -0,0 +1,48 @@ +easyblock = 'PythonBundle' + +name = 'MAGIC' +version = '3.0.0' + +homepage = 'https://krishnaswamylab.org/projects/magic' +description = """Markov Affinity-based Graph Imputation of Cells (MAGIC) is an algorithm for denoising high-dimensional + data most commonly applied to single-cell RNA sequencing data.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('matplotlib', '3.7.2'), + ('scikit-learn', '1.3.1'), +] + +use_pip = True + +exts_list = [ + ('wrapt', '1.16.0', { + 'checksums': ['5f370f952971e7d17c7d1ead40e49f32345a7f7a5373571ef44d800d06b1899d'], + }), + ('Deprecated', '1.2.14', { + 'checksums': ['e5323eb936458dccc2582dc6f9c322c852a775a27065ff2b0c4970b9d53d01b3'], + }), + ('PyGSP', '0.5.1', { + 'checksums': ['4874ad88793d622d4f578b40c6617a99b1f02bc6c6c4077f0e48cd71c7275800'], + }), + ('graphtools', '1.5.3', { + 'checksums': ['b35ae2974d24c507fe01b110d10b1d8c949e20bc49ff9d7d04f94849f9795907'], + }), + ('scprep', '1.2.3', { + 'checksums': ['cc4ba4cedbba256935298f2ba6a973b4e74ea8cb9ad2632b693b6d4e6ab77c3f'], + }), + ('tasklogger', '1.2.0', { + 'checksums': ['b0a390dbe1d4c6f7465e58ee457b5bb381657b5ede3a85bcf45199cb56ac01a4'], + }), + ('magic-impute', version, { + 'modulename': 'magic', + 'checksums': ['0c3f6d17baf586c412c174709a19164f04e693fd1933a8c0399ae5c5bf1cfd7a'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MATES/MATES-0.1.2-20240813-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/m/MATES/MATES-0.1.2-20240813-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 000000000000..dbba96ddf2f8 --- /dev/null +++ b/easybuild/easyconfigs/m/MATES/MATES-0.1.2-20240813-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,58 @@ +easyblock = 'PythonBundle' + +name = 'MATES' +version = '0.1.2-20240813' +local_commit = 'd5ee15b' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/mcgilldinglab/MATES' +description = "A Deep Learning-Based Model for Quantifying Transposable Elements in Single-Cell Sequencing Data." + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('CUDA', '12.1.1', '', SYSTEM), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('matplotlib', '3.7.2'), + ('anndata', '0.10.5.post1'), + ('SAMtools', '1.18'), + ('pybedtools', '0.9.1'), + ('PyTorch-bundle', '2.1.2', versionsuffix), + ('Pysam', '0.22.0'), + ('tqdm', '4.66.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('sorted_nearest', '0.0.39', { + 'checksums': ['16a51d5db87ae226b47ace43c176bb672477a1b7ba8052ea9291a6356c9c69b1'], + }), + ('ncls', '0.0.68', { + 'checksums': ['81aaa5abb123bb21797ed2f8ef921e20222db14a3ecbc61ccf447532f2b7ba93'], + }), + ('natsort', '8.4.0', { + 'checksums': ['45312c4a0e5507593da193dedd04abb1469253b601ecaf63445ad80f0a1ea581'], + }), + ('pyranges', '0.0.129', { + 'checksums': ['bee83b4fad0062be9586668c6b0fc4270d5e761951975e018202993680071fb3'], + }), + (name, version, { + 'modulename': 'MATES', + # unpin exact versions of dependencies + 'preinstallopts': r"sed -i 's/==.*//g' requirements.txt && sed -i 's/==.*/\",/g' setup.py && ", + 'source_urls': ['https://github.com/mcgilldinglab/MATES/archive'], + 'sources': [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}], + 'checksums': ['aca36b2b99ebed975fdf61670a9b551c1ab7882ff2b9d4ed3f25f2e13805652c'], + }), +] + +sanity_check_commands = [ + "python -c 'from MATES import bam_processor, data_processor, MATES_model'", + "python -c 'from MATES import TE_quantifier, TE_quantifier_LongRead, TE_quantifier_Intronic'", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MATES/MATES-0.1.2-20240813-foss-2023a.eb b/easybuild/easyconfigs/m/MATES/MATES-0.1.2-20240813-foss-2023a.eb new file mode 100644 index 000000000000..e7e73a89e808 --- /dev/null +++ b/easybuild/easyconfigs/m/MATES/MATES-0.1.2-20240813-foss-2023a.eb @@ -0,0 +1,56 @@ +easyblock = 'PythonBundle' + +name = 'MATES' +version = '0.1.2-20240813' +local_commit = 'd5ee15b' + +homepage = 'https://github.com/mcgilldinglab/MATES' +description = "A Deep Learning-Based Model for Quantifying Transposable Elements in Single-Cell Sequencing Data." + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('matplotlib', '3.7.2'), + ('anndata', '0.10.5.post1'), + ('SAMtools', '1.18'), + ('pybedtools', '0.9.1'), + ('PyTorch-bundle', '2.1.2'), + ('Pysam', '0.22.0'), + ('tqdm', '4.66.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('sorted_nearest', '0.0.39', { + 'checksums': ['16a51d5db87ae226b47ace43c176bb672477a1b7ba8052ea9291a6356c9c69b1'], + }), + ('ncls', '0.0.68', { + 'checksums': ['81aaa5abb123bb21797ed2f8ef921e20222db14a3ecbc61ccf447532f2b7ba93'], + }), + ('natsort', '8.4.0', { + 'checksums': ['45312c4a0e5507593da193dedd04abb1469253b601ecaf63445ad80f0a1ea581'], + }), + ('pyranges', '0.0.129', { + 'checksums': ['bee83b4fad0062be9586668c6b0fc4270d5e761951975e018202993680071fb3'], + }), + (name, version, { + 'modulename': 'MATES', + # unpin exact versions of dependencies + 'preinstallopts': r"sed -i 's/==.*//g' requirements.txt && sed -i 's/==.*/\",/g' setup.py && ", + 'source_urls': ['https://github.com/mcgilldinglab/MATES/archive'], + 'sources': [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}], + 'checksums': ['aca36b2b99ebed975fdf61670a9b551c1ab7882ff2b9d4ed3f25f2e13805652c'], + }), +] + +sanity_check_commands = [ + "python -c 'from MATES import bam_processor, data_processor, MATES_model'", + "python -c 'from MATES import TE_quantifier, TE_quantifier_LongRead, TE_quantifier_Intronic'", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MBX/MBX-1.1.0-foss-2023a.eb b/easybuild/easyconfigs/m/MBX/MBX-1.1.0-foss-2023a.eb new file mode 100644 index 000000000000..3f6da986d620 --- /dev/null +++ b/easybuild/easyconfigs/m/MBX/MBX-1.1.0-foss-2023a.eb @@ -0,0 +1,48 @@ +easyblock = 'ConfigureMake' + +name = 'MBX' +version = '1.1.0' + +homepage = 'https://github.com/paesanilab/MBX' +description = "MBX is an energy and force calculator for data-driven many-body simulations" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'pic': True, 'openmp': True} + +source_urls = ['https://github.com/paesanilab/MBX/archive/'] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['0f55f4950226defb46fd0814ad97f906ce4ffd6403af6817bd98cb3c68996692'] + +builddependencies = [('Autotools', '20220317')] +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('GSL', '2.7'), +] + +preconfigopts = 'export MBX_HOME=$PWD && autoreconf -fi && ' + +configopts = '--enable-shared --enable-verbose CXX="$CXX"' + +postinstallcmds = ["cp -a plugins %(installdir)s"] + +maxparallel = 2 + +runtest = 'check' + +modextrapaths = {'PYTHONPATH': 'plugins/python'} + +modextravars = {'MBX_HOME': '%(installdir)s'} + +sanity_check_paths = { + 'files': ['bin/mb_decomp', 'bin/optimize', 'bin/order_frames', 'bin/single_point', + 'lib/libmbx.a', 'lib/libmbx.%s' % SHLIB_EXT], + 'dirs': ['include', 'plugins/python/mbx', 'plugins/lammps/USER-MBX'], +} + +sanity_check_commands = [ + "optimize", + "python -c 'import mbx'", +] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/m/MCR/MCR-R2024a.4.eb b/easybuild/easyconfigs/m/MCR/MCR-R2024a.4.eb new file mode 100644 index 000000000000..bb746ac5151f --- /dev/null +++ b/easybuild/easyconfigs/m/MCR/MCR-R2024a.4.eb @@ -0,0 +1,18 @@ +name = 'MCR' +version = 'R2024a' # runtime version 24.1 +local_update = '4' +versionsuffix = '.%s' % local_update + +homepage = 'https://www.mathworks.com/products/compiler/mcr/' +description = """The MATLAB Runtime is a standalone set of shared libraries + that enables the execution of compiled MATLAB applications + or components on computers that do not have MATLAB installed.""" + +toolchain = SYSTEM + +source_urls = ['https://ssd.mathworks.com/supportfiles/downloads/%%(version)s/Release/%s/deployment_files/' + 'installer/complete/glnxa64/' % local_update] +sources = ['MATLAB_Runtime_%%(version)s_Update_%s_glnxa64.zip' % local_update] +checksums = ['ceed37dc342660c934b9f6297491f57b6d51a7f49cd1fb80b775b1f748b72d03'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..417e4750ef90 --- /dev/null +++ b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-GCCcore-13.3.0.eb @@ -0,0 +1,36 @@ +name = 'METIS' +version = '5.1.0' + +homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/metis/overview' + +description = """ + METIS is a set of serial programs for partitioning graphs, partitioning + finite element meshes, and producing fill reducing orderings for sparse + matrices. The algorithms implemented in METIS are based on the multilevel + recursive-bisection, multilevel k-way, and multi-constraint partitioning + schemes. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis', + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/OLD', +] +sources = [SOURCELOWER_TAR_GZ] +patches = ['%(name)s-%(version)s-use-doubles.patch'] +checksums = [ + {'metis-5.1.0.tar.gz': '76faebe03f6c963127dbb73c13eab58c9a3faeae48779f049066a21c087c5db2'}, + {'METIS-5.1.0-use-doubles.patch': '7e38a3ec8f2b8e3d189239bade5b28c0dd1c564485050109164fa71a6a767c67'}, +] + +# We use 32bit for indices and 64bit for content +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] + +configopts = ['', 'shared=1'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MONAI/MONAI-1.3.0-foss-2022b.eb b/easybuild/easyconfigs/m/MONAI/MONAI-1.3.0-foss-2022b.eb new file mode 100644 index 000000000000..29dbbe424bae --- /dev/null +++ b/easybuild/easyconfigs/m/MONAI/MONAI-1.3.0-foss-2022b.eb @@ -0,0 +1,96 @@ +easyblock = 'PythonBundle' + +name = 'MONAI' +version = '1.3.0' + +homepage = 'https://monai.io/' +description = """ +MONAI is a PyTorch-based, open-source framework for deep learning in healthcare +imaging, part of PyTorch Ecosystem. +""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +github_account = 'Project-MONAI' + +builddependencies = [ + ('Ninja', '1.11.1'), +] + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('PyTorch', '1.13.1'), + ('einops', '0.7.0'), + ('ITK', '5.3.0'), + ('NiBabel', '5.2.0'), + ('scikit-image', '0.21.0'), + ('tensorboard', '2.15.1'), + ('torchvision', '0.14.1'), + ('tqdm', '4.64.1'), + ('Pillow', '9.4.0'), + ('openslide-python', '1.3.1'), + ('BeautifulSoup', '4.11.1'), +] + +use_pip = True + +# install MONAI with list of 'extras', which require additional dependencies +local_pip_extras = "einops,fire,gdown,ignite,itk,jsonschema,lmdb,nibabel," +local_pip_extras += "openslide,pandas,pillow,psutil,pydicom,pyyaml,scipy," +local_pip_extras += "skimage,tensorboard,torchvision,tqdm" + +# PyTorch-Ignite v0.4.11 bundled as an extension because MONAI v1.3.0 has a strict requirement on it +exts_list = [ + ('gdown', '4.7.1', { + 'checksums': ['347f23769679aaf7efa73e5655270fcda8ca56be65eb84a4a21d143989541045'], + }), + ('lmdb', '1.4.1', { + 'checksums': ['1f4c76af24e907593487c904ef5eba1993beb38ed385af82adb25a858f2d658d'], + }), + ('termcolor', '2.3.0', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['3afb05607b89aed0ffe25202399ee0867ad4d3cb4180d98aaf8eefa6a5f7d475'], + }), + ('fire', '0.5.0', { + 'checksums': ['a6b0d49e98c8963910021f92bba66f65ab440da2982b78eb1bbf95a0a34aacc6'], + }), + ('pytorch-ignite', '0.4.11', { + 'modulename': 'ignite', + 'patches': ['PyTorch-Ignite-0.4.11_fix_error_on_importing_Events.patch'], + 'checksums': [ + {'pytorch-ignite-0.4.11.tar.gz': 'ee31096a58679417097ef7f3f27d88bec40b789ac5e13cd9ed08bc89ca8ce2e2'}, + {'PyTorch-Ignite-0.4.11_fix_error_on_importing_Events.patch': + 'd45c0da30c01f7ce47b7be49a6d5d6eb9529c94a0b9de89260d4b07d9d2359e0'}, + ], + }), + (name, version, { + 'preinstallopts': 'BUILD_MONAI=1', + 'source_urls': ['https://github.com/%(github_account)s/%(name)s/archive'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'use_pip_extras': local_pip_extras, + # 2 valid checksums, as source tarball provided by GitHub for MONAI 1.3.0 slightly changed at some point + # see also https://github.com/easybuilders/easybuild-easyconfigs/issues/20617 + 'checksums': [('67e0f55678faad4bd38b1ea69d5de94586b20b551b8ad745415623a8b6c1c5e2', + '076d75458d490b4f2dafbf5974fcc8e07a86c03f39f5ef48c6689ab6e4347da9')], + }), +] + +sanity_pip_check = True + +# 'pip check' does not verify whether all optional dependencies required to support 'extras' +# are actually available, so we do it here via an import check; +local_extra_mod_check = {x: x for x in local_pip_extras.split(",")} +# Some special cases with different module name than extra name +local_extra_mod_check['pillow'] = 'PIL' +local_extra_mod_check['pyyaml'] = 'yaml' + +sanity_check_commands = ["python -c 'import monai; monai.config.print_config()'"] +sanity_check_commands += ["python -c 'import %s'" % local_extra_mod_check[x] for x in local_extra_mod_check] + +sanity_check_paths = { + 'files': ['lib/python%%(pyshortver)s/site-packages/%%(namelower)s/_C.%s' % SHLIB_EXT], + 'dirs': ['lib/python%(pyshortver)s/site-packages/ignite'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/MPICH/MPICH-4.2.1-GCC-12.3.0.eb b/easybuild/easyconfigs/m/MPICH/MPICH-4.2.1-GCC-12.3.0.eb new file mode 100644 index 000000000000..08f9b0e3d4df --- /dev/null +++ b/easybuild/easyconfigs/m/MPICH/MPICH-4.2.1-GCC-12.3.0.eb @@ -0,0 +1,20 @@ +name = 'MPICH' +version = '4.2.1' + +homepage = 'https://www.mpich.org/' +description = """MPICH is a high-performance and widely portable implementation +of the Message Passing Interface (MPI) standard (MPI-1, MPI-2 and MPI-3).""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://www.mpich.org/static/downloads/%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['23331b2299f287c3419727edc2df8922d7e7abbb9fd0ac74e03b9966f9ad42d7'] + +configopts = 'FFLAGS="-w -fallow-argument-mismatch -O2" --with-devices=ch4:ucx --with-ucx=$EBROOTUCX' + +dependencies = [ + ('UCX', '1.14.1'), +] + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.6.1-foss-2023b-metis.eb b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.6.1-foss-2023b-metis.eb new file mode 100644 index 000000000000..b9fb9f3ce74d --- /dev/null +++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.6.1-foss-2023b-metis.eb @@ -0,0 +1,35 @@ +name = 'MUMPS' +version = '5.6.1' +versionsuffix = '-metis' + +homepage = 'https://graal.ens-lyon.fr/MUMPS/' +description = "A parallel sparse direct solver" + +toolchain = {'name': 'foss', 'version': '2023b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://graal.ens-lyon.fr/MUMPS/'] +sources = ['%(name)s_%(version)s.tar.gz'] +patches = [ + '%(name)s-%(version)s_shared-pord.patch', # builds the shared libs of PORD + '%(name)s-%(version)s_shared-mumps.patch', # builds shared libs of MUMPS +] +checksums = [ + {'MUMPS_5.6.1.tar.gz': '1920426d543e34d377604070fde93b8d102aa38ebdf53300cbce9e15f92e2896'}, + {'MUMPS-5.6.1_shared-pord.patch': '51d3685208a42581b462592eea977f185d87e871fb65e8e90a54dd2ad18ac715'}, + {'MUMPS-5.6.1_shared-mumps.patch': '27f788a5f85e8c9a6a7ec1651097b87c1de0ede0be943df7a10fa7c1ff5f494f'}, +] + +dependencies = [ + ('SCOTCH', '7.0.4'), + ('METIS', '5.1.0'), +] + +parallel = 1 + +# fix 'Type mismatch between actual argument' errors with GCC 10.x +prebuildopts = 'export FFLAGS="$FFLAGS -fallow-argument-mismatch" && ' + +buildopts = 'all SONAME_VERSION="%(version)s"' + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.7.2-foss-2023b-parmetis.eb b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.7.2-foss-2023b-parmetis.eb new file mode 100644 index 000000000000..1b7b70075c21 --- /dev/null +++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.7.2-foss-2023b-parmetis.eb @@ -0,0 +1,27 @@ +name = 'MUMPS' +version = '5.7.2' +versionsuffix = '-parmetis' + +homepage = 'https://graal.ens-lyon.fr/MUMPS/' +description = "A parallel sparse direct solver" + +toolchain = {'name': 'foss', 'version': '2023b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['http://mumps-solver.org/'] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['1362d377ce7422fc886c55212b4a4d2c381918b5ca4478f682a22d0627a8fbf8'] + +dependencies = [ + ('SCOTCH', '7.0.4'), + ('ParMETIS', '4.0.3'), +] + +parallel = 1 + +# fix 'Type mismatch between actual argument' errors with GCC 10.x +prebuildopts = 'export FFLAGS="$FFLAGS -fallow-argument-mismatch" && ' + +buildopts = 'all SONAME_VERSION="%(version)s"' + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.7.2-intel-2023b-parmetis.eb b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.7.2-intel-2023b-parmetis.eb new file mode 100644 index 000000000000..589710ed6ee4 --- /dev/null +++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.7.2-intel-2023b-parmetis.eb @@ -0,0 +1,27 @@ +name = 'MUMPS' +version = '5.7.2' +versionsuffix = '-parmetis' + +homepage = 'https://graal.ens-lyon.fr/MUMPS/' +description = "A parallel sparse direct solver" + +toolchain = {'name': 'intel', 'version': '2023b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['http://mumps-solver.org/'] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['1362d377ce7422fc886c55212b4a4d2c381918b5ca4478f682a22d0627a8fbf8'] + +dependencies = [ + ('SCOTCH', '7.0.4'), + ('ParMETIS', '4.0.3'), +] + +parallel = 1 + +# fix 'Type mismatch between actual argument' errors with GCC 10.x +prebuildopts = 'export FFLAGS="$FFLAGS -fallow-argument-mismatch" && ' + +buildopts = 'all SONAME_VERSION="%(version)s"' + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-5.1.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-5.1.0-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..8af917599378 --- /dev/null +++ b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-5.1.0-GCCcore-12.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'MakeCp' + +name = 'MUSCLE' +version = '5.1.0' + +homepage = 'https://drive5.com/muscle/' +description = """MUSCLE is one of the best-performing multiple alignment programs + according to published benchmark tests, with accuracy and speed that are consistently + better than CLUSTALW. MUSCLE can align hundreds of sequences in seconds. Most users + learn everything they need to know about MUSCLE in a few minutes-only a handful of + command-line options are needed to perform common alignment tasks.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +github_account = 'rcedgar' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['2bba8b06e3ccabf6465fa26f459763b2029d7e7b9596881063e3aaba60d9e87d'] + +builddependencies = [ + ('binutils', '2.39'), +] + +start_dir = 'src' + +# Use build environment defined by EasyBuild +prebuildopts = "sed -i 's/$(CPPOPTS)/$(CPPOPTS) $(CXXFLAGS) $(CPPFLAGS)/g' Makefile &&" +buildopts = "CPP=${CXX} CC=${CC}" + +files_to_copy = [(['Linux/muscle'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/muscle'], + 'dirs': [], +} + +sanity_check_commands = ["muscle -h"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-11.6.0-GCC-12.3.0.eb b/easybuild/easyconfigs/m/MariaDB/MariaDB-11.6.0-GCC-12.3.0.eb new file mode 100644 index 000000000000..357433434404 --- /dev/null +++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-11.6.0-GCC-12.3.0.eb @@ -0,0 +1,65 @@ +easyblock = 'CMakeMake' + +name = 'MariaDB' +version = '11.6.0' + +homepage = 'https://mariadb.org/' +description = """MariaDB is an enhanced, drop-in replacement for MySQL. +Included engines: myISAM, Aria, InnoDB, RocksDB, TokuDB, OQGraph, Mroonga.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = [ + 'https://archive.mariadb.org/mariadb-%(version)s/source/', + 'http://ftp.hosteurope.de/mirror/archive.mariadb.org/mariadb-%(version)s/source', +] +sources = [SOURCELOWER_TAR_GZ] +patches = ['MariaDB-10.1.13-link-rt-for-jemalloc.patch'] +checksums = [ + {'mariadb-11.6.0.tar.gz': '8fd5b593aee3920eb434c37ec44779d565fe96ef7dfd6b35a646fe7221103e11'}, + {'MariaDB-10.1.13-link-rt-for-jemalloc.patch': '8295837e623f6c782e1d64b00e0877ea98cce4bf8846755bb86c8a7732797c19'}, +] + +builddependencies = [ + ('CMake', '3.26.3'), + ('libaio', '0.3.113'), +] + +dependencies = [ + ('ncurses', '6.4'), + ('zlib', '1.2.13'), + ('LZO', '2.10'), # optional + ('lz4', '1.9.4'), # optional + ('XZ', '5.4.2'), # optional + ('jemalloc', '5.3.0'), # optional + ('snappy', '1.1.10'), # needed by RocksDB; optional for InnoDB + ('libxml2', '2.11.4'), # needed by Connect XML + ('Boost', '1.82.0'), # needed by OQGraph + ('Judy', '1.0.5'), # needed by OQGraph + ('PCRE2', '10.42'), + ('OpenSSL', '1.1', '', SYSTEM), # runtime dep for mysql and PCRE2 for mysqltest +] + +configopts = "-DCMAKE_SHARED_LINKER_FLAGS='-fuse-ld=bfd' " # Linking fails with default gold linker +configopts += "-DMYSQL_MAINTAINER_MODE=OFF " # disabled to not treat warnings as errors (-Werror) +configopts += "-DWITH_PCRE=auto " # External download sometimes fails so we build PCRE2 directly. +configopts += "-DWITH_ZLIB=system " +configopts += "-DWITH_EMBEDDED_SERVER=ON " # for libmysqld.so & co +configopts += "-DWITH_SAFEMALLOC=OFF " # Disable memory debugger with jemalloc + +sanity_check_commands = ["mysql --help", "mysqltest --help"] + +sanity_check_paths = { + 'files': ['bin/mysql', 'bin/mysqld_safe', 'lib/libmysqlclient.%s' % SHLIB_EXT, 'lib/libmysqld.%s' % SHLIB_EXT, + 'lib/plugin/ha_connect.%s' % SHLIB_EXT, 'lib/plugin/ha_rocksdb.%s' % SHLIB_EXT, + 'lib/plugin/ha_oqgraph.%s' % SHLIB_EXT, 'scripts/mysql_install_db'], + 'dirs': ['include', 'share'], +} + +modextrapaths = {'PATH': 'scripts'} + +# Ensure that jemalloc does not use transparent hugepages. +# Database workloads with THP can cause memory bloat, potentially hiting OOM errors. +modextravars = {'MALLOC_CONF': 'thp:never'} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/m/Maven/Maven-3.9.7.eb b/easybuild/easyconfigs/m/Maven/Maven-3.9.7.eb new file mode 100644 index 000000000000..63a55f376dfe --- /dev/null +++ b/easybuild/easyconfigs/m/Maven/Maven-3.9.7.eb @@ -0,0 +1,26 @@ +# Contribution from the Crick HPC team +# uploaded by J. Sassmannshausen + +easyblock = 'PackedBinary' + +name = 'Maven' +version = '3.9.7' + +homepage = 'https://maven.apache.org/index.html' +description = """Binary maven install, Apache Maven is a software project management and comprehension tool. Based on +the concept of a project object model (POM), Maven can manage a project's build, reporting and documentation from a +central piece of information. +""" + +toolchain = SYSTEM + +source_urls = ['https://archive.apache.org/dist/maven/maven-%(version_major)s/%(version)s/binaries/'] +sources = ['apache-maven-%(version)s-bin.tar.gz'] +checksums = ['c8fb9f620e5814588c2241142bbd9827a08e3cb415f7aa437f2ed44a3eeab62c'] + +sanity_check_paths = { + 'files': ['bin/mvn'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/Mercurial/Mercurial-6.8.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/m/Mercurial/Mercurial-6.8.1-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..a733004f29a6 --- /dev/null +++ b/easybuild/easyconfigs/m/Mercurial/Mercurial-6.8.1-GCCcore-13.3.0.eb @@ -0,0 +1,31 @@ +# # +# Author: Robert Mijakovic +# # +easyblock = 'PythonPackage' + +name = 'Mercurial' +version = '6.8.1' + +homepage = 'https://www.mercurial-scm.org' +description = """Mercurial is a free, distributed source control management tool. It efficiently handles projects +of any size and offers an easy and intuitive interface. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://www.%(namelower)s-scm.org/release/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['030e8a7a6d590e4eaeb403ee25675615cd80d236f3ab8a0b56dcc84181158b05'] + +dependencies = [ + ('binutils', '2.42'), + ('Python', '3.12.3'), +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +sanity_check_commands = ['hg --help'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-24.1.3-GCCcore-13.3.0.eb b/easybuild/easyconfigs/m/Mesa/Mesa-24.1.3-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..5eda042c4947 --- /dev/null +++ b/easybuild/easyconfigs/m/Mesa/Mesa-24.1.3-GCCcore-13.3.0.eb @@ -0,0 +1,68 @@ +# This is a Mesa using software rendering via Gallium-DRI and libglvnd +# - libglvnd can dynamically choose between system-installed NVidia +# libGLX/libEGL or the software renderers provided by this Mesa +# - EGL is available +# +# Software renderers enabled (swr deprecated as of v22): +# - llvmpipe: uses LLVM for JIT code generation (multi-threaded) +# - softpipe: a reference Gallium driver +# Default renderer is llvmpipe. To use softpipe, set the environment +# variable GALLIUM_DRIVER=softpipe + +name = 'Mesa' +version = '24.1.3' + +homepage = 'https://www.mesa3d.org/' +description = """Mesa is an open-source implementation of the OpenGL specification - + a system for rendering interactive 3D graphics.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [ + 'https://mesa.freedesktop.org/archive/', + 'https://mesa.freedesktop.org/archive/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x', +] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['63236426b25a745ba6aa2d6daf8cd769d5ea01887b0745ab7124d2ef33a9020d'] + +builddependencies = [ + ('binutils', '2.42'), + ('Meson', '1.4.0'), + ('Ninja', '1.12.1'), + ('flex', '2.6.4'), + ('Bison', '3.8.2'), + ('pkgconf', '2.2.0'), + ('Mako', '1.3.5'), + ('libxml2', '2.12.7'), + ('expat', '2.6.2'), + ('gettext', '0.22.5'), +] + +dependencies = [ + ('zlib', '1.3.1'), + ('zstd', '1.5.6'), + ('libdrm', '2.4.122'), + ('libglvnd', '1.7.0'), + ('libunwind', '1.8.1'), + ('LLVM', '18.1.8'), + ('X11', '20240607'), + ('Wayland', '1.23.0'), +] + +configopts = "-Dplatforms=x11,wayland -Dosmesa=true -Dvulkan-drivers='swrast' -Dvulkan-layers='device-select' " +configopts += "-Dllvm=enabled -Dshared-llvm=enabled -Dlibunwind=enabled -Dglvnd=true " +configopts += "-Dvideo-codecs=vc1dec,h264dec,h264enc,h265dec,h265enc " + +# Easybuild will automatically add appropriate Gallium drivers for the processor architecture of the host +# If you need a different configuration, it possible to override those values by setting your own configopts +# configopts += " -Dgallium-drivers=swrast" + +# symlink indirect to mesa GLX, similar to Debian, see +# https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=881789 +# This helps in certain X forwarding situations (e.g. XQuartz) +postinstallcmds = ["ln -s libGLX_mesa.so.0 %(installdir)s/lib/libGLX_indirect.so.0"] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/MeshLab/MeshLab-2023.12-GCC-12.3.0.eb b/easybuild/easyconfigs/m/MeshLab/MeshLab-2023.12-GCC-12.3.0.eb new file mode 100644 index 000000000000..ca152c147be4 --- /dev/null +++ b/easybuild/easyconfigs/m/MeshLab/MeshLab-2023.12-GCC-12.3.0.eb @@ -0,0 +1,47 @@ +easyblock = 'CMakeNinja' + +name = 'MeshLab' +version = '2023.12' + +homepage = 'https://github.com/cnr-isti-vclab/meshlab' +description = 'The open source mesh processing system.' + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +sources = [{ + 'filename': '%(name)s-%(version)s.tar.gz', + 'git_config': { + 'url': 'https://github.com/cnr-isti-vclab', + 'repo_name': '%(namelower)s', + 'tag': '%(name)s-%(version)s', + 'recursive': True, + 'keep_git_dir': True, + }, +}] +checksums = [None] + +builddependencies = [ + ('CMake', '3.26.3'), + ('Ninja', '1.11.1'), + ('pkgconf', '1.9.5'), + ('patchelf', '0.18.0'), + ('Eigen', '3.4.0'), +] + +dependencies = [ + ('Qt5', '5.15.10'), + ('Mesa', '23.1.4'), + ('libGLU', '9.0.3'), + ('CGAL', '5.6'), + ('Boost', '1.82.0'), + ('MPFR', '4.2.0'), +] + +sanity_check_paths = { + 'files': ['bin/meshlab'], + 'dirs': ['share'], +} + +sanity_check_commands = ['meshlab --help'] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/Miniconda3/Miniconda3-23.10.0-1.eb b/easybuild/easyconfigs/m/Miniconda3/Miniconda3-23.10.0-1.eb new file mode 100644 index 000000000000..3fd68df4e5c8 --- /dev/null +++ b/easybuild/easyconfigs/m/Miniconda3/Miniconda3-23.10.0-1.eb @@ -0,0 +1,27 @@ +easyblock = 'EB_Anaconda' + +name = 'Miniconda3' +version = '23.10.0-1' + +homepage = 'https://docs.conda.io/en/latest/miniconda.html' +description = """Miniconda is a free minimal installer for conda. It is a small, + bootstrap version of Anaconda that includes only conda, Python, the packages they + depend on, and a small number of other useful packages.""" + +toolchain = SYSTEM + +source_urls = ['https://repo.anaconda.com/miniconda/'] +local_arch = {'arm64': 'aarch64'}.get(ARCH, ARCH) +sources = ['%%(name)s-py311_%%(version)s-Linux-%s.sh' % local_arch] +checksums = [ + { + '%(name)s-py311_%(version)s-Linux-x86_64.sh': + 'd0643508fa49105552c94a523529f4474f91730d3e0d1f168f1700c43ae67595', + '%(name)s-py311_%(version)s-Linux-ppc64le.sh': + '1a2eda0a9a52a4bd058abbe9de5bb2bc751fcd7904c4755deffdf938d6f4436e', + '%(name)s-py311_%(version)s-Linux-aarch64.sh': + 'a60e70ad7e8ac5bb44ad876b5782d7cdc66e10e1f45291b29f4f8d37cc4aa2c8', + } +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/m/MultiQC/MultiQC-1.22.3-foss-2023b.eb b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.22.3-foss-2023b.eb new file mode 100644 index 000000000000..ef34f8747cf0 --- /dev/null +++ b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.22.3-foss-2023b.eb @@ -0,0 +1,80 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Adam Huffman +# The Francis Crick Institute +# Elements derived from work by Pablo Escobar +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +# Note that Click in Python 3 requires that you change your locale to unicode before invoking your Python script. +# See: https://click.palletsprojects.com/en/7.x/python3/ + +easyblock = 'PythonBundle' + +name = 'MultiQC' +version = '1.22.3' + +homepage = 'https://multiqc.info' +description = """Aggregate results from bioinformatics analyses across many samples into a single report. + + MultiQC searches a given directory for analysis logs and compiles an HTML report. It's a general + use tool, perfect for summarising the output from numerous bioinformatics tools.""" + +toolchain = {'name': 'foss', 'version': '2023b'} + +builddependencies = [('hatchling', '1.18.0')] + +dependencies = [ + ('Python', '3.11.5'), + ('Python-bundle-PyPI', '2023.10'), + ('Kaleido', '0.2.1'), + ('matplotlib', '3.8.2'), + ('plotly.py', '5.18.0'), + ('pydantic', '2.7.4'), + ('tqdm', '4.66.2'), + ('Pillow', '10.2.0'), + ('PyYAML', '6.0.1'), + ('networkx', '3.2.1'), +] + +use_pip = True + +exts_list = [ + ('colormath', '3.0.0', { + 'checksums': ['3d4605af344527da0e4f9f504fad7ddbebda35322c566a6c72e28edb1ff31217'], + }), + ('humanfriendly', '10.0', { + 'checksums': ['6b0b831ce8f15f7300721aa49829fc4e83921a9a301cc7f606be6686a2288ddc'], + }), + ('Markdown', '3.6', { + 'checksums': ['ed4f41f6daecbeeb96e576ce414c41d2d876daa9a16cb35fa8ed8c2ddfad0224'], + }), + ('coloredlogs', '15.0.1', { + 'checksums': ['7c991aa71a4577af2f82600d8f8f3a89f936baeaf9b50a9c197da014e5bf16b0'], + }), + ('humanize', '4.9.0', { + 'checksums': ['582a265c931c683a7e9b8ed9559089dea7edcf6cc95be39a3cbc2c5d5ac2bcfa'], + }), + ('pyaml_env', '1.2.1', { + 'checksums': ['6d5dc98c8c82df743a132c196e79963050c9feb05b0a6f25f3ad77771d3d95b0'], + }), + ('spectra', '0.0.11', { + 'checksums': ['8eb362a5187cb63cee13cd01186799c0c791a3ad3bec57b279132e12521762b8'], + }), + ('typeguard', '4.3.0', { + 'checksums': ['92ee6a0aec9135181eae6067ebd617fd9de8d75d714fb548728a4933b1dea651'], + }), + ('multiqc', version, { + 'checksums': ['5f2cc3c417b5ed4ad57bdff02d93bb7f4c6e6677768ddad1cde7b9b1e04b5854'], + }), +] + +sanity_check_paths = { + 'files': ['bin/multiqc'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["multiqc --help"] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/maeparser/maeparser-1.3.1-gompi-2024a.eb b/easybuild/easyconfigs/m/maeparser/maeparser-1.3.1-gompi-2024a.eb new file mode 100644 index 000000000000..a757e81653a3 --- /dev/null +++ b/easybuild/easyconfigs/m/maeparser/maeparser-1.3.1-gompi-2024a.eb @@ -0,0 +1,26 @@ +easyblock = 'CMakeMake' + +name = 'maeparser' +version = '1.3.1' + +homepage = 'https://github.com/schrodinger/maeparser' +description = "maeparser is a parser for Schrodinger Maestro files." + +toolchain = {'name': 'gompi', 'version': '2024a'} + +source_urls = ['https://github.com/schrodinger/maeparser/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['a8d80f67d1b9be6e23b9651cb747f4a3200132e7d878a285119c86bf44568e36'] + +builddependencies = [ + ('CMake', '3.29.3'), +] + +dependencies = [('Boost', '1.85.0')] + +sanity_check_paths = { + 'files': ['lib/libmaeparser.%s' % SHLIB_EXT], + 'dirs': ['include/maeparser', 'lib/cmake'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.9-GCCcore-13.2.0.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.9-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..94178adcc236 --- /dev/null +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.9-GCCcore-13.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'makedepend' +version = '1.0.9' + +homepage = 'https://linux.die.net/man/1/makedepend' +description = "The makedepend package contains a C-preprocessor like utility to determine build-time dependencies." + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = [XORG_UTIL_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['bc94ffda6cd4671603a69c39dbe8f96b317707b9185b2aaa3b54b5d134b41884'] + +builddependencies = [ + ('binutils', '2.40'), + ('xproto', '7.0.31'), + ('xorg-macros', '1.20.0'), +] + +sanity_check_paths = { + 'files': ['bin/makedepend'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/mallard-ducktype/mallard-ducktype-1.0.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/m/mallard-ducktype/mallard-ducktype-1.0.2-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..65102800699b --- /dev/null +++ b/easybuild/easyconfigs/m/mallard-ducktype/mallard-ducktype-1.0.2-GCCcore-12.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'mallard-ducktype' +version = '1.0.2' + +homepage = 'https://github.com/projectmallard/mallard-ducktype' +description = """Parser for the lightweight Ducktype syntax for Mallard""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +sources = ['mallard_ducktype-%(version)s-py3-none-any.whl'] +checksums = ['90c2d9e40934c634f3e83e0758285e2803f62c2c5db405702af2f5884e1a2918'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('Python', '3.11.3'), +] + +options = {'modulename': 'mallard.ducktype'} + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.9.2-contourpy-fix-pybind-module.patch b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.9.2-contourpy-fix-pybind-module.patch new file mode 100644 index 000000000000..9a34eb1cdaee --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.9.2-contourpy-fix-pybind-module.patch @@ -0,0 +1,14 @@ +Fixes: error: macro "PYBIND11_MODULE" passed 3 arguments, but takes just 2 +Author: Anke Kreuzer (JSC) +diff -ruN src/wrap.cpp.orig src/wrap.cpp +--- src/wrap.cpp.orig 2024-09-02 21:07:13.893013182 +0200 ++++ src/wrap.cpp 2024-09-02 21:07:39.973005828 +0200 +@@ -18,7 +18,7 @@ + static contourpy::LineType mpl20xx_line_type = contourpy::LineType::SeparateCode; + static contourpy::FillType mpl20xx_fill_type = contourpy::FillType::OuterCode; + +-PYBIND11_MODULE(_contourpy, m, py::mod_gil_not_used()) { ++PYBIND11_MODULE(_contourpy, m) { + m.doc() = + "C++11 extension module wrapped using `pybind11`_.\n\n" + "It should not be necessary to access classes and functions in this extension module " diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.9.2-gfbf-2024a.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.9.2-gfbf-2024a.eb new file mode 100644 index 000000000000..33ddf00eb934 --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.9.2-gfbf-2024a.eb @@ -0,0 +1,79 @@ +easyblock = 'PythonBundle' + +name = 'matplotlib' +version = '3.9.2' + +homepage = 'https://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'gfbf', 'version': '2024a'} + +builddependencies = [ + ('pkgconf', '2.2.0'), + ('cppy', '1.2.1'), + ('meson-python', '0.16.0'), +] + +dependencies = [ + ('Python', '3.12.3'), + ('SciPy-bundle', '2024.05'), + ('libpng', '1.6.43'), + ('freetype', '2.13.2'), + ('Tkinter', '%(pyver)s'), + ('Pillow-SIMD', '10.4.0'), + ('Qhull', '2020.2'), +] + +use_pip = True +sanity_pip_check = True + +_include_path = "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && " + +local_configopts = "--config-settings=setup-args='-Dsystem-qhull=true' && " +local_configopts += " --config-settings=setup-args='-Dsystem-freetype=true' && " +local_configopts += "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && " + +exts_list = [ + ('fonttools', '4.53.1', { + 'modulename': 'fontTools', + 'source_tmpl': '%(name)s-%(version)s.tar.gz', + 'checksums': ['e128778a8e9bc11159ce5447f76766cefbd876f44bd79aff030287254e4752c4'], + }), + ('Cycler', '0.12.1', { + 'modulename': 'cycler', + 'source_tmpl': 'cycler-%(version)s.tar.gz', + 'checksums': ['88bb128f02ba341da8ef447245a9e138fae777f6a23943da4540077d3601eb1c'], + }), + ('kiwisolver', '1.4.5', { + 'patches': ['kiwisolver-1.4.4-fix_version.patch'], + 'checksums': [ + {'kiwisolver-1.4.5.tar.gz': 'e57e563a57fb22a142da34f38acc2fc1a5c864bc29ca1517a88abc963e60d6ec'}, + {'kiwisolver-1.4.4-fix_version.patch': '6753afbb3a88856493fcfa0b33989f35742f57bfd41ff3b7f71a98797e1bfbd0'}, + ], + }), + ('contourpy', '1.3.0', { + 'patches': ['matplotlib-3.9.2-contourpy-fix-pybind-module.patch'], + 'checksums': [ + {'contourpy-1.3.0.tar.gz': '7ffa0db17717a8ffb127efd0c95a4362d996b892c2904db72428d5b52e1938a4'}, + {'matplotlib-3.9.2-contourpy-fix-pybind-module.patch': + 'a998438a1048524a550bf3bb607197658b13dce56e8e54169e24ce7c3c022a8f'}, + ], + }), + (name, version, { + 'configopts': "%(local_configopts)s", + 'checksums': ['96ab43906269ca64a6366934106fa01534454a69e471b7bf3d79083981aaab92'], + }), +] + +sanity_check_commands = [ + """python -c 'import matplotlib; matplotlib.use("Agg"); import matplotlib.pyplot' """, + "python -c 'from mpl_toolkits.mplot3d import Axes3D'", +] + +# use non-interactive plotting backend as default +# see https://matplotlib.org/tutorials/introductory/usage.html#what-is-a-backend +modextravars = {'MPLBACKEND': 'Agg'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/maturin/maturin-1.6.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/m/maturin/maturin-1.6.0-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..b7a45d6c37ae --- /dev/null +++ b/easybuild/easyconfigs/m/maturin/maturin-1.6.0-GCCcore-13.3.0.eb @@ -0,0 +1,659 @@ +easyblock = 'CargoPythonPackage' + +name = 'maturin' +version = '1.6.0' + +homepage = 'https://github.com/pyo3/maturin' +description = """This project is meant as a zero configuration +replacement for setuptools-rust and milksnake. It supports building +wheels for python 3.5+ on windows, linux, mac and freebsd, can upload +them to pypi and has basic pypy and graalpy support.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +crates = [ + ('adler', '1.0.2'), + ('ahash', '0.8.7'), + ('aho-corasick', '1.1.2'), + ('allocator-api2', '0.2.16'), + ('anstream', '0.6.11'), + ('anstyle', '1.0.4'), + ('anstyle-parse', '0.2.3'), + ('anstyle-query', '1.0.2'), + ('anstyle-wincon', '3.0.2'), + ('anyhow', '1.0.80'), + ('autocfg', '1.1.0'), + ('base64', '0.13.1'), + ('base64', '0.21.7'), + ('bitflags', '1.3.2'), + ('bitflags', '2.4.2'), + ('block-buffer', '0.10.4'), + ('bstr', '1.9.0'), + ('byteorder', '1.5.0'), + ('bytes', '1.5.0'), + ('bytesize', '1.3.0'), + ('bzip2', '0.4.4'), + ('bzip2-sys', '0.1.11+1.0.8'), + ('cab', '0.4.1'), + ('camino', '1.1.6'), + ('cargo-config2', '0.1.24'), + ('cargo-options', '0.7.4'), + ('cargo-platform', '0.1.6'), + ('cargo-xwin', '0.16.4'), + ('cargo-zigbuild', '0.18.4'), + 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'7a4191c47f15cc3ec71fcb4913cb83d58def65dd3787610213c649283b5ce178'}, + {'xattr-1.3.1.tar.gz': '8da84f1a25939b27f6820d92aed108f83ff920fdf11a7b19366c27c4cda81d4f'}, + {'xwin-0.5.0.tar.gz': 'c43e0202f5457b48558096cb7b36d0e473f267551a89c82ed72d73b01dfd4007'}, + {'yansi-0.5.1.tar.gz': '09041cd90cf85f7f8b2df60c646f853b7f535ce68f85244eb6731cf89fa498ec'}, + {'zerocopy-0.7.32.tar.gz': '74d4d3961e53fa4c9a25a8637fc2bfaf2595b3d3ae34875568a5cf64787716be'}, + {'zerocopy-derive-0.7.32.tar.gz': '9ce1b18ccd8e73a9321186f97e46f9f04b778851177567b1975109d26a08d2a6'}, + {'zeroize-1.7.0.tar.gz': '525b4ec142c6b68a2d10f01f7bbf6755599ca3f81ea53b8431b7dd348f5fdb2d'}, + {'zip-0.6.6.tar.gz': '760394e246e4c28189f19d488c058bf16f564016aefac5d32bb1f3b51d5e9261'}, +] + +builddependencies = [ + ('binutils', '2.42'), + ('setuptools-rust', '1.9.0'), +] +dependencies = [ + ('Python', '3.12.3'), + ('Rust', '1.78.0'), +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/mcqd/mcqd-1.0.0-GCC-13.2.0.eb b/easybuild/easyconfigs/m/mcqd/mcqd-1.0.0-GCC-13.2.0.eb new file mode 100644 index 000000000000..87f925535482 --- /dev/null +++ b/easybuild/easyconfigs/m/mcqd/mcqd-1.0.0-GCC-13.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'CmdCp' + +name = 'mcqd' +version = '1.0.0' + +homepage = 'https://gitlab.com/janezkonc/mcqd' +description = """MaxCliqueDyn is a fast exact algorithm for finding a maximum clique in an undirected graph.""" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +source_urls = ['https://gitlab.com/janezkonc/mcqd/-/archive/v%(version)s/'] +sources = ['mcqd-v%(version)s.tar.gz'] +checksums = ['37ff68ff88e047c929990d4c12ce474753f6f9c49324661a3aa1cfe77c26ad9d'] + +cmds_map = [('.*', '$CXX $CXXFLAGS $LDFLAGS mcqd.cpp -o mcqd')] + +files_to_copy = [ + (['mcqd'], 'bin'), + (['mcqd.h'], 'include'), +] + +sanity_check_paths = { + 'files': [ + 'bin/mcqd', + 'include/mcqd.h', + ], + 'dirs': [], +} + +sanity_check_commands = ["command -v mcqd"] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/medaka/medaka-1.12.0-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/m/medaka/medaka-1.12.0-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 000000000000..c9ac4870bf56 --- /dev/null +++ b/easybuild/easyconfigs/m/medaka/medaka-1.12.0-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,85 @@ +# This is a contribution from HPCNow! (http://hpcnow.com) +# Copyright:: HPCNow! +# Authors:: Danilo Gonzalez +# License:: GPL-v3.0 +# Updated to foss-2020b to use with artic tool +# J. Sassmannshausen (GSTT/NHS UK) +# Updated to 1.5.0 +# Jasper Grimm (UoY) +# Updated: Petr Král (INUITS) + +easyblock = 'PythonBundle' + +name = 'medaka' +version = '1.12.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/nanoporetech/medaka' +description = "medaka is a tool to create a consensus sequence from nanopore sequencing data." + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'pic': True} + +builddependencies = [('Autotools', '20220317')] + +_minimap_ver = '2.26' +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), # includes cffi + ('TensorFlow', '2.15.1', versionsuffix), + ('Pysam', '0.22.0'), + ('SAMtools', '1.18'), + ('minimap2', _minimap_ver), + ('HTSlib', '1.18'), # for tabix, bgzip + ('Racon', '1.5.0'), + ('edlib', '1.3.9'), + ('pyspoa', '0.2.1'), + ('python-parasail', '1.3.4'), + ('ont-fast5-api', '4.1.2'), + ('WhatsHap', '2.2'), + ('intervaltree-python', '3.1.0'), + ('BCFtools', '1.18'), +] + +use_pip = True +sanity_pip_check = True + +local_sed_commands = [ + "sed -i 's/tensorflow.*/tensorflow/g;s/cffi==1.15.0/cffi/g' requirements.txt pyproject.toml", + # Python 3.11 support + "sed -i 's/8, 9, 10/8, 9, 10, 11/g;s/,<3.11//g' setup.py", +] + +exts_list = [ + ('mappy', _minimap_ver, { + 'checksums': ['e53fbe9a3ea8762a64b8103f4f779c9fb16d418eaa0a731f45cebc83867a9b71'], + }), + ('wurlitzer', '3.1.1', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['0b2749c2cde3ef640bf314a9f94b24d929fe1ca476974719a6909dfc568c3aac'], + }), + ('h5py', '3.10.0', { + 'checksums': ['d93adc48ceeb33347eb24a634fb787efc7ae4644e6ea4ba733d099605045c049'], + }), + ('pyabpoa', '1.5.1', { + 'checksums': ['878f981e890a421d92a0d7606705d0ad9813ae6086239460dfe4b0cfc7476174'], + }), + (name, version, { + 'checksums': ['039219204111a8114b1f72d87d0d3463e43473790cff4520c8afbd79cc8784d6'], + # Some requirements are too strict. + 'preinstallopts': " && ".join(local_sed_commands) + " && ", + }), +] + +sanity_check_paths = { + 'files': ['bin/medaka', 'bin/medaka_consensus', 'bin/medaka_version_report'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "medaka --help", + "medaka_version_report", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/medaka/medaka-1.12.0-foss-2023a.eb b/easybuild/easyconfigs/m/medaka/medaka-1.12.0-foss-2023a.eb new file mode 100644 index 000000000000..af21d1b6a0df --- /dev/null +++ b/easybuild/easyconfigs/m/medaka/medaka-1.12.0-foss-2023a.eb @@ -0,0 +1,84 @@ +# This is a contribution from HPCNow! (http://hpcnow.com) +# Copyright:: HPCNow! +# Authors:: Danilo Gonzalez +# License:: GPL-v3.0 +# Updated to foss-2020b to use with artic tool +# J. Sassmannshausen (GSTT/NHS UK) +# Updated to 1.5.0 +# Jasper Grimm (UoY) +# Updated: Petr Král (INUITS) + +easyblock = 'PythonBundle' + +name = 'medaka' +version = '1.12.0' + +homepage = 'https://github.com/nanoporetech/medaka' +description = "medaka is a tool to create a consensus sequence from nanopore sequencing data." + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'pic': True} + +builddependencies = [('Autotools', '20220317')] + +_minimap_ver = '2.26' +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), # includes cffi + ('TensorFlow', '2.13.0'), + ('Pysam', '0.22.0'), + ('SAMtools', '1.18'), + ('minimap2', _minimap_ver), + ('HTSlib', '1.18'), # for tabix, bgzip + ('Racon', '1.5.0'), + ('edlib', '1.3.9'), + ('pyspoa', '0.2.1'), + ('python-parasail', '1.3.4'), + ('ont-fast5-api', '4.1.2'), + ('WhatsHap', '2.2'), + ('intervaltree-python', '3.1.0'), + ('BCFtools', '1.18'), +] + +use_pip = True +sanity_pip_check = True + +local_sed_commands = [ + "sed -i 's/tensorflow.*/tensorflow/g;s/cffi==1.15.0/cffi/g' requirements.txt pyproject.toml", + # Python 3.11 support + "sed -i 's/8, 9, 10/8, 9, 10, 11/g;s/,<3.11//g' setup.py", +] + +exts_list = [ + ('mappy', _minimap_ver, { + 'checksums': ['e53fbe9a3ea8762a64b8103f4f779c9fb16d418eaa0a731f45cebc83867a9b71'], + }), + ('wurlitzer', '3.1.1', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['0b2749c2cde3ef640bf314a9f94b24d929fe1ca476974719a6909dfc568c3aac'], + }), + # medaka 1.12.0 requires h5py ~=3.10.0 + ('h5py', '3.10.0', { + 'checksums': ['d93adc48ceeb33347eb24a634fb787efc7ae4644e6ea4ba733d099605045c049'], + }), + ('pyabpoa', '1.5.1', { + 'checksums': ['878f981e890a421d92a0d7606705d0ad9813ae6086239460dfe4b0cfc7476174'], + }), + (name, version, { + 'checksums': ['039219204111a8114b1f72d87d0d3463e43473790cff4520c8afbd79cc8784d6'], + # Some requirements are too strict. + 'preinstallopts': " && ".join(local_sed_commands) + " && ", + }), +] + +sanity_check_paths = { + 'files': ['bin/medaka', 'bin/medaka_consensus', 'bin/medaka_version_report'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "medaka --help", + "medaka_version_report", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/medaka/medaka-1.12.1-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/m/medaka/medaka-1.12.1-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 000000000000..3e055e5d8dd8 --- /dev/null +++ b/easybuild/easyconfigs/m/medaka/medaka-1.12.1-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,88 @@ +# This is a contribution from HPCNow! (http://hpcnow.com) +# Copyright:: HPCNow! +# Authors:: Danilo Gonzalez +# License:: GPL-v3.0 +# Updated to foss-2020b to use with artic tool +# J. Sassmannshausen (GSTT/NHS UK) +# Updated to 1.5.0 +# Jasper Grimm (UoY) +# Updated: Petr Král (INUITS) + +easyblock = 'PythonBundle' + +name = 'medaka' +version = '1.12.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/nanoporetech/medaka' +description = "medaka is a tool to create a consensus sequence from nanopore sequencing data." + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'pic': True} + +builddependencies = [('Autotools', '20220317')] + +_minimap_ver = '2.26' +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), # includes cffi + ('TensorFlow', '2.15.1', versionsuffix), + ('Pysam', '0.22.0'), + ('SAMtools', '1.18'), + ('minimap2', _minimap_ver), + ('HTSlib', '1.18'), # for tabix, bgzip + ('Racon', '1.5.0'), + ('edlib', '1.3.9'), + ('pyspoa', '0.2.1'), + ('python-parasail', '1.3.4'), + ('ont-fast5-api', '4.1.2'), + ('WhatsHap', '2.2'), + ('intervaltree-python', '3.1.0'), + ('BCFtools', '1.18'), +] + +use_pip = True +sanity_pip_check = True + +local_sed_commands = [ + "sed -i 's/tensorflow.*/tensorflow/g;s/cffi==1.15.0/cffi/g' requirements.txt pyproject.toml", + # Python 3.11 support + "sed -i 's/8, 9, 10/8, 9, 10, 11/g;s/,<3.11//g' setup.py", + # ont-parasail on PyPI is just pre-built wheels for (python-)parasail + "sed -i 's/ont-parasail/parasail/g' requirements.txt", +] + +exts_list = [ + ('mappy', _minimap_ver, { + 'checksums': ['e53fbe9a3ea8762a64b8103f4f779c9fb16d418eaa0a731f45cebc83867a9b71'], + }), + ('wurlitzer', '3.1.1', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['0b2749c2cde3ef640bf314a9f94b24d929fe1ca476974719a6909dfc568c3aac'], + }), + # medaka 1.12.0 requires h5py ~=3.10.0 + ('h5py', '3.10.0', { + 'checksums': ['d93adc48ceeb33347eb24a634fb787efc7ae4644e6ea4ba733d099605045c049'], + }), + ('pyabpoa', '1.5.2', { + 'checksums': ['be39c83b12e923c9e47073cb8f0abc4c42f609fa2c0ec13d6f6a4f5a0537ee06'], + }), + (name, version, { + 'checksums': ['df4baf7d1e9154de85229aef237919619ff6ae7f7d103abb0828e449ff977adf'], + # Some requirements are too strict. + 'preinstallopts': " && ".join(local_sed_commands) + " && ", + }), +] + +sanity_check_paths = { + 'files': ['bin/medaka', 'bin/medaka_consensus', 'bin/medaka_version_report'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "medaka --help", + "medaka_version_report", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/medaka/medaka-1.12.1-foss-2023a.eb b/easybuild/easyconfigs/m/medaka/medaka-1.12.1-foss-2023a.eb new file mode 100644 index 000000000000..f95d01c89d98 --- /dev/null +++ b/easybuild/easyconfigs/m/medaka/medaka-1.12.1-foss-2023a.eb @@ -0,0 +1,86 @@ +# This is a contribution from HPCNow! (http://hpcnow.com) +# Copyright:: HPCNow! +# Authors:: Danilo Gonzalez +# License:: GPL-v3.0 +# Updated to foss-2020b to use with artic tool +# J. Sassmannshausen (GSTT/NHS UK) +# Updated to 1.5.0 +# Jasper Grimm (UoY) +# Updated: Petr Král (INUITS) + +easyblock = 'PythonBundle' + +name = 'medaka' +version = '1.12.1' + +homepage = 'https://github.com/nanoporetech/medaka' +description = "medaka is a tool to create a consensus sequence from nanopore sequencing data." + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'pic': True} + +builddependencies = [('Autotools', '20220317')] + +_minimap_ver = '2.26' +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), # includes cffi + ('TensorFlow', '2.13.0'), + ('Pysam', '0.22.0'), + ('SAMtools', '1.18'), + ('minimap2', _minimap_ver), + ('HTSlib', '1.18'), # for tabix, bgzip + ('Racon', '1.5.0'), + ('edlib', '1.3.9'), + ('pyspoa', '0.2.1'), + ('python-parasail', '1.3.4'), + ('ont-fast5-api', '4.1.2'), + ('WhatsHap', '2.2'), + ('intervaltree-python', '3.1.0'), + ('BCFtools', '1.18'), +] + +use_pip = True +sanity_pip_check = True + +local_sed_commands = [ + "sed -i 's/tensorflow.*/tensorflow/g;s/cffi==1.15.0/cffi/g' requirements.txt pyproject.toml", + # Python 3.11 support + "sed -i 's/8, 9, 10/8, 9, 10, 11/g;s/,<3.11//g' setup.py", + # ont-parasail on PyPI is just pre-built wheels for (python-)parasail + "sed -i 's/ont-parasail/parasail/g' requirements.txt", +] + +exts_list = [ + ('mappy', _minimap_ver, { + 'checksums': ['e53fbe9a3ea8762a64b8103f4f779c9fb16d418eaa0a731f45cebc83867a9b71'], + }), + ('wurlitzer', '3.1.1', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['0b2749c2cde3ef640bf314a9f94b24d929fe1ca476974719a6909dfc568c3aac'], + }), + # medaka 1.12.0 requires h5py ~=3.10.0 + ('h5py', '3.10.0', { + 'checksums': ['d93adc48ceeb33347eb24a634fb787efc7ae4644e6ea4ba733d099605045c049'], + }), + ('pyabpoa', '1.5.2', { + 'checksums': ['be39c83b12e923c9e47073cb8f0abc4c42f609fa2c0ec13d6f6a4f5a0537ee06'], + }), + (name, version, { + 'checksums': ['df4baf7d1e9154de85229aef237919619ff6ae7f7d103abb0828e449ff977adf'], + # Some requirements are too strict. + 'preinstallopts': " && ".join(local_sed_commands) + " && ", + }), +] + +sanity_check_paths = { + 'files': ['bin/medaka', 'bin/medaka_consensus', 'bin/medaka_version_report'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "medaka --help", + "medaka_version_report", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/meshio/meshio-5.3.5-foss-2023b.eb b/easybuild/easyconfigs/m/meshio/meshio-5.3.5-foss-2023b.eb new file mode 100644 index 000000000000..d4b1a912aa31 --- /dev/null +++ b/easybuild/easyconfigs/m/meshio/meshio-5.3.5-foss-2023b.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonBundle' + +name = 'meshio' +version = '5.3.5' + +homepage = 'https://github.com/nschloe/meshio' +description = "meshio is a tool for reading/writing various mesh formats representing unstructured meshes" + +toolchain = {'name': 'foss', 'version': '2023b'} + +dependencies = [ + ('Python', '3.11.5'), + ('Python-bundle-PyPI', '2023.10'), # includes rich + ('SciPy-bundle', '2023.11'), # includes numpy + ('h5py', '3.11.0'), + ('VTK', '9.3.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('appdirs', '1.4.4', { + 'checksums': ['7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41'], + }), + ('pipdate', '0.5.6', { + 'checksums': ['1b6b7ec2c5468fb7036ec9d6b2ced7a8a538db55aaca03f30199216d3bbd264b'], + }), + (name, version, { + 'checksums': ['f21f01abd9f29ba06ea119304b3d39e610421cfe93b9dd23362834919f87586d'], + }), +] + +sanity_check_paths = { + 'files': ['bin/meshio', 'bin/pipdate'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/m/meson-python/meson-python-0.16.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/m/meson-python/meson-python-0.16.0-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..1724208584ff --- /dev/null +++ b/easybuild/easyconfigs/m/meson-python/meson-python-0.16.0-GCCcore-13.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonBundle' + +name = 'meson-python' +version = '0.16.0' + +homepage = 'https://github.com/mesonbuild/meson-python' +description = "Python build backend (PEP 517) for Meson projects" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('binutils', '2.42'), +] + +dependencies = [ + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), # provides 'packaging' + ('Meson', '1.4.0'), +] + +use_pip = True + +exts_list = [ + ('pyproject-metadata', '0.8.0', { + 'sources': ['pyproject_metadata-%(version)s.tar.gz'], + 'checksums': ['376d5a00764ac29440a54579f88e66b7d9cb7e629d35c35a1c7248bfebc9b455'], + }), + (name, version, { + 'modulename': 'mesonpy', + 'sources': ['meson_python-%(version)s.tar.gz'], + 'checksums': ['9068c17e36c89d6c7ff709fffb2a8a9925e8cd0b02629728e5ceaf2ec505cb5f'], + }), +] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/meteogrid/meteogrid-20240627-gfbf-2023a-R-4.3.2.eb b/easybuild/easyconfigs/m/meteogrid/meteogrid-20240627-gfbf-2023a-R-4.3.2.eb new file mode 100644 index 000000000000..8fca99e52988 --- /dev/null +++ b/easybuild/easyconfigs/m/meteogrid/meteogrid-20240627-gfbf-2023a-R-4.3.2.eb @@ -0,0 +1,34 @@ +easyblock = 'RPackage' + +name = 'meteogrid' +version = '20240627' +local_commit = '9da2345' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/harphub/meteogrid' +description = """ +R package for working with gridded meteorological data. +""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +source_urls = ['https://github.com/harphub/%(name)s/archive/'] +sources = [{ + 'download_filename': '%s.tar.gz' % local_commit, + 'filename': '%%(name)s-%%(version)s-%s.tar.gz' % local_commit, +}] +checksums = ['ab89739e2e85d62bbdc8ee1a96d409654b19ebd2acf8251c2563a88f9d53d5c0'] + +dependencies = [ + ('R', '4.3.2'), + ('PROJ', '9.2.0'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +sanity_check_commands = ['Rscript -e "library(meteogrid)"'] + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/m/micro-sam/micro-sam-1.0.1-foss-2023a.eb b/easybuild/easyconfigs/m/micro-sam/micro-sam-1.0.1-foss-2023a.eb new file mode 100644 index 000000000000..418740280e54 --- /dev/null +++ b/easybuild/easyconfigs/m/micro-sam/micro-sam-1.0.1-foss-2023a.eb @@ -0,0 +1,43 @@ +easyblock = 'PythonBundle' + +name = 'micro-sam' +version = '1.0.1' + +homepage = 'https://github.com/computational-cell-analytics/micro-sam/' +description = "Tools for segmentation and tracking in microscopy build on top of SegmentAnything." + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('torchvision', '0.16.0'), + ('napari', '0.4.18'), + ('zarr', '2.17.1'), + ('vigra', '1.11.2'), + ('python-elf', '0.5.1'), + ('z5py', '2.0.17'), + ('python-xxhash', '3.4.1'), + ('segment-anything', '1.0'), + ('torch-em', '0.7.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'source_urls': ['https://github.com/computational-cell-analytics/micro-sam/archive/'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['5b7cc562a639d68de4f9462f3696f17b479ea0d669eaedb34687b65ceac715e9'], + }), +] + +sanity_check_commands = [ + "python -c 'import affogato'", + "python -c 'import napari.viewer'", + "micro_sam.annotator_2d -h", + "micro_sam.annotator_3d -h", +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/miniasm/miniasm-0.3-20191007-GCCcore-12.3.0.eb b/easybuild/easyconfigs/m/miniasm/miniasm-0.3-20191007-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..a34b456c98c7 --- /dev/null +++ b/easybuild/easyconfigs/m/miniasm/miniasm-0.3-20191007-GCCcore-12.3.0.eb @@ -0,0 +1,46 @@ +easyblock = 'MakeCp' + +name = 'miniasm' +version = '0.3-20191007' +local_commit = 'ce615d1d6b8678d38f2f9d27c9dccd944436ae75' + +homepage = 'https://github.com/lh3/miniasm' +description = """Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It +takes all-vs-all read self-mappings (typically by minimap) as input and outputs +an assembly graph in the GFA format. Different from mainstream assemblers, +miniasm does not have a consensus step. It simply concatenates pieces of read +sequences to generate the final unitig sequences. Thus the per-base error rate +is similar to the raw input reads.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +github_account = 'lh3' +source_urls = [GITHUB_SOURCE] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['31d62309e8b802d3aebd492c1fed8d2a9197a3243c128345745dccb762457e3d'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('zlib', '1.2.13'), +] + +buildopts = 'CC="${CC}" CFLAGS="${CFLAGS}" CPPFLAGS="${CPPFLAGS}"' + +files_to_copy = [ + (['%(name)s', 'minidot'], 'bin'), + (['*.h'], 'include'), + (['LICENSE.txt', 'PAF.md', 'README.md'], 'share'), + (['%(name)s.1'], 'share/man/man1'), +] + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'bin/minidot'], + 'dirs': ['include', 'share'] +} + +sanity_check_commands = ["miniasm -V"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/miniprot/miniprot-0.13-GCCcore-12.3.0.eb b/easybuild/easyconfigs/m/miniprot/miniprot-0.13-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..aa598c6869b4 --- /dev/null +++ b/easybuild/easyconfigs/m/miniprot/miniprot-0.13-GCCcore-12.3.0.eb @@ -0,0 +1,33 @@ +easyblock = "MakeCp" + +name = 'miniprot' +version = '0.13' + +homepage = 'https://github.com/lh3/miniprot' +description = """Miniprot aligns a protein sequence against a genome with affine gap penalty, splicing and frameshift. +It is primarily intended for annotating protein-coding genes in a new species using known genes from other species. +Miniprot is similar to GeneWise and Exonerate in functionality but it can map proteins to whole genomes and is much +faster at the residue alignment step.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/lh3/miniprot/archive'] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['be12d98d998beb78e4e06350c03d2f188bcdf3245d6bcaf43e2cc80785a617a4'] + +builddependencies = [('binutils', '2.40')] +dependencies = [('zlib', '1.2.13')] + +files_to_copy = [ + (['*.h', 'miniprot.1', 'test', 'tex'], 'lib'), + (['miniprot'], 'bin'), + 'README.md', + 'LICENSE.txt', +] + +sanity_check_paths = { + 'files': ['bin/miniprot'], + 'dirs': ['lib'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/ml-collections/ml-collections-0.1.1-foss-2023a.eb b/easybuild/easyconfigs/m/ml-collections/ml-collections-0.1.1-foss-2023a.eb new file mode 100644 index 000000000000..79034a7433db --- /dev/null +++ b/easybuild/easyconfigs/m/ml-collections/ml-collections-0.1.1-foss-2023a.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonBundle' + +name = 'ml-collections' +version = '0.1.1' + +homepage = 'https://github.com/google/ml_collections' +description = """ +ML Collections is a library of Python Collections designed for ML use cases. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('PyYAML', '6.0'), +] + +use_pip = True + +exts_list = [ + ('absl-py', '2.1.0', { + 'modulename': 'absl', + 'checksums': ['7820790efbb316739cde8b4e19357243fc3608a152024288513dd968d7d959ff'], + }), + ('contextlib2', '21.6.0', { + 'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'], + }), + ('ml_collections', version, { + 'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ", + 'checksums': ['3fefcc72ec433aa1e5d32307a3e474bbb67f405be814ea52a2166bfc9dbe68cc'], + }), +] + +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/mm-common/mm-common-1.0.6-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/mm-common/mm-common-1.0.6-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..9a06d985675c --- /dev/null +++ b/easybuild/easyconfigs/m/mm-common/mm-common-1.0.6-GCCcore-11.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'MesonNinja' + +name = 'mm-common' +version = '1.0.6' + +homepage = 'https://gitlab.gnome.org/GNOME/mm-common' +description = """The mm-common module provides the build infrastructure and +utilities shared among the GNOME C++ binding libraries.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['b55c46037dbcdabc5cee3b389ea11cc3910adb68ebe883e9477847aa660862e7'] + +builddependencies = [ + ('binutils', '2.38'), + ('Meson', '0.62.1'), + ('Ninja', '1.10.2'), +] + +dependencies = [ + ('Python', '3.10.4'), +] + +sanity_check_paths = { + 'files': ['bin/mm-common-get', 'bin/mm-common-prepare', 'share/pkgconfig/mm-common-util.pc'], + 'dirs': ['share/man/man1'], +} + +sanity_check_commands = ["mm-common-prepare --help"] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/mm-common/mm-common-1.0.6-GCCcore-12.2.0.eb b/easybuild/easyconfigs/m/mm-common/mm-common-1.0.6-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..48aae0caae0e --- /dev/null +++ b/easybuild/easyconfigs/m/mm-common/mm-common-1.0.6-GCCcore-12.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'MesonNinja' + +name = 'mm-common' +version = '1.0.6' + +homepage = 'https://gitlab.gnome.org/GNOME/mm-common' +description = """The mm-common module provides the build infrastructure and +utilities shared among the GNOME C++ binding libraries.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['b55c46037dbcdabc5cee3b389ea11cc3910adb68ebe883e9477847aa660862e7'] + +builddependencies = [ + ('binutils', '2.39'), + ('Meson', '0.64.0'), + ('Ninja', '1.11.1'), +] + +dependencies = [ + ('Python', '3.10.8'), +] + +sanity_check_paths = { + 'files': ['bin/mm-common-get', 'bin/mm-common-prepare', 'share/pkgconfig/mm-common-util.pc'], + 'dirs': ['share/man/man1'], +} + +sanity_check_commands = ["mm-common-prepare --help"] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/mm-common/mm-common-1.0.6-GCCcore-12.3.0.eb b/easybuild/easyconfigs/m/mm-common/mm-common-1.0.6-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..0078e0948e90 --- /dev/null +++ b/easybuild/easyconfigs/m/mm-common/mm-common-1.0.6-GCCcore-12.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'MesonNinja' + +name = 'mm-common' +version = '1.0.6' + +homepage = 'https://gitlab.gnome.org/GNOME/mm-common' +description = """The mm-common module provides the build infrastructure and +utilities shared among the GNOME C++ binding libraries.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['b55c46037dbcdabc5cee3b389ea11cc3910adb68ebe883e9477847aa660862e7'] + +builddependencies = [ + ('binutils', '2.40'), + ('Meson', '1.1.1'), + ('Ninja', '1.11.1'), +] + +dependencies = [ + ('Python', '3.11.3'), +] + +sanity_check_paths = { + 'files': ['bin/mm-common-get', 'bin/mm-common-prepare', 'share/pkgconfig/mm-common-util.pc'], + 'dirs': ['share/man/man1'], +} + +sanity_check_commands = ["mm-common-prepare --help"] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/mm-common/mm-common-1.0.6-GCCcore-13.2.0.eb b/easybuild/easyconfigs/m/mm-common/mm-common-1.0.6-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..f545595fd963 --- /dev/null +++ b/easybuild/easyconfigs/m/mm-common/mm-common-1.0.6-GCCcore-13.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'MesonNinja' + +name = 'mm-common' +version = '1.0.6' + +homepage = 'https://gitlab.gnome.org/GNOME/mm-common' +description = """The mm-common module provides the build infrastructure and +utilities shared among the GNOME C++ binding libraries.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['b55c46037dbcdabc5cee3b389ea11cc3910adb68ebe883e9477847aa660862e7'] + +builddependencies = [ + ('binutils', '2.40'), + ('Meson', '1.2.3'), + ('Ninja', '1.11.1'), +] + +dependencies = [ + ('Python', '3.11.5'), +] + +sanity_check_paths = { + 'files': ['bin/mm-common-get', 'bin/mm-common-prepare', 'share/pkgconfig/mm-common-util.pc'], + 'dirs': ['share/man/man1'], +} + +sanity_check_commands = ["mm-common-prepare --help"] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2022a.eb b/easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2022a.eb new file mode 100644 index 000000000000..e2e6b2f69cd2 --- /dev/null +++ b/easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2022a.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonPackage' + +name = 'molmod' +version = '1.4.8' + +homepage = 'https://molmod.github.io/molmod/' +description = "MolMod is a Python library with many compoments that are useful to write molecular modeling programs." + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://github.com/molmod/molmod/releases/download/%(version)s'] +sources = [SOURCE_TAR_GZ] +patches = ['molmod-1.4.8_fix-git-version-check.patch'] +checksums = [ + {'molmod-1.4.8.tar.gz': '759f8894f8a206e8d83f3f88882f29fcf73a7f9be375026e03c58e19496f42e8'}, + {'molmod-1.4.8_fix-git-version-check.patch': '6d1455f9dc3af07b723b05d144f6d8c3c0e5184e094eced1a6f59822f97dcf47'}, +] + +dependencies = [ + ('Python', '3.10.4'), + ('matplotlib', '3.5.2'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +# disable tests that require X11 by specifying "backend: agg" in matplotlibrc +runtest = "export MATPLOTLIBRC=$PWD; echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc;" +runtest += "python setup.py build_ext -i && pytest -ra" + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/molmod/molmod-1.4.8-gfbf-2022b.eb b/easybuild/easyconfigs/m/molmod/molmod-1.4.8-gfbf-2022b.eb new file mode 100644 index 000000000000..3f20a89299fe --- /dev/null +++ b/easybuild/easyconfigs/m/molmod/molmod-1.4.8-gfbf-2022b.eb @@ -0,0 +1,42 @@ +easyblock = 'PythonPackage' + +name = 'molmod' +version = '1.4.8' + +homepage = 'https://molmod.github.io/molmod/' +description = "MolMod is a Python library with many compoments that are useful to write molecular modeling programs." + +toolchain = {'name': 'gfbf', 'version': '2022b'} + +source_urls = ['https://github.com/molmod/molmod/releases/download/%(version)s'] +sources = [SOURCE_TAR_GZ] +patches = [ + 'molmod-1.4.8_fix-git-version-check.patch', + 'molmod-1.4.8_fix-np-unicode.patch', +] +checksums = [ + {'molmod-1.4.8.tar.gz': '759f8894f8a206e8d83f3f88882f29fcf73a7f9be375026e03c58e19496f42e8'}, + {'molmod-1.4.8_fix-git-version-check.patch': '6d1455f9dc3af07b723b05d144f6d8c3c0e5184e094eced1a6f59822f97dcf47'}, + {'molmod-1.4.8_fix-np-unicode.patch': + '85bd2e2981d2cdd8cfab5d1c2cf37432e2967ff82de603700383d7c31530327c'}, +] + +dependencies = [ + ('Python', '3.10.8'), + ('matplotlib', '3.7.0'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +# disable tests that require X11 by specifying "backend: agg" in matplotlibrc +runtest = "export MATPLOTLIBRC=$PWD; echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc;" +runtest += "python setup.py build_ext -i && pytest -ra" + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/mpifileutils/mpifileutils-0.11.1-gompi-2024a.eb b/easybuild/easyconfigs/m/mpifileutils/mpifileutils-0.11.1-gompi-2024a.eb new file mode 100644 index 000000000000..f486ed4effd4 --- /dev/null +++ b/easybuild/easyconfigs/m/mpifileutils/mpifileutils-0.11.1-gompi-2024a.eb @@ -0,0 +1,45 @@ +easyblock = 'CMakeMake' + +name = 'mpifileutils' +version = "0.11.1" + +homepage = 'https://hpc.github.io/mpifileutils/' + +description = """ + MPI-Based File Utilities For Distributed Systems +""" + +toolchain = {'name': 'gompi', 'version': '2024a'} + +github_account = 'hpc' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['e2cba53309b5b3ee581b6ff82e4e66f54628370cce694c34224ed947fece32d4'] + +builddependencies = [ + ('CMake', '3.29.3'), +] + +dependencies = [ + ('attr', '2.5.2'), + ('bzip2', '1.0.8'), + ('lwgrp', '1.0.6'), + ('dtcmp', '1.1.5'), + ('libarchive', '3.7.4'), + ('libcircle', '0.3'), +] + +_binaries = [ + 'dbcast', 'dbz2', 'dchmod', 'dcmp', 'dcp', 'ddup', 'dfind', + 'dreln', 'drm', 'dstripe', 'dsync', 'dtar', 'dwalk' +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in _binaries] + + ['include/mfu.h', 'lib/libmfu.%s' % SHLIB_EXT], + 'dirs': [] +} + +sanity_check_commands = ['%s --help 2>&1 | grep Usage' % x for x in _binaries] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/mrcfile/mrcfile-1.4.3-gfbf-2022b.eb b/easybuild/easyconfigs/m/mrcfile/mrcfile-1.4.3-gfbf-2022b.eb new file mode 100644 index 000000000000..42492460fd9e --- /dev/null +++ b/easybuild/easyconfigs/m/mrcfile/mrcfile-1.4.3-gfbf-2022b.eb @@ -0,0 +1,40 @@ +# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2022/11 +easyblock = 'PythonPackage' + +name = 'mrcfile' +version = '1.4.3' + +homepage = 'https://github.com/ccpem/mrcfile' +description = """mrcfile is a Python implementation of the MRC2014 file format, which is used in +structural biology to store image and volume data. + +It allows MRC files to be created and opened easily using a very simple API, +which exposes the file’s header and data as numpy arrays. The code runs in +Python 2 and 3 and is fully unit-tested. + +This library aims to allow users and developers to read and write standard- +compliant MRC files in Python as easily as possible, and with no dependencies on +any compiled libraries except numpy. You can use it interactively to inspect +files, correct headers and so on, or in scripts and larger software packages to +provide basic MRC file I/O functions. """ + +toolchain = {'name': 'gfbf', 'version': '2022b'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['43c358c59ff8f583fc4dc2079a0099028719109ebf92066e388772bab389c5f5'] + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/multichoose/multichoose-1.0.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/m/multichoose/multichoose-1.0.3-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..9c2a1b09cfc9 --- /dev/null +++ b/easybuild/easyconfigs/m/multichoose/multichoose-1.0.3-GCCcore-12.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'MakeCp' + +name = 'multichoose' +version = '1.0.3' + +homepage = 'https://github.com/ekg/multichoose' +description = """generate multiset combinations (n multichoose k).""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +github_account = 'ekg' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_improve-build-system.patch'] +checksums = [ + '74f0a223c670f5aa81b14191c53ad8d84281838a47471c10253ae391f736c877', # v1.0.3.tar.gz + '96abf6ac1105ee596be078d6e8fb478f870a4ae33fffe70f93e627c0360cfc77', # multichoose-1.0.3_improve-build-system.patch +] + +builddependencies = [('binutils', '2.39')] + +local_bins = [name, 'multipermute'] +files_to_copy = [(local_bins, 'bin'), (['*.h'], 'include/%(name)s')] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_bins], + 'dirs': [], +} + +sanity_check_commands = ['%(name)s 1 a'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/multiprocess/multiprocess-0.70.15-gfbf-2022b.eb b/easybuild/easyconfigs/m/multiprocess/multiprocess-0.70.15-gfbf-2022b.eb new file mode 100644 index 000000000000..2bac0d9bfe60 --- /dev/null +++ b/easybuild/easyconfigs/m/multiprocess/multiprocess-0.70.15-gfbf-2022b.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'multiprocess' +version = '0.70.15' + +homepage = 'https://github.com/uqfoundation/multiprocess' +description = "better multiprocessing and multithreading in python" + +toolchain = {'name': 'gfbf', 'version': '2022b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['f20eed3036c0ef477b07a4177cf7c1ba520d9a2677870a4f47fe026f0cd6787e'] + +dependencies = [ + ('Python', '3.10.8'), + ('dill', '0.3.7'), + ('Arrow', '11.0.0'), # if needed rebuild --from-pr 19758 +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/mygene/mygene-3.2.2-foss-2023a.eb b/easybuild/easyconfigs/m/mygene/mygene-3.2.2-foss-2023a.eb new file mode 100644 index 000000000000..1c49c2ece325 --- /dev/null +++ b/easybuild/easyconfigs/m/mygene/mygene-3.2.2-foss-2023a.eb @@ -0,0 +1,34 @@ +# Author: Pavel Grochal (INUITS) +# Update: Pavel Tománek (INUITS) +# License: GPLv2 + +easyblock = 'PythonBundle' + +name = 'mygene' +version = '3.2.2' + +homepage = 'https://github.com/biothings/mygene.py' +description = "Python Client for MyGene.Info services." + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), +] + +use_pip = True + +exts_list = [ + ('biothings_client', '0.3.1', { + 'checksums': ['c972bf2e02b6f9cc78f7f2fbc5ef02cc56fe4f8a2adcb8801ec902f4ab7011e6'], + }), + (name, version, { + 'checksums': ['e729cabbc28cf5afb221bca1ab637883b375cb1a3e2f067587ec79f71affdaea'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.18.3-GCCcore-12.3.0-CUDA-12.1.1.eb b/easybuild/easyconfigs/n/NCCL/NCCL-2.18.3-GCCcore-12.3.0-CUDA-12.1.1.eb index c85b7a97e481..569d09f98593 100644 --- a/easybuild/easyconfigs/n/NCCL/NCCL-2.18.3-GCCcore-12.3.0-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/n/NCCL/NCCL-2.18.3-GCCcore-12.3.0-CUDA-12.1.1.eb @@ -11,11 +11,15 @@ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} github_account = 'NVIDIA' source_urls = [GITHUB_SOURCE] sources = ['v%(version)s-1.tar.gz'] -patches = ['NCCL-2.16.2_fix-cpuid.patch'] +patches = [ + 'NCCL-2.16.2_fix-cpuid.patch', + 'NCCL-2.18.3_fix-cudaMemcpyAsync.patch', +] checksums = [ ('6477d83c9edbb34a0ebce6d751a1b32962bc6415d75d04972b676c6894ceaef9', 'b4f5d7d9eea2c12e32e7a06fe138b2cfc75969c6d5c473aa6f819a792db2fc96'), {'NCCL-2.16.2_fix-cpuid.patch': '0459ecadcd32b2a7a000a2ce4f675afba908b2c0afabafde585330ff4f83e277'}, + {'NCCL-2.18.3_fix-cudaMemcpyAsync.patch': '7dc8d0d1b78e4f8acefbc400860f47432ef67c225b50d73c732999c23483de90'}, ] builddependencies = [('binutils', '2.40')] diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.18.3_fix-cudaMemcpyAsync.patch b/easybuild/easyconfigs/n/NCCL/NCCL-2.18.3_fix-cudaMemcpyAsync.patch new file mode 100644 index 000000000000..685426567335 --- /dev/null +++ b/easybuild/easyconfigs/n/NCCL/NCCL-2.18.3_fix-cudaMemcpyAsync.patch @@ -0,0 +1,174 @@ +Backported from (original message attached below): +https://github.com/NVIDIA/nccl/commit/4365458757e4107ecbf629b2fd6e0e19a5d237c2 + +From: Kaiming Ouyang +Date: Wed, 20 Sep 2023 05:51:14 -0700 +Subject: [PATCH] Fix cudaMemcpyAsync bug + +We are trying to use the copy result of first cudaMemcpyAsync in the +second cudaMemcpyAsync without sync in between. This patch fixes it +by allocating a CPU side array to cache device side addr so that we +can avoid this consecutive cuda mem copy. + +Fixes #957 +--- + src/channel.cc | 12 ++++++++++++ + src/include/comm.h | 2 ++ + src/init.cc | 2 +- + src/transport.cc | 8 ++------ + src/transport/nvls.cc | 10 ++++------ + 5 files changed, 21 insertions(+), 13 deletions(-) + +diff --git a/src/channel.cc b/src/channel.cc +index 3edcc2f..245dfd5 100644 +--- a/src/channel.cc ++++ b/src/channel.cc +@@ -42,9 +42,11 @@ ncclResult_t initChannel(struct ncclComm* comm, int channelId) { + /* channel->devPeers is not shared, so just free it when calling commFree() */ + NCCLCHECK(ncclCudaCallocAsync(&channel->devPeers, nPeers, sharedRes->deviceStream.cudaStream)); + ncclCommPushCudaFree(comm, channel->devPeers); ++ NCCLCHECK(ncclCalloc(&channel->devPeersHostPtr, nPeers)); + for (int r = 0; r < nRanks; r++) { + uintptr_t addr = (uintptr_t)(comm->sharedRes->devPeers[channelId] + comm->topParentRanks[r]); + NCCLCHECK(ncclCudaMemcpyAsync((uintptr_t*)(channel->devPeers + r), (uintptr_t*)&addr, 1, sharedRes->deviceStream.cudaStream)); ++ channel->devPeersHostPtr[r] = (struct ncclDevChannelPeer*)addr; + } + } + +@@ -52,6 +54,8 @@ ncclResult_t initChannel(struct ncclComm* comm, int channelId) { + NCCLCHECK(ncclCudaCallocAsync(&channel->devRingUserRanks, nRanks, sharedRes->deviceStream.cudaStream)); + ncclCommPushCudaFree(comm, channel->devRingUserRanks); + ++ /* guarantee addr has been copied into channel->devPeers */ ++ NCCLCHECK(ncclStrongStreamSynchronize(&sharedRes->deviceStream)); + NCCLCHECK(ncclStrongStreamRelease(ncclCudaGraphNone(), &sharedRes->deviceStream)); + + return ncclSuccess; +@@ -77,6 +81,7 @@ ncclResult_t initNvlsChannel(struct ncclComm* comm, int channelId, struct ncclCo + uintptr_t addr = (uintptr_t)(parent->channels[channelId].nvlsDevPeers + tr); + channel->peers[comm->nRanks + 1 + r] = parent->channels[channelId].nvlsPeers + tr; + NCCLCHECK(ncclCudaMemcpyAsync((uintptr_t*)(channel->devPeers + comm->nRanks + 1 + r), (uintptr_t*)&addr, 1, sharedRes->deviceStream.cudaStream)); ++ channel->devPeersHostPtr[comm->nRanks + 1 + r] = (struct ncclDevChannelPeer*)addr; + ncclAtomicRefCountIncrement(&parent->channels[channelId].nvlsPeers[tr].refCount); + } + } else { +@@ -86,10 +91,12 @@ ncclResult_t initNvlsChannel(struct ncclComm* comm, int channelId, struct ncclCo + uintptr_t addr = (uintptr_t)(channel->nvlsDevPeers + r); + channel->peers[comm->nRanks + 1 + r] = channel->nvlsPeers + r; + NCCLCHECK(ncclCudaMemcpyAsync((uintptr_t*)(channel->devPeers + comm->nRanks + 1 + r), (uintptr_t*)&addr, 1, sharedRes->deviceStream.cudaStream)); ++ channel->devPeersHostPtr[comm->nRanks + 1 + r] = (struct ncclDevChannelPeer*)addr; + ncclAtomicRefCountIncrement(&channel->nvlsPeers[r].refCount); + } + } + ++ NCCLCHECK(ncclStrongStreamSynchronize(&sharedRes->deviceStream)); + NCCLCHECK(ncclStrongStreamRelease(ncclCudaGraphNone(), &sharedRes->deviceStream)); + + return ncclSuccess; +@@ -114,6 +121,7 @@ ncclResult_t initCollnetChannel(struct ncclComm* comm, int channelId, struct ncc + addr = (uintptr_t)parent->channels[channelId].collnetDevPeers; + channel->peers[comm->nRanks] = parent->channels[channelId].collnetPeers; + NCCLCHECK(ncclCudaMemcpyAsync((uintptr_t*)(channel->devPeers + comm->nRanks), (uintptr_t*)&addr, 1, sharedRes->deviceStream.cudaStream)); ++ channel->devPeersHostPtr[comm->nRanks] = (struct ncclDevChannelPeer*)addr; + ncclAtomicRefCountIncrement(&parent->channels[channelId].collnetPeers->refCount); + } else { + NCCLCHECK(ncclCalloc(&channel->collnetPeers, 1)); +@@ -121,9 +129,11 @@ ncclResult_t initCollnetChannel(struct ncclComm* comm, int channelId, struct ncc + addr = (uintptr_t)channel->collnetDevPeers; + channel->peers[comm->nRanks] = channel->collnetPeers; + NCCLCHECK(ncclCudaMemcpyAsync((uintptr_t*)(channel->devPeers + comm->nRanks), (uintptr_t*)&addr, 1, sharedRes->deviceStream.cudaStream)); ++ channel->devPeersHostPtr[comm->nRanks] = (struct ncclDevChannelPeer*)addr; + ncclAtomicRefCountIncrement(&channel->collnetPeers->refCount); + } + ++ NCCLCHECK(ncclStrongStreamSynchronize(&sharedRes->deviceStream)); + NCCLCHECK(ncclStrongStreamRelease(ncclCudaGraphNone(), &sharedRes->deviceStream)); + + return ncclSuccess; +@@ -156,5 +166,7 @@ ncclResult_t freeChannel(struct ncclChannel* channel, int nRanks, int collnetNRa + } + } + } ++ ++ free(channel->devPeersHostPtr); + return ncclSuccess; + } +diff --git a/src/include/comm.h b/src/include/comm.h +index e79bf54..8986f93 100644 +--- a/src/include/comm.h ++++ b/src/include/comm.h +@@ -124,6 +124,8 @@ struct ncclSharedResources { + struct ncclChannel { + struct ncclChannelPeer** peers; + struct ncclDevChannelPeer** devPeers; ++ /* devPeer pointer array used for host side access */ ++ struct ncclDevChannelPeer** devPeersHostPtr; + struct ncclRing ring; + int* devRingUserRanks; + struct ncclTree tree; +diff --git a/src/init.cc b/src/init.cc +index 1ea1d7e..309ce10 100644 +--- a/src/init.cc ++++ b/src/init.cc +@@ -437,7 +437,7 @@ static ncclResult_t devCommSetup(ncclComm_t comm) { + + NCCLCHECKGOTO(ncclCudaMemcpyAsync(devCommAndChans, &tmpCommAndChans, 1, comm->sharedRes->deviceStream.cudaStream), ret, fail); + exit: +- CUDACHECK(cudaStreamSynchronize(comm->sharedRes->deviceStream.cudaStream)); ++ NCCLCHECK(ncclStrongStreamSynchronize(&comm->sharedRes->deviceStream)); + NCCLCHECK(ncclStrongStreamRelease(ncclCudaGraphNone(), &comm->sharedRes->deviceStream)); + return ret; + fail: +diff --git a/src/transport.cc b/src/transport.cc +index f4b8a2a..9817beb 100644 +--- a/src/transport.cc ++++ b/src/transport.cc +@@ -147,11 +147,9 @@ ncclResult_t ncclTransportP2pSetup(struct ncclComm* comm, struct ncclTopoGraph* + if (conn->connected == 0) { + NCCLCHECKGOTO(conn->transportComm->connect(comm, sendData[i] + sendDataOffset++, 1, comm->rank, conn), ret, fail); + if (ret == ncclSuccess) { +- struct ncclDevChannelPeer* addr; + conn->connected = 1; + /* comm->channels[c].devPeers[sendPeer]->send[connIndex] is a device memory access. */ +- CUDACHECKGOTO(cudaMemcpyAsync(&addr, &comm->channels[c].devPeers[sendPeer], sizeof(struct ncclDevChannelPeer*), cudaMemcpyDeviceToHost, comm->sharedRes->hostStream.cudaStream), ret, fail); +- CUDACHECKGOTO(cudaMemcpyAsync(&addr->send[connIndex], &conn->conn, sizeof(struct ncclConnInfo), cudaMemcpyHostToDevice, comm->sharedRes->hostStream.cudaStream), ret, fail); ++ CUDACHECKGOTO(cudaMemcpyAsync(&comm->channels[c].devPeersHostPtr[sendPeer]->send[connIndex], &conn->conn, sizeof(struct ncclConnInfo), cudaMemcpyHostToDevice, comm->sharedRes->hostStream.cudaStream), ret, fail); + } else if (ret == ncclInProgress) { + allChannelsConnected = false; + } +@@ -167,11 +165,9 @@ ncclResult_t ncclTransportP2pSetup(struct ncclComm* comm, struct ncclTopoGraph* + if (conn->connected == 0) { + NCCLCHECKGOTO(conn->transportComm->connect(comm, recvData[i] + recvDataOffset++, 1, comm->rank, conn), ret, fail); + if (ret == ncclSuccess) { +- struct ncclDevChannelPeer* addr; + conn->connected = 1; + /* comm->channels[c].devPeers[recvPeer]->recv[connIndex] is a device memory access. */ +- CUDACHECKGOTO(cudaMemcpyAsync(&addr, &comm->channels[c].devPeers[recvPeer], sizeof(struct ncclDevChannelPeer*), cudaMemcpyDeviceToHost, comm->sharedRes->hostStream.cudaStream), ret, fail); +- CUDACHECKGOTO(cudaMemcpyAsync(&addr->recv[connIndex], &conn->conn, sizeof(struct ncclConnInfo), cudaMemcpyHostToDevice, comm->sharedRes->hostStream.cudaStream), ret, fail); ++ CUDACHECKGOTO(cudaMemcpyAsync(&comm->channels[c].devPeersHostPtr[recvPeer]->recv[connIndex], &conn->conn, sizeof(struct ncclConnInfo), cudaMemcpyHostToDevice, comm->sharedRes->hostStream.cudaStream), ret, fail); + } else if (ret == ncclInProgress) { + allChannelsConnected = false; + } +diff --git a/src/transport/nvls.cc b/src/transport/nvls.cc +index 633cb04..07be99d 100644 +--- a/src/transport/nvls.cc ++++ b/src/transport/nvls.cc +@@ -359,12 +359,10 @@ ncclResult_t ncclNvlsSetup(struct ncclComm* comm, struct ncclComm* parent) { + peer->send[0].conn.tail = (uint64_t*)(mem + buffSize + memSize / 2); + peer->send[0].conn.flags |= NCCL_NVLS_MIN_POLL; + +- struct ncclDevChannelPeer* addr; +- CUDACHECKGOTO(cudaMemcpyAsync(&addr, comm->channels[c].devPeers + nvlsPeer, sizeof(struct ncclDevChannelPeer*), cudaMemcpyDeviceToHost, comm->sharedRes->hostStream.cudaStream), res, cleanup); +- CUDACHECKGOTO(cudaMemcpyAsync(&addr->send[0], &peer->send[0].conn, sizeof(struct ncclConnInfo), cudaMemcpyHostToDevice, comm->sharedRes->hostStream.cudaStream), res, cleanup); +- CUDACHECKGOTO(cudaMemcpyAsync(&addr->recv[0], &peer->recv[0].conn, sizeof(struct ncclConnInfo), cudaMemcpyHostToDevice, comm->sharedRes->hostStream.cudaStream), res, cleanup); +- CUDACHECKGOTO(cudaMemcpyAsync(&addr->send[1], &peer->send[1].conn, sizeof(struct ncclConnInfo), cudaMemcpyHostToDevice, comm->sharedRes->hostStream.cudaStream), res, cleanup); +- CUDACHECKGOTO(cudaMemcpyAsync(&addr->recv[1], &peer->recv[1].conn, sizeof(struct ncclConnInfo), cudaMemcpyHostToDevice, comm->sharedRes->hostStream.cudaStream), res, cleanup); ++ CUDACHECKGOTO(cudaMemcpyAsync(&comm->channels[c].devPeersHostPtr[nvlsPeer]->send[0], &peer->send[0].conn, sizeof(struct ncclConnInfo), cudaMemcpyHostToDevice, comm->sharedRes->hostStream.cudaStream), res, cleanup); ++ CUDACHECKGOTO(cudaMemcpyAsync(&comm->channels[c].devPeersHostPtr[nvlsPeer]->recv[0], &peer->recv[0].conn, sizeof(struct ncclConnInfo), cudaMemcpyHostToDevice, comm->sharedRes->hostStream.cudaStream), res, cleanup); ++ CUDACHECKGOTO(cudaMemcpyAsync(&comm->channels[c].devPeersHostPtr[nvlsPeer]->send[1], &peer->send[1].conn, sizeof(struct ncclConnInfo), cudaMemcpyHostToDevice, comm->sharedRes->hostStream.cudaStream), res, cleanup); ++ CUDACHECKGOTO(cudaMemcpyAsync(&comm->channels[c].devPeersHostPtr[nvlsPeer]->recv[1], &peer->recv[1].conn, sizeof(struct ncclConnInfo), cudaMemcpyHostToDevice, comm->sharedRes->hostStream.cudaStream), res, cleanup); + + /*INFO(NCCL_INIT|NCCL_NVLS, "Peer %d Channel %d MC buff %p/%p UC Buff %p/%p", + nvlsPeer, c, +-- +2.45.2 diff --git a/easybuild/easyconfigs/n/NCO/NCO-5.1.9-foss-2023a.eb b/easybuild/easyconfigs/n/NCO/NCO-5.1.9-foss-2023a.eb new file mode 100644 index 000000000000..0e7dd9be31aa --- /dev/null +++ b/easybuild/easyconfigs/n/NCO/NCO-5.1.9-foss-2023a.eb @@ -0,0 +1,44 @@ +easyblock = 'ConfigureMake' + +name = 'NCO' +version = '5.1.9' + +homepage = "https://github.com/nco/nco" +description = """The NCO toolkit manipulates and analyzes data stored in netCDF-accessible formats, +including DAP, HDF4, and HDF5.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/nco/nco/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['9cd90345c1e3860a690b53fd6c08b721d631a646d169431927884c99841c34e9'] + +builddependencies = [ + ('Bison', '3.8.2'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('UDUNITS', '2.2.28'), + ('expat', '2.5.0'), + ('ANTLR', '2.7.7', '-Java-11'), + ('libdap', '3.20.11'), + ('GSL', '2.7'), + ('netCDF', '4.9.2'), + ('ESMF', '8.6.0'), # ncremap needs ESMF_RegridWeightGen +] + +configopts = "--enable-nco_cplusplus" + +sanity_check_paths = { + 'files': ['bin/nc%s' % x for x in ('ap2', 'atted', 'bo', 'diff', 'ea', 'ecat', 'es', + 'flint', 'ks', 'pdq', 'ra', 'rcat', 'rename', 'wa')] + + ['lib/libnco.a', 'lib/libnco.%s' % SHLIB_EXT, 'lib/libnco_c++.a', 'lib/libnco_c++.%s' % SHLIB_EXT], + 'dirs': ['include'], +} +sanity_check_commands = [ + "ncks -O -7 --cnk_dmn time,10 " + "%(builddir)s/%(namelower)s-%(version)s/data/in.nc %(builddir)s/%(namelower)s-%(version)s/data/in4.cdl" +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/NECAT/NECAT-0.0.1-foss-2023a.eb b/easybuild/easyconfigs/n/NECAT/NECAT-0.0.1-foss-2023a.eb new file mode 100644 index 000000000000..dbc35f62054b --- /dev/null +++ b/easybuild/easyconfigs/n/NECAT/NECAT-0.0.1-foss-2023a.eb @@ -0,0 +1,32 @@ +easyblock = 'MakeCp' + +name = 'NECAT' +version = '0.0.1' + +homepage = 'https://github.com/xiaochuanle/NECAT' +description = """NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads.).""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/xiaochuanle/NECAT/archive/'] +sources = ['v%(version)s_update20200803.tar.gz'] +checksums = ['5ddd147b5be6b1fac2f6c10b18c9b587838f2304d2584087c4ed6f628eced06c'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [('Perl', '5.36.1')] + +start_dir = 'src' + +files_to_copy = [ + (['../Linux-amd64/bin/*'], 'bin'), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s.pl'], + 'dirs': [], +} + +sanity_check_commands = ['%(namelower)s.pl --help'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/NLopt/NLopt-2.7.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/n/NLopt/NLopt-2.7.1-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..17c0db0f1615 --- /dev/null +++ b/easybuild/easyconfigs/n/NLopt/NLopt-2.7.1-GCCcore-13.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'CMakeMake' + +name = 'NLopt' +version = '2.7.1' + +homepage = 'http://ab-initio.mit.edu/wiki/index.php/NLopt' +description = """ NLopt is a free/open-source library for nonlinear optimization, + providing a common interface for a number of different free optimization routines + available online as well as original implementations of various other algorithms. """ + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/stevengj/nlopt/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['db88232fa5cef0ff6e39943fc63ab6074208831dc0031cf1545f6ecd31ae2a1a'] + +builddependencies = [ + ('CMake', '3.27.6'), + ('binutils', '2.40'), +] + +configopts = [ + '-DBUILD_SHARED_LIBS=ON', + '-DBUILD_SHARED_LIBS=OFF' +] + +sanity_check_paths = { + 'files': ['lib/libnlopt.a', 'lib/libnlopt.%s' % SHLIB_EXT, 'include/nlopt.h'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/n/NLopt/NLopt-2.7.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/n/NLopt/NLopt-2.7.1-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..b9bb438dc948 --- /dev/null +++ b/easybuild/easyconfigs/n/NLopt/NLopt-2.7.1-GCCcore-13.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'CMakeMake' + +name = 'NLopt' +version = '2.7.1' + +homepage = 'http://ab-initio.mit.edu/wiki/index.php/NLopt' +description = """ NLopt is a free/open-source library for nonlinear optimization, + providing a common interface for a number of different free optimization routines + available online as well as original implementations of various other algorithms. """ + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/stevengj/nlopt/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['db88232fa5cef0ff6e39943fc63ab6074208831dc0031cf1545f6ecd31ae2a1a'] + +builddependencies = [ + ('CMake', '3.29.3'), + ('binutils', '2.42'), +] + +configopts = [ + '-DBUILD_SHARED_LIBS=ON', + '-DBUILD_SHARED_LIBS=OFF' +] + +sanity_check_paths = { + 'files': ['lib/libnlopt.a', 'lib/libnlopt.%s' % SHLIB_EXT, 'include/nlopt.h'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/n/NanoCaller/NanoCaller-3.6.0-foss-2022b.eb b/easybuild/easyconfigs/n/NanoCaller/NanoCaller-3.6.0-foss-2022b.eb new file mode 100644 index 000000000000..037b70ab15ed --- /dev/null +++ b/easybuild/easyconfigs/n/NanoCaller/NanoCaller-3.6.0-foss-2022b.eb @@ -0,0 +1,44 @@ +easyblock = 'Tarball' + +name = 'NanoCaller' +version = '3.6.0' + +homepage = 'https://github.com/WGLab/NanoCaller' +description = """NanoCaller is a computational method that integrates long reads in deep + convolutional neural network for the detection of SNPs/indels from long-read sequencing data.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +source_urls = ['https://github.com/WGLab/%(name)s/archive/'] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}] +checksums = ['d3df57ca47617365ed891f7acc6976ec5dec3c224e5e213f8bba2d3b2d973303'] + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('BCFtools', '1.17'), + ('python-parasail', '1.3.4'), + ('MUSCLE', '5.1.0'), + ('Pysam', '0.21.0'), + ('SAMtools', '1.17'), + ('TensorFlow', '2.13.0'), + ('WhatsHap', '2.1'), + ('vcflib', '1.0.9', '-R-4.2.2'), + ('intervaltree-python', '3.1.0'), + ('tqdm', '4.64.1'), + ('RTG-Tools', '3.12.1', '-Java-11', SYSTEM), +] + +modextrapaths = { + 'PATH': '', + 'PYTHONPATH': '', +} + +sanity_check_paths = { + 'files': ['NanoCaller'], + 'dirs': [], +} + +sanity_check_commands = ["NanoCaller --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/NextPolish/NextPolish-1.4.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/n/NextPolish/NextPolish-1.4.1-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..857ec88ff805 --- /dev/null +++ b/easybuild/easyconfigs/n/NextPolish/NextPolish-1.4.1-GCCcore-12.3.0.eb @@ -0,0 +1,72 @@ +easyblock = 'MakeCp' + +name = 'NextPolish' +version = '1.4.1' + +homepage = 'https://github.com/Nextomics/NextPolish' +description = 'NextDenovo is a string graph-based de novo assembler for long reads.' + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/Nextomics/NextPolish/releases/download/'] +sources = [{ + 'download_filename': 'v%(version)s/%(name)s.tgz', + 'filename': SOURCE_TAR_GZ, +}] +checksums = ['2a5f66f3db7f76e583a6b6e28f9c1f3c392258b8d755050d7abe129a2fbb48c4'] + +builddependencies = [('binutils', '2.40')] +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('BWA', '0.7.17'), +] + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'download_dep_fail': True, + 'use_pip': True, + 'sanity_pip_check': True, + 'preinstallopts': '', + 'installopts': '', +} + +exts_list = [ + ('Paralleltask', '0.2.3', { + 'modulename': 'paralleltask', + 'checksums': ['8015a8311d5021bc44edbfbf45ff2557a529999e235d25190bac62993fdf7b66'], + }), +] + +# fix make -C util - warning: jobserver unavailable +parallel = 1 + +# fix bwa bug - https://github.com/Nextomics/NextPolish/issues/83 +prebuildopts = "sed -i 's/seq_count bwa samtools minimap2/seq_count samtools minimap2/' Makefile && " +prebuildopts += "rm -rf util/bwa && " +prebuildopts += ( + "sed -i" + " -e 's/seq_count bwa_ samtools_/seq_count samtools_/'" + " -e '29d'" # @+make clean -C $(BWADIR) + " -e '18,20d'" # bwa_: @+make -C $(BWADIR) + " -e '1d'" # BWADIR = ./bwa + " util/Makefile && " +) +postinstallcmds = ['cd %(installdir)s/bin && ln -s $EBROOTBWA/bin/bwa'] + +files_to_copy = ['bin', 'lib', 'test_data', 'LICENSE', 'nextPolish'] + +sanity_check_paths = { + 'files': ['nextPolish', 'bin/minimap2', 'bin/paralleltask', 'bin/bwa'], + 'dirs': ['test_data', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['nextPolish --help'] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + 'PATH': '', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/NiBabel/NiBabel-5.2.0-gfbf-2022b.eb b/easybuild/easyconfigs/n/NiBabel/NiBabel-5.2.0-gfbf-2022b.eb new file mode 100644 index 000000000000..a930785f65b5 --- /dev/null +++ b/easybuild/easyconfigs/n/NiBabel/NiBabel-5.2.0-gfbf-2022b.eb @@ -0,0 +1,46 @@ +easyblock = 'PythonBundle' + +name = 'NiBabel' +version = '5.2.0' + +homepage = 'https://nipy.github.io/nibabel' +description = """NiBabel provides read/write access to some common medical and neuroimaging file formats, + including: ANALYZE (plain, SPM99, SPM2 and later), GIFTI, NIfTI1, NIfTI2, MINC1, MINC2, MGH and ECAT + as well as Philips PAR/REC. We can read and write Freesurfer geometry, and read Freesurfer morphometry and + annotation files. There is some very limited support for DICOM. NiBabel is the successor of PyNIfTI.""" + +toolchain = {'name': 'gfbf', 'version': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('Pillow', '9.4.0'), + ('pydicom', '2.4.4'), +] + +use_pip = True + +exts_list = [ + ('bz2file', '0.98', { + 'checksums': ['64c1f811e31556ba9931953c8ec7b397488726c63e09a4c67004f43bdd28da88'], + }), + ('nibabel', version, { + 'checksums': ['3df8f1ab981d1bd92f4331d565528d126ab9717fdbd4cfe68f43fcd1c2bf3f52'], + }), +] + +fix_python_shebang_for = ['bin/*'] + +sanity_check_paths = { + 'files': ['bin/nib-dicomfs', 'bin/nib-diff', 'bin/nib-ls', 'bin/nib-nifti-dx', 'bin/parrec2nii'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "nib-diff --help", + "parrec2nii --help", +] + +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/n/Normaliz/Normaliz-3.10.3-gfbf-2023b.eb b/easybuild/easyconfigs/n/Normaliz/Normaliz-3.10.3-gfbf-2023b.eb new file mode 100644 index 000000000000..6651c1a848d0 --- /dev/null +++ b/easybuild/easyconfigs/n/Normaliz/Normaliz-3.10.3-gfbf-2023b.eb @@ -0,0 +1,47 @@ +easyblock = 'ConfigureMake' + +name = 'Normaliz' +version = '3.10.3' + +homepage = 'https://www.normaliz.uni-osnabrueck.de/' +description = """Normaliz is a open source tool for computations in affine monoids, vector +configurations, rational polyhedra and rational cones. Normaliz now computes +rational and algebraic polyhedra, i.e., polyhedra defined over real algebraic +extensions of QQ.""" + +toolchain = {'name': 'gfbf', 'version': '2023b'} +toolchainopts = {'pic': True, 'openmp': True, 'cstd': 'c++14'} + +github_account = 'Normaliz' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['d9536ab3568053a8dd9aeabe09ef901c1c0ebbda37be50775a120eb9e7ff47cb'] + +builddependencies = [ + ('Autotools', '20220317'), +] + +dependencies = [ + ('Boost', '1.83.0'), + ('GMP', '6.3.0'), + ('CoCoALib', '0.99850'), + ('FLINT', '3.1.1'), + ('E-ANTIC', '2.0.2'), + ('nauty', '2.8.8'), +] + +preconfigopts = "autoreconf -f -i && " + +configopts = "--with-gmp=$EBROOTGMP --with-cocoalib=$EBROOTCOCOALIB --with-flint=$EBROOTFLINT " +configopts += "--with-e-antic=$EBROOTEMINANTIC --with-nauty=$EBROOTNAUTY" + +runtest = 'check' + +sanity_check_paths = { + 'files': ['bin/normaliz'] + ['lib/libnormaliz.%s' % e for e in ['a', SHLIB_EXT]], + 'dirs': ['include/libnormaliz'] +} + +sanity_check_commands = ["normaliz --help"] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/n/n2v/n2v-0.3.3-foss-2023a.eb b/easybuild/easyconfigs/n/n2v/n2v-0.3.3-foss-2023a.eb new file mode 100644 index 000000000000..dfc99c9d4d37 --- /dev/null +++ b/easybuild/easyconfigs/n/n2v/n2v-0.3.3-foss-2023a.eb @@ -0,0 +1,87 @@ +easyblock = 'PythonBundle' + +name = 'n2v' +version = '0.3.3' + +homepage = 'https://github.com/juglab/n2v' +description = "Learning Denoising from Single Noisy Images" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('Pillow', '10.0.0'), + ('imagecodecs', '2024.1.1'), + ('ruamel.yaml', '0.17.32'), + ('CSBDeep', '0.7.4'), + ('xarray', '2023.9.0'), + ('imageio', '2.33.1'), + ('pydantic', '2.5.3'), +] + +use_pip = True + +exts_list = [ + ('typer', '0.12.3', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['070d7ca53f785acbccba8e7d28b08dcd88f79f1fbda035ade0aecec71ca5c914'], + }), + ('marshmallow_union', '0.1.15.post1', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['1e21b759c76735305f99179c1a16759ebb9629733159628241b3f2117ff55e86'], + }), + ('marshmallow_jsonschema', '0.13.0', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['2814f2afb94a6e01b3c0a5795b3dfb142b628763655f20378400af5c0a2307fb'], + }), + ('marshmallow', '3.21.3', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['86ce7fb914aa865001a4b2092c4c2872d13bc347f3d42673272cabfdbad386f1'], + }), + ('fire', '0.6.0', { + 'checksums': ['54ec5b996ecdd3c0309c800324a0703d6da512241bc73b553db959d98de0aa66'], + }), + ('ruyaml', '0.91.0', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['50e0ee3389c77ad340e209472e0effd41ae0275246df00cdad0a067532171755'], + }), + ('python_dotenv', '1.0.1', { + 'source_tmpl': SOURCE_PY3_WHL, + 'modulename': 'dotenv', + 'checksums': ['f7b63ef50f1b690dddf550d03497b66d609393b40b564ed0d674909a68ebf16a'], + }), + ('pydantic_settings', '2.2.1', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['0235391d26db4d2190cb9b31051c4b46882d28a51533f97440867f012d4da091'], + }), + ('loguru', '0.7.2', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['003d71e3d3ed35f0f8984898359d65b79e5b21943f78af86aa5491210429b8eb'], + }), + ('dnspython', '2.6.1', { + 'source_tmpl': SOURCE_PY3_WHL, + 'modulename': 'dns', + 'checksums': ['5ef3b9680161f6fa89daf8ad451b5f1a33b18ae8a1c6778cdf4b43f08c0a6e50'], + }), + ('email_validator', '2.2.0', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['561977c2d73ce3611850a06fa56b414621e0c8faa9d66f2611407d87465da631'], + }), + ('bioimageio.spec', '0.4.9.post5', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['a24ef7c0d6506d080655fbd8f322bc153a147329bd2258a8e958982d31885865'], + }), + ('bioimageio.core', '0.5.11', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['af8138f0c75fcebf7abbb873d01af8055d6209b2fd611269990b72e51fb991b5'], + }), + (name, version, { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['be5b24fe0bf3cdc15cd4771c50e577a81b7d83b27300a0b90035cc87bb95c33c'], + }), +] + +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/n/nano/nano-8.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/n/nano/nano-8.1-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..64684d1ff42c --- /dev/null +++ b/easybuild/easyconfigs/n/nano/nano-8.1-GCCcore-13.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'nano' +version = '8.1' + +homepage = 'https://www.nano-editor.org/' +docurls = 'https://www.nano-editor.org/docs.php' +description = """a simple editor, inspired by Pico""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://www.nano-editor.org/dist/v%(version_major)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['6508bfbcfe38153ecbdc1b7d3479323564353f134acc8c501910220371390675'] + +builddependencies = [('binutils', '2.42')] + +dependencies = [('ncurses', '6.5')] + +sanity_check_paths = { + 'files': ['bin/nano'], + 'dirs': ['bin', 'share'], +} + +sanity_check_commands = ['nano --version'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/nanopolish/nanopolish-0.14.0-foss-2023a.eb b/easybuild/easyconfigs/n/nanopolish/nanopolish-0.14.0-foss-2023a.eb new file mode 100644 index 000000000000..d32ee79a46a9 --- /dev/null +++ b/easybuild/easyconfigs/n/nanopolish/nanopolish-0.14.0-foss-2023a.eb @@ -0,0 +1,61 @@ +easyblock = 'MakeCp' + +name = 'nanopolish' +version = '0.14.0' + +homepage = 'https://github.com/jts/nanopolish' +description = "Software package for signal-level analysis of Oxford Nanopore sequencing data." + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = [ + 'https://github.com/jts/nanopolish/archive/', + 'https://github.com/mateidavid/fast5/archive/', +] +sources = [ + { + 'source_urls': ['https://github.com/jts/nanopolish/archive/'], + 'download_filename': 'v%(version)s.tar.gz', + 'filename': SOURCE_TAR_GZ, + }, + { + 'source_urls': ['https://github.com/hasindu2008/slow5lib/archive/'], + 'download_filename': 'v1.1.0.tar.gz', + 'filename': 'slow5lib-v1.1.0.tar.gz', + }, +] +checksums = [ + {'nanopolish-0.14.0.tar.gz': 'bcc1a7e2d23941592d817da3af9165b3843ae52b11a3ca5983d6417f1614ef78'}, + {'slow5lib-v1.1.0.tar.gz': 'f13f08b85a9a11086b5d9378251093d1858d0dc29d8e727eabacfa57a73f4277'}, +] + +builddependencies = [('Eigen', '3.4.0')] + +dependencies = [ + ('zlib', '1.2.13'), + ('Python', '3.11.3'), + ('Biopython', '1.83'), + ('Pysam', '0.22.0'), + ('HDF5', '1.14.0'), + ('HTSlib', '1.18'), + ('minimap2', '2.26'), + ('VBZ-Compression', '1.0.3'), +] + +prebuildopts = "rmdir slow5lib && ln -s %(builddir)s/slow5lib-*/ slow5lib && " +buildopts = "HDF5=noinstall EIGEN=noinstall HTS=noinstall MINIMAP2=noinstall" + +runtest = 'test ' + buildopts + +files_to_copy = [(['nanopolish'], 'bin'), 'scripts'] + +postinstallcmds = ["chmod a+rx %(installdir)s/scripts/*"] + +sanity_check_paths = { + 'files': ['bin/nanopolish'], + 'dirs': ['scripts'], +} + +modextrapaths = {'PATH': 'scripts'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/napari-denoiseg/napari-denoiseg-0.0.1-foss-2023a.eb b/easybuild/easyconfigs/n/napari-denoiseg/napari-denoiseg-0.0.1-foss-2023a.eb new file mode 100644 index 000000000000..8335ad90cba5 --- /dev/null +++ b/easybuild/easyconfigs/n/napari-denoiseg/napari-denoiseg-0.0.1-foss-2023a.eb @@ -0,0 +1,57 @@ +easyblock = 'PythonBundle' + +name = 'napari-denoiseg' +version = '0.0.1' + +homepage = 'https://juglab.github.io/napari-denoiseg/index.html' +description = """A napari plugin performing joint denoising and segmentation of microscopy images using DenoiSeg.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('napari', '0.4.18'), + ('PyQtGraph', '0.13.7'), + ('QtPy', '2.4.1'), + ('TensorFlow', '2.13.0'), + ('CSBDeep', '0.7.4'), + ('n2v', '0.3.3'), + ('numba', '0.58.1'), + ('scikit-learn', '1.3.1'), + ('autopep8', '2.2.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('napari-workflows', '0.2.10', { + 'checksums': ['d48f2020693b4b8c1dd639668a3b1588115beac8f19f42394fc241fc1672be12'], + }), + ('napari-tools-menu', '0.1.19', { + 'checksums': ['6b58ac45d7fe84bc5975e7a53142340d5d62beff9ade0f2f58d7a3a4a0a8e8f8'], + }), + ('magicgui', '0.8.3', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['ee763f3908a344cc73e1ed0981885114937ce3077e60e4feb8148e64f0e762a3'], + }), + ('napari_time_slicer', '0.5.0', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['6c7f53f762cb3410da097be43ba47b4f4213e89930a3ade3ec1c7c1beb9d605f'], + }), + ('denoiseg', '0.3.1', { + 'preinstallopts': 'sed -i "s/wrapt<=1.12.1/wrapt/g" setup.py && ', + 'checksums': ['fd720b78910b84ea5d65deda8c193d64e583c78090d9867990b7a39f72ed7ea3'], + }), + ('napari-denoiseg', '%(version)src2', { + 'preinstallopts': 'sed -i "s/vispy<=0.9.6/vispy/g;s/napari<=0.4.15/napari<=0.4.18/g" setup.cfg && ', + 'checksums': ['e244dbb820ee7d35212ee198d28eabf987439a70ce6695cbf63cfa52baab1ea8'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-3.1.1-gompi-2023b.eb b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-3.1.1-gompi-2023b.eb new file mode 100644 index 000000000000..a7b4d99b54de --- /dev/null +++ b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-3.1.1-gompi-2023b.eb @@ -0,0 +1,38 @@ +easyblock = 'CMakeMake' + +name = 'ncbi-vdb' +version = '3.1.1' + +homepage = 'https://github.com/ncbi/ncbi-vdb' +description = """The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for + using data in the INSDC Sequence Read Archives.""" + +toolchain = {'name': 'gompi', 'version': '2023b'} + +github_account = 'ncbi' +source_urls = [GITHUB_SOURCE] +sources = [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['e9766f259853c696be48e289b08cb5ae6e198d82d7ffee79f09ce7f720487991'] + +builddependencies = [ + ('Perl', '5.38.0'), + ('Python', '3.11.5'), + ('CMake', '3.27.6'), +] + +dependencies = [ + ('HDF5', '1.14.3'), + ('libxml2', '2.11.5'), + ('bzip2', '1.0.8'), +] + +configopts = "-DHDF5_INCDIR=$EBROOTHDF5/include -DHDF5_LIBDIR=$EBROOTHDF5/lib " +configopts += "-DXML2_INCDIR=$EBROOTLIBXML2/include -DXML2_LIBDIR=$EBROOTLIBXML2/lib " + +sanity_check_paths = { + 'files': ['include/ncbi/ncbi.h', 'include/ncbi/vdb-blast.h'] + + [('lib/libncbi-%s.%s' % (k, e)) for k in ['vdb', 'wvdb'] for e in ['a', SHLIB_EXT]], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/nellie/nellie-0.3.1-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/n/nellie/nellie-0.3.1-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 000000000000..35d0c5778dde --- /dev/null +++ b/easybuild/easyconfigs/n/nellie/nellie-0.3.1-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,55 @@ +easyblock = 'PythonBundle' + +name = 'nellie' +version = '0.3.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/aelefebv/nellie/' +description = """ +Napari plugin for automated organelle segmentation, +tracking, and hierarchical feature extraction in 2D/3D live-cell microscopy. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('CUDA', '12.1.1', '', SYSTEM), + ('SciPy-bundle', '2023.07'), + ('napari', '0.4.18'), + ('scikit-image', '0.22.0'), + ('imagecodecs', '2024.1.1'), + ('matplotlib', '3.7.2'), + ('ome-types', '0.5.1.post1'), + ('CuPy', '13.0.0', versionsuffix), +] + +use_pip = True +sanity_pip_check = True + +local_preinstallopts = ( + "sed -i" + " -e 's/numpy==1.26.4/numpy/'" + " -e 's/scipy==1.12.0/scipy/'" + " -e 's/nd2==0.9.0/nd2/'" + " -e 's/pandas==2.2.1/pandas/'" + " -e 's/matplotlib==3.8.3/matplotlib/'" + " -e 's/napari[all]/napari/'" + " setup.cfg && " +) + +exts_list = [ + ('resource_backed_dask_array', '0.1.0', { + 'checksums': ['8fabcccf5c7e29059b5badd6786dd7675a258a203c58babf10077d9c90ada54f'], + }), + ('nd2', '0.10.1', { + 'checksums': ['88ee60f6ba39392722a162da58fb81bf0cdb8ed6c772772e4db91e90f97e490a'], + }), + (name, version, { + 'preinstallopts': local_preinstallopts, + 'checksums': ['3fd85bd1c7df5a8f24bff2118805cd7c82140b08871d520b2131d4d9a8c00d94'], + }), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/n/nellie/nellie-0.3.1-foss-2023a.eb b/easybuild/easyconfigs/n/nellie/nellie-0.3.1-foss-2023a.eb new file mode 100644 index 000000000000..34b3ce6299a6 --- /dev/null +++ b/easybuild/easyconfigs/n/nellie/nellie-0.3.1-foss-2023a.eb @@ -0,0 +1,52 @@ +easyblock = 'PythonBundle' + +name = 'nellie' +version = '0.3.1' + +homepage = 'https://github.com/aelefebv/nellie/' +description = """ +Napari plugin for automated organelle segmentation, +tracking, and hierarchical feature extraction in 2D/3D live-cell microscopy. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('napari', '0.4.18'), + ('scikit-image', '0.22.0'), + ('imagecodecs', '2024.1.1'), + ('matplotlib', '3.7.2'), + ('ome-types', '0.5.1.post1'), +] + +use_pip = True +sanity_pip_check = True + +local_preinstallopts = ( + "sed -i" + " -e 's/numpy==1.26.4/numpy/'" + " -e 's/scipy==1.12.0/scipy/'" + " -e 's/nd2==0.9.0/nd2/'" + " -e 's/pandas==2.2.1/pandas/'" + " -e 's/matplotlib==3.8.3/matplotlib/'" + " -e 's/napari[all]/napari/'" + " setup.cfg && " +) + +exts_list = [ + ('resource_backed_dask_array', '0.1.0', { + 'checksums': ['8fabcccf5c7e29059b5badd6786dd7675a258a203c58babf10077d9c90ada54f'], + }), + ('nd2', '0.10.1', { + 'checksums': ['88ee60f6ba39392722a162da58fb81bf0cdb8ed6c772772e4db91e90f97e490a'], + }), + (name, version, { + 'preinstallopts': local_preinstallopts, + 'checksums': ['3fd85bd1c7df5a8f24bff2118805cd7c82140b08871d520b2131d4d9a8c00d94'], + }), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/n/nettle/nettle-3.10-GCCcore-13.3.0.eb b/easybuild/easyconfigs/n/nettle/nettle-3.10-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..ef91cf135fe3 --- /dev/null +++ b/easybuild/easyconfigs/n/nettle/nettle-3.10-GCCcore-13.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'nettle' +version = '3.10' + +homepage = 'https://www.lysator.liu.se/~nisse/nettle/' +description = """Nettle is a cryptographic library that is designed to fit easily + in more or less any context: In crypto toolkits for object-oriented + languages (C++, Python, Pike, ...), in applications like LSH or GNUPG, + or even in kernel space.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['b4c518adb174e484cb4acea54118f02380c7133771e7e9beb98a0787194ee47c'] + +builddependencies = [ + ('binutils', '2.42'), + ('Autotools', '20231222'), +] + +dependencies = [ + ('GMP', '6.3.0'), +] + +configopts = '--disable-openssl ' # openssl is just used for the nettle-openssl example and requires openssl 1.1 + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['nettle-hash', 'nettle-lfib-stream', 'pkcs1-conv', 'sexp-conv']] + + [('lib/libhogweed.a', 'lib64/libhogweed.a'), + ('lib/libhogweed.%s' % SHLIB_EXT, 'lib64/libhogweed.%s' % SHLIB_EXT), + ('lib/libnettle.a', 'lib64/libnettle.a'), + ('lib/libnettle.%s' % SHLIB_EXT, 'lib64/libnettle.%s' % SHLIB_EXT)], + 'dirs': ['include/nettle'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/nifty/nifty-1.2.1-foss-2023a.eb b/easybuild/easyconfigs/n/nifty/nifty-1.2.1-foss-2023a.eb new file mode 100644 index 000000000000..37d6c62dec72 --- /dev/null +++ b/easybuild/easyconfigs/n/nifty/nifty-1.2.1-foss-2023a.eb @@ -0,0 +1,54 @@ +easyblock = 'CMakeMakeCp' + +name = 'nifty' +version = '1.2.1' + +homepage = 'https://github.com/DerThorsten/nifty/' +description = """A nifty library for 2D and 3D image segmentation, graph based segmentation an opt. +This library provided building blocks for segmentation algorithms and complex segmentation pipelines.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/DerThorsten/nifty/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['a5fd611463336ba18be828da3154da8828b6486603e2a04f14a4520cb357661a'] + +builddependencies = [('CMake', '3.26.3')] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('Boost', '1.82.0'), + ('h5py', '3.9.0'), + ('nlohmann_json', '3.11.2'), + ('scikit-image', '0.22.0'), + ('vigra', '1.11.2'), + ('xtensor', '0.24.7'), + ('zlib', '1.2.13'), + ('HDF5', '1.14.0'), +] + +# Add flags (nifty/.github/workflows/build_unix.sh) +configopts = '-DWITH_QPBO=OFF -DWITH_HDF5=ON -DWITH_Z5=OFF -DWITH_ZLIB=ON -DWITH_CPLEX=OFF -DWITH_GUROBI=OFF ' +# Fix path to python executable - it finds v3.6.8 from /usr/bin/ without this fix +configopts += '-DPYTHON_EXECUTABLE="$EBROOTPYTHON/bin/python" -DBUILD_NIFTY_PYTHON=ON ' + +# export PYTHON_MODULE_INSTALL_DIR to fix make install +preinstallopts = 'export PYTHON_MODULE_INSTALL_DIR="%(builddir)s/easybuild_obj/python/" && ' + +files_to_copy = [(['python/nifty'], 'lib/python%(pyshortver)s/site-packages')] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/nifty'], +} + +sanity_check_commands = [ + "python -c 'import nifty'", + "python -c 'from nifty.graph import UndirectedGraph'", + "python -c 'import nifty.tools'", +] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/n/nlohmann_json/nlohmann_json-3.11.3-GCCcore-13.3.0.eb b/easybuild/easyconfigs/n/nlohmann_json/nlohmann_json-3.11.3-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..8be75746afa3 --- /dev/null +++ b/easybuild/easyconfigs/n/nlohmann_json/nlohmann_json-3.11.3-GCCcore-13.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'CMakeMake' + +name = 'nlohmann_json' +version = '3.11.3' + +homepage = 'https://github.com/nlohmann/json' +description = """JSON for Modern C++""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/nlohmann/json/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['0d8ef5af7f9794e3263480193c491549b2ba6cc74bb018906202ada498a79406'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] + +sanity_check_paths = { + 'files': ['include/nlohmann/json.hpp'], + 'dirs': ['share/cmake', 'share/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/nose3/nose3-1.3.8-GCCcore-12.2.0.eb b/easybuild/easyconfigs/n/nose3/nose3-1.3.8-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..3fb61c98db7a --- /dev/null +++ b/easybuild/easyconfigs/n/nose3/nose3-1.3.8-GCCcore-12.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'nose3' +version = '1.3.8' + +homepage = 'https://nose.readthedocs.io/' +description = """Nose extends unittest to make testing easier.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['762aae22cadb898b00b9d4f4bbb9f8e87f8e0dde6c49a88cd0c554f4e5925b76'] + +builddependencies = [('binutils', '2.39')] + +dependencies = [ + ('Python', '3.10.8'), + ('coverage', '7.2.3'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +sanity_check_paths = { + 'files': ['bin/nosetests'], + 'dirs': [], +} + +options = {'modulename': 'nose'} + +sanity_check_commands = ["nosetests --help"] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/nsync/nsync-1.29.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/n/nsync/nsync-1.29.2-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..e7c2035444b7 --- /dev/null +++ b/easybuild/easyconfigs/n/nsync/nsync-1.29.2-GCCcore-13.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'CMakeNinja' + +name = 'nsync' +version = '1.29.2' + +homepage = 'https://github.com/google/nsync' +description = """nsync is a C library that exports various synchronization primitives, such as mutexes""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/google/nsync/archive/refs/tags/'] +sources = ['%(version)s.tar.gz'] +checksums = ['1d63e967973733d2c97e841e3c05fac4d3fa299f01d14c86f2695594c7a4a2ec'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), + ('Ninja', '1.12.1'), +] + +sanity_check_paths = { + 'files': ['include/nsync.h', 'lib/libnsync.a', 'lib/libnsync_cpp.a'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/numexpr/numexpr-2.9.0-foss-2023a.eb b/easybuild/easyconfigs/n/numexpr/numexpr-2.9.0-foss-2023a.eb new file mode 100644 index 000000000000..74e99150d4bf --- /dev/null +++ b/easybuild/easyconfigs/n/numexpr/numexpr-2.9.0-foss-2023a.eb @@ -0,0 +1,21 @@ +name = 'numexpr' +version = '2.9.0' + +homepage = 'https://numexpr.readthedocs.io/en/latest/' +description = """The numexpr package evaluates multiple-operator array expressions many times faster than NumPy can. + It accepts the expression as a string, analyzes it, rewrites it more efficiently, and compiles it on the fly into + code for its internal virtual machine (VM). Due to its integrated just-in-time (JIT) compiler, it does not require a + compiler at runtime.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/pydata/numexpr/archive/refs/tags'] +sources = ['v%(version)s.tar.gz'] +checksums = ['4df4163fcab20030137e8f2aa23e88e1e42e6fe702387cfd95d7675e1d84645e'] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0.8-GCCcore-13.3.0.eb b/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0.8-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..503a56951d05 --- /dev/null +++ b/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0.8-GCCcore-13.3.0.eb @@ -0,0 +1,45 @@ +# # +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2013-2024 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# Markus Geimer +# Jan André Reuter +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +# # + +easyblock = 'ConfigureMake' + +name = 'OPARI2' +version = '2.0.8' + +homepage = 'https://www.score-p.org' +description = """ + OPARI2, the successor of Forschungszentrum Juelich's OPARI, is a + source-to-source instrumentation tool for OpenMP and hybrid codes. + It surrounds OpenMP directives and runtime library calls with calls + to the POMP2 measurement interface. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['http://perftools.pages.jsc.fz-juelich.de/cicd/%(namelower)s/tags/%(namelower)s-%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['196e59a2a625e6c795a6124c61e784bad142f9f38df0b4fa4d435ba9b9c19721'] + +builddependencies = [ + ('binutils', '2.42'), +] + + +sanity_check_paths = { + 'files': ['bin/opari2', 'include/opari2/pomp2_lib.h'], + 'dirs': [], +} + +sanity_check_commands = ['opari2-config --help'] + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-6.0.0-foss-2023b-avx2.eb b/easybuild/easyconfigs/o/ORCA/ORCA-6.0.0-foss-2023b-avx2.eb new file mode 100644 index 000000000000..ff3112bb0844 --- /dev/null +++ b/easybuild/easyconfigs/o/ORCA/ORCA-6.0.0-foss-2023b-avx2.eb @@ -0,0 +1,37 @@ +name = 'ORCA' +version = '6.0.0' +versionsuffix = '-avx2' + +homepage = 'https://orcaforum.kofo.mpg.de' +description = """ +ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum +chemistry with specific emphasis on spectroscopic properties of open-shell +molecules. It features a wide variety of standard quantum chemical methods +ranging from semiempirical methods to DFT to single- and multireference +correlated ab initio methods. It can also treat environmental and relativistic +effects.""" + +toolchain = {'name': 'foss', 'version': '2023b'} + +download_instructions = "Shared build of ORCA: download from https://orcaforum.kofo.mpg.de" +# mostly dynamically linked (SCALAPACK, OpenBLAS are still embedded) +sources = ['%%(namelower)s_%s_linux_%%(orcaarch)s_avx2_shared_openmpi416.tar.xz' % version.replace('.', '_')] +checksums = [ + # orca_6_0_0_linux_x86-64_avx2_shared_openmpi416.tar.xz + '02c21294efe7b1b721e26cb90f98ee15ad682d02807201b7d217dfe67905a2fd', +] + +# optional dependency for ORCA, +# see also https://xtb-docs.readthedocs.io/en/latest/setup.html#using-xtb-with-orca +dependencies = [('xtb', '6.7.1')] + +postinstallcmds = ["cd %(installdir)s/bin && ln -s $EBROOTXTB/bin/xtb otool_xtb"] + +enhance_sanity_check = True + +sanity_check_paths = { + 'files': ['bin/orca', 'bin/otool_xtb'], + 'dirs': [], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-6.0.0-foss-2023b.eb b/easybuild/easyconfigs/o/ORCA/ORCA-6.0.0-foss-2023b.eb new file mode 100644 index 000000000000..f28a5a3ff99a --- /dev/null +++ b/easybuild/easyconfigs/o/ORCA/ORCA-6.0.0-foss-2023b.eb @@ -0,0 +1,36 @@ +name = 'ORCA' +version = '6.0.0' + +homepage = 'https://orcaforum.kofo.mpg.de' +description = """ +ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum +chemistry with specific emphasis on spectroscopic properties of open-shell +molecules. It features a wide variety of standard quantum chemical methods +ranging from semiempirical methods to DFT to single- and multireference +correlated ab initio methods. It can also treat environmental and relativistic +effects.""" + +toolchain = {'name': 'foss', 'version': '2023b'} + +download_instructions = "Shared build of ORCA: download from https://orcaforum.kofo.mpg.de" +# mostly dynamically linked (SCALAPACK, OpenBLAS are still embedded) +sources = ['%%(namelower)s_%s_linux_%%(orcaarch)s_shared_openmpi416.tar.xz' % version.replace('.', '_')] +checksums = [ + # orca_6_0_0_linux_x86-64_shared_openmpi416.tar.xz + '219bd1deb6d64a63cb72471926cb81665cbbcdec19f9c9549761be67d49a29c6', +] + +# optional dependency for ORCA, +# see also https://xtb-docs.readthedocs.io/en/latest/setup.html#using-xtb-with-orca +dependencies = [('xtb', '6.7.1')] + +postinstallcmds = ["cd %(installdir)s/bin && ln -s $EBROOTXTB/bin/xtb otool_xtb"] + +enhance_sanity_check = True + +sanity_check_paths = { + 'files': ['bin/orca', 'bin/otool_xtb'], + 'dirs': [], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-6.0.0-gompi-2023a-avx2.eb b/easybuild/easyconfigs/o/ORCA/ORCA-6.0.0-gompi-2023a-avx2.eb new file mode 100644 index 000000000000..cdc92c16f64e --- /dev/null +++ b/easybuild/easyconfigs/o/ORCA/ORCA-6.0.0-gompi-2023a-avx2.eb @@ -0,0 +1,24 @@ +name = 'ORCA' +version = '6.0.0' +versionsuffix = '-avx2' + +homepage = 'https://orcaforum.kofo.mpg.de' +description = """ +ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum +chemistry with specific emphasis on spectroscopic properties of open-shell +molecules. It features a wide variety of standard quantum chemical methods +ranging from semiempirical methods to DFT to single- and multireference +correlated ab initio methods. It can also treat environmental and relativistic +effects.""" + +toolchain = {'name': 'gompi', 'version': '2023a'} + +download_instructions = "Shared build of ORCA: download from https://orcaforum.kofo.mpg.de" +# mostly dynamically linked (SCALAPACK, OpenBLAS are still embedded) +sources = ['%%(namelower)s_%s_linux_%%(orcaarch)s_avx2_shared_openmpi416.tar.xz' % version.replace('.', '_')] +checksums = [ + # orca_6_0_0_linux_x86-64_avx2_shared_openmpi416.tar.xz + '02c21294efe7b1b721e26cb90f98ee15ad682d02807201b7d217dfe67905a2fd', +] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-6.0.0-gompi-2023a.eb b/easybuild/easyconfigs/o/ORCA/ORCA-6.0.0-gompi-2023a.eb new file mode 100644 index 000000000000..8bf88fa8129f --- /dev/null +++ b/easybuild/easyconfigs/o/ORCA/ORCA-6.0.0-gompi-2023a.eb @@ -0,0 +1,23 @@ +name = 'ORCA' +version = '6.0.0' + +homepage = 'https://orcaforum.kofo.mpg.de' +description = """ +ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum +chemistry with specific emphasis on spectroscopic properties of open-shell +molecules. It features a wide variety of standard quantum chemical methods +ranging from semiempirical methods to DFT to single- and multireference +correlated ab initio methods. It can also treat environmental and relativistic +effects.""" + +toolchain = {'name': 'gompi', 'version': '2023a'} + +download_instructions = "Shared build of ORCA: download from https://orcaforum.kofo.mpg.de" +# mostly dynamically linked (SCALAPACK, OpenBLAS are still embedded) +sources = ['%%(namelower)s_%s_linux_%%(orcaarch)s_shared_openmpi416.tar.xz' % version.replace('.', '_')] +checksums = [ + # orca_6_0_0_linux_x86-64_shared_openmpi416.tar.xz + '219bd1deb6d64a63cb72471926cb81665cbbcdec19f9c9549761be67d49a29c6', +] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-7.4-gompi-2024a.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-7.4-gompi-2024a.eb new file mode 100644 index 000000000000..0d9573028ddd --- /dev/null +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-7.4-gompi-2024a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'OSU-Micro-Benchmarks' +version = '7.4' + +homepage = 'https://mvapich.cse.ohio-state.edu/benchmarks/' +description = """OSU Micro-Benchmarks""" + +toolchain = {'name': 'gompi', 'version': '2024a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://mvapich.cse.ohio-state.edu/download/mvapich/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['1edd0c2efa61999409bfb28740a7f39689a5b42b1a1b4c66d1656e5637f7cefc'] + +local_benchmark_dirs = [ + 'libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup'] +] +modextrapaths = {'PATH': local_benchmark_dirs} + +sanity_check_paths = { + 'files': [], + 'dirs': local_benchmark_dirs, +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-7.4-iimpi-2024a.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-7.4-iimpi-2024a.eb new file mode 100644 index 000000000000..3122923be15f --- /dev/null +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-7.4-iimpi-2024a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'OSU-Micro-Benchmarks' +version = '7.4' + +homepage = 'https://mvapich.cse.ohio-state.edu/benchmarks/' +description = """OSU Micro-Benchmarks""" + +toolchain = {'name': 'iimpi', 'version': '2024a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://mvapich.cse.ohio-state.edu/download/mvapich/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['1edd0c2efa61999409bfb28740a7f39689a5b42b1a1b4c66d1656e5637f7cefc'] + +local_benchmark_dirs = [ + 'libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup'] +] +modextrapaths = {'PATH': local_benchmark_dirs} + +sanity_check_paths = { + 'files': [], + 'dirs': local_benchmark_dirs, +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-3.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/o/OTF2/OTF2-3.0-GCCcore-11.3.0.eb index 6e982449e9ef..fe8a5244c124 100644 --- a/easybuild/easyconfigs/o/OTF2/OTF2-3.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/o/OTF2/OTF2-3.0-GCCcore-11.3.0.eb @@ -3,6 +3,7 @@ # Copyright:: Copyright 2013-2019 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr # Markus Geimer +# Jan Andre Reuter # License:: 3-clause BSD # # This work is based on experiences from the UNITE project @@ -34,17 +35,21 @@ builddependencies = [ dependencies = [ # SIONlib container support (optional): ('SIONlib', '1.7.7', '-tools'), + # OTF2 Python bindings + ('Python', '3.10.4'), ] +local_pyshortver = '3.10' configopts = '--enable-shared' +modextrapaths = {'PYTHONPATH': ['lib64/python%s/site-packages' % local_pyshortver]} sanity_check_paths = { 'files': ['bin/otf2-config', 'include/otf2/otf2.h', 'lib/libotf2.a', 'lib/libotf2.%s' % SHLIB_EXT], 'dirs': [], } - -sanity_check_commands = ['%(namelower)s-config --help'] +sanity_check_commands = ['%(namelower)s-config --help', + 'python -c "import %(namelower)s"'] moduleclass = 'perf' diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-3.0.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/o/OTF2/OTF2-3.0.2-GCCcore-11.2.0.eb index 7c4d60f05143..488b8e0de0de 100644 --- a/easybuild/easyconfigs/o/OTF2/OTF2-3.0.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/o/OTF2/OTF2-3.0.2-GCCcore-11.2.0.eb @@ -3,6 +3,7 @@ # Copyright:: Copyright 2013-2019 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr # Markus Geimer +# Jan Andre Reuter # License:: 3-clause BSD # # This work is based on experiences from the UNITE project @@ -34,17 +35,22 @@ builddependencies = [ dependencies = [ # SIONlib container support (optional): ('SIONlib', '1.7.7', '-tools'), + # OTF2 Python bindings + ('Python', '3.9.6'), ] +local_pyshortver = '3.9' configopts = '--enable-shared' +modextrapaths = {'PYTHONPATH': ['lib64/python%s/site-packages' % local_pyshortver]} sanity_check_paths = { 'files': ['bin/otf2-config', 'include/otf2/otf2.h', 'lib/libotf2.a', 'lib/libotf2.%s' % SHLIB_EXT], 'dirs': [], } +sanity_check_commands = ['%(namelower)s-config --help', + 'python -c "import %(namelower)s"'] -sanity_check_commands = ['%(namelower)s-config --help'] moduleclass = 'perf' diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-3.0.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/o/OTF2/OTF2-3.0.2-GCCcore-11.3.0.eb index 61eba75f5f0f..6756aa72eac3 100644 --- a/easybuild/easyconfigs/o/OTF2/OTF2-3.0.2-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/o/OTF2/OTF2-3.0.2-GCCcore-11.3.0.eb @@ -3,6 +3,7 @@ # Copyright:: Copyright 2013-2019 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr # Markus Geimer +# Jan Andre Reuter # License:: 3-clause BSD # # This work is based on experiences from the UNITE project @@ -34,17 +35,21 @@ builddependencies = [ dependencies = [ # SIONlib container support (optional): ('SIONlib', '1.7.7', '-tools'), + # OTF2 Python bindings + ('Python', '3.10.4'), ] +local_pyshortver = '3.10' configopts = '--enable-shared' +modextrapaths = {'PYTHONPATH': ['lib64/python%s/site-packages' % local_pyshortver]} sanity_check_paths = { 'files': ['bin/otf2-config', 'include/otf2/otf2.h', 'lib/libotf2.a', 'lib/libotf2.%s' % SHLIB_EXT], 'dirs': [], } - -sanity_check_commands = ['%(namelower)s-config --help'] +sanity_check_commands = ['%(namelower)s-config --help', + 'python -c "import %(namelower)s"'] moduleclass = 'perf' diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-12.2.0.eb index 54478bf62fae..f4c842e04509 100644 --- a/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-12.2.0.eb @@ -3,6 +3,7 @@ # Copyright:: Copyright 2013-2019 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr # Markus Geimer +# Jan Andre Reuter # License:: 3-clause BSD # # This work is based on experiences from the UNITE project @@ -34,17 +35,21 @@ builddependencies = [ dependencies = [ # SIONlib container support (optional): ('SIONlib', '1.7.7', '-tools'), + # OTF2 Python bindings + ('Python', '3.10.8'), ] +local_pyshortver = '3.10' configopts = '--enable-shared' +modextrapaths = {'PYTHONPATH': ['lib64/python%s/site-packages' % local_pyshortver]} sanity_check_paths = { 'files': ['bin/otf2-config', 'include/otf2/otf2.h', 'lib/libotf2.a', 'lib/libotf2.%s' % SHLIB_EXT], 'dirs': [], } - -sanity_check_commands = ['%(namelower)s-config --help'] +sanity_check_commands = ['%(namelower)s-config --help', + 'python -c "import %(namelower)s"'] moduleclass = 'perf' diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-12.3.0.eb index 17595d97acbf..db786b12a413 100644 --- a/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-12.3.0.eb @@ -3,6 +3,7 @@ # Copyright:: Copyright 2013-2019 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr # Markus Geimer +# Jan Andre Reuter # License:: 3-clause BSD # # This work is based on experiences from the UNITE project @@ -34,17 +35,22 @@ builddependencies = [ dependencies = [ # SIONlib container support (optional): ('SIONlib', '1.7.7', '-tools'), + # OTF2 Python bindings + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), ] +local_pyshortver = '3.11' configopts = '--enable-shared' +modextrapaths = {'PYTHONPATH': ['lib64/python%s/site-packages' % local_pyshortver]} sanity_check_paths = { 'files': ['bin/otf2-config', 'include/otf2/otf2.h', 'lib/libotf2.a', 'lib/libotf2.%s' % SHLIB_EXT], 'dirs': [], } - -sanity_check_commands = ['%(namelower)s-config --help'] +sanity_check_commands = ['%(namelower)s-config --help', + 'python -c "import %(namelower)s"'] moduleclass = 'perf' diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-13.2.0.eb b/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-13.2.0.eb index 48cbf931ec51..c5108c8daca9 100644 --- a/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-13.2.0.eb @@ -3,6 +3,7 @@ # Copyright:: Copyright 2013-2019 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr # Markus Geimer +# Jan Andre Reuter # License:: 3-clause BSD # # This work is based on experiences from the UNITE project @@ -34,17 +35,22 @@ builddependencies = [ dependencies = [ # SIONlib container support (optional): ('SIONlib', '1.7.7', '-tools'), + # OTF2 Python bindings + ('Python', '3.11.5'), + ('Python-bundle-PyPI', '2023.10'), ] +local_pyshortver = '3.11' configopts = '--enable-shared' +modextrapaths = {'PYTHONPATH': ['lib64/python%s/site-packages' % local_pyshortver]} sanity_check_paths = { 'files': ['bin/otf2-config', 'include/otf2/otf2.h', 'lib/libotf2.a', 'lib/libotf2.%s' % SHLIB_EXT], 'dirs': [], } - -sanity_check_commands = ['%(namelower)s-config --help'] +sanity_check_commands = ['%(namelower)s-config --help', + 'python -c "import %(namelower)s"'] moduleclass = 'perf' diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-13.3.0.eb b/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..fdf78e0772d5 --- /dev/null +++ b/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-13.3.0.eb @@ -0,0 +1,60 @@ +# # +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# Copyright:: Copyright 2013-2024 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# Markus Geimer +# Jan André Reuter +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +# # + +easyblock = 'EB_Score_minus_P' + +name = 'OTF2' +version = '3.0.3' + +homepage = 'https://www.score-p.org' +description = """ + The Open Trace Format 2 is a highly scalable, memory efficient event trace + data format plus support library. It is the new standard trace format for + Scalasca, Vampir, and TAU and is open for other tools. + +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['http://perftools.pages.jsc.fz-juelich.de/cicd/%(namelower)s/tags/%(namelower)s-%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['otf2-3.0.3-update-py-compile.patch'] +checksums = [ + '18a3905f7917340387e3edc8e5766f31ab1af41f4ecc5665da6c769ca21c4ee8', # otf2-3.0.3.tar.gz + '5b1dad8788642eaa97bc03003c9329380340ba10649e556a30ce541165cf8da4', # otf2-3.0.3-update-py-compile.patch +] + +builddependencies = [ + ('binutils', '2.42'), +] +dependencies = [ + # SIONlib container support (optional): + ('SIONlib', '1.7.7', '-tools'), + # OTF2 Python bindings + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), +] + +local_pyshortver = '3.12' +configopts = '--enable-shared' + +modextrapaths = {'PYTHONPATH': ['lib64/python%s/site-packages' % local_pyshortver]} + +sanity_check_paths = { + 'files': ['bin/otf2-config', 'include/otf2/otf2.h', + 'lib/libotf2.a', 'lib/libotf2.%s' % SHLIB_EXT], + 'dirs': [], +} +sanity_check_commands = ['%(namelower)s-config --help', + 'python -c "import %(namelower)s"'] + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/o/OTF2/otf2-3.0.3-update-py-compile.patch b/easybuild/easyconfigs/o/OTF2/otf2-3.0.3-update-py-compile.patch new file mode 100644 index 000000000000..539726fbf145 --- /dev/null +++ b/easybuild/easyconfigs/o/OTF2/otf2-3.0.3-update-py-compile.patch @@ -0,0 +1,252 @@ +This patch updates the py-compile file used by OTF2 during the install process +to fix the removal of the imp module in Python 3.12 which was long deprecated. +With this, OTF2 can be installed with Python 3.12, which would previously fail +with a module not found error. + +--- build-config/py-compile 2023-02-12 17:32:31.274132086 +0100 ++++ ../../otf2/build-config/py-compile 2024-08-22 17:44:59.939242651 +0200 +@@ -1,7 +1,7 @@ + #!/bin/sh + # py-compile - Compile a Python program + +-scriptversion=2011-06-08.12; # UTC ++scriptversion=2023-03-30.00; # UTC + + # Copyright (C) 2000-2013 Free Software Foundation, Inc. + +@@ -27,7 +27,7 @@ + # bugs to or send patches to + # . + +-if [ -z "$PYTHON" ]; then ++if test -z "$PYTHON"; then + PYTHON=python + fi + +@@ -79,13 +79,20 @@ + ;; + -h|--help) + cat <<\EOF +-Usage: py-compile [--help] [--version] [--basedir DIR] [--destdir DIR] [--silent] FILES..." ++Usage: py-compile [options] FILES... + + Byte compile some python scripts FILES. Use --destdir to specify any + leading directory path to the FILES that you don't want to include in the + byte compiled file. Specify --basedir for any additional path information you + do want to be shown in the byte compiled file. + ++Options: ++ --basedir DIR Prefix all FILES with DIR, and include in error messages. ++ --destdir DIR Prefix all FILES with DIR before compiling. ++ -v, --version Display version information. ++ -h, --help This help screen. ++ --silent Operate silently. ++ + Example: + py-compile --destdir /tmp/pkg-root --basedir /usr/share/test test.py test2.py + +@@ -114,87 +121,165 @@ + shift + done + +-files=$* +-if test -z "$files"; then +- usage_error "no files given" ++if test $# -eq 0; then ++ usage_error "no files given" + fi + + # if basedir was given, then it should be prepended to filenames before + # byte compilation. +-if [ -z "$basedir" ]; then +- pathtrans="path = file" ++if test -z "$basedir"; then ++ pathtrans="path = file" + else +- pathtrans="path = os.path.join('$basedir', file)" ++ pathtrans="path = os.path.join('$basedir', file)" + fi + + # if destdir was given, then it needs to be prepended to the filename to + # byte compile but not go into the compiled file. +-if [ -z "$destdir" ]; then +- filetrans="filepath = path" ++if test -z "$destdir"; then ++ filetrans="filepath = path" + else +- filetrans="filepath = os.path.normpath('$destdir' + os.sep + path)" ++ filetrans="filepath = os.path.normpath('$destdir' + os.sep + path)" ++fi ++ ++python_major=`$PYTHON -c 'import sys; print(sys.version_info[0])'` ++if test -z "$python_major"; then ++ usage_error "could not determine $PYTHON major version" + fi + ++case $python_major in ++[01]) ++ usage_error "python version 0.x and 1.x not supported" ++ ;; ++esac ++ ++python_minor=`$PYTHON -c 'import sys; print(sys.version_info[1])'` ++ ++# NB: When adding support for newer versions, prefer copying & adding new cases ++# rather than try to keep things merged with shell variables. ++ ++# First byte compile (no optimization) all the modules. ++# This works for all currently known Python versions. + $PYTHON -c " +-import sys, os, py_compile, imp ++import sys, os, py_compile ++ ++try: ++ import importlib ++except ImportError: ++ importlib = None ++ ++# importlib.util.cache_from_source was added in 3.4 ++if ( ++ hasattr(importlib, 'util') ++ and hasattr(importlib.util, 'cache_from_source') ++): ++ destpath = importlib.util.cache_from_source ++else: ++ destpath = lambda filepath: filepath + 'c' + +-files = '''$files''' + silent = $silent + blu = '''$blu''' + std = '''$std''' + + if not silent: +- sys.stdout.write('Byte-compiling python modules...') +-for file in files.split(): ++ sys.stdout.write('Byte-compiling python modules...\n') ++for file in sys.argv[1:]: + $pathtrans + $filetrans +- if not os.path.exists(filepath) or not (len(filepath) >= 3 +- and filepath[-3:] == '.py'): +- continue ++ if ( ++ not os.path.exists(filepath) ++ or not (len(filepath) >= 3 and filepath[-3:] == '.py') ++ ): ++ continue + if not silent: +- sys.stdout.write(' ' + file) ++ sys.stdout.write(file + ' ') + sys.stdout.flush() + else: +- sys.stdout.write(' PYTHON {}{}{}\n'.format(blu, filepath + 'c', std)) +- if hasattr(imp, 'get_tag'): +- py_compile.compile(filepath, imp.cache_from_source(filepath), path) +- else: +- py_compile.compile(filepath, filepath + 'c', path) ++ sys.stdout.write(' PYCACHE {}{}{}\n'.format(blu, destpath(filepath), std)) ++ py_compile.compile(filepath, destpath(filepath), path) + if not silent: +- sys.stdout.write('\n')" || exit $? ++ sys.stdout.write('\n')" "$@" || exit $? + +-# this will fail for python < 1.5, but that doesn't matter ... ++# Then byte compile w/optimization all the modules. + $PYTHON -O -c " +-import sys, os, py_compile, imp ++import sys, os, py_compile ++ ++try: ++ import importlib ++except ImportError: ++ importlib = None ++ ++# importlib.util.cache_from_source was added in 3.4 ++if ( ++ hasattr(importlib, 'util') ++ and hasattr(importlib.util, 'cache_from_source') ++): ++ destpath = importlib.util.cache_from_source ++else: ++ destpath = lambda filepath: filepath + 'o' + +-# pypy does not use .pyo optimization +-if hasattr(sys, 'pypy_translation_info'): ++# pypy2 does not use .pyo optimization ++if sys.version_info.major <= 2 and hasattr(sys, 'pypy_translation_info'): + sys.exit(0) + +-files = '''$files''' + silent = $silent + blu = '''$blu''' + std = '''$std''' + + if not silent: +- sys.stdout.write('Byte-compiling python modules (optimized versions)...') +-for file in files.split(): ++ sys.stdout.write('Byte-compiling python modules (optimized versions) ...\n') ++for file in sys.argv[1:]: + $pathtrans + $filetrans +- if not os.path.exists(filepath) or not (len(filepath) >= 3 +- and filepath[-3:] == '.py'): +- continue ++ if ( ++ not os.path.exists(filepath) ++ or not (len(filepath) >= 3 and filepath[-3:] == '.py') ++ ): ++ continue + if not silent: +- sys.stdout.write(' ' + file) ++ sys.stdout.write(file + ' ') + sys.stdout.flush() + else: +- sys.stdout.write(' PYTHON {}{}{}\n'.format(blu, filepath + 'o', std)) +- if hasattr(imp, 'get_tag'): +- py_compile.compile(filepath, imp.cache_from_source(filepath, False), path) ++ sys.stdout.write(' PYCACHE {}{}{}\n'.format(blu, destpath(filepath), std)) ++ py_compile.compile(filepath, destpath(filepath), path) ++if not silent: ++ sys.stdout.write('\n')" "$@" 2>/dev/null || exit $? ++ ++# Then byte compile w/more optimization. ++# Only do this for Python 3.5+, see https://bugs.gnu.org/38043 for background. ++case $python_major.$python_minor in ++2.*|3.[0-4]) ++ ;; ++*) ++ $PYTHON -OO -c " ++import sys, os, py_compile, importlib ++ ++destpath = importlib.util.cache_from_source ++ ++silent = $silent ++blu = '''$blu''' ++std = '''$std''' ++ ++if not silent: ++ sys.stdout.write('Byte-compiling python modules (more optimized versions)' ++ ' ...\n') ++for file in sys.argv[1:]: ++ $pathtrans ++ $filetrans ++ if ( ++ not os.path.exists(filepath) ++ or not (len(filepath) >= 3 and filepath[-3:] == '.py') ++ ): ++ continue ++ if not silent: ++ sys.stdout.write(file + ' ') ++ sys.stdout.flush() + else: +- py_compile.compile(filepath, filepath + 'o', path) ++ sys.stdout.write(' PYCACHE {}{}{}\n'.format(blu, destpath(filepath), std)) ++ py_compile.compile(filepath, destpath(filepath), path) + if not silent: +- sys.stdout.write('\n')" 2>/dev/null || : ++ sys.stdout.write('\n')" "$@" 2>/dev/null || exit $? ++ ;; ++esac + + # Local Variables: + # mode: shell-script diff --git a/easybuild/easyconfigs/o/OpenAI-Gym/OpenAI-Gym-0.26.2-foss-2023a.eb b/easybuild/easyconfigs/o/OpenAI-Gym/OpenAI-Gym-0.26.2-foss-2023a.eb new file mode 100644 index 000000000000..c7ad7c7c04f9 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenAI-Gym/OpenAI-Gym-0.26.2-foss-2023a.eb @@ -0,0 +1,53 @@ +easyblock = 'PythonBundle' + +name = 'OpenAI-Gym' +version = '0.26.2' + +homepage = 'https://gym.openai.com' +description = "A toolkit for developing and comparing reinforcement learning algorithms." + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('CMake', '3.26.3'), + ('SWIG', '4.1.1'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('Arcade-Learning-Environment', '0.8.1'), + ('OpenCV', '4.8.1', '-contrib'), + ('lz4', '1.9.4'), + ('pygame', '2.5.2'), + ('MuJoCo', '3.1.4'), +] + +use_pip = True + +exts_list = [ + ('cloudpickle', '3.0.0', { + 'checksums': ['996d9a482c6fb4f33c1a35335cf8afd065d2a56e973270364840712d9131a882'], + }), + ('gym-notices', '0.0.8', { + 'checksums': ['ad25e200487cafa369728625fe064e88ada1346618526102659b4640f2b4b911'], + }), + ('box2d-py', '2.3.8', { + 'modulename': 'Box2D', + 'checksums': ['bdacfbbc56079bb317548efe49d3d5a86646885cc27f4a2ee97e4b2960921ab7'], + }), + ('lz4', '4.3.3', { + 'checksums': ['01fe674ef2889dbb9899d8a67361e0c4a2c833af5aeb37dd505727cf5d2a131e'], + }), + ('gym', version, { + 'use_pip_extras': 'all', + 'checksums': ['e0d882f4b54f0c65f203104c24ab8a38b039f1289986803c7d02cdbe214fbcc4'], + }), +] + +local_envs = ['box2d', 'classic_control', 'mujoco', 'toy_text'] +sanity_check_commands = ["python -c 'import gym.envs.%s'" % e for e in local_envs] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.24-GCC-13.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.24-GCC-13.2.0.eb index 4835813e357a..8d2315fbe6ed 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.24-GCC-13.2.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.24-GCC-13.2.0.eb @@ -20,6 +20,7 @@ patches = [ 'OpenBLAS-0.3.21_fix-order-vectorization.patch', 'OpenBLAS-0.3.23_disable-xDRGES-LAPACK-test.patch', 'OpenBLAS-0.3.24_fix-czasum.patch', + 'OpenBLAS-0.3.24_fix-A64FX.patch', ] checksums = [ {'v0.3.24.tar.gz': 'ceadc5065da97bd92404cac7254da66cc6eb192679cf1002098688978d4d5132'}, @@ -33,8 +34,8 @@ checksums = [ '08af834e5d60441fd35c128758ed9c092ba6887c829e0471ecd489079539047d'}, {'OpenBLAS-0.3.23_disable-xDRGES-LAPACK-test.patch': 'ab7e0af05f9b2a2ced32f3875e1e3767d9c3531a455421a38f7324350178a0ff'}, - {'OpenBLAS-0.3.24_fix-czasum.patch': - '8132b87c519fb08caa3bd7291fe8a1d0e1afe6fcb667d16f3020b46122afe20c'}, + {'OpenBLAS-0.3.24_fix-czasum.patch': '8132b87c519fb08caa3bd7291fe8a1d0e1afe6fcb667d16f3020b46122afe20c'}, + {'OpenBLAS-0.3.24_fix-A64FX.patch': '3712e8c3f0024c7bb327958779c388ad0234ad6d58b7b118e605256ec089964c'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.24_fix-A64FX.patch b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.24_fix-A64FX.patch new file mode 100644 index 000000000000..ff4a16dea8dc --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.24_fix-A64FX.patch @@ -0,0 +1,138 @@ +fix installation of OpenBLAS 0.3.24 on Arm A64FX, +see https://github.com/OpenMathLib/OpenBLAS/pull/4258 + https://github.com/OpenMathLib/OpenBLAS/issues/4257 +diff --git a/kernel/arm64/KERNEL.A64FX b/kernel/arm64/KERNEL.A64FX +index bd25f7cd8a..ccbce27e1b 100644 +--- a/kernel/arm64/KERNEL.A64FX ++++ b/kernel/arm64/KERNEL.A64FX +@@ -57,7 +57,7 @@ CAMAXKERNEL = zamax.S + ZAMAXKERNEL = zamax.S + + SAXPYKERNEL = axpy.S +-DAXPYKERNEL = axpy.S ++DAXPYKERNEL = daxpy_thunderx2t99.S + CAXPYKERNEL = zaxpy.S + ZAXPYKERNEL = zaxpy.S + +@@ -81,45 +81,35 @@ DGEMVTKERNEL = gemv_t.S + CGEMVTKERNEL = zgemv_t.S + ZGEMVTKERNEL = zgemv_t.S + +- +-SASUMKERNEL = asum.S +-DASUMKERNEL = asum.S +-CASUMKERNEL = casum.S +-ZASUMKERNEL = zasum.S +- +-SCOPYKERNEL = copy.S +-DCOPYKERNEL = copy.S +-CCOPYKERNEL = copy.S +-ZCOPYKERNEL = copy.S +- +-SSWAPKERNEL = swap.S +-DSWAPKERNEL = swap.S +-CSWAPKERNEL = swap.S +-ZSWAPKERNEL = swap.S +- +-ISAMAXKERNEL = iamax.S +-IDAMAXKERNEL = iamax.S +-ICAMAXKERNEL = izamax.S +-IZAMAXKERNEL = izamax.S +- +-SNRM2KERNEL = nrm2.S +-DNRM2KERNEL = nrm2.S +-CNRM2KERNEL = znrm2.S +-ZNRM2KERNEL = znrm2.S +- +-DDOTKERNEL = dot.S +-ifneq ($(C_COMPILER), PGI) +-SDOTKERNEL = ../generic/dot.c +-else +-SDOTKERNEL = dot.S +-endif +-ifneq ($(C_COMPILER), PGI) +-CDOTKERNEL = zdot.S +-ZDOTKERNEL = zdot.S +-else +-CDOTKERNEL = ../arm/zdot.c +-ZDOTKERNEL = ../arm/zdot.c +-endif ++SASUMKERNEL = sasum_thunderx2t99.c ++DASUMKERNEL = dasum_thunderx2t99.c ++CASUMKERNEL = casum_thunderx2t99.c ++ZASUMKERNEL = zasum_thunderx2t99.c ++ ++SCOPYKERNEL = copy_thunderx2t99.c ++DCOPYKERNEL = copy_thunderx2t99.c ++CCOPYKERNEL = copy_thunderx2t99.c ++ZCOPYKERNEL = copy_thunderx2t99.c ++ ++SSWAPKERNEL = swap_thunderx2t99.S ++DSWAPKERNEL = swap_thunderx2t99.S ++CSWAPKERNEL = swap_thunderx2t99.S ++ZSWAPKERNEL = swap_thunderx2t99.S ++ ++ISAMAXKERNEL = iamax_thunderx2t99.c ++IDAMAXKERNEL = iamax_thunderx2t99.c ++ICAMAXKERNEL = izamax_thunderx2t99.c ++IZAMAXKERNEL = izamax_thunderx2t99.c ++ ++SNRM2KERNEL = scnrm2_thunderx2t99.c ++DNRM2KERNEL = dznrm2_thunderx2t99.c ++CNRM2KERNEL = scnrm2_thunderx2t99.c ++ZNRM2KERNEL = dznrm2_thunderx2t99.c ++ ++DDOTKERNEL = dot.c ++SDOTKERNEL = dot.c ++CDOTKERNEL = zdot_thunderx2t99.c ++ZDOTKERNEL = zdot_thunderx2t99.c + DSDOTKERNEL = dot.S + + DGEMM_BETA = dgemm_beta.S +@@ -128,10 +118,10 @@ SGEMM_BETA = sgemm_beta.S + SGEMMKERNEL = sgemm_kernel_sve_v2x$(SGEMM_UNROLL_N).S + STRMMKERNEL = strmm_kernel_sve_v1x$(SGEMM_UNROLL_N).S + +-SGEMMINCOPY = sgemm_ncopy_sve_v1.c +-SGEMMITCOPY = sgemm_tcopy_sve_v1.c +-SGEMMONCOPY = sgemm_ncopy_$(DGEMM_UNROLL_N).S +-SGEMMOTCOPY = sgemm_tcopy_$(DGEMM_UNROLL_N).S ++SGEMMINCOPY = gemm_ncopy_sve_v1x$(SGEMM_UNROLL_N).c ++SGEMMITCOPY = gemm_tcopy_sve_v1x$(SGEMM_UNROLL_N).c ++SGEMMONCOPY = sgemm_ncopy_$(SGEMM_UNROLL_N).S ++SGEMMOTCOPY = sgemm_tcopy_$(SGEMM_UNROLL_N).S + + SGEMMINCOPYOBJ = sgemm_incopy$(TSUFFIX).$(SUFFIX) + SGEMMITCOPYOBJ = sgemm_itcopy$(TSUFFIX).$(SUFFIX) +@@ -149,8 +139,8 @@ SSYMMLCOPY_M = symm_lcopy_sve.c + DGEMMKERNEL = dgemm_kernel_sve_v2x$(DGEMM_UNROLL_N).S + DTRMMKERNEL = dtrmm_kernel_sve_v1x$(DGEMM_UNROLL_N).S + +-DGEMMINCOPY = dgemm_ncopy_sve_v1.c +-DGEMMITCOPY = dgemm_tcopy_sve_v1.c ++DGEMMINCOPY = gemm_ncopy_sve_v1x$(DGEMM_UNROLL_N).c ++DGEMMITCOPY = gemm_tcopy_sve_v1x$(DGEMM_UNROLL_N).c + DGEMMONCOPY = dgemm_ncopy_$(DGEMM_UNROLL_N).S + DGEMMOTCOPY = dgemm_tcopy_$(DGEMM_UNROLL_N).S + +@@ -170,8 +160,8 @@ DSYMMLCOPY_M = symm_lcopy_sve.c + CGEMMKERNEL = cgemm_kernel_sve_v1x$(ZGEMM_UNROLL_N).S + CTRMMKERNEL = ctrmm_kernel_sve_v1x$(ZGEMM_UNROLL_N).S + +-CGEMMINCOPY = cgemm_ncopy_sve_v1.c +-CGEMMITCOPY = cgemm_tcopy_sve_v1.c ++CGEMMINCOPY = gemm_ncopy_complex_sve_v1x$(ZGEMM_UNROLL_N).c ++CGEMMITCOPY = gemm_tcopy_complex_sve_v1x$(ZGEMM_UNROLL_N).c + CGEMMONCOPY = ../generic/zgemm_ncopy_$(ZGEMM_UNROLL_N).c + CGEMMOTCOPY = ../generic/zgemm_tcopy_$(ZGEMM_UNROLL_N).c + +@@ -194,8 +184,8 @@ CSYMMLCOPY_M = zsymm_lcopy_sve.c + ZGEMMKERNEL = zgemm_kernel_sve_v1x$(ZGEMM_UNROLL_N).S + ZTRMMKERNEL = ztrmm_kernel_sve_v1x$(ZGEMM_UNROLL_N).S + +-ZGEMMINCOPY = zgemm_ncopy_sve_v1.c +-ZGEMMITCOPY = zgemm_tcopy_sve_v1.c ++ZGEMMINCOPY = gemm_ncopy_complex_sve_v1x$(ZGEMM_UNROLL_N).c ++ZGEMMITCOPY = gemm_tcopy_complex_sve_v1x$(ZGEMM_UNROLL_N).c + ZGEMMONCOPY = ../generic/zgemm_ncopy_$(ZGEMM_UNROLL_N).c + ZGEMMOTCOPY = ../generic/zgemm_tcopy_$(ZGEMM_UNROLL_N).c + diff --git a/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.2.4-GCCcore-13.3.0.eb b/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.2.4-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..f6e66db69aee --- /dev/null +++ b/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.2.4-GCCcore-13.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'CMakeMake' + +name = 'OpenEXR' +version = '3.2.4' + +homepage = 'https://www.openexr.com/' +description = """OpenEXR is a high dynamic-range (HDR) image file format developed by Industrial Light & Magic + for use in computer imaging applications""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/%(namelower)s/%(namelower)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['81e6518f2c4656fdeaf18a018f135e96a96e7f66dbe1c1f05860dd94772176cc'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] +dependencies = [ + ('Imath', '3.1.11'), + ('zlib', '1.3.1') +] + +local_libs, local_bins = [ + ['Iex', 'IlmThread', 'OpenEXR', 'OpenEXRUtil'], + ['envmap', 'header', 'makepreview', 'maketiled', 'multipart', 'multiview', 'stdattr'] +] + +sanity_check_paths = { + 'files': ( + ['lib/lib%s.%s' % (s, SHLIB_EXT) for s in local_libs] + + ['bin/exr%s' % b for b in local_bins] + ), + 'dirs': ['include/%(name)s', 'share'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2022a-20230119-int64.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2022a-20230119-int64.eb new file mode 100644 index 000000000000..5c5f4d70f9fa --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2022a-20230119-int64.eb @@ -0,0 +1,42 @@ +name = 'OpenFOAM' + +version = '10' +_version_patch = '20230119' +versionsuffix = '-%s-int64' % _version_patch + +homepage = 'https://www.openfoam.org/' +description = """OpenFOAM is a free, open source CFD software package. + OpenFOAM has an extensive range of features to solve anything from complex fluid flows + involving chemical reactions, turbulence and heat transfer, + to solid dynamics and electromagnetics.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'vectorize': False, 'i8': True} + +source_urls = ['https://github.com/OpenFOAM/OpenFOAM-%(version_major)s/archive'] +sources = [{ + 'download_filename': '%s.tar.gz' % _version_patch, + 'filename': 'OpenFOAM-%s-%s.tar.gz' % (version, _version_patch), +}] +patches = ['OpenFOAM-%(version_major)s-ThirdParty.patch'] +checksums = [ + {'OpenFOAM-10-20230119.tar.gz': '86f8cb18d4f59812b129ce7d669e8ff498da442fbdb46705492fbba3cbda82ab'}, + {'OpenFOAM-10-ThirdParty.patch': '307df0206cdb24533f4974378843332064f4a2d85cf0638c20fc4c87b1524b43'}, +] + +builddependencies = [ + ('Bison', '3.8.2'), + ('CMake', '3.23.1'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('ncurses', '6.3'), + ('METIS', '5.1.0', '-int64'), + ('SCOTCH', '7.0.1', '-int64'), + ('CGAL', '4.14.3'), + ('ParaView', '5.10.1', '-mpi'), + ('gnuplot', '5.4.4'), +] + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2022a-20230119.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2022a-20230119.eb index f9ebf346635a..fd18ec3e2876 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2022a-20230119.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2022a-20230119.eb @@ -11,6 +11,7 @@ description = """OpenFOAM is a free, open source CFD software package. to solid dynamics and electromagnetics.""" toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'vectorize': False} source_urls = ['https://github.com/OpenFOAM/OpenFOAM-%(version_major)s/archive'] sources = [{ diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2022a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2022a.eb index 7fafa63937ce..3bdaaf4f06e9 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2022a.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2022a.eb @@ -8,6 +8,7 @@ description = """OpenFOAM is a free, open source CFD software package. to solid dynamics and electromagnetics.""" toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'vectorize': False} source_urls = ['https://github.com/OpenFOAM/OpenFOAM-%(version_major)s/archive'] sources = ['version-%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2023a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2023a.eb index c4358543285e..4989e318c7cd 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2023a.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2023a.eb @@ -8,6 +8,7 @@ description = """OpenFOAM is a free, open source CFD software package. to solid dynamics and electromagnetics.""" toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'vectorize': False} source_urls = ['https://github.com/OpenFOAM/OpenFOAM-%(version_major)s/archive'] sources = ['version-%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-11-foss-2022a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-11-foss-2022a.eb index 9481f562349b..e4abfa2f3e21 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-11-foss-2022a.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-11-foss-2022a.eb @@ -8,6 +8,7 @@ description = """OpenFOAM is a free, open source CFD software package. to solid dynamics and electromagnetics.""" toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'vectorize': False} source_urls = ['https://github.com/OpenFOAM/OpenFOAM-%(version_major)s/archive'] sources = ['version-%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-11-foss-2023a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-11-foss-2023a.eb index 1ce1045701de..c2cabe755a31 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-11-foss-2023a.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-11-foss-2023a.eb @@ -8,6 +8,7 @@ description = """OpenFOAM is a free, open source CFD software package. to solid dynamics and electromagnetics.""" toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'vectorize': False} source_urls = ['https://github.com/OpenFOAM/OpenFOAM-%(version_major)s/archive'] sources = ['version-%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-12-ThirdParty.patch b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-12-ThirdParty.patch new file mode 100644 index 000000000000..e8a0b33adf76 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-12-ThirdParty.patch @@ -0,0 +1,397 @@ +# This patch removes all need for the ThirdParty files of OpenFOAM: +# we use EB dependencies for everything. It adjusts the paths, variables, etc +# We also let the install dir, compiler, etc be set by EB. +# Aligned hunks by Leon Kos and updated by Simon Branford (University of Birmingham). +# Based on patch for OpenFOAM 5.0 and 4.1 by Kenneth Hoste (HPC-UGent) and Ward Poelmans + +diff -ru OpenFOAM-12-version-12/applications/utilities/postProcessing/graphics/PVReaders/Allwmake OpenFOAM-12/applications/utilities/postProcessing/graphics/PVReaders/Allwmake +--- OpenFOAM-12-version-12/applications/utilities/postProcessing/graphics/PVReaders/Allwmake ++++ OpenFOAM-12/applications/utilities/postProcessing/graphics/PVReaders/Allwmake +@@ -11,8 +11,8 @@ + fi + + # Ensure CMake gets the correct C/C++ compilers +-[ -n "$WM_CC" ] && export CC="$WM_CC" +-[ -n "$WM_CXX" ] && export CXX="$WM_CXX" ++#[ -n "$WM_CC" ] && export CC="$WM_CC" ++#[ -n "$WM_CXX" ] && export CXX="$WM_CXX" + + wmake $targetType vtkPVblockMesh + wmake $targetType vtkPVFoam +diff -ru OpenFOAM-12-version-12/applications/utilities/postProcessing/graphics/PVReaders/CMakeLists.txt OpenFOAM-12/applications/utilities/postProcessing/graphics/PVReaders/CMakeLists.txt +--- OpenFOAM-12-version-12/applications/utilities/postProcessing/graphics/PVReaders/CMakeLists.txt ++++ OpenFOAM-12/applications/utilities/postProcessing/graphics/PVReaders/CMakeLists.txt +@@ -2,6 +2,8 @@ + + PROJECT(PVReaders) + ++FIND_PACKAGE(MPI REQUIRED) ++ + FIND_PACKAGE(ParaView REQUIRED) + + INCLUDE(GNUInstallDirs) +diff -ru OpenFOAM-12-version-12/etc/bashrc OpenFOAM-12/etc/bashrc +--- OpenFOAM-12-version-12/etc/bashrc ++++ OpenFOAM-12/etc/bashrc +@@ -43,12 +43,13 @@ + # + [ "$BASH" ] && bashrcFile=${BASH_SOURCE} + [ "$ZSH_NAME" ] && bashrcFile=$0 +-if [ -n "$bashrcFile" ] +-then +- export FOAM_INST_DIR=$(cd $(dirname $bashrcFile)/../.. && pwd -P) +-else +- export FOAM_INST_DIR=$HOME/$WM_PROJECT +-fi ++#if [ -n "$bashrcFile" ] ++#then ++# export FOAM_INST_DIR=$(cd $(dirname $bashrcFile)/../.. && pwd -P) ++#else ++# export FOAM_INST_DIR=$HOME/$WM_PROJECT ++#fi ++# For Easybuild: set by the module + unset bashrcFile + # + # Please set to the appropriate path if the above default is not correct. E.g., +diff -ru OpenFOAM-12-version-12/etc/config.sh/gperftools OpenFOAM-12/etc/config.sh/gperftools +--- OpenFOAM-12-version-12/etc/config.sh/gperftools ++++ OpenFOAM-12/etc/config.sh/gperftools +@@ -29,13 +29,7 @@ + # + #------------------------------------------------------------------------------ + +-version=svn +-gperftools_install=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER +- +-GPERFTOOLS_VERSION=gperftools-$version +-GPERFTOOLS_ARCH_PATH=$gperftools_install/$GPERFTOOLS_VERSION +- +-export PATH=$GPERFTOOLS_ARCH_PATH/bin:$PATH +-export LD_LIBRARY_PATH=$GPERFTOOLS_ARCH_PATH/lib:$LD_LIBRARY_PATH ++GPERFTOOLS_VERSION=gperftools-$EBVERSIONGPERFTOOLS ++GPERFTOOLS_ARCH_PATH=$EBROOTGPERFTOOLS + + #------------------------------------------------------------------------------ +diff -ru OpenFOAM-12-version-12/etc/config.sh/metis OpenFOAM-12/etc/config.sh/metis +--- OpenFOAM-12-version-12/etc/config.sh/metis ++++ OpenFOAM-12/etc/config.sh/metis +@@ -37,32 +37,8 @@ + # Load functions + . $WM_PROJECT_DIR/etc/config.sh/functions + +-# Find the path to the metis installation +-case "$METIS_TYPE" in +-none) +- ;; +-system) +- export METIS_VERSION=system +- export METIS_ARCH_PATH=/usr +- ;; +-OpenFOAM | ThirdParty) +- # Look for the source directory +- if [ -z "$METIS_VERSION" ] +- then +- metisSrcDir=$(_foamMostRecentDir "$WM_THIRD_PARTY_DIR"/metis-*) +- else +- metisSrcDir=$WM_THIRD_PARTY_DIR/metis-$METIS_VERSION +- fi +- # Set the version and the installation path +- if [ -d "$metisSrcDir" ] +- then +- export METIS_VERSION=${metisSrcDir##*metis-} +- export METIS_ARCH_PATH=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER$WM_PRECISION_OPTION$WM_LABEL_OPTION/metis-$METIS_VERSION +- fi +- # Clean up +- unset metisSrcDir +- ;; +-esac ++export METIS_VERSION=metis-$EBVERSIONMETIS ++export METIS_ARCH_PATH=$EBROOTMETIS + + # Unload functions + . $WM_PROJECT_DIR/etc/config.sh/functions +diff -ru OpenFOAM-12-version-12/etc/config.sh/mpi OpenFOAM-12/etc/config.sh/mpi +--- OpenFOAM-12-version-12/etc/config.sh/mpi ++++ OpenFOAM-12/etc/config.sh/mpi +@@ -254,6 +254,9 @@ + _foamAddPath $MPI_ARCH_PATH/bin64 + _foamAddLib $MPI_ARCH_PATH/lib/release + ;; ++EASYBUILDMPI) ++ export FOAM_MPI=mpi ++ ;; + *) + export FOAM_MPI=dummy + ;; +diff -ru OpenFOAM-12-version-12/etc/config.sh/paraview OpenFOAM-12/etc/config.sh/paraview +--- OpenFOAM-12-version-12/etc/config.sh/paraview ++++ OpenFOAM-12/etc/config.sh/paraview +@@ -38,117 +38,13 @@ + ) \ + && PATH="$cleaned" + +-# Detect the most recent version of cmake available and add to the PATH +-cmakeDir=$(_foamMostRecentDir "$WM_THIRD_PARTY_DIR"/platforms/$WM_ARCH$WM_COMPILER/cmake-*) +-if [ -n "$cmakeDir" ] +-then +- export PATH=$cmakeDir/bin:$PATH +-fi +-unset cmakeDir +- +-# Set up the paraview environment +-case "$ParaView_TYPE" in +-none) +- ;; +- +-system) +- +- # Look for a paraview installation +- if pvserverExe=$(which pvserver 2> /dev/null) +- then +- paraviewBinDir=$(dirname $pvserverExe) +- paraviewBinDir=$(cd $paraviewBinDir && pwd -P) +- fi +- +- # Set the environment +- if [ -d "$paraviewBinDir" ] +- then +- export ParaView_DIR=$(dirname $paraviewBinDir) +- export ParaView_LIB_DIR=$(unset LD_LIBRARY_PATH && \ +- ldd $paraviewBinDir/paraview | \ +- grep -o "/.*/libpqCore-pv.*.so" | \ +- xargs dirname) +- export ParaView_VERSION=$(unset LD_LIBRARY_PATH && \ +- pvserver --version 2> /dev/null | \ +- awk '{print $NF}') +- export ParaView_MAJOR=${ParaView_VERSION%.*} +- export ParaView_INCLUDE_DIR=$ParaView_DIR/include/paraview-$ParaView_MAJOR +- export PV_PLUGIN_PATH=$FOAM_LIBBIN/paraview-$ParaView_MAJOR +- +- # Add to the library path +- export LD_LIBRARY_PATH=$ParaView_LIB_DIR:$PV_PLUGIN_PATH:$LD_LIBRARY_PATH +- fi +- +- unset pvserverExe paraviewBinDir +- ;; +- +-paraviewopenfoam) +- +- # Look for a paraview installation. The version should be set externally. +- if [ -n "$ParaView_VERSION" ] +- then +- export ParaView_MAJOR=${ParaView_VERSION%.*} +- paraviewDir=/opt/paraviewopenfoam$(echo "$ParaView_MAJOR" | tr -d '.') +- fi +- +- # Set the environment +- if [ -d "$paraviewDir" ] +- then +- export ParaView_DIR=$paraviewDir +- export ParaView_LIB_DIR=$(echo "$ParaView_DIR"/lib* | tr ' ' ':') +- export ParaView_INCLUDE_DIR=$ParaView_DIR/include/paraview-$ParaView_MAJOR +- export PV_PLUGIN_PATH=$FOAM_LIBBIN/paraview-$ParaView_MAJOR +- +- # Add to the path and the library path +- export PATH=$ParaView_DIR/bin:$PATH +- export LD_LIBRARY_PATH=$ParaView_LIB_DIR:$PV_PLUGIN_PATH:$LD_LIBRARY_PATH +- fi +- +- unset paraviewDir +- ;; +- +-OpenFOAM | ThirdParty) +- +- # Look for a paraview installation +- if [ -z "$ParaView_VERSION" ] +- then +- paraviewDir=$(_foamMostRecentDir "$WM_THIRD_PARTY_DIR"/platforms/$WM_ARCH$WM_COMPILER/ParaView-*) +- else +- paraviewDir=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/ParaView-$ParaView_VERSION +- fi +- +- # Set the environment +- if [ -d "$paraviewDir" ] +- then +- export ParaView_DIR=$paraviewDir +- export ParaView_LIB_DIR=$(echo "$ParaView_DIR"/lib* | tr ' ' ':') +- export ParaView_VERSION=${paraviewDir##*ParaView-} +- export ParaView_MAJOR=${ParaView_VERSION%.*} +- export ParaView_INCLUDE_DIR=$paraviewDir/include/paraview-$ParaView_MAJOR +- export PV_PLUGIN_PATH=$FOAM_LIBBIN/paraview-$ParaView_MAJOR +- +- # Add to the path and the library path +- export PATH=$ParaView_DIR/bin:$PATH +- export LD_LIBRARY_PATH=$ParaView_LIB_DIR:$PV_PLUGIN_PATH:$LD_LIBRARY_PATH +- +- # Add in python libraries if required +- paraviewPython=$ParaView_DIR/Utilities/VTKPythonWrapping +- if [ -r "$paraviewPython" ] +- then +- if [ "$PYTHONPATH" ] +- then +- export PYTHONPATH=$PYTHONPATH:$paraviewPython:$ParaView_LIB_DIR +- else +- export PYTHONPATH=$paraviewPython:$ParaView_LIB_DIR +- fi +- fi +- unset paraviewPython +- fi +- +- unset paraviewDir +- ;; +- +-esac ++export ParaView_VERSION=$EBVERSIONPARAVIEW ++export ParaView_MAJOR=${ParaView_VERSION%.*} ++export ParaView_DIR=$EBROOTPARAVIEW ++export ParaView_LIB_DIR=$ParaView_DIR/lib ++export ParaView_INCLUDE_DIR=$ParaView_DIR/include/paraview-$ParaView_MAJOR ++export PV_PLUGIN_PATH=$FOAM_LIBBIN/paraview-$ParaView_MAJOR ++export LD_LIBRARY_PATH=$ParaView_LIB_DIR:$PV_PLUGIN_PATH:$LD_LIBRARY_PATH + + # Report + if [ "$FOAM_VERBOSE" ] && [ "$PS1" ] && [ -d "$ParaView_DIR" ] +diff -ru OpenFOAM-12-version-12/etc/config.sh/scotch OpenFOAM-12/etc/config.sh/scotch +--- OpenFOAM-12-version-12/etc/config.sh/scotch ++++ OpenFOAM-12/etc/config.sh/scotch +@@ -37,32 +37,8 @@ + # Load functions + . $WM_PROJECT_DIR/etc/config.sh/functions + +-# Find the path to the scotch installation +-case "$SCOTCH_TYPE" in +-none) +- ;; +-system) +- export SCOTCH_VERSION=system +- export SCOTCH_ARCH_PATH=/usr +- ;; +-OpenFOAM | ThirdParty) +- # Look for the source directory +- if [ -z "$SCOTCH_VERSION" ] +- then +- scotchSrcDir=$(_foamMostRecentDir "$WM_THIRD_PARTY_DIR"/scotch_*) +- else +- scotchSrcDir=$WM_THIRD_PARTY_DIR/scotch_$SCOTCH_VERSION +- fi +- # Set the version and the installation path +- if [ -d "$scotchSrcDir" ] +- then +- export SCOTCH_VERSION=${scotchSrcDir##*scotch_} +- export SCOTCH_ARCH_PATH=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER$WM_PRECISION_OPTION$WM_LABEL_OPTION/scotch_$SCOTCH_VERSION +- fi +- # Clean up +- unset scotchSrcDir +- ;; +-esac ++export SCOTCH_VERSION=scotch_$EBVERSIONSCOTCH ++export SCOTCH_ARCH_PATH=$EBROOTSCOTCH + + # Unload functions + . $WM_PROJECT_DIR/etc/config.sh/functions +diff -ru OpenFOAM-12-version-12/etc/config.sh/zoltan OpenFOAM-12/etc/config.sh/zoltan +--- OpenFOAM-12-version-12/etc/config.sh/zoltan ++++ OpenFOAM-12/etc/config.sh/zoltan +@@ -37,32 +37,8 @@ + # Load functions + . $WM_PROJECT_DIR/etc/config.sh/functions + +-# Find the path to the zoltan installation +-case "$ZOLTAN_TYPE" in +-none) +- ;; +-system) +- export ZOLTAN_VERSION=system +- export ZOLTAN_ARCH_PATH=/usr +- ;; +-OpenFOAM | ThirdParty) +- # Look for the source directory +- if [ -z "$ZOLTAN_VERSION" ] +- then +- zoltanSrcDir=$(_foamMostRecentDir "$WM_THIRD_PARTY_DIR"/Zoltan-*) +- else +- zoltanSrcDir=$WM_THIRD_PARTY_DIR/Zoltan-$ZOLTAN_VERSION +- fi +- # Set the version and the installation path +- if [ -d "$zoltanSrcDir" ] +- then +- export ZOLTAN_VERSION=${zoltanSrcDir##*Zoltan-} +- export ZOLTAN_ARCH_PATH=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER$WM_PRECISION_OPTION$WM_LABEL_OPTION/Zoltan-$ZOLTAN_VERSION +- fi +- # Clean up +- unset zoltanSrcDir +- ;; +-esac ++export ZOLTAN_VERSION=Zoltan-$EBVERSIONZOLTAN ++export ZOLTAN_ARCH_PATH=$EBROOTZOLTAN + + # Unload functions + . $WM_PROJECT_DIR/etc/config.sh/functions +diff -ru OpenFOAM-12-version-12/etc/config.sh/settings OpenFOAM-12/etc/config.sh/settings +--- OpenFOAM-12-version-12/etc/config.sh/settings ++++ OpenFOAM-12/etc/config.sh/settings +@@ -63,11 +63,11 @@ + 64) + WM_ARCH=linux64 + export WM_COMPILER_LIB_ARCH=64 +- export WM_CC='gcc' +- export WM_CXX='g++' +- export WM_CFLAGS='-m64 -fPIC' +- export WM_CXXFLAGS='-m64 -fPIC -std=c++0x' +- export WM_LDFLAGS='-m64' ++ export WM_CC=$CC ++ export WM_CXX=$CXX ++ export WM_CFLAGS=$CFLAGS ++ export WM_CXXFLAGS=$CXXFLAGS ++ export WM_LDFLAGS=$LDFLAGS + ;; + *) + echo "Unknown WM_ARCH_OPTION '$WM_ARCH_OPTION', should be 32 or 64"\ +diff -ru OpenFOAM-12-version-12/src/parallel/decompose/ptscotch/Make/options OpenFOAM-12/src/parallel/decompose/ptscotch/Make/options +--- OpenFOAM-12-version-12/src/parallel/decompose/ptscotch/Make/options ++++ OpenFOAM-12/src/parallel/decompose/ptscotch/Make/options +@@ -6,15 +6,7 @@ + $(PFLAGS) $(PINC) \ + -I$(FOAM_SRC)/Pstream/mpi/lnInclude \ + -I$(SCOTCH_ARCH_PATH)/include/$(FOAM_MPI) \ +- -I$(SCOTCH_ARCH_PATH)/include \ +- -I$(or $(PTSCOTCH_INCLUDE_DIR),/usr/include/scotch) \ + -I../decompositionMethods/lnInclude + + LIB_LIBS = \ +- -L$(SCOTCH_ARCH_PATH)/lib \ +- $(if $(PTSCOTCH_LIB_DIR),-L$(PTSCOTCH_LIB_DIR)) \ +- -L$(FOAM_EXT_LIBBIN)/$(FOAM_MPI) \ +- -lptscotch \ +- -lptscotcherrexit \ +- -lscotch \ +- -lrt ++ -L$(SCOTCH_ARCH_PATH)/lib -L$(FOAM_EXT_LIBBIN)/$(FOAM_MPI) -lptscotch -lptscotcherrexit -lscotch ${LINK_FLAGS} -lrt +diff -ru OpenFOAM-12-version-12/src/parallel/decompose/ptscotch/ptscotch.C OpenFOAM-12/src/parallel/decompose/ptscotch/ptscotch.C +--- OpenFOAM-12-version-12/src/parallel/decompose/ptscotch/ptscotch.C ++++ OpenFOAM-12/src/parallel/decompose/ptscotch/ptscotch.C +@@ -31,10 +31,11 @@ + #include "SubField.H" + #include "PstreamGlobals.H" + ++#include ++#include ++ + extern "C" + { + #include +- #include +- #include "ptscotch.h" + } + +diff -ru OpenFOAM-12-version-12/src/parallel/decompose/scotch/Make/options OpenFOAM-12/src/parallel/decompose/scotch/Make/options +--- OpenFOAM-12-version-12/src/parallel/decompose/scotch/Make/options ++++ OpenFOAM-12/src/parallel/decompose/scotch/Make/options +@@ -6,7 +6,6 @@ + EXE_INC = \ + $(PFLAGS) $(PINC) \ + -I$(SCOTCH_ARCH_PATH)/include \ +- -I$(or $(SCOTCH_INCLUDE_DIR),/usr/include/scotch) \ + -I../decompositionMethods/lnInclude + + LIB_LIBS = \ diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-12-foss-2023a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-12-foss-2023a.eb new file mode 100644 index 000000000000..ed565315859a --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-12-foss-2023a.eb @@ -0,0 +1,38 @@ +name = 'OpenFOAM' +version = '12' + +homepage = 'https://www.openfoam.org/' +description = """OpenFOAM is a free, open source CFD software package. + OpenFOAM has an extensive range of features to solve anything from complex fluid flows + involving chemical reactions, turbulence and heat transfer, + to solid dynamics and electromagnetics.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'vectorize': False} + +source_urls = ['https://github.com/OpenFOAM/OpenFOAM-%(version_major)s/archive'] +sources = ['version-%(version)s.tar.gz'] +patches = ['OpenFOAM-12-ThirdParty.patch'] +checksums = [ + {'version-12.tar.gz': 'e59fad54c62e64f1bb89dbaebe5f99a76dc0a6a91d9aad86042a7c4cef6d0744'}, + {'OpenFOAM-12-ThirdParty.patch': 'b8a9abf3b8479d32d87654d833501f54abe57ceb9f06f7d2412a3e52d20108ec'}, +] + +builddependencies = [ + ('Bison', '3.8.2'), + ('CMake', '3.26.3'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('ncurses', '6.4'), + # OpenFOAM requires 64 bit METIS using 32 bit indexes (array indexes) + ('METIS', '5.1.0'), + ('SCOTCH', '7.0.3'), + ('CGAL', '5.6'), + ('ParaView', '5.11.2'), + ('gnuplot', '5.4.8'), + ('Zoltan', '3.901'), +] + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2306-foss-2022b.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2306-foss-2022b.eb index f43803749296..02ee224e98b9 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2306-foss-2022b.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2306-foss-2022b.eb @@ -30,6 +30,8 @@ builddependencies = [ ('CMake', '3.24.3'), ('flex', '2.6.4'), ('CGAL', '5.5.2'), # header only + ('GMP', '6.2.1'), + ('MPFR', '4.2.0'), ] dependencies = [ diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2312-foss-2023a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2312-foss-2023a.eb index bc5f33912b5f..b7f522ba479f 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2312-foss-2023a.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2312-foss-2023a.eb @@ -39,6 +39,8 @@ dependencies = [ ('SCOTCH', '7.0.3'), ('KaHIP', '3.16'), ('CGAL', '5.6'), + ('GMP', '6.2.1'), + ('MPFR', '4.2.0'), ('ParaView', '5.11.2'), ('gnuplot', '5.4.8'), ] diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2406-cleanup.patch b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2406-cleanup.patch new file mode 100644 index 000000000000..ac5229788c51 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2406-cleanup.patch @@ -0,0 +1,182 @@ +# Replaces OpenFOAM third-party libraries with EASYBUILD variants. +# Uses the OpenFOAM prefs mechanism and the FOAM_CONFIG_ETC variable +# to define the preferred settings without patching the original files +# +# Authors: Mark Olesen +# +# ChangeLog: +# - v2312 - activate METIS, KaHIP and readline support in etc/config.sh/setup +# author: Jiri Furst +# - v2406 - set MPFR_ARCH_PATH and GMP_ARCH_PATH to CGAL config +# author: Jiri Furst +# +# ------------------------------------------------------------------------- +--- /dev/null 2020-12-14 09:05:45.272769166 +0100 ++++ OpenFOAM-v2012/etc/prefs.sh 2020-12-14 10:02:26.488430802 +0100 +@@ -0,0 +1,7 @@ ++##Easybuild## settings -*- sh -*- ++ ++export FOAM_CONFIG_ETC="etc/easybuild" ++ ++export WM_MPLIB=EASYBUILDMPI ++ ++##Easybuild## +--- /dev/null 2020-12-14 09:05:45.272769166 +0100 ++++ OpenFOAM-v2012/etc/easybuild/config.sh/CGAL 2020-12-14 10:10:55.991841204 +0100 +@@ -0,0 +1,8 @@ ++##Easybuild## settings -*- sh -*- ++ ++export MPFR_ARCH_PATH="$EBROOTMPFR" ++export GMP_ARCH_PATH="$EBROOTGMP" ++export BOOST_ARCH_PATH="$EBROOTBOOST" ++export CGAL_ARCH_PATH="$EBROOTCGAL" ++ ++##Easybuild## +--- /dev/null 2020-12-14 09:05:45.272769166 +0100 ++++ OpenFOAM-v2012/etc/easybuild/config.sh/FFTW 2020-12-14 10:10:53.735843322 +0100 +@@ -0,0 +1,5 @@ ++##Easybuild## settings -*- sh -*- ++ ++export FFTW_ARCH_PATH="$EBROOTFFTW" ++ ++##EasyBuild## +--- /dev/null 2020-12-14 09:05:45.272769166 +0100 ++++ OpenFOAM-v2012/etc/easybuild/config.sh/metis 2020-12-11 21:23:28.774934024 +0100 +@@ -0,0 +1,6 @@ ++##Easybuild## settings -*- sh -*- ++ ++METIS_VERSION="metis-$EBVERSIONMETIS" ++[ -d "$METIS_ARCH_PATH" ] || METIS_ARCH_PATH="$EBROOTMETIS" ++ ++##Easybuild## +--- /dev/null 2022-12-01 18:21:35.103878336 +0100 ++++ OpenFOAM-v2206/etc/easybuild/config.sh/kahip 2022-12-12 20:24:07.538408981 +0100 +@@ -0,0 +1,6 @@ ++##Easybuild## settings -*- sh -*- ++ ++KAHIP_VERSION="kahip-$EBVERSIONKAHIP" ++export KAHIP_ARCH_PATH="$EBROOTKAHIP" ++ ++##Easybuild## +--- /dev/null 2020-12-14 09:05:45.272769166 +0100 ++++ OpenFOAM-v2012/etc/easybuild/config.sh/readline 2020-12-11 21:23:22.534951043 +0100 +@@ -0,0 +1,5 @@ ++##Easybuild## settings -*- sh -*- ++ ++export READLINE_ARCH_PATH="$EBROOTLIBREADLINE" ++ ++##Easybuild## +--- /dev/null 2020-12-14 09:05:45.272769166 +0100 ++++ OpenFOAM-v2012/etc/easybuild/config.sh/scotch 2020-12-11 21:23:17.586964539 +0100 +@@ -0,0 +1,7 @@ ++##Easybuild## settings -*- sh -*- ++ ++export SCOTCH_VERSION="scotch_$EBVERSIONSCOTCH" ++export SCOTCH_ARCH_PATH="$EBROOTSCOTCH" ++[ -d "$SCOTCH_ARCH_PATH" ] || SCOTCH_ARCH_PATH="$SCOTCH_ROOT" ++ ++##Easybuild## +--- /dev/null 2020-12-14 09:05:45.272769166 +0100 ++++ OpenFOAM-v2012/etc/easybuild/config.sh/vtk 2020-12-11 21:22:55.463024882 +0100 +@@ -0,0 +1,9 @@ ++##Easybuild## settings -*- sh -*- ++ ++export VTK_DIR="$EBROOTVTK" ++export MESA_ARCH_PATH="$EBROOTMESA" ++ ++# Define paraview-mesa directory as required ++unset ParaView_MESA_DIR ++ ++##Easybuild## +--- /dev/null 2020-12-14 09:05:45.272769166 +0100 ++++ OpenFOAM-v2012/etc/easybuild/config.sh/paraview 2020-12-14 10:13:53.583674383 +0100 +@@ -0,0 +1,75 @@ ++##Easybuild## settings -*- sh -*- ++# ++# Largely a knockoff of the OpenFOAM etc/config.sh/paraview-system ++# readjusted for easybuild ++# ++# Copyright (C) 2020 OpenCFD Ltd. ++# ++#------------------------------------------------------------------------------ ++# Compiler-specific location for ThirdParty installations ++archDir="$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER" ++ ++# Clean path and library path of previous settings ++eval \ ++ "$($WM_PROJECT_DIR/bin/foamCleanPath -sh-env=PATH \ ++ $ParaView_DIR $archDir/ParaView- $archDir/qt-)" ++ ++eval \ ++ "$($WM_PROJECT_DIR/bin/foamCleanPath -sh-env=LD_LIBRARY_PATH \ ++ $ParaView_DIR $archDir/ParaView- $archDir/qt-)" ++ ++ ++#------------------------------------------------------------------------------ ++ ++##Easybuild## settings ++ ++ParaView_VERSION="$EBVERSIONPARAVIEW" ++export ParaView_DIR="$EBROOTPARAVIEW" ++ ++#------------------------------------------------------------------------------ ++ ++unset PV_PLUGIN_PATH ++ ++# Set API to correspond to VERSION ++# pv_api is . from ParaView_VERSION ++#- ++# Extract API from VERSION ++pv_api=$(echo "$ParaView_VERSION" | \ ++ sed -ne 's/^[^0-9]*\([0-9][0-9]*\.[0-9][0-9]*\).*$/\1/p') ++ ++pv_plugin_dir="$FOAM_LIBBIN/paraview-$pv_api" ++ ++# Set paths if binaries are present ++if [ -r "$ParaView_DIR" ] ++then ++ export PATH="$ParaView_DIR/bin:$PATH" ++ ++ # ParaView libraries ++ # - 5.5 and later: lib/, but could also be lib64/ ++ for libDir in lib64 lib ++ do ++ pvLibDir="$libDir/paraview-$pv_api" ++ if [ -d "$ParaView_DIR/$pvLibDir" ] ++ then ++ export LD_LIBRARY_PATH="$ParaView_DIR/$libDir:$LD_LIBRARY_PATH" ++ break ++ fi ++ done ++ ++ # OpenFOAM plugin directory must be the first in PV_PLUGIN_PATH ++ # and have paraview-major.minor encoded in its name ++ if [ -d "$pv_plugin_dir" ] ++ then ++ export PV_PLUGIN_PATH="$pv_plugin_dir" ++ fi ++fi ++ ++ ++#------------------------------------------------------------------------------ ++ ++unset ParaView_VERSION ++ ++unset archDir libDir ++unset pv_api pv_plugin_dir pvLibDir ++ ++#------------------------------------------------------------------------------ +--- OpenFOAM-v2312/etc/config.sh/setup.orig 2024-01-11 09:49:24.823571481 +0100 ++++ OpenFOAM-v2312/etc/config.sh/setup 2024-01-11 09:51:40.545969774 +0100 +@@ -207,7 +207,9 @@ + _foamEtc -config CGAL + _foamEtc -config scotch + _foamEtc -config FFTW +- ++_foamEtc -config metis ++_foamEtc -config kahip ++_foamEtc -config readline + + # Finalize library paths + # ~~~~~~~~~~~~~~~~~~~~~~ + diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2406-foss-2023a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2406-foss-2023a.eb new file mode 100644 index 000000000000..0e2885c064fc --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2406-foss-2023a.eb @@ -0,0 +1,55 @@ +name = 'OpenFOAM' +version = 'v2406' + +homepage = 'https://www.openfoam.com/' +description = """OpenFOAM is a free, open source CFD software package. + OpenFOAM has an extensive range of features to solve anything from complex fluid flows + involving chemical reactions, turbulence and heat transfer, + to solid dynamics and electromagnetics.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +# Users have found that vectorizion caused OpenFOAM to produce some very incorrect results. +# Disabling vectorize was confirmed to fix the the known issues. +# With no test suite, sticking to known working toolchain options until proven otherwise. +toolchainopts = {'cstd': 'c++14', 'vectorize': False} + +source_urls = ['https://sourceforge.net/projects/openfoam/files/%(version)s/'] +sources = [ + SOURCE_TGZ, + { + 'filename': '%(name)s-plugins-%(version)s.tgz', + 'extract_cmd': 'tar --strip-components=1 -C %(installdir)s/%(name)s-%(version)s/ -xzf %s' + } +] +patches = [ + ('OpenFOAM-v2406-cleanup.patch', 1), + ('OpenFOAM-v2212-wmake-OpenMPI.patch', 1), +] +checksums = [ + {'OpenFOAM-v2406.tgz': '8d1450fb89eec1e7cecc55c3bb7bc486ccbf63d069379d1d5d7518fa16a4686a'}, + {'OpenFOAM-plugins-v2406.tgz': '1d008f86fad06a4a568d194c6e3d5ab52be2b20c83a3b9b1b0230e2de2d0558b'}, + {'OpenFOAM-v2406-cleanup.patch': '3abff48a517fb63719ad57fa32af746bc379a1e80c72d3e5852aa17cd13cf03e'}, + {'OpenFOAM-v2212-wmake-OpenMPI.patch': '241dc4898c22aab0cbd10c1ea931a07a786508ee03462d45dbc1c202fee3ebe8'}, +] + +builddependencies = [ + ('Bison', '3.8.2'), + ('CMake', '3.26.3'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('libreadline', '8.2'), + ('ncurses', '6.4'), + # OpenFOAM requires 64 bit METIS using 32 bit indexes (array indexes) + ('METIS', '5.1.0'), + ('SCOTCH', '7.0.3'), + ('KaHIP', '3.16'), + ('CGAL', '5.6'), + ('GMP', '6.2.1'), + ('MPFR', '4.2.0'), + ('ParaView', '5.11.2'), + ('gnuplot', '5.4.8'), +] + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/o/OpenForceField-Toolkit/OpenForceField-Toolkit-0.16.0-foss-2023a.eb b/easybuild/easyconfigs/o/OpenForceField-Toolkit/OpenForceField-Toolkit-0.16.0-foss-2023a.eb new file mode 100644 index 000000000000..f323c61f0657 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenForceField-Toolkit/OpenForceField-Toolkit-0.16.0-foss-2023a.eb @@ -0,0 +1,144 @@ +easyblock = 'PythonBundle' + +name = 'OpenForceField-Toolkit' +version = '0.16.0' + +homepage = 'https://github.com/openforcefield/openff-toolkit' +description = """The Open Force Field Toolkit provides implementations of the SMIRNOFF format, +parameterization engine, and other tools.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [('poetry', '1.5.1')] +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('networkx', '3.1'), + ('typing-extensions', '4.9.0'), + ('pydantic', '2.5.3'), + ('tqdm', '4.66.1'), + ('OpenMM', '8.0.0'), + ('PyYAML', '6.0'), + ('RDKit', '2024.03.3'), + ('MDTraj', '1.9.9'), + ('JupyterNotebook', '7.0.2'), + ('AmberTools', '23.6'), + ('Pint', '0.23'), + ('nglview', '3.1.2'), +] + +use_pip = True + +exts_list = [ + ('qcelemental', '0.26.0', { + 'checksums': ['a14e8510cdbfda645ef1461c1afd02efb599311733dbba5f83fcd1d6168a6ddd'], + }), + ('PyJWT', '2.8.0', { + 'modulename': 'jwt', + 'checksums': ['57e28d156e3d5c10088e0c68abb90bfac3df82b40a71bd0daa20c65ccd5c23de'], + }), + ('apsw', '3.46.0.0', { + 'checksums': ['e128ccaab511f9a7fc48be6414f99a9197f83a69624d8ba40c1ca241bdef418e'], + }), + ('zstandard', '0.18.0', { + 'checksums': ['0ac0357a0d985b4ff31a854744040d7b5754385d1f98f7145c30e02c6865cb6f'], + }), + ('qcportal', '0.55', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['f6eb86d6ace4ae6a71bbd8e2ee054305aff2c1da0198a3741b0d589c572a31b3'], + }), + ('cached-property', '1.5.2', { + 'checksums': ['9fa5755838eecbb2d234c3aa390bd80fbd3ac6b6869109bfc1b499f7bd89a130'], + }), + ('cachetools', '5.3.3', { + 'checksums': ['ba29e2dfa0b8b556606f097407ed1aa62080ee108ab0dc5ec9d6a723a007d105'], + }), + ('python-constraint', '1.4.0', { + 'modulename': 'constraint', + 'source_tmpl': '%(name)s-%(version)s.tar.bz2', + 'checksums': ['501d6f17afe0032dfc6ea6c0f8acc12e44f992733f00e8538961031ef27ccb8e'], + }), + ('bson', '0.5.10', { + 'checksums': ['d6511b2ab051139a9123c184de1a04227262173ad593429d21e443d6462d6590'], + }), + ('xmltodict', '0.13.0', { + 'checksums': ['341595a488e3e01a85a9d8911d8912fd922ede5fecc4dce437eb4b6c8d037e56'], + }), + ('intermol', '0.1.2', { + 'source_urls': ['https://github.com/shirtsgroup/InterMol/archive/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['a3065133ba16585a5db3807466a36242d191156525c33079cf46a97cedcfe835'], + }), + ('SMIRNOFF99Frosst', '1.1.0', { + 'source_urls': ['https://github.com/openforcefield/smirnoff99Frosst/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['940c4ed3cd720e746549a3335f10b7b0d9047a67bc216ad45dd875be5c8ec467'], + }), + ('SMIRNOFF-Plugins', '2024.01.0', { + 'source_urls': ['https://github.com/openforcefield/smirnoff-plugins/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['8ba4dbc6ed320f06f30bf42e8f70399bc3818becd668990693b51ddca183ff74'], + }), + ('OpenForceField-ForceFields', '2024.04.0', { + 'modulename': 'openforcefields', + 'source_urls': ['https://github.com/openforcefield/openff-forcefields/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['fc7094cdb74bf9f0ed665dfc716cc62c5a37def3fc7e852adeae0ae4b60169c7'], + }), + ('OpenForceField-Amber-FF-Ports', '0.0.4', { + 'modulename': 'openff.amber_ff_ports', + 'source_urls': ['https://github.com/openforcefield/openff-amber-ff-ports/archive/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['dbf2d1ccce06b0627b1eccae7e227ad800ff1cbac3e869344de265b178cc0207'], + }), + ('OpenForceField-Utilities', '0.1.12', { + 'modulename': 'openff.utilities', + 'source_urls': ['https://github.com/openforcefield/openff-utilities/archive/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['92882c5b87b40bdb4ee1e8c84c0ecc0fc83f26eaf3e3befde41bfdcf93d75dea'], + }), + ('OpenForceField-Units', '0.2.2', { + 'modulename': 'openff.units', + 'source_urls': ['https://github.com/openforcefield/openff-units/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['532746534c1937938580d5cfe98f414aff9bfbcc66970e115a88a38f6d5a2581'], + }), + ('OpenForceField-NAGL-Models', '0.2.0', { + 'modulename': 'openff.nagl_models', + 'source_urls': ['https://github.com/openforcefield/openff-nagl-models/archive/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['5ccc55d7f0fcd24577796fd8b2bfd85b035ee8060e441c1f7dfc6f1949b9dee5'], + }), + ('OpenForceField-Models', '0.1.2', { + 'modulename': 'openff.models', + 'source_urls': ['https://github.com/openforcefield/openff-models/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['cf2aa7ef467721f141149e4ce96134db390b27012f09996c4442a3fad2371653'], + }), + ('OpenForceField-Interchange', '0.3.27', { + 'modulename': 'openff.interchange', + 'source_urls': ['https://github.com/openforcefield/openff-interchange/archive/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['6b44ba8a89921b3843a5f9fc41dc4f8a0c784ba12221e3ea0fb8c1b01a10cf2e'], + }), + (name, version, { + 'modulename': 'openff.toolkit', + 'source_urls': ['https://github.com/openforcefield/openff-toolkit/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['70a81e914e86efd933819a5db05fc4400dcd23e12ad29398fdad46f2765b5634'], + }), +] + +sanity_check_commands = [ + "python -c 'from openff.toolkit import Molecule, Topology, ForceField'", + "python -c 'from openff.interchange import Interchange'", + "python -c 'from openff.units import unit'", + "python -c 'from openff.interchange.components.mdconfig import MDConfig'", + "python -c 'from openff.interchange.models import TopologyKey'", + "python -c 'from openff.toolkit.typing.engines.smirnoff import ForceField'", +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.5.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.5.2-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..8ee5d1477f8d --- /dev/null +++ b/easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.5.2-GCCcore-13.3.0.eb @@ -0,0 +1,42 @@ +easyblock = 'CMakeMake' + +name = 'OpenJPEG' +version = '2.5.2' + +homepage = 'https://www.openjpeg.org/' +description = """OpenJPEG is an open-source JPEG 2000 codec written in + C language. It has been developed in order to promote the use of JPEG 2000, + a still-image compression standard from the Joint Photographic Experts Group + (JPEG). Since may 2015, it is officially recognized by ISO/IEC and ITU-T as + a JPEG 2000 Reference Software.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/uclouvain/%(namelower)s/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['90e3896fed910c376aaf79cdd98bdfdaf98c6472efd8e1debf0a854938cbda6a'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] +# for running the binary of openjpeg like opj_compress you need the libraries like zlib etc. +dependencies = [ + ('zlib', '1.3.1'), + ('libpng', '1.6.43'), + ('LibTIFF', '4.6.0'), +] + +sanity_check_paths = { + 'files': [ + 'bin/opj_compress', + 'bin/opj_decompress', + 'bin/opj_dump', + 'include/openjpeg-%(version_major)s.%(version_minor)s/openjpeg.h', + 'lib/libopenjp2.%s' % SHLIB_EXT + ], + 'dirs': ['bin', 'include', 'lib'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 000000000000..8cf271071e78 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,70 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# Update to 7.5.1 +# J. Sassmannshausen / GSTT + +easyblock = 'CMakeMake' + +name = 'OpenMM' +version = '8.0.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://openmm.org' +description = "OpenMM is a toolkit for molecular simulation." + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'opt': True} + +source_urls = ['https://github.com/openmm/openmm/archive/'] +sources = ['%(version)s.tar.gz'] +patches = ['OpenMM-8.0.0_add_no_tree_vectorize.patch'] +checksums = [ + 'dc63d7b47c8bb7b169c409cfd63d909ed0ce1ae114d37c627bf7a4231acf488e', # 8.0.0.tar.gz + '4bacf45443a2472e59798743f27d07481e065d784cbbea7be22aa6427af0d2bd', # OpenMM-8.0.0_add_no_tree_vectorize.patch +] + +builddependencies = [ + ('CMake', '3.26.3'), + ('Doxygen', '1.9.7'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('SWIG', '4.1.1'), + ('CUDA', '12.1.1', '', SYSTEM), +] + +# Set the OPENMM_CUDA_COMPILER variable to make sure that all tests use the right nvcc, +# Otherwise they will use the wrong path: `/usr/local/cuda/bin/nvcc` +pretestopts = ' export OPENMM_CUDA_COMPILER=${EBROOTCUDA}/bin/nvcc && ' +pretestopts += " CTEST_OUTPUT_ON_FAILURE=1" +# Skip CudaCompiler test as it doesn't work when the OPENMM_CUDA_COMPILER variable is set +local_ignore_pattern = "(Integrator)|(Thermostat)|(Barostat)|(Rpmd)|(Amoeba)|(CudaCompiler)" +runtest = """test -e ARGS="-E \'%s\'" """ % local_ignore_pattern + +preinstallopts = ' export OPENMM_INCLUDE_PATH=%(installdir)s/include && ' +preinstallopts += ' export OPENMM_LIB_PATH=%(installdir)s/lib && ' + +# required to install the python API +installopts = ' && cd python && python setup.py build && python setup.py install --prefix=%(installdir)s' + +sanity_check_paths = { + 'files': ['lib/libOpenMM.%s' % SHLIB_EXT], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +sanity_check_commands = [ + "python -c 'import simtk.openmm'", + "python -m openmm.testInstallation", +] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages/OpenMM-%(version)s-py%(pyshortver)s-linux-%(arch)s.egg', + 'OPENMM_INCLUDE_PATH': 'include', + 'OPENMM_LIB_PATH': 'lib', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-GCC-11.3.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-GCC-11.3.0.eb index 6471a45d999a..06b168671f7c 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-GCC-11.3.0.eb @@ -11,6 +11,7 @@ sources = [SOURCELOWER_TAR_BZ2] patches = [ 'OpenMPI-4.1.1_build-with-internal-cuda-header.patch', 'OpenMPI-4.1.1_opal-datatype-cuda-performance.patch', + 'OpenMPI-4.1.4_fix-implicit-cuda-function-declaration.patch', 'OpenMPI-4.1.x_add_atomic_wmb.patch', ] checksums = [ @@ -19,6 +20,8 @@ checksums = [ '63eac52736bdf7644c480362440a7f1f0ae7c7cae47b7565f5635c41793f8c83'}, {'OpenMPI-4.1.1_opal-datatype-cuda-performance.patch': 'b767c7166cf0b32906132d58de5439c735193c9fd09ec3c5c11db8d5fa68750e'}, + {'OpenMPI-4.1.4_fix-implicit-cuda-function-declaration.patch': + 'ec1c2f07d03574b86fc5fb462eed96eb6f5658deb8a6412cf37007d687a28673'}, {'OpenMPI-4.1.x_add_atomic_wmb.patch': '9494bbc546d661ba5189e44b4c84a7f8df30a87cdb9d96ce2e73a7c8fecba172'}, ] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-GCC-12.2.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-GCC-12.2.0.eb index fbb50478eecd..f4fbe865280a 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-GCC-12.2.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-GCC-12.2.0.eb @@ -11,6 +11,7 @@ sources = [SOURCELOWER_TAR_BZ2] patches = [ 'OpenMPI-4.1.1_build-with-internal-cuda-header.patch', 'OpenMPI-4.1.1_opal-datatype-cuda-performance.patch', + 'OpenMPI-4.1.4_fix-implicit-cuda-function-declaration.patch', 'OpenMPI-4.1.x_add_atomic_wmb.patch', ] checksums = [ @@ -19,6 +20,8 @@ checksums = [ '63eac52736bdf7644c480362440a7f1f0ae7c7cae47b7565f5635c41793f8c83'}, {'OpenMPI-4.1.1_opal-datatype-cuda-performance.patch': 'b767c7166cf0b32906132d58de5439c735193c9fd09ec3c5c11db8d5fa68750e'}, + {'OpenMPI-4.1.4_fix-implicit-cuda-function-declaration.patch': + 'ec1c2f07d03574b86fc5fb462eed96eb6f5658deb8a6412cf37007d687a28673'}, {'OpenMPI-4.1.x_add_atomic_wmb.patch': '9494bbc546d661ba5189e44b4c84a7f8df30a87cdb9d96ce2e73a7c8fecba172'}, ] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-NVHPC-22.7-CUDA-11.7.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-NVHPC-22.7-CUDA-11.7.0.eb index 9ef5b5d1bb40..a69c1e2b8d48 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-NVHPC-22.7-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-NVHPC-22.7-CUDA-11.7.0.eb @@ -11,6 +11,7 @@ sources = [SOURCELOWER_TAR_BZ2] patches = [ 'OpenMPI-4.1.1_build-with-internal-cuda-header.patch', 'OpenMPI-4.1.1_opal-datatype-cuda-performance.patch', + 'OpenMPI-4.1.4_fix-implicit-cuda-function-declaration.patch', 'OpenMPI-4.1.x_add_atomic_wmb.patch', ] checksums = [ @@ -19,6 +20,8 @@ checksums = [ '63eac52736bdf7644c480362440a7f1f0ae7c7cae47b7565f5635c41793f8c83'}, {'OpenMPI-4.1.1_opal-datatype-cuda-performance.patch': 'b767c7166cf0b32906132d58de5439c735193c9fd09ec3c5c11db8d5fa68750e'}, + {'OpenMPI-4.1.4_fix-implicit-cuda-function-declaration.patch': + 'ec1c2f07d03574b86fc5fb462eed96eb6f5658deb8a6412cf37007d687a28673'}, {'OpenMPI-4.1.x_add_atomic_wmb.patch': '9494bbc546d661ba5189e44b4c84a7f8df30a87cdb9d96ce2e73a7c8fecba172'}, ] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4_fix-implicit-cuda-function-declaration.patch b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4_fix-implicit-cuda-function-declaration.patch new file mode 100644 index 000000000000..3ccb7d43d826 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4_fix-implicit-cuda-function-declaration.patch @@ -0,0 +1,31 @@ +Fix a left-over function causing compilation warnings or errors: +mtl_ofi_component.c:298:5: error: implicit declaration of function 'mca_common_cuda_fini'; did you mean 'ompi_comm_cid_init'? [-Werror=implicit-function-declaration] + mca_common_cuda_fini(); + ^~~~~~~~~~~~~~~~~~~~ + +See https://github.com/open-mpi/ompi/issues/11381 + +From 7676618c43d489b145e730d1d7603f0292a031c0 Mon Sep 17 00:00:00 2001 +From: Jingyin Tang +Date: Mon, 6 Feb 2023 13:48:51 -0500 +Subject: [PATCH] Fix compilation issue in OFI with CUDA + +Signed-off-by: Jingyin Tang +--- + ompi/mca/mtl/ofi/mtl_ofi_component.c | 3 --- + 1 file changed, 3 deletions(-) + +diff --git a/ompi/mca/mtl/ofi/mtl_ofi_component.c b/ompi/mca/mtl/ofi/mtl_ofi_component.c +index c1aac6934d0..e36f020b206 100644 +--- a/ompi/mca/mtl/ofi/mtl_ofi_component.c ++++ b/ompi/mca/mtl/ofi/mtl_ofi_component.c +@@ -294,9 +294,6 @@ ompi_mtl_ofi_component_query(mca_base_module_t **module, int *priority) + static int + ompi_mtl_ofi_component_close(void) + { +-#if OPAL_CUDA_SUPPORT +- mca_common_cuda_fini(); +-#endif + return opal_common_ofi_close(); + } + diff --git a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-13.3.0.eb b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..cbf6bca94d7c --- /dev/null +++ b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-13.3.0.eb @@ -0,0 +1,44 @@ +easyblock = 'ConfigureMake' + +name = 'OpenPGM' +version = '5.2.122' + +homepage = 'https://code.google.com/p/openpgm/' +description = """ + OpenPGM is an open source implementation of the Pragmatic General Multicast + (PGM) specification in RFC 3208 available at www.ietf.org. PGM is a reliable + and scalable multicast protocol that enables receivers to detect loss, request + retransmission of lost data, or notify an application of unrecoverable loss. + PGM is a receiver-reliable protocol, which means the receiver is responsible + for ensuring all data is received, absolving the sender of reception + responsibility. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/%(namelower)s/'] +sources = ['libpgm-%(version)s.tar.gz'] +patches = [ + '%(name)s-%(version)s-pkgconfig_includes.patch', + '%(name)s-%(version)s-python3-compliant.patch', +] +checksums = [ + '6b895f550b95284dcde7189b01e04a9a1c1f94579af31b1eebd32c2207a1ba2c', # libpgm-%(version)s.tar.gz + '4a9fc7fbb6e73e325639a895cd19c1ac6918b575f715c057caa01f826de40114', # %(name)s-%(version)s-pkgconfig_includes.patch + 'a3bf6b4127473d287d72767b0335b8705940e56ffbccc8d4d3bdbf23a2fc8618', # %(name)s-%(version)s-python3-compliant.patch +] + +builddependencies = [ + ('binutils', '2.42'), + ('Python', '3.12.3'), +] + +start_dir = 'pgm' + +sanity_check_paths = { + 'files': ['lib/libpgm.%s' % SHLIB_EXT, 'lib/libpgm.a'], + 'dirs': ['include'], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/o/OpenSlide/OpenSlide-3.4.1-GCCcore-12.2.0-largefiles.eb b/easybuild/easyconfigs/o/OpenSlide/OpenSlide-3.4.1-GCCcore-12.2.0-largefiles.eb new file mode 100644 index 000000000000..a8bdbafa429b --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSlide/OpenSlide-3.4.1-GCCcore-12.2.0-largefiles.eb @@ -0,0 +1,56 @@ +easyblock = 'ConfigureMake' + +name = 'OpenSlide' +version = '3.4.1' +versionsuffix = '-largefiles' + +homepage = 'https://openslide.org/' +description = """OpenSlide is a C library that provides a simple interface to +read whole-slide images (also known as virtual slides).""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [GITHUB_SOURCE] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +patches = ['%(name)s-%(version)s_large_file_support.patch'] +checksums = [ + # v3.4.1.tar.gz + 'a5d869916e370125421535dcce778b2ba625dc50d920aa4ca93bbaaa6a7b470c', + # %(name)s-%(version_major_minor)s.1_large_file_support.patch + 'cb618053f4ae6c3ce37d1b8b0e4ef7c55fd17378776d13be4aa4efab91706b8c', +] + +builddependencies = [ + ('Autotools', '20220317'), + ('M4', '1.4.19'), + ('pkgconf', '1.9.3'), + ('binutils', '2.39'), +] + +dependencies = [ + ('zlib', '1.2.12'), + ('libpng', '1.6.38'), + ('libjpeg-turbo', '2.1.4'), + ('LibTIFF', '4.4.0'), + ('OpenJPEG', '2.5.0'), + ('libxml2', '2.10.3'), + ('SQLite', '3.39.4'), + ('cairo', '1.17.4'), + ('Gdk-Pixbuf', '2.42.10'), +] + +preconfigopts = "autoreconf -f -i && " + +sanity_check_paths = { + 'files': [ + 'bin/openslide-quickhash1sum', + 'bin/openslide-show-properties', + 'bin/openslide-write-png', + 'lib/libopenslide.la', + 'lib/libopenslide.%s' % SHLIB_EXT + ], + 'dirs': ['include/openslide'] +} + + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-5.5.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-5.5.0-GCCcore-10.2.0.eb index b013362d2e5d..50dab938d40c 100644 --- a/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-5.5.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-5.5.0-GCCcore-10.2.0.eb @@ -16,9 +16,9 @@ dependencies = [ ] builddependencies = [('binutils', '2.35')] -exts_default_options = { - 'use_pip': True, -} +sanity_pip_check = True +use_pip = True + exts_list = [ ('pbr', '5.6.0', { 'checksums': ['42df03e7797b796625b1029c0400279c7c34fd7df24a7d7818a1abb5b38710dd'], @@ -121,7 +121,6 @@ exts_list = [ }), ] -sanity_pip_check = True enhance_sanity_check = True sanity_check_commands = ['openstack -h'] diff --git a/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-5.8.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-5.8.0-GCCcore-11.2.0.eb index e590dd730ca7..d92bda87180a 100644 --- a/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-5.8.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-5.8.0-GCCcore-11.2.0.eb @@ -16,9 +16,9 @@ dependencies = [ ] builddependencies = [('binutils', '2.37')] -exts_default_options = { - 'use_pip': True, -} +sanity_pip_check = True +use_pip = True + exts_list = [ ('pyperclip', '1.8.2', { 'checksums': ['105254a8b04934f0bc84e9c24eb360a591aaf6535c9def5f29d92af107a9bf57'], @@ -121,7 +121,6 @@ exts_list = [ }), ] -sanity_pip_check = True enhance_sanity_check = True sanity_check_commands = ['openstack -h'] diff --git a/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-6.0.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-6.0.0-GCCcore-12.2.0.eb index 6b695f632798..bdf0b5c45a68 100644 --- a/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-6.0.0-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-6.0.0-GCCcore-12.2.0.eb @@ -15,9 +15,9 @@ dependencies = [ ] builddependencies = [('binutils', '2.39')] -exts_default_options = { - 'use_pip': True, -} +sanity_pip_check = True +use_pip = True + exts_list = [ ('pyperclip', '1.8.2', { 'checksums': ['105254a8b04934f0bc84e9c24eb360a591aaf6535c9def5f29d92af107a9bf57'], @@ -114,7 +114,6 @@ exts_list = [ }), ] -sanity_pip_check = True enhance_sanity_check = True sanity_check_commands = ['openstack -h'] diff --git a/easybuild/easyconfigs/o/Optax/Optax-0.2.2-gfbf-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/o/Optax/Optax-0.2.2-gfbf-2023a-CUDA-12.1.1.eb new file mode 100644 index 000000000000..61000b1388ca --- /dev/null +++ b/easybuild/easyconfigs/o/Optax/Optax-0.2.2-gfbf-2023a-CUDA-12.1.1.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonBundle' + +name = 'Optax' +version = '0.2.2' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/deepmind/optax' +description = """Optax is a gradient processing and optimization library for JAX.""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('jax', '0.4.25', versionsuffix), +] + +use_pip = True + +exts_list = [ + ('toolz', '0.12.1', { + 'checksums': ['ecca342664893f177a13dac0e6b41cbd8ac25a358e5f215316d43e2100224f4d'], + }), + ('chex', '0.1.86', { + 'checksums': ['e8b0f96330eba4144659e1617c0f7a57b161e8cbb021e55c6d5056c7378091d1'], + }), + ('optax', version, { + 'checksums': ['f09bf790ef4b09fb9c35f79a07594c6196a719919985f542dc84b0bf97812e0e'], + }), +] + +sanity_pip_check = True + +sanity_check_commands = ["python -c 'from optax import GradientTransformation'"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/Optax/Optax-0.2.2-gfbf-2023a.eb b/easybuild/easyconfigs/o/Optax/Optax-0.2.2-gfbf-2023a.eb new file mode 100644 index 000000000000..d447a77bbd21 --- /dev/null +++ b/easybuild/easyconfigs/o/Optax/Optax-0.2.2-gfbf-2023a.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonBundle' + +name = 'Optax' +version = '0.2.2' + +homepage = 'https://github.com/deepmind/optax' +description = """Optax is a gradient processing and optimization library for JAX.""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('jax', '0.4.25'), +] + +use_pip = True + +exts_list = [ + ('toolz', '0.12.1', { + 'checksums': ['ecca342664893f177a13dac0e6b41cbd8ac25a358e5f215316d43e2100224f4d'], + }), + ('chex', '0.1.86', { + 'checksums': ['e8b0f96330eba4144659e1617c0f7a57b161e8cbb021e55c6d5056c7378091d1'], + }), + ('optax', version, { + 'checksums': ['f09bf790ef4b09fb9c35f79a07594c6196a719919985f542dc84b0bf97812e0e'], + }), +] + +sanity_pip_check = True + +sanity_check_commands = ["python -c 'from optax import GradientTransformation'"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/Optuna/Optuna-3.6.1-foss-2023b.eb b/easybuild/easyconfigs/o/Optuna/Optuna-3.6.1-foss-2023b.eb new file mode 100644 index 000000000000..35dec40e2343 --- /dev/null +++ b/easybuild/easyconfigs/o/Optuna/Optuna-3.6.1-foss-2023b.eb @@ -0,0 +1,50 @@ +easyblock = 'PythonBundle' + +name = 'Optuna' +version = '3.6.1' + +homepage = "https://optuna.org/" +description = """Optuna is an automatic hyperparameter optimization software framework, +particularly designed for machine learning. It features an imperative, +define-by-run style user API. Thanks to our define-by-run API, the code written +with Optuna enjoys high modularity, and the user of Optuna can dynamically +construct the search spaces for the hyperparameters.""" + + +toolchain = {'name': 'foss', 'version': '2023b'} + +dependencies = [ + ('Python', '3.11.5'), + ('PyYAML', '6.0.1'), + ('SciPy-bundle', '2023.11'), + ('tqdm', '4.66.2'), + ('matplotlib', '3.8.2'), # optional + ('plotly.py', '5.18.0'), # optional + ('redis-py', '5.0.9'), # optional + ('scikit-learn', '1.4.0'), # optional + ('SQLAlchemy', '2.0.29'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('cmaes', '0.11.1', { + 'checksums': ['cf71fa3679814723be771f2c9edd85f465b1bc1e409e1ad6d8a9e481efcd5160'], + }), + ('colorlog', '6.8.2', { + 'checksums': ['3e3e079a41feb5a1b64f978b5ea4f46040a94f11f0e8bbb8261e3dbbeca64d44'], + }), + ('optuna', version, { + 'use_pip_extras': 'optional', + 'checksums': ['146e530b57b4b9afd7526b3e642fbe65491f7e292b405913355f8e438e361ecf'], + }), +] + +sanity_check_paths = { + 'files': ['bin/optuna'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} +sanity_check_commands = [('optuna', '--help')] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/o/ome-types/ome-types-0.5.1.post1-foss-2023a.eb b/easybuild/easyconfigs/o/ome-types/ome-types-0.5.1.post1-foss-2023a.eb new file mode 100644 index 000000000000..0de34e3542ba --- /dev/null +++ b/easybuild/easyconfigs/o/ome-types/ome-types-0.5.1.post1-foss-2023a.eb @@ -0,0 +1,52 @@ +easyblock = 'PythonBundle' + +name = 'ome-types' +version = '0.5.1.post1' + +homepage = 'https://github.com/tlambert03/ome-types/' +description = """ +ome_types provides a set of python dataclasses and utility functions for parsing +the OME-XML format into fully-typed python objects for interactive or programmatic access in python. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('poetry', '1.5.1'), + ('hatchling', '1.18.0'), + ('maturin', '1.4.0', '-Rust-1.75.0'), +] +dependencies = [ + ('Python', '3.11.3'), + ('pydantic', '2.5.3'), + ('Python-bundle-PyPI', '2023.06'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('ruff', '0.3.0', { + 'checksums': ['0886184ba2618d815067cf43e005388967b67ab9c80df52b32ec1152ab49f53a'], + }), + ('pydantic_compat', '0.1.2', { + 'checksums': ['c5c5bca39ca2d22cad00c02898e400e1920e5127649a8e860637f15566739373'], + }), + ('untokenize', '0.1.1', { + 'checksums': ['3865dbbbb8efb4bb5eaa72f1be7f3e0be00ea8b7f125c69cbd1f5fda926f37a2'], + }), + ('docformatter', '1.7.5', { + 'checksums': ['ffed3da0daffa2e77f80ccba4f0e50bfa2755e1c10e130102571c890a61b246e'], + }), + ('toposort', '1.10', { + 'checksums': ['bfbb479c53d0a696ea7402601f4e693c97b0367837c8898bc6471adfca37a6bd'], + }), + ('xsdata', '23.8', { + 'checksums': ['55f03d4c88236f047266affe550ba0dd19476adfce6a01f3e0aefac7c8078e56'], + }), + ('ome_types', version, { + 'checksums': ['cadda5e36ad4d33dad2034fd43f32113a736fe47c67fd9e06bbb8d3858d1dc58'], + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/openai-python/openai-python-1.30.5-foss-2023a.eb b/easybuild/easyconfigs/o/openai-python/openai-python-1.30.5-foss-2023a.eb new file mode 100644 index 000000000000..e5fa3228a075 --- /dev/null +++ b/easybuild/easyconfigs/o/openai-python/openai-python-1.30.5-foss-2023a.eb @@ -0,0 +1,53 @@ +easyblock = 'PythonBundle' + +name = 'openai-python' +version = '1.30.5' + +homepage = 'https://github.com/openai/openai-python' +description = """ +The OpenAI Python library provides convenient access to the OpenAI REST API from any +Python 3.7+ application. The library includes type definitions for all request params and +response fields, and offers both synchronous and asynchronous clients powered by httpx. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('hatchling', '1.18.0'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('pydantic', '2.5.3'), + ('typing-extensions', '4.9.0'), + ('tqdm', '4.66.1'), +] + +exts_list = [ + ('h11', '0.14.0', { + 'checksums': ['8f19fbbe99e72420ff35c00b27a34cb9937e902a8b810e2c88300c6f0a3b699d'], + }), + ('httpcore', '1.0.5', { + 'checksums': ['34a38e2f9291467ee3b44e89dd52615370e152954ba21721378a87b2960f7a61'], + }), + ('httpx', '0.27.0', { + 'checksums': ['a0cb88a46f32dc874e04ee956e4c2764aba2aa228f650b06788ba6bda2962ab5'], + }), + ('anyio', '4.4.0', { + 'checksums': ['5aadc6a1bbb7cdb0bede386cac5e2940f5e2ff3aa20277e991cf028e0585ce94'], + }), + ('sniffio', '1.3.1', { + 'checksums': ['f4324edc670a0f49750a81b895f35c3adb843cca46f0530f79fc1babb23789dc'], + }), + ('openai', version, { + # needs a README or will get "Fragment file 'README.md' not found." error + 'preinstallopts': "touch README.md && ", + 'checksums': ['5366562eb2c5917e6116ae0391b7ae6e3acd62b0ae3f565ada32b35d8fcfa106'], + }), +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/openslide-python/openslide-python-1.3.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/o/openslide-python/openslide-python-1.3.1-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..bbbaa753b406 --- /dev/null +++ b/easybuild/easyconfigs/o/openslide-python/openslide-python-1.3.1-GCCcore-12.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'openslide-python' +version = '1.3.1' + +homepage = 'https://github.com/openslide/openslide-python' +description = "OpenSlide Python is a Python interface to the OpenSlide library." + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/openslide/openslide-python/archive'] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['3f56bc9d02ae4a5b7257cf5e35214c5cc45f429ff3d5ef849c6c8e2460c1f9cd'] + +builddependencies = [('binutils', '2.39')] + +dependencies = [ + ('Python', '3.10.8'), + ('OpenSlide', '3.4.1', '-largefiles'), + ('Pillow-SIMD', '9.5.0'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +options = {'modulename': 'openslide'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/o/orjson/orjson-3.9.15-GCCcore-12.3.0.eb b/easybuild/easyconfigs/o/orjson/orjson-3.9.15-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..410c8131df9a --- /dev/null +++ b/easybuild/easyconfigs/o/orjson/orjson-3.9.15-GCCcore-12.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonBundle' + +name = 'orjson' +version = '3.9.15' + +homepage = 'https://github.com/ijl/orjson' +description = """Fast, correct Python JSON library supporting dataclasses, datetimes, and numpy.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('maturin', '1.4.0', '-Rust-1.75.0'), +] +dependencies = [ + ('Python', '3.11.3'), +] + +use_pip = True + +exts_list = [ + ('ruff', '0.4.8', { + 'checksums': ['16d717b1d57b2e2fd68bd0bf80fb43931b79d05a7131aa477d66fc40fbd86268'], + }), + ('mypy_extensions', '1.0.0', { + 'checksums': ['75dbf8955dc00442a438fc4d0666508a9a97b6bd41aa2f0ffe9d2f2725af0782'], + }), + ('mypy', '1.10.0', { + 'checksums': ['3d087fcbec056c4ee34974da493a826ce316947485cef3901f511848e687c131'], + }), + (name, version, { + 'checksums': ['95cae920959d772f30ab36d3b25f83bb0f3be671e986c72ce22f8fa700dae061'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PAPI/PAPI-7.1.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/PAPI/PAPI-7.1.0-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..5c653a9d5154 --- /dev/null +++ b/easybuild/easyconfigs/p/PAPI/PAPI-7.1.0-GCCcore-13.3.0.eb @@ -0,0 +1,53 @@ +## +# Author: Robert Mijakovic +# Updated: Alexander Grund +## + +easyblock = 'ConfigureMake' + +name = 'PAPI' +version = '7.1.0' + +homepage = 'https://icl.cs.utk.edu/projects/papi/' +description = """ + PAPI provides the tool designer and application engineer with a consistent + interface and methodology for use of the performance counter hardware found + in most major microprocessors. PAPI enables software engineers to see, in near + real time, the relation between software performance and processor events. + In addition Component PAPI provides access to a collection of components + that expose performance measurement opportunites across the hardware and + software stack. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://icl.utk.edu/projects/papi/downloads'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['%(name)s-%(version)s_add_initial_riscv_support.patch'] +checksums = [ + '5818afb6dba3ece57f51e65897db5062f8e3464e6ed294b654ebf34c3991bc4f', + {'PAPI-7.1.0_add_initial_riscv_support.patch': '6c7d0d63ccf2b8c46f2ed736fbd4c58303038fb2a45315aed94c026b773af35a'} +] + +builddependencies = [ + ('binutils', '2.42'), +] + +start_dir = 'src' + +configopts = "--with-components=rapl " # for energy measurements + +# There is also "fulltest" that is a superset of "test" but hangs on some processors +# indefinitely with a defunct `make` process. So use only "test". +runtest = 'test' + +sanity_check_paths = { + 'files': ["bin/papi_%s" % x + for x in ["avail", "clockres", "command_line", "component_avail", + "cost", "decode", "error_codes", "event_chooser", + "mem_info", "multiplex_cost", "native_avail", + "version", "xml_event_info"]], + 'dirs': [], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/p/PDT/PDT-3.25.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/PDT/PDT-3.25.2-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..74328c99ae7e --- /dev/null +++ b/easybuild/easyconfigs/p/PDT/PDT-3.25.2-GCCcore-13.3.0.eb @@ -0,0 +1,40 @@ +# # +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2013-2019 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +# # + +name = 'PDT' +version = '3.25.2' + +homepage = 'https://www.cs.uoregon.edu/research/pdt/' +description = """ + Program Database Toolkit (PDT) is a framework for analyzing source code + written in several programming languages and for making rich program + knowledge accessible to developers of static and dynamic analysis tools. + PDT implements a standard program representation, the program database + (PDB), that can be accessed in a uniform way through a class library + supporting common PDB operations. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['http://tau.uoregon.edu/pdt_releases/'] +sources = ['pdtoolkit-%(version)s.tar.gz'] +# Might now be available as direct download although e.g. http://tau.uoregon.edu/pdt.tgz may work +download_instructions = ("Download from https://www.cs.uoregon.edu/research/pdt/downloads.php " + + "and rename to " + sources[0]) +checksums = ['01c2d403bc6672b2b264a182c325806541066c5ed5713878eb598f5506428cbe'] + +builddependencies = [ + ('binutils', '2.42'), +] + + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/p/PEcAn/PEcAn-1.8.0.9000-foss-2023a-R-4.3.2.eb b/easybuild/easyconfigs/p/PEcAn/PEcAn-1.8.0.9000-foss-2023a-R-4.3.2.eb new file mode 100644 index 000000000000..b57478152463 --- /dev/null +++ b/easybuild/easyconfigs/p/PEcAn/PEcAn-1.8.0.9000-foss-2023a-R-4.3.2.eb @@ -0,0 +1,217 @@ +easyblock = 'Bundle' + +name = 'PEcAn' +version = '1.8.0.9000' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/PecanProject/pecan' +description = """Ecosystem science, policy, and management informed by the best available data and models.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('R', '4.3.2'), + ('R-bundle-Bioconductor', '3.18', versionsuffix), + ('PostgreSQL', '16.1'), + ('CDO', '2.2.2'), + ('HDF5', '1.14.0'), + ('netCDF', '4.9.2'), + ('UDUNITS', '2.2.28'), + ('texlive', '20230313'), + ('NCO', '5.1.9'), + ('ncview', '2.1.8'), + ('rjags', '4-15', versionsuffix), + ('Redland', '1.0.17'), +] + +exts_defaultclass = 'RPackage' +exts_default_options = { + 'sources': ['%(name)s_%(version)s.tar.gz'], + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + 'https://pecanproject.r-universe.dev/src/contrib/', # PEcAn sources + ], +} + +exts_list = [ + ('PEcAn.logger', '1.8.2.9000', { + 'checksums': ['1092f72fa63d58d83ca939a06bfa51ad3b3b4cd94ca4e68202cdb08fd3ada099'], + }), + ('PEcAn.remote', version, { + 'checksums': ['b3c7208c85d37aa6c12ca99182262a9886e57e2591faefd909232b8c89111b20'], + }), + ('PEcAn.utils', version, { + 'checksums': ['524c3231a21a1e5fc48ebc53d17e49c82f018b87c274095cd0362103fe322ec5'], + }), + ('PEcAn.DB', version, { + 'checksums': ['9b7e9b40a07879c1265d9ab6087b7448dfd34c3601c64ddcb41511c97399fece'], + }), + ('PEcAn.settings', version, { + 'checksums': ['555a7d81eec7e97b8457cef51888087af6b5d7d07f527ca58cbab07ed847fabc'], + }), + ('PEcAn.MA', '1.7.3.9000', { + 'checksums': ['680290e0ee52526db1242d95c4ca06a1e0ad117337ff721d79387797bc7e40ed'], + }), + ('PEcAn.emulator', version, { + 'checksums': ['68944ebdf1f37ff84f9b09bf02c709de9eda823728bbdea073a36d7ef19cfb9c'], + }), + ('PEcAn.priors', '1.7.3.9000', { + 'checksums': ['e942a31ae02af61b1b8e36d1c5df58f39829b3d0c29421edc151f2f063ff4c1f'], + }), + ('PEcAn.uncertainty', version, { + 'checksums': ['65e392536e17e1de2bf8f66c2cd8f46fcb26dcb3294acf0132551b6736722196'], + }), + ('amerifluxr', '1.0.0', { + 'checksums': ['ec54dce4b8e4108832eaadb60f7ef8ad28b459d3381316537492dcd755d83b25'], + }), + ('geonames', '0.999', { + 'checksums': ['1dd7bbd82d9425d14eb36f8e5bf431feaccfe3b0c4e70bf38f44f13dfc59e17b'], + }), + ('solartime', '0.0.2', { + 'checksums': ['5dd7a28db2bd4881ab740cd7004b88cd05c61e0954e3a10c8e18ebbe07d3e7d1'], + }), + ('bigleaf', '0.8.2', { + 'checksums': ['e41d82fb6298150c46f57128e959a1f1c6cfa55e916c32544bab7be69b0b6df7'], + }), + ('REddyProc', '1.3.3', { + 'checksums': ['3f673bd24f41813f631bf25139c9595bd91483e898ec31b7207c4eb8b7ff486b'], + }), + ('suntools', '1.0.0', { + 'checksums': ['42b7b39bd23ad48ded002150a0e7798fab94ed9828e5b5fdd8e5e1c9040697e2'], + }), + ('fauxpas', '0.5.2', { + 'checksums': ['84d07361a146b419cb1dcb7751654e3d5f159cf2704faf498e5ea56c8de61ef6'], + }), + ('nneo', '0.1.0', { + 'checksums': ['ca503e78cf4f4c85de6e18ad3ffde0c08d6a507ff5dc5ff91a50b3e04bf84a49'], + }), + ('PEcAn.data.atmosphere', version, { + 'checksums': ['28fb884cdeeff6405252352a261c3a884ad33202e556e88cee262aba96e1aea4'], + }), + ('redland', '1.0.17-18', { + 'checksums': ['e999ba22321733df7ed056f528e38fc4be535d36bbac8106395c14f9f60a75a0'], + }), + ('datapack', '1.4.1', { + 'checksums': ['6149733ae90e6bbbb53d5f85ca29cec5f811825e794b56029b7f325de6637493'], + }), + ('dplR', '1.7.7', { + 'checksums': ['0e35a4d2a22773499f9e4592d1a198a08c9842388ce1e5a35394990ed4cdb2bd'], + }), + ('neonUtilities', '2.4.2', { + 'checksums': ['37b4efd0ed3b724de999d08d4d430954a6c717b1d943bc84c513c4fe8dbca057'], + }), + ('storr', '1.2.5', { + 'checksums': ['4224c3991d9c043a45ce530d0698d7f2cdca231b26fe31b45e0db865026e5f63'], + }), + ('thor', '1.1.5', { + 'checksums': ['99802d8c8471ce351403f8428c1efab48ccf20f359fbd368db84f25ef8f7ecae'], + }), + ('duckdb', '1.0.0-2', { + 'patches': ['PEcAn-1.8.0.9000_duckdb.patch'], + 'checksums': [ + {'duckdb_1.0.0-2.tar.gz': '3735d51f22d62a7411aa514142cd569ce28bdaec4eb58d5f0893a476b9ccbf01'}, + {'PEcAn-1.8.0.9000_duckdb.patch': 'fb47b668b23e6c9274ce5365725af71e56f2d99771efdd343dc4283f68ab0c21'}, + ], + }), + ('duckdbfs', '0.0.4', { + 'checksums': ['90b2aff2bdefff1db4f855e2a9c9b19a404f522027105424aebd3c7e45944334'], + }), + ('neonstore', '0.5.1', { + 'checksums': ['f911e957861d558adead8ca77e4d1575a47dceb9553f1aa9d818460126deab9b'], + }), + ('HDInterval', '0.2.4', { + 'checksums': ['bb07f0edd660a02ed18e578c2798eb8c2db0e181a5e0c3e23db182d13e9494f6'], + }), + ('kknn', '1.3.1', { + 'checksums': ['22840e70ec2afa40371e274b583634c8f6d27149a87253ee411747d5db78f3db'], + }), + ('timeSeries', '4032.109', { + 'checksums': ['5e0c47584e0b01ea4011ed5ced217d95f8bb872611f6b029b0797d95eebd731f'], + }), + ('gss', '2.2-7', { + 'checksums': ['3b13144702c570c83462b4ea2ad17f4bd630cff5bf2ab0347a33c7e86a4f3f6a'], + }), + ('fBasics', '4032.96', { + 'checksums': ['e1556909871c836668b10bf90e1676aac6a2892a04663d7ab00c22a64c0b8690'], + }), + ('rmutil', '1.1.10', { + 'checksums': ['819fd7ce695cc742b4594705986eb06764460fc88521ea32de793c49de7ca5f9'], + }), + ('stable', '1.1.6', { + 'checksums': ['2238788a35b5aa9e175ad7b92348640c3dcad68b6ab0a0bc04aeec9084d29da4'], + }), + ('statip', '0.2.3', { + 'checksums': ['56a81a1882856cd1c5711ba133417b64f09071dda356e74280a0dba0db60d54f'], + }), + ('modeest', '2.4.0', { + 'checksums': ['1a949409bf64679d32400d20aa3d53e65a9a20f5bd1a40993b95f81100e0ed20'], + }), + ('runjags', '2.2.2-4', { + 'checksums': ['6f656e4d0620c0806e596ddb4bfec3934534ec17c02da699fcbfd6720a6f424f'], + }), + ('swfscMisc', '1.6.5', { + 'checksums': ['a49cb390643c4079f02986862eb2dfd33db4e6b6498e849bb418f73ffd6882e1'], + }), + ('CDM', '8.2-6', { + 'checksums': ['144a85e36c120e9f8a5bd35c1db50cf089ea4807721ac14460137b9a4b1c98d1'], + }), + ('TAM', '4.2-21', { + 'checksums': ['0d1782e42e89c1863edab12c1861d0e2628ea9ee1a1e37d268f27a3deaf3d568'], + }), + ('pbv', '0.5-47', { + 'checksums': ['e17a04efa96a601ab72172b59f555f36d28bb824f02f363cc5806b05d7d7c792'], + }), + ('sirt', '4.1-15', { + 'checksums': ['c12ffcb83bea5b549c7a34c12561f3e57798b83d68a887c5da0d9a66efac3066'], + }), + ('hoardr', '0.5.4', { + 'checksums': ['4e031ac1317584451c09bc8288ed73fb2d6ceea3c10d29dbb4be08157e489a37'], + }), + ('traits', '0.5.1', { + 'checksums': ['3080887a454d69814cd6cb9683a6750db02cf4c77b40b022ef50d40171ba6aca'], + }), + ('SimilarityMeasures', '1.4', { + 'checksums': ['b26bbc3a402d21f030cc8e4ff6baca644eb4c63a4fb33423dbc9436229a393f0'], + }), + ('PEcAn.benchmark', '1.7.3.9000', { + 'checksums': ['2e8b285869b4df148228cdde5de44a67dfe0b584b2a7cd614280134259e33ed4'], + }), + ('PEcAn.visualization', version, { + 'checksums': ['f77dcb756871a419a85e46cde4a1fb0a1993c29cce8578255d5a46db722ece43'], + }), + ('PEcAn.data.land', version, { + 'checksums': ['19c572e95c11362f4714d9c3d9cc7b2d17c2e3a34513c7ed629e7bdb99bdd0ec'], + }), + ('MODISTools', '1.1.5', { + 'checksums': ['0a6b3762865424e299e1a5ec28de78b8dcca3f673e61f42a37dae19ed78db3e3'], + }), + ('PEcAn.data.remote', version, { + 'checksums': ['c097d9395d9dbb6c123f404525cae7fdb1a99b142b32c1a40b0143060444e184'], + }), + ('SparseGrid', '0.8.2', { + 'checksums': ['1d84ae83db2a390b111589a10570d55b378c2dd3310d3bc588a94ab8845cfd14'], + }), + ('lqmm', '1.5.8', { + 'checksums': ['11eddeeeed6b9d3190a80a3b3cc3d64519c6e9cb208746a3736139340df691fb'], + }), + ('PEcAn.workflow', version, { + 'checksums': ['91a1849c040089da1088c02469b973a5f301a419237db7c840fe4ca2922f4b9d'], + }), + ('PEcAn.assim.batch', version, { + 'checksums': ['a1403a5a4591791e37e7e48ca9e9d49f66f4270757711b68b72fd38aadd411cb'], + }), + ('PEcAn.all', version, { + 'checksums': ['6fe594fb890b5680977d1bf58232b941c6d522456e7803e3dc9c4418b92db737'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['%(name)s.all'], +} + +modextrapaths = {'R_LIBS_SITE': ''} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/PEcAn/PEcAn-1.8.0.9000_duckdb.patch b/easybuild/easyconfigs/p/PEcAn/PEcAn-1.8.0.9000_duckdb.patch new file mode 100644 index 000000000000..940992bf5ba9 --- /dev/null +++ b/easybuild/easyconfigs/p/PEcAn/PEcAn-1.8.0.9000_duckdb.patch @@ -0,0 +1,16 @@ +Fixes the `prefix_back_ was not declared` error, see https://github.com/duckdb/duckdb/pull/12344 +Source: https://patch-diff.githubusercontent.com/raw/duckdb/duckdb/pull/12344.diff +diff -u src/duckdb/third_party/re2/re2/prog.cc.orig src/duckdb/third_party/re2/re2/prog.cc +--- src/duckdb/third_party/re2/re2/prog.cc.orig 2024-07-19 14:46:13.000000000 +0200 ++++ src/duckdb/third_party/re2/re2/prog.cc 2024-08-21 15:51:17.394266979 +0200 +@@ -1143,8 +1143,8 @@ + const __m256i* bp = reinterpret_cast( + reinterpret_cast(data) + prefix_size_-1); + const __m256i* endfp = fp + size/sizeof(__m256i); +- const __m256i f_set1 = _mm256_set1_epi8(prefix_front_); +- const __m256i b_set1 = _mm256_set1_epi8(prefix_back_); ++ const __m256i f_set1 = _mm256_set1_epi8(prefix_front_back.prefix_front_); ++ const __m256i b_set1 = _mm256_set1_epi8(prefix_front_back.prefix_back_); + do { + const __m256i f_loadu = _mm256_loadu_si256(fp++); + const __m256i b_loadu = _mm256_loadu_si256(bp++); diff --git a/easybuild/easyconfigs/p/PLY/PLY-3.11-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/PLY/PLY-3.11-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..74ab008fb997 --- /dev/null +++ b/easybuild/easyconfigs/p/PLY/PLY-3.11-GCCcore-13.2.0.eb @@ -0,0 +1,22 @@ +easyblock = 'PythonPackage' + +name = 'PLY' +version = '3.11' + +homepage = "https://www.dabeaz.com/ply/" +description = """PLY is yet another implementation of lex and yacc for Python.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [('Python', '3.11.5')] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PLY/PLY-3.11-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/PLY/PLY-3.11-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..a5620c426d65 --- /dev/null +++ b/easybuild/easyconfigs/p/PLY/PLY-3.11-GCCcore-13.3.0.eb @@ -0,0 +1,22 @@ +easyblock = 'PythonPackage' + +name = 'PLY' +version = '3.11' + +homepage = "https://www.dabeaz.com/ply/" +description = """PLY is yet another implementation of lex and yacc for Python.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3'] + +builddependencies = [('binutils', '2.42')] + +dependencies = [('Python', '3.12.3')] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1-GCCcore-10.3.0.eb index a7f0ee5d4695..1f6981d1daec 100644 --- a/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1-GCCcore-10.3.0.eb @@ -15,15 +15,17 @@ source_urls = ['https://github.com/cornelisnetworks/opa-psm2/archive/refs/tags'] sources = ['%(name)s_%(version)s.tar.gz'] patches = [ ('PSM2-11.2.80_hfi-user.patch', 1), + ('PSM2-12.0.1_build-with-internal-cuda-header.patch', 1), ] checksums = [ {'PSM2_12.0.1.tar.gz': 'e41af2d7d36a6ab67639ecbd5c1012aa20b2b464bf5cfbdac60e7eb37bfe58de'}, {'PSM2-11.2.80_hfi-user.patch': 'e43138859387213506050af9b76e193c3cd0a162d148998c39e551f220392abb'}, + {'PSM2-12.0.1_build-with-internal-cuda-header.patch': + '0016327d7eade9e763ffbc468cf25c182d743074dca2885dea7ef0cf7e3b23cf'}, ] builddependencies = [ ('binutils', '2.36.1'), - ('CUDA', '11.3.1', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1-GCCcore-11.2.0.eb index 779d6bcdd0ac..325c404a0550 100644 --- a/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1-GCCcore-11.2.0.eb @@ -15,15 +15,17 @@ source_urls = ['https://github.com/cornelisnetworks/opa-psm2/archive/refs/tags'] sources = ['%(name)s_%(version)s.tar.gz'] patches = [ ('PSM2-11.2.80_hfi-user.patch', 1), + ('PSM2-12.0.1_build-with-internal-cuda-header.patch', 1), ] checksums = [ {'PSM2_12.0.1.tar.gz': 'e41af2d7d36a6ab67639ecbd5c1012aa20b2b464bf5cfbdac60e7eb37bfe58de'}, {'PSM2-11.2.80_hfi-user.patch': 'e43138859387213506050af9b76e193c3cd0a162d148998c39e551f220392abb'}, + {'PSM2-12.0.1_build-with-internal-cuda-header.patch': + '0016327d7eade9e763ffbc468cf25c182d743074dca2885dea7ef0cf7e3b23cf'}, ] builddependencies = [ ('binutils', '2.37'), - ('CUDA', '11.5.2', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1-GCCcore-11.3.0.eb index 7fa4c192e3b4..b93b34dc43e4 100644 --- a/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1-GCCcore-11.3.0.eb @@ -15,15 +15,17 @@ source_urls = ['https://github.com/cornelisnetworks/opa-psm2/archive/refs/tags'] sources = ['%(name)s_%(version)s.tar.gz'] patches = [ ('PSM2-11.2.80_hfi-user.patch', 1), + ('PSM2-12.0.1_build-with-internal-cuda-header.patch', 1), ] checksums = [ {'PSM2_12.0.1.tar.gz': 'e41af2d7d36a6ab67639ecbd5c1012aa20b2b464bf5cfbdac60e7eb37bfe58de'}, {'PSM2-11.2.80_hfi-user.patch': 'e43138859387213506050af9b76e193c3cd0a162d148998c39e551f220392abb'}, + {'PSM2-12.0.1_build-with-internal-cuda-header.patch': + '0016327d7eade9e763ffbc468cf25c182d743074dca2885dea7ef0cf7e3b23cf'}, ] builddependencies = [ ('binutils', '2.38'), - ('CUDA', '11.7.0', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1-GCCcore-12.2.0.eb index fbf417d2bc8d..fa91a78538eb 100644 --- a/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1-GCCcore-12.2.0.eb @@ -15,15 +15,17 @@ source_urls = ['https://github.com/cornelisnetworks/opa-psm2/archive/refs/tags'] sources = ['%(name)s_%(version)s.tar.gz'] patches = [ ('PSM2-11.2.80_hfi-user.patch', 1), + ('PSM2-12.0.1_build-with-internal-cuda-header.patch', 1), ] checksums = [ {'PSM2_12.0.1.tar.gz': 'e41af2d7d36a6ab67639ecbd5c1012aa20b2b464bf5cfbdac60e7eb37bfe58de'}, {'PSM2-11.2.80_hfi-user.patch': 'e43138859387213506050af9b76e193c3cd0a162d148998c39e551f220392abb'}, + {'PSM2-12.0.1_build-with-internal-cuda-header.patch': + '0016327d7eade9e763ffbc468cf25c182d743074dca2885dea7ef0cf7e3b23cf'}, ] builddependencies = [ ('binutils', '2.39'), - ('CUDA', '12.0.0', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1-GCCcore-12.3.0.eb index 0470fe64363b..169b08b1e36c 100644 --- a/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1-GCCcore-12.3.0.eb @@ -15,15 +15,17 @@ source_urls = ['https://github.com/cornelisnetworks/opa-psm2/archive/refs/tags'] sources = ['%(name)s_%(version)s.tar.gz'] patches = [ ('PSM2-11.2.80_hfi-user.patch', 1), + ('PSM2-12.0.1_build-with-internal-cuda-header.patch', 1), ] checksums = [ {'PSM2_12.0.1.tar.gz': 'e41af2d7d36a6ab67639ecbd5c1012aa20b2b464bf5cfbdac60e7eb37bfe58de'}, {'PSM2-11.2.80_hfi-user.patch': 'e43138859387213506050af9b76e193c3cd0a162d148998c39e551f220392abb'}, + {'PSM2-12.0.1_build-with-internal-cuda-header.patch': + '0016327d7eade9e763ffbc468cf25c182d743074dca2885dea7ef0cf7e3b23cf'}, ] builddependencies = [ ('binutils', '2.40'), - ('CUDA', '12.1.1', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1-GCCcore-13.2.0.eb index cfe3fe9f1e48..ee265c55610f 100644 --- a/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1-GCCcore-13.2.0.eb @@ -15,15 +15,17 @@ source_urls = ['https://github.com/cornelisnetworks/opa-psm2/archive/refs/tags'] sources = ['%(name)s_%(version)s.tar.gz'] patches = [ ('PSM2-11.2.80_hfi-user.patch', 1), + ('PSM2-12.0.1_build-with-internal-cuda-header.patch', 1), ] checksums = [ {'PSM2_12.0.1.tar.gz': 'e41af2d7d36a6ab67639ecbd5c1012aa20b2b464bf5cfbdac60e7eb37bfe58de'}, {'PSM2-11.2.80_hfi-user.patch': 'e43138859387213506050af9b76e193c3cd0a162d148998c39e551f220392abb'}, + {'PSM2-12.0.1_build-with-internal-cuda-header.patch': + '0016327d7eade9e763ffbc468cf25c182d743074dca2885dea7ef0cf7e3b23cf'}, ] builddependencies = [ ('binutils', '2.40'), - ('CUDA', '12.4.0', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1-GCCcore-13.3.0.eb index 78d99d2efecc..aff3d686fc74 100644 --- a/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1-GCCcore-13.3.0.eb @@ -15,15 +15,17 @@ source_urls = ['https://github.com/cornelisnetworks/opa-psm2/archive/refs/tags'] sources = ['%(name)s_%(version)s.tar.gz'] patches = [ ('PSM2-11.2.80_hfi-user.patch', 1), + ('PSM2-12.0.1_build-with-internal-cuda-header.patch', 1), ] checksums = [ {'PSM2_12.0.1.tar.gz': 'e41af2d7d36a6ab67639ecbd5c1012aa20b2b464bf5cfbdac60e7eb37bfe58de'}, {'PSM2-11.2.80_hfi-user.patch': 'e43138859387213506050af9b76e193c3cd0a162d148998c39e551f220392abb'}, + {'PSM2-12.0.1_build-with-internal-cuda-header.patch': + '0016327d7eade9e763ffbc468cf25c182d743074dca2885dea7ef0cf7e3b23cf'}, ] builddependencies = [ ('binutils', '2.42'), - ('CUDA', '12.4.0', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1_build-with-internal-cuda-header.patch b/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1_build-with-internal-cuda-header.patch new file mode 100644 index 000000000000..3e3ffd8038e8 --- /dev/null +++ b/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1_build-with-internal-cuda-header.patch @@ -0,0 +1,88 @@ +Allow building PSM2 without a CUDA builddependency, by providing an +internal minimal cuda.h header file. +As long as the runtime CUDA version is 8.0+, libcuda.so will be dlopen'ed and +used successfully. + +Author: Bart Oldeman +diff -urN opa-psm2-PSM2_12.0.1.orig/include/cuda.h opa-psm2-PSM2_12.0.1/include/cuda.h +--- opa-psm2-PSM2_12.0.1.orig/include/cuda.h 1970-01-01 00:00:00.000000000 +0000 ++++ opa-psm2-PSM2_12.0.1/include/cuda.h 2024-06-11 18:39:38.242975935 +0000 +@@ -0,0 +1,73 @@ ++/* This header provides minimal parts of the CUDA Driver API, without having to ++ rely on the proprietary CUDA toolkit. ++ ++ References (to avoid copying from NVidia's proprietary cuda.h): ++ https://github.com/gcc-mirror/gcc/blob/master/include/cuda/cuda.h ++ https://github.com/Theano/libgpuarray/blob/master/src/loaders/libcuda.h ++ https://github.com/CPFL/gdev/blob/master/cuda/driver/cuda.h ++ https://github.com/CudaWrangler/cuew/blob/master/include/cuew.h ++*/ ++ ++#ifndef PSM2_CUDA_H ++#define PSM2_CUDA_H ++ ++#include ++ ++#define CUDA_VERSION 8000 ++ ++typedef void *CUcontext; ++typedef int CUdevice; ++#if defined(__LP64__) || defined(_WIN64) ++typedef unsigned long long CUdeviceptr; ++#else ++typedef unsigned CUdeviceptr; ++#endif ++typedef void *CUevent; ++typedef void *CUstream; ++ ++typedef enum { ++ CUDA_SUCCESS = 0, ++ CUDA_ERROR_ALREADY_MAPPED = 208, ++ CUDA_ERROR_NOT_READY = 600, ++} CUresult; ++ ++enum { ++ CU_EVENT_DEFAULT = 0x0, ++}; ++ ++enum { ++ CU_IPC_MEM_LAZY_ENABLE_PEER_ACCESS = 0x1, ++}; ++ ++typedef enum { ++ CU_POINTER_ATTRIBUTE_MEMORY_TYPE = 2, ++ CU_POINTER_ATTRIBUTE_SYNC_MEMOPS = 6, ++ CU_POINTER_ATTRIBUTE_IS_MANAGED = 8, ++} CUpointer_attribute; ++ ++ ++typedef enum { ++ CU_MEMORYTYPE_HOST = 0x01, ++ CU_MEMORYTYPE_DEVICE = 0x02, ++} CUmemorytype; ++ ++#define CU_IPC_HANDLE_SIZE 64 ++ ++typedef struct CUipcMemHandle_st { ++ char reserved[CU_IPC_HANDLE_SIZE]; ++} CUipcMemHandle; ++ ++typedef enum { ++ CU_DEVICE_ATTRIBUTE_UNIFIED_ADDRESSING = 41, ++ CU_DEVICE_ATTRIBUTE_COMPUTE_CAPABILITY_MAJOR = 75, ++} CUdevice_attribute; ++ ++enum { ++ CU_STREAM_NON_BLOCKING = 1 ++}; ++ ++enum { ++ CU_MEMHOSTALLOC_PORTABLE = 0x01, ++}; ++ ++#endif +diff -urN opa-psm2-PSM2_12.0.1.orig/include/driver_types.h opa-psm2-PSM2_12.0.1/include/driver_types.h +--- opa-psm2-PSM2_12.0.1.orig/include/driver_types.h 1970-01-01 00:00:00.000000000 +0000 ++++ opa-psm2-PSM2_12.0.1/include/driver_types.h 2024-06-12 13:46:04.123858352 +0000 +@@ -0,0 +1 @@ ++/* this file is empty */ diff --git a/easybuild/easyconfigs/p/PaStiX/PaStiX-6.3.2-foss-2023b.eb b/easybuild/easyconfigs/p/PaStiX/PaStiX-6.3.2-foss-2023b.eb new file mode 100644 index 000000000000..64b3fd907c72 --- /dev/null +++ b/easybuild/easyconfigs/p/PaStiX/PaStiX-6.3.2-foss-2023b.eb @@ -0,0 +1,47 @@ +easyblock = 'CMakeMake' + +name = 'PaStiX' +version = '6.3.2' + +homepage = 'http://pastix.gforge.inria.fr/' +description = """PaStiX (Parallel Sparse matriX package) is a scientific library that provides a high performance + parallel solver for very large sparse linear systems based on direct methods.""" + +toolchain = {'name': 'foss', 'version': '2023b'} +toolchainopts = {'pic': True} + +source_urls = ['https://files.inria.fr/pastix/releases/v6/'] +sources = ['%(namelower)s-%(version)s.tar.gz'] +checksums = ['c4da8802d1933eecf8c09d7e63c014c81ccf353fe623142e9f5c5fc65ed82ee0'] + +builddependencies = [ + ('CMake', '3.27.6'), + ('pkgconf', '2.0.3'), +] + +dependencies = [ + ('hwloc', '2.9.2'), + ('SCOTCH', '7.0.4'), +] + +configopts = [ + '-DBUILD_SHARED_LIBS=OFF -DPASTIX_INT64=OFF -DPASTIX_WITH_MPI=ON', + '-DBUILD_SHARED_LIBS=ON -DPASTIX_INT64=OFF -DPASTIX_WITH_MPI=ON' +] + +sanity_check_paths = { + 'files': ['bin/pastix_env.sh', + 'bin/spm_env.sh', + 'lib/libpastix.a', + 'lib/libpastixf.a', + 'lib/libpastix.%s' % SHLIB_EXT, + 'lib/libpastixf.%s' % SHLIB_EXT, + 'lib/libspm.a', + 'lib/libspmf.a', + 'lib/libspm.%s' % SHLIB_EXT, + 'lib/libspmf.%s' % SHLIB_EXT, + ], + 'dirs': ['bin', 'include', 'lib/pkgconfig', 'share'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/PaStiX/PaStiX-6.3.2-intel-2023b.eb b/easybuild/easyconfigs/p/PaStiX/PaStiX-6.3.2-intel-2023b.eb new file mode 100644 index 000000000000..d53ebd66755e --- /dev/null +++ b/easybuild/easyconfigs/p/PaStiX/PaStiX-6.3.2-intel-2023b.eb @@ -0,0 +1,47 @@ +easyblock = 'CMakeMake' + +name = 'PaStiX' +version = '6.3.2' + +homepage = 'http://pastix.gforge.inria.fr/' +description = """PaStiX (Parallel Sparse matriX package) is a scientific library that provides a high performance + parallel solver for very large sparse linear systems based on direct methods.""" + +toolchain = {'name': 'intel', 'version': '2023b'} +toolchainopts = {'pic': True} + +source_urls = ['https://files.inria.fr/pastix/releases/v6/'] +sources = ['%(namelower)s-%(version)s.tar.gz'] +checksums = ['c4da8802d1933eecf8c09d7e63c014c81ccf353fe623142e9f5c5fc65ed82ee0'] + +builddependencies = [ + ('CMake', '3.27.6'), + ('pkgconf', '2.0.3'), +] + +dependencies = [ + ('hwloc', '2.9.2'), + ('SCOTCH', '7.0.4'), +] + +configopts = [ + '-DBUILD_SHARED_LIBS=OFF -DPASTIX_INT64=OFF -DPASTIX_WITH_MPI=ON', + '-DBUILD_SHARED_LIBS=ON -DPASTIX_INT64=OFF -DPASTIX_WITH_MPI=ON' +] + +sanity_check_paths = { + 'files': ['bin/pastix_env.sh', + 'bin/spm_env.sh', + 'lib/libpastix.a', + 'lib/libpastixf.a', + 'lib/libpastix.%s' % SHLIB_EXT, + 'lib/libpastixf.%s' % SHLIB_EXT, + 'lib/libspm.a', + 'lib/libspmf.a', + 'lib/libspm.%s' % SHLIB_EXT, + 'lib/libspmf.%s' % SHLIB_EXT, + ], + 'dirs': ['bin', 'include', 'lib/pkgconfig', 'share'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-gompi-2023b.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-gompi-2023b.eb new file mode 100644 index 000000000000..ae247e2b7c5b --- /dev/null +++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-gompi-2023b.eb @@ -0,0 +1,29 @@ +## +# Author: Robert Mijakovic +## +name = 'ParMETIS' +version = '4.0.3' + +homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview' +description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning + unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the + functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and + large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way + graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes.""" + +toolchain = {'name': 'gompi', 'version': '2023b'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = [ + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis', + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/OLD', +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f2d9a231b7cf97f1fee6e8c9663113ebf6c240d407d3c118c55b3633d6be6e5f'] + +builddependencies = [('CMake', '3.27.6')] + +# Build static and shared libraries +configopts = ['', '-DSHARED=1'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-iimpi-2023b.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-iimpi-2023b.eb new file mode 100644 index 000000000000..a2804c40d1cd --- /dev/null +++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-iimpi-2023b.eb @@ -0,0 +1,29 @@ +## +# Author: Robert Mijakovic +## +name = 'ParMETIS' +version = '4.0.3' + +homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview' +description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning + unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the + functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and + large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way + graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes.""" + +toolchain = {'name': 'iimpi', 'version': '2023b'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = [ + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis', + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/OLD', +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f2d9a231b7cf97f1fee6e8c9663113ebf6c240d407d3c118c55b3633d6be6e5f'] + +builddependencies = [('CMake', '3.27.6')] + +# Build static and shared libraries +configopts = ['', '-DSHARED=1'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.12.0-foss-2023b-Qt5.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.12.0-foss-2023b-Qt5.eb new file mode 100644 index 000000000000..abec428859fa --- /dev/null +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.12.0-foss-2023b-Qt5.eb @@ -0,0 +1,72 @@ +easyblock = 'CMakeMake' + +name = 'ParaView' +version = '5.12.0' +versionsuffix = '-Qt5' + +homepage = 'https://www.paraview.org' +description = "ParaView is a scientific parallel visualizer." + +toolchain = {'name': 'foss', 'version': '2023b'} +toolchainopts = {'pic': True, 'usempi': True} + +local_download_suffix = 'download.php?submit=Download&version=v%(version_major_minor)s&type=source&os=all&downloadFile=' +source_urls = ['https://www.paraview.org/paraview-downloads/%s' % local_download_suffix] +sources = ["%(name)s-v%(version)s.tar.gz"] +patches = ['ParaView-5.11.1-remove_glew_init_warning.patch'] +checksums = [ + {'ParaView-v5.12.0.tar.gz': '2cc5733608fd508e2da8fc5d4ee693523d350dc1e1f89f9a89a78dc63107f70e'}, + {'ParaView-5.11.1-remove_glew_init_warning.patch': + 'dd86134f3a5b2c1b834224c69665dd31f99ef7d367688fe77dbaada212758710'}, +] + +builddependencies = [('CMake', '3.27.6')] + +dependencies = [ + ('Python', '3.11.5'), + ('SciPy-bundle', '2023.11'), + ('Boost', '1.83.0'), + ('XZ', '5.4.4'), + ('HDF5', '1.14.3'), + ('netCDF', '4.9.2'), + ('libdrm', '2.4.117'), + ('Mesa', '23.1.9'), + ('Qt5', '5.15.13'), + ('zlib', '1.2.13'), + ('FFmpeg', '6.0'), + ('Szip', '2.1.1'), +] + +_copts = [ + # Basic configuration + '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON', + '-DPARAVIEW_BUILD_SHARED_LIBS=ON', + '-DPARAVIEW_USE_MPI=ON', + '-DPARAVIEW_ENABLE_FFMPEG=ON', + '-DPARAVIEW_USE_PYTHON=ON', + '-DPython3_ROOT_DIR=$EBROOTPYTHON', + # Useful input formats + '-DPARAVIEW_ENABLE_XDMF2=ON', + '-DPARAVIEW_ENABLE_XDMF3=ON', + # EGL, X and Mesa + '-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s' % SHLIB_EXT, + '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include', + '-DEGL_INCLUDE_DIR=$EBROOTLIBGLVND/include', + '-DEGL_LIBRARY=$EBROOTLIBGLVND/lib/libEGL.%s' % SHLIB_EXT, + '-DEGL_opengl_LIBRARY=$EBROOTLIBGLVND/libOpenGL.%s' % SHLIB_EXT, + '-DVTK_OPENGL_HAS_EGL=ON', + '-DVTK_USE_X=ON', + '-DVTK_OPENGL_HAS_OSMESA=OFF', + '-DVTK_PYTHON_OPTIONAL_LINK=OFF'] +configopts = ' '.join(_copts) + +sanity_check_paths = { + 'files': ['bin/paraview', 'bin/pvserver', 'bin/pvpython'], + 'dirs': ['include/paraview-%(version_major_minor)s', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['python -c "import paraview"'] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.12.0-foss-2023b.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.12.0-foss-2023b.eb index 018edd704319..ed8408c93010 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-5.12.0-foss-2023b.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.12.0-foss-2023b.eb @@ -12,11 +12,15 @@ toolchainopts = {'pic': True, 'usempi': True} local_download_suffix = 'download.php?submit=Download&version=v%(version_major_minor)s&type=source&os=all&downloadFile=' source_urls = ['https://www.paraview.org/paraview-downloads/%s' % local_download_suffix] sources = ["%(name)s-v%(version)s.tar.gz"] -patches = ['ParaView-5.11.1-remove_glew_init_warning.patch'] +patches = [ + 'ParaView-5.11.1-remove_glew_init_warning.patch', + 'ParaView-5.12.0-qt6_fixes.patch', +] checksums = [ {'ParaView-v5.12.0.tar.gz': '2cc5733608fd508e2da8fc5d4ee693523d350dc1e1f89f9a89a78dc63107f70e'}, {'ParaView-5.11.1-remove_glew_init_warning.patch': 'dd86134f3a5b2c1b834224c69665dd31f99ef7d367688fe77dbaada212758710'}, + {'ParaView-5.12.0-qt6_fixes.patch': '015d07ac6b74c7355b56ed7f67166f0d5b765f9d6ac135b7246a675a317063df'}, ] builddependencies = [('CMake', '3.27.6')] @@ -58,7 +62,9 @@ _copts = [ '-DEGL_opengl_LIBRARY=$EBROOTLIBGLVND/libOpenGL.%s' % SHLIB_EXT, '-DVTK_OPENGL_HAS_EGL=ON', '-DVTK_USE_X=ON', - '-DVTK_OPENGL_HAS_OSMESA=OFF'] + '-DVTK_OPENGL_HAS_OSMESA=OFF', + '-DVTK_PYTHON_OPTIONAL_LINK=OFF'] + configopts = ' '.join(_copts) sanity_check_paths = { diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.12.0-qt6_fixes.patch b/easybuild/easyconfigs/p/ParaView/ParaView-5.12.0-qt6_fixes.patch new file mode 100644 index 000000000000..838d6fe5d32a --- /dev/null +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.12.0-qt6_fixes.patch @@ -0,0 +1,126 @@ +This patch solves qt6 compatibility issues. For details see +https://gitlab.kitware.com/paraview/paraview/-/merge_requests/6836 + +diff --git a/Plugins/CAVEInteraction/pqVRDockPanel.cxx b/Plugins/CAVEInteraction/pqVRDockPanel.cxx +index 7a3d352b993f2930716b47dd98512ca88697374c..448ac4d3833ec1582d99139b3f3fea6bbdf7d3ce 100644 +--- a/Plugins/CAVEInteraction/pqVRDockPanel.cxx ++++ b/Plugins/CAVEInteraction/pqVRDockPanel.cxx +@@ -159,8 +159,8 @@ void pqVRDockPanel::initStyles() + this->Internals->stylesCombo->addItem(QString::fromStdString(styleDescs[i])); + } + +- connect(this->Internals->stylesCombo, SIGNAL(currentIndexChanged(QString)), this, +- SLOT(styleComboChanged(QString)), Qt::UniqueConnection); ++ QObject::connect(this->Internals->stylesCombo, &QComboBox::currentTextChanged, this, ++ &pqVRDockPanel::styleComboChanged, Qt::UniqueConnection); + } + + //----------------------------------------------------------------------------- +diff --git a/Qt/Components/pqCustomFilterDefinitionWizard.cxx b/Qt/Components/pqCustomFilterDefinitionWizard.cxx +index 9c140a37abca11b19f0c04bf7c41645b756457d6..acd7bd99e19017a5557a41c4585586b39e5ffc58 100644 +--- a/Qt/Components/pqCustomFilterDefinitionWizard.cxx ++++ b/Qt/Components/pqCustomFilterDefinitionWizard.cxx +@@ -134,8 +134,8 @@ pqCustomFilterDefinitionWizard::pqCustomFilterDefinitionWizard( + SLOT(clearNameOverwrite(const QString&))); + + // When combo selection changes, update new label to be same as old. +- QObject::connect(this->Form->PropertyCombo, SIGNAL(currentIndexChanged(const QString&)), +- this->Form->PropertyName, SLOT(setText(const QString&))); ++ QObject::connect(this->Form->PropertyCombo, &QComboBox::currentTextChanged, ++ this->Form->PropertyName, &QLineEdit::setText); + } + + //----------------------------------------------------------------------------- +diff --git a/Qt/Components/pqDataInformationWidget.cxx b/Qt/Components/pqDataInformationWidget.cxx +index f151d584fc8b683b5666c11c7dfad85219c1e94f..7079507a14bad98dd10bff7ddf65af896cf5e919 100644 +--- a/Qt/Components/pqDataInformationWidget.cxx ++++ b/Qt/Components/pqDataInformationWidget.cxx +@@ -103,8 +103,8 @@ pqDataInformationWidget::pqDataInformationWidget(QWidget* _parent /*=0*/) + this->Model->setActiveView(pqActiveObjects::instance().activeView()); + + // Clicking on the header should sort the column. +- QObject::connect(this->View->horizontalHeader(), SIGNAL(sectionClicked(int)), this->View, +- SLOT(sortByColumn(int))); ++ QObject::connect(this->View->horizontalHeader(), &QHeaderView::sectionClicked, this->View, ++ [=](int col) { this->View->sortByColumn(col, Qt::AscendingOrder); }); + + // Set the context menu policy for the header. + this->View->horizontalHeader()->setContextMenuPolicy(Qt::CustomContextMenu); +diff --git a/Qt/Components/pqDisplayRepresentationWidget.cxx b/Qt/Components/pqDisplayRepresentationWidget.cxx +index 3e08e05e560618457e628afc9bf1fdbf3167b9f0..4d9bc9958a0034e3e2b1e7920a333a5d7f794db6 100644 +--- a/Qt/Components/pqDisplayRepresentationWidget.cxx ++++ b/Qt/Components/pqDisplayRepresentationWidget.cxx +@@ -111,8 +111,8 @@ pqDisplayRepresentationWidget::pqDisplayRepresentationWidget(QWidget* _p) + { + this->Internal = new pqDisplayRepresentationWidget::pqInternals(); + this->Internal->setupUi(this); +- this->connect(this->Internal->comboBox, SIGNAL(currentIndexChanged(const QString&)), +- SLOT(comboBoxChanged(const QString&))); ++ QObject::connect(this->Internal->comboBox, &QComboBox::currentTextChanged, this, ++ &pqDisplayRepresentationWidget::comboBoxChanged); + } + + //----------------------------------------------------------------------------- +diff --git a/Qt/Components/pqLinksEditor.cxx b/Qt/Components/pqLinksEditor.cxx +index 6f02d16d44b82f616a236557f16174d3ffa96425..ae66b1c97c3d82425c2f8b849c6d656deecc64a8 100644 +--- a/Qt/Components/pqLinksEditor.cxx ++++ b/Qt/Components/pqLinksEditor.cxx +@@ -452,8 +452,8 @@ pqLinksEditor::pqLinksEditor(vtkSMLink* link, QWidget* p) + QObject::connect(this->Ui->lineEdit, SIGNAL(textChanged(const QString&)), this, + SLOT(updateEnabledState()), Qt::QueuedConnection); + +- QObject::connect(this->Ui->comboBox, SIGNAL(currentIndexChanged(const QString&)), this, +- SLOT(updateSelectedProxies()), Qt::QueuedConnection); ++ QObject::connect(this->Ui->comboBox, &QComboBox::currentTextChanged, this, ++ &pqLinksEditor::updateSelectedProxies, Qt::QueuedConnection); + + QObject::connect( + this->Ui->interactiveViewLinkCheckBox, &QCheckBox::stateChanged, this, +diff --git a/Qt/Core/pqFileDialog.cxx b/Qt/Core/pqFileDialog.cxx +index 2a87c723a5ef4af856c71e3589ce9a5efa95b65b..6f369d1163a32e5ae3c7e3bcc00a22081e81e2a2 100644 +--- a/Qt/Core/pqFileDialog.cxx ++++ b/Qt/Core/pqFileDialog.cxx +@@ -322,7 +322,7 @@ pqFileDialog::pqFileDialog(pqServer* server, QWidget* p, const QString& title, + QObject::connect( + impl.Ui.NavigateForward, SIGNAL(clicked(bool)), this, SLOT(onNavigateForward())); + impl.Ui.NavigateUp->setIcon(style()->standardPixmap(QStyle::SP_FileDialogToParent)); +- impl.Ui.NavigateUp->setShortcut(Qt::ALT + Qt::Key_Up); ++ impl.Ui.NavigateUp->setShortcut(Qt::ALT | Qt::Key_Up); + impl.Ui.NavigateUp->setToolTip( + tr("Navigate Up (%1)").arg(impl.Ui.NavigateUp->shortcut().toString())); + impl.Ui.CreateFolder->setIcon(style()->standardPixmap(QStyle::SP_FileDialogNewFolder)); +@@ -378,8 +378,8 @@ pqFileDialog::pqFileDialog(pqServer* server, QWidget* p, const QString& title, + QObject::connect( + impl.Ui.Parents, SIGNAL(activated(const QString&)), this, SLOT(onNavigate(const QString&))); + +- QObject::connect(impl.Ui.EntityType, SIGNAL(currentIndexChanged(const QString&)), this, +- SLOT(onFilterChange(const QString&))); ++ QObject::connect( ++ impl.Ui.EntityType, &QComboBox::currentTextChanged, this, &pqFileDialog::onFilterChange); + + QObject::connect(impl.Ui.Favorites, SIGNAL(clicked(const QModelIndex&)), this, + SLOT(onClickedFavorite(const QModelIndex&))); +diff --git a/Qt/Widgets/pqSignalAdaptors.cxx b/Qt/Widgets/pqSignalAdaptors.cxx +index 0015c9148b80eddd926ba37c17b7d777250c1a78..8e218b945c5f7a8962ffaced17d4a011c00db153 100644 +--- a/Qt/Widgets/pqSignalAdaptors.cxx ++++ b/Qt/Widgets/pqSignalAdaptors.cxx +@@ -16,10 +16,15 @@ + pqSignalAdaptorComboBox::pqSignalAdaptorComboBox(QComboBox* p) + : QObject(p) + { +- QObject::connect(p, SIGNAL(currentIndexChanged(const QString&)), this, +- SIGNAL(currentTextChanged(const QString&))); +- +- QObject::connect(p, SIGNAL(currentIndexChanged(int)), this, SIGNAL(currentIndexChanged(int))); ++ QObject::connect( ++ p, &QComboBox::currentTextChanged, this, &pqSignalAdaptorComboBox::currentTextChanged); ++ ++#if QT_VERSION > QT_VERSION_CHECK(6, 0, 0) ++ QObject::connect( ++ p, &QComboBox::currentIndexChanged, this, &pqSignalAdaptorComboBox::currentIndexChanged); ++#else ++ QObject::connect(p, SIGNAL(currentIndexChanged(int)), this, SLOT(currentIndexChanged(int))); ++#endif + } + + //---------------------------------------------------------------------------- diff --git a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.36.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.36.1-GCCcore-12.3.0.eb index 3921d7fefac6..7e166bd251fc 100644 --- a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.36.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.36.1-GCCcore-12.3.0.eb @@ -1767,12 +1767,6 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JD/JDHEDDEN'], 'checksums': ['9dfd6ca2822724347e0eb6759d00709425814703ad5c66bdb6214579868bcac4'], }), - ('Time::HiRes', '1.9764', { - 'runtest': False, # https://github.com/easybuilders/easybuild-easyconfigs/issues/20145 unreliable atime tests - 'source_tmpl': 'Time-HiRes-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AT/ATOOMIC'], - 'checksums': ['9841be5587bfb7cd1f2fe267b5e5ac04ce25e79d5cc77e5ef9a9c5abd101d7b1'], - }), ('Term::ReadLine::Gnu', '1.45', { 'modulename': 'Term::ReadLine', 'source_tmpl': 'Term-ReadLine-Gnu-%(version)s.tar.gz', diff --git a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.0-GCCcore-13.2.0.eb index 9754ce8b0aea..154ff6fee8f5 100644 --- a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.0-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.0-GCCcore-13.2.0.eb @@ -1770,11 +1770,6 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JD/JDHEDDEN'], 'checksums': ['9dfd6ca2822724347e0eb6759d00709425814703ad5c66bdb6214579868bcac4'], }), - ('Time::HiRes', '1.9764', { - 'source_tmpl': 'Time-HiRes-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AT/ATOOMIC'], - 'checksums': ['9841be5587bfb7cd1f2fe267b5e5ac04ce25e79d5cc77e5ef9a9c5abd101d7b1'], - }), ('Term::ReadLine::Gnu', '1.46', { 'modulename': 'Term::ReadLine', 'source_tmpl': 'Term-ReadLine-Gnu-%(version)s.tar.gz', diff --git a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.2-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..7ea28abbcbb3 --- /dev/null +++ b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.2-GCCcore-13.3.0.eb @@ -0,0 +1,2153 @@ +easyblock = 'PerlBundle' + +name = 'Perl-bundle-CPAN' +version = '5.38.2' + +homepage = 'https://www.perl.org/' +description = """A set of common packages from CPAN""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +builddependencies = [ + ('binutils', '2.42'), + ('groff', '1.23.0'), +] + +dependencies = [ + ('Perl', version), + ('zlib', '1.3.1'), # for Net::SSLeay + ('expat', '2.6.2'), # for XML::Parser + ('ncurses', '6.5'), # for Term::ReadLine::Gnu + ('libreadline', '8.2'), # for Term::ReadLine::Gnu + ('OpenSSL', '3', '', SYSTEM), # required for Net::SSLeay +] + +# !! order of extensions is important !! +# extensions updated on 2024-07-08 +exts_list = [ + ('Config::General', '2.65', { + 'source_tmpl': 'Config-General-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TL/TLINDEN'], + 'checksums': ['4d6d5754be3a9f30906836f0cc10e554c8832e14e7a1341efb15b05d706fc58f'], + }), + ('HTTP::Date', '6.06', { + 'source_tmpl': 'HTTP-Date-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + 'checksums': ['7b685191c6acc3e773d1fc02c95ee1f9fae94f77783175f5e78c181cc92d2b52'], + }), + ('File::Listing', '6.16', { + 'source_tmpl': 'File-Listing-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + 'checksums': ['189b3a13fc0a1ba412b9d9ec5901e9e5e444cc746b9f0156d4399370d33655c6'], + }), + ('ExtUtils::Config', '0.009', { + 'source_tmpl': 'ExtUtils-Config-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['4ef84e73aad50a3be332885d2a3b12f3cab1b1e0bad24e88297a123b4f39f3ce'], + }), + ('ExtUtils::InstallPaths', '0.013', { + 'source_tmpl': 'ExtUtils-InstallPaths-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['65969d3ad8a3a2ea8ef5b4213ed5c2c83961bb5bd12f7ad35128f6bd5b684aa0'], + }), + ('ExtUtils::Helpers', '0.027', { + 'source_tmpl': 'ExtUtils-Helpers-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['9d592131dc5845a86dc28be9143f764e73cb62db06fedf50a895be1324b6cec5'], + }), + ('Test::Harness', '3.48', { + 'source_tmpl': 'Test-Harness-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['e73ff89c81c1a53f6baeef6816841b89d3384403ad97422a7da9d1eeb20ef9c5'], + }), + ('CPAN::Meta::Requirements', '2.143', { + 'source_tmpl': 'CPAN-Meta-Requirements-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS/'], + 'checksums': ['6ec7e4697bb5a8cea0ee3c8bd5d4b20ce086168a8084778d6e7a4c37356fdf8b'], + }), + ('CPAN::Requirements::Dynamic', '0.001', { + 'source_tmpl': 'CPAN-Requirements-Dynamic-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['4b590e712b9aca680c3631855ee16a50b84fa0227c362e13b237a75a01489ef5'], + }), + ('Module::Build::Tiny', '0.048', { + 'source_tmpl': 'Module-Build-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['79a73e506fb7badabdf79137a45c6c5027daaf6f9ac3dcfb9d4ffcce92eb36bd'], + }), + ('aliased', '0.34', { + 'source_tmpl': 'aliased-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['c350524507cd827fab864e5d4c2cc350b1babaa12fa95aec0ca00843fcc7deeb'], + }), + ('Text::Glob', '0.11', { + 'source_tmpl': 'Text-Glob-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + 'checksums': ['069ccd49d3f0a2dedb115f4bdc9fbac07a83592840953d1fcdfc39eb9d305287'], + }), + ('Regexp::Common', '2017060201', { + 'source_tmpl': 'Regexp-Common-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AB/ABIGAIL'], + 'checksums': ['ee07853aee06f310e040b6bf1a0199a18d81896d3219b9b35c9630d0eb69089b'], + }), + ('IO::String', '1.08', { + 'source_tmpl': 'IO-String-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + 'checksums': ['2a3f4ad8442d9070780e58ef43722d19d1ee21a803bf7c8206877a10482de5a0'], + }), + ('Data::Stag', '0.14', { + 'source_tmpl': 'Data-Stag-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CM/CMUNGALL'], + 'checksums': ['4ab122508d2fb86d171a15f4006e5cf896d5facfa65219c0b243a89906258e59'], + }), + ('GO::Utils', '0.15', { + 'source_tmpl': 'go-perl-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CM/CMUNGALL'], + 'checksums': ['423d26155ee85ca51ab2270cee59f4e85b193e57ac3a29aff827298c0a396b12'], + }), + ('Module::Pluggable', '5.2', { + 'source_tmpl': 'Module-Pluggable-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SI/SIMONW'], + 'checksums': ['b3f2ad45e4fd10b3fb90d912d78d8b795ab295480db56dc64e86b9fa75c5a6df'], + }), + ('Try::Tiny', '0.31', { + 'source_tmpl': 'Try-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['3300d31d8a4075b26d8f46ce864a1d913e0e8467ceeba6655d5d2b2e206c11be'], + }), + ('Test::Fatal', '0.017', { + 'source_tmpl': 'Test-Fatal-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['37dfffdafb84b762efe96b02fb2aa41f37026c73e6b83590db76229697f3c4a6'], + }), + ('Test::Warnings', '0.033', { + 'source_tmpl': 'Test-Warnings-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['b9c375719f2c61c5f97aa5ee6cf4c901a972347c415969379b0b51f67c48bbcb'], + }), + ('Class::Inspector', '1.36', { + 'source_tmpl': 'Class-Inspector-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + 'checksums': ['cc295d23a472687c24489d58226ead23b9fdc2588e522f0b5f0747741700694e'], + }), + ('File::ShareDir::Install', '0.14', { + 'source_tmpl': 'File-ShareDir-Install-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['8f9533b198f2d4a9a5288cbc7d224f7679ad05a7a8573745599789428bc5aea0'], + }), + ('File::ShareDir', '1.118', { + 'source_tmpl': 'File-ShareDir-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + 'checksums': ['3bb2a20ba35df958dc0a4f2306fc05d903d8b8c4de3c8beefce17739d281c958'], + }), + ('IPC::System::Simple', '1.30', { + 'source_tmpl': 'IPC-System-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JK/JKEENAN'], + 'checksums': ['22e6f5222b505ee513058fdca35ab7a1eab80539b98e5ca4a923a70a8ae9ba9e'], + }), + ('Importer', '0.026', { + 'source_tmpl': 'Importer-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + 'checksums': ['e08fa84e13cb998b7a897fc8ec9c3459fcc1716aff25cc343e36ef875891b0ef'], + }), + ('Term::Table', '0.018', { + 'source_tmpl': 'Term-Table-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + 'checksums': ['9159b9131ee6b3f3956b74f45422985553574babbfaeba60be5c17bc114ac011'], + }), + ('Scope::Guard', '0.21', { + 'source_tmpl': 'Scope-Guard-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CH/CHOCOLATE'], + 'checksums': ['8c9b1bea5c56448e2c3fadc65d05be9e4690a3823a80f39d2f10fdd8f777d278'], + }), + ('Sub::Info', '0.002', { + 'source_tmpl': 'Sub-Info-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + 'checksums': ['ea3056d696bdeff21a99d340d5570887d39a8cc47bff23adfc82df6758cdd0ea'], + }), + ('Test2::Require::Module', '0.000163', { + 'source_tmpl': 'Test2-Suite-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + 'checksums': ['e336c2d92d43c4f0068aa0d67019d56723ab82471e1bd9028300bb6a1602c0a9'], + }), + ('Test2::Plugin::NoWarnings', '0.10', { + 'source_tmpl': 'Test2-Plugin-NoWarnings-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['c97cb1122cc6e3e4a079059da71e12f65760bfb0671d19d25a7ec7c5f1f240fb'], + }), + ('Class::Tiny', '1.008', { + 'source_tmpl': 'Class-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + 'checksums': ['ee058a63912fa1fcb9a72498f56ca421a2056dc7f9f4b67837446d6421815615'], + }), + ('Path::Tiny', '0.146', { + 'source_tmpl': 'Path-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + 'checksums': ['861ef09bca68254e9ab24337bb6ec9d58593a792e9d68a27ee6bec2150f06741'], + }), + ('Test::Deep', '1.204', { + 'source_tmpl': 'Test-Deep-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['b6591f6ccdd853c7efc9ff3c5756370403211cffe46047f082b1cd1611a84e5f'], + }), + ('Test::File', '1.993', { + 'source_tmpl': 'Test-File-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BD/BDFOY'], + 'checksums': ['ef2ffe1aaec7b42d874ad411ec647547b9b9bc2f5fb93e49e3399488456afc7a'], + }), + ('Test::Needs', '0.002010', { + 'source_tmpl': 'Test-Needs-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + 'checksums': ['923ffdc78fcba96609753e4bae26b0ba0186893de4a63cd5236e012c7c90e208'], + }), + ('Test::Requires', '0.11', { + 'source_tmpl': 'Test-Requires-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TOKUHIROM'], + 'checksums': ['4b88de549597eecddf7c3c38a4d0204a16f59ad804577b671896ac04e24e040f'], + }), + ('File::Copy::Recursive', '0.45', { + 'source_tmpl': 'File-Copy-Recursive-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DM/DMUEY'], + 'checksums': ['d3971cf78a8345e38042b208bb7b39cb695080386af629f4a04ffd6549df1157'], + }), + ('Test::File::ShareDir::Dist', '1.001002', { + 'source_tmpl': 'Test-File-ShareDir-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KE/KENTNL'], + 'checksums': ['b33647cbb4b2f2fcfbde4f8bb4383d0ac95c2f89c4c5770eb691f1643a337aad'], + }), + ('CPAN::Meta::Check', '0.018', { + 'source_tmpl': 'CPAN-Meta-Check-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['f619d2df5ea0fd91c8cf83eb54acccb5e43d9e6ec1a3f727b3d0ac15d0cf378a'], + }), + ('Sub::Exporter::Progressive', '0.001013', { + 'source_tmpl': 'Sub-Exporter-Progressive-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/F/FR/FREW'], + 'checksums': ['d535b7954d64da1ac1305b1fadf98202769e3599376854b2ced90c382beac056'], + }), + ('Module::Runtime', '0.016', { + 'source_tmpl': 'Module-Runtime-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/Z/ZE/ZEFRAM'], + 'checksums': ['68302ec646833547d410be28e09676db75006f4aa58a11f3bdb44ffe99f0f024'], + }), + ('Module::Implementation', '0.09', { + 'source_tmpl': 'Module-Implementation-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['c15f1a12f0c2130c9efff3c2e1afe5887b08ccd033bd132186d1e7d5087fd66d'], + }), + ('B::Hooks::EndOfScope', '0.28', { + 'source_tmpl': 'B-Hooks-EndOfScope-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['edac77a17fc36620c8324cc194ce1fad2f02e9fcbe72d08ad0b2c47f0c7fd8ef'], + }), + ('Package::Stash', '0.40', { + 'source_tmpl': 'Package-Stash-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['5a9722c6d9cb29ee133e5f7b08a5362762a0b5633ff5170642a5b0686e95e066'], + }), + ('namespace::clean', '0.27', { + 'source_tmpl': 'namespace-clean-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RI/RIBASUSHI'], + 'checksums': ['8a10a83c3e183dc78f9e7b7aa4d09b47c11fb4e7d3a33b9a12912fd22e31af9d'], + }), + ('Sub::Identify', '0.14', { + 'source_tmpl': 'Sub-Identify-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RG/RGARCIA'], + 'checksums': ['068d272086514dd1e842b6a40b1bedbafee63900e5b08890ef6700039defad6f'], + }), + ('namespace::autoclean', '0.29', { + 'source_tmpl': 'namespace-autoclean-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['45ebd8e64a54a86f88d8e01ae55212967c8aa8fed57e814085def7608ac65804'], + }), + ('Eval::Closure', '0.14', { + 'source_tmpl': 'Eval-Closure-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DO/DOY'], + 'checksums': ['ea0944f2f5ec98d895bef6d503e6e4a376fea6383a6bc64c7670d46ff2218cad'], + }), + ('Exporter::Tiny', '1.006002', { + 'source_tmpl': 'Exporter-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TOBYINK'], + 'checksums': ['6f295e2cbffb1dbc15bdb9dadc341671c1e0cd2bdf2d312b17526273c322638d'], + }), + ('Type::Tiny', '2.004000', { + 'source_tmpl': 'Type-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TOBYINK'], + 'checksums': ['697e7f775edfc85f4cf07792d04fd19b09c25285f98f5938e8efc4f74507a128'], + }), + ('Class::Data::Inheritable', '0.09', { + 'source_tmpl': 'Class-Data-Inheritable-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSHERER'], + 'checksums': ['44088d6e90712e187b8a5b050ca5b1c70efe2baa32ae123e9bd8f59f29f06e4d'], + }), + ('Devel::StackTrace', '2.05', { + 'source_tmpl': 'Devel-StackTrace-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['63cb6196e986a7e578c4d28b3c780e7194835bfc78b68eeb8f00599d4444888c'], + }), + ('Exception::Class', '1.45', { + 'source_tmpl': 'Exception-Class-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['5482a77ef027ca1f9f39e1f48c558356e954936fc8fbbdee6c811c512701b249'], + }), + ('Role::Tiny', '2.002004', { + 'source_tmpl': 'Role-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + 'checksums': ['d7bdee9e138a4f83aa52d0a981625644bda87ff16642dfa845dcb44d9a242b45'], + }), + ('MRO::Compat', '0.15', { + 'source_tmpl': 'MRO-Compat-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + 'checksums': ['0d4535f88e43babd84ab604866215fc4d04398bd4db7b21852d4a31b1c15ef61'], + }), + ('Sub::Quote', '2.006008', { + 'source_tmpl': 'Sub-Quote-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + 'checksums': ['94bebd500af55762e83ea2f2bc594d87af828072370c7110c60c238a800d15b2'], + }), + ('Specio', '0.48', { + 'source_tmpl': 'Specio-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['0c85793580f1274ef08173079131d101f77b22accea7afa8255202f0811682b2'], + }), + ('Test::Without::Module', '0.22', { + 'source_tmpl': 'Test-Without-Module-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CO/CORION'], + 'checksums': ['27cde4394891028c7d8ecef22a2806308a3389597b70f6a9a421b4247e69052f'], + }), + ('Params::ValidationCompiler', '0.31', { + 'source_tmpl': 'Params-ValidationCompiler-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['7b6497173f1b6adb29f5d51d8cf9ec36d2f1219412b4b2410e9d77a901e84a6d'], + }), + ('DateTime::Locale', '1.42', { + 'source_tmpl': 'DateTime-Locale-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['7d8a138fa32faf24af30a1dbdee4dd11988ddb6a129138004d220b6cc4053cb0'], + }), + ('Class::Singleton', '1.6', { + 'source_tmpl': 'Class-Singleton-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHAY'], + 'checksums': ['27ba13f0d9512929166bbd8c9ef95d90d630fc80f0c9a1b7458891055e9282a4'], + }), + ('DateTime::TimeZone', '2.62', { + 'source_tmpl': 'DateTime-TimeZone-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['6214f9c9c8dfa2000bae912ef2b8ebc5b163a83a0b5b2a82705162dad63466fa'], + }), + ('Module::Build', '0.4234', { + 'source_tmpl': 'Module-Build-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['66aeac6127418be5e471ead3744648c766bd01482825c5b66652675f2bc86a8f'], + }), + ('Params::Validate', '1.31', { + 'source_tmpl': 'Params-Validate-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['1bf2518ef2c4869f91590e219f545c8ef12ed53cf313e0eb5704adf7f1b2961e'], + }), + ('List::MoreUtils::XS', '0.430', { + 'source_tmpl': 'List-MoreUtils-XS-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + 'checksums': ['e8ce46d57c179eecd8758293e9400ff300aaf20fefe0a9d15b9fe2302b9cb242'], + }), + ('List::MoreUtils', '0.430', { + 'source_tmpl': 'List-MoreUtils-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + 'checksums': ['63b1f7842cd42d9b538d1e34e0330de5ff1559e4c2737342506418276f646527'], + }), + ('DateTime', '1.65', { + 'source_tmpl': 'DateTime-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['0bfda7ff0253fb3d88cf4bdb5a14afb8cea24d147975d5bdf3c88b40e7ab140e'], + }), + ('Number::Compare', '0.03', { + 'source_tmpl': 'Number-Compare-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + 'checksums': ['83293737e803b43112830443fb5208ec5208a2e6ea512ed54ef8e4dd2b880827'], + }), + ('File::Find::Rule', '0.34', { + 'source_tmpl': 'File-Find-Rule-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + 'checksums': ['7e6f16cc33eb1f29ff25bee51d513f4b8a84947bbfa18edb2d3cc40a2d64cafe'], + }), + ('Params::Util', '1.102', { + 'source_tmpl': 'Params-Util-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + 'checksums': ['499bb1b482db24fda277a51525596ad092c2bd51dd508fa8fec2e9f849097402'], + }), + ('File::Find::Rule::Perl', '1.16', { + 'source_tmpl': 'File-Find-Rule-Perl-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['ae1886050d9ca21223c073e2870abdc80dc30e3f55289a11c37da3820a8321ff'], + }), + ('Readonly', '2.05', { + 'source_tmpl': 'Readonly-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SA/SANKO'], + 'checksums': ['4b23542491af010d44a5c7c861244738acc74ababae6b8838d354dfb19462b5e'], + }), + ('Git', '0.42', { + 'source_tmpl': 'Git-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MS/MSOUTH'], + 'checksums': ['9469a9f398f3a2bf2b0500566ee41d3ff6fae460412a137185767a1cc4783a6d'], + }), + ('File::Slurp::Tiny', '0.004', { + 'source_tmpl': 'File-Slurp-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['452995beeabf0e923e65fdc627a725dbb12c9e10c00d8018c16d10ba62757f1e'], + }), + ('Tree::DAG_Node', '1.32', { + 'source_tmpl': 'Tree-DAG_Node-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + 'checksums': ['22d9de3d6e6f4afd89e6d825c664f9482878bd49e29cb81342a707af40542d3d'], + }), + ('Template', '3.102', { + 'source_tmpl': 'Template-Toolkit-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + 'checksums': ['d161c89dee9b213a7c55709ea782e2dd5923dbd1215b9576612889e6e74a2e06'], + }), + ('DBI', '1.643', { + 'source_tmpl': 'DBI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TI/TIMB'], + 'checksums': ['8a2b993db560a2c373c174ee976a51027dd780ec766ae17620c20393d2e836fa'], + 'pretestopts': 'LC_ALL=C ', # Test fails if run in localized environments + }), + ('DBD::SQLite', '1.74', { + 'source_tmpl': 'DBD-SQLite-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IS/ISHIGAKI'], + 'checksums': ['8994997d84b9feb4547795f78746c661fb72e3cb6a25dbdd789b731f5688a4dd'], + }), + ('Math::Bezier', '0.01', { + 'source_tmpl': 'Math-Bezier-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AB/ABW'], + 'checksums': ['11a815fc45fdf0efabb1822ab77faad8b9eea162572c5f0940c8ed7d56e6b8b8'], + }), + ('Archive::Extract', '0.88', { + 'source_tmpl': 'Archive-Extract-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': ['cffcf135cd0622287d3b02154f7d6716495449fcaed03966621948e25ea5f742'], + }), + ('DBIx::Simple', '1.37', { + 'source_tmpl': 'DBIx-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JU/JUERD'], + 'checksums': ['46d311aa2ce08907401c56119658426dbb044c5a40de73d9a7b79bf50390cae3'], + }), + ('Shell', '0.73', { + 'source_tmpl': 'Shell-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/F/FE/FERREIRA'], + 'checksums': ['f7dbebf65261ed0e5abd0f57052b64d665a1a830bab4c8bbc220f235bd39caf5'], + }), + ('Test::Simple', '1.302199', { + 'source_tmpl': 'Test-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + 'checksums': ['7b4b03cee7f9e928fe10e8a3efef02b2a286f0877979694b2a9ef99250bd8c5c'], + }), + ('Set::Scalar', '1.29', { + 'source_tmpl': 'Set-Scalar-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAVIDO'], + 'checksums': ['a3dc1526f3dde72d3c64ea00007b86ce608cdcd93567cf6e6e42dc10fdc4511d'], + }), + ('IO::Stringy', '2.113', { + 'source_tmpl': 'IO-Stringy-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CA/CAPOEIRAB'], + 'checksums': ['51220fcaf9f66a639b69d251d7b0757bf4202f4f9debd45bdd341a6aca62fe4e'], + }), + ('Encode::Locale', '1.05', { + 'source_tmpl': 'Encode-Locale-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + 'checksums': ['176fa02771f542a4efb1dbc2a4c928e8f4391bf4078473bd6040d8f11adb0ec1'], + }), + ('XML::SAX::Base', '1.09', { + 'source_tmpl': 'XML-SAX-Base-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GR/GRANTM'], + 'checksums': ['66cb355ba4ef47c10ca738bd35999723644386ac853abbeb5132841f5e8a2ad0'], + }), + ('XML::NamespaceSupport', '1.12', { + 'source_tmpl': 'XML-NamespaceSupport-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PERIGRIN'], + 'checksums': ['47e995859f8dd0413aa3f22d350c4a62da652e854267aa0586ae544ae2bae5ef'], + }), + ('XML::SAX', '1.02', { + 'source_tmpl': 'XML-SAX-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GR/GRANTM'], + 'checksums': ['4506c387043aa6a77b455f00f57409f3720aa7e553495ab2535263b4ed1ea12a'], + }), + ('Test::LeakTrace', '0.17', { + 'source_tmpl': 'Test-LeakTrace-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEEJO'], + 'checksums': ['777d64d2938f5ea586300eef97ef03eacb43d4c1853c9c3b1091eb3311467970'], + }), + ('Sub::Uplevel', '0.2800', { + 'source_tmpl': 'Sub-Uplevel-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + 'checksums': ['b4f3f63b80f680a421332d8851ddbe5a8e72fcaa74d5d1d98f3c8cc4a3ece293'], + }), + ('Test::Exception', '0.43', { + 'source_tmpl': 'Test-Exception-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + 'checksums': ['156b13f07764f766d8b45a43728f2439af81a3512625438deab783b7883eb533'], + }), + ('Text::Aligner', '0.16', { + 'source_tmpl': 'Text-Aligner-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + 'checksums': ['5c857dbce586f57fa3d7c4ebd320023ab3b2963b2049428ae01bd3bc4f215725'], + }), + ('Text::Table', '1.135', { + 'source_tmpl': 'Text-Table-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + 'checksums': ['fca3c16e83127f7c44dde3d3f7e3c73ea50d109a1054445de8082fea794ca5d2'], + }), + ('MIME::Types', '2.26', { + 'source_tmpl': 'MIME-Types-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], + 'checksums': ['bc738483cb4cdb47d61e85fe9304fa929aa9ab927e3171ec2ba2ab1cd7cefdff'], + }), + ('Cwd::Guard', '0.05', { + 'source_tmpl': 'Cwd-Guard-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KAZEBURO'], + 'checksums': ['7afc7ca2b9502e440241938ad97a3e7ebd550180ebd6142e1db394186b268e77'], + }), + ('Capture::Tiny', '0.48', { + 'source_tmpl': 'Capture-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + 'checksums': ['6c23113e87bad393308c90a207013e505f659274736638d8c79bac9c67cc3e19'], + }), + ('File::Copy::Recursive::Reduced', '0.008', { + 'source_tmpl': 'File-Copy-Recursive-Reduced-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JK/JKEENAN'], + 'checksums': ['462bd66bf55e74b78f29ebdc9626af622d4f0115b5191b03167e82164db98f5a'], + }), + ('Module::Build::XSUtil', '0.19', { + 'source_tmpl': 'Module-Build-XSUtil-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HI/HIDEAKIO'], + 'checksums': ['9063b3c346edeb422807ffe49ffb23038c4f900d4a77b845ce4b53d97bf29400'], + }), + ('Tie::Function', '0.02', { + 'source_tmpl': 'Tie-Function-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAVIDNICO/handy_tied_functions'], + 'checksums': ['0b1617af218dfab911ba0fbd72210529a246efe140332da77fe3e03d11000117'], + }), + ('Number::Format', '1.76', { + 'source_tmpl': 'Number-Format-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['0e0060eb363635a885706c6a26f5fcaafeae759f7b2acae49dda70e195dd44d6'], + }), + ('Template::Plugin::Number::Format', '1.06', { + 'source_tmpl': 'Template-Plugin-Number-Format-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DARREN'], + 'checksums': ['0865836a1bcbc34d4a0ee34b5ccc14d7b511f1fd300bf390f002dac349539843'], + }), + ('HTML::Tagset', '3.24', { + 'source_tmpl': 'HTML-Tagset-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PETDANCE'], + 'checksums': ['eb89e145a608ed1f8f141a57472ee5f69e67592a432dcd2e8b1dbb445f2b230b'], + }), + ('URI', '5.28', { + 'source_tmpl': 'URI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + 'checksums': ['e7985da359b15efd00917fa720292b711c396f2f9f9a7349e4e7dec74aa79765'], + }), + ('B::COW', '0.007', { + 'source_tmpl': 'B-COW-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AT/ATOOMIC'], + 'checksums': ['1290daf227e8b09889a31cf182e29106f1cf9f1a4e9bf7752f9de92ed1158b44'], + }), + ('Clone', '0.46', { + 'source_tmpl': 'Clone-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GARU'], + 'checksums': ['aadeed5e4c8bd6bbdf68c0dd0066cb513e16ab9e5b4382dc4a0aafd55890697b'], + }), + ('IO::HTML', '1.004', { + 'source_tmpl': 'IO-HTML-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJM'], + 'checksums': ['c87b2df59463bbf2c39596773dfb5c03bde0f7e1051af339f963f58c1cbd8bf5'], + }), + ('LWP::MediaTypes', '6.04', { + 'source_tmpl': 'LWP-MediaTypes-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + 'checksums': ['8f1bca12dab16a1c2a7c03a49c5e58cce41a6fec9519f0aadfba8dad997919d9'], + }), + ('HTTP::Message', '6.46', { + 'source_tmpl': 'HTTP-Message-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + 'checksums': ['e27443434150d2d1259bb1e5c964429f61559b0ae34b5713090481994936e2a5'], + }), + ('HTML::Parser', '3.82', { + 'source_tmpl': 'HTML-Parser-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + 'checksums': ['5b1f20dd0e471a049c13a53d0fcd0442f58518889180536c6f337112c9a430d8'], + }), + ('Date::Handler', '1.2', { + 'source_tmpl': 'Date-Handler-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BB/BBEAUSEJ'], + 'checksums': ['c36fd2b68d48c2e17417bf2873c78820f3ae02460fdf5976b8eeab887d59e16c'], + }), + ('XML::Parser', '2.47', { + 'source_tmpl': 'XML-Parser-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + 'checksums': ['ad4aae643ec784f489b956abe952432871a622d4e2b5c619e8855accbfc4d1d8'], + }), + ('Data::Grove', '0.08', { + 'source_tmpl': 'libxml-perl-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KM/KMACLEOD'], + 'checksums': ['4571059b7b5d48b7ce52b01389e95d798bf5cf2020523c153ff27b498153c9cb'], + }), + ('Class::ISA', '0.36', { + 'source_tmpl': 'Class-ISA-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SM/SMUELLER'], + 'checksums': ['8816f34e9a38e849a10df756030dccf9fe061a196c11ac3faafd7113c929b964'], + }), + ('DBIx::ContextualFetch', '1.03', { + 'source_tmpl': 'DBIx-ContextualFetch-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TM/TMTM'], + 'checksums': ['85e2f805bfc81cd738c294316b27a515397036f397a0ff1c6c8d754c38530306'], + }), + ('Ima::DBI', '0.35', { + 'source_tmpl': 'Ima-DBI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PERRIN'], + 'checksums': ['8b481ceedbf0ae4a83effb80581550008bfdd3885ef01145e3733c7097c00a08'], + }), + ('Tie::IxHash', '1.23', { + 'source_tmpl': 'Tie-IxHash-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CH/CHORNY'], + 'checksums': ['fabb0b8c97e67c9b34b6cc18ed66f6c5e01c55b257dcf007555e0b027d4caf56'], + }), + ('Parse::RecDescent', '1.967015', { + 'source_tmpl': 'Parse-RecDescent-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JT/JTBRAUN'], + 'checksums': ['1943336a4cb54f1788a733f0827c0c55db4310d5eae15e542639c9dd85656e37'], + }), + ('GO', '0.04', { + 'runtest': False, # Problem with indirect dependency DBD::Pg + 'source_tmpl': 'go-db-perl-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SJ/SJCARBON'], + 'checksums': ['8eb73d591ad767e7cf26def40cffd84833875f1ad51e456960b9ed73dc23641b'], + }), + ('Class::Trigger', '0.15', { + 'source_tmpl': 'Class-Trigger-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], + 'checksums': ['b7a878d44dea67d64df2ca18020d9d868a95596debd16f1a264874209332b07f'], + }), + ('Class::Accessor', '0.51', { + 'source_tmpl': 'Class-Accessor-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KASEI'], + 'checksums': ['bf12a3e5de5a2c6e8a447b364f4f5a050bf74624c56e315022ae7992ff2f411c'], + }), + ('UNIVERSAL::moniker', '0.08', { + 'source_tmpl': 'UNIVERSAL-moniker-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KASEI'], + 'checksums': ['94ce27a546cd57cb52e080a8f2533a7cc2350028388582485bd1039a37871f9c'], + }), + ('Class::DBI', 'v3.0.17', { + 'source_tmpl': 'Class-DBI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TM/TMTM'], + 'checksums': ['541354fe361c56850cb11261f6ca089a14573fa764792447444ff736ae626206'], + }), + ('Class::DBI::SQLite', '0.11', { + 'source_tmpl': 'Class-DBI-SQLite-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], + 'checksums': ['c4661b00afb7e53c97ac36e13f34dde43c1a93540a2f4ff97e6182b0c731e4e7'], + }), + ('File::Slurper', '0.014', { + 'source_tmpl': 'File-Slurper-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['d5a36487339888c3cd758e648160ee1d70eb4153cacbaff57846dbcefb344b0c'], + }), + ('Pod::POM', '2.01', { + 'source_tmpl': 'Pod-POM-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + 'checksums': ['1b50fba9bbdde3ead192beeba0eaddd0c614e3afb1743fa6fff805f57c56f7f4'], + }), + ('Math::Round', '0.08', { + 'source_tmpl': 'Math-Round-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + 'checksums': ['7b4d2775ad3b859a5fd61f7f3fc5cfba42b1a10df086d2ed15a0ae712c8fd402'], + }), + ('Algorithm::Diff', '1.201', { + 'source_tmpl': 'Algorithm-Diff-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['0022da5982645d9ef0207f3eb9ef63e70e9713ed2340ed7b3850779b0d842a7d'], + }), + ('Text::Diff', '1.45', { + 'source_tmpl': 'Text-Diff-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + 'checksums': ['e8baa07b1b3f53e00af3636898bbf73aec9a0ff38f94536ede1dbe96ef086f04'], + }), + ('Log::Message', '0.08', { + 'source_tmpl': 'Log-Message-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': ['bd697dd62aaf26d118e9f0a0813429deb1c544e4501559879b61fcbdfe99fe46'], + }), + ('Log::Message::Simple', '0.10', { + 'source_tmpl': 'Log-Message-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': ['aa12d1a4c0ac260b94d448fa01feba242a8a85cb6cbfdc66432e3b5b468add96'], + }), + ('Net::SSLeay', '1.94', { + 'preconfigopts': "export OPENSSL_PREFIX=$EBROOTOPENSSL && ", + 'source_tmpl': 'Net-SSLeay-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CH/CHRISN'], + 'checksums': ['9d7be8a56d1bedda05c425306cc504ba134307e0c09bda4a788c98744ebcd95d'], + }), + ('IO::Socket::SSL', '2.087', { + 'source_tmpl': 'IO-Socket-SSL-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SU/SULLR'], + 'checksums': ['936a46c58312df272313fedb4bb39faea7481629c163d83a8cdd283a0e28c578'], + }), + ('Fennec::Lite', '0.004', { + 'source_tmpl': 'Fennec-Lite-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + 'checksums': ['dce28e3932762c2ff92aa52d90405c06e898e81cb7b164ccae8966ae77f1dcab'], + }), + ('Meta::Builder', '0.004', { + 'source_tmpl': 'Meta-Builder-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + 'checksums': ['acb499aa7206eb9db21eb85357a74521bfe3bdae4a6416d50a7c75b939cf56fe'], + }), + ('Exporter::Declare', '0.114', { + 'source_tmpl': 'Exporter-Declare-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + 'checksums': ['4bd70d6ca76f6f6ba7e4c618d4ac93b8593a58f1233ccbe18b10f5f204f1d4e4'], + }), + ('Mouse', 'v2.5.10', { + 'source_tmpl': 'Mouse-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SK/SKAJI'], + 'checksums': ['ce8dc23946153a467ff09765167ee2590f5c502120f48a2d9441733f39aa32ee'], + }), + ('Test::Version', '2.09', { + 'source_tmpl': 'Test-Version-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + 'checksums': ['9ce1dd2897a5f30e1b7f8966ec66f57d8d8f280f605f28c7ca221fa79aca38e0'], + }), + ('Class::Method::Modifiers', '2.15', { + 'source_tmpl': 'Class-Method-Modifiers-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['65cd85bfe475d066e9186f7a8cc636070985b30b0ebb1cde8681cf062c2e15fc'], + }), + ('Moo', '2.005005', { + 'source_tmpl': 'Moo-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + 'checksums': ['fb5a2952649faed07373f220b78004a9c6aba387739133740c1770e9b1f4b108'], + }), + ('Data::Dumper::Concise', '2.023', { + 'source_tmpl': 'Data-Dumper-Concise-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['a6c22f113caf31137590def1b7028a7e718eface3228272d0672c25e035d5853'], + }), + ('DBIx::Admin::CreateTable', '2.11', { + 'source_tmpl': 'DBIx-Admin-CreateTable-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + 'checksums': ['07b1427fbc15455657ca57217749004162a50c04abb243022a5b479e4b2a5912'], + }), + ('Config::Tiny', '2.30', { + 'source_tmpl': 'Config-Tiny-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + 'checksums': ['b2f7345619b3b8e636dd39ea010731c9dc2bfb8f022bcbd86ae6ad17866e110d'], + }), + ('File::Slurp', '9999.32', { + 'source_tmpl': 'File-Slurp-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CA/CAPOEIRAB'], + 'checksums': ['4c3c21992a9d42be3a79dd74a3c83d27d38057269d65509a2f555ea0fb2bc5b0'], + }), + ('DBIx::Admin::DSNManager', '2.02', { + 'source_tmpl': 'DBIx-Admin-DSNManager-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + 'checksums': ['c25511f42328ccb606a0cd78413a74181c87fb37a382d38aa3fad106b540adcb'], + }), + ('Lingua::EN::PluralToSingular', '0.21', { + 'source_tmpl': 'Lingua-EN-PluralToSingular-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BK/BKB'], + 'checksums': ['f8a8b7de28c25c96190d7f48c90b5ad9b9bf517f3835c77641f0e8fa546c0d1d'], + }), + ('Test::Warn', '0.37', { + 'source_tmpl': 'Test-Warn-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BIGJ'], + 'checksums': ['98ca32e7f2f5ea89b8bfb9a0609977f3d153e242e2e51705126cb954f1a06b57'], + }), + ('Test::Differences', '0.71', { + 'runtest': False, # Cryptic test failing + 'source_tmpl': 'Test-Differences-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DC/DCANTRELL'], + 'checksums': ['cac16a56cd843b0809e5b49199d60d75a8dbad7ca9a08380dbf3f5cc3aaa38d9'], + }), + ('Test::Most', '0.38', { + 'source_tmpl': 'Test-Most-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OV/OVID'], + 'checksums': ['089eb894f7bace4c37c6334e0e290eb20338ee10223af0c82cbe7281c78382df'], + }), + ('Const::Fast', '0.014', { + 'source_tmpl': 'Const-Fast-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['f805953a08c57846a16a4d85d7b766398afaf7c36c1465fcb1dea09e5fa394db'], + }), + ('Ref::Util', '0.204', { + 'source_tmpl': 'Ref-Util-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AR/ARC'], + 'checksums': ['415fa73dbacf44f3d5d79c14888cc994562720ab468e6f71f91cd1f769f105e1'], + }), + ('Class::XSAccessor', '1.19', { + 'source_tmpl': 'Class-XSAccessor-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SM/SMUELLER'], + 'checksums': ['99c56b395f1239af19901f2feeb125d9ecb4e351a0d80daa9529211a4700a6f2'], + }), + ('Hash::Objectify', '0.008', { + 'source_tmpl': 'Hash-Objectify-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + 'checksums': ['236d5829cdebf3ba648d34e1295cd9099a20506d8d0284668e617e0058cebeed'], + }), + ('Const::Exporter', 'v1.2.3', { + 'source_tmpl': 'Const-Exporter-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RR/RRWO'], + 'checksums': ['53e59b4764aebcf79bbed533ab5a6107339fe516b7f2f607b1bae8dd9dcf7015'], + }), + ('HTML::Entities::Interpolate', '1.10', { + 'source_tmpl': 'HTML-Entities-Interpolate-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + 'checksums': ['f15a9df92c282419f7010964aca1ada844ddfae7afc735cd2ba1bb20883e955c'], + }), + ('List::SomeUtils', '0.59', { + 'source_tmpl': 'List-SomeUtils-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['fab30372e4c67bf5a46062da38d1d0c8756279feada866eb439fa29571a2dc7b'], + }), + ('List::UtilsBy', '0.12', { + 'source_tmpl': 'List-UtilsBy-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PEVANS'], + 'checksums': ['fff1281fd469fe982b1a58044becfd970f313bff3a26e1c7b2b3f4c0a5ed71e0'], + }), + ('List::AllUtils', '0.19', { + 'source_tmpl': 'List-AllUtils-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['30a8146ab21a7787b8c56d5829cf9a7f2b15276d3b3fca07336ac38d3002ffbc'], + }), + ('Unicode::EastAsianWidth', '12.0', { + 'source_tmpl': 'Unicode-EastAsianWidth-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AU/AUDREYT'], + 'checksums': ['2a5bfd926c4fe5f77e6137da2c31ac2545282ae5fec6e9af0fdd403555a90ff4'], + }), + ('String::TtyLength', '0.03', { + 'source_tmpl': 'String-TtyLength-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + 'checksums': ['4fedaf72028511d80eb6afba523993e9aaa245d7af558345d5d4ed46e2e82ce1'], + }), + ('Text::Table::Manifold', '1.03', { + 'source_tmpl': 'Text-Table-Manifold-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + 'checksums': ['e680713169557b0768952fa6932f25576a61dccfb96bd9036dcf6fcefb35e09e'], + }), + ('DBIx::Admin::TableInfo', '3.04', { + 'source_tmpl': 'DBIx-Admin-TableInfo-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + 'checksums': ['b9625992683b97378bea0947773f50e3c9f81974048b84f4c3422cae7e6082f4'], + }), + ('Net::HTTP', '6.23', { + 'runtest': False, # Fragile tests + 'source_tmpl': 'Net-HTTP-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + 'checksums': ['0d65c09dd6c8589b2ae1118174d3c1a61703b6ecfc14a3442a8c74af65e0c94e'], + }), + ('Clone::Choose', '0.010', { + 'source_tmpl': 'Clone-Choose-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HE/HERMES'], + 'checksums': ['5623481f58cee8edb96cd202aad0df5622d427e5f748b253851dfd62e5123632'], + }), + ('Hash::Merge', '0.302', { + 'source_tmpl': 'Hash-Merge-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HE/HERMES'], + 'checksums': ['ae0522f76539608b61dde14670e79677e0f391036832f70a21f31adde2538644'], + }), + ('SQL::Abstract', '2.000001', { + 'source_tmpl': 'SQL-Abstract-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MS/MSTROUT'], + 'checksums': ['35a642662c349420d44be6e0ef7d8765ea743eb12ad14399aa3a232bb94e6e9a'], + }), + ('HTML::Form', '6.11', { + 'source_tmpl': 'HTML-Form-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SI/SIMBABQUE'], + 'checksums': ['43bfaa7087393487d2d51261a1aa7f6f81a97b1d8fef7a48fcf6ef32b16d6454'], + }), + ('IPC::Run', '20231003.0', { + 'source_tmpl': 'IPC-Run-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + 'checksums': ['eb25bbdf5913d291797ef1bfe998f15130b455d3ed02aacde6856f0b25e4fe57'], + }), + ('File::Remove', '1.61', { + 'source_tmpl': 'File-Remove-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + 'checksums': ['fd857f585908fc503461b9e48b3c8594e6535766bc14beb17c90ba58d5dc4975'], + }), + ('YAML::Tiny', '1.74', { + 'source_tmpl': 'YAML-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['7b38ca9f5d3ce24230a6b8bdc1f47f5b2db348e7f7f9666c26f5955636e33d6c'], + }), + ('Module::Install', '1.21', { + 'source_tmpl': 'Module-Install-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['fbf91007f30565f3920e106055fd0d4287981d5e7dad8b35323ce4b733f15a7b'], + }), + ('Test::ClassAPI', '1.07', { + 'source_tmpl': 'Test-ClassAPI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['30e9dbfc5e0cc2ee14eae8f3465a908a710daecbd0a3ebdb2888fc4504fa18aa'], + }), + ('HTTP::Tiny', '0.088', { + 'source_tmpl': 'HTTP-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + 'checksums': ['7ce6367e861883b6868d6dd86168af33524717d8cc94100c2abf9bd86a82b4d8'], + }), + ('Sub::Install', '0.929', { + 'source_tmpl': 'Sub-Install-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['80b1e281d8cd3b2b31dac711f5c8a1657a87cd80bbe69af3924bcbeb4e5db077'], + }), + ('Package::DeprecationManager', '0.18', { + 'source_tmpl': 'Package-DeprecationManager-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['b68d3f0ced55b7615fddbb6029b89f92a34fe0dd8c6fd6bceffc157d56834fe8'], + }), + ('Digest::SHA1', '2.13', { + 'source_tmpl': 'Digest-SHA1-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + 'checksums': ['68c1dac2187421f0eb7abf71452a06f190181b8fc4b28ededf5b90296fb943cc'], + }), + ('Date::Language', '2.33', { + 'source_tmpl': 'TimeDate-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AT/ATOOMIC'], + 'checksums': ['c0b69c4b039de6f501b0d9f13ec58c86b040c1f7e9b27ef249651c143d605eb2'], + }), + ('version', '0.9932', { + 'source_tmpl': 'version-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['e7b5e8fcb8dfd1d6147b931a382e9dc377b3485ade18bea342dad11226be6f7f'], + }), + ('XML::Bare', '0.53', { + 'source_tmpl': 'XML-Bare-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CO/CODECHILD'], + 'checksums': ['865e198e98d904be1683ef5a53a4948f02dabdacde59fc554a082ffbcc5baefd'], + }), + ('Dist::CheckConflicts', '0.11', { + 'source_tmpl': 'Dist-CheckConflicts-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DO/DOY'], + 'checksums': ['ea844b9686c94d666d9d444321d764490b2cde2f985c4165b4c2c77665caedc4'], + }), + ('Sub::Name', '0.27', { + 'source_tmpl': 'Sub-Name-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['ecf36fba1c47ca93e1daa394968ed39c4186867459d9cd173c421e2b972043e8'], + }), + ('Time::Piece', '1.3401', { + 'source_tmpl': 'Time-Piece-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ES/ESAYM'], + 'checksums': ['4b55b7bb0eab45cf239a54dfead277dfa06121a43e63b3fce0853aecfdb04c27'], + }), + ('Digest::HMAC', '1.04', { + 'source_tmpl': 'Digest-HMAC-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AR/ARODLAND'], + 'checksums': ['d6bc8156aa275c44d794b7c18f44cdac4a58140245c959e6b19b2c3838b08ed4'], + }), + ('HTTP::Negotiate', '6.01', { + 'source_tmpl': 'HTTP-Negotiate-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + 'checksums': ['1c729c1ea63100e878405cda7d66f9adfd3ed4f1d6cacaca0ee9152df728e016'], + }), + ('Email::Date::Format', '1.008', { + 'source_tmpl': 'Email-Date-Format-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['432b7c83ff88749af128003f5257c573aec1a463418db90ed22843cbbc258b4f'], + }), + ('MIME::Lite', '3.033', { + 'source_tmpl': 'MIME-Lite-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['78a279f1d2e242551c347ef97a13fc675766602cb84c2a80c569400f4f368bab'], + }), + ('Crypt::Rijndael', '1.16', { + 'source_tmpl': 'Crypt-Rijndael-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['6540085e3804b82a6f0752c1122cf78cadd221990136dd6fd4c097d056c84d40'], + }), + ('B::Lint', '1.20', { + 'runtest': False, # One failing subtest + 'source_tmpl': 'B-Lint-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['dc49408964fd8b7963859c92e013f0b9f92f74be5a7c2a78e3996279827c10b3'], + }), + ('Canary::Stability', '2013', { + 'source_tmpl': 'Canary-Stability-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], + 'checksums': ['a5c91c62cf95fcb868f60eab5c832908f6905221013fea2bce3ff57046d7b6ea'], + }), + ('AnyEvent', '7.17', { + 'source_tmpl': 'AnyEvent-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], + 'checksums': ['50beea689c098fe4aaeb83806c40b9fe7f946d5769acf99f849f099091a4b985'], + }), + ('Object::Accessor', '0.48', { + 'source_tmpl': 'Object-Accessor-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': ['76cb824a27b6b4e560409fcf6fd5b3bfbbd38b72f1f3d37ed0b54bd9c0baeade'], + }), + ('Data::UUID', '1.227', { + 'source_tmpl': 'Data-UUID-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GT/GTERMARS'], + 'checksums': ['95bda7276265f57bc48ffdeddec5ef28cd6f765e3a183757fa5f09f0ce6b98ac'], + }), + ('Test::Pod', '1.52', { + 'source_tmpl': 'Test-Pod-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['60a8dbcc60168bf1daa5cc2350236df9343e9878f4ab9830970a5dde6fe8e5fc'], + }), + ('AppConfig', '1.71', { + 'source_tmpl': 'AppConfig-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + 'checksums': ['1177027025ecb09ee64d9f9f255615c04db5e14f7536c344af632032eb887b0f'], + }), + ('Net::SMTP::SSL', '1.04', { + 'source_tmpl': 'Net-SMTP-SSL-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['7b29c45add19d3d5084b751f7ba89a8e40479a446ce21cfd9cc741e558332a00'], + }), + ('XML::Tiny', '2.07', { + 'source_tmpl': 'XML-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DC/DCANTRELL'], + 'checksums': ['ce39fcb53e0fe9f1cbcd86ddf152e1db48566266b70ec0769ef364eeabdd8941'], + }), + ('HTML::Tree', '5.07', { + 'source_tmpl': 'HTML-Tree-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KE/KENTNL'], + 'checksums': ['f0374db84731c204b86c1d5b90975fef0d30a86bd9def919343e554e31a9dbbf'], + }), + ('Devel::GlobalDestruction', '0.14', { + 'source_tmpl': 'Devel-GlobalDestruction-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + 'checksums': ['34b8a5f29991311468fe6913cadaba75fd5d2b0b3ee3bb41fe5b53efab9154ab'], + }), + ('WWW::RobotRules', '6.02', { + 'source_tmpl': 'WWW-RobotRules-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + 'checksums': ['46b502e7a288d559429891eeb5d979461dd3ecc6a5c491ead85d165b6e03a51e'], + }), + ('IO::Tty', '1.20', { + 'source_tmpl': 'IO-Tty-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + 'checksums': ['b15309fc85623893289cb9b2b88dfa9ed1e69156b75f29938553a45be6d730af'], + }), + ('Expect', '1.38', { + 'source_tmpl': 'Expect-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JA/JACOBY'], + 'checksums': ['7b1048335f327958903867cea079dc072ea07f4eafae1b40c2e6f25db21686c0'], + }), + ('Term::UI', '0.50', { + 'source_tmpl': 'Term-UI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': ['60bfdd6d4c158b88d370133fc65b20485a36a45b12d906000b81c78ca524163d'], + }), + ('Net::SNMP', 'v6.0.1', { + 'source_tmpl': 'Net-SNMP-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DT/DTOWN'], + 'checksums': ['14c37bc1cbb3f3cdc7d6c13e0f27a859f14cdcfd5ea54a0467a88bc259b0b741'], + }), + ('XML::Filter::BufferText', '1.01', { + 'source_tmpl': 'XML-Filter-BufferText-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RB/RBERJON'], + 'checksums': ['8fd2126d3beec554df852919f4739e689202cbba6a17506e9b66ea165841a75c'], + }), + ('XML::SAX::Writer', '0.57', { + 'source_tmpl': 'XML-SAX-Writer-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PERIGRIN'], + 'checksums': ['3d61d07ef43b0126f5b4de4f415a256fa859fa88dc4fdabaad70b7be7c682cf0'], + }), + ('Statistics::Descriptive', '3.0801', { + 'source_tmpl': 'Statistics-Descriptive-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + 'checksums': ['047b70a63fdcaa916168e0ff2d58e155e0ebbc68ed4ccbd73a7213dca3028f65'], + }), + ('Data::OptList', '0.114', { + 'source_tmpl': 'Data-OptList-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['9fd1093b917a21fb79ae1607db53d113b4e0ad8fe0ae776cb077a7e50044fdf3'], + }), + ('Class::Load', '0.25', { + 'source_tmpl': 'Class-Load-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['2a48fa779b5297e56156380e8b32637c6c58decb4f4a7f3c7350523e11275f8f'], + }), + ('HTTP::Daemon', '6.16', { + 'source_tmpl': 'HTTP-Daemon-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + 'checksums': ['b38d092725e6fa4e0c4dc2a47e157070491bafa0dbe16c78a358e806aa7e173d'], + }), + ('Test::RequiresInternet', '0.05', { + 'source_tmpl': 'Test-RequiresInternet-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MALLEN'], + 'checksums': ['bba7b32a1cc0d58ce2ec20b200a7347c69631641e8cae8ff4567ad24ef1e833e'], + }), + ('HTTP::Cookies', '6.11', { + 'source_tmpl': 'HTTP-Cookies-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + 'checksums': ['8c9a541a4a39f6c0c7e3d0b700b05dfdb830bd490a1b1942a7dedd1b50d9a8c8'], + }), + ('HTTP::CookieJar', '0.014', { + 'source_tmpl': 'HTTP-CookieJar-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + 'checksums': ['7094ea5c91f536d263b85e83ab4e9a963e11c4408ce08ecae553fa9c0cc47e73'], + }), + ('LWP::Simple', '6.77', { + 'source_tmpl': 'libwww-perl-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + 'checksums': ['94a907d6b3ea8d966ef43deffd4fa31f5500142b4c00489bfd403860a5f060e4'], + }), + ('Time::Piece::MySQL', '0.06', { + 'source_tmpl': 'Time-Piece-MySQL-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KASEI'], + 'checksums': ['319601feec17fae344988a5ee91cfc6a0bcfe742af77dba254724c3268b2a60f'], + }), + ('Package::Stash::XS', '0.30', { + 'source_tmpl': 'Package-Stash-XS-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['26bad65c1959c57379b3e139dc776fbec5f702906617ef27cdc293ddf1239231'], + }), + ('Want', '0.29', { + 'source_tmpl': 'Want-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RO/ROBIN'], + 'checksums': ['b4e4740b8d4cb783591273c636bd68304892e28d89e88abf9273b1de17f552f7'], + }), + ('Set::Array', '0.30', { + 'source_tmpl': 'Set-Array-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + 'checksums': ['d9f024c8e3637feccdebcf6479b6754b6c92f1209f567feaf0c23818af31ee3c'], + }), + ('boolean', '0.46', { + 'source_tmpl': 'boolean-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IN/INGY'], + 'checksums': ['95c088085c3e83bf680fe6ce16d8264ec26310490f7d1680e416ea7a118f156a'], + }), + ('Test::NoWarnings', '1.06', { + 'source_tmpl': 'Test-NoWarnings-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + 'checksums': ['c2dc51143b7eb63231210e27df20d2c8393772e0a333547ec8b7a205ed62f737'], + }), + ('Crypt::DES', '2.07', { + 'source_tmpl': 'Crypt-DES-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DP/DPARIS'], + 'checksums': ['2db1ebb5837b4cb20051c0ee5b733b4453e3137df0a92306034c867621edd7e7'], + }), + ('XML::XPath', '1.48', { + 'source_tmpl': 'XML-XPath-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MANWAR'], + 'checksums': ['7bc75be36b239e5b2e700a9570d2b53b43093d467f2abe6a743f9ff9093790cd'], + }), + ('JSON', '4.10', { + 'source_tmpl': 'JSON-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IS/ISHIGAKI'], + 'checksums': ['df8b5143d9a7de99c47b55f1a170bd1f69f711935c186a6dc0ab56dd05758e35'], + }), + ('Sub::Exporter', '0.991', { + 'source_tmpl': 'Sub-Exporter-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['2a95695d35c5d0d5373a7e145c96b9b016113b74e94116835ac05450cae4d445'], + }), + ('Class::Load::XS', '0.10', { + 'source_tmpl': 'Class-Load-XS-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['5bc22cf536ebfd2564c5bdaf42f0d8a4cee3d1930fc8b44b7d4a42038622add1'], + }), + ('Data::Types', '0.17', { + 'source_tmpl': 'Data-Types-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MANWAR'], + 'checksums': ['860751feb79b7dfc1af71c4b7fe920220ec6d31c4ab9402b8f178f7f4b8293c1'], + }), + ('Set::IntSpan::Fast', '1.15', { + 'source_tmpl': 'Set-IntSpan-Fast-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AN/ANDYA'], + 'checksums': ['cfb1768c24f55208e87405b17f537f0f303fa141891d0b22d509a941aa57e24e'], + }), + ('Text::Iconv', '1.7', { + 'source_tmpl': 'Text-Iconv-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MP/MPIOTR'], + 'checksums': ['5b80b7d5e709d34393bcba88971864a17b44a5bf0f9e4bcee383d029e7d2d5c3'], + }), + ('Text::Balanced', '2.06', { + 'source_tmpl': 'Text-Balanced-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHAY'], + 'checksums': ['773e0f0f21c0cb2cf664cee6ba28ff70259babcc892f9b650f9cbda00be092ad'], + }), + ('strictures', '2.000006', { + 'source_tmpl': 'strictures-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + 'checksums': ['09d57974a6d1b2380c802870fed471108f51170da81458e2751859f2714f8d57'], + }), + ('Switch', '2.17', { + 'source_tmpl': 'Switch-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CH/CHORNY'], + 'checksums': ['31354975140fe6235ac130a109496491ad33dd42f9c62189e23f49f75f936d75'], + }), + ('File::Which', '1.27', { + 'source_tmpl': 'File-Which-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + 'checksums': ['3201f1a60e3f16484082e6045c896842261fc345de9fb2e620fd2a2c7af3a93a'], + }), + ('Error', '0.17029', { + 'source_tmpl': 'Error-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + 'checksums': ['1a23f7913032aed6d4b68321373a3899ca66590f4727391a091ec19c95bf7adc'], + }), + ('Mock::Quick', '1.111', { + 'source_tmpl': 'Mock-Quick-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + 'checksums': ['ff786008bf8c022064ececd3b7ed89c76b35e8d1eac6cf472a9f51771c1c9f2c'], + }), + ('Text::CSV', '2.04', { + 'source_tmpl': 'Text-CSV-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IS/ISHIGAKI'], + 'checksums': ['4f80122e4ea0b05079cad493e386564030f18c8d7b1f9af561df86985a653fe3'], + }), + ('Test::Output', '1.034', { + 'source_tmpl': 'Test-Output-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BD/BDFOY'], + 'checksums': ['cd42e2801c0d2b482d18c9fb4b06c757054818bcbb2824e5dfbf33ad7a3d69a0'], + }), + ('File::CheckTree', '4.42', { + 'source_tmpl': 'File-CheckTree-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['66fb417f8ff8a5e5b7ea25606156e70e204861c59fa8c3831925b4dd3f155f8a'], + }), + ('Math::VecStat', '0.08', { + 'source_tmpl': 'Math-VecStat-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AS/ASPINELLI'], + 'checksums': ['409a8e0e4b1025c8e80f628f65a9778aa77ab285161406ca4a6c097b13656d0d'], + }), + ('Pod::Parser', '1.67', { + 'configopts': 'INSTALLDIRS=site', + 'source_tmpl': 'Pod-Parser-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MAREKR'], + 'checksums': ['5deccbf55d750ce65588cd211c1a03fa1ef3aaa15d1ac2b8d85383a42c1427ea'], + }), + ('Pod::LaTeX', '0.61', { + 'source_tmpl': 'Pod-LaTeX-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TJ/TJENNESS'], + 'checksums': ['15a840ea1c8a76cd3c865fbbf2fec33b03615c0daa50f9c800c54e0cf0659d46'], + }), + ('XML::Twig', '3.52', { + 'source_tmpl': 'XML-Twig-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIROD'], + 'checksums': ['fef75826c24f2b877d0a0d2645212fc4fb9756ed4d2711614ac15c497e8680ad'], + }), + ('XML::Simple', '2.25', { + 'source_tmpl': 'XML-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GR/GRANTM'], + 'checksums': ['531fddaebea2416743eb5c4fdfab028f502123d9a220405a4100e68fc480dbf8'], + }), + ('Pod::Plainer', '1.04', { + 'source_tmpl': 'Pod-Plainer-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RM/RMBARKER'], + 'checksums': ['1bbfbf7d1d4871e5a83bab2137e22d089078206815190eb1d5c1260a3499456f'], + }), + ('Data::Section::Simple', '0.07', { + 'source_tmpl': 'Data-Section-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], + 'checksums': ['0b3035ffdb909aa1f7ded6b608fa9d894421c82c097d51e7171170d67579a9cb'], + }), + ('File::HomeDir', '1.006', { + 'source_tmpl': 'File-HomeDir-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + 'checksums': ['593737c62df0f6dab5d4122e0b4476417945bb6262c33eedc009665ef1548852'], + }), + ('Authen::SASL', '2.1700', { + 'source_tmpl': 'Authen-SASL-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EH/EHUELS'], + 'checksums': ['b86d5a576b8d387aee24f39f47a54afd14bb66b09003db5065001f1de03a8ece'], + }), + ('Import::Into', '1.002005', { + 'source_tmpl': 'Import-Into-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + 'checksums': ['bd9e77a3fb662b40b43b18d3280cd352edf9fad8d94283e518181cc1ce9f0567'], + }), + ('DateTime::Tiny', '1.07', { + 'runtest': False, # One subset fails due to locale + 'source_tmpl': 'DateTime-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + 'checksums': ['83568a22838cb518fbeb9e060460ec7f59d5a0b0a1cc06562954c3674d7cf7e4'], + }), + ('Text::Format', '0.62', { + 'source_tmpl': 'Text-Format-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + 'checksums': ['7d429057319e123c590ba0765334f0ade4a5eb9ea8db7c0ec4d3902de5f90404'], + }), + ('Devel::CheckCompiler', '0.07', { + 'source_tmpl': 'Devel-CheckCompiler-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SY/SYOHEX'], + 'checksums': ['768b7697b4b8d4d372c7507b65e9dd26aa4223f7100183bbb4d3af46d43869b5'], + }), + ('Log::Handler', '0.90', { + 'source_tmpl': 'Log-Handler-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BL/BLOONIX'], + 'checksums': ['3a5c80e7128454770f83acab8cbd3e70e5ec3d59a61dc32792a178f0b31bf74d'], + }), + ('Term::ReadKey', '2.38', { + 'source_tmpl': 'TermReadKey-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JS/JSTOWE'], + 'checksums': ['5a645878dc570ac33661581fbb090ff24ebce17d43ea53fd22e105a856a47290'], + }), + ('Set::IntSpan', '1.19', { + 'source_tmpl': 'Set-IntSpan-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SW/SWMCD'], + 'checksums': ['11b7549b13ec5d87cc695dd4c777cd02983dd5fe9866012877fb530f48b3dfd0'], + }), + ('Module::Runtime::Conflicts', '0.003', { + 'source_tmpl': 'Module-Runtime-Conflicts-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['707cdc75038c70fe91779b888ac050f128565d3967ba96680e1b1c7cc9733875'], + }), + ('File::pushd', '1.016', { + 'source_tmpl': 'File-pushd-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + 'checksums': ['d73a7f09442983b098260df3df7a832a5f660773a313ca273fa8b56665f97cdc'], + }), + ('Test::CleanNamespaces', '0.24', { + 'source_tmpl': 'Test-CleanNamespaces-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['338d5569e8e89a654935f843ec0bc84aaa486fe8dd1898fb9cab3eccecd5327a'], + }), + ('Devel::OverloadInfo', '0.007', { + 'source_tmpl': 'Devel-OverloadInfo-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IL/ILMARI'], + 'checksums': ['21a184163b90f91f06ffc7f5de0b968356546ae9b400a9d75c573c958c246222'], + }), + ('Moose', '2.2207', { + 'source_tmpl': 'Moose-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['7c2daddc49754ded93f65b8ce9e3ac9b6d11ab27d111ec77f95a8528cf4ac409'], + }), + ('Algorithm::Dependency', '1.112', { + 'source_tmpl': 'Algorithm-Dependency-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['7e0fb7c39f56a2dccf9d0295c82f3031ee116e807f6a12a438fa4dd41b0ec187'], + }), + ('Font::TTF', '1.06', { + 'source_tmpl': 'Font-TTF-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BH/BHALLISSY'], + 'checksums': ['4b697d444259759ea02d2c442c9bffe5ffe14c9214084a01f743693a944cc293'], + }), + ('IPC::Run3', '0.049', { + 'source_tmpl': 'IPC-Run3-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['9d048ae7b9ae63871bae976ba01e081d887392d904e5d48b04e22d35ed22011a'], + }), + ('SQL::Statement', '1.414', { + 'source_tmpl': 'SQL-Statement-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + 'checksums': ['dde8bdcfa6a136eedda06519ba0f3efaec085c39db0df9c472dc0ec6cd781a49'], + }), + ('Package::Constants', '0.06', { + 'source_tmpl': 'Package-Constants-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': ['0b58be78706ccc4e4bd9bbad41767470427fd7b2cfad749489de101f85bc5df5'], + }), + ('CPANPLUS', '0.9914', { + 'source_tmpl': 'CPANPLUS-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': ['76c3e5da623a4af60fe64adec448fb1f8e0cae9f6798a36b68865974044e9b67'], + }), + ('IO::Tty', '1.20', { + 'source_tmpl': 'IO-Tty-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + 'checksums': ['b15309fc85623893289cb9b2b88dfa9ed1e69156b75f29938553a45be6d730af'], + }), + ('Text::Soundex', '3.05', { + 'source_tmpl': 'Text-Soundex-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['f6dd55b4280b25dea978221839864382560074e1d6933395faee2510c2db60ed'], + }), + ('Mail::Util', '2.21', { + 'source_tmpl': 'MailTools-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], + 'checksums': ['4ad9bd6826b6f03a2727332466b1b7d29890c8d99a32b4b3b0a8d926ee1a44cb'], + }), + ('Test::More::UTF8', '0.05', { + 'source_tmpl': 'Test-More-UTF8-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MO/MONS'], + 'checksums': ['b9f1c4b36a97cdfefaa53ed1115dd38f4b483037775f6559ee1df14acfd1ce04'], + }), + ('Text::Template', '1.61', { + 'source_tmpl': 'Text-Template-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MS/MSCHOUT'], + 'checksums': ['a295ea7d1ef241ae2640c1f7864b628f8e6f99ec14fb1da781b2f5f2168dcf09'], + }), + ('PadWalker', '2.5', { + 'source_tmpl': 'PadWalker-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RO/ROBIN'], + 'checksums': ['07b26abb841146af32072a8d68cb90176ffb176fd9268e6f2f7d106f817a0cd0'], + }), + ('Devel::Cycle', '1.12', { + 'source_tmpl': 'Devel-Cycle-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LD/LDS'], + 'checksums': ['fd3365c4d898b2b2bddbb78a46d507a18cca8490a290199547dab7f1e7390bc2'], + }), + ('Test::Memory::Cycle', '1.06', { + 'source_tmpl': 'Test-Memory-Cycle-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PETDANCE'], + 'checksums': ['9d53ddfdc964cd8454cb0da4c695b6a3ae47b45839291c34cb9d8d1cfaab3202'], + }), + ('PDF::API2', '2.047', { + 'source_tmpl': 'PDF-API2-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SS/SSIMMS'], + 'checksums': ['84d6318279d77844923e4de4275fe4345cd08b225edd7f9ed6a16f87a91aca39'], + }), + ('Devel::CheckLib', '1.16', { + 'source_tmpl': 'Devel-CheckLib-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MATTN'], + 'checksums': ['869d38c258e646dcef676609f0dd7ca90f085f56cf6fd7001b019a5d5b831fca'], + }), + ('SVG', '2.87', { + 'source_tmpl': 'SVG-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MANWAR'], + 'checksums': ['b3fa58c1c59942b4ebef003da97c3e01e531480ca29e8efbe327ff0589c0bd3c'], + }), + ('Statistics::Basic', '1.6611', { + 'source_tmpl': 'Statistics-Basic-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JE/JETTERO'], + 'checksums': ['6855ce5615fd3e1af4cfc451a9bf44ff29a3140b4e7130034f1f0af2511a94fb'], + }), + ('Log::Log4perl', '1.57', { + 'source_tmpl': 'Log-Log4perl-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETJ'], + 'checksums': ['0f8fcb7638a8f3db4c797df94fdbc56013749142f2f94cbc95b43c9fca096a13'], + }), + ('Math::CDF', '0.1', { + 'source_tmpl': 'Math-CDF-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CA/CALLAHAN'], + 'checksums': ['7896bf250835ce47dcc813cb8cf9dc576c5455de42e822dcd7d8d3fef2125565'], + }), + ('Array::Utils', '0.5', { + 'source_tmpl': 'Array-Utils-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/Z/ZM/ZMIJ/Array'], + 'checksums': ['89dd1b7fcd9b4379492a3a77496e39fe6cd379b773fd03a6b160dd26ede63770'], + }), + ('File::Grep', '0.02', { + 'source_tmpl': 'File-Grep-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MN/MNEYLON'], + 'checksums': ['462e15274eb6278521407ea302d9eea7252cd44cab2382871f7de833d5f85632'], + }), + ('File::Temp', '0.2311', { + 'source_tmpl': 'File-Temp-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['2290d61bf5c39882fc3311da9ce1c7f42dbdf825ae169e552c59fe4598b36f4a'], + }), + ('Set::Object', '1.42', { + 'source_tmpl': 'Set-Object-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RU/RURBAN'], + 'checksums': ['d18c5a8a233eabbd0206cf3da5b00fcdd7b37febf12a93dcc3d1c026e6fdec45'], + }), + ('Heap', '0.80', { + 'source_tmpl': 'Heap-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JM/JMM'], + 'checksums': ['ccda29f3c93176ad0fdfff4dd6f5e4ac90b370cba4b028386b7343bf64139bde'], + }), + ('Graph', '0.9729', { + 'source_tmpl': 'Graph-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETJ'], + 'checksums': ['3efbed46ca82f78f25253d034232b0cc9cfadfbd867437e63f9275850f85abb0'], + }), + ('XML::Writer', '0.900', { + 'source_tmpl': 'XML-Writer-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JO/JOSEPHW'], + 'checksums': ['73c8f5bd3ecf2b350f4adae6d6676d52e08ecc2d7df4a9f089fa68360d400d1f'], + }), + ('Parse::Yapp', '1.21', { + 'source_tmpl': 'Parse-Yapp-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/W/WB/WBRASWELL'], + 'checksums': ['3810e998308fba2e0f4f26043035032b027ce51ce5c8a52a8b8e340ca65f13e5'], + }), + ('Graph::ReadWrite', '2.10', { + 'source_tmpl': 'Graph-ReadWrite-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + 'checksums': ['516c1ea9facb995dbc38d1735d58974b2399862567e731b729c8d0bc2ee5a14b'], + }), + ('PerlIO::utf8_strict', '0.010', { + 'source_tmpl': 'PerlIO-utf8_strict-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['bcd2848b72df290b5e984fae8b1a6ca96f6d072003cf222389a8c9e8e1c570cd'], + }), + ('Digest::MD5::File', '0.08', { + 'source_tmpl': 'Digest-MD5-File-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DM/DMUEY'], + 'checksums': ['adb43a54e32627b4f7e57c9640e6eb06d0bb79d8ea54cd0bd79ed35688fb1218'], + }), + ('String::RewritePrefix', '0.009', { + 'source_tmpl': 'String-RewritePrefix-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['44918bec96a54af8ca37ca897e436709ec284a07b28516ef3cce4666869646d5'], + }), + ('Getopt::Long::Descriptive', '0.114', { + 'source_tmpl': 'Getopt-Long-Descriptive-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['410e842114a9cbfd3fd3a5fd248a96703c07c5d879b2aa5f9db0333f23276016'], + }), + ('IO::TieCombine', '1.005', { + 'source_tmpl': 'IO-TieCombine-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['402d4db8300b3d271632f4995e0ade329d89280a7e47f2badf8b38af6e5569af'], + }), + ('App::Cmd', '0.336', { + 'source_tmpl': 'App-Cmd-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['df966b57d59abb196e00304885e5bf117ca958182ae3f4eedf17218ea2838e81'], + }), + ('Carp::Clan', '6.08', { + 'source_tmpl': 'Carp-Clan-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['c75f92e34422cc5a65ab05d155842b701452434e9aefb649d6e2289c47ef6708'], + }), + ('Sub::Exporter::ForMethods', '0.100055', { + 'source_tmpl': 'Sub-Exporter-ForMethods-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['791f4203ba7c0f7d8380bc01bec20215f7c8bc70d7ed03e552eee44541abe94e'], + }), + ('MooseX::Types', '0.50', { + 'source_tmpl': 'MooseX-Types-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['9cd87b3492cbf0be9d2df9317b2adf9fc30663770e69906654bea3f41b17cb08'], + }), + ('Variable::Magic', '0.64', { + 'source_tmpl': 'Variable-Magic-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/V/VP/VPIT'], + 'checksums': ['9f7853249c9ea3b4df92fb6b790c03a60680fc029f44c8bf9894dccf019516bd'], + 'pretestopts': 'LC_ALL=C ', # Test fails if run in localized environments + }), + ('MooseX::Types::Perl', '0.101344', { + 'source_tmpl': 'MooseX-Types-Perl-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['87644354f74fa65235cb2bfca44277930a7eabe51acc5f81fb631530a8355e24'], + }), + ('Log::Dispatch', '2.71', { + 'source_tmpl': 'Log-Dispatch-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['9d60d9648c35ce2754731eb4deb7f05809ece1bd633b74d74795aed9ec732570'], + }), + ('JSON::MaybeXS', '1.004005', { + 'source_tmpl': 'JSON-MaybeXS-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['f5b6bc19f579e66b7299f8748b8ac3e171936dc4e7fcb72a8a257a9bd482a331'], + }), + ('String::Flogger', '1.101246', { + 'source_tmpl': 'String-Flogger-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['15f8491e07818bb3cfa9f6bd3aabf6430ba9b4e309f18114358be3d81bff3a0f'], + }), + ('Log::Dispatch::Array', '1.005', { + 'source_tmpl': 'Log-Dispatch-Array-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['311640b7a967f8dd7c9bb41a227073565636d70df4fcc1d44fed8a8223b347ca'], + }), + ('Sub::Exporter::GlobExporter', '0.006', { + 'source_tmpl': 'Sub-Exporter-GlobExporter-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['de743f08026701c2a6a222a8b41c4cdc254b1a4afe7ef98987cd3aba4ce52696'], + }), + ('Log::Dispatchouli', '3.007', { + 'source_tmpl': 'Log-Dispatchouli-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['988118965952ba49a8fa791a6536880c89017f4eb9d72c1745ed67d15c0d272c'], + }), + ('Test::FailWarnings', '0.008', { + 'source_tmpl': 'Test-FailWarnings-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + 'checksums': ['da34ef9029f6849d6026201d49127d054ee6ac4b979c82210315f5721964a96f'], + }), + ('Data::Section', '0.200008', { + 'source_tmpl': 'Data-Section-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['83acc7a55d3dd7ed36e9d78d350af3138c69cfa178a44765822712ff433b990e'], + }), + ('Test::CheckDeps', '0.010', { + 'source_tmpl': 'Test-CheckDeps-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['66fccca6c6f330e7ecc898bd6a51846e2145b3e02d78c4997ba6b7de23b551ee'], + }), + ('Software::License', '0.104006', { + 'runtest': False, # This test just suddenly started to fail + 'source_tmpl': 'Software-License-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['65c8ee1c2da2a4de10139863df668fa6b3b3e24a39d69a7cca39f284fb6b9c0f'], + }), + ('MooseX::SetOnce', '0.203', { + 'source_tmpl': 'MooseX-SetOnce-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['3cd2f3664e438382cf844b679350a2e428b760927e2cf18fccdc468a7bc3066f'], + }), + ('Term::Encoding', '0.03', { + 'source_tmpl': 'Term-Encoding-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], + 'checksums': ['95ba9687d735d25a3cbe64508d7894f009c7fa2a1726c3e786e9e21da2251d0b'], + }), + ('Throwable', '1.001', { + 'source_tmpl': 'Throwable-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['d0cb5e9d7d06d70f2cc56eecf857a83a45eaca43850dcdda91d3feb4ddde4c51'], + }), + ('Role::Identifiable::HasIdent', '0.009', { + 'source_tmpl': 'Role-Identifiable-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['5a735e9f7177f9ebae047eb7bae29b7ec29ec020ae37637aea5350d30c087b76'], + }), + ('MooseX::Role::Parameterized', '1.11', { + 'source_tmpl': 'MooseX-Role-Parameterized-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['1cfe766c5d7f0ecab57f733dcca430a2a2acd6b995757141b940ade3692bec9e'], + }), + ('MooseX::OneArgNew', '0.007', { + 'source_tmpl': 'MooseX-OneArgNew-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['84282435f1169cf09d7513fa9387e2091791635cf35a078b500b829aeea06138'], + }), + ('MooseX::LazyRequire', '0.11', { + 'source_tmpl': 'MooseX-LazyRequire-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['ef620c1e019daf9cf3f23a943d25a94c91e93ab312bcd63be2e9740ec0b94288'], + }), + ('String::Formatter', '1.235', { + 'source_tmpl': 'String-Formatter-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['08236a913b911ce652cf08598e7c07d2df3f369fc47bf401a485a504a1660783'], + }), + ('String::Errf', '0.009', { + 'source_tmpl': 'String-Errf-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['e1fedbf9b4fd64b64ea81038ddb76a4c6cd85f5db15bc21f10656a298349dc1f'], + }), + ('Role::HasMessage', '0.007', { + 'source_tmpl': 'Role-HasMessage-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['5e267a4d7620b368481204c88ea2044b8b2a58ff8b05577f2717b2754c0414ce'], + }), + ('Config::MVP', '2.200013', { + 'source_tmpl': 'Config-MVP-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['018d161623ee3a67f860d9e680e22e61b79eae6018f0e7c3b525fc934f5b7d45'], + }), + ('Mixin::Linewise::Readers', '0.111', { + 'source_tmpl': 'Mixin-Linewise-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['d28e88516ce9b5295c31631dcccdc0fc8f2ab7d8a5cc876bb1b20131087b01db'], + }), + ('Config::INI', '0.029', { + 'source_tmpl': 'Config-INI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['0bbe797a730210644a907d90cd4aa2b23ad580cb27bd39393bfc6a7ef9fdfdea'], + }), + ('String::Truncate', '1.100603', { + 'source_tmpl': 'String-Truncate-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['ab45602cce2dd9515edfbb2e6e5cde19cdd5498d61a23afd8c46c1f11f8eec62'], + }), + ('Pod::Eventual', '0.094003', { + 'source_tmpl': 'Pod-Eventual-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['7f060cc34d11656ce069db061e3d60edc0cabc8f89a4a2dc7eaae95dac856d2d'], + }), + ('Pod::Elemental', '0.103006', { + 'source_tmpl': 'Pod-Elemental-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['750c3a79d8e1824758a6ef7d2dd077dcddca503542b8c34eccd5acbb779dc423'], + }), + ('Test::Object', '0.08', { + 'source_tmpl': 'Test-Object-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['65278964147837313f4108e55b59676e8a364d6edf01b3dc198aee894ab1d0bb'], + }), + ('Hook::LexWrap', '0.26', { + 'source_tmpl': 'Hook-LexWrap-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['b60bdc5f98f94f9294b06adef82b1d996da192d5f183f9f434b610fd1137ec2d'], + }), + ('Test::SubCalls', '1.10', { + 'source_tmpl': 'Test-SubCalls-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['cbc1e9b35a05e71febc13e5ef547a31c8249899bb6011dbdc9d9ff366ddab6c2'], + }), + ('PPI', '1.278', { + 'source_tmpl': 'PPI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + 'checksums': ['1c867b2e9b10056978db9ddaadab599af9a5c9a66805ed03ef4b201f1105d427'], + }), + ('Config::MVP::Reader::INI', '2.101465', { + 'source_tmpl': 'Config-MVP-Reader-INI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['13c7aa27c1df98cd33ada399e59ff38fabfa9d65513e42af02f72c2d3f636247'], + }), + ('Pod::Weaver', '4.020', { + 'source_tmpl': 'Pod-Weaver-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['655fcf261206c1adbc3038981790b116c31508485135c648093b99b3b3de09d2'], + }), + ('CPAN::Uploader', '0.103018', { + 'source_tmpl': 'CPAN-Uploader-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['c4ffe4ede9db79b396e3bfc5e7cdf0e2e9821e1f1e087f523bcfa74c9fc9e248'], + }), + ('Devel::FindPerl', '0.016', { + 'source_tmpl': 'Devel-FindPerl-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['43a2bf2f787a3f1b881179063162b2aa3e7cb044f6e5e76ec6466ae90a861138'], + }), + ('Module::Path', '0.19', { + 'source_tmpl': 'Module-Path-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + 'checksums': ['b33179ce4dd73dfcde7d46808804b9ffbb11db0245fe455a7d001747562feaca'], + }), + ('Perl::PrereqScanner', '1.100', { + 'source_tmpl': 'Perl-PrereqScanner-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['01181d38a2e7aff838d262122563c50636ba4b3652ee5d1d4f8ef5ba3f5b186b'], + }), + ('Dist::Zilla', '6.032', { + 'source_tmpl': 'Dist-Zilla-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['5c771a1dc2daab5afae0fd59e5046111970f73bf3eaec9df70d8e07346f8165e'], + }), + ('XML::RegExp', '0.04', { + 'source_tmpl': 'XML-RegExp-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TJ/TJMATHER'], + 'checksums': ['df1990096036085c8e2d45904fe180f82bfed40f1a7e05243f334ea10090fc54'], + }), + ('XML::DOM', '1.46', { + 'source_tmpl': 'XML-DOM-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TJ/TJMATHER'], + 'checksums': ['8ba24b0b459b01d6c5e5b0408829c7d5dfe47ff79b3548c813759048099b175e'], + }), + ('Data::Dump', '1.25', { + 'source_tmpl': 'Data-Dump-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GARU'], + 'checksums': ['a4aa6e0ddbf39d5ad49bddfe0f89d9da864e3bc00f627125d1bc580472f53fbd'], + }), + ('File::Next', '1.18', { + 'source_tmpl': 'File-Next-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PETDANCE'], + 'checksums': ['f900cb39505eb6e168a9ca51a10b73f1bbde1914b923a09ecd72d9c02e6ec2ef'], + }), + ('App::cpanminus', '1.7047', { + 'source_tmpl': 'App-cpanminus-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], + 'checksums': ['963e63c6e1a8725ff2f624e9086396ae150db51dd0a337c3781d09a994af05a5'], + }), + ('Parallel::ForkManager', '2.02', { + 'source_tmpl': 'Parallel-ForkManager-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/Y/YA/YANICK'], + 'checksums': ['c1b2970a8bb666c3de7caac4a8f4dbcc043ab819bbc337692ec7bf27adae4404'], + }), + ('Object::InsideOut', '4.05', { + 'source_tmpl': 'Object-InsideOut-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JD/JDHEDDEN'], + 'checksums': ['9dfd6ca2822724347e0eb6759d00709425814703ad5c66bdb6214579868bcac4'], + }), + ('Logger::Simple', '2.0', { + 'source_tmpl': 'Logger-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TS/TSTANLEY'], + 'checksums': ['2e63fd3508775b5902132ba1bfb03b42bee468dfaf35dfe42e1909ff6d291b2d'], + }), + ('Scalar::Util::Numeric', '0.40', { + 'source_tmpl': 'Scalar-Util-Numeric-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CH/CHOCOLATE'], + 'checksums': ['d7501b6d410703db5b1c1942fbfc41af8964a35525d7f766058acf5ca2cc4440'], + }), + ('Spiffy', '0.46', { + 'source_tmpl': 'Spiffy-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IN/INGY'], + 'checksums': ['8f58620a8420255c49b6c43c5ff5802bd25e4f09240c51e5bf2b022833d41da3'], + }), + ('Test::Base', '0.89', { + 'source_tmpl': 'Test-Base-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IN/INGY'], + 'checksums': ['2794a1aaaeb1d3a287dd2c7286258663796562f7db9ccc6b424bc4f1de8ad014'], + }), + ('Test::YAML', '1.07', { + 'source_tmpl': 'Test-YAML-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TI/TINITA'], + 'checksums': ['1f300d034f46298cb92960912cc04bac33fb27f05b8852d8f051e110b9cd995f'], + }), + ('YAML', '1.31', { + 'source_tmpl': 'YAML-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IN/INGY'], + 'checksums': ['a0ce30381657dce8e694df9a09e95d818d13beb03698fd2cf79d0c8d564a9b8e'], + }), + ('Object::InsideOut', '4.05', { + 'source_tmpl': 'Object-InsideOut-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JD/JDHEDDEN'], + 'checksums': ['9dfd6ca2822724347e0eb6759d00709425814703ad5c66bdb6214579868bcac4'], + }), + ('Term::ReadLine::Gnu', '1.46', { + 'modulename': 'Term::ReadLine', + 'source_tmpl': 'Term-ReadLine-Gnu-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAYASHI'], + 'checksums': ['b13832132e50366c34feac12ce82837c0a9db34ca530ae5d27db97cf9c964c7b'], + }), + ('ExtUtils::MakeMaker', '7.70', { + 'source_tmpl': 'ExtUtils-MakeMaker-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': ['f108bd46420d2f00d242825f865b0f68851084924924f92261d684c49e3e7a74'], + }), + ('Scalar::Util', '1.63', { + 'source_tmpl': 'Scalar-List-Utils-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PEVANS'], + 'checksums': ['cafbdf212f6827dc9a0dd3b57b6ee50e860586d7198228a33262d55c559eb2a9'], + }), + ('Module::CoreList', '5.20240702', { + 'source_tmpl': 'Module-CoreList-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': ['f2fa93960b1419ab3aaa186d4ce2a538de229d1af8a9eecd76265c78252c011b'], + }), + ('Module::Metadata', '1.000038', { + 'source_tmpl': 'Module-Metadata-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['b599d8770a9a9fa0a8ae3cd0ed395a9cf71b4eb53aed82989a6bece33485a9cd'], + }), + ('Params::Check', '0.38', { + 'configopts': 'INSTALLDIRS=site', # Force it to correctly use site_perl + 'source_tmpl': 'Params-Check-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': ['f0c9d33876c36b1bca1475276d26d2efaf449b256d7cc8118fae012e89a26290'], + }), + ('Locale::Maketext::Simple', '0.21', { + 'configopts': 'INSTALLDIRS=site', # Force it to correctly use site_perl + 'source_tmpl': 'Locale-Maketext-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JE/JESSE'], + 'checksums': ['b009ff51f4fb108d19961a523e99b4373ccf958d37ca35bf1583215908dca9a9'], + }), + ('Perl::OSType', '1.010', { + 'source_tmpl': 'Perl-OSType-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + 'checksums': ['e7ed4994b5d547cb23aadb84dc6044c5eb085d5a67a6c5624f42542edd3403b2'], + }), + ('IPC::Cmd', '1.04', { + 'source_tmpl': 'IPC-Cmd-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': ['d110a0f60e35c65721454200f0d2f0f8965529a2add9649d1fa6f4f9eccb6430'], + }), + ('Pod::Escapes', '1.07', { + 'source_tmpl': 'Pod-Escapes-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + 'checksums': ['dbf7c827984951fb248907f940fd8f19f2696bc5545c0a15287e0fbe56a52308'], + }), + ('if', '0.0608', { + 'configopts': 'INSTALLDIRS=site', # Force it to correctly use site_perl + 'modulename': False, + 'source_tmpl': 'if-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'], + 'checksums': ['37206e10919c4d99273020008a3581bf0947d364e859b8966521c3145b4b3700'], + }), + ('Test', '1.26', { + 'configopts': 'INSTALLDIRS=site', # Force it to correctly use site_perl + 'source_tmpl': 'Test-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JE/JESSE'], + 'checksums': ['f7701bd28e05e7f82fe9a181bbab38f53fa6aeae48d2a810da74d1b981d4f392'], + }), + ('ExtUtils::Constant', '0.25', { + 'runtest': False, # Somehow has syntax errors in tests + 'source_tmpl': 'ExtUtils-Constant-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NW/NWCLARK'], + 'checksums': ['6933d0e963b62281ef7561068e6aecac8c4ac2b476b2bba09ab0b90fbac9d757'], + }), + ('ExtUtils::CBuilder', '0.280236', { + 'source_tmpl': 'ExtUtils-CBuilder-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AM/AMBS'], + 'checksums': ['abc21827eb8a513171bf7fdecefce9945132cb76db945036518291f607b1491f'], + }), + ('Carp::Heavy', '1.50', { + 'source_tmpl': 'Carp-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'], + 'checksums': ['f5273b4e1a6d51b22996c48cb3a3cbc72fd456c4038f5c20b127e2d4bcbcebd9'], + }), + ('Pod::Simple', '3.45', { + 'source_tmpl': 'Pod-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KH/KHW'], + 'checksums': ['8483bb95cd3e4307d66def092a3779f843af772482bfdc024e3e00d0c4db0cfa'], + }), + ('Socket', '2.038', { + 'source_tmpl': 'Socket-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PEVANS'], + 'checksums': ['563d11731ff44307fa2779a6958fd2d2f6643fbd9a3174cbf350228b159681f8'], + }), + ('Time::Local', '1.35', { + 'source_tmpl': 'Time-Local-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['1d136b71bd041cbe6f66c43180ee79e675b72ad5a3596abd6a44d211072ada29'], + }), + ('Storable', '3.25', { + 'source_tmpl': 'Storable-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NW/NWCLARK'], + 'checksums': ['e1e96b24a076792fde52154789fe4b76034b9ad39c8a1a819ead77d50d5f1817'], + }), + ('ExtUtils::ParseXS', '3.51', { + 'source_tmpl': 'ExtUtils-ParseXS-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['82431a57425d78682acefb3a2cc9287683d091c8d034b825c584d9805bed6535'], + }), + ('Pod::Man', '5.01', { + 'source_tmpl': 'podlators-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RR/RRA'], + 'checksums': ['ccfd1df9f1a47f095bce6d718fad5af40f78ce2491f2c7239626e15b7020bc71'], + }), + ('Mozilla::CA', '20240313', { + 'source_tmpl': 'Mozilla-CA-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LW/LWP'], + 'checksums': ['624873939e309833894f881464a95dfe74ab77cab5d557308c010487161698e7'], + }), + ('LWP::Protocol::https', '6.14', { + 'source_tmpl': 'LWP-Protocol-https-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + 'checksums': ['59cdeabf26950d4f1bef70f096b0d77c5b1c5a7b5ad1b66d71b681ba279cbb2a'], + }), + ('Module::Load', '0.36', { + 'source_tmpl': 'Module-Load-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': ['d825020ac00b220e89f9524e24d838f9438b072fcae8c91938e4026677bef6e0'], + }), + ('Module::Load::Conditional', '0.74', { + 'source_tmpl': 'Module-Load-Conditional-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': ['54c354a9393820f1ebc2a095da084ea0392dcbccb0cb38a187a71831cc60a730'], + }), + ('parent', '0.241', { + 'source_tmpl': 'parent-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CO/CORION'], + 'checksums': ['b10b3960ab3997dab7571ffe975ba462d979d086450740a1e08b3959e75128fe'], + }), + ('Net::Domain', '3.15', { + 'source_tmpl': 'libnet-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHAY'], + 'checksums': ['a71f4db580e1a767d6936faa5baf38f1fa617824342da078b561283e86f8f4a2'], + }), + ('Encode', '3.21', { + 'source_tmpl': 'Encode-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DANKOGAI'], + 'checksums': ['eacf71c5eb49e0e590de797f1982d7fb95d8481e4d13c3ce79eb32ef9373b3db'], + }), + ('Cwd', '3.75', { + 'runtest': False, # Single failure about a tainted PATH + 'source_tmpl': 'PathTools-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'], + 'patches': ['PathTools-3.75_fix-cwd_enoent-test.patch'], + 'checksums': [ + {'PathTools-3.75.tar.gz': 'a558503aa6b1f8c727c0073339081a77888606aa701ada1ad62dd9d8c3f945a2'}, + {'PathTools-3.75_fix-cwd_enoent-test.patch': + '7a456a99d9b04a36359f3623f0deef8fe7f472c742f99cdcf0215c50afbbe7b1'}, + ], + }), + ('MIME::Base64', '3.16', { + 'source_tmpl': 'MIME-Base64-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CA/CAPOEIRAB'], + 'checksums': ['77f73d6f7aeb8d33be08b0d8c2617f9b6c77fb7fc45422d507ca8bafe4246017'], + }), + ('ExtUtils::CppGuess', '0.27', { + 'runtest': False, # Poorly written test + 'source_tmpl': 'ExtUtils-CppGuess-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETJ'], + 'checksums': ['b2c7b581901054a32dfcea12536fda8626457ed0bfbc02600bd354bde7e2a9b4'], + }), + ('XSLoader', '0.24', { + 'source_tmpl': 'XSLoader-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SA/SAPER'], + 'checksums': ['e819a35a6b8e55cb61b290159861f0dc00fe9d8c4f54578eb24f612d45c8d85f'], + }), + ('AutoLoader', '5.74', { + 'source_tmpl': 'AutoLoader-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SM/SMUELLER'], + 'checksums': ['2fac75b05309f71a6871804cd25e1a3ba0a28f43f294fb54528077558da3aff4'], + }), + ('Set::IntervalTree', '0.12', { + 'source_tmpl': 'Set-IntervalTree-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SL/SLOYD'], + 'checksums': ['6fd4000e4022968e2ce5b83c07b189219ef1925ecb72977b52a6f7d76adbc349'], + }), + ('MCE::Mutex', '1.897', { + 'runtest': False, # Single failing subtest + 'source_tmpl': 'MCE-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARIOROY'], + 'checksums': ['673d337d14fc2d7a12576ca6615c729821dc616ee76e0ecc9c0f32de8a9f9c39'], + }), + ('Text::CSV_XS', '1.55', { + 'source_tmpl': 'Text-CSV_XS-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HM/HMBRAND'], + 'checksums': ['e4b623b31b4ac35e99d7b797d5b7c2205a5b984bcd88dee1a9460a6a39d40b5e'], + }), + ('DBD::CSV', '0.60', { + 'source_tmpl': 'DBD-CSV-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HM/HMBRAND'], + 'checksums': ['018b83a30f799979bc8c3c3044c8b1c8001cdf60bdc3e746848818195254b4e7'], + }), + ('Array::Transpose', '0.06', { + 'source_tmpl': 'Array-Transpose-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MR/MRDVT'], + 'checksums': ['d58667f64381a105f375226f592d0af71068e640a5a9f4d5ecf27c90feb32676'], + }), + ('Config::Simple', '4.58', { + 'source_tmpl': 'Config-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHERZODR'], + 'checksums': ['dd9995706f0f9384a15ccffe116c3b6e22f42ba2e58d8f24ed03c4a0e386edb4'], + }), + ('Business::ISBN::Data', '20240614.001', { + 'source_tmpl': 'Business-ISBN-Data-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BR/BRIANDFOY'], + 'checksums': ['38d7f0e24152e1aef07b1517a16104c1763b6669095dbad5083c3b91fc27232b'], + }), + ('Business::ISBN', '3.009', { + 'source_tmpl': 'Business-ISBN-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BR/BRIANDFOY'], + 'checksums': ['d2ec1970454af1b2c099dd34caa7a348ca6fd323bb7ddbfad55389bd7f96789b'], + }), + ('common::sense', '3.75', { + 'source_tmpl': 'common-sense-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], + 'checksums': ['a86a1c4ca4f3006d7479064425a09fa5b6689e57261fcb994fe67d061cba0e7e'], + }), + ('Compress::Raw::Zlib', '2.212', { + 'source_tmpl': 'Compress-Raw-Zlib-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PM/PMQS'], + 'checksums': ['6d9de0c11921fd520dfd99a3f6b0ca9f1fd9850274f8bec10bbaa4f6803cc049'], + }), + ('Compress::Raw::Bzip2', '2.212', { + 'source_tmpl': 'Compress-Raw-Bzip2-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PM/PMQS'], + 'checksums': ['6caeee843c428f45fa9646ea98dc675470db63dbac0ee3e2d8e9ee4eb58a856d'], + }), + ('IO::Compress::Zip', '2.212', { + 'source_tmpl': 'IO-Compress-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PM/PMQS'], + 'checksums': ['687490dbf9c4be42c22a945c4601812be5f4d38a9836018148915ba9e0ea65b1'], + }), + ('Types::Serialiser', '1.01', { + 'source_tmpl': 'Types-Serialiser-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], + 'checksums': ['f8c7173b0914d0e3d957282077b366f0c8c70256715eaef3298ff32b92388a80'], + }), + ('JSON::XS', '4.03', { + 'source_tmpl': 'JSON-XS-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], + 'checksums': ['515536f45f2fa1a7e88c8824533758d0121d267ab9cb453a1b5887c8a56b9068'], + }), + ('Authen::NTLM', '1.09', { + 'source_tmpl': 'NTLM-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NB/NBEBOUT'], + 'checksums': ['c823e30cda76bc15636e584302c960e2b5eeef9517c2448f7454498893151f85'], + }), + ('Types::Serialiser', '1.01', { + 'source_tmpl': 'Types-Serialiser-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], + 'checksums': ['f8c7173b0914d0e3d957282077b366f0c8c70256715eaef3298ff32b92388a80'], + }), + ('XML::SAX::Expat', '0.51', { + 'source_tmpl': 'XML-SAX-Expat-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BJ/BJOERN'], + 'checksums': ['4c016213d0ce7db2c494e30086b59917b302db8c292dcd21f39deebd9780c83f'], + }), + ('Inline', '0.86', { + 'source_tmpl': 'Inline-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IN/INGY'], + 'checksums': ['510a7de2d011b0db80b0874e8c0f7390010991000ae135cff7474df1e6d51e3a'], + }), + ('Test::Sys::Info', '0.23', { + # test fails on systems without /etc/fstab - so comment it out + 'preconfigopts': "sed -i 's/ok( my %fs/# ok( my %fs/' lib/Test/Sys/Info/Driver.pm && ", + 'source_tmpl': 'Test-Sys-Info-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BU/BURAK'], + 'checksums': ['30c5f2c4cfee8e1ae6d9fb6291f79addbff5739ba4efa5b1e034520f18fbc95a'], + }), + ('Sys::Info::Base', '0.7807', { + 'source_tmpl': 'Sys-Info-Base-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BU/BURAK'], + 'checksums': ['132362b0046e8dc4f12e1560903623a88a8871d09bf1c29d93d48d3f4a582acb'], + }), + ('Sys::Info::Driver::Unknown::Device::CPU', '0.79', { + 'source_tmpl': 'Sys-Info-Driver-Unknown-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BU/BURAK'], + 'checksums': ['02408843c8e36ea3d507e9f33fee48d6908543829ebe320f13d1bfe76af31e09'], + }), + ('Unix::Processors', '2.046', { + 'source_tmpl': 'Unix-Processors-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/W/WS/WSNYDER'], + 'checksums': ['3973ebdc44682c9c15c776f66e8be242cb4ff1dd52caf43ff446b74d4dccca06'], + }), + ('Sys::Info::Driver::Linux::Device::CPU', '0.7905', { + 'source_tmpl': 'Sys-Info-Driver-Linux-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BU/BURAK'], + 'checksums': ['899c329bd3508ec5849ad0e5dadfa7c3679bbacaea9dda12404a7893032e8b7b'], + }), + ('Sys::Info', '0.7811', { + 'source_tmpl': 'Sys-Info-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BU/BURAK'], + 'checksums': ['566482bff3427c198d7955468ed945a8e736c4a2925151fdef96801ef8a401e1'], + }), + ('CGI', '4.66', { + 'source_tmpl': 'CGI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEEJO'], + 'checksums': ['4697437688a193e3f02556e1d223015590c1f2800b40becf83dc12d5cc5ed8e1'], + }), + ('HTML::Template', '2.97', { + 'source_tmpl': 'HTML-Template-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SA/SAMTREGAR'], + 'checksums': ['6547af61f3aa85793f8616190938d677d7995fb3b720c16258040bc935e2129f'], + }), + ('MIME::Charset', 'v1.013.1', { + 'source_tmpl': 'MIME-Charset-1.013.1.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEZUMI'], + 'checksums': ['1bb7a6e0c0d251f23d6e60bf84c9adefc5b74eec58475bfee4d39107e60870f0'], + }), + ('Unicode::LineBreak', '2019.001', { + 'source_tmpl': 'Unicode-LineBreak-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEZUMI'], + 'checksums': ['486762e4cacddcc77b13989f979a029f84630b8175e7fef17989e157d4b6318a'], + }), + ('String::Print', '0.94', { + 'source_tmpl': 'String-Print-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], + 'checksums': ['9b3cd677adb7a40cb183bd6c60db80d96adcabd5aae27e324e3ee37e3275229b'], + }), + ('Log::Report::Optional', '1.07', { + 'source_tmpl': 'Log-Report-Optional-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], + 'checksums': ['b2658b53176df5afa5d02789368715c86b98c8d04ecd930252bcd7f832cc6224'], + }), + ('Log::Report', '1.37', { + 'source_tmpl': 'Log-Report-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], + 'checksums': ['9135798e9cb391e949a3c829c101631d182baa4feaaf821efcee8deba7fdee67'], + }), + ('Sys::Info::Driver::Unknown', '0.79', { + 'source_tmpl': 'Sys-Info-Driver-Unknown-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BU/BURAK'], + 'checksums': ['02408843c8e36ea3d507e9f33fee48d6908543829ebe320f13d1bfe76af31e09'], + }), + ('Sys::Info::Driver::Linux', '0.7905', { + 'source_tmpl': 'Sys-Info-Driver-Linux-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BU/BURAK'], + 'checksums': ['899c329bd3508ec5849ad0e5dadfa7c3679bbacaea9dda12404a7893032e8b7b'], + }), + ('Unix::Processors', '2.046', { + 'source_tmpl': 'Unix-Processors-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/W/WS/WSNYDER'], + 'checksums': ['3973ebdc44682c9c15c776f66e8be242cb4ff1dd52caf43ff446b74d4dccca06'], + }), + ('local::lib', '2.000029', { + 'source_tmpl': 'local-lib-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + 'checksums': ['8df87a10c14c8e909c5b47c5701e4b8187d519e5251e87c80709b02bb33efdd7'], + }), + ('Module::Path', '0.19', { + 'source_tmpl': 'Module-Path-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + 'checksums': ['b33179ce4dd73dfcde7d46808804b9ffbb11db0245fe455a7d001747562feaca'], + }), + ('Devel::Size', '0.84', { + 'source_tmpl': 'Devel-Size-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NW/NWCLARK'], + 'checksums': ['db2e4d65f688dbf59273b5e82101ac3f1a66f665afb0594dce168b8650a4d0e4'], + }), + ('Math::Utils', '1.14', { + 'source_tmpl': 'Math-Utils-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JG/JGAMBLE'], + 'checksums': ['88a20ae0736a622671b92bb2a350969af424d7610284530b277c8020235f2695'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-10.4.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-10.4.0-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..e752171a582d --- /dev/null +++ b/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-10.4.0-GCCcore-13.3.0.eb @@ -0,0 +1,48 @@ +easyblock = 'PythonPackage' + +name = 'Pillow-SIMD' +version = '10.4.0' + +homepage = 'https://github.com/uploadcare/pillow-simd' +description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. + PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/uploadcare/pillow-simd/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['8c7c3c0fc2952ff11b9a8c60365e098ee5334427dd5688c3584e77c25a7e1b3f'] + +builddependencies = [('binutils', '2.42')] + +dependencies = [ + ('Python', '3.12.3'), + ('libjpeg-turbo', '3.0.1'), + ('libpng', '1.6.43'), + ('zlib', '1.3.1'), + ('LibTIFF', '4.6.0'), + ('freetype', '2.13.2'), + ('libwebp', '1.4.0'), + ('OpenJPEG', '2.5.2'), + ('LittleCMS', '2.16'), +] + +use_pip = True +download_dep_fail = True + +# patch setup.py to prefix hardcoded /usr/* and /lib paths with value of %(sysroot) template +# (which will be empty if EasyBuild is not configured to use an alternate sysroot); +# see also https://gitlab.com/eessi/support/-/issues/9 +preinstallopts = """sed -i 's@"/usr/@"%(sysroot)s/usr/@g' setup.py && """ +preinstallopts += """sed -i 's@"/lib@"%(sysroot)s/lib@g' setup.py && """ + +options = {'modulename': 'PIL'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/PIL'], +} + +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Pint/Pint-0.24-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/Pint/Pint-0.24-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..40b50dbb060c --- /dev/null +++ b/easybuild/easyconfigs/p/Pint/Pint-0.24-GCCcore-13.2.0.eb @@ -0,0 +1,43 @@ +easyblock = 'PythonBundle' + +name = 'Pint' +version = '0.24' + +homepage = 'https://github.com/hgrecco/pint' +description = """Pint is a Python package to define, operate and +manipulate physical quantities: the product of a numerical value and a +unit of measurement. It allows arithmetic operations between them and +conversions from and to different units.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('hatchling', '1.18.0'), +] + +dependencies = [ + ('Python', '3.11.5'), +] + +use_pip = True + +exts_list = [ + ('appdirs', '1.4.4', { + 'checksums': ['7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41'], + }), + ('flexcache', '0.3', { + 'checksums': ['18743bd5a0621bfe2cf8d519e4c3bfdf57a269c15d1ced3fb4b64e0ff4600656'], + }), + ('flexparser', '0.3.1', { + 'checksums': ['36f795d82e50f5c9ae2fde1c33f21f88922fdd67b7629550a3cc4d0b40a66856'], + }), + (name, version, { + 'sources': [SOURCELOWER_TAR_GZ], + 'checksums': ['c6c7c027b821413db1ac46b3b7bd296592848b5aec29a88cfc6e378fd1371903'], + }), +] + +sanity_pip_check = True + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/p/Platypus-Opt/Platypus-Opt-1.2.0-foss-2022b.eb b/easybuild/easyconfigs/p/Platypus-Opt/Platypus-Opt-1.2.0-foss-2022b.eb new file mode 100644 index 000000000000..a0e995d4f45e --- /dev/null +++ b/easybuild/easyconfigs/p/Platypus-Opt/Platypus-Opt-1.2.0-foss-2022b.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'Platypus-Opt' +version = '1.2.0' + +homepage = 'https://github.com/Project-Platypus/Platypus' +description = """Platypus is a framework for evolutionary computing in Python with a focus on + multiobjective evolutionary algorithms (MOEAs).""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['f7150de2e24f8003c911259c575493c9351a7dcfb132445a3f3b096728634e6a'] + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('mpi4py', '3.1.4'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +options = {'modulename': 'platypus'} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-16.4-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-16.4-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..9b4c1f628550 --- /dev/null +++ b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-16.4-GCCcore-13.3.0.eb @@ -0,0 +1,43 @@ +easyblock = 'ConfigureMake' + +name = 'PostgreSQL' +version = '16.4' + +homepage = 'https://www.postgresql.org/' +description = """PostgreSQL is a powerful, open source object-relational database system. + It is fully ACID compliant, has full support for foreign keys, + joins, views, triggers, and stored procedures (in multiple languages). + It includes most SQL:2008 data types, including INTEGER, + NUMERIC, BOOLEAN, CHAR, VARCHAR, DATE, INTERVAL, and TIMESTAMP. + It also supports storage of binary large objects, including pictures, + sounds, or video. It has native programming interfaces for C/C++, Java, + .Net, Perl, Python, Ruby, Tcl, ODBC, among others, and exceptional documentation.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['http://ftp.postgresql.org/pub/source/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['2e17a90062403e15d6540480fdec50c8b005eb48729a91cb4989ffeb04df193c'] + +builddependencies = [ + ('binutils', '2.42'), + ('Bison', '3.8.2'), + ('flex', '2.6.4'), + ('Perl', '5.38.2'), + ('Python', '3.12.3'), +] + +dependencies = [ + ('libreadline', '8.2'), + ('zlib', '1.3.1'), + ('OpenSSL', '3', '', SYSTEM), +] + +configopts = '--with-python --with-openssl --without-icu' + +sanity_check_paths = { + 'files': ['bin/psql', 'bin/pg_config', 'lib/libpq.a', 'lib/libpq.%s' % SHLIB_EXT], + 'dirs': ['share/postgresql'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/PretextMap/PretextMap-0.1.9-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/PretextMap/PretextMap-0.1.9-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..699729719367 --- /dev/null +++ b/easybuild/easyconfigs/p/PretextMap/PretextMap-0.1.9-GCCcore-12.3.0.eb @@ -0,0 +1,41 @@ +easyblock = 'MesonNinja' + +name = 'PretextMap' +version = '0.1.9' + +homepage = 'https://github.com/sanger-tol/PretextMap/' +description = """Paired REad TEXTure Mapper. Converts SAM formatted read pairs into genome contact maps.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +sources = [{ + 'filename': '%(version)s.tar.gz', + 'git_config': { + 'url': 'https://github.com/sanger-tol', + 'repo_name': '%(name)s', + 'tag': '%(version)s', + 'recursive': True, + 'keep_git_dir': True, + }, +}] +checksums = [None] + +builddependencies = [ + ('binutils', '2.40'), + ('Meson', '1.1.1'), + ('Ninja', '1.11.1'), + ('Clang', '16.0.6'), +] + +preconfigopts = 'CXX=clang && ' +configure_cmd = 'meson setup --buildtype=release --unity on' +runtest = 'meson test' + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin'] +} + +sanity_check_commands = ["command -v PretextMap"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/ProteinMPNN/ProteinMPNN-1.0.1-20230627-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/ProteinMPNN/ProteinMPNN-1.0.1-20230627-foss-2022a-CUDA-11.7.0.eb index 258c21fef240..db7151ab47f3 100644 --- a/easybuild/easyconfigs/p/ProteinMPNN/ProteinMPNN-1.0.1-20230627-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/p/ProteinMPNN/ProteinMPNN-1.0.1-20230627-foss-2022a-CUDA-11.7.0.eb @@ -27,17 +27,20 @@ dependencies = [ ('torchaudio', '0.12.0', '-PyTorch-1.12.0' + versionsuffix), ] -postinstallcmds = ['chmod a+x %(installdir)s/protein_mpnn_run.py'] +postinstallcmds = [ + 'chmod a+x %(installdir)s/protein_mpnn_run.py', + 'chmod a+x %(installdir)s/helper_scripts/*.py' +] sanity_check_paths = { 'files': ['protein_mpnn_run.py'], 'dirs': ['examples'], } -fix_python_shebang_for = ['protein_mpnn_run.py'] +fix_python_shebang_for = ['protein_mpnn_run.py', 'helper_scripts/*.py'] sanity_check_commands = ['protein_mpnn_run.py --help'] -modextrapaths = {'PATH': ''} +modextrapaths = {'PATH': ['', 'helper_scripts']} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PyAEDT/PyAEDT-0.8.7-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/PyAEDT/PyAEDT-0.8.7-GCCcore-12.3.0.eb index aee9ba9ea19a..894b488cd3e0 100644 --- a/easybuild/easyconfigs/p/PyAEDT/PyAEDT-0.8.7-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/PyAEDT/PyAEDT-0.8.7-GCCcore-12.3.0.eb @@ -43,6 +43,7 @@ exts_list = [ ('ansys-pythonnet', '3.1.0rc3', { 'checksums': ['369a0a5a838a0991f755b6d63c319ab6997f9dc464d016187227be5cd860a9cb'], 'modulename': 'pythonnet', + 'preinstallopts': 'export OPENSSL_ENABLE_SHA1_SIGNATURES=1 &&', }), ('pytomlpp', '1.0.13', { 'checksums': ['a0bd639a8f624d1bdf5b3ea94363ca23dbfef38ab7b5b9348881a84afab434ad'], diff --git a/easybuild/easyconfigs/p/PyAEDT/PyAEDT-0.9.9-gfbf-2023b.eb b/easybuild/easyconfigs/p/PyAEDT/PyAEDT-0.9.9-gfbf-2023b.eb new file mode 100644 index 000000000000..f2436367baa8 --- /dev/null +++ b/easybuild/easyconfigs/p/PyAEDT/PyAEDT-0.9.9-gfbf-2023b.eb @@ -0,0 +1,78 @@ +easyblock = 'PythonBundle' + +name = 'PyAEDT' +version = '0.9.9' + +homepage = 'https://aedt.docs.pyansys.com/version/stable' +description = """PyAEDT is a Python library that interacts directly with the +Ansys Electronics Desktop (AEDT) API, enabling straightforward and efficient +automation in your workflow.""" + +toolchain = {'name': 'gfbf', 'version': '2023b'} + +builddependencies = [ + ('binutils', '2.40'), + ('hatchling', '1.18.0'), +] + +dependencies = [ + ('dotNET-Core', '8.0', '', SYSTEM), + ('libspatialindex', '1.9.3'), + ('Python', '3.11.5'), + ('Python-bundle-PyPI', '2023.10'), + ('Pillow', '10.2.0'), + ('pydantic', '2.6.4'), + ('SciPy-bundle', '2023.11'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('dotnetcore2', '3.1.23', { + 'sources': ['dotnetcore2-3.1.23-py3-none-manylinux1_x86_64.whl'], + 'checksums': ['5f076ddc39da0c685e7de20ecb91ee81185928918ec86fbeb3bffc55dd867ab5'], + }), + ('clr_loader', '0.2.6', { + 'checksums': ['019348ae6b6a83c7a406d14537c277cecf7a3a53b263ec342c81ded5845a67ee'], + }), + ('defusedxml', '0.7.1', { + 'checksums': ['1bb3032db185915b62d7c6209c5a8792be6a32ab2fedacc84e01b52c51aa3e69'], + }), + ('fonttools', '4.53.1', { + 'modulename': 'fontTools', + 'checksums': ['e128778a8e9bc11159ce5447f76766cefbd876f44bd79aff030287254e4752c4'], + }), + ('ansys-pythonnet', '3.1.0rc3', { + 'modulename': 'pythonnet', + 'checksums': ['369a0a5a838a0991f755b6d63c319ab6997f9dc464d016187227be5cd860a9cb'], + 'preinstallopts': 'export OPENSSL_ENABLE_SHA1_SIGNATURES=1 &&', + }), + ('pytomlpp', '1.0.13', { + 'checksums': ['a0bd639a8f624d1bdf5b3ea94363ca23dbfef38ab7b5b9348881a84afab434ad'], + }), + ('fpdf2', '2.7.9', { + 'modulename': 'fpdf', + 'checksums': ['f364c0d816a5e364eeeda9761cf5c961bae8c946f080cf87fed7f38ab773b318'], + }), + ('plumbum', '1.8.3', { + 'checksums': ['6092c85ab970b7a7a9d5d85c75200bc93be82b33c9bdf640ffa87d2d7c8709f0'], + }), + ('rpyc', '6.0.0', { + 'checksums': ['a7e12b31f40978cbd6b74e0b713da389d4b2565cef612adcb0f4b41aeb188230'], + }), + ('rtree', '1.3.0', { + 'modulename': 'rtree', + 'checksums': ['b36e9dd2dc60ffe3d02e367242d2c26f7281b00e1aaf0c39590442edaaadd916'], + }), + ('pyedb', '0.21.0', { + 'checksums': ['3c91cb8a72a080864d3582ae7ec1de2f04d90aee477dadc096a7144f7823258d'], + }), + ('pyaedt', version, { + 'checksums': ['714728230ab3ede4744a30a7c0d45aaa104cdc1887bfbfe8feb928a8f10cc72f'], + }), +] + +modloadmsg = "NOTE: You also need load a AEDT module before you start using PyAEDT." + +moduleclass = "phys" diff --git a/easybuild/easyconfigs/p/PyBEL/PyBEL-0.15.5-gfbf-2023a.eb b/easybuild/easyconfigs/p/PyBEL/PyBEL-0.15.5-gfbf-2023a.eb new file mode 100644 index 000000000000..40c17e035ce8 --- /dev/null +++ b/easybuild/easyconfigs/p/PyBEL/PyBEL-0.15.5-gfbf-2023a.eb @@ -0,0 +1,76 @@ +easyblock = 'PythonBundle' + +name = 'PyBEL' +version = '0.15.5' + +homepage = 'https://github.com/pybel/pybel' +description = """ +PyBEL is a pure Python software package that parses BEL (Biological Expression Language) +documents, validates their semantics, and facilitates data interchange between common formats +and database systems like JSON, CSV, Excel, SQL, CX, and Neo4J. +""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +builddependencies = [ + ('hatchling', '1.18.0'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('networkx', '3.1'), + ('SQLAlchemy', '2.0.25'), + ('tqdm', '4.66.1'), + ('pydantic', '2.5.3'), # for bioregistry +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('multisplitby', '0.0.1', { + 'checksums': ['e40489fa174fd7afd28a895477e6eefc64d6cfd863cca6900530e436a40e356f'], + }), + ('bel_resources', '0.0.3', { + 'checksums': ['ec2d6390f89c0a98d67868bf02f7538709df0ba5b5ba6ddeb105512da07e82b5'], + }), + ('PyTrie', '0.4.0', { + 'checksums': ['8f4488f402d3465993fb6b6efa09866849ed8cda7903b50647b7d0342b805379'], + }), + ('curies', '0.7.9', { + 'checksums': ['3b63c5fea7b0e967629a3a384b1a8c59b56c503487c1dcbacddeab59e25db4d8'], + }), + ('more_click', '0.1.2', { + 'checksums': ['085da66d5a9b823c5d912a888dca1fa0c8b3a14ed1b21ea9c8a1b814857a3981'], + }), + ('bioregistry', '0.11.10', { + 'checksums': ['d3e155ba38d88f5e4a84a2d337c33109f3434f6b2e64a285eba14817ed5c4492'], + }), + ('click-plugins', '1.1.1', { + 'checksums': ['46ab999744a9d831159c3411bb0c79346d94a444df9a3a3742e9ed63645f264b'], + }), + ('humanize', '4.8.0', { + 'checksums': ['9783373bf1eec713a770ecaa7c2d7a7902c98398009dfa3d8a2df91eec9311e8'], + }), + ('psycopg2-binary', '2.9.9', { + 'modulename': 'psycopg2', + 'checksums': ['7f01846810177d829c7692f1f5ada8096762d9172af1b1a28d4ab5b77c923c1c'], + }), + ('pystow', '0.5.4', { + 'checksums': ['2692180cb405bd77259bee6c7f4db545d10e81939980064730609f21750567ff'], + }), + ('ratelimit', '2.2.1', { + 'checksums': ['af8a9b64b821529aca09ebaf6d8d279100d766f19e90b5059ac6a718ca6dee42'], + }), + ('requests_file', '2.1.0', { + 'checksums': ['0f549a3f3b0699415ac04d167e9cb39bccfb730cb832b4d20be3d9867356e658'], + }), + ('pybel', version, { + 'checksums': ['c2aabd0ad65b9f205f9ed6eae126d19875c1312f8e35641f4f42bcc1fc573f9e'], + }), +] + +sanity_check_commands = ["pybel --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PyCharm/PyCharm-2024.1.6.eb b/easybuild/easyconfigs/p/PyCharm/PyCharm-2024.1.6.eb new file mode 100644 index 000000000000..37d00512c279 --- /dev/null +++ b/easybuild/easyconfigs/p/PyCharm/PyCharm-2024.1.6.eb @@ -0,0 +1,20 @@ +easyblock = 'Tarball' + +name = 'PyCharm' +version = "2024.1.6" + +homepage = 'https://www.jetbrains.com/pycharm/' +description = """PyCharm Community Edition: Python IDE for Professional Developers""" + +toolchain = SYSTEM + +source_urls = ['https://download-cf.jetbrains.com/python'] +sources = ['pycharm-community-%(version)s.tar.gz'] +checksums = ['539961408de4217a68b84d666d5c10ddb8d7bcf919e3a569f2489438a3237f1a'] + +sanity_check_paths = { + 'files': ["bin/pycharm.sh"], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PyClone/PyClone-2020.9b2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/PyClone/PyClone-2020.9b2-GCCcore-10.2.0.eb index ee4425b49c5d..96d813edcceb 100644 --- a/easybuild/easyconfigs/p/PyClone/PyClone-2020.9b2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/PyClone/PyClone-2020.9b2-GCCcore-10.2.0.eb @@ -21,9 +21,8 @@ dependencies = [ ('Python', '3.8.6'), ] -exts_default_options = { - 'use_pip': True -} +sanity_pip_check = True +use_pip = True exts_list = [ ('Logbook', '1.5.3', { @@ -37,6 +36,4 @@ exts_list = [ }), ] -sanity_pip_check = True - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/PyRosetta/PyRosetta-4.release-384-gompi-2022a.eb b/easybuild/easyconfigs/p/PyRosetta/PyRosetta-4.release-384-gompi-2022a.eb new file mode 100644 index 000000000000..5769add932d0 --- /dev/null +++ b/easybuild/easyconfigs/p/PyRosetta/PyRosetta-4.release-384-gompi-2022a.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonBundle' + +name = 'PyRosetta' +version = '4.release-384' + +homepage = 'https://www.pyrosetta.org/' +description = """ +PyRosetta is an interactive Python-based interface to the powerful Rosetta molecular modeling +suite. It enables users to design their own custom molecular modeling algorithms using Rosetta +sampling methods and energy functions. +""" + +toolchain = {'name': 'gompi', 'version': '2022a'} +toolchainopts = {'usempi': True} + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('Python', '3.10.4'), +] + +use_pip = True + +local_source_tmpl = '%(name)s%(version_major)s.Release.python%(pymajver)s%(pyminver)s.linux.%(version_minor)s.tar.bz2' +local_source_urls = 'https://graylab.jhu.edu/download/PyRosetta4/archive/release/PyRosetta4.Release.python310.linux/' + +exts_list = [ + (name, version, { + 'source_tmpl': local_source_tmpl, + 'source_urls': [local_source_urls], + 'start_dir': 'setup', + 'checksums': ['630108f2bac166563fd2a4046a1d82e51e14693bb0e20dd3174e71c02b0760c2'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-2.5.0-foss-2023a-PyTorch-2.1.2.eb b/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-2.5.0-foss-2023a-PyTorch-2.1.2.eb new file mode 100644 index 000000000000..9c8f282ccee8 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-2.5.0-foss-2023a-PyTorch-2.1.2.eb @@ -0,0 +1,100 @@ +easyblock = 'PythonBundle' + +name = 'PyTorch-Geometric' +version = '2.5.0' +local_pytorchver = '2.1.2' +versionsuffix = '-PyTorch-%s' % local_pytorchver + +homepage = 'https://github.com/rusty1s/pytorch_geometric' +description = "PyTorch Geometric (PyG) is a geometric deep learning extension library for PyTorch." + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('PDM', '2.12.4'), + ('Parallel-Hashmap', '1.3.12'), # header only +] + +dependencies = [ + ('Python', '3.11.3'), + ('PyTorch', local_pytorchver), + ('scikit-learn', '1.3.1'), + ('scikit-image', '0.22.0'), + ('numba', '0.58.1'), + ('h5py', '3.9.0'), + ('tqdm', '4.66.1'), + ('RDFlib', '7.0.0'), + ('ASE', '3.22.1'), + ('YACS', '0.1.8'), + ('aiohttp', '3.8.5'), +] + +use_pip = True + +exts_list = [ + ('googledrivedownloader', '0.4', { + 'modulename': 'google_drive_downloader', + 'checksums': ['4b34c1337b2ff3bf2bd7581818efbdcaea7d50ffd484ccf80809688f5ca0e204'], + }), + ('plyfile', '1.0.3', { + 'patches': ['plyfile-1.0.3_use_pdm_backend.patch'], + 'checksums': [ + {'plyfile-1.0.3.tar.gz': '0ecbe8e7ce55a7bbc6c9dea24242fffa0ab7d9bed33fbd5ad567ca013bcc5222'}, + {'plyfile-1.0.3_use_pdm_backend.patch': '815611863f16e785ef03a7992a0b99e433150212ff03559c7f6fce4e86d9e0a7'}, + ], + }), + ('torch_scatter', '2.1.2', { + 'source_urls': ['https://github.com/rusty1s/pytorch_scatter/archive/refs/tags/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['6f375dbc9cfe03f330aa29ea553e9c7432e9b040d039b041f08bf05df1a8bf37'], + 'runtest': 'pytest', + 'testinstall': True, + }), + ('torch_sparse', '0.6.18', { + 'source_urls': ['https://github.com/rusty1s/pytorch_sparse/archive/refs/tags/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['a9e194cddc17481001ac4592a058450493ce13780e8ce3eb54d4f79706e69c91'], + 'runtest': 'pytest -k "not test_spmm[dtype10-device10-sum] and not test_spmm[dtype16-device16-add]"', # flaky + 'testinstall': True, + }), + ('torch_cluster', '1.6.3', { + 'source_urls': ['https://github.com/rusty1s/pytorch_cluster/archive/refs/tags/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['0e2b08095e03cf87ce9b23b7a7352236a25d3ed92d92351dc020fd927ea8dbfe'], + 'runtest': 'pytest', + 'testinstall': True, + }), + ('torch_spline_conv', '1.2.2', { + 'source_urls': ['https://github.com/rusty1s/pytorch_spline_conv/archive/refs/tags/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['258947394514ba487b2617268ae7102e9a06fd15d79f5d8239a96211a85adc3d'], + 'runtest': 'pytest', + 'testinstall': True, + }), + ('python-louvain', '0.16', { + 'modulename': 'community.community_louvain', + 'checksums': ['b7ba2df5002fd28d3ee789a49532baad11fe648e4f2117cf0798e7520a1da56b'], + }), + ('torch_geometric', version, { + 'source_urls': ['https://github.com/pyg-team/pytorch_geometric/archive/refs/tags/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['f9abf00dc7fd1039ef1d9734a0fbd8c52196e39ca9fc4816afd98a8f311265be'], + 'runtest': ( + 'pytest' + ' --ignore=test/test_edge_index.py' # many tests require PyTorch with MKL + ' --ignore=test/nn/models/test_graph_unet.py' # requires PyTorch with MKL + ' --ignore=test/nn/pool/test_asap.py' # requires PyTorch with MKL + ' --ignore=test/transforms/test_add_metapaths.py' # requires PyTorch with MKL + ' --ignore=test/transforms/test_two_hop.py' # requires PyTorch with MKL + ' --ignore=test/test_inspector.py' # test failing due to typing change + ' --ignore=test/nn/conv/test_hetero_conv.py' # unknown jit compilation issue + ' --ignore=test/nn/conv/test_sage_conv.py' # unknown jit compilation issue + ' -k "not test_multithreading_neighbor_loader" ' # picky about number of cores in the environment + ), + 'testinstall': True, + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2022a.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2022a.eb index 0f6d51fd1bb4..4c9324b74791 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2022a.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2022a.eb @@ -46,6 +46,7 @@ patches = [ 'PyTorch-2.1.2_fix-vsx-vector-abs.patch', 'PyTorch-2.1.2_fix-vsx-vector-div.patch', 'PyTorch-2.1.2_skip-cpu_repro-test-without-vectorization.patch', + 'PyTorch-2.1.2_skip-memory-leak-test.patch', 'PyTorch-2.1.2_workaround_dynamo_failure_without_nnpack.patch', ] checksums = [ @@ -111,6 +112,7 @@ checksums = [ {'PyTorch-2.1.2_fix-vsx-vector-div.patch': '11f497a6892eb49b249a15320e4218e0d7ac8ae4ce67de39e4a018a064ca1acc'}, {'PyTorch-2.1.2_skip-cpu_repro-test-without-vectorization.patch': '7ace835af60c58d9e0754a34c19d4b9a0c3a531f19e5d0eba8e2e49206eaa7eb'}, + {'PyTorch-2.1.2_skip-memory-leak-test.patch': '8d9841208e8a00a498295018aead380c360cf56e500ef23ca740adb5b36de142'}, {'PyTorch-2.1.2_workaround_dynamo_failure_without_nnpack.patch': 'fb96eefabf394617bbb3fbd3a7a7c1aa5991b3836edc2e5d2a30e708bfe49ba1'}, ] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2022b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2022b.eb index 146e42cb2b82..ee2c8731bb89 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2022b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2022b.eb @@ -47,6 +47,7 @@ patches = [ 'PyTorch-2.1.2_fix-vsx-vector-abs.patch', 'PyTorch-2.1.2_fix-vsx-vector-div.patch', 'PyTorch-2.1.2_skip-cpu_repro-test-without-vectorization.patch', + 'PyTorch-2.1.2_skip-memory-leak-test.patch', 'PyTorch-2.1.2_workaround_dynamo_failure_without_nnpack.patch', ] checksums = [ @@ -113,6 +114,7 @@ checksums = [ {'PyTorch-2.1.2_fix-vsx-vector-div.patch': '11f497a6892eb49b249a15320e4218e0d7ac8ae4ce67de39e4a018a064ca1acc'}, {'PyTorch-2.1.2_skip-cpu_repro-test-without-vectorization.patch': '7ace835af60c58d9e0754a34c19d4b9a0c3a531f19e5d0eba8e2e49206eaa7eb'}, + {'PyTorch-2.1.2_skip-memory-leak-test.patch': '8d9841208e8a00a498295018aead380c360cf56e500ef23ca740adb5b36de142'}, {'PyTorch-2.1.2_workaround_dynamo_failure_without_nnpack.patch': 'fb96eefabf394617bbb3fbd3a7a7c1aa5991b3836edc2e5d2a30e708bfe49ba1'}, ] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb index 7990dd1511b8..65dfced17011 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb @@ -59,6 +59,7 @@ patches = [ 'PyTorch-2.1.2_remove-nccl-backend-default-without-gpus.patch', 'PyTorch-2.1.2_skip-cpu_repro-test-without-vectorization.patch', 'PyTorch-2.1.2_skip-failing-test_dtensor_ops-subtests.patch', + 'PyTorch-2.1.2_skip-memory-leak-test.patch', 'PyTorch-2.1.2_skip-test_fsdp_tp_checkpoint_integration.patch', 'PyTorch-2.1.2_workaround_dynamo_failure_without_nnpack.patch', ] @@ -145,6 +146,7 @@ checksums = [ '7ace835af60c58d9e0754a34c19d4b9a0c3a531f19e5d0eba8e2e49206eaa7eb'}, {'PyTorch-2.1.2_skip-failing-test_dtensor_ops-subtests.patch': '6cf711bf26518550903b09ed4431de9319791e79d61aab065785d6608fd5cc88'}, + {'PyTorch-2.1.2_skip-memory-leak-test.patch': '8d9841208e8a00a498295018aead380c360cf56e500ef23ca740adb5b36de142'}, {'PyTorch-2.1.2_skip-test_fsdp_tp_checkpoint_integration.patch': '943ee92f5fd518f608a59e43fe426b9bb45d7e7ad0ba04639e516db2d61fa57d'}, {'PyTorch-2.1.2_workaround_dynamo_failure_without_nnpack.patch': diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a.eb index 413e3254f8ac..a79f709480ca 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a.eb @@ -48,6 +48,7 @@ patches = [ 'PyTorch-2.1.2_fix-vsx-vector-abs.patch', 'PyTorch-2.1.2_fix-vsx-vector-div.patch', 'PyTorch-2.1.2_skip-cpu_repro-test-without-vectorization.patch', + 'PyTorch-2.1.2_skip-memory-leak-test.patch', 'PyTorch-2.1.2_workaround_dynamo_failure_without_nnpack.patch', ] checksums = [ @@ -116,6 +117,7 @@ checksums = [ {'PyTorch-2.1.2_fix-vsx-vector-div.patch': '11f497a6892eb49b249a15320e4218e0d7ac8ae4ce67de39e4a018a064ca1acc'}, {'PyTorch-2.1.2_skip-cpu_repro-test-without-vectorization.patch': '7ace835af60c58d9e0754a34c19d4b9a0c3a531f19e5d0eba8e2e49206eaa7eb'}, + {'PyTorch-2.1.2_skip-memory-leak-test.patch': '8d9841208e8a00a498295018aead380c360cf56e500ef23ca740adb5b36de142'}, {'PyTorch-2.1.2_workaround_dynamo_failure_without_nnpack.patch': 'fb96eefabf394617bbb3fbd3a7a7c1aa5991b3836edc2e5d2a30e708bfe49ba1'}, ] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023b.eb index 151e13356fec..bce1b68aa7be 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023b.eb @@ -48,6 +48,7 @@ patches = [ 'PyTorch-2.1.2_fix-vsx-vector-abs.patch', 'PyTorch-2.1.2_fix-vsx-vector-div.patch', 'PyTorch-2.1.2_skip-cpu_repro-test-without-vectorization.patch', + 'PyTorch-2.1.2_skip-memory-leak-test.patch', 'PyTorch-2.1.2_workaround_dynamo_failure_without_nnpack.patch', ] checksums = [ @@ -116,6 +117,7 @@ checksums = [ {'PyTorch-2.1.2_fix-vsx-vector-div.patch': '11f497a6892eb49b249a15320e4218e0d7ac8ae4ce67de39e4a018a064ca1acc'}, {'PyTorch-2.1.2_skip-cpu_repro-test-without-vectorization.patch': '7ace835af60c58d9e0754a34c19d4b9a0c3a531f19e5d0eba8e2e49206eaa7eb'}, + {'PyTorch-2.1.2_skip-memory-leak-test.patch': '8d9841208e8a00a498295018aead380c360cf56e500ef23ca740adb5b36de142'}, {'PyTorch-2.1.2_workaround_dynamo_failure_without_nnpack.patch': 'fb96eefabf394617bbb3fbd3a7a7c1aa5991b3836edc2e5d2a30e708bfe49ba1'}, ] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_skip-memory-leak-test.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_skip-memory-leak-test.patch new file mode 100644 index 000000000000..cbebd761d98b --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_skip-memory-leak-test.patch @@ -0,0 +1,17 @@ +Reports from various sites show that this test is unreliable. +As it is not critical just skip it. + +@Author: Alexander Grund (TU Dresden) + +diff --git a/test/test_jit.py b/test/test_jit.py +index 2cdc5413dfe..5b145458630 100644 +--- a/test/test_jit.py ++++ b/test/test_jit.py +@@ -12838,6 +12838,7 @@ dedent """ + data = reader.get_record(str(offset)) + assert(data == buffers[i]) + ++ @unittest.skip("The memory allocation tracking is not reliable on all systems") + def test_file_reader_no_memory_leak(self): + num_iters = 10000 + filename, _, _ = self._make_filereader_test_file() diff --git a/easybuild/easyconfigs/p/PyWavelets/PyWavelets-1.7.0-foss-2023a.eb b/easybuild/easyconfigs/p/PyWavelets/PyWavelets-1.7.0-foss-2023a.eb new file mode 100644 index 000000000000..f68a1a2ba06d --- /dev/null +++ b/easybuild/easyconfigs/p/PyWavelets/PyWavelets-1.7.0-foss-2023a.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'PyWavelets' +version = '1.7.0' + +homepage = 'https://pywavelets.readthedocs.io' +description = "PyWavelets is open source wavelet transform software for Python." + +toolchain = {'name': 'foss', 'version': '2023a'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['b47250e5bb853e37db5db423bafc82847f4cde0ffdf7aebb06336a993bc174f6'] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), # for numpy + ('meson-python', '0.13.2'), + ('Cython', '3.0.8'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +options = {'modulename': 'pywt'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-6.0.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-6.0.2-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..50b9ad427e64 --- /dev/null +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-6.0.2-GCCcore-13.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'PyYAML' +version = '6.0.2' + +homepage = 'https://github.com/yaml/pyyaml' +description = "PyYAML is a YAML parser and emitter for the Python programming language." + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +sources = ['https://github.com/yaml/pyyaml/archive/refs/tags/%(version)s.tar.gz'] +checksums = ['9377c381ac3fccad8df73d96b5139ef8b1a2c57a0d913e95ab0a2275d66b5caa'] + +builddependencies = [ + ('binutils', '2.42'), + ('Cython', '3.0.10'), +] +dependencies = [ + ('Python', '3.12.3'), + ('libyaml', '0.2.5'), + ('Python-bundle-PyPI', '2024.06'), +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True +options = {'modulename': 'yaml'} + +sanity_check_commands = ["python -c 'import yaml; yaml.CLoader'"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/Pygments/Pygments-2.18.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/Pygments/Pygments-2.18.0-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..54edd0b830e8 --- /dev/null +++ b/easybuild/easyconfigs/p/Pygments/Pygments-2.18.0-GCCcore-12.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'Pygments' +version = '2.18.0' + +homepage = 'https://pygments.org/' +description = """Generic syntax highlighter suitable for use in code hosting, forums, wikis or other applications + that need to prettify source code.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +sources = [SOURCELOWER_PY3_WHL] +checksums = ['b8e6aca0523f3ab76fee51799c488e38782ac06eafcf95e7ba832985c8e7b13a'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('Python', '3.11.3'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/pygmentize'], + 'dirs': [], +} + +sanity_check_commands = ['pygmentize --help'] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/Pylint/Pylint-3.2.5-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/Pylint/Pylint-3.2.5-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..c919c6c4dd4f --- /dev/null +++ b/easybuild/easyconfigs/p/Pylint/Pylint-3.2.5-GCCcore-13.2.0.eb @@ -0,0 +1,56 @@ +easyblock = 'PythonBundle' + +name = 'Pylint' +version = '3.2.5' + +homepage = 'https://www.pylint.org/' +description = """Pylint is a tool that checks for errors in Python code, tries to enforce + a coding standard and looks for code smells. It can also look for certain type errors, + it can recommend suggestions about how particular blocks can be refactored and + can offer you details about the code's complexity.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('poetry', '1.6.1'), +] + +dependencies = [ + ('Python', '3.11.5'), +] + +use_pip = True + +exts_list = [ + ('dill', '0.3.8', { + 'checksums': ['3ebe3c479ad625c4553aca177444d89b486b1d84982eeacded644afc0cf797ca'], + }), + ('platformdirs', '4.2.2', { + 'checksums': ['38b7b51f512eed9e84a22788b4bce1de17c0adb134d6becb09836e37d8654cd3'], + }), + ('tomlkit', '0.12.5', { + 'checksums': ['eef34fba39834d4d6b73c9ba7f3e4d1c417a4e56f89a7e96e090dd0d24b8fb3c'], + }), + ('astroid', '3.2.2', { + 'checksums': ['8ead48e31b92b2e217b6c9733a21afafe479d52d6e164dd25fb1a770c7c3cf94'], + }), + ('isort', '5.13.2', { + 'checksums': ['48fdfcb9face5d58a4f6dde2e72a1fb8dcaf8ab26f95ab49fab84c2ddefb0109'], + }), + ('mccabe', '0.7.0', { + 'checksums': ['348e0240c33b60bbdf4e523192ef919f28cb2c3d7d5c7794f74009290f236325'], + }), + ('pylint', version, { + 'checksums': ['e9b7171e242dcc6ebd0aaa7540481d1a72860748a0a7816b8fe6cf6c80a6fe7e'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/pylint'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/Pyomo/Pyomo-6.7.3-foss-2023a.eb b/easybuild/easyconfigs/p/Pyomo/Pyomo-6.7.3-foss-2023a.eb new file mode 100644 index 000000000000..64ee6de4f2b4 --- /dev/null +++ b/easybuild/easyconfigs/p/Pyomo/Pyomo-6.7.3-foss-2023a.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonBundle' + +name = 'Pyomo' +version = '6.7.3' + +homepage = 'https://www.pyomo.org/' +description = """ Pyomo is a Python-based open-source software package that supports a diverse set of optimization + capabilities for formulating and analyzing optimization models. """ + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('mpi4py', '3.1.4'), + ('PLY', '3.11'), +] + +exts_list = [ + ('PyUtilib', '6.0.0', { + 'preinstallopts': """sed -i "s/'nose',//g" setup.py && """, + 'checksums': ['d3c14f8ed9028a831b2bf51b8ab7776eba87e66cfc58a06b99c359aaa640f040'], + }), + (name, version, { + 'checksums': ['b7f0441c405af4f42f38527ae38826a5c0a4984dd7bea1fe07172789d8594770'], + }), +] + +use_pip = True +sanity_pip_check = True + +sanity_check_commands = ['pyomo -h'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2023.06-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2023.06-GCCcore-12.3.0.eb index 6a91bcca5e41..808285d9f26c 100644 --- a/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2023.06-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2023.06-GCCcore-12.3.0.eb @@ -26,11 +26,8 @@ dependencies = [ ('virtualenv', '20.23.1'), ] -exts_default_options = { - 'download_dep_fail': True, - 'sanity_pip_check': True, - 'use_pip': True, -} +sanity_pip_check = True +use_pip = True # order is important! # package versions updated 2023-06-26 diff --git a/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2023.10-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2023.10-GCCcore-13.2.0.eb index d551945f5e7d..d97f7a93c0f7 100644 --- a/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2023.10-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2023.10-GCCcore-13.2.0.eb @@ -26,11 +26,8 @@ dependencies = [ ('virtualenv', '20.24.6'), ] -exts_default_options = { - 'download_dep_fail': True, - 'sanity_pip_check': True, - 'use_pip': True, -} +sanity_pip_check = True +use_pip = True # order is important! # package versions updated 2023-10-29 diff --git a/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2024.06-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2024.06-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..42df4fd52a1b --- /dev/null +++ b/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2024.06-GCCcore-13.3.0.eb @@ -0,0 +1,497 @@ +easyblock = 'PythonBundle' + +name = 'Python-bundle-PyPI' +version = '2024.06' + +homepage = 'https://python.org/' +description = "Bundle of Python packages from PyPI" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +builddependencies = [ + ('binutils', '2.42'), + ('UnZip', '6.0'), + ('pkgconf', '2.2.0'), + ('git', '2.45.1'), # required for pbr + ('hatchling', '1.24.2'), + ('poetry', '1.8.3'), + ('scikit-build', '0.17.6'), + ('flit', '3.9.0'), + ('setuptools-rust', '1.9.0'), # required for dulwich + ('maturin', '1.6.0'), # required for rpds-py +] + +dependencies = [ + ('Python', '3.12.3'), + ('cryptography', '42.0.8'), + ('virtualenv', '20.26.2'), +] + +sanity_pip_check = True +use_pip = True + +# order is important! +# package versions updated 2024-06-14 +exts_list = [ + ('blist', '1.3.6', { + 'patches': [ + 'Python-3_9-blist-1.3.6-fix-undefined_symbol_PyObject_GC_IS_TRACKED.patch', + 'Python-3.10-bist-1.3.6-compatibility.patch', + 'Python-3.11-bist-1.3.6-compatibility.patch', + ], + 'checksums': [ + {'blist-1.3.6.tar.gz': '3a12c450b001bdf895b30ae818d4d6d3f1552096b8c995f0fe0c74bef04d1fc3'}, + {'Python-3_9-blist-1.3.6-fix-undefined_symbol_PyObject_GC_IS_TRACKED.patch': + '18a643d1d1565b05df7dcc9a612a86dcf7b3b352435032f6425a61b597f911d0'}, + {'Python-3.10-bist-1.3.6-compatibility.patch': + '0fb2d92e06b2c39bfc79e229e6fde6053f9aa9538733029377c9a743650a4741'}, + {'Python-3.11-bist-1.3.6-compatibility.patch': + 'da283300bc5f0524b9982c9d9de4670908711634667849d3d81ccd87fc82c4ee'}, + ], + }), + ('pbr', '6.0.0', { + 'checksums': ['d1377122a5a00e2f940ee482999518efe16d745d423a670c27773dfbc3c9a7d9'], + }), + ('six', '1.16.0', { + 'checksums': ['1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926'], + }), + ('toml', '0.10.2', { + 'checksums': ['b3bda1d108d5dd99f4a20d24d9c348e91c4db7ab1b749200bded2f839ccbe68f'], + }), + ('tomli', '2.0.1', { + 'checksums': ['de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f'], + }), + ('packaging', '24.1', { + 'checksums': ['026ed72c8ed3fcce5bf8950572258698927fd1dbda10a5e981cdf0ac37f4f002'], + }), + ('python-dateutil', '2.9.0.post0', { + 'modulename': 'dateutil', + 'checksums': ['37dd54208da7e1cd875388217d5e00ebd4179249f90fb72437e91a35459a0ad3'], + }), + ('decorator', '5.1.1', { + 'checksums': ['637996211036b6385ef91435e4fae22989472f9d571faba8927ba8253acbc330'], + }), + ('liac-arff', '2.5.0', { + 'modulename': 'arff', + 'checksums': ['3220d0af6487c5aa71b47579be7ad1d94f3849ff1e224af3bf05ad49a0b5c4da'], + }), + ('pycryptodome', '3.20.0', { + 'modulename': 'Crypto.PublicKey.RSA', + 'checksums': ['09609209ed7de61c2b560cc5c8c4fbf892f8b15b1faf7e4cbffac97db1fffda7'], + }), + ('ecdsa', '0.19.0', { + 'checksums': ['60eaad1199659900dd0af521ed462b793bbdf867432b3948e87416ae4caf6bf8'], + }), + ('ipaddress', '1.0.23', { + 'checksums': ['b7f8e0369580bb4a24d5ba1d7cc29660a4a6987763faf1d8a8046830e020e7e2'], + }), + ('asn1crypto', '1.5.1', { + 'checksums': ['13ae38502be632115abf8a24cbe5f4da52e3b5231990aff31123c805306ccb9c'], + }), + ('idna', '3.7', { + 'checksums': ['028ff3aadf0609c1fd278d8ea3089299412a7a8b9bd005dd08b9f8285bcb5cfc'], + }), + ('pycparser', '2.22', { + 'checksums': ['491c8be9c040f5390f5bf44a5b07752bd07f56edf992381b05c701439eec10f6'], + }), + ('cffi', '1.16.0', { + 'checksums': ['bcb3ef43e58665bbda2fb198698fcae6776483e0c4a631aa5647806c25e02cc0'], + }), + ('semantic-version', '2.10.0', { + 'sources': ['semantic_version-%(version)s.tar.gz'], + 'checksums': ['bdabb6d336998cbb378d4b9db3a4b56a1e3235701dc05ea2690d9a997ed5041c'], + }), + ('pyasn1', '0.6.0', { + 'checksums': ['3a35ab2c4b5ef98e17dfdec8ab074046fbda76e281c5a706ccd82328cfc8f64c'], + }), + ('PyNaCl', '1.5.0', { + 'modulename': 'nacl', + 'checksums': ['8ac7448f09ab85811607bdd21ec2464495ac8b7c66d146bf545b0f08fb9220ba'], + }), + ('pyparsing', '3.1.2', { + 'checksums': ['a1bac0ce561155ecc3ed78ca94d3c9378656ad4c94c1270de543f621420f94ad'], + }), + ('netifaces', '0.11.0', { + 'checksums': ['043a79146eb2907edf439899f262b3dfe41717d34124298ed281139a8b93ca32'], + }), + ('netaddr', '1.3.0', { + 'checksums': ['5c3c3d9895b551b763779ba7db7a03487dc1f8e3b385af819af341ae9ef6e48a'], + }), + ('mock', '5.1.0', { + 'checksums': ['5e96aad5ccda4718e0a229ed94b2024df75cc2d55575ba5762d31f5767b8767d'], + }), + ('pytz', '2024.1', { + 'checksums': ['2a29735ea9c18baf14b448846bde5a48030ed267578472d8955cd0e7443a9812'], + }), + ('bitarray', '2.9.2', { + 'checksums': ['a8f286a51a32323715d77755ed959f94bef13972e9a2fe71b609e40e6d27957e'], + }), + ('bitstring', '4.2.3', { + 'checksums': ['e0c447af3fda0d114f77b88c2d199f02f97ee7e957e6d719f40f41cf15fbb897'], + }), + ('appdirs', '1.4.4', { + 'checksums': ['7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41'], + }), + ('distlib', '0.3.8', { + 'checksums': ['1530ea13e350031b6312d8580ddb6b27a104275a31106523b8f123787f494f64'], + }), + ('zipp', '3.19.2', { + 'checksums': ['bf1dcf6450f873a13e952a29504887c89e6de7506209e5b1bcc3460135d4de19'], + }), + ('importlib-metadata', '7.1.0', { + 'sources': ['importlib_metadata-%(version)s.tar.gz'], + 'checksums': ['b78938b926ee8d5f020fc4772d487045805a55ddbad2ecf21c6d60938dc7fcd2'], + }), + ('backports.entry-points-selectable', '1.3.0', { + 'sources': ['backports.entry_points_selectable-%(version)s.tar.gz'], + 'checksums': ['17a8b44ae700fba548686dd274ddc91c060371565cd63806c20a1d33911746e6'], + }), + ('pathspec', '0.12.1', { + 'checksums': ['a482d51503a1ab33b1c67a6c3813a26953dbdc71c31dacaef9a838c4e29f5712'], + }), + ('pluggy', '1.5.0', { + 'checksums': 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['pytest_xdist-%(version)s.tar.gz'], + 'checksums': ['ead156a4db231eec769737f57668ef58a2084a34b2e55c4a8fa20d861107300d'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/packmol/packmol-20.14.4-GCC-12.3.0.eb b/easybuild/easyconfigs/p/packmol/packmol-20.14.4-GCC-12.3.0.eb new file mode 100644 index 000000000000..4f5dd6ed6b81 --- /dev/null +++ b/easybuild/easyconfigs/p/packmol/packmol-20.14.4-GCC-12.3.0.eb @@ -0,0 +1,24 @@ +easyblock = 'MakeCp' + +name = 'packmol' +version = '20.14.4' + +homepage = 'http://m3g.iqm.unicamp.br/packmol' +description = "Packing Optimization for Molecular Dynamics Simulations" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/m3g/packmol/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['45ec33798d5f10c0aac6046675531a0e98567890c1a76f753450c5fc6b1aaa2f'] + +buildopts = 'FORTRAN="$F90"' + +files_to_copy = [(['packmol'], 'bin'), 'AUTHORS', 'LICENSE'] + +sanity_check_paths = { + 'files': ['bin/packmol', 'AUTHORS', 'LICENSE'], + 'dirs': [], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/pagmo/pagmo-2.19.0-gfbf-2022b.eb b/easybuild/easyconfigs/p/pagmo/pagmo-2.19.0-gfbf-2022b.eb new file mode 100644 index 000000000000..6f64905045c8 --- /dev/null +++ b/easybuild/easyconfigs/p/pagmo/pagmo-2.19.0-gfbf-2022b.eb @@ -0,0 +1,35 @@ +easyblock = 'CMakeMake' + +name = 'pagmo' +version = '2.19.0' + +homepage = 'https://esa.github.io/pagmo2' +description = "pagmo is a C++ scientific library for massively parallel optimization." + +toolchain = {'name': 'gfbf', 'version': '2022b'} + +source_urls = ['https://github.com/esa/pagmo2/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['701ada528de7d454201e92a5d88903dd1c22ea64f43861d9694195ddfef82a70'] + +builddependencies = [ + ('CMake', '3.24.3'), +] + +dependencies = [ + ('Boost', '1.81.0'), + ('tbb', '2021.9.0'), + ('Eigen', '3.4.0'), + ('NLopt', '2.7.1'), +] + +configopts = "-DPAGMO_WITH_EIGEN3=ON -DPAGMO_WITH_NLOPT=ON -DPAGMO_BUILD_TESTS=ON" + +runtest = 'test' + +sanity_check_paths = { + 'files': ['lib/libpagmo.%s' % SHLIB_EXT], + 'dirs': ['include/pagmo', 'lib/cmake/pagmo'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/parallel/parallel-20240722-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/parallel/parallel-20240722-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..92658cc24b76 --- /dev/null +++ b/easybuild/easyconfigs/p/parallel/parallel-20240722-GCCcore-13.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'parallel' +version = '20240722' + +homepage = 'https://savannah.gnu.org/projects/parallel/' +description = """parallel: Build and execute shell commands in parallel""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['c7335471f776af28bea9464ad85a50f2ed120f78fbf75ead6647aeea8e0e53f0'] + +builddependencies = [('binutils', '2.42')] + +dependencies = [('Perl', '5.38.2')] + +sanity_check_paths = { + 'files': ['bin/parallel'], + 'dirs': [] +} + +sanity_check_commands = ["parallel --help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/parasail/parasail-2.6.2-GCC-13.2.0.eb b/easybuild/easyconfigs/p/parasail/parasail-2.6.2-GCC-13.2.0.eb new file mode 100644 index 000000000000..ddb3e791f305 --- /dev/null +++ b/easybuild/easyconfigs/p/parasail/parasail-2.6.2-GCC-13.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'CMakeMake' + +name = 'parasail' +version = '2.6.2' + +homepage = 'https://github.com/jeffdaily/parasail' +description = """parasail is a SIMD C (C99) library containing implementations + of the Smith-Waterman (local), Needleman-Wunsch (global), and semi-global + pairwise sequence alignment algorithms. """ + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +github_account = 'jeffdaily' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['9057041db8e1cde76678f649420b85054650414e5de9ea84ee268756c7ea4b4b'] + +builddependencies = [('CMake', '3.27.6')] + +sanity_check_paths = { + 'files': ['bin/parasail_aligner', 'bin/parasail_stats', + 'lib/libparasail.%s' % SHLIB_EXT, 'include/parasail.h'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/phonopy/phonopy-2.12.0-foss-2020b.eb b/easybuild/easyconfigs/p/phonopy/phonopy-2.12.0-foss-2020b.eb index 3a1f3d0bc3b4..2aa223e2c831 100644 --- a/easybuild/easyconfigs/p/phonopy/phonopy-2.12.0-foss-2020b.eb +++ b/easybuild/easyconfigs/p/phonopy/phonopy-2.12.0-foss-2020b.eb @@ -3,7 +3,7 @@ easyblock = 'PythonPackage' name = 'phonopy' version = '2.12.0' -homepage = 'https://atztogo.github.io/phonopy/' +homepage = 'https://phonopy.github.io/phonopy/' description = """Phonopy is an open source package of phonon calculations based on the supercell approach.""" toolchain = {'name': 'foss', 'version': '2020b'} diff --git a/easybuild/easyconfigs/p/phonopy/phonopy-2.16.3-foss-2022a.eb b/easybuild/easyconfigs/p/phonopy/phonopy-2.16.3-foss-2022a.eb index d06fecee5a29..bd922d7ded0c 100644 --- a/easybuild/easyconfigs/p/phonopy/phonopy-2.16.3-foss-2022a.eb +++ b/easybuild/easyconfigs/p/phonopy/phonopy-2.16.3-foss-2022a.eb @@ -3,7 +3,7 @@ easyblock = 'PythonPackage' name = 'phonopy' version = '2.16.3' -homepage = 'https://atztogo.github.io/phonopy/' +homepage = 'https://phonopy.github.io/phonopy/' description = """Phonopy is an open source package of phonon calculations based on the supercell approach.""" toolchain = {'name': 'foss', 'version': '2022a'} diff --git a/easybuild/easyconfigs/p/phonopy/phonopy-2.20.0-foss-2023a.eb b/easybuild/easyconfigs/p/phonopy/phonopy-2.20.0-foss-2023a.eb index aa68af8a4959..9e6b6c5f6e6c 100644 --- a/easybuild/easyconfigs/p/phonopy/phonopy-2.20.0-foss-2023a.eb +++ b/easybuild/easyconfigs/p/phonopy/phonopy-2.20.0-foss-2023a.eb @@ -3,7 +3,7 @@ easyblock = 'PythonPackage' name = 'phonopy' version = '2.20.0' -homepage = 'https://atztogo.github.io/phonopy/' +homepage = 'https://phonopy.github.io/phonopy/' description = """Phonopy is an open source package of phonon calculations based on the supercell approach.""" toolchain = {'name': 'foss', 'version': '2023a'} diff --git a/easybuild/easyconfigs/p/phonopy/phonopy-2.7.1-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/phonopy/phonopy-2.7.1-intel-2019b-Python-3.7.4.eb index 694e7938d28d..310c8045b347 100644 --- a/easybuild/easyconfigs/p/phonopy/phonopy-2.7.1-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/p/phonopy/phonopy-2.7.1-intel-2019b-Python-3.7.4.eb @@ -4,7 +4,7 @@ name = 'phonopy' version = '2.7.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'https://atztogo.github.io/phonopy/' +homepage = 'https://phonopy.github.io/phonopy/' description = """Phonopy is an open source package of phonon calculations based on the supercell approach.""" toolchain = {'name': 'intel', 'version': '2019b'} diff --git a/easybuild/easyconfigs/p/phonopy/phonopy-2.7.1-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/p/phonopy/phonopy-2.7.1-intel-2020a-Python-3.8.2.eb index 5744c456a632..2d2fef61b173 100644 --- a/easybuild/easyconfigs/p/phonopy/phonopy-2.7.1-intel-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/p/phonopy/phonopy-2.7.1-intel-2020a-Python-3.8.2.eb @@ -4,7 +4,7 @@ name = 'phonopy' version = '2.7.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'https://atztogo.github.io/phonopy/' +homepage = 'https://phonopy.github.io/phonopy/' description = """Phonopy is an open source package of phonon calculations based on the supercell approach.""" toolchain = {'name': 'intel', 'version': '2020a'} diff --git a/easybuild/easyconfigs/p/pixman/pixman-0.43.4-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/pixman/pixman-0.43.4-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..b15cf9f2ef62 --- /dev/null +++ b/easybuild/easyconfigs/p/pixman/pixman-0.43.4-GCCcore-13.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'MesonNinja' + +name = 'pixman' +version = '0.43.4' + +homepage = 'http://www.pixman.org/' +description = """ + Pixman is a low-level software library for pixel manipulation, providing + features such as image compositing and trapezoid rasterization. Important + users of pixman are the cairo graphics library and the X server. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://cairographics.org/releases/'] +sources = [SOURCE_TAR_GZ] +checksums = ['a0624db90180c7ddb79fc7a9151093dc37c646d8c38d3f232f767cf64b85a226'] + +builddependencies = [ + ('binutils', '2.42'), + ('Meson', '1.4.0'), + ('Ninja', '1.12.1'), +] + +sanity_check_paths = { + 'files': ['lib/libpixman-1.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.5-GCCcore-13.3.0-python.eb b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.5-GCCcore-13.3.0-python.eb new file mode 100644 index 000000000000..f66c2f133580 --- /dev/null +++ b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.5-GCCcore-13.3.0-python.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'pkgconfig' +version = '1.5.5' +# The -python versionsuffix is used to avoid confusion between +# pkg-config (the tool) and pkgconfig (the Python wrappers) +versionsuffix = '-python' + +homepage = 'https://github.com/matze/pkgconfig' +description = """pkgconfig is a Python module to interface with the pkg-config command line tool""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['deb4163ef11f75b520d822d9505c1f462761b4309b1bb713d08689759ea8b899'] + +builddependencies = [ + ('binutils', '2.42'), + ('poetry', '1.8.3'), +] + +dependencies = [ + ('Python', '3.12.3'), + ('pkgconf', '2.2.0'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.3.10-foss-2023a.eb b/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.3.10-foss-2023a.eb new file mode 100644 index 000000000000..9db2243c96ec --- /dev/null +++ b/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.3.10-foss-2023a.eb @@ -0,0 +1,110 @@ +easyblock = 'CMakeMake' + +name = 'pod5-file-format' +version = '0.3.10' + +homepage = 'https://github.com/nanoporetech/pod5-file-format' +description = """POD5 is a file format for storing nanopore dna data in an easily accessible way. + The format is able to be written in a streaming manner which allows a sequencing + instrument to directly write the format.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/nanoporetech/%(name)s/archive/'] +sources = [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +patches = ['pod5-file-format-0.3.10_dep_fix.patch'] +checksums = [ + {'pod5-file-format-0.3.10.tar.gz': 'eb177018b310e508f7ad6b5d486cc29166404dd5f82879d0c26aceaff51d3768'}, + {'pod5-file-format-0.3.10_dep_fix.patch': '20dc87ab82d4b52ff7fb769d17c2478daf95f787b2a184c9d985e33e03038e31'}, +] + +builddependencies = [ + ('poetry', '1.5.1'), + ('CMake', '3.26.3'), + ('pkgconfig', '1.5.5', '-python'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('Arrow', '14.0.1'), + ('SciPy-bundle', '2023.07'), + ('zstd', '1.5.5'), + ('flatbuffers', '23.5.26'), + ('pybind11', '2.11.1'), + ('Boost', '1.82.0'), + ('build', '1.0.3'), + ('HDF5', '1.14.0'), + ('h5py', '3.9.0'), + ('tqdm', '4.66.1'), + ('polars', '0.20.2'), +] + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'download_dep_fail': True, + 'use_pip': True, + 'sanity_pip_check': True, + 'installopts': '', +} + +# unpin polars and h5py versions in pod5 +local_preinstallopts = ( + "sed -i" + " -e 's/polars~=0.19/polars/'" + " -e 's/h5py~=3.10.0/h5py/'" + " pyproject.toml && " +) + +exts_list = [ + ('vbz_h5py_plugin', '1.0.1', { + 'checksums': ['c784458bb0aad6303474cb2f10956179116b35555803fd1154eb4ef362519341'], + }), + ('iso8601', '2.1.0', { + 'checksums': ['6b1d3829ee8921c4301998c909f7829fa9ed3cbdac0d3b16af2d743aed1ba8df'], + }), + ('pod5', version, { + 'preinstallopts': local_preinstallopts, + 'checksums': ['f2dcb1938fcf51c725393345e480c1d12711089d542a27446fb92fbe2e18ae60'], + }), +] + +# create POD5Version.cmake +# python -m setuptools_scm && python -m pod5_make_version shows wrong version +local_ver_sub_minor = version.split('.')[2] +preconfigopts = ( + 'cd %%(builddir)s/%%(name)s-%%(version)s/cmake && ' + 'touch POD5Version.cmake && ' + 'echo "set(POD5_VERSION_MAJOR %%(version_major)s)">POD5Version.cmake && ' + 'echo "set(POD5_VERSION_MINOR %%(version_minor)s)">>POD5Version.cmake && ' + 'echo "set(POD5_VERSION_REV %s)">>POD5Version.cmake && ' + 'echo "set(POD5_NUMERIC_VERSION %%(version)s)">>POD5Version.cmake && ' + 'echo "set(POD5_FULL_VERSION %%(version)s)">>POD5Version.cmake && ' % local_ver_sub_minor +) + +# delete add_subdirectory(third_party/pybind11) from CMakeLists.txt +preconfigopts += "cd %(builddir)s/%(name)s-%(version)s && sed -i '/add_subdirectory(third_party/d' CMakeLists.txt && " +preconfigopts += 'cd %(builddir)s/easybuild_obj && ' + +configopts = ' -DBUILD_PYTHON_WHEEL=ON -DZSTD_LIB="$EBROOTZSTD/lib" -DZSTD_INCLUDE_DIR="$EBROOTZSTD/include"' + +# install lib_pod5 from wheel - dependency of pod5 +installopts = ' && export XDG_CACHE_HOME=%(builddir)s && cd %(installdir)s' +installopts += ' && pip install --no-deps --ignore-installed --prefix %(installdir)s lib_pod5-%(version)s-*.whl' + +postinstallcmds = ['rm %(installdir)s/lib_pod5-%(version)s-*.whl'] + +sanity_check_paths = { + 'files': ['bin/pod5', 'lib/libpod5_format.a'], + 'dirs': ['include/pod5_format', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "pod5 subset --help", + "python -c 'import lib_pod5'", +] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.3.10_dep_fix.patch b/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.3.10_dep_fix.patch new file mode 100644 index 000000000000..a053f870ebe6 --- /dev/null +++ b/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.3.10_dep_fix.patch @@ -0,0 +1,32 @@ +Flatbuffers 2.0.7 uses capital 'B' in 'FlatBuffersConfig.cmake' +We want to use our pybind11 instead of the one in git submodules +Author: Petr Král (INUITS) +diff -u c++/CMakeLists.txt.orig c++/CMakeLists.txt +--- c++/CMakeLists.txt.orig 2023-02-23 19:17:13.000000000 +0100 ++++ c++/CMakeLists.txt 2023-04-25 14:07:28.174884834 +0200 +@@ -3,7 +3,7 @@ + if (ENABLE_CONAN) + find_package(Arrow REQUIRED CONFIG) + find_package(Boost REQUIRED CONFIG) +- find_package(Flatbuffers REQUIRED CONFIG) ++ find_package(FlatBuffers REQUIRED CONFIG) + find_package(zstd REQUIRED CONFIG) + find_package(ZLIB REQUIRED CONFIG) + +@@ -17,7 +17,7 @@ + COMPONENTS + headers + ) +- find_package(Flatbuffers REQUIRED) ++ find_package(FlatBuffers REQUIRED) + find_package(zstd REQUIRED) + find_package(ZLIB REQUIRED) + +@@ -27,6 +27,7 @@ + endif() + + find_package(Threads REQUIRED) ++find_package(pybind11 REQUIRED) + + find_program( + FLATBUFFERS_FLATC_EXECUTABLE diff --git a/easybuild/easyconfigs/p/poetry/poetry-1.8.3-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/poetry/poetry-1.8.3-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..030ca7ce42ea --- /dev/null +++ b/easybuild/easyconfigs/p/poetry/poetry-1.8.3-GCCcore-13.3.0.eb @@ -0,0 +1,181 @@ +easyblock = 'PythonBundle' + +name = 'poetry' +version = '1.8.3' + +homepage = 'https://python-poetry.org' +description = """Python packaging and dependency management made easy. Poetry helps you declare, manage and install + dependencies of Python projects, ensuring you have the right stack everywhere.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), + ('scikit-build', '0.17.6'), + ('Rust', '1.78.0'), + ('setuptools-rust', '1.9.0'), + ('maturin', '1.6.0'), +] + +dependencies = [ + ('Python', '3.12.3'), + ('hatchling', '1.24.2'), + ('cryptography', '42.0.8'), + ('virtualenv', '20.26.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('six', '1.16.0', { + 'checksums': ['1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926'], + }), + ('idna', '3.7', { + 'checksums': ['028ff3aadf0609c1fd278d8ea3089299412a7a8b9bd005dd08b9f8285bcb5cfc'], + }), + ('certifi', '2024.6.2', { + 'checksums': ['3cd43f1c6fa7dedc5899d69d3ad0398fd018ad1a17fba83ddaf78aa46c747516'], + }), + ('urllib3', '2.2.1', { + 'checksums': ['d0570876c61ab9e520d776c38acbbb5b05a776d3f9ff98a5c8fd5162a444cf19'], + }), + ('charset-normalizer', '3.3.2', { + 'checksums': ['f30c3cb33b24454a82faecaf01b19c18562b1e89558fb6c56de4d9118a032fd5'], + }), + ('dulwich', '0.21.7', { + 'checksums': ['a9e9c66833cea580c3ac12927e4b9711985d76afca98da971405d414de60e968'], + }), + ('crashtest', '0.4.1', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['8d23eac5fa660409f57472e3851dab7ac18aba459a8d19cbbba86d3d5aecd2a5'], + }), + ('zipp', '3.19.2', { + 'checksums': ['bf1dcf6450f873a13e952a29504887c89e6de7506209e5b1bcc3460135d4de19'], + }), + ('importlib-metadata', '7.1.0', { + 'sources': ['importlib_metadata-%(version)s.tar.gz'], + 'checksums': ['b78938b926ee8d5f020fc4772d487045805a55ddbad2ecf21c6d60938dc7fcd2'], + }), + ('jeepney', '0.8.0', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['c0a454ad016ca575060802ee4d590dd912e35c122fa04e70306de3d076cce755'], + }), + ('SecretStorage', '3.3.3', { + 'checksums': ['2403533ef369eca6d2ba81718576c5e0f564d5cca1b58f73a8b23e7d4eeebd77'], + }), + ('more-itertools', '10.3.0', { + 'checksums': ['e5d93ef411224fbcef366a6e8ddc4c5781bc6359d43412a65dd5964e46111463'], + }), + ('jaraco.classes', '3.4.0', { + 'checksums': ['47a024b51d0239c0dd8c8540c6c7f484be3b8fcf0b2d85c13825780d3b3f3acd'], + }), + ('keyring', '24.3.1', { + 'modulename': False, + 'checksums': ['c3327b6ffafc0e8befbdb597cacdb4928ffe5c1212f7645f186e6d9957a898db'], + }), + ('pyproject-hooks', '1.1.0', { + 'sources': ['pyproject_hooks-%(version)s.tar.gz'], + 'checksums': ['4b37730834edbd6bd37f26ece6b44802fb1c1ee2ece0e54ddff8bfc06db86965'], + }), + ('build', '1.2.1', { + 'checksums': ['526263f4870c26f26c433545579475377b2b7588b6f1eac76a001e873ae3e19d'], + }), + ('installer', '0.7.0', { + 'checksums': ['a26d3e3116289bb08216e0d0f7d925fcef0b0194eedfa0c944bcaaa106c4b631'], + }), + ('webencodings', '0.5.1', { + 'checksums': ['b36a1c245f2d304965eb4e0a82848379241dc04b865afcc4aab16748587e1923'], + }), + ('html5lib', '1.1', { + 'checksums': ['b2e5b40261e20f354d198eae92afc10d750afb487ed5e50f9c4eaf07c184146f'], + }), + ('rapidfuzz', '3.9.3', { + 'checksums': ['b398ea66e8ed50451bce5997c430197d5e4b06ac4aa74602717f792d8d8d06e2'], + }), + ('cleo', '2.1.0', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['4a31bd4dd45695a64ee3c4758f583f134267c2bc518d8ae9a29cf237d009b07e'], + }), + ('attrs', '23.2.0', { + 'modulename': 'attr', + 'checksums': ['935dc3b529c262f6cf76e50877d35a4bd3c1de194fd41f47a2b7ae8f19971f30'], + }), + ('pyrsistent', '0.20.0', { + 'checksums': ['4c48f78f62ab596c679086084d0dd13254ae4f3d6c72a83ffdf5ebdef8f265a4'], + }), + ('requests-toolbelt', '1.0.0', { + 'checksums': ['7681a0a3d047012b5bdc0ee37d7f8f07ebe76ab08caeccfc3921ce23c88d5bc6'], + }), + ('pkginfo', '1.11.1', { + 'checksums': ['2e0dca1cf4c8e39644eed32408ea9966ee15e0d324c62ba899a393b3c6b467aa'], + }), + ('ptyprocess', '0.7.0', { + 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'checksums': ['4b41f3967fce3af57cc7e94b888626c18bf37a083e3651ca8feeb66d492fef35'], + }), + ('pexpect', '4.9.0', { + 'checksums': ['ee7d41123f3c9911050ea2c2dac107568dc43b2d3b0c7557a33212c398ead30f'], + }), + ('jsonschema-specifications', '2023.12.1', { + 'sources': ['jsonschema_specifications-%(version)s.tar.gz'], + 'checksums': ['48a76787b3e70f5ed53f1160d2b81f586e4ca6d1548c5de7085d1682674764cc'], + }), + ('referencing', '0.35.1', { + 'checksums': ['25b42124a6c8b632a425174f24087783efb348a6f1e0008e63cd4466fedf703c'], + }), + ('rpds-py', '0.18.1', { + 'sources': ['rpds_py-%(version)s.tar.gz'], + 'checksums': ['dc48b479d540770c811fbd1eb9ba2bb66951863e448efec2e2c102625328e92f'], + 'modulename': 'rpds', + }), + ('jsonschema', '4.22.0', { + 'checksums': ['5b22d434a45935119af990552c862e5d6d564e8f6601206b305a61fdf661a2b7'], + }), + ('platformdirs', '4.2.2', { + 'checksums': ['38b7b51f512eed9e84a22788b4bce1de17c0adb134d6becb09836e37d8654cd3'], + }), + ('shellingham', '1.5.4', { + 'checksums': ['8dbca0739d487e5bd35ab3ca4b36e11c4078f3a234bfce294b0a0291363404de'], + }), + ('tomlkit', '0.12.5', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['af914f5a9c59ed9d0762c7b64d3b5d5df007448eb9cd2edc8a46b1eafead172f'], + }), + ('requests', '2.32.3', { + 'checksums': ['55365417734eb18255590a9ff9eb97e9e1da868d4ccd6402399eaf68af20a760'], + }), + ('msgpack', '1.0.8', { + 'checksums': ['95c02b0e27e706e48d0e5426d1710ca78e0f0628d6e89d5b5a5b91a5f12274f3'], + }), + ('CacheControl', '0.14.0', { + 'sources': ['cachecontrol-%(version)s.tar.gz'], + 'checksums': ['7db1195b41c81f8274a7bbd97c956f44e8348265a1bc7641c37dfebc39f0c938'], + }), + ('lockfile', '0.12.2', { + 'checksums': ['6aed02de03cba24efabcd600b30540140634fc06cfa603822d508d5361e9f799'], + }), + ('poetry-core', '1.9.0', { + 'modulename': 'poetry.core', + 'sources': ['poetry_core-%(version)s.tar.gz'], + 'checksums': ['fa7a4001eae8aa572ee84f35feb510b321bd652e5cf9293249d62853e1f935a2'], + }), + ('poetry-plugin-export', '1.8.0', { + 'sources': ['poetry_plugin_export-%(version)s.tar.gz'], + 'checksums': ['1fa6168a85d59395d835ca564bc19862a7c76061e60c3e7dfaec70d50937fc61'], + }), + ('fastjsonschema', '2.19.1', { + 'checksums': ['e3126a94bdc4623d3de4485f8d468a12f02a67921315ddc87836d6e456dc789d'], + }), + (name, version, { + 'checksums': ['67f4eb68288eab41e841cc71a00d26cf6bdda9533022d0189a145a34d0a35f48'], + }), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/popt/popt-1.19-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/popt/popt-1.19-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..91b5c7c74ba4 --- /dev/null +++ b/easybuild/easyconfigs/p/popt/popt-1.19-GCCcore-13.3.0.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'popt' +version = '1.19' + +homepage = 'https://github.com/rpm-software-management/popt' +description = 'Popt is a C library for parsing command line parameters.' + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['http://ftp.rpm.org/popt/releases/popt-1.x'] +sources = [SOURCE_TAR_GZ] +checksums = ['c25a4838fc8e4c1c8aacb8bd620edb3084a3d63bf8987fdad3ca2758c63240f9'] + +builddependencies = [ + ('binutils', '2.42') +] + +sanity_check_paths = { + 'files': ['include/%(name)s.h', ('lib/libpopt.a', 'lib64/libpopt.a'), ('lib/libpopt.so', 'lib64/libpopt.so')], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pretty-yaml/pretty-yaml-24.7.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/pretty-yaml/pretty-yaml-24.7.0-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..ef58228ef610 --- /dev/null +++ b/easybuild/easyconfigs/p/pretty-yaml/pretty-yaml-24.7.0-GCCcore-13.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'pretty-yaml' +local_mod = 'pyaml' +version = '24.7.0' + +homepage = 'https://github.com/mk-fg/pretty-yaml' +description = """PyYAML-based python module to produce pretty and readable YAML-serialized data. +This module is for serialization only, see ruamel.yaml module for literate YAML +parsing (keeping track of comments, spacing, line/column numbers of values, etc).""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://pypi.python.org/packages/source/p/%s/' % local_mod] +sources = ['%s-%%(version)s.tar.gz' % local_mod] +checksums = ['5d0fdf9e681036fb263a783d0298fc3af580a6e2a6cf1a3314ffc48dc3d91ccb'] + +builddependencies = [('binutils', '2.42')] + +dependencies = [ + ('Python', '3.12.3'), + ('PyYAML', '6.0.2'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +options = {'modulename': local_mod} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/primecount/primecount-7.14-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/primecount/primecount-7.14-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..556cc0f1507d --- /dev/null +++ b/easybuild/easyconfigs/p/primecount/primecount-7.14-GCCcore-13.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'CMakeMake' + +name = 'primecount' +version = '7.14' + +homepage = 'https://github.com/kimwalisch/primecount' +description = """primecount is a command-line program and C/C++ library that counts the number of primes ≤ x + (maximum 1031) using highly optimized implementations of the combinatorial prime counting algorithms.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://github.com/kimwalisch/primecount/archive/refs/tags'] +sources = ['v%(version)s.tar.gz'] +checksums = ['d867ac18cc52c0f7014682169988a76f39e4cd56f8ce78fb56e064499b1d66bb'] + +builddependencies = [ + ('CMake', '3.27.6'), + ('binutils', '2.40'), +] + +configopts = '-DBUILD_SHARED_LIBS=ON ' + +sanity_check_paths = { + 'files': ['bin/primecount', 'include/primecount.h'] + + ['lib/libprimecount.%s' % e for e in ['a', SHLIB_EXT]], + 'dirs': ['share'], +} + +sanity_check_commands = ["primecount -h"] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/primecountpy/primecountpy-0.1.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/primecountpy/primecountpy-0.1.0-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..11244361d59d --- /dev/null +++ b/easybuild/easyconfigs/p/primecountpy/primecountpy-0.1.0-GCCcore-13.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'primecountpy' +version = '0.1.0' + +homepage = 'https://pypi.org/project/primecountpy' +description = "This is a Cython interface to the C++ library primecount." + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['78fe7cc32115f0669a45d7c90faaf39f7ce3939e39e2e7e5f14c17fe4bff0676'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('Python', '3.11.5'), + ('Cython', '3.0.10'), + ('cysignals', '1.11.4'), + ('primecount', '7.14'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-3.0.36-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-3.0.36-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..dfcdad173d10 --- /dev/null +++ b/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-3.0.36-GCCcore-12.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'prompt-toolkit' +version = '3.0.36' + +homepage = 'https://github.com/jonathanslenders/python-prompt-toolkit' +description = """prompt_toolkit is a Python library for building powerful interactive command lines and + terminal applications.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), +] + +sources = ['prompt_toolkit-%(version)s-py3-none-any.whl'] +checksums = ['aa64ad242a462c5ff0363a7b9cfe696c20d55d9fc60c11fd8e632d064804d305'] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +options = {'modulename': 'prompt_toolkit'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/psycopg/psycopg-3.2.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/psycopg/psycopg-3.2.1-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..5c0aab8a54ef --- /dev/null +++ b/easybuild/easyconfigs/p/psycopg/psycopg-3.2.1-GCCcore-12.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonBundle' + +name = 'psycopg' +version = '3.2.1' + +homepage = 'https://psycopg.org/' +description = "Psycopg is the most popular PostgreSQL adapter for the Python programming language." + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [('binutils', '2.40')] +dependencies = [ + ('Python', '3.11.3'), + ('PostgreSQL', '16.1'), +] + +exts_list = [ + (name, version, { + 'checksums': ['dc8da6dc8729dacacda3cc2f17d2c9397a70a66cf0d2b69c91065d60d5f00cb7'], + }), +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.22-foss-2023a.eb b/easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.22-foss-2023a.eb deleted file mode 100644 index fc2cc3e8efc8..000000000000 --- a/easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.22-foss-2023a.eb +++ /dev/null @@ -1,36 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'pyBigWig' -version = '0.3.22' - -github_account = 'deeptools' -homepage = 'https://github.com/%(github_account)s/%(name)s' -description = """A python extension, written in C, for quick access to bigBed - files and access to and creation of bigWig files.""" - -toolchain = {'name': 'foss', 'version': '2023a'} - -source_urls = [GITHUB_SOURCE] -sources = ['%(version)s.tar.gz'] -checksums = ['3b8d62b2bedcee0545a586884466c97a64b64283a309b211300b670f41dd2046'] - -dependencies = [ - ('Python', '3.11.3'), - ('cURL', '8.0.1'), - ('NSS', '3.89.1'), # provides libfreebl3 - ('SciPy-bundle', '2023.07'), # optional, for numpy support -] - -# fix version of '0.0.0' issue -preinstallopts = """sed -i 's/setup(/setup(version="%(version)s",/g' setup.py && """ -# do not use setuptools-scm to detect version -preinstallopts += """sed -i 's/[tool.setuptools_scm]//' pyproject.toml && """ - -use_pip = True -download_dep_fail = True - -options = {'modulename': name} - -sanity_pip_check = True - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.22-gfbf-2023a.eb b/easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.22-gfbf-2023a.eb new file mode 100644 index 000000000000..8e9947f8e5bc --- /dev/null +++ b/easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.22-gfbf-2023a.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'pyBigWig' +version = '0.3.22' + +homepage = 'https://github.com/deeptools/pyBigWig' +description = """A python extension, written in C, for quick access to bigBed +files and access to and creation of bigWig files.""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['5d4426f754bd7b7f6dc21d6c3f93b58a96a65b6eb2e578ae03b31a71272d2243'] + +dependencies = [ + ('Python', '3.11.3'), + ('cURL', '8.0.1'), + ('NSS', '3.89.1'), # provides libfreebl3 + ('SciPy-bundle', '2023.07'), # optional, for numpy support +] + +use_pip = True +download_dep_fail = True + +options = {'modulename': name} + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/pyGenomeTracks/pyGenomeTracks-3.9-foss-2023a.eb b/easybuild/easyconfigs/p/pyGenomeTracks/pyGenomeTracks-3.9-foss-2023a.eb new file mode 100644 index 000000000000..aa1c89854765 --- /dev/null +++ b/easybuild/easyconfigs/p/pyGenomeTracks/pyGenomeTracks-3.9-foss-2023a.eb @@ -0,0 +1,58 @@ +easyblock = 'PythonBundle' + +name = 'pyGenomeTracks' +version = '3.9' + +homepage = 'https://pygenometracks.readthedocs.io' +description = "pyGenomeTracks aims to produce high-quality genome browser tracks that are highly customizable." + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('matplotlib', '3.7.2'), + ('bx-python', '0.10.0'), + ('pybedtools', '0.9.1'), + ('pyBigWig', '0.3.22'), + ('pyfaidx', '0.8.1.1'), + ('Pysam', '0.22.0'), + ('tqdm', '4.66.1'), + ('PyTables', '3.8.0'), + ('h5py', '3.9.0'), + ('PyYAML', '6.0'), + ('cooler', '0.10.2'), + ('HiCMatrix', '17.2'), +] + +use_pip = True +exts_list = [ + ('argcomplete', '3.4.0', { + 'checksums': ['c2abcdfe1be8ace47ba777d4fce319eb13bf8ad9dace8d085dcad6eded88057f'], + }), + ('argh', '0.31.2', { + 'checksums': ['db1c34885804f7d4646c385dc2fb19b45298561322f4c15eae1b133993f9e323'], + }), + ('gffutils', '0.13', { + 'checksums': ['b0d52f35c014cc0330fb5c4e3c6fea127c90ccf4c5384a825cdb5c8ff330d4eb'], + }), + ('pypairix', '0.3.7', { + 'checksums': ['c1b47c05f92b5be628923c60a27344503ddeba5d8f35a3752d646271d38e0525'], + }), + (name, version, { + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/deeptools/pyGenomeTracks/archive/refs/tags'], + 'checksums': ['4318cb642422ee16d83675d571f4cd49b14784d7ee135ab53d8946fc7ad663f6'], + }), +] + +sanity_check_paths = { + 'files': ['bin/pyGenomeTracks'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["pyGenomeTracks --help"] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/pyMBE/pyMBE-0.8.0-foss-2023b.eb b/easybuild/easyconfigs/p/pyMBE/pyMBE-0.8.0-foss-2023b.eb new file mode 100644 index 000000000000..6e676c324559 --- /dev/null +++ b/easybuild/easyconfigs/p/pyMBE/pyMBE-0.8.0-foss-2023b.eb @@ -0,0 +1,67 @@ +easyblock = 'PythonBundle' + +name = 'pyMBE' +version = '0.8.0' + +homepage = '' +description = """pyMBE: the Python-based Molecule Builder for ESPResSo + +pyMBE provides tools to facilitate building up molecules with complex architectures +in the Molecular Dynamics software ESPResSo.""" + +toolchain = {'name': 'foss', 'version': '2023b'} + +builddependencies = [('hatchling', '1.18.0')] + +dependencies = [ + ('Python', '3.11.5'), + ('SciPy-bundle', '2023.11'), + ('Pint', '0.24'), + ('tqdm', '4.66.2'), + ('matplotlib', '3.8.2'), + ('ESPResSo', '4.2.2'), +] + +use_pip = True +# pyMBE is not installable and should just be copied to the installation directory +exts_classmap = {'pyMBE': 'Tarball'} + +# pyMBE itself should be the first one in the list, +# otherwise the Tarball easyblock will copy the sources of all extensions to the installation directory +exts_list = [ + (name, version, { + 'source_urls': ['https://github.com/pyMBE-dev/pyMBE/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['f143ae655b477d6d2ab6d97190a387fa9c7e854502a38c72c24eac48e37ea663'], + }), + ('looseversion', '1.1.2', { + 'checksums': ['94d80bdbd0b6d57c11b886147ba1601f7d1531571621b81933b34537cbe469ad'], + }), + ('mmtf-python', '1.1.3', { + 'modulename': 'mmtf', + 'checksums': ['12a02fe1b7131f0a2b8ce45b46f1e0cdd28b9818fe4499554c26884987ea0c32'], + }), + ('Pint-Pandas', '0.5', { + 'checksums': ['48ec96d457f802a347763dee1d3e1a273f11f90e4e595df17fd44613dd14a61c'], + }), + ('biopandas', '0.5.1.dev0', { + 'checksums': ['6dc9de631babf8221c1ac60230133717039e08911f15e8ac48498c787022de12'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['pyMBE.py'], + 'dirs': ['figs', 'lib', 'maintainer', 'parameters', 'refs', 'samples', 'testsuite', 'tutorials', 'visualization'], +} + +sanity_check_commands = [ + 'python -c "import pyMBE"', + # running the full test suite takes a long time, so just stick to the unit tests + 'cd %(installdir)s && make unit_tests' +] + +modextrapaths = {'PYTHONPATH': ['.']} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/pybind11/pybind11-2.12.0-GCC-13.3.0.eb b/easybuild/easyconfigs/p/pybind11/pybind11-2.12.0-GCC-13.3.0.eb new file mode 100644 index 000000000000..e4e0460d13eb --- /dev/null +++ b/easybuild/easyconfigs/p/pybind11/pybind11-2.12.0-GCC-13.3.0.eb @@ -0,0 +1,33 @@ +name = 'pybind11' +version = '2.12.0' + +homepage = 'https://pybind11.readthedocs.io' +description = """pybind11 is a lightweight header-only library that exposes C++ types in Python and vice versa, + mainly to create Python bindings of existing C++ code.""" + +toolchain = {'name': 'GCC', 'version': '13.3.0'} + +source_urls = ['https://github.com/pybind/pybind11/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'pybind11-2.10.3_require-catch.patch', +] +checksums = [ + {'v2.12.0.tar.gz': 'bf8f242abd1abcd375d516a7067490fb71abd79519a282d22b6e4d19282185a7'}, + {'pybind11-2.10.3_require-catch.patch': '4a27ba3ef1d5c535d120d6178a6e876ae678e4899a07500aab37908357b0b60b'}, +] + +builddependencies = [ + ('CMake', '3.29.3'), + # Test dependencies + ('Eigen', '3.4.0'), + ('Catch2', '2.13.10'), + ('Python-bundle-PyPI', '2024.06'), # to provide pytest +] + +dependencies = [ + ('Boost', '1.85.0'), + ('Python', '3.12.3'), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pycocotools/pycocotools-2.0.7-foss-2023a.eb b/easybuild/easyconfigs/p/pycocotools/pycocotools-2.0.7-foss-2023a.eb new file mode 100644 index 000000000000..666074add240 --- /dev/null +++ b/easybuild/easyconfigs/p/pycocotools/pycocotools-2.0.7-foss-2023a.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'pycocotools' +version = '2.0.7' + +homepage = 'https://pypi.org/project/pycocotools' +description = "Official APIs for the MS-COCO dataset" + +toolchain = {'name': 'foss', 'version': '2023a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['da8b7815196eebf0adabf67fcc459126cbc6498bbc6ab1fd144c371465d86879'] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('matplotlib', '3.7.2'), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/pydantic/pydantic-2.7.4-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/pydantic/pydantic-2.7.4-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..efc3388a0730 --- /dev/null +++ b/easybuild/easyconfigs/p/pydantic/pydantic-2.7.4-GCCcore-13.2.0.eb @@ -0,0 +1,126 @@ +easyblock = 'CargoPythonBundle' + +name = 'pydantic' +version = '2.7.4' + +homepage = 'https://github.com/samuelcolvin/pydantic' +description = """Data validation and settings management using Python type hinting.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('Rust', '1.76.0'), + ('maturin', '1.5.0', '-Rust-1.76.0'), + ('hatchling', '1.18.0'), +] + +dependencies = [ + ('Python', '3.11.5'), + ('typing-extensions', '4.10.0'), +] + +use_pip = True +sanity_pip_check = True + +crates = [ + ('ahash', '0.8.10'), + ('aho-corasick', '1.0.2'), + ('autocfg', '1.1.0'), + ('base64', '0.21.7'), + ('bitflags', '1.3.2'), + ('bitvec', '1.0.1'), + ('cc', '1.0.79'), + ('cfg-if', '1.0.0'), + ('enum_dispatch', '0.3.13'), + ('equivalent', '1.0.1'), + ('form_urlencoded', '1.2.1'), + ('funty', '2.0.0'), + ('getrandom', '0.2.10'), + ('hashbrown', '0.14.3'), + ('heck', '0.4.1'), + ('idna', '0.5.0'), + ('indexmap', '2.2.2'), + ('indoc', '2.0.4'), + ('itoa', '1.0.8'), + ('jiter', '0.4.1'), + ('lexical-parse-float', '0.8.5'), + ('lexical-parse-integer', '0.8.6'), + ('lexical-util', '0.8.5'), + ('libc', '0.2.147'), + ('lock_api', '0.4.10'), + ('memchr', '2.6.3'), + ('memoffset', '0.9.0'), + ('num-bigint', '0.4.4'), + ('num-integer', '0.1.45'), + ('num-traits', '0.2.16'), + ('once_cell', '1.18.0'), + ('parking_lot', '0.12.1'), + ('parking_lot_core', '0.9.8'), + ('percent-encoding', '2.3.1'), + ('portable-atomic', '1.6.0'), + ('proc-macro2', '1.0.76'), + ('pyo3', '0.21.2'), + ('pyo3-build-config', '0.21.2'), + ('pyo3-ffi', '0.21.2'), + ('pyo3-macros', '0.21.2'), + ('pyo3-macros-backend', '0.21.2'), + ('python3-dll-a', '0.2.9'), + ('quote', '1.0.35'), + ('radium', '0.7.0'), + ('redox_syscall', '0.3.5'), + ('regex', '1.10.4'), + ('regex-automata', '0.4.5'), + ('regex-syntax', '0.8.2'), + ('rustversion', '1.0.13'), + ('ryu', '1.0.14'), + ('scopeguard', '1.1.0'), + ('serde', '1.0.203'), + ('serde_derive', '1.0.203'), + ('serde_json', '1.0.116'), + ('smallvec', '1.13.2'), + ('speedate', '0.14.0'), + ('static_assertions', '1.1.0'), + ('strum', '0.25.0'), + ('strum_macros', '0.25.3'), + ('strum_macros', '0.26.1'), + ('syn', '2.0.48'), + ('tap', '1.0.1'), + ('target-lexicon', '0.12.9'), + ('tinyvec', '1.6.0'), + ('tinyvec_macros', '0.1.1'), + ('unicode-bidi', '0.3.13'), + ('unicode-ident', '1.0.10'), + ('unicode-normalization', '0.1.22'), + ('unindent', '0.2.3'), + ('url', '2.5.0'), + ('uuid', '1.8.0'), + ('version_check', '0.9.4'), + ('wasi', '0.11.0+wasi-snapshot-preview1'), + ('windows-targets', '0.48.1'), + ('windows_aarch64_gnullvm', '0.48.0'), + ('windows_aarch64_msvc', '0.48.0'), + ('windows_i686_gnu', '0.48.0'), + ('windows_i686_msvc', '0.48.0'), + ('windows_x86_64_gnu', '0.48.0'), + ('windows_x86_64_gnullvm', '0.48.0'), + ('windows_x86_64_msvc', '0.48.0'), + ('wyz', '0.5.1'), + ('zerocopy', '0.7.32'), + ('zerocopy-derive', '0.7.32'), +] + +exts_list = [ + ('annotated_types', '0.6.0', { + 'checksums': ['563339e807e53ffd9c267e99fc6d9ea23eb8443c08f112651963e24e22f84a5d'], + }), + ('pydantic_core', '2.18.4', { + 'checksums': ['ec3beeada09ff865c344ff3bc2f427f5e6c26401cc6113d77e372c3fdac73864'], + }), + (name, version, { + 'preinstallopts': "sed -i '/Framework :: Pydantic/d' pyproject.toml && ", + 'checksums': ['0c84efd9548d545f63ac0060c1e4d39bb9b14db8b3c0652338aecc07b5adec52'], + }), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/pydicom/pydicom-2.4.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/pydicom/pydicom-2.4.4-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..a1071f66e075 --- /dev/null +++ b/easybuild/easyconfigs/p/pydicom/pydicom-2.4.4-GCCcore-12.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'pydicom' +version = '2.4.4' + +homepage = 'https://pydicom.github.io/' +description = "Pure python package for DICOM medical file reading and writing." + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [GITHUB_SOURCE] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['42c06ed74331174111dd42c89db774a13fc472abe18015f22c5aba80cddb7843'] + +builddependencies = [ + ('binutils', '2.39'), +] +dependencies = [ + ('Python', '3.10.8'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/pydot/pydot-2.0.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/pydot/pydot-2.0.0-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..d39e368e0cd6 --- /dev/null +++ b/easybuild/easyconfigs/p/pydot/pydot-2.0.0-GCCcore-12.2.0.eb @@ -0,0 +1,25 @@ +# updated: Denis Kristak, Pavel Tománek (INUITS) +easyblock = 'PythonBundle' + +name = 'pydot' +version = '2.0.0' + +homepage = 'https://github.com/pydot/pydot' +description = "Python interface to Graphviz's Dot language." + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +builddependencies = [('binutils', '2.39')] + +dependencies = [('Python', '3.10.8')] + +exts_list = [ + (name, version, { + 'checksums': ['60246af215123fa062f21cd791be67dda23a6f280df09f68919e637a1e4f3235'], + }), +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/pyfasta/pyfasta-0.5.2-foss-2023a.eb b/easybuild/easyconfigs/p/pyfasta/pyfasta-0.5.2-foss-2023a.eb new file mode 100644 index 000000000000..127a798d38a6 --- /dev/null +++ b/easybuild/easyconfigs/p/pyfasta/pyfasta-0.5.2-foss-2023a.eb @@ -0,0 +1,44 @@ +easyblock = 'PythonBundle' + +name = 'pyfasta' +version = '0.5.2' + +homepage = 'https://pypi.org/project/pyfasta/' +description = """fast, memory-efficient, pythonic (and command-line) access to fasta sequence files""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), +] + +use_pip = True + +local_preinstallopts = ( + "sed -i" + " -e 's/from fasta/from pyfasta.fasta/'" + " -e 's/from records/from pyfasta.records/'" + " -e 's/from split_fasta/from pyfasta.split_fasta/'" + " %(name)s/__init__.py && " +) +local_preinstallopts += "sed -i 's/from collections/from collections.abc/' pyfasta/fasta.py && " +local_preinstallopts += "sed -i 's/from records/from pyfasta.records/' pyfasta/fasta.py && " +local_preinstallopts += "sed -i 's/import cPickle/import _pickle as cPickle/' pyfasta/records.py && " +local_preinstallopts += "sed -i 's/from cStringIO import StringIO/from io import StringIO/' pyfasta/split_fasta.py && " + +exts_list = [ + (name, version, { + 'preinstallopts': local_preinstallopts, + 'checksums': ['ab08d75fa90253bc91933d10567d5d9cca2718f4796ef3bdc36b68df0e45b258'], + }), +] + +sanity_check_paths = { + 'files': ['bin/pyfasta'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} +sanity_check_commands = ['pyfasta extract --help'] +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pygmo/pygmo-2.19.5-gfbf-2022b.eb b/easybuild/easyconfigs/p/pygmo/pygmo-2.19.5-gfbf-2022b.eb new file mode 100644 index 000000000000..20109f005543 --- /dev/null +++ b/easybuild/easyconfigs/p/pygmo/pygmo-2.19.5-gfbf-2022b.eb @@ -0,0 +1,58 @@ +easyblock = 'CMakePythonPackage' + +name = 'pygmo' +version = '2.19.5' + +homepage = 'https://esa.github.io/pygmo2' +description = "pygmo is a scientific Python library for massively parallel optimization." + +toolchain = {'name': 'gfbf', 'version': '2022b'} + +source_urls = ['https://github.com/esa/pygmo2/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['742ff0c3d535cb2af94d5095968d8f29c23ed7bdbd4ddd8259ca787eef881aa2'] + +builddependencies = [ + ('CMake', '3.24.3'), + ('pybind11', '2.10.3'), +] + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('Boost', '1.81.0'), + ('pagmo', '2.19.0'), + ('matplotlib', '3.7.0'), + ('networkx', '3.0'), +] + +# make sure that all files are installed in the correct location (-DCMAKE_INSTALL_PREFIX is not enough)... +configopts = "-DPYGMO_INSTALL_PATH=%(installdir)s/lib/python%(pyshortver)s/site-packages" + +runtest = False + +exts_defaultclass = 'PythonPackage' + +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'download_dep_fail': True, + 'use_pip': True, +} + +exts_list = [ + ('cloudpickle', '2.2.1', { + 'checksums': ['d89684b8de9e34a2a43b3460fbca07d09d6e25ce858df4d5a44240403b6178f5'], + }), + ('dill', '0.3.6', { + 'checksums': ['e5db55f3687856d8fbdab002ed78544e1c4559a130302693d839dfe8f93f2373'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/pygmo'], +} + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pyperf/pyperf-2.7.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/pyperf/pyperf-2.7.0-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..0c4a15042488 --- /dev/null +++ b/easybuild/easyconfigs/p/pyperf/pyperf-2.7.0-GCCcore-12.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'pyperf' +version = '2.7.0' + +homepage = 'https://github.com/psf/pyperf' +description = "The Python pyperf module is a toolkit to write, run and analyze benchmarks" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['4201c6601032f374e9c900c6d2544a2f5891abedc1a96eec0e7b2338a6247589'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('psutil', '5.9.8'), +] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': ['bin/pyperf'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["pyperf --help"] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pyseer/pyseer-1.3.12-foss-2023a.eb b/easybuild/easyconfigs/p/pyseer/pyseer-1.3.12-foss-2023a.eb new file mode 100644 index 000000000000..16cf7b1a00c9 --- /dev/null +++ b/easybuild/easyconfigs/p/pyseer/pyseer-1.3.12-foss-2023a.eb @@ -0,0 +1,56 @@ +# Borrowed from the BEAR RSG team, University of Birmingham +# Update: Petr Král (INUITS) +easyblock = 'PythonBundle' + +name = 'pyseer' +version = '1.3.12' + +homepage = 'https://github.com/mgalardini/pyseer' +description = """pyseer was first written a python reimplementation of seer, which was written in C++. pyseer uses + linear models with fixed or mixed effects to estimate the effect of genetic variation in a bacterial population + on a phenotype of interest, while accounting for potentially very strong confounding population structure. + This allows for genome-wide association studies (GWAS) to be performed in clonal organisms + such as bacteria and viruses.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('pybedtools', '0.9.1'), + ('statsmodels', '0.14.1'), + ('scikit-learn', '1.3.1'), + ('Pysam', '0.22.0'), + ('DendroPy', '4.6.1'), + ('matplotlib', '3.7.2'), + ('tqdm', '4.66.1'), +] + +use_pip = True + +exts_list = [ + ('glmnet-python', '1.0.2', { + 'source_urls': ['https://github.com/johnlees/glmnet_python/archive'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['7a5550514140dabbd27ad4eb1c04db64199d9bb89541e088d9bb162570205e76'], + }), + (name, version, { + 'source_urls': ['https://github.com/mgalardini/pyseer/archive'], + 'sources': ['%(version)s.tar.gz'], + 'checksums': ['aa07fc1bd5346d02123ff36ba64a1ff4dbbb85a21c37a12f35ad7d5be7e21e9c'], + }), +] + +sanity_check_paths = { + 'files': ['bin/pyseer', 'bin/square_mash'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + '%(namelower)s --help', + 'square_mash --help', +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/pyspoa/pyspoa-0.2.1-GCC-13.2.0.eb b/easybuild/easyconfigs/p/pyspoa/pyspoa-0.2.1-GCC-13.2.0.eb new file mode 100644 index 000000000000..127ab6861d92 --- /dev/null +++ b/easybuild/easyconfigs/p/pyspoa/pyspoa-0.2.1-GCC-13.2.0.eb @@ -0,0 +1,62 @@ +easyblock = 'PythonPackage' + +name = 'pyspoa' +version = '0.2.1' + +local_cereal_version = '1.3.2' + +homepage = 'https://github.com/nanoporetech/pyspoa' +description = "Python bindings to spoa." + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +toolchainopts = {'extra_cflags': "-fpermissive"} + +sources = [ + { + 'filename': '%(name)s-%(version)s.tar.gz', + 'git_config': { + 'url': 'https://github.com/nanoporetech', + 'repo_name': 'pyspoa', + 'tag': 'v%(version)s', + 'recursive': True, + 'keep_git_dir': True, + } + }, + { + 'source_urls': ['https://github.com/USCiLab/cereal/archive/'], + 'download_filename': 'v%s.tar.gz' % local_cereal_version, + 'filename': 'cereal-%s.tar.gz' % local_cereal_version, + }, +] + +patches = ['pyspoa-%(version)s_use-spoa-dep.patch'] + +checksums = [ + None, + '16a7ad9b31ba5880dac55d62b5d6f243c3ebc8d46a3514149e56b5e7ea81f85f', + 'dffd946e3b36e4872846fe983d287f992b5bf177798e11141bf0d645cfc0664d', +] + +builddependencies = [('CMake', '3.27.6')] + +dependencies = [ + ('Python', '3.11.5'), + ('pybind11', '2.11.1'), + ('spoa', '4.1.0'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +preinstallopts = "mkdir -p src/vendor/cereal && ln -s %(builddir)s/cereal-*/include src/vendor/cereal/include && " +# strip out cmake requirements, since we provide that as proper dependency +preinstallopts += "sed -i 's/.cmake==[0-9.]*.//g' setup.py && " +preinstallopts += "export libspoa=$EBROOTSPOA/lib/libspoa.a && " + +options = {'modulename': 'spoa'} + +sanity_check_commands = ["cd %(builddir)s/*/tests && python test_pyspoa.py"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pystencils/pystencils-1.3.4-gfbf-2023b.eb b/easybuild/easyconfigs/p/pystencils/pystencils-1.3.4-gfbf-2023b.eb new file mode 100644 index 000000000000..2c08948afa05 --- /dev/null +++ b/easybuild/easyconfigs/p/pystencils/pystencils-1.3.4-gfbf-2023b.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonBundle' + +name = 'pystencils' +version = '1.3.4' + +homepage = 'https://pycodegen.pages.i10git.cs.fau.de/pystencils' +description = "pystencils uses sympy to define stencil operations, that can be executed on numpy arrays" + +toolchain = {'name': 'gfbf', 'version': '2023b'} + +dependencies = [ + ('Python', '3.11.5'), + ('SciPy-bundle', '2023.11'), + ('sympy', '1.12'), + ('PyYAML', '6.0.1'), +] + +use_pip = True + +exts_list = [ + (name, version, { + 'checksums': ['d8c502ad27d5e270c5048558a3c8b316beef8d7ac6a8a9f72b78632a6e0ca317'], + # remove strict version requirement for sympy + 'preinstallopts': """sed -i 's/"sympy[^"]*"/"sympy"/g' pyproject.toml && """, + }), +] + +sanity_pip_check = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/pysteps/pysteps-1.10.0-foss-2023a.eb b/easybuild/easyconfigs/p/pysteps/pysteps-1.10.0-foss-2023a.eb new file mode 100644 index 000000000000..f60f3a18e872 --- /dev/null +++ b/easybuild/easyconfigs/p/pysteps/pysteps-1.10.0-foss-2023a.eb @@ -0,0 +1,41 @@ +easyblock = 'PythonBundle' + +name = 'pysteps' +version = '1.10.0' + +homepage = 'https://pysteps.github.io/' +description = """Pysteps is an open-source and community-driven Python library for probabilistic +precipitation nowcasting, i.e. short-term ensemble prediction systems.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('OpenCV', '4.8.1', '-contrib'), + ('Pillow', '10.0.0'), + ('pyproj', '3.6.0'), + ('matplotlib', '3.7.2'), + ('netcdf4-python', '1.6.4'), + ('dask', '2023.9.2'), # needed by pysteps-nwp-importers + ('xarray', '2023.9.0'), # needed by pysteps-nwp-importers +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('jsmin', '3.0.1', { + 'checksums': ['c0959a121ef94542e807a674142606f7e90214a2b3d1eb17300244bbb5cc2bfc'], + }), + (name, version, { + 'checksums': ['28b51d61c3411fccf5c5f80792b9effe8f92a515e5984ffc5ad9ce810603a62d'], + }), + ('pysteps-nwp-importers', '20240624', { + 'source_urls': ['https://github.com/pySTEPS/pysteps-nwp-importers/archive/'], + 'sources': [{'download_filename': '73b3573.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['d5835023c739056aa04c6938e256e6ba24ed9585a252cdf3f10b6dc0b92f0730'], + }), +] + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/p/pytest/pytest-7.4.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/pytest/pytest-7.4.2-GCCcore-12.3.0.eb index 9d0b6f0c25de..45ab5fae484b 100644 --- a/easybuild/easyconfigs/p/pytest/pytest-7.4.2-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/pytest/pytest-7.4.2-GCCcore-12.3.0.eb @@ -13,11 +13,12 @@ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} builddependencies = [ ('binutils', '2.40'), ('hatchling', '1.18.0'), + ('flit', '3.9.0'), ] dependencies = [ ('Python', '3.11.3'), - ('Python-bundle-PyPI', '2023.06'), + ('hypothesis', '6.82.0'), ] use_pip = True @@ -39,15 +40,14 @@ _skip_tests = [ _ignore_tests = ' --ignore='.join(_skip_tests) exts_list = [ - ('setuptools-scm', '8.0.4', { - 'checksums': ['b5f43ff6800669595193fd09891564ee9d1d7dcb196cab4b2506d53a2e1c95c7'], + ('iniconfig', '2.0.0', { + 'checksums': ['2d91e135bf72d31a410b17c16da610a82cb55f6b0477d1a902134b24a455b8b3'], }), - ('flit-core', '3.9.0', { - 'source_tmpl': 'flit_core-%(version)s.tar.gz', - 'checksums': ['72ad266176c4a3fcfab5f2930d76896059851240570ce9a98733b658cb786eba'], + ('exceptiongroup', '1.1.1', { + 'checksums': ['d484c3090ba2889ae2928419117447a14daf3c1231d5e30d0aae34f354f01785'], }), - ('hypothesis', '6.88.1', { - 'checksums': ['f4c2c004b9ec3e0e25332ad2cb6b91eba477a855557a7b5c6e79068809ff8b51'], + ('pluggy', '1.2.0', { + 'checksums': ['d12f0c4b579b15f5e054301bb226ee85eeeba08ffec228092f8defbaa3a4c4b3'], }), ('elementpath', '4.1.5', { 'checksums': ['c2d6dc524b29ef751ecfc416b0627668119d8812441c555d7471da41d4bacb8d'], diff --git a/easybuild/easyconfigs/p/python-blosc/python-blosc-1.11.0-foss-2023a.eb b/easybuild/easyconfigs/p/python-blosc/python-blosc-1.11.0-foss-2023a.eb new file mode 100644 index 000000000000..3a8083cc0d5f --- /dev/null +++ b/easybuild/easyconfigs/p/python-blosc/python-blosc-1.11.0-foss-2023a.eb @@ -0,0 +1,36 @@ +easyblock = 'PythonBundle' + +name = 'python-blosc' +version = '1.11.0' + +homepage = 'https://github.com/Blosc/python-blosc/' +description = "A Python wrapper for the extremely fast Blosc compression library." + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('scikit-build', '0.17.6'), + ('CMake', '3.26.3'), +] +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('Blosc', '1.21.5'), +] + +use_pip = True +sanity_pip_check = True + +local_preinstallopts = 'export USE_SYSTEM_BLOSC=1 && ' +local_preinstallopts += 'export Blosc_ROOT=$EBROOTBLOSC && ' + +exts_list = [ + ('blosc', version, { + 'preinstallopts': local_preinstallopts, + 'checksums': ['c985b8f435dbc49b190fe88947539ed710ad0e9aaaf83778acc506a71ada7bd2'], + }), +] + +sanity_check_commands = ["python -m blosc.test"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/python-elf/python-elf-0.5.1-foss-2023a.eb b/easybuild/easyconfigs/p/python-elf/python-elf-0.5.1-foss-2023a.eb new file mode 100644 index 000000000000..c3fe23a272a0 --- /dev/null +++ b/easybuild/easyconfigs/p/python-elf/python-elf-0.5.1-foss-2023a.eb @@ -0,0 +1,72 @@ +easyblock = 'PythonBundle' + +name = 'python-elf' +version = '0.5.1' + +homepage = 'https://github.com/constantinpape/elf' +description = "Utils and convenience functions for large-scale bio-image analysis." + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('scikit-build', '0.17.6'), + ('CMake', '3.26.3'), +] +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('imageio', '2.33.1'), + ('scikit-image', '0.22.0'), + ('scikit-learn', '1.3.1'), + ('h5py', '3.9.0'), + ('zarr', '2.17.1'), + ('mrcfile', '1.5.0'), + ('numba', '0.58.1'), + ('tqdm', '4.66.1'), + ('vigra', '1.11.2'), + ('python-blosc', '1.11.0'), + ('openpyxl', '3.1.2'), + ('nifty', '1.2.1'), + ('z5py', '2.0.17'), + ('affogato', '0.3.3'), + ('napari', '0.4.18'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('nose2', '0.14.1', { + 'checksums': ['7f8f03a21c9de2c33015933afcef72bf8e4a2d5dfec3b40092287de6e41b093a'], + }), + ('intern', '1.4.1', { + 'checksums': ['7cdc6caa66716760f93dbbadaa67cc8a03866d6c5f33a6a3285cb9e5f4994315'], + }), + ('skan', '0.11.1', { + 'checksums': ['d5439c17fbf5f86386a7548acb6ab11482961164a6284047b9bdc6652a0d1faf'], + }), + (name, version, { + 'modulename': 'elf', + 'source_urls': ['https://github.com/constantinpape/elf/archive/'], + 'sources': ['%(version)s.tar.gz'], + 'checksums': ['29c542dfb953a1975e2d45f72c84b8f8a2f79fcb0cb2d855dae5493cadbbaa9d'], + }), +] + +sanity_check_commands = [ + "python -c 'import elf.segmentation.multicut'", + "python -c 'import elf.segmentation.features'", + "python -c 'import elf.segmentation.embeddings'", + "python -c 'from elf.segmentation.mutex_watershed import mutex_watershed_clustering'", + "python -c 'from elf.segmentation.utils import load_mutex_watershed_problem'", + "python -c 'import elf.htm'", + "python -c 'from elf.parallel.label import label'", + "python -c 'from elf.evaluation import rand_index'", + "python -c 'from elf.io import open_file'", + "python -c 'from elf.visualisation import visualise_edges'", + "python -c 'import elf.tracking.tracking_utils'", + "python -c 'import elf.transformation'", + "python -c 'import elf.util'", +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/python-igraph/python-igraph-0.10.6-foss-2022b.eb b/easybuild/easyconfigs/p/python-igraph/python-igraph-0.10.6-foss-2022b.eb index 01e1aa2d9c6e..3b61ec3f8693 100644 --- a/easybuild/easyconfigs/p/python-igraph/python-igraph-0.10.6-foss-2022b.eb +++ b/easybuild/easyconfigs/p/python-igraph/python-igraph-0.10.6-foss-2022b.eb @@ -20,6 +20,7 @@ dependencies = [ ('Clang', '16.0.4'), ('libxml2', '2.10.3'), ('zlib', '1.2.12'), + ('cairo', '1.17.4'), ] use_pip = True diff --git a/easybuild/easyconfigs/p/python-louvain/python-louvain-0.16-foss-2022b.eb b/easybuild/easyconfigs/p/python-louvain/python-louvain-0.16-foss-2022b.eb new file mode 100644 index 000000000000..5c6085a41e68 --- /dev/null +++ b/easybuild/easyconfigs/p/python-louvain/python-louvain-0.16-foss-2022b.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'python-louvain' +version = '0.16' + +homepage = 'https://pypi.org/project/python-louvain' +description = "Louvain algorithm for community detection" + +toolchain = {'name': 'foss', 'version': '2022b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['b7ba2df5002fd28d3ee789a49532baad11fe648e4f2117cf0798e7520a1da56b'] + +dependencies = [ + ('Python', '3.10.8'), + ('networkx', '3.0'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +options = {'modulename': 'community'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/python-parasail/python-parasail-1.3.4-foss-2023b.eb b/easybuild/easyconfigs/p/python-parasail/python-parasail-1.3.4-foss-2023b.eb new file mode 100644 index 000000000000..46bbb77dda99 --- /dev/null +++ b/easybuild/easyconfigs/p/python-parasail/python-parasail-1.3.4-foss-2023b.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'python-parasail' +version = '1.3.4' + +homepage = 'https://github.com/jeffdaily/parasail-python' +description = "Python Bindings for the Parasail C Library" + +toolchain = {'name': 'foss', 'version': '2023b'} + +sources = ['parasail-%(version)s.tar.gz'] +checksums = ['d6a7035dfae3ef5aafdd7e6915711214c22b572ea059fa69d9d7ecbfb9b61b0f'] + +builddependencies = [ + ('parasail', '2.6.2'), +] + +dependencies = [ + ('Python', '3.11.5'), + ('SciPy-bundle', '2023.11'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +# make sure setup.py finds the parasail library +preinstallopts = "ln -s $EBROOTPARASAIL/lib/libparasail.so parasail/libparasail.%s && " % SHLIB_EXT + +options = {'modulename': 'parasail'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/q/Qhull/Qhull-2020.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/q/Qhull/Qhull-2020.2-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..400fecee609d --- /dev/null +++ b/easybuild/easyconfigs/q/Qhull/Qhull-2020.2-GCCcore-13.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'CMakeMake' + +name = 'Qhull' +version = '2020.2' + +homepage = 'http://www.qhull.org' + +description = """ + Qhull computes the convex hull, Delaunay triangulation, Voronoi diagram, + halfspace intersection about a point, furthest-site Delaunay triangulation, + and furthest-site Voronoi diagram. The source code runs in 2-d, 3-d, 4-d, and + higher dimensions. Qhull implements the Quickhull algorithm for computing the + convex hull. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.qhull.org/download/'] +sources = ['%(namelower)s-%(version_major)s-src-8.0.2.tgz'] +checksums = ['b5c2d7eb833278881b952c8a52d20179eab87766b00b865000469a45c1838b7e'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] + +sanity_check_paths = { + 'files': ['bin/qhull', 'lib/libqhull_r.%s' % SHLIB_EXT, + 'lib/pkgconfig/qhull_r.pc'], + 'dirs': [], +} + +modextrapaths = { + 'CPATH': ['qhull/include'], +} + +parallel = 1 + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/q/Qualimap/Qualimap-2.3-foss-2022b-R-4.2.2.eb b/easybuild/easyconfigs/q/Qualimap/Qualimap-2.3-foss-2022b-R-4.2.2.eb new file mode 100644 index 000000000000..c6a3e40d231e --- /dev/null +++ b/easybuild/easyconfigs/q/Qualimap/Qualimap-2.3-foss-2022b-R-4.2.2.eb @@ -0,0 +1,33 @@ +easyblock = 'Tarball' + +name = 'Qualimap' +version = '2.3' +versionsuffix = '-R-%(rver)s' + +homepage = 'http://qualimap.bioinfo.cipf.es/' +description = """Qualimap 2 is a platform-independent application written in Java and R that provides both + a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of + alignment sequencing data and its derivatives like feature counts.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +source_urls = ['https://bitbucket.org/kokonech/qualimap/downloads/'] +sources = ['qualimap_v%(version)s.zip'] +checksums = ['2a04dd864b712da30923cce3bc8dfc6ea59612118e8b0ff1a246fe43b8d34c40'] + +dependencies = [ + ('Java', '11', '', SYSTEM), + ('R', '4.2.2'), + ('R-bundle-Bioconductor', '3.16', versionsuffix), +] + +sanity_check_paths = { + 'files': ['qualimap'], + 'dirs': [], +} + +sanity_check_commands = ["qualimap --help"] + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-foss-2021a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-foss-2021a.eb index 5438527c1583..bdff659a888c 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-foss-2021a.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-foss-2021a.eb @@ -29,7 +29,8 @@ checksums = [ dependencies = [ ('HDF5', '1.10.7'), - ('ELPA', '2021.05.001'), + # From the QE configure help, this version of ELPA is not compatible + # ('ELPA', '2021.05.001'), ('libxc', '5.1.5'), ] @@ -41,4 +42,7 @@ buildopts = 'all gwl xspectra couple epw gipaw w90' # parallel build tends to fail parallel = 1 +# allow some test failures (not investigated for old easyconfig) +test_suite_max_failed = 4 + moduleclass = 'chem' diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-intel-2021a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-intel-2021a.eb index 90cb839d1f7a..99d05042d925 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-intel-2021a.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-intel-2021a.eb @@ -29,7 +29,8 @@ checksums = [ dependencies = [ ('HDF5', '1.10.7'), - ('ELPA', '2021.05.001'), + # From the QE configure help, this version of ELPA is not compatible + # ('ELPA', '2021.05.001'), ('libxc', '5.1.5'), ] @@ -41,4 +42,7 @@ buildopts = 'all gwl xspectra couple epw gipaw w90' # parallel build tends to fail parallel = 1 +# allow some test failures (not investigated for old easyconfig) +test_suite_max_failed = 2 + moduleclass = 'chem' diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.8-foss-2021b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.8-foss-2021b.eb index fc8ad3175476..aedc3282d148 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.8-foss-2021b.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.8-foss-2021b.eb @@ -41,4 +41,7 @@ buildopts = 'all gwl xspectra couple epw gipaw w90' # parallel build tends to fail parallel = 1 +# don't run the tests (not investigated for old easyconfig) +skipsteps = ['test'] + moduleclass = 'chem' diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.8-intel-2021a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.8-intel-2021a.eb index 4b187cd70ee4..5982b4efde67 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.8-intel-2021a.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.8-intel-2021a.eb @@ -41,4 +41,7 @@ buildopts = 'all gwl xspectra couple epw gipaw w90' # parallel build tends to fail parallel = 1 +# allow some test failures (not investigated for old easyconfig) +test_suite_max_failed = 4 + moduleclass = 'chem' diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.0-foss-2021b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.0-foss-2021b.eb index a0a1ebea9ea5..9f62ca5ad84e 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.0-foss-2021b.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.0-foss-2021b.eb @@ -41,4 +41,7 @@ buildopts = 'all gwl xspectra couple epw gipaw w90' # parallel build tends to fail parallel = 1 +# allow some test failures (not investigated for old easyconfig) +test_suite_max_failed = 3 + moduleclass = 'chem' diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.0-intel-2021b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.0-intel-2021b.eb index febc60c8c61d..3aef60958a62 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.0-intel-2021b.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.0-intel-2021b.eb @@ -41,4 +41,7 @@ buildopts = 'all gwl xspectra couple epw gipaw w90' # parallel build tends to fail parallel = 1 +# don't run the tests (not investigated for old easyconfig) +skipsteps = ['test'] + moduleclass = 'chem' diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-foss-2022a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-foss-2022a.eb index 87066c6ae6d7..3f34e98c9709 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-foss-2022a.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-foss-2022a.eb @@ -48,4 +48,7 @@ buildopts = 'all gwl xspectra couple epw gipaw w90' # parallel build tends to fail parallel = 1 +# don't run the tests (not investigated for old easyconfig) +skipsteps = ['test'] + moduleclass = 'chem' diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-intel-2022a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-intel-2022a.eb index a81be226c253..931d16c7f635 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-intel-2022a.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-intel-2022a.eb @@ -48,4 +48,7 @@ buildopts = 'all gwl xspectra couple epw gipaw w90' # parallel build tends to fail parallel = 1 +# don't run the tests (not investigated for old easyconfig) +skipsteps = ['test'] + moduleclass = 'chem' diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2022b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2022b.eb index 376073c68087..9362d5a9fb84 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2022b.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2022b.eb @@ -45,6 +45,8 @@ dependencies = [ # which depends on qe source buildopts = 'all gwl xspectra couple epw gipaw w90' +with_fox = True + # parallel build tends to fail parallel = 1 diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2023a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2023a.eb index 4a79d7df97a7..8369f3fb31a2 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2023a.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2023a.eb @@ -46,6 +46,8 @@ dependencies = [ # which depends on qe source buildopts = "all gwl xspectra couple epw gipaw w90" +with_fox = True + # parallel build tends to fail parallel = 1 diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-intel-2022b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-intel-2022b.eb index 8b78a44b1f61..53852bd770bd 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-intel-2022b.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-intel-2022b.eb @@ -9,7 +9,9 @@ It is based on density-functional theory, plane waves, and pseudopotentials """ toolchain = {'name': 'intel', 'version': '2022b'} -toolchainopts = {'usempi': True, 'openmp': True} +# OpenMP is not working with Intel ifort/ifx compilers (Fortran) starting from version 2021.2.0 +# toolchainopts = {'usempi': True, 'openmp': True} +toolchainopts = {'usempi': True} sources = [ { @@ -45,6 +47,8 @@ dependencies = [ # which depends on qe source buildopts = 'all gwl xspectra couple epw gipaw w90' +with_fox = True + # parallel build tends to fail parallel = 1 diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3-foss-2023a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3-foss-2023a.eb index 208c30416899..dff22dff1e6d 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3-foss-2023a.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3-foss-2023a.eb @@ -52,4 +52,7 @@ buildopts = "all gwl xspectra couple epw gipaw w90" # parallel build tends to fail parallel = 1 +# allow some test failures (see https://github.com/EESSI/software-layer/pull/504#issuecomment-2039605740) +test_suite_max_failed = 2 + moduleclass = 'chem' diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-foss-2023a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-foss-2023a.eb new file mode 100644 index 000000000000..ff3277e87b30 --- /dev/null +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-foss-2023a.eb @@ -0,0 +1,158 @@ +name = "QuantumESPRESSO" +version = "7.3.1" + +homepage = "https://www.quantum-espresso.org" +description = """Quantum ESPRESSO is an integrated suite of computer codes +for electronic-structure calculations and materials modeling at the nanoscale. +It is based on density-functional theory, plane waves, and pseudopotentials +(both norm-conserving and ultrasoft). +""" + +toolchain = {"name": "foss", "version": "2023a"} +toolchainopts = { + "usempi": True, + "openmp": True, +} + +# Check hashes inside external/submodule_commit_hash_records when making file for new version +local_lapack_hash = "12d825396fcef1e0a1b27be9f119f9e554621e55" +local_mbd_hash = "82005cbb65bdf5d32ca021848eec8f19da956a77" +local_devxlib_hash = "a6b89ef77b1ceda48e967921f1f5488d2df9226d" +local_fox_hash = "3453648e6837658b747b895bb7bef4b1ed2eac40" +# Different from the one at tag qe-7.3.1 because of: +# https://gitlab.com/QEF/q-e/-/issues/666 +local_d3q_hash = "de4718351e7bbb9d1d12aad2b7ca232d06775b83" +# Different from the one at tag qe-7.3.1 because of: +# https://github.com/dceresoli/qe-gipaw/issues/19 +local_qe_gipaw_hash = "79d3a03b7bdc4325e66f3fad02a24c6e6e3e5806" +local_qmcpack_hash = "f72ab25fa4ea755c1b4b230ae8074b47d5509c70" +local_w90_hash = "1d6b187374a2d50b509e5e79e2cab01a79ff7ce1" + + +sources = [ + { + "filename": "q-e-qe-%(version)s.tar.gz", + "extract_cmd": "mkdir -p %(builddir)s/qe-%(version)s && tar xzvf %s --strip-components=1 -C $_", + "source_urls": ["https://gitlab.com/QEF/q-e/-/archive/qe-%(version)s"], + }, + { + "filename": "lapack-%s.tar.gz" % local_lapack_hash, + "git_config": { + "url": "https://github.com/Reference-LAPACK", + "repo_name": "lapack", + "commit": local_lapack_hash, + }, + }, + { + "filename": "mbd-%s.tar.gz" % local_mbd_hash, + "git_config": { + "url": "https://github.com/libmbd", + "repo_name": "libmbd", + "commit": local_mbd_hash, + 'clone_into': 'mbd', + }, + }, + { + "filename": "devxlib-%s.tar.gz" % local_devxlib_hash, + "git_config": { + "url": "https://gitlab.com/max-centre/components", + "repo_name": "devicexlib", + "commit": local_devxlib_hash, + 'clone_into': 'devxlib', + }, + }, + { + "filename": "d3q-%s.tar.gz" % local_d3q_hash, + "git_config": { + "url": "https://github.com/anharmonic", + "repo_name": "d3q", + "commit": local_d3q_hash, + }, + }, + { + "filename": "fox-%s.tar.gz" % local_fox_hash, + "git_config": { + "url": "https://github.com/pietrodelugas", + "repo_name": "fox", + "commit": local_fox_hash, + }, + }, + { + "filename": "qe-gipaw-%s.tar.gz" % local_qe_gipaw_hash, + "git_config": { + "url": "https://github.com/dceresoli", + "repo_name": "qe-gipaw", + "commit": local_qe_gipaw_hash, + }, + }, + { + "filename": "pw2qmcpack-%s.tar.gz" % local_qmcpack_hash, + "git_config": { + "url": "https://github.com/QMCPACK", + "repo_name": "pw2qmcpack", + "commit": local_qmcpack_hash, + }, + }, + { + "filename": "wannier90-%s.tar.gz" % local_w90_hash, + "git_config": { + "url": "https://github.com/wannier-developers", + "repo_name": "wannier90", + "commit": local_w90_hash, + }, + }, +] +# Holding off checksum checks untill 5.0.x +# https://github.com/easybuilders/easybuild-framework/pull/4248 +# checksums = [ +# {'q-e-qe-7.3.1.tar.gz': '2c58b8fadfe4177de5a8b69eba447db5e623420b070dea6fd26c1533b081d844'}, +# {'lapack-%s.tar.gz' % local_lapack_hash: 'c05532ae0e5fe35f473206dda12970da5f2e2214620487d71837ddcf0ea6b21d'}, +# {'mbd-%s.tar.gz' % local_mbd_hash: 'a180682c00bb890c9b1e26a98addbd68e32f970c06439acf7582415f4c589800'}, +# {'devxlib-%s.tar.gz' % local_devxlib_hash: '76da8fe5a2050f58efdc92fa8831efec25c19190df7f4e5e39c173a5fbae83b4'}, +# {'d3q-%s.tar.gz' % local_d3q_hash: '43e50753a56af05d181b859d3e29d842fb3fc4352f00cb7fe229a435a1f20c31'}, +# {'fox-%s.tar.gz' % local_fox_hash: '99b6a899a3f947d7763aa318e86f9f08db684568bfdcd293f3318bee9d7f1948'}, +# {'qe-gipaw-%s.tar.gz' % local_qe_gipaw_hash: '9ac8314363d29cc2f1ce85abd8f26c1a3ae311d54f6e6034d656442dd101c928'}, +# {'pw2qmcpack-%s.tar.gz' % local_qmcpack_hash: 'a8136da8429fc49ab560ef7356cd6f0a2714dfbb137baff7961f46dfe32061eb'}, +# {'wannier90-%s.tar.gz' % local_w90_hash: 'f989497790ec9777bdc159945bbf42156edb7268011f972874dec67dd4f58658'}, +# ] +checksums = [ + '2c58b8fadfe4177de5a8b69eba447db5e623420b070dea6fd26c1533b081d844', + None, None, None, None, None, None, None, None +] + +builddependencies = [ + ("M4", "1.4.19"), + ("CMake", "3.26.3"), + ("pkgconf", "1.9.5"), +] +dependencies = [ + ("HDF5", "1.14.0"), + ("ELPA", "2023.05.001"), + ("libxc", "6.2.2"), +] + +# Disabled because of +# https://gitlab.com/QEF/q-e/-/issues/667 +# https://github.com/anharmonic/d3q/issues/15 +build_shared_libs = False +with_scalapack = True +with_fox = True +with_gipaw = True +with_d3q = True +with_qmcpack = True + +moduleclass = "chem" + +test_suite_threshold = ( + 0.4 # Low threshold because of https://gitlab.com/QEF/q-e/-/issues/665 +) +test_suite_max_failed = ( + 5 # Allow for some flaky tests (failed due to strict thresholds) +) +test_suite_allow_failures = [ + "test_qe_xclib_", # 7.3.1: https://gitlab.com/QEF/q-e/-/issues/640 + "--hp_", # 7.3.1: Broken testsuite (https://gitlab.com/QEF/q-e/-/issues/665) + "--ph_", # 7.3.1: Broken testsuite (https://gitlab.com/QEF/q-e/-/issues/665) + "--epw_", # 7.3.1: Broken testsuite (https://gitlab.com/QEF/q-e/-/issues/665) + "--tddfpt_", # 7.3.1: Broken testsuite (https://gitlab.com/QEF/q-e/-/issues/665) +] diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-intel-2023a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-intel-2023a.eb new file mode 100644 index 000000000000..d6ffe3c80c16 --- /dev/null +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-intel-2023a.eb @@ -0,0 +1,150 @@ +name = 'QuantumESPRESSO' +version = '7.3.1' + +homepage = 'https://www.quantum-espresso.org' +description = """Quantum ESPRESSO is an integrated suite of computer codes +for electronic-structure calculations and materials modeling at the nanoscale. +It is based on density-functional theory, plane waves, and pseudopotentials +(both norm-conserving and ultrasoft). +""" + +toolchain = {'name': 'intel', 'version': '2023a'} +toolchainopts = { + 'usempi': True, + 'openmp': True, +} + +# Check hashes inside external/submodule_commit_hash_records when making file for new version +local_lapack_hash = "12d825396fcef1e0a1b27be9f119f9e554621e55" +local_mbd_hash = "82005cbb65bdf5d32ca021848eec8f19da956a77" +local_devxlib_hash = "a6b89ef77b1ceda48e967921f1f5488d2df9226d" +local_fox_hash = "3453648e6837658b747b895bb7bef4b1ed2eac40" +# Different from the one at tag qe-7.3.1 because of: +# https://gitlab.com/QEF/q-e/-/issues/666 +local_d3q_hash = "de4718351e7bbb9d1d12aad2b7ca232d06775b83" +local_qe_gipaw_hash = "75b01b694c9ba4df55d294cacc27cf28591b2161" +local_qmcpack_hash = "f72ab25fa4ea755c1b4b230ae8074b47d5509c70" +local_w90_hash = "1d6b187374a2d50b509e5e79e2cab01a79ff7ce1" + +sources = [ + { + 'filename': 'q-e-qe-%(version)s.tar.gz', + 'extract_cmd': 'mkdir -p %(builddir)s/qe-%(version)s && tar xzvf %s --strip-components=1 -C $_', + 'source_urls': ['https://gitlab.com/QEF/q-e/-/archive/qe-%(version)s'] + }, + { + "filename": "lapack-%s.tar.gz" % local_lapack_hash, + "git_config": { + "url": "https://github.com/Reference-LAPACK", + "repo_name": "lapack", + "commit": local_lapack_hash, + }, + }, + { + "filename": "mbd-%s.tar.gz" % local_mbd_hash, + "git_config": { + "url": "https://github.com/libmbd", + "repo_name": "libmbd", + "commit": local_mbd_hash, + 'clone_into': 'mbd', + }, + }, + { + "filename": "devxlib-%s.tar.gz" % local_devxlib_hash, + "git_config": { + "url": "https://gitlab.com/max-centre/components", + "repo_name": "devicexlib", + "commit": local_devxlib_hash, + 'clone_into': 'devxlib', + }, + }, + { + "filename": "d3q-%s.tar.gz" % local_d3q_hash, + "git_config": { + "url": "https://github.com/anharmonic", + "repo_name": "d3q", + "commit": local_d3q_hash, + }, + }, + { + "filename": "fox-%s.tar.gz" % local_fox_hash, + "git_config": { + "url": "https://github.com/pietrodelugas", + "repo_name": "fox", + "commit": local_fox_hash, + }, + }, + { + "filename": "qe-gipaw-%s.tar.gz" % local_qe_gipaw_hash, + "git_config": { + "url": "https://github.com/dceresoli", + "repo_name": "qe-gipaw", + "commit": local_qe_gipaw_hash, + }, + }, + { + "filename": "pw2qmcpack-%s.tar.gz" % local_qmcpack_hash, + "git_config": { + "url": "https://github.com/QMCPACK", + "repo_name": "pw2qmcpack", + "commit": local_qmcpack_hash, + }, + }, + { + "filename": "wannier90-%s.tar.gz" % local_w90_hash, + "git_config": { + "url": "https://github.com/wannier-developers", + "repo_name": "wannier90", + "commit": local_w90_hash, + }, + }, +] +# Holding off checksum checks untill 5.0.x +# https://github.com/easybuilders/easybuild-framework/pull/4248 +# checksums = [ +# {'q-e-qe-7.3.1.tar.gz': '2c58b8fadfe4177de5a8b69eba447db5e623420b070dea6fd26c1533b081d844'}, +# {'lapack-%s.tar.gz' % local_lapack_hash: 'c05532ae0e5fe35f473206dda12970da5f2e2214620487d71837ddcf0ea6b21d'}, +# {'mbd-%s.tar.gz' % local_mbd_hash: 'a180682c00bb890c9b1e26a98addbd68e32f970c06439acf7582415f4c589800'}, +# {'devxlib-%s.tar.gz' % local_devxlib_hash: '76da8fe5a2050f58efdc92fa8831efec25c19190df7f4e5e39c173a5fbae83b4'}, +# {'d3q-%s.tar.gz' % local_d3q_hash: '43e50753a56af05d181b859d3e29d842fb3fc4352f00cb7fe229a435a1f20c31'}, +# {'fox-%s.tar.gz' % local_fox_hash: '99b6a899a3f947d7763aa318e86f9f08db684568bfdcd293f3318bee9d7f1948'}, +# {'qe-gipaw-%s.tar.gz' % local_qe_gipaw_hash: '9ac8314363d29cc2f1ce85abd8f26c1a3ae311d54f6e6034d656442dd101c928'}, +# {'pw2qmcpack-%s.tar.gz' % local_qmcpack_hash: 'a8136da8429fc49ab560ef7356cd6f0a2714dfbb137baff7961f46dfe32061eb'}, +# {'wannier90-%s.tar.gz' % local_w90_hash: 'f989497790ec9777bdc159945bbf42156edb7268011f972874dec67dd4f58658'}, +# ] +checksums = [ + '2c58b8fadfe4177de5a8b69eba447db5e623420b070dea6fd26c1533b081d844', + None, None, None, None, None, None, None, None +] + +builddependencies = [ + ('M4', '1.4.19'), + ('CMake', '3.26.3'), + ("pkgconf", "1.9.5"), +] +dependencies = [ + ('HDF5', '1.14.0'), + ('ELPA', '2023.05.001'), + ('libxc', '6.2.2'), +] + +# Disabled because of +# https://gitlab.com/QEF/q-e/-/issues/667 +# https://github.com/anharmonic/d3q/issues/15 +build_shared_libs = False +with_scalapack = True +with_gipaw = False # https://github.com/dceresoli/qe-gipaw/issues/19 +with_d3q = True +with_qmcpack = True + +moduleclass = 'chem' + +test_suite_threshold = 0.4 # Low threshold because of https://gitlab.com/QEF/q-e/-/issues/665 +test_suite_max_failed = 5 # Allow for some flaky tests (failed due to strict thresholds) +test_suite_allow_failures = [ + 'test_qe_xclib_', # 7.3.1: https://gitlab.com/QEF/q-e/-/issues/640 + '--hp_', # 7.3.1: Broken testsuite (https://gitlab.com/QEF/q-e/-/issues/665) + '--ph_', # 7.3.1: Broken testsuite (https://gitlab.com/QEF/q-e/-/issues/665) + '--epw_', # 7.3.1: Broken testsuite (https://gitlab.com/QEF/q-e/-/issues/665) + '--tddfpt_', # 7.3.1: Broken testsuite (https://gitlab.com/QEF/q-e/-/issues/665) +] diff --git a/easybuild/easyconfigs/q/Qwt/Qwt-6.3.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/q/Qwt/Qwt-6.3.0-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..f208a0345428 --- /dev/null +++ b/easybuild/easyconfigs/q/Qwt/Qwt-6.3.0-GCCcore-12.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'Qwt' +version = '6.3.0' + +homepage = 'https://qwt.sourceforge.io/' +description = """The Qwt library contains GUI Components and utility classes which are primarily useful for programs + with a technical background.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_BZ2] +patches = ['Qwt-6.2.0_fix-install-prefix.patch'] +checksums = [ + {'qwt-6.3.0.tar.bz2': 'dcb085896c28aaec5518cbc08c0ee2b4e60ada7ac929d82639f6189851a6129a'}, + {'Qwt-6.2.0_fix-install-prefix.patch': 'ac5c329c0693d565b461cdd3b36c1b96b4d09885e1e0c10929fc7a9021c03bad'}, +] + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '1.9.5'), +] + +dependencies = [ + ('Qt5', '5.15.10'), +] + +skipsteps = ['configure'] + +prebuildopts = 'export QWT_PREFIX=%(installdir)s && ' +prebuildopts += "qmake qwt.pro && " + +sanity_check_paths = { + 'files': ['lib/libqwt.%s' % SHLIB_EXT, 'lib/pkgconfig/Qt5Qwt6.pc'], + 'dirs': ['doc', 'features', 'include', 'plugins'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/q/qnorm/qnorm-0.8.1-foss-2022b.eb b/easybuild/easyconfigs/q/qnorm/qnorm-0.8.1-foss-2022b.eb new file mode 100644 index 000000000000..99c6ebe1e239 --- /dev/null +++ b/easybuild/easyconfigs/q/qnorm/qnorm-0.8.1-foss-2022b.eb @@ -0,0 +1,36 @@ +easyblock = 'PythonPackage' + +name = 'qnorm' +version = '0.8.1' + +homepage = 'https://github.com/Maarten-vd-Sande/qnorm' +description = "Fast-ish (and correct!) quantile normalization in Python" + +toolchain = {'name': 'foss', 'version': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('numba', '0.58.1'), +] + +sources = [SOURCE_TAR_GZ] +checksums = ['61b2f3ef09a9c552a4f3b83dc438cb13f191fa190164361a3a508c4777eed3c7'] + +download_dep_fail = True +use_pip = True + +# pyproject.toml included in qnorm source tarball does not include standard fields, +# it's only there to be read by setup.py... +preinstallopts = "sed -i 's/pyproject.toml/pyproject.toml_/g' setup.py && mv pyproject.toml pyproject.toml_ && " + +sanity_check_paths = { + 'files': ['bin/qnorm'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["qnorm --help"] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2023.12-foss-2023a.eb b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2023.12-foss-2023a.eb index bbc343accac8..972a8488f6ad 100644 --- a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2023.12-foss-2023a.eb +++ b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2023.12-foss-2023a.eb @@ -867,7 +867,10 @@ exts_list = [ 'checksums': ['8e50415e415702402473caf622d86b89ddc881f6e5d888079a4818a8807ac9a2'], }), ('bold', '1.3.0', { - 'checksums': ['0ead11d4386c4c0cd578d3a956f809db2001e387e449a431b4ad503f3da38f5f'], + 'checksums': [ + ('0ead11d4386c4c0cd578d3a956f809db2001e387e449a431b4ad503f3da38f5f', + '4920fbebd22fb1d0f1a31ccc09c98aec446bb6cb5f65a2610437e405c0512c68'), + ], }), ('rredlist', '0.7.1', { 'checksums': ['92a10c37a211dc19b41b93f9ceb13d7ce1c3d3a7290cbba4c1688d944353ae85'], @@ -3424,6 +3427,9 @@ exts_list = [ ('rhandsontable', '0.3.8', { 'checksums': ['901ed9c59936f7fa52ad8db3111c8904ab962f9c74f1b6cd40f81683af35d21d'], }), + ('missMDA', '1.19', { + 'checksums': ['f9675884829b2fef75237c335b21991d163674320e766523c71c7a853f95e65c'], + }), ] modextrapaths = {'R_LIBS_SITE': ''} diff --git a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb new file mode 100644 index 000000000000..0ff705e97888 --- /dev/null +++ b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb @@ -0,0 +1,3463 @@ +easyblock = 'Bundle' + +name = 'R-bundle-CRAN' +version = '2024.06' + +homepage = 'https://www.r-project.org/' +description = "Bundle of R packages from CRAN" + +toolchain = {'name': 'foss', 'version': '2023b'} + +builddependencies = [ + ('pkgconf', '2.0.3'), + ('Xvfb', '21.1.9'), + ('Autotools', '20220317'), + ('CMake', '3.27.6'), +] + +dependencies = [ + ('R', '4.4.1'), + ('libxml2', '2.11.5'), # for XML + ('GMP', '6.3.0'), # for igraph + ('NLopt', '2.7.1'), # for nlopt + ('FFTW', '3.3.10'), # for fftw + ('libsndfile', '1.2.2'), # for seewave + ('ICU', '74.1'), # for rJava & gdsfmt + ('HDF5', '1.14.3'), # for hdf5r + ('UDUNITS', '2.2.28'), # for units + ('GSL', '2.7'), # for RcppGSL + ('ImageMagick', '7.1.1-34'), + ('GLPK', '5.0'), # for Rglpk + ('nodejs', '20.9.0'), # for V8 (required by rstan) + ('GDAL', '3.9.0'), # for sf + ('MPFR', '4.2.1'), # for Rmpfr + ('PostgreSQL', '16.1'), # for RPostgreSQL +] + +# Some R extensions (mclust, quantreg, waveslim for example) require the math library (-lm) to avoid undefined symbols. +# Adding it to FLIBS makes sure it is present when needed. +preconfigopts = 'export FLIBS="$FLIBS -lm" && ' + +configopts = "--with-pic --enable-threads --enable-R-shlib" +# some recommended packages may fail in a parallel build (e.g. Matrix), and +# we're installing them anyway below +configopts += " --with-recommended-packages=no" + +exts_defaultclass = 'RPackage' + +exts_default_options = { + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz', +} + +# check whether correct version is installed in extension filter +# (some versions in this bundle may be newer than the ones provided by R) +local_ext_version_check = "pkgver = packageVersion('%(ext_name)s'); if (pkgver != '%(ext_version)s') " +local_stop_msg = "stop('%(ext_name)s %(ext_version)s not installed, found ', pkgver, ' instead')" +exts_filter = ("R -q --no-save", "%s { %s }" % (local_ext_version_check, local_stop_msg)) + +# the dbarts extension needs an additional compiler flag on Arm systems to prevent "incompatible types" errors +# cfr. https://github.com/vdorie/dbarts/issues/66 +if ARCH == 'aarch64': + local_dbarts_preinstallopts = 'sed -i "s|-c partition_neon.c|-flax-vector-conversions -c partition_neon.c|"' + local_dbarts_preinstallopts += ' src/misc/Makefile && ' +else: + local_dbarts_preinstallopts = '' + +# !! order of packages is important !! +# packages updated on 24 June 2024 +exts_list = [ + ('abind', '1.4-5', { + 'checksums': ['3a3ace5afbcb86e56889efcebf3bf5c3bb042a282ba7cc4412d450bb246a3f2c'], + }), + ('magic', '1.6-1', { + 'checksums': ['ca79ec7ae92b736cb128556c081abf547f49956c326e053a76579889cbcb7976'], + }), + ('RcppProgress', '0.4.2', { + 'checksums': ['b1624b21b7aeb1dafb30f092b2a4bef4c3504efd2d6b00b2cdf55dc9df194b48'], + }), + ('lpSolve', '5.6.20', { + 'checksums': ['3ffe06a0685123c36cd306b874f89a59a70c864c8f78c5569f82a86abedc21db'], + }), + ('linprog', '0.9-4', { + 'checksums': ['81a6aa2fdc075f12dc912794d0554f87705a8b872b99c89a90a69ee9ada864b4'], + }), + ('geometry', '0.4.7', { + 'checksums': ['96204205f51b4d63c2e7a7b00365def27d131f3c9ec66db56b510046e5d2013b'], + }), + ('bit', '4.0.5', { + 'checksums': ['f0f2536a8874b6a30b80baefbc68cb21f0ffbf51f3877bda8038c3f9f354bfbc'], + }), + ('filehash', '2.4-5', { + 'checksums': ['3b1ee2794dd61e525ee44db16611c65957691d77bb26ae481eba988bb55da22c'], + }), + ('ff', '4.0.12', { + 'checksums': ['08af355a9a10fe29d48d085abc7cf1f975e1a4a670668a4f8d9632d087fb41bf'], + }), + ('bnlearn', '4.9.4', { + 'checksums': ['ce3d8d89451fed9277f879c03bb02bc17acab13f1f35587aab8175b80246eeea'], + }), + ('bootstrap', '2019.6', { + 'checksums': ['5252fdfeb944cf1fae35016d35f9333b1bd1fc8c6d4a14e33901160e21968694'], + }), + ('combinat', '0.0-8', { + 'checksums': ['1513cf6b6ed74865bfdd9f8ca58feae12b62f38965d1a32c6130bef810ca30c1'], + }), + ('deal', '1.2-42', { + 'checksums': ['a17f452a94fc3964c939c5b147ad6d4f326a0990493519d376d6700cf733a134'], + }), + ('fdrtool', '1.2.17', { + 'checksums': ['3452601adbead9be4820794e3af2666f710fdf9b801186df565b80b43629c5dd'], + }), + ('formatR', '1.14', { + 'checksums': ['4ebaab2c3f8527871655246b62abd060bc75dae1cec7f962ca4752b8080f474c'], + }), + ('gtools', '3.9.5', { + 'checksums': 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('NLP', '0.2-1', { + 'checksums': ['05eaa453ad2757311c073fd30093c738b20a977c5089031eb454345a1d01f2b6'], + }), + ('mclust', '6.1.1', { + 'checksums': ['ddd7018e5e6ea7f92c7fc9872b391491b7e91c2cd89ef1dcaf4408afb5116775'], + }), + ('RANN', '2.6.1', { + 'checksums': ['b299c3dfb7be17aa41e66eff5674fddd2992fb6dd3b10bc59ffbf0c401697182'], + }), + ('rmeta', '3.0', { + 'checksums': ['b9f9d405935cffcd7a5697ff13b033f9725de45f4dc7b059fd68a7536eb76b6e'], + }), + ('MASS', '7.3-61', { + 'checksums': ['3144c8bf579dd7b7c47c259728c27f53f53e294e7ed307da434dfd144e800a90'], + }), + ('lattice', '0.22-6', { + 'checksums': ['4b377211e472ece7872b9d6759f9b9c660b09594500462eb6146312a1d4d00f7'], + }), + ('nlme', '3.1-165', { + 'checksums': ['fc37bba493c2138be2f38fcfd2a67327d81ab91a37bad6f698226bb400ec9499'], + }), + ('segmented', '2.1-0', { + 'checksums': ['6d7ba0248cb5aa23dfdfc3fc53b6aab2f564323c671420fc73c5274e03640cf2'], + }), + ('som', '0.3-5.1', { + 'checksums': 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['d06bcaa1ccb52ef775f7c8b2d6d4676408dbc2813dfc128da34ffa4c7740f3e4'], + }), + ('minerva', '1.5.10', { + 'checksums': ['2f26353d8fcc989ac698c4e45bb683801b1a7bb60b14903d05a4d73c629c590f'], + }), + ('RcppTOML', '0.2.2', { + 'checksums': ['371391f9ca82221e76a424082ea9ebc5ea2c50f14e8408469b09d7dc3e6f63aa'], + }), + ('here', '1.0.1', { + 'checksums': ['08ed908033420d3d665c87248b3a14d1b6e2b37844bf736be620578c20ca346b'], + }), + ('reticulate', '1.38.0', { + 'checksums': ['cb2f313e2351a3cde03be55561b592318ec5376fba3b10e371eeff1986deca8d'], + }), + ('umap', '0.2.10.0', { + 'checksums': ['8d4786929345e8980bb8be8bb4b6300a679bba03a5984eed59e5e00c626b6ea9'], + }), + ('KODAMA', '2.4', { + 'checksums': ['78f2ea3596f3697fc06a080947e82a54c5270ed90f86916b91902e5db6ec85e7'], + }), + ('locfdr', '1.1-8', { + 'checksums': ['42d6e12593ae6d541e6813a140b92591dabeb1df94432a515507fc2eee9a54b9'], + }), + ('ica', '1.0-3', { + 'checksums': ['474d3530b16b76a1bf1a1114d24092678ea7215fa57c6fdcee6333f1e768b865'], + }), + ('dtw', '1.23-1', { + 'checksums': ['6ed6a3b52be673ce2617b8d48723c7c488c95aab88fe2912d7e00507838e826d'], + }), + ('SDMTools', '1.1-221.2', { + 'checksums': ['f0dd8c5f98d2f2c012536fa56d8f7a58aaf0c11cbe3527e66d4ee3194f6a6cf7'], + }), + ('ggridges', '0.5.6', { + 'checksums': ['efccaa309a150d11c6b402b912e618ea041f25cca3101f32cd821a6f41684e35'], + }), + ('TFisher', '0.2.0', { + 'checksums': ['bd9b7484d6fba0165841596275b446f85ba446d40e92f3b9cb37381a3827e76f'], + }), + ('lsei', '1.3-0', { + 'checksums': ['6289058f652989ca8a5ad6fa324ce1762cc9e36c42559c00929b70f762066ab6'], + }), + ('npsurv', '0.5-0', { + 'checksums': ['bc87db76e7017e178c2832a684fcd49c42e20054644b21b586413d26c8821dc6'], + }), + ('fitdistrplus', '1.1-11', { + 'checksums': ['26274f2b710b2417a8bca314d400abf320d4ccf0387ad082743056699501b53d'], + }), + ('hdf5r', '1.3.10', { + 'installopts': '--configure-args="--with-hdf5=$EBROOTHDF5/bin/h5pcc"', + 'preinstallopts': "unset LIBS && ", + 'checksums': ['92496e0693a27c0a1c8caba671c51fcecc3a120f8ef7eb0cb3cd686a3e49124e'], + }), + ('DTRreg', '2.2', { + 'checksums': ['9c8954d5c342af85611d13dab5be64c4a7a5904644a6e04ff21d5494559e2fc7'], + }), + ('pulsar', '0.3.11', { + 'checksums': ['ee82ef25b2be4bbac713c34bca85d8ea1fa0e32eb8c800dad7256e145fc79393'], + }), + ('bayesm', '3.1-6', { + 'checksums': ['17d72b9cdc090845f98e7a04640380d0baef8bc23d1487c8f64dc192fdb93cb5'], + }), + ('gsl', '2.1-8', { + 'checksums': ['f33609bf485abd190e65ff5d0fdab438b759294c47b921d983d89d6f053a2d95'], + }), + ('energy', '1.7-11', { + 'checksums': ['c29f8fb000c979d2504f6f6d3a99c773004f77d58793e7e2a5766155272b6511'], + }), + ('compositions', '2.0-8', { + 'checksums': ['c5063488f456992b5821458b3237322addffd3451ae91f9474707886971ef290'], + }), + ('clustree', '0.5.1', { + 'checksums': ['b5f2496e596e3fd140ace69c4837085e13f3abb850f5eb57d496380691fdd117'], + }), + ('tweedie', '2.3.5', { + 'checksums': ['983c745fee5a780d46e8dd04c2eb1c10cb2e222d3679654f0d6934d3db7b1c3e'], + }), + ('RcppGSL', '0.3.13', { + 'checksums': ['fe5e73bc119c6424e1a40b6fea17417a7bba93e81dbe9b7cf86dde9b8e8d93e7'], + }), + ('mvabund', '4.2.1', { + 'checksums': ['ed6946c95609443584081100cd38624d2309f7f5d210fd4b8ec12ad25bd27a06'], + }), + ('fishMod', '0.29', { + 'checksums': ['5989e49ca6d6b2c5d514655e61f75b019528a8c975f0d6056143f17dc4277a5d'], + }), + ('alabama', '2023.1.0', { + 'checksums': ['925f67c72d9cdb677105377777bd09e9b56a61573bea7e3f69e0a49595c7bf1c'], + }), + ('gllvm', '1.4.3', { + 'checksums': ['63b77040e9cf2694882d1d80a3bc3030b3a348819ea38e6728417e4c5de07ecc'], + }), + ('grpreg', '3.4.0', { + 'checksums': ['fd57d20baf63d2cc5821998bca5c3fdcbe46c933c9553caa492911b12654d6ad'], + }), + ('trust', '0.1-8', { + 'checksums': ['952e348b62aec35988b103fd152329662cb6a451538f184549252fbf49d7dcac'], + }), + ('lpSolveAPI', '5.5.2.0-17.11', { + 'checksums': ['b08d6cae4fc17575adf5df0113ea5f4f819bb2c7f87987e0d66c8eabfc933fa4'], + }), + ('ergm', '4.6.0', { + 'checksums': ['b471a60c39eb5b478e06dd0caf1d085f4b0927f1c260de699f1c8d4fe831a7f7'], + }), + ('networkLite', '1.0.5', { + 'checksums': ['aaab55d4f8f0b330fe7c1ecbab3c44746c52c2fda99c53c6b46042bb8775718b'], + }), + ('networkDynamic', '0.11.4', { + 'checksums': ['6bf3e216a444f183ff925e29560fae4c2362cc2a9fed19b3e116a9d9f1184a46'], + }), + ('ergm.multi', '0.2.1', { + 'checksums': ['e09dd0d7207a8214746ea251a50c93f6f5de255175309dc8757206f419a01902'], + }), + ('tergm', '4.2.0', { + 'checksums': ['dcf5a26cc2c4d165766706af08f8ea4f36e328158f5b682490c2a351f7fbda69'], + }), + ('ergm.count', '4.1.2', { + 'checksums': ['9bce70b64a2f60b242603b771370b40d7f7aeed37ed426670131fd966c13b020'], + }), + ('tsna', '0.3.5', { + 'checksums': ['4ee2f773d573f0f4bd93131156fdccf01d7f1a3f725eff3e885021098c6bff65'], + }), + ('statnet', '2019.6', { + 'checksums': ['0903e1a81ed1b6289359cefd12da1424c92456d19e062c3f74197b69e536b29d'], + }), + ('aggregation', '1.0.1', { + 'checksums': ['86f88a02479ddc8506bafb154117ebc3b1a4a44fa308e0193c8c315109302f49'], + }), + ('ComICS', '1.0.4', { + 'checksums': ['0af7901215876f95f309d7da6e633c38e4d7faf04112dd6fd343bc15fc593a2f'], + }), + ('dtangle', '2.0.9', { + 'checksums': ['c375068c1877c2e8cdc5601cfd5a9c821645c3dff90ddef64817f788f372e179'], + }), + ('mcmc', '0.9-8', { + 'checksums': ['6a06440d4b58e8a7f122747d92046ff40da4bb58a20bf642228a648a0c826ea7'], + }), + ('MCMCpack', '1.7-0', { + 'checksums': ['846073d710017ec1dc9a2b4616cb6aeb60ce04e3500a37214522818d34045def'], + }), + ('shinythemes', '1.2.0', { + 'checksums': ['37d68569ce838c7da9f0ea7e2b162ecf38fba2ae448a4888b6dd29c4bb5b2963'], + }), + ('csSAM', '1.2.4', { + 'checksums': ['3d6442ad8c41fa84633cbbc275cd67e88490a160927a5c55d29da55a36e148d7'], + }), + ('bridgedist', '0.1.2', { + 'checksums': ['7210c97fc864e78ea8502067359d642bbd95bf2df30d33da193fc5c004e45baf'], + }), + ('asnipe', '1.1.17', { + 'checksums': ['e7b4010fa1adf27534420db2971dae3c63190920a4323c86fd586842e22d9b07'], + }), + ('liquidSVM', '1.2.4', { + 'patches': ['liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch'], + # Don't add optimization flags by liquidSVM which may not be known e.g. on PPC + 'preinstallopts': 'LIQUIDSVM_TARGET="empty"', + 'checksums': [ + {'liquidSVM_1.2.4.tar.gz': '15a9c7f2930e2ed3f4c5bcd9b042884ea580d2b2e52e1c68041600c196046aba'}, + {'liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch': + '46b09e441c3b59af535f20d8db0dee7f1d6a7ddd511175d252115b53cb8b86f8'}, + ], + }), + ('oddsratio', '2.0.1', { + 'checksums': ['2097e7a8bf623379d55652de5dce4946d05163e85d30df50dc19055962bf60b5'], + }), + ('mltools', '0.3.5', { + 'checksums': ['7093ffceccdf5d4c3f045d8c8143deaa8ab79935cc6d5463973ffc7d3812bb10'], + }), + ('h2o', '3.44.0.3', { + 'checksums': ['61a85f6c2f15e8e96839f8a4fd3a45eaa6bca90517bb20a4dd36e951d6fd0c82'], + }), + ('mlegp', '3.1.9', { + 'checksums': ['63296d17a162fdce0958b10f45cb7d5dab4b3ee29340528d33cedcae08a040b3'], + }), + ('itertools', '0.1-3', { + 'checksums': ['b69b0781318e175532ad2d4f2840553bade9637e04de215b581704b5635c45d3'], + }), + ('missForest', '1.5', { + 'checksums': ['417055a03b02ad8359cf1bdc8f89d49531a3a8ee2c98edf90c8a01432f44838d'], + }), + ('bartMachineJARs', '1.2.1', { + 'checksums': ['9f7a20acf4aec249e16f83d81f5ec796aa718deb1b8bc24393fc0421eb8ce1c0'], + }), + ('bartMachine', '1.3.4.1', { + 'checksums': ['3b0a5250f5425a8efe460adcb58ea1342f1d845ae3a8db29dbf4806653884b89'], + }), + ('lqa', '1.0-3', { + 'checksums': ['3889675dc4c8cbafeefe118f4f20c3bd3789d4875bb725933571f9991a133990'], + }), + ('PresenceAbsence', '1.1.11', { + 'checksums': ['c63a6453783865b7c69c580a09a769e99390dd8b2e0f63e48fbfc86da3bee4b7'], + }), + ('GUTS', '1.2.5', { + 'checksums': ['9d983a566daa07d3e0036fe7011efe94f29e31a611493ba16bd316b61730a7b7'], + }), + ('GenSA', '1.1.14', { + 'checksums': ['66e455bb0e66d3c04af84d9dddc9b89f40b4cf9fe9ad1cf0714bcf30aa1b6837'], + }), + ('parsedate', '1.3.1', { + 'checksums': ['1fc31ab9813b61680abf4f4c2705b8f484d56d1d3ef256df84b342b628b6d1b1'], + }), + ('circular', '0.5-0', { + 'checksums': ['4bf4da5de29e555d1a7ae7ea64f8a5dda037e5c423f1078944f0bbb6eb9a7b92'], + }), + ('cobs', '1.3-8', { + 'checksums': ['2c2049c7cb868a2e4e1a530fe7218fac56e6157ef64ad57b91c5bb457dbc9821'], + }), + ('resample', '0.6', { + 'checksums': ['1b958009b18c92a47971847c782af76952ea4e85d5f1e3e1e70fa35c67b95265'], + }), + ('MIIVsem', '0.5.8', { + 'checksums': ['a908f51e1598290d25864c358d57201bd50c1c40775d4d0405cbc8077bee61e1'], + }), + ('medflex', '0.6-10', { + 'checksums': ['bd89a8fe939f3becd71a9dab30fe27fa43c96572d8309d2c1a70633117d4cb33'], + }), + ('Rserve', '1.8-13', { + 'checksums': ['7e5d312fca8029d746f60e7d9e701129561942f97dfc33b036b123f159d69a4c'], + }), + ('spls', '2.2-3', { + 'checksums': ['bbd693da80487eef2939c37aba199f6d811ec289828c763d9416a05fa202ab2e'], + }), + ('Boruta', '8.0.0', { + 'checksums': ['38e75b1ebc8b2d1c54b3373a42529b819c7b4773fd4932f57bc9701d1e3e3dc7'], + }), + ('dr', '3.0.10', { + 'checksums': ['ce523c1bdb62a9dda30afc12b1dd96975cc34695c61913012236f3b80e24bf36'], + }), + ('CovSel', '1.2.1', { + 'checksums': ['b375d00cc567e125ff106b4357654f43bba3abcadeed2238b6dea4b7a68fda09'], + }), + ('tmle', '2.0.1.1', { + 'checksums': ['8c2448f176ed94201affb8a9c42a5d0f56f26e88131ff2c1f4a9d14c5a0d87f6'], + }), + ('ctmle', '0.1.2', { + 'checksums': ['e3fa0722cd87aa0e0b209c2dddf3fc44c6d09993f1e66a6c43285fe950948161'], + }), + ('BayesPen', '1.0', { + 'checksums': ['772df9ae12cd8a3da1d5b7d1f1629602c7693f0eb03945784df2809e2bb061b0'], + }), + ('inline', '0.3.19', { + 'checksums': ['0ee9309bb7dab0b97761ddd18381aa12bd7d54678ccd7bec00784e831f4c99d5'], + }), + ('BMA', '3.18.17', { + 'checksums': ['6d8c514fa179f8a48c2105b551a8a08e28ea4375d06150a4b8ab4ccda577daf5'], + }), + ('BCEE', '1.3.2', { + 'checksums': ['f0e0a6a4eb11213073aa2f0cd6c76d87e8b3965124d8ca509538eb3c128533a0'], + }), + ('bacr', '1.0.1', { + 'checksums': ['c847272e2c03fd08ed79b3b739f57fe881af77404b6fd087caa0c398c90ef993'], + }), + ('clue', '0.3-65', { + 'checksums': ['bdf8fdd35fb2b1c65d09766da79d930fa664a00aa497f03b636400eecb623ef8'], + }), + ('bdsmatrix', '1.3-7', { + 'checksums': ['c3505e5ac06d5e01b3a6bad94177f8375cd9867bb0146cc9c63d92424ecb7922'], + }), + ('fftwtools', '0.9-11', { + 'checksums': ['f1f0c9a9086c7b2f72c5fb0334717cc917213a004eaef8448eab4940c9852c7f'], + }), + ('imagerExtra', '1.3.2', { + 'checksums': ['0ebfa1eabb89459d774630ab73c7a97a93b9481ea5afc55482975475acebd5b8'], + }), + ('MALDIquant', '1.22.2', { + 'checksums': ['6051b07019003c698ae016d79f13945bfe2edec26f8a688126b978cb90adcfff'], + }), + ('threejs', '0.3.3', { + 'checksums': ['76c759c8b20fb34f4f7a01cbd1b961296e1f19f4df6dded69aae7f1bca80219c'], + }), + ('LaplacesDemon', '16.1.6', { + 'checksums': ['57b53882fd7a195b38bbdbbf0b17745405eb3159b1b42f7f11ce80c78ab94eb7'], + }), + ('rda', '1.2-1', { + 'checksums': ['37038a9131c9133519f5e64fa1a86dbe28b21f519cf6528503234648a139ae9a'], + }), + ('sampling', '2.10', { + 'checksums': ['fdec976ec0abfb5c690049d76f89ebcb8ab3650e2eb28a5b54c3984d17372775'], + }), + ('lda', '1.5.2', { + 'checksums': ['95d354786e002352a973052df993b9d3acfc9f9598a053afb95ac27c7e150fd4'], + }), + ('jiebaRD', '0.1', { + 'checksums': ['045ee670f5378fe325a45b40fd55136b355cbb225e088cb229f512c51abb4df1'], + }), + ('jiebaR', '0.11', { + 'checksums': ['adde8b0b21c01ec344735d49cd33929511086719c99f8e10dce4ca9479276623'], + }), + ('hdm', '0.3.2', { + 'checksums': ['3354b22752f0aa0c0d9c8c12b38810202b6380f2587e539be11d9a358412fe6a'], + }), + ('abe', '3.0.1', { + 'checksums': ['66d2e9ac78ba64b7d27b22b647fc00378ea832f868e51c18df50d6fffb8029b8'], + }), + ('SignifReg', '4.3', { + 'checksums': ['f755808fcb618582acb862729b20e267d9c2214f22e6e7a0c8d29073d8faa7b8'], + }), + ('bbmle', '1.0.25.1', { + 'checksums': ['d92a0cf819fe4c08b8eb17f5e03275c8accde7f3b54f990cbba5ab926575b60b'], + }), + ('emdbook', '1.3.13', { + 'checksums': ['26044b7ea1b42304b4dfde48afa94dd487acf979da4db2bf670ba41222083c19'], + }), + ('SOAR', '0.99-11', { + 'checksums': ['d5a0fba3664087308ce5295a1d57d10bad149eb9771b4fe67478deae4b7f68d8'], + }), + ('rasterVis', '0.51.6', { + 'checksums': ['61bd0d19d045b50c6764f3a7c95ce1e734af9e5f964449825d002afe02109489'], + }), + ('tictoc', '1.2.1', { + 'checksums': ['8fcdb7c9a1e4b4817bcab654effd64dea6ec749a7901d4060d5b5c625fc88833'], + }), + ('ISOcodes', '2024.02.12', { + 'checksums': ['02cb7b918034085dffcba0d329a2bc52514873f898a3a716560ebf17b57ae2e6'], + }), + ('stopwords', '2.3', { + 'checksums': ['c5ec1c6ab1bad1786d87d7823d4b63abc94d2fd84ed7d8e985906e96fb6321b2'], + }), + ('janeaustenr', '1.0.0', { + 'checksums': ['b4c32ee1395ee4a8efe714c535c0fe578b0dbf5f3bb85b41fa5cc87569b8e8aa'], + }), + ('SnowballC', '0.7.1', { + 'checksums': ['753cf13f3206751662c03b1cf39bce9e680024f6d9f8503b836a83797181c034'], + }), + ('tokenizers', '0.3.0', { + 'checksums': ['24571e4642a1a2d9f4f4c7a363b514eece74788d59c09012a5190ee718a91c29'], + }), + ('hunspell', '3.0.3', { + 'checksums': ['fdaa1473a62dff2a5923b9bd958d87e546069ca22ce113f44e88c761338442f3'], + }), + ('topicmodels', '0.2-16', { + 'checksums': ['0d5c9c65dd7ba031ba81adc0984d3e36b0309ada2204644bf816370ae656e905'], + }), + ('tidytext', '0.4.2', { + 'checksums': ['0cf4180c2ab9fdb158337a7bfb6ba32f15fb61aae28abce425deaa5933ed2d54'], + }), + ('splitstackshape', '1.4.8', { + 'checksums': ['656032c3f1e3dd5b8a3ee19ffcae617e07104c0e342fc3da4d863637a770fe56'], + }), + ('grImport2', '0.3-1', { + 'checksums': ['216a1a5bb18c7a7dfb13c6c162228c6c81c45408f04d7784b6e60ae6cd4745d2'], + }), + ('preseqR', '4.0.0', { + 'checksums': ['0143db473fb9a811f9cf582a348226a5763e62d9857ce3ef4ec41412abb559bc'], + }), + ('idr', '1.3', { + 'checksums': ['6b3910dc48495439cd01828f8999823864a6712f73560ee3e6c903065c67d1e4'], + }), + ('entropy', '1.3.1', { + 'checksums': ['6f5a89f5ce0e90cbed1695b81259326c976e7a8f538157e223ee5f63b54412b8'], + }), + ('kedd', '1.0.4', { + 'checksums': ['bb944389a61cff22bb3bdde938a0ff6c16700a1ca725ef36b391b97812c45b26'], + }), + ('HiddenMarkov', '1.8-13', { + 'checksums': ['7186d23e561818f3e1f01376a4fb2af9ccee775ce5afc1e3175f3b07a81db515'], + }), + ('lmerTest', '3.1-3', { + 'checksums': ['35aa75e9f5f2871398ff56a482b013e6828135ef04916ced7d1d7e35257ea8fd'], + }), + ('distributional', '0.4.0', { + 'checksums': ['09b5f3279bed4c79575f75d5f7f5e3e593c7838434a78c89f0b7184e8f20e602'], + }), + ('posterior', '1.5.0', { + 'checksums': ['4a10307fcae321f2cd4ca7871504a0c6c9152b8473dc9a033721e8dcda18e2de'], + }), + ('loo', '2.7.0', { + 'checksums': ['7664f331555e569d6037100048681e3a696fb9ca2e87907712eb54faa85bcb36'], + }), + ('RcppParallel', '5.1.7', { + 'checksums': ['f9c30eb9ce1abffc590825d513d6d28dcbe970e36032dd7521febf04e905b29c'], + }), + ('StanHeaders', '2.32.9', { + 'checksums': ['27b0feb34e1200193e3a31a951d28c5adc91c93dc0454732545b8078132e0b33'], + }), + ('V8', '4.4.2', { + 'installopts': '--configure-vars="INCLUDE_DIR=$CPATH LIB_DIR=$LIBRARY_PATH"', + 'preinstallopts': "export CPATH=$EBROOTNODEJS/include/node:$CPATH && ", + 'checksums': ['e7bc35f3420f5f537121d681a90c16a74b36dc17210c9425e7f03842493a9670'], + }), + ('QuickJSR', '1.2.2', { + 'checksums': ['51842f846585c8dfdab155eb5a26be0735cae280fa1c1bff1907d718525968ed'], + }), + ('rstan', '2.32.6', { + 'checksums': ['3390d00191bbd3b0739dd19fe437b99a041a6b04be208877b48419d1348a1a70'], + }), + ('Rborist', '0.3-7', { + 'checksums': ['011efef9e6f304f752bd5013627dc8482f0e9d4cf1ec49503e97d3718f542596'], + }), + ('VSURF', '1.2.0', { + 'checksums': ['c027b1e19762f1eaf4a559c2592f3530210fefd21ee3d7c787c73b776c683393'], + }), + ('mRMRe', '2.1.2.1', { + 'checksums': ['d53c392e82a437005b71d0e8b97350d0237608fffafe087700fe7f6770167fd9'], + }), + ('dHSIC', '2.1', { + 'checksums': ['94c86473790cf69f11c68ed8ba9d6ae98218c7c69b7a9a093f235d175cf83db0'], + }), + ('ggsci', '3.2.0', { + 'checksums': ['41d8ed4c01c3740028bdf2ba9c5550f1142061e4a40c93b1d2160719c59c3c4a'], + }), + ('ggsignif', '0.6.4', { + 'checksums': ['112051af425a0c0f2998ce187dacad066bc16f55af01e3e7b76d62ff6954b20a'], + }), + ('corrplot', '0.92', { + 'checksums': ['e8c09f963f9c4837036c439ebfe00fa3a6e462ccbb786d2cf90850ddcd9428bd'], + }), + ('rstatix', '0.7.2', { + 'checksums': ['e0c6f5ab1d9c5d84713defabc5d149aad3d55944cffdb903cc128b694e5221a1'], + }), + ('ggfan', '0.1.3', { + 'checksums': ['5c888b203ecf5e3dc7a317a790ca059c733002fbca4b4bc1a4f62b7ded5f70dc'], + }), + ('ggpubr', '0.6.0', { + 'checksums': ['2e6ec5d8151991d17ef8832259cf545fa0d1a50b326ba8c1c4657700171df774'], + }), + ('yaImpute', '1.0-34', { + 'checksums': ['b4c898c95fca784480bbbc239c78c85dc9f45a96c34c563ea7e81248ef8a8a73'], + }), + ('intrinsicDimension', '1.2.0', { + 'checksums': ['6cc9180a83aa0d123f1e420136bb959c0d5877867fa170b79536f5ee22106a32'], + }), + ('leiden', '0.4.3.1', { + 'checksums': ['a9ecbbcfa2724d8fdd0133af569278e036b25b6e2cbb23d453092cc6b3fc30e2'], + }), + ('sctransform', '0.4.1', { + 'checksums': ['5f6be7f8be543e4c32c8007207b603a750881459370b7bb5afd63e8c8fabf171'], + }), + ('packrat', '0.9.2', { + 'checksums': ['69df5943257e6c4d06f3d907241b668b53dedece72158ca935260b8b8e1672d7'], + }), + ('colourpicker', '1.3.0', { + 'checksums': ['c7f2618cd1ae1f7ac15aee072c648e6494dfff6714e13dc7cd1da993d1102510'], + }), + ('ggExtra', '0.10.1', { + 'checksums': ['6879edfe8e3905a2c299cbd18777422223ad30042bc6e20614ca5109a75de82c'], + }), + ('findpython', '1.0.8', { + 'checksums': ['0f8a90cbafd4949c0333a86808383a358fb7ec3268953d8a4887d5d22264cdb7'], + }), + ('argparse', '2.2.3', { + 'checksums': ['a50cc4e1221f063e472a8cfe7e881a1d4abed5ef93cf40d5f65a2528cdfd2674'], + }), + ('intergraph', '2.0-4', { + 'checksums': ['585f2f9fa92aa52022dfdcbe597a3654099ca63c1d4110a0f8e895fa32fc59c9'], + }), + ('ggnetwork', '0.5.13', { + 'checksums': ['6c297ead19dbd89de3278f3705410b757f2d9744bc466d8175105833a4e1fd46'], + }), + ('qqman', '0.1.9', { + 'checksums': ['3f6a931771d375174b78f220471ddd601def9b5c69631931b0992ebbc8c5bc13'], + }), + ('rstantools', '2.4.0', { + 'checksums': ['bff72ca2f0352c6c5d2868823e286fdb73a6ead74508a4124cbcb222c83b4faa'], + }), + ('bayesplot', '1.11.1', { + 'checksums': ['4f71e67391e0135acd3e890989b87025f3f8160242f532a8e1a0ed74ed0f3830'], + }), + ('dygraphs', '1.1.1.6', { + 'checksums': ['c3d331f30012e721a048e04639f60ea738cd7e54e4f930ac9849b95f0f005208'], + }), + ('renv', '1.0.7', { + 'checksums': ['7b60b58a23743803ab167f82f78663e86f778947b2bda07afa12689338794507'], + }), + ('PKI', '0.1-14', { + 'checksums': ['c024e81977b978b705460df96639e3369420bd7e8f4f3242ec796255dc1b7966'], + }), + ('rsconnect', '1.3.1', { + 'checksums': ['47de8a832da493e2a1b3243fb42459a53eb193f75a1143348b7d8c7478cb5557'], + }), + ('shinystan', '2.6.0', { + 'checksums': ['a084856a2d66d8744f2c72e3e19ca35e600a508ed7ef1f7ebed8c7fc0738d529'], + }), + ('optimx', '2023-10.21', { + 'checksums': ['0d732d5604c26af59cfb95b80ed4e226c9c10422e2d82a6cc06b92f9ba6a44b5'], + }), + ('gamm4', '0.2-6', { + 'checksums': ['57c5b66582b2adc32f6a3bb6a259f5b95198e283a96d966a6007e8e48b380c89'], + }), + ('memisc', '0.99.31.7', { + 'checksums': ['b403185850520db18ebd608df85c76df80e6c64af428cdc4e49c2fe487483637'], + }), + ('mclogit', '0.9.6', { + 'checksums': ['9adc5f6d8649960abe009c30d9b4c448ff7d174c455a594cbf104a33d5a36f69'], + }), + ('projpred', '2.8.0', { + 'checksums': ['b383ddc5eca275737b96e4e3e14256b4f4abc4b29d292b5cebf3828d0921a1f6'], + }), + ('brms', '2.21.0', { + 'checksums': ['7289ff33c2a4b83584b7fece0a6aa53fd14b5881a467d417fbca5dbf62ec5d58'], + }), + ('drgee', '1.1.10', { + 'checksums': ['e684f07f7dfec922380d4202922c11094f859721f77b31ff38b0d35d0f42c743'], + }), + ('stdReg', '3.4.1', { + 'checksums': ['285335dbe29b6898641e1151ab2f06acf76c6f4d6fbeadd66d151c25d7e38a74'], + }), + ('mcmcse', '1.5-0', { + 'checksums': ['4a820dc22c48efd32b7f9d1e1b897b4b3f165cd64b2ff85ba7029621cf9e7463'], + }), + ('copCAR', '2.0-4', { + 'checksums': ['8b4ed53c58a665f70e48bdca689a992a81d5ecb5a6051ca7361d3870e13c77f3'], + }), + ('batchmeans', '1.0-4', { + 'checksums': ['8694573009d9070a76007281407d3314da78902e122a9d8aec1f819d3bbe562c'], + }), + ('ngspatial', '1.2-2', { + 'checksums': ['3fa79e45d3a502a58c1454593ec83dfc73144e92b34c14f617a6126557dd0d26'], + }), + ('BIGL', '1.9.1', { + 'checksums': ['c2136a7a5b3a6b71c8ba3cdfc7e83c14b400c9197c1544f0967297659e3b8631'], + }), + ('drugCombo', '1.2.1', { + 'checksums': ['9a605c655c159604033558d757711e6d83d33dfc286c1280f722d4cb7d130f80'], + }), + ('betareg', '3.1-4', { + 'checksums': ['5106986096a68b2b516215968158589b71969ce7912879253d6e930355a18101'], + }), + ('unmarked', '1.4.1', { + 'checksums': ['1c277248ad00122f404aabd0f0bbdeaf1cd69c58b65faaf23e36ee39f1e750c7'], + }), + ('maxlike', '0.1-11', { + 'checksums': ['6dde7bb4a46d5509a1fee024c2fd1d13c82e14a80806969ec89359103ade01e9'], + }), + ('coxme', '2.2-20', { + 'checksums': ['a0eeeadaabe81458b4fe80d26ca9770ff17dc3a2a41a37b2d1b09fadb887cb62'], + }), + ('AICcmodavg', '2.3-3', { + 'checksums': ['4055b5f1fc12917b9f812c056e6a2dbf23bbd0169e468f567306ddf29d699f7a'], + }), + ('pacman', '0.5.1', { + 'checksums': ['9ec9a72a15eda5b8f727adc877a07c4b36f8372fe7ed80a1bc6c2068dab3ef7c'], + }), + ('spaa', '0.2.2', { + 'checksums': ['a5a54454d4a7af473ce797875f849bd893005cb04325bf3e0dbddb19fe8d7198'], + }), + ('maxnet', '0.1.4', { + 'checksums': ['fd21e5ecf3c1ac00ef1bbe79fab4cdd62789e0c4c45f126f1b64bda667238216'], + }), + ('oai', '0.4.0', { + 'checksums': ['f540de066de5538e303cd535cbd2e771b40474bc2c6e8d08a4894a868543ee33'], + }), + ('wellknown', '0.7.4', { + 'checksums': ['483e6fc43edf09ed583e74ce5ca7e2d7838ef8a32291e06d774c37546eed1a34'], + }), + ('rgbif', '3.8.0', { + 'checksums': ['8b5cd096404291d39778ec4fed36cd25719fa0ca4225866e67566c4d346d2ce8'], + }), + ('rgdal', '1.6-7', { + 'checksums': ['555cedfdadb05db90b061d4b056f96d8b7010c00ea54bc6c1bbcc7684fadae33'], + }), + ('rgeos', '0.6-4', { + 'checksums': ['9d03c4de96fd3fad55ff8d1ff8113dcaaa00f15d9d0588e54c9f91751bcede11'], + }), + ('mapproj', '1.2.11', { + 'checksums': ['db2d201cc939de26717566066bf44225a967ccde6fc34731af845f03c086347d'], + }), + ('rbison', '1.0.0', { + 'checksums': ['9957e5f85ce68f5dd0ddc3c4b2b3c9d2f52d6f37587e1022ab8a44863534a83c'], + }), + ('rebird', '1.3.0', { + 'checksums': ['b238d3f246aa0249145894e1f3a90f46902f6615fc2f23b24c99bb5feecc55d3'], + }), + ('rvertnet', '0.8.4', { + 'checksums': ['b1826899f33640541752f2b68ed4d23530fe62744ac4714adf79ff748fc6701a'], + }), + ('ridigbio', '0.3.8', { + 'checksums': ['e518dbaeaf7f0dd0b833d83a6a094e07c5bd84935279c9e35bb69fe35ee00288'], + }), + ('spocc', '1.2.3', { + 'checksums': ['ee14de78a9a91bf4220b3317d724f9e4953fda8b5478b2083690c984903db951'], + }), + ('spThin', '0.2.0', { + 'checksums': ['2e997afb79a2a990eded34c71afaac83986669cfa9ac51b15ae3f2b558902048'], + }), + ('RPostgreSQL', '0.7-6', { + 'checksums': ['385939708b6a3657663409f91e165ded0ff5268d1dc6225e0f9b34764baf2d2c'], + }), + ('fasterize', '1.0.5', { + 'checksums': ['d44f101aec29aee285c4c7b578e26d11b6add423336ace90a7c22e07cfc1c3b4'], + }), + ('BIEN', '1.2.6', { + 'checksums': ['fa7a25d89f26c10686fb4ab4d0aa704beb50dc44b173ff56abe4ab3e5991f99f'], + }), + ('rangeModelMetadata', '0.1.5', { + 'checksums': ['289620500522d489aafbb03c85f68182ef0a6701fed5f9d09b55fae337e2647b'], + }), + ('ENMeval', '2.0.4', { + 'checksums': ['6d9f3c460fa7ab3131cede904fcb9280cf69f4fdd43f67115a3abcb8ed5b64d1'], + }), + ('plotmo', '3.6.3', { + 'checksums': ['6917cd8185325f1f2998fb14def9e6a8d93f1b708cf70d7c443d3960c9189b7b'], + }), + ('earth', '5.3.3', { + 'checksums': ['786a0fcabb3db13e0e0a4ba61ecccb7e171030b39bc97926f8e7159485d2f572'], + }), + ('mda', '0.5-4', { + 'checksums': ['f25f7f28807d0fa478b1b55eb9d026ebc30577d9d5ff288f9abfe1f3fdb8a759'], + }), + ('xgboost', '1.7.7.1', { + 'checksums': ['f7912ccf3a583a27208f74ca15c3b272cc930bae6b10ae7e5958ff2951ee9723'], + }), + ('biomod2', '4.2-5-2', { + 'checksums': ['1c4ca427b8d6af54de548023dcbe25c7e9cbea7afb684c58b66f4210af9eb4e5'], + }), + ('poLCA', '1.6.0.1', { + 'checksums': ['ed8c60a42bff0402c9ba2f9ce1422dd171e711c1a64498c4d96010ddb29f6b16'], + }), + ('PermAlgo', '1.2', { + 'checksums': ['aa2c774d6c6dcfeec882c1936e8723ef49bd36030fb10c17ca60bb9d4a519443'], + }), + ('coxed', '0.3.3', { + 'checksums': ['d0d6cb8fea9516b3c63b34d0d81f3804c18a07f97a83e51555575c8ed4c75626'], + }), + ('testit', '0.13', { + 'checksums': ['90d47168ab6bdbd1274b600b457626ac07697ce09792c92b2043be5f5b678d80'], + }), + ('NISTunits', '1.0.1', { + 'checksums': ['eaccd68db5c73d6a089ce5b323cdd51bc6a6a58ce467987158ba8c9be6a0a94e'], + }), + ('celestial', '1.4.6', { + 'checksums': ['9f647f41465ac65b254717698f1978871c378ad8e6ccaa693abf579437069abe'], + }), + ('RPMM', '1.25', { + 'checksums': ['f04a524b13918062616beda50c4e759ce2719ce14150a0e677d07132086c88c8'], + }), + ('RefFreeEWAS', '2.2', { + 'checksums': ['de2812f166caabf6ea01c0533402e5cd9d8a525a2a7583e4757decf22319caab'], + }), + ('wordcloud', '2.6', { + 'checksums': ['53716954430acd4f164bfd8eacd7068a908ee3358293ded6cd992d53b7f72649'], + }), + ('JADE', '2.0-4', { + 'checksums': ['d4b3d65a33cae454d3ab13343bceabfb3f6b8004ac64ae7bd86dee92a1cd2055'], + }), + ('awsMethods', '1.1-1', { + 'checksums': ['50934dc20cf4e015f1304a89de6703fed27e7bd54c6b9fc9fb253cdf2ecb7541'], + }), + ('aws', '2.5-5', { + 'checksums': ['b27cb2795cb59592d474cfaf49a21657a8878404da4f01c556f7323e953b4c5b'], + }), + ('ruv', '0.9.7.1', { + 'checksums': ['a0c54e56ba3d8f6ae178ae4d0e417a79295abf5dcb68bbae26c4b874734d98d8'], + }), + ('mhsmm', '0.4.21', { + 'checksums': ['293544afb194934b1d58cf88c6f8c372f537745514b6e428cf83ae62e87d2bba'], + }), + ('dbarts', '0.9-28', { + 'checksums': ['d2e4b4ee1c191e7c506be3fec5a5e877c1b36754cba558bd75eaac9cc6ac0138'], + 'preinstallopts': local_dbarts_preinstallopts, + }), + ('proftools', '0.99-3', { + 'checksums': ['e034eb1531af54013143da3e15229e1d4c2260f8eb79c93846014db3bdefb724'], + }), + ('NCmisc', '1.2.0', { + 'checksums': ['26fcfbc79810f23a28389a5ce5519e6ddc2470c5e924ba8cf4dd19a1b0fd9f83'], + }), + ('reader', '1.0.6', { + 'checksums': ['905c7c5a1b035ac8213fc533fa26e511abfeea40bd22e3edfde42a49074e88f4'], + }), + ('gnumeric', '0.7-10', { + 'checksums': ['f6fcd9012f2fa777127c86ba520d8dc834f4ea746a6e29623edd072479191c75'], + }), + ('tcltk2', '1.2-11', { + 'checksums': ['ad183ae3b7190501504a0589e0b3be480f04267303e3384fef00987446a37dc5'], + }), + ('minty', '0.0.1', { + 'checksums': ['cfbdc6603c8fb54ea4d43091e2aee4c99212e6e20a335ed89576156d86237acd'], + }), + ('readODS', '2.3.0', { + 'checksums': ['1e120ff8fdb34c7e00f07726b4843cfaeee9c680bfdc2982e83422c24e4c0491'], + }), + ('nortest', '1.0-4', { + 'checksums': ['a3850a048181d5d059c1e74903437569873b430c915b709808237d71fee5209f'], + }), + ('EnvStats', '2.8.1', { + 'checksums': ['12952b9eaa64b7bdbaaa5c6b7acb3aa1028ddfa4e5de7ddfea54f900c452d6a6'], + }), + ('outliers', '0.15', { + 'checksums': ['cc31d7f2faefd2c3a27f8ce78c7e67d3b321dcd6690292fad2468125e5e635fb'], + }), + ('gWidgets2', '1.0-9', { + 'checksums': ['d4d9ef7b2788efeb8209aa8dd610af4cd86286392fbdf9ea70bcfeafda95d4c5'], + }), + ('gWidgets2tcltk', '1.0-8', { + # need to run installation via xvfb-run to avoid problems on headless systems: + # no DISPLAY variable so Tk is not available + # [tcl] invalid command name "font" + 'preinstallopts': "xvfb-run ", + 'checksums': ['10399cc636eeeb5484c3379970c37c56df10d979bf866a35b66d0c75b7222c0a'], + # skip 'import' check with library(gWidgets2tcltk), since it also fails on headless systems... + 'modulename': False, + }), + ('mgsub', '1.7.3', { + 'checksums': ['c9ae2560fe2690bedc5248af3fc89e7ef2bc6c147d46ced28f9824584c3791d5'], + }), + ('ie2misc', '0.9.1', { + 'checksums': ['f1db0c66c8fa05e99c4059c1799abc3eb7effd7113baf03f38d26853ac05c425'], + }), + ('assertive.base', '0.0-9', { + 'checksums': ['4bf0910b0eaa507e0e11c3c43c316b524500c548d307eb045d6f89047e6ba01e'], + }), + ('assertive.properties', '0.0-5', { + 'checksums': ['b68954f53082561f0242682611bf3373e0bf30d8ac2256d82474edc5f992f4dd'], + }), + ('assertive.types', '0.0-3', { + 'checksums': ['ab6db2eb926e7bc885f2043fab679330aa336d07755375282d89bf9f9d0cb87f'], + }), + ('assertive.numbers', '0.0-2', { + 'checksums': ['bae18c0b9e5b960a20636e127eb738ecd8a266e5fc29d8bc5ca712498cd68349'], + }), + ('assertive.strings', '0.0-3', { + 'checksums': ['d541d608a01640347d661cc9a67af8202904142031a20caa270f1c83d0ccd258'], + }), + ('assertive.datetimes', '0.0-3', { + 'checksums': ['014e2162f5a8d95138ed8330f7477e71c908a29341697c09a1b7198b7e012d94'], + }), + ('assertive.files', '0.0-2', { + 'checksums': ['be6adda6f18a0427449249e44c2deff4444a123244b16fe82c92f15d24faee0a'], + }), + ('assertive.sets', '0.0-3', { + 'checksums': ['876975a16ed911ea1ad12da284111c6eada6abfc0118585033abc0edb5801bb3'], + }), + ('assertive.matrices', '0.0-2', { + 'checksums': ['3462a7a7e11d7cc24180330d48cc3067cf92eab1699b3e4813deec66d99f5e9b'], + }), + ('assertive.models', '0.0-2', { + 'checksums': ['b9a6d8786f352d53371dbe8c5f2f2a62a7866e30313f268e69626d5c3691c42e'], + }), + ('assertive.data', '0.0-3', { + 'checksums': ['5a00fb48ad870d9b3c872ce3d6aa20a7948687a980f49fe945b455339e789b01'], + }), + ('assertive.data.uk', '0.0-2', { + 'checksums': ['ab48dab6977e8f43d6fffb33228d158865f68dde7026d123c693d77339dcf2bb'], + }), + ('assertive.data.us', '0.0-2', { + 'checksums': ['180e64dfe6339d25dd27d7fe9e77619ef697ef6e5bb6a3cf4fb732a681bdfaad'], + }), + ('assertive.reflection', '0.0-5', { + 'checksums': ['c2ca9b27cdddb9b9876351afd2ebfaf0fbe72c636cd12aa2af5d64e33fbf34bd'], + }), + ('assertive.code', '0.0-4', { + 'checksums': ['2f820474ed20e06f65b284962c87cd1e85220a11cc7fcde09716f0eee5821387'], + }), + ('assertive', '0.3-6', { + 'checksums': ['c403169e83c433b65e911f7fd640b378e2a4a4765a36063584b8458168a4ea0a'], + }), + ('rdrop2', '0.8.2.1', { + 'checksums': ['b9add765fe8e7c966f0d36eef939a9e38f253958bd2a3c656b890cbb0366300b'], + }), + ('Exact', '3.2', { + 'checksums': ['53b4e20cbb57615970c572fc4e7a780a510bde8b5deadec3880095f6e17a6328'], + }), + ('lmom', '3.0', { + 'checksums': ['4b0ae8638a63b45ddedfd65c15e3206d34e947a2b5d31e9aa8c55446d69a0291'], + }), + ('gld', '2.6.6', { + 'checksums': ['ea23e9781207b5d47ed04e4d5758d9652cab5d1eedcf9fbc9c2ee4d3babffdc4'], + }), + ('DescTools', '0.99.54', { + 'checksums': ['470a16405d52d7e8595ac025a0d2bf50b78edaebe83af358903e201168a80b9b'], + }), + ('orthopolynom', '1.0-6.1', { + 'checksums': ['ec4a6ed266532f2f6d37a4ca6bd1b74c1df28a8c2caeab60e5d6af15bdbfe2c5'], + }), + ('gaussquad', '1.0-3', { + 'checksums': ['a3337ce52bc53435cb4565a38bf48b72b384be397d2e86bb66f62973004dc810'], + }), + ('nlsem', '0.8-1', { + 'checksums': ['0674ec2a1ae7e50b08ee1b156674c2f2100258b14d6a9068f7dd6ad1ee128377'], + }), + ('tableone', '0.13.2', { + 'checksums': ['b1cf15579abd4240e24435d2d9aad255c839d2a0293e28cb2eef0c808c4727af'], + }), + ('jstable', '1.2.6', { + 'checksums': ['b759553446892a4b8697be0c696f5d2c5aafdb64cff1ca1b22557687ea7218bd'], + }), + ('RCAL', '2.0', { + 'checksums': ['10f5f938a8322d8737159e1e49ce9d12419a5130699b8a19c6ca53d6508da8cc'], + }), + ('stargazer', '5.2.3', { + 'checksums': ['208e9b48a11cf56ce142731c204f3d2bcb5b68719f84309a36362cd925414265'], + }), + ('sensemakr', '0.1.4', { + 'checksums': ['6a1354f05392fa9343b90f69a54022c995651fb3c3d05cb08fa088ef52258caf'], + }), + ('CompQuadForm', '1.4.3', { + 'checksums': ['042fc56c800dd8f5f47a017e2efa832caf74f0602824abf7099898d9708660c4'], + }), + ('nonnest2', '0.5-7', { + 'checksums': ['e440c2464b3bd3b452e02583bb280eecba6acecf0f2c04b6b9fe4dcdd128db3e'], + }), + ('blavaan', '0.5-5', { + 'checksums': ['a8d3bc5e9d15a2e8496950e87ed3c6bc6d769e761ec068e1f063f2d255330b6d'], + }), + ('mathjaxr', '1.6-0', { + 'checksums': ['ecc47607111b788d84789459af7f4f9102719f98640b7a23bd5a4eb1a6d3c179'], + }), + ('metadat', '1.2-0', { + 'checksums': ['f0cce5e30c3d256eaf5a41e4f52ffc7108e195016a4b99409e0ab4c2ef58f5b8'], + }), + ('metafor', '4.6-0', { + 'checksums': ['07344cc3bd87b8bd25ef998e9a6ce322ae8e448ef5af06ec3e79631724e18666'], + }), + ('RNifti', '1.7.0', { + 'checksums': ['e58cf73a0f5fbf5d6a2c845bfdeea193eb5262c73d0f329beae17d68f40e18e8'], + }), + ('oro.nifti', '0.11.4', { + 'checksums': ['efe4f5d2c2e37ff6c3e9250f54ef775e4d452c1334f781f22f219ed53148b606'], + }), + ('fmri', '1.9.12', { + 'checksums': ['d8b55f8867bb0487d1a8241b340099c41d990ae5aa49768b2dc0f9db58af65b3'], + }), + ('linkcomm', '1.0-14', { + 'checksums': ['36f1557c65d862fc87635eedfad77f18a5deb66da00895e50e2d5eac0f23b597'], + }), + ('rnetcarto', '0.2.6', { + 'checksums': ['4f28ae62748654cb6f90e1ffa17b05bb8b89eb6a20262d9c5d39cb862f71dc91'], + }), + ('optextras', '2019-12.4', { + 'checksums': ['59006383860826be502ea8757e39ed94338f04d246c4fc398a088e004d8b13eb'], + }), + ('setRNG', '2024.2-1', { + 'checksums': ['e3b21b08b7db3c2c06543a21718e1c18a2b2d2ddf4c92f0e44841d10f55d5c40'], + }), + ('Rvmmin', '2018-4.17.1', { + 'checksums': ['55000ac4ff57d42f172c46c7d6b0a603da3b65866d6440d6b32bac4d2b81814e'], + }), + ('Rcgmin', '2022-4.30', { + 'checksums': ['2684b8e7fb970da2afbc00e482031cf4447416249d04c4c1740400ad112fb911'], + }), + ('optimr', '2019-12.16', { + 'checksums': ['73b1ed560ffd74599517e8baa4c5b293aa062e9c8d50219a3a24b63e72fa7c00'], + }), + ('DMCfun', '3.5.4', { + 'checksums': ['2c2ab38ed5ae140e1d5d045a1d4b95ef9d286b13467301be37477258de87804f'], + }), + ('miceadds', '3.17-44', { + 'checksums': ['6ef69dd1ac3b547a1450ca54c719c5d1f983a585207cb09ae3ad6b42a8cc2165'], + }), + ('visdat', '0.6.0', { + 'checksums': ['104acdbb9d41167b861ab24de0e1e1e14f61c1b476bac112fcbc6e47c157e598'], + }), + ('UpSetR', '1.4.0', { + 'checksums': ['351e5fee64204cf77fd378cf2a2c0456cc19d4d98a2fd5f3dac74b69a505f100'], + }), + ('norm', '1.0-11.1', { + 'checksums': ['c2ffe6c30fc203337bde49ef630a740141604d8e648c558e58c20116c47963bc'], + }), + ('naniar', '1.1.0', { + 'checksums': ['a94c46c3a78893bd935a0a51adb6a523915afb35427a56ce650b1e1ab28c6f44'], + }), + ('stringdist', '0.9.12', { + 'checksums': ['e1843452ff4184b8d3bc5168732c0c65d3fce11f0df9fcf92173a22ef92e66c4'], + }), + ('image.binarization', '0.1.3', { + 'checksums': ['ecc844bdd9bf15b88ce1e1afc8321c177bdc8ec32618c22102b1e8b02b36e00e'], + }), + ('lassosum', '0.4.5', { + 'source_urls': ['https://github.com/tshmak/%(name)s/releases/download/v%(version)s/'], + 'sources': ['%(name)s_%(version)s.tar.gz'], + 'checksums': ['18c0d0b5022bcf81a9bf1b3b6647da3e080f221828b473ea2a45a9bf98474fbc'], + }), + ('lslx', '0.6.11', { + 'checksums': ['373cfb1e79174b568dac254fab02d99bf79b830218bf18f0cc592af6fef853d6'], + }), + ('truncnorm', '1.0-9', { + 'checksums': ['5156acc4d63243bf95326d6285b0ba3cdf710697d67c233a12ae56f3d87ec708'], + }), + ('Rsolnp', '1.16', { + 'checksums': ['3142776062beb8e2b45cdbc4fe6e5446b6d33505253d79f2890fe4178d9cf670'], + }), + ('regsem', '1.9.5', { + 'checksums': ['7392bd644efe82f96da0df470a962de398f1d0162273cba1ff31c2ecd7f17a53'], + }), + ('semPLS', '1.0-10', { + 'checksums': ['cb587ccfdaf970f426dc7146035c7e010b1c51c17bf4fc089fd796eda58db460'], + }), + ('GxEScanR', '2.0.2', { + 'checksums': ['6d42fd15d83dd1491405b282d26fa472f9f9902a9dc68836d6a48b459ada6a4c'], + }), + ('admisc', '0.35', { + 'checksums': ['cf4b5b3f09f0fd0ad085d97bd589be0cfe6652e5a365f7b09c0e93515b5aed3f'], + }), + ('polycor', '0.8-1', { + 'checksums': ['f05f53e0b5c992de0e5b4c6b2e998148cf83310358821e1bba180d81face0509'], + }), + ('multipol', '1.0-9', { + 'checksums': ['4ec305565c214872705f7d5ea4928c8761750663d664a77f1676d81a1ca0c632'], + }), + ('symmoments', '1.2.1', { + 'checksums': ['9a6be1f8fe44f6ab5a1790e870fd8b18de1686a48a14a9fca2d035bfb5458672'], + }), + ('rngWELL', '0.10-9', { + 'checksums': ['9969cc10be6d18155d2b2de93381c52e7f720c2b1b3f2554fa8bfa84ceb7cacb'], + }), + ('randtoolbox', '2.0.4', { + 'checksums': ['94da14953e4ffc7981d7a9398622082c4eda3bd9d912d1437b527d949da39e4b'], + }), + ('TruncatedNormal', '2.2.2', { + 'checksums': ['aef567e8962a64d1afbdfd98ab8f385f32966c3c42acb54ee20f02dceab18e15'], + }), + ('cSEM', '0.5.0', { + 'checksums': ['25ae115520aab7d916da9ded1f87b8519c4e15101c4adef2284c51eb03d81728'], + }), + ('cubelyr', '1.0.2', { + 'checksums': ['18b10f1fe561305a1e115a438460264b88b301b3e8c086b931500a798be39b94'], + }), + ('furrr', '0.3.1', { + 'checksums': ['0d91735e2e9be759b1ab148d115c2c7429b79740514778828e5dab631dc0e48b'], + }), + ('broom.mixed', '0.2.9.5', { + 'checksums': ['959fa6cd26135ad408d3ee447d4423919c9cdaa9a6ecc4396f858c90d30b5ab3'], + }), + ('DiceKriging', '1.6.0', { + 'checksums': ['ab5d1332809f2bb16d156ed234b102eb9fbd6de792e4291f9f6ea4652215cb49'], + }), + ('grf', '2.3.2', { + 'checksums': ['c0392b6f6e20058cc6d5cdd5b5c1e5298bc42906cee45d04143adc4d6162427d'], + }), + ('twang', '2.6', { + 'checksums': ['0b28382af11cebf675cdffc66990e011d751e9703d27e2ed41895ead5e667fdb'], + }), + ('neuralnet', '1.44.2', { + 'checksums': ['5f66cd255db633322c0bd158b9320cac5ceff2d56f93e4864a0540f936028826'], + }), + ('PCAmatchR', '0.3.3', { + 'checksums': ['5dc9d8bb4c0020b5e51a53a4fa71afa9adc6b907ea618b231f5cfc2877a49779'], + }), + ('origami', '1.0.7', { + 'checksums': ['b44034541ac358e0686682684c40e9a1de8d78c7913e56e4d3dbe41a2a55c62c'], + }), + ('hal9001', '0.4.6', { + 'checksums': ['1123288b603f97de98b42178ab5b4809536f64d7884a46b829795245eacd08dd'], + }), + ('cobalt', '4.5.5', { + 'checksums': ['076c1956e1a24d3ded5ac6227bf05cb294e103dc0d02d825e65b72d2c5f62ec0'], + }), + ('CBPS', '0.23', { + 'checksums': ['ed8fe09b642db459a516bdeb03a49e718a7d5ad915cbf82400029508efe9b32d'], + }), + ('SBdecomp', '1.2', { + 'checksums': ['0be4e1c9e8bed87fd1712e62346a97148a1a295ff56981e832921cc390006e5c'], + }), + ('naturalsort', '0.1.3', { + 'checksums': ['cd38a9c5f323f61459e6096cdbf4493851d40497baf671af4f8dfe9a7c00e857'], + }), + ('lwgeom', '0.2-14', { + 'checksums': ['26db6cf7dbc8cf43a70e5e2a34941a1c4b65e182f86f58d64ff9f614b3be929c'], + }), + ('finalfit', '1.0.7', { + 'checksums': ['4fb9fa3a8eae9ea80277ca3f256947d6f9485ab66ad2e3bbe429a586e79eda12'], + }), + ('bigD', '0.2.0', { + 'checksums': ['bca9eb0c9a231b159b97650884b1a7a490bc3bf4edef11cc12db06fb15c6ff5f'], + }), + ('juicyjuice', '0.1.0', { + 'checksums': ['64f5418b2a4794b47f0525baaf101beb4f1374ea22f38d7d604f5118bdb6e12a'], + }), + ('reactR', '0.5.0', { + 'checksums': ['e79e3f37c2f28ae70c912efe203dbca35094ce017e497421c049e1221817f192'], + }), + ('reactable', '0.4.4', { + 'checksums': ['b4aae6be2dd85aaa5226067415e501abc139e99499bc62c539630eeafdaf6af2'], + }), + ('gt', '0.10.1', { + 'checksums': ['c56760e2dd4490b755c569d5fbc25f38b33096cefec5bf24a01cb198e4cc3387'], + }), + ('gtsummary', '1.7.2', { + 'checksums': ['ddc225f1c3a629b47bce85b64229d2a99c46c7bf22b88a6bb6cc728e76d34b0a'], + }), + ('ncdf4', '1.22', { + 'checksums': ['b9a9a2004f4c008d665afbe617f4e4b45e57dc70e303c8ec341aa5a51fbb1210'], + }), + ('geex', '1.1.1', { + 'checksums': ['a1aebb9f73ba8dfe26ee3dc7b0725ccb814b3db5358ba17e417bdfc7eb3e4143'], + }), + ('momentfit', '0.5', { + 'checksums': ['5f68e90545f123790d6ba149a21f07d1885361e4ca748cc93fb13bc443f7c720'], + }), + ('StatMatch', '1.4.2', { + 'checksums': ['852f9f923e18f528af86858e10142800182f87c216636b4d7de4345661ee954f'], + }), + ('stars', '0.6-5', { + 'checksums': ['4fcb12f25ce4351840d24489b8d6ca61eecc0da12f93bfab702701a430d0afac'], + }), + ('rapidjsonr', '1.2.0', { + 'checksums': ['62c94fcdcf5d0fbdfa2f6168affe526bf547c37c16d94e2e1b78d7bf608eed1f'], + }), + ('jsonify', '1.2.2', { + 'checksums': ['3745e962592f021a3deaed8b2f6b99c4f7181f28e095300a96d1c2b08af4af2f'], + 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a/easybuild/easyconfigs/r/R/R-4.4.1-gfbf-2023b.eb b/easybuild/easyconfigs/r/R/R-4.4.1-gfbf-2023b.eb new file mode 100644 index 000000000000..09a46feeaa15 --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-4.4.1-gfbf-2023b.eb @@ -0,0 +1,371 @@ +name = 'R' +version = '4.4.1' + +homepage = 'https://www.r-project.org/' +description = """R is a free software environment for statistical computing + and graphics.""" + +toolchain = {'name': 'gfbf', 'version': '2023b'} + +source_urls = ['https://cloud.r-project.org/src/base/R-%(version_major)s'] +sources = [SOURCE_TAR_GZ] +checksums = ['b4cb675deaaeb7299d3b265d218cde43f192951ce5b89b7bb1a5148a36b2d94d'] + +builddependencies = [ + ('pkgconf', '2.0.3'), + ('Autotools', '20220317'), +] +dependencies = [ + ('X11', '20231019'), + ('Mesa', '23.1.9'), + ('libGLU', '9.0.3'), + ('cairo', '1.18.0'), + ('libreadline', '8.2'), + ('ncurses', '6.4'), + ('bzip2', '1.0.8'), + ('XZ', '5.4.4'), + ('zlib', '1.2.13'), + ('SQLite', '3.43.1'), + ('PCRE2', '10.42'), + ('libpng', '1.6.40'), # for plotting in R + ('libjpeg-turbo', '3.0.1'), # for plottting in R + ('LibTIFF', '4.6.0'), + ('Java', '11', '', SYSTEM), + ('libgit2', '1.7.2'), + ('OpenSSL', '1.1', '', SYSTEM), + ('cURL', '8.3.0'), + ('Tk', '8.6.13'), # for tcltk + ('HarfBuzz', '8.2.2'), # for textshaping + ('FriBidi', '1.0.13'), # for textshaping + +] + +# Some R extensions (mclust, quantreg, waveslim for example) require the math library (-lm) to avoid undefined symbols. +# Adding it to FLIBS makes sure it is present when needed. +preconfigopts = 'export FLIBS="$FLIBS -lm" && ' + +configopts = "--with-pic --enable-threads --enable-R-shlib" +# some recommended packages may fail in a parallel build (e.g. Matrix), and +# we're installing them anyway below +configopts += " --with-recommended-packages=no" + +exts_default_options = { + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz', +} + +# !! order of packages is important !! +# packages updated on 24 June 2024 +exts_list = [ + # include packages that are part of the base installation of R, + # both to make sure they are available (via sanity check), + # and to be able to pass the check for required dependencies when installing extensions in parallel + 'base', + 'compiler', + 'datasets', + 'graphics', + 'grDevices', + 'grid', + 'methods', + 'parallel', + 'splines', + 'stats', + 'stats4', + 'tcltk', + 'tools', + 'utils', + ('rlang', '1.1.4', { + 'checksums': ['f2d74527508bf3287102470beb27de0d234c3cbba399c28d3312f2c83c64a6e1'], + }), + ('Rcpp', '1.0.12', { + 'checksums': ['0c7359cc43beee02761aa3df2baccede1182d29d28c9cd49964b609305062bd0'], + }), + ('R6', '2.5.1', { + 'checksums': ['8d92bd29c2ed7bf15f2778618ffe4a95556193d21d8431a7f75e7e5fc102bf48'], + }), + ('cli', 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['d785ce3975939e28b61048b0e28d881c80904534ff21e5b1a79a0a934124e9f7'], + }), + ('xml2', '1.3.6', { + 'checksums': ['e81991ff99bff3616dde8683c1327194e3ea64fa3b8062f52d8ce32673dd308f'], + }), + ('curl', '5.2.1', { + 'checksums': ['4a7a4d8c08aa1bca2fcd9c58ade7b4b0ea2ed9076d0521071be29baac8adfa90'], + }), + ('sys', '3.4.2', { + 'checksums': ['b7bdce66f0fb681830ea6fb77b5a2c6babb43920abb1eddc733f95c0a63ce5b3'], + }), + ('askpass', '1.2.0', { + 'checksums': ['b922369781934d0ffc8d0c0177e8ace56796c2e6a726f65e460c16f792592cef'], + }), + ('openssl', '2.2.0', { + 'checksums': ['18b8b46ae8db4bd57c7bcc8e10d0bb549ae63e383502051cef86102ab617ddb3'], + }), + ('httr', '1.4.7', { + 'checksums': ['1555e6c2fb67bd38ff11b479f74aa287b2d93f4add487aec53b836ff07de3a3a'], + }), + ('jquerylib', '0.1.4', { + 'checksums': ['f0bcc11dcde3a6ff180277e45c24642d3da3c8690900e38f44495efbc9064411'], + }), + ('rappdirs', '0.3.3', { + 'checksums': ['49959f65b45b0b189a2792d6c1339bef59674ecae92f8c2ed9f26ff9e488c184'], + }), + ('sass', '0.4.9', { + 'checksums': ['e133049aad7964e0f6150257e1470b3748f36029322265ee797b8caf7517d4d2'], + }), + ('purrr', '1.0.2', { + 'checksums': ['2c1bc6bb88433dff0892b41136f2f5c23573b335ff35a4775c72aa57b48bbb63'], + }), + ('cachem', '1.1.0', { + 'checksums': ['550839fc2ae5d865db475ba2c1714144f07fa0c052c72135b0e4a70287492e21'], + }), + ('memoise', '2.0.1', { + 'checksums': ['f85034ee98c8ca07fb3cd826142c1cd1e1e5747075a94c75a45783bbc4fe2deb'], + }), + ('bslib', '0.7.0', { + 'checksums': ['2135d9841af382673b815a14454abff2f2ce0f5dc97484d1499298b85b752ca0'], + }), + ('fontawesome', '0.5.2', { + 'checksums': ['da3de2a9717084d1400d48edd783f06c66b8c910ce9c8d753d1b7d99be1c5cc9'], + }), + ('tinytex', '0.51', { + 'checksums': ['bb113b51b4b58e78902a0220d709650c1458a8c6d3fa03f58ba007f0eb74c8ea'], + }), + ('rmarkdown', '2.27', { + 'checksums': ['61e9cb3eab4f8587fea98d3358652695b7e77eda858caa4c8985241ba6502b9f'], + }), + ('downlit', '0.4.4', { + 'checksums': ['55c377dcee4adc48c1060e14079f3d1832453d066a2cf070530caa210c48f828'], + }), + ('cpp11', '0.4.7', { + 'checksums': ['801d1266824c3972642bce2db2a5fd0528a65ec845c58eb5a886edf082264344'], + }), + ('systemfonts', '1.1.0', { + 'checksums': ['1941069bd20320284ec026a38c53cb736be60bda431303ceaf8fd27ae13fb644'], + }), + ('textshaping', '0.4.0', { + 'checksums': ['35e940786bb278560de61bb55d4f46f8c86c878d0461613ceb8c98ba9b239d7a'], + }), + ('ragg', '1.3.2', { + 'checksums': ['8037a45209fdd50acf101208af8e832b840a11ad4201cf7fb480de432e6b6931'], + }), + ('whisker', '0.4.1', { + 'checksums': ['bf5151494508032f68ac41e211bda80da9087c65c7068ffdd12f16669bf1f2bc'], + }), + ('pkgdown', '2.0.9', { + 'checksums': ['6e542216c03b5286cb9901175d1a7937a664db2572bc28bb51e9000269fcdda0'], + }), + ('htmlwidgets', '1.6.4', { + 'checksums': ['7cb08f0b30485dac26f72e4056ec4ed8825d1398e8b9f25ed63db228fe3a0ed0'], + }), + ('profvis', '0.3.8', { + 'checksums': ['ec02c75bc9907a73564e691adfa8e06651ca0bd73b7915412960231cd265b4b2'], + }), + ('urlchecker', '1.0.1', { + 'checksums': ['62165ddbe1b748b58c71a50c8f07fdde6f3d19a7b39787b9fa2b4f9216250318'], + }), + ('later', '1.3.2', { + 'checksums': ['52f5073d33cd0d3c12e56526c9c53c323ebafcc79b22cc6e51fb0c41ee2b561e'], + }), + ('promises', '1.3.0', { + 'checksums': ['f8209df3bab33340c1bc8c0d26caee2890fafb93129ff1423302abae5931fad3'], + }), + ('xtable', '1.8-4', { + 'checksums': ['5abec0e8c27865ef0880f1d19c9f9ca7cc0fd24eadaa72bcd270c3fb4075fd1c'], + }), + ('httpuv', '1.6.15', { + 'checksums': ['5e6ded3623a39df3e1db6cb7e7292b4c03c80b3c6c5faaac3b78b711cb205ed0'], + }), + ('sourcetools', '0.1.7-1', { + 'checksums': ['96812bdb7a0dd99690d84e4b0a3def91389e4290f53f01919ef28a50554e31d1'], + }), + ('shiny', '1.8.1.1', { + 'checksums': ['a38d5fb5d750e2c2091ce9101f138c1f9bc7009bbb195227a3519c5d97e36753'], + }), + ('miniUI', '0.1.1.1', { + 'checksums': ['452b41133289f630d8026507263744e385908ca025e9a7976925c1539816b0c0'], + }), + ('brew', '1.0-10', { + 'checksums': ['4181f7334e032ae0775c5dec49d6137eb25d5430ca3792d321793307b3dda38f'], + }), + ('roxygen2', '7.3.1', { + 'checksums': ['215e9fa9c0e73cb33f9870854c97b25c1a6386f519f69f397123f1a66656e2c8'], + }), + ('rversions', '2.1.2', { + 'checksums': ['de5818233e8271132fe8ea70145618950b35786e0d2f270e39bf3338f3b8b160'], + }), + ('sessioninfo', '1.2.2', { + 'checksums': ['f56283857c53ac8691e3747ed48fe03e893d8ff348235bff7364658bcfb0c7cb'], + }), + ('xopen', '1.0.1', { + 'checksums': ['e3b278b8c324a1aa2650141dd89d01253eea5c2555007422c797915689b29aec'], + }), + ('rcmdcheck', '1.4.0', { + 'checksums': ['bbd4ef7d514b8c2076196a7c4a6041d34623d55fbe73f2771758ce61fd32c9d0'], + }), + ('remotes', '2.5.0', { + 'checksums': ['4d663f1426cd88d42f4070f23d969305c575e0499ed1397be6607b0770d2850c'], + }), + ('clipr', '0.8.0', { + 'checksums': ['32c2931992fbec9c31b71de3e27059f1cbb45b4b1f45fd42e0e8dbcec6de3be9'], + }), + ('ini', '0.3.1', { + 'checksums': ['7b191a54019c8c52d6c2211c14878c95564154ec4865f57007953742868cd813'], + }), + ('gitcreds', '0.1.2', { + 'checksums': ['41c6abcca5635062b123ffb5af2794770eca5ebd97b05c5a64b24fa1c803c75d'], + }), + ('httr2', '1.0.1', { + 'checksums': ['33e92d830981b33cd5e55068b500c57dbfb72329c2fce54be3163c63b217f1b2'], + }), + ('gh', '1.4.1', { + 'checksums': ['76bd3f2a31eeaf76a633362899a20b0f7e8fb6159d4777baf3da2a47854292af'], + }), + ('credentials', '2.0.1', { + 'checksums': ['2c7cfc45bd4afa9a2c2b85d43e907b212da3468781e1b617737bd095253c358b'], + }), + ('zip', '2.3.1', { + 'checksums': ['83754408781c525917f36535865d28214893de0778b5f337e050cb543cacc28f'], + }), + ('gert', '2.0.1', { + 'checksums': ['0ed784837809ce89797ea77834d420e89351728f70d8d2f4b34487df813cd092'], + }), + ('usethis', '2.2.3', { + 'checksums': ['8d0c98995c23b5f4b5b95cd453557d2d15faa7399cc01bff304f5b15cb0cdeb3'], + }), + ('devtools', '2.4.5', { + 'checksums': ['38160ebd839acdec7ebf0699a085b4ab1ebd5500d3c57a9fa7ae484f1909904b'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/RDKit/RDKit-2024.03.3-foss-2023a.eb b/easybuild/easyconfigs/r/RDKit/RDKit-2024.03.3-foss-2023a.eb new file mode 100644 index 000000000000..5af2865d609e --- /dev/null +++ b/easybuild/easyconfigs/r/RDKit/RDKit-2024.03.3-foss-2023a.eb @@ -0,0 +1,73 @@ +easyblock = 'CMakeMake' + +name = 'RDKit' +version = '2024.03.3' + +homepage = 'https://www.rdkit.org' +description = "RDKit is a collection of cheminformatics and machine-learning software written in C++ and Python." + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/rdkit/rdkit/archive/'] +sources = ['Release_%s.tar.gz' % version.replace('.', '_')] +checksums = ['52f79c6bf1d446cdb5c86a35de655d96bad0c52a5f4ecbe15f08eaf334e6f76a'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('Eigen', '3.4.0'), + ('pkgconf', '1.9.5'), +] +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('SQLite', '3.42.0'), + ('matplotlib', '3.7.2'), + ('Pillow', '10.0.0'), + ('Boost.Python', '1.82.0'), + ('cairo', '1.17.8'), +] + +separate_build_dir = True + +configopts = "-DPy_ENABLE_SHARED=1 -DRDK_INSTALL_STATIC_LIBS=OFF -DRDK_INSTALL_INTREE=OFF " +configopts += "-DRDK_BUILD_INCHI_SUPPORT=ON " +configopts += "-DBOOST_ROOT=$EBROOTBOOST" + +# ingnore failing test pythonSourceTests - from . import rdBase failing +prebuildopts = "sed -i '22d' %(builddir)s/rdkit-Release_2024_03_3/rdkit/CMakeLists.txt && " +# ignore failing testUFFAngleConstraints +# https://github.com/rdkit/rdkit/discussions/7588 +prebuildopts += "sed -i 's/def testUFFAngleConstraints(self):/def ignore_testUFFAngleConstraints(self):/' " +prebuildopts += "%(builddir)s/rdkit-Release_2024_03_3/Code/ForceField/Wrap/testConstraints.py && " + +# merge source directory into build directory in order to run the tests +buildopts = '&& cp -RT %(builddir)s/%(namelower)s-*/ ./ && ' +buildopts += 'export RDBASE=$PWD && export PYTHONPATH=$PWD:$PYTHONPATH && ' + +# Specify path for libraries so that they are found during the tests when the module is built with --rpath flag. +buildopts += 'export LD_LIBRARY_PATH=%(builddir)s/easybuild_obj/lib:${LD_LIBRARY_PATH} && ' + +# 'ctest' allows to pass additional arguments opposed to 'make test' +buildopts += 'ctest --output-on-failure' + +local_libs = ['Alignment', 'Catalogs', 'ChemicalFeatures', 'ChemReactions', 'ChemTransforms', 'coordgen', 'DataStructs', + 'Depictor', 'Descriptors', 'DistGeometry', 'DistGeomHelpers', 'EigenSolvers', 'FileParsers', + 'FilterCatalog', 'Fingerprints', 'FMCS', 'ForceFieldHelpers', 'ForceField', 'FragCatalog', 'GraphMol', + 'hc', 'InfoTheory', 'maeparser', 'MMPA', 'MolAlign', 'MolCatalog', 'MolChemicalFeatures', 'MolDraw2D', + 'MolHash', 'MolInterchange', 'MolStandardize', 'MolTransforms', 'Optimizer', 'PartialCharges', 'RDBoost', + 'RDGeneral', 'RDGeometryLib', 'RDStreams', 'ReducedGraphs', 'RGroupDecomposition', 'RingDecomposerLib', + 'ScaffoldNetwork', 'ShapeHelpers', 'SimDivPickers', 'SLNParse', 'SmilesParse', 'Subgraphs', + 'SubstructLibrary', 'SubstructMatch', 'Trajectory'] + +sanity_check_paths = { + 'files': ['lib/libRDKit%s.%s' % (x, SHLIB_EXT) for x in local_libs], + 'dirs': ['include/rdkit', 'lib/python%(pyshortver)s/site-packages/rdkit'], +} + +sanity_check_commands = [ + "python -c 'import rdkit.rdBase'", +] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2023.09.1+494-foss-2023a-Java-11-R-4.3.2.eb b/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2023.09.1+494-foss-2023a-Java-11-R-4.3.2.eb new file mode 100644 index 000000000000..56585dad1c09 --- /dev/null +++ b/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2023.09.1+494-foss-2023a-Java-11-R-4.3.2.eb @@ -0,0 +1,108 @@ +easyblock = 'CMakeNinja' + +name = 'RStudio-Server' +version = "2023.09.1+494" +versionsuffix = '-Java-%(javaver)s-R-%(rver)s' +local_git_rev = 'cd7011dce393115d3a7c3db799dda4b1c7e88711' + +homepage = 'https://www.rstudio.com/' +description = """This is the RStudio Server version. +RStudio is a set of integrated tools designed to help you be more productive with R. + +The server can be started with: + rserver --server-daemonize=0 --www-port=8787 + +If you need a database config one can be created with: + MYTMP=`mktemp -d` && echo -e "provider=sqlite\\ndirectory=${MYTMP}/sqlite" > "${MYTMP}/db.conf" +and then used with: + rserver ... --database-config-file="${MYTMP}/db.conf" +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/rstudio/rstudio/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['38526a5816e980b12aeaef7debd2151f08ef2e54fed83af2622eb7cdeeb479a2'] + +builddependencies = [ + ('ant', '1.10.14', '-Java-%(javaver)s', SYSTEM), + ('CMake', '3.26.3'), + ('Ninja', '1.11.1'), + ('pkgconf', '1.9.5'), + ('nodejs', '18.17.1'), +] + +dependencies = [ + ('Boost', '1.82.0'), + ('Java', '11', '', SYSTEM), + ('R', '4.3.2'), + ('R-bundle-CRAN', '2023.12'), + ('SOCI', '4.0.3'), + ('yaml-cpp', '0.7.0'), +] + +osdependencies = [ + ('pam-devel', 'libpam0g-dev') +] + +preconfigopts = " && ".join([ + # Install dependencies via scripts. Done in subshell to preserve PWD + "(export RSTUDIO_TOOLS_ROOT='%(builddir)s'", + "cd '%(start_dir)s/dependencies/common'", + "./install-cef", + "./install-dictionaries", + "./install-mathjax", + "./install-pandoc", + "./install-panmirror", + "./install-npm-dependencies)", + "" +]) + +configopts = " ".join([ + "-DRSTUDIO_TOOLS_ROOT='%(builddir)s'", + "-DRSTUDIO_TARGET=Server", + "-DRSTUDIO_USE_SYSTEM_BOOST=ON", + "-DRSTUDIO_USE_SYSTEM_SOCI=ON", + "-DRSTUDIO_USE_SYSTEM_YAML_CPP=ON", + "-DQUARTO_ENABLED=OFF", # Not available on all archs, use pandoc fallback + "-DRSTUDIO_GIT_REVISION_HASH=" + local_git_rev +]) + +sanity_check_commands = [ + # RSession requires environment variables R_HOME and R_DOC_DIR + 'R_HOME="$EBROOTR/lib64/R" R_DOC_DIR="$R_HOME/doc" rsession --verify-installation=1', + # RServer requires a db conf (this may also be needed for live use) + # Also create and set a soem dirs so it doesn't try to use $HOME + ' '.join([ + 'MYTMP=`mktemp -d`', + '&& export RSTUDIO_CONFIG_DIR="$MYTMP"', + '&& export XDG_DATA_HOME="$MYTMP/.data"', + '&& export XDG_CACHE_HOME="$MYTMP/.cache"', + '&& mkdir "$XDG_DATA_HOME" "$XDG_CACHE_HOME"', + '&& export RS_LOG_DIR="$MYTMP/log"', + '&& echo -e "provider=sqlite\\ndirectory=$MYTMP/db" >> "$MYTMP/db.conf"', + '&& rserver', + '--verify-installation=1', + '--server-user="$USER"', + '--database-config-file="$MYTMP/db.conf"', + '--server-data-dir="$MYTMP/sdd"', + '--secure-cookie-key-file="$MYTMP/secure-cookie-key"', + ]), +] + +sanity_check_paths = { + 'files': ['bin/rstudio-server'], + 'dirs': ['bin', 'extras', 'resources', 'www', 'www-symbolmaps', 'R'], +} + +modloadmsg = """ +The server can be started with: + rserver --server-daemonize=0 --www-port=8787 + +If you need a database config one can be created with: + MYTMP=`mktemp -d` && echo -e "provider=sqlite\\ndirectory=${MYTMP}/sqlite" > "${MYTMP}/db.conf" +and then used with: + rserver ... --database-config-file="${MYTMP}/db.conf" +""" + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-20240409-GCCcore-13.2.0.eb b/easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-20240409-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..4f36c473ec48 --- /dev/null +++ b/easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-20240409-GCCcore-13.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'CMakeMake' + +name = 'RapidJSON' +# no new release since Aug'16 so using latest commit; +# see also https://github.com/Tencent/rapidjson/issues/2202 +version = '1.1.0-20240409' +local_commit = 'ab1842a' + +homepage = 'https://rapidjson.org' +description = "A fast JSON parser/generator for C++ with both SAX/DOM style API" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://github.com/Tencent/%(namelower)s/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': 'v%(version)s.tar.gz'}] +checksums = ['39f96f17b40f7201042c9b45d6444cb7eae1b7adfb7455412a86f6140450d32d'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.27.6'), +] + +# strip out hardcoded use of -march=native, EasyBuild should be in control of this +preconfigopts = "sed -i 's/-march=native//g' ../rapidjson-*/CMakeLists.txt && " + +sanity_check_paths = { + 'files': ['lib/pkgconfig/%(name)s.pc'], + 'dirs': ['include/%(namelower)s', 'lib/cmake', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/r/Raptor/Raptor-2.0.16-GCCcore-12.3.0.eb b/easybuild/easyconfigs/r/Raptor/Raptor-2.0.16-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..61c358020c87 --- /dev/null +++ b/easybuild/easyconfigs/r/Raptor/Raptor-2.0.16-GCCcore-12.3.0.eb @@ -0,0 +1,55 @@ +## +# This is a contribution from SIB Swiss Institute of Bioinformatics +# Homepage: https://www.sib.swiss/research-infrastructure/competence-centers/vital-it +# +# Authors:: Sebastien Moretti +# +# Based on Raptor2 RPM spec file: +# https://git.rockylinux.org/staging/rpms/raptor2/-/blob/r8/SPECS/raptor2.spec +# The RPM patches have been integrated in the version 2.0.16 +# +# Update: Petr Král (INUITS) +## +easyblock = 'ConfigureMake' + +name = 'Raptor' +version = '2.0.16' +homepage = 'https://librdf.org/raptor/' +description = """Set of parsers and serializers that generate Resource Description Framework +(RDF) triples by parsing syntaxes or serialize the triples into a syntax.""" +# software_license = 'LicenseLGPLv2.1 + LicenseGPLv2 + LicenseApachev2' + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://download.librdf.org/source'] +sources = ['raptor2-%(version)s.tar.gz'] +checksums = ['089db78d7ac982354bdbf39d973baf09581e6904ac4c92a98c5caadb3de44680'] + +builddependencies = [ + ('Autotools', '20220317'), + ('binutils', '2.40'), + ('make', '4.4.1'), +] + +dependencies = [ + ('libxml2', '2.11.4'), + ('libxslt', '1.1.38'), + ('cURL', '8.0.1'), + ('ICU', '73.2'), +] + +configopts = "--disable-static --enable-release --disable-gtk-doc --with-yajl=no" + +# fix error: 'xmlEntity' {aka 'struct _xmlEntity'} has no member named 'checked' +# see https://github.com/dajobe/raptor/pull/58 +local_sed_replacement = r's/LIBXML_VERSION >= 20627/LIBXML_VERSION >= 2062 \&\& LIBXML_VERSION < 21100/g' +prebuildopts = "sed -i '%s' src/raptor_libxml.c && " % local_sed_replacement + +sanity_check_paths = { + 'files': ['bin/rapper', 'lib/libraptor2.%s' % SHLIB_EXT], + 'dirs': ['include/raptor2/'] +} + +sanity_check_commands = ["rapper --help"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/r/Rasqal/Rasqal-0.9.33-GCCcore-12.3.0.eb b/easybuild/easyconfigs/r/Rasqal/Rasqal-0.9.33-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..3d5e0ad9d836 --- /dev/null +++ b/easybuild/easyconfigs/r/Rasqal/Rasqal-0.9.33-GCCcore-12.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'Rasqal' +version = '0.9.33' +homepage = 'hhttps://librdf.org/rasqal' +description = """A library handling RDF query syntaxes, construction and execution""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://download.librdf.org/source'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['6924c9ac6570bd241a9669f83b467c728a322470bf34f4b2da4f69492ccfd97c'] + +builddependencies = [ + ('Autotools', '20220317'), + ('binutils', '2.40'), + ('Raptor', '2.0.16'), +] + +dependencies = [ + ('libgcrypt', '1.10.3'), + ('MPFR', '4.2.0'), + ('PCRE', '8.45'), + ('gtk-doc', '1.34.0'), + ('ICU', '73.2'), +] + +preconfigopts = "autoreconf -f -i && " +configopts = "--disable-static --enable-release" + +sanity_check_paths = { + 'files': ['bin/roqet', 'lib/librasqal.%s' % SHLIB_EXT], + 'dirs': ['include/rasqal/'] +} + +sanity_check_commands = ["roqet --help"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/r/Ray-project/Ray-project-2.9.1-foss-2023a.eb b/easybuild/easyconfigs/r/Ray-project/Ray-project-2.9.1-foss-2023a.eb new file mode 100644 index 000000000000..67ab662077d2 --- /dev/null +++ b/easybuild/easyconfigs/r/Ray-project/Ray-project-2.9.1-foss-2023a.eb @@ -0,0 +1,73 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'PythonBundle' + +name = 'Ray-project' +version = '2.9.1' + +homepage = "https://docs.ray.io/en/latest/" +description = "Ray is a fast and simple framework for building and running distributed applications." + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'usempi': True} + +builddependencies = [ + ('redis-py', '5.0.1'), + ('hatchling', '1.18.0'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('protobuf-python', '4.24.0'), + ('PyYAML', '6.0'), + ('lz4', '1.9.4'), + ('mpi4py', '3.1.4'), +] + +use_pip = True + +exts_list = [ + ('grpcio', '1.62.1', { + 'modulename': 'grpc', + 'preinstallopts': "export GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS=%(parallel)s && ", + 'checksums': ['6c455e008fa86d9e9a9d85bb76da4277c0d7d9668a3bfa70dbe86e9f3c759947'], + }), + ('aiosignal', '1.3.1', { + 'checksums': ['54cd96e15e1649b75d6c87526a6ff0b6c1b0dd3459f43d9ca11d48c339b68cfc'], + }), + ('expandvars', '0.12.0', { + 'checksums': ['7d1adfa55728cf4b5d812ece3d087703faea953e0c0a1a78415de9df5024d844'], + }), + ('frozenlist', '1.4.1', { + 'checksums': ['c037a86e8513059a2613aaba4d817bb90b9d9b6b69aace3ce9c877e8c8ed402b'], + }), + ('lz4', '4.3.3', { + 'checksums': ['01fe674ef2889dbb9899d8a67361e0c4a2c833af5aeb37dd505727cf5d2a131e'], + }), + ('Ray', version, { + 'source_tmpl': '%(namelower)s-%(version)s-cp311-cp311-manylinux2014_%(arch)s.whl', + 'checksums': [{ + '%(namelower)s-%(version)s-cp311-cp311-manylinux2014_x86_64.whl': ( + 'fabc520990c1b98dde592813d62737e5e817460e0ac359f32ba029ace292cbe2' + ), + '%(namelower)s-%(version)s-cp311-cp311-manylinux2014_aarch64.whl': ( + '1907649d69efdc1b9ffbc03db086f6d768216cb73908ebd4038ac5030effef9e' + ), + }], + }), +] + +sanity_check_paths = { + 'files': ['bin/ray'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + 'ray --help' +] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.3.2.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.3.2.eb index b8237231c173..7e01526d78c9 100644 --- a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.3.2.eb +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.3.2.eb @@ -29,6 +29,8 @@ exts_list = [ }), ('reframe', version, { 'preinstallopts': "export PATH=%(installdir)s/bin:$PATH && " + # use PyYAML 6.0.1 to solve Cython 3 incompatibility issues + "sed -i 's@PyYAML==6.0@PyYAML==6.0.1@' requirements.txt && " "./bootstrap.sh +docs +pygelf && cp -r external %(installdir)s && " "PYTHONPATH=%(builddir)s/reframe/reframe-%(version)s/external:$PYTHONPATH ", 'source_tmpl': 'v%(version)s.tar.gz', diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.3.3.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.3.3.eb index af6b22f48468..f4319b13ae56 100644 --- a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.3.3.eb +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.3.3.eb @@ -30,6 +30,8 @@ exts_list = [ }), ('reframe', version, { 'preinstallopts': "export PATH=%(installdir)s/bin:$PATH && " + # use PyYAML 6.0.1 to solve Cython 3 incompatibility issues + "sed -i 's@PyYAML==6.0@PyYAML==6.0.1@' requirements.txt && " "./bootstrap.sh +docs +pygelf && cp -r external %(installdir)s && " "PYTHONPATH=%(builddir)s/reframe/reframe-%(version)s/external:$PYTHONPATH ", 'source_tmpl': 'v%(version)s.tar.gz', diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..9046d5c93625 --- /dev/null +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-12.3.0.eb @@ -0,0 +1,76 @@ +easyblock = 'PythonBundle' + +name = 'ReFrame' +version = '4.6.2' + +homepage = 'https://github.com/reframe-hpc/reframe' +description = '''ReFrame is a framework for writing regression tests for HPC systems.''' + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('cURL', '8.0.1'), # Used by ReFrame to download pip in the bootstrap +] + +# Note that for ReFrame's CPU autodetect to work +# the system also needs to provide (new enough versions of) these dependencies +dependencies = [ + ('Python', '3.11.3'), + ('libxslt', '1.1.38'), # Required by lxml, which is installed by ReFrame's bootstrap installer + ('libxml2', '2.11.4'), # Required by lxml, which is installed by ReFrame's bootstrap installer +] + +use_pip = True + +exts_list = [ + # ReFrame's bootstrap script is intended to run with zero dependencies. It downloads all python deps for ReFrame + # into a %(installdir)/external directory. ReFrame's main executable (reframe) adds this dir to python's sys.path + # so that ReFrame (and only ReFrame) will find & use all of these dependencies. + # In EasyBuild, we should adhere to this installation method because a) it is how ReFrame is meant to be used and + # b) it isolates all of ReFrame dependencies from any other python code you run. Thus, there is no chance that + # a test will pick up on any python deps from ReFrame itself. + # For this to work, we need to disable download_dep_fail and sanity_pip_check, as both are _expected_ to fail + # for this setup. + ('reframe', version, { + # Deps are downloaded to %(installdir)/external, which won't polute the PYTHONPATH, so is ok + 'download_dep_fail': False, + # ReFrame uses its custom sys.path to find necessary packages, they are not on PYTYHONPATH + # Thus, the regular pip sanity check is expected to fail, even if ReFrame would run just fine + 'sanity_pip_check': False, + # Set modulename to False, as to skip the sanity_check-step from extension.py (python -c "import reframe") + # This step would fail, since the regular python interpreter wouldn't find the additional packages in + # %(installdir)/external. That's fine, as ReFrame should never be imported directly, only through the + # reframe command. + 'modulename': False, + 'preinstallopts': "export PATH=%(installdir)s/bin:$PATH && " + "./bootstrap.sh +docs +pygelf && cp -r external %(installdir)s && ", + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/reframe-hpc/reframe/archive/'], + 'checksums': ['d3343815ee3d2c330b91a1cdb924ba184119ed7d9fc88a4a754b939a4259df82'], + }), +] + +postinstallcmds = [ + "cp -a tools examples %(installdir)s", + "mkdir -p %(installdir)s/share && cp -a share/completions %(installdir)s/share/completions", + r"sed -i 's@/\(python[0-9.]*\)$@/\1 -S@g' %(installdir)s/bin/reframe", +] + +sanity_check_paths = { + 'files': ['bin/reframe', + 'share/completions/reframe.bash', + 'share/completions/reframe.fish', + 'share/completions/reframe.tcsh'], + 'dirs': ['external', 'lib', 'tools', 'examples'] +} + +sanity_check_commands = ['reframe -V'] + +# Since this is at the GCCcore toolchain level, make sure ReFrame is configured to purge modules before running +# any tests by default +modextravars = { + 'RFM_PURGE_ENVIRONMENT': '1', +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..e2adb9db1d94 --- /dev/null +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb @@ -0,0 +1,76 @@ +easyblock = 'PythonBundle' + +name = 'ReFrame' +version = '4.6.2' + +homepage = 'https://github.com/reframe-hpc/reframe' +description = '''ReFrame is a framework for writing regression tests for HPC systems.''' + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('cURL', '8.3.0'), # Used by ReFrame to download pip in the bootstrap +] + +# Note that for ReFrame's CPU autodetect to work +# the system also needs to provide (new enough versions of) these dependencies +dependencies = [ + ('Python', '3.11.5'), + ('libxslt', '1.1.38'), # Required by lxml, which is installed by ReFrame's bootstrap installer + ('libxml2', '2.11.5'), # Required by lxml, which is installed by ReFrame's bootstrap installer +] + +use_pip = True + +exts_list = [ + # ReFrame's bootstrap script is intended to run with zero dependencies. It downloads all python deps for ReFrame + # into a %(installdir)/external directory. ReFrame's main executable (reframe) adds this dir to python's sys.path + # so that ReFrame (and only ReFrame) will find & use all of these dependencies. + # In EasyBuild, we should adhere to this installation method because a) it is how ReFrame is meant to be used and + # b) it isolates all of ReFrame dependencies from any other python code you run. Thus, there is no chance that + # a test will pick up on any python deps from ReFrame itself. + # For this to work, we need to disable download_dep_fail and sanity_pip_check, as both are _expected_ to fail + # for this setup. + ('reframe', version, { + # Deps are downloaded to %(installdir)/external, which won't polute the PYTHONPATH, so is ok + 'download_dep_fail': False, + # ReFrame uses its custom sys.path to find necessary packages, they are not on PYTYHONPATH + # Thus, the regular pip sanity check is expected to fail, even if ReFrame would run just fine + 'sanity_pip_check': False, + # Set modulename to False, as to skip the sanity_check-step from extension.py (python -c "import reframe") + # This step would fail, since the regular python interpreter wouldn't find the additional packages in + # %(installdir)/external. That's fine, as ReFrame should never be imported directly, only through the + # reframe command. + 'modulename': False, + 'preinstallopts': "export PATH=%(installdir)s/bin:$PATH && " + "./bootstrap.sh +docs +pygelf && cp -r external %(installdir)s && ", + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/reframe-hpc/reframe/archive/'], + 'checksums': ['d3343815ee3d2c330b91a1cdb924ba184119ed7d9fc88a4a754b939a4259df82'], + }), +] + +postinstallcmds = [ + "cp -a tools examples %(installdir)s", + "mkdir -p %(installdir)s/share && cp -a share/completions %(installdir)s/share/completions", + r"sed -i 's@/\(python[0-9.]*\)$@/\1 -S@g' %(installdir)s/bin/reframe", +] + +sanity_check_paths = { + 'files': ['bin/reframe', + 'share/completions/reframe.bash', + 'share/completions/reframe.fish', + 'share/completions/reframe.tcsh'], + 'dirs': ['external', 'lib', 'tools', 'examples'] +} + +sanity_check_commands = ['reframe -V'] + +# Since this is at the GCCcore toolchain level, make sure ReFrame is configured to purge modules before running +# any tests by default +modextravars = { + 'RFM_PURGE_ENVIRONMENT': '1', +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/r/Redland/Redland-1.0.17-GCC-12.3.0.eb b/easybuild/easyconfigs/r/Redland/Redland-1.0.17-GCC-12.3.0.eb new file mode 100644 index 000000000000..7217999a898e --- /dev/null +++ b/easybuild/easyconfigs/r/Redland/Redland-1.0.17-GCC-12.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'Redland' +version = '1.0.17' + +homepage = 'https://librdf.org/raptor' +description = """Redland is a set of free software C libraries that + provide support for the Resource Description Framework (RDF).""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://download.librdf.org/source'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['de1847f7b59021c16bdc72abb4d8e2d9187cd6124d69156f3326dd34ee043681'] + +dependencies = [ + ('Rasqal', '0.9.33'), + ('Raptor', '2.0.16'), + ('PostgreSQL', '16.1'), + ('MariaDB', '11.6.0'), + ('unixODBC', '2.3.12'), + ('SQLite', '3.42.0'), + ('libtool', '2.4.7'), +] + +sanity_check_paths = { + 'files': [ + 'include/%(namelower)s.h', + 'bin/%(namelower)s-config', + 'bin/%(namelower)s-db-upgrade', + 'lib/librdf.%s' % SHLIB_EXT, + ], + 'dirs': ['share/%(namelower)s'], +} + +sanity_check_commands = ['%(namelower)s-config --help'] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/r/Regenie/Regenie-3.1.2-GCC-11.2.0.eb b/easybuild/easyconfigs/r/Regenie/Regenie-3.1.2-GCC-11.2.0.eb new file mode 100644 index 000000000000..09b2ac462d61 --- /dev/null +++ b/easybuild/easyconfigs/r/Regenie/Regenie-3.1.2-GCC-11.2.0.eb @@ -0,0 +1,47 @@ +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen +# we recommend to use --download-timeout=1000 when fetching the files + +easyblock = 'MakeCp' + +name = 'Regenie' +version = '3.1.2' + +homepage = 'https://rgcgithub.github.io/regenie' +description = """Regenie is a C++ program for whole genome regression modelling of large genome-wide +association studies. It is developed and supported by a team of scientists at the Regeneron Genetics Center.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://github.com/rgcgithub/regenie/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['%(namelower)s-%(version)s_Makefile.patch'] +checksums = [ + 'b2e5e98bb310d9b9071ae5c63c5207be853bb1ec7918574e1acfdd0c83e744ff', # v3.1.2.tar.gz + '8be5d4b3b237d7a1820727061227857770554970aa136da614b71c14767e655e', # regenie-3.1.2_Makefile.patch +] + +dependencies = [ + ('Boost', '1.55.0'), + ('BGEN-enkre', '1.1.7'), + ('OpenBLAS', '0.3.18'), +] + +build_cmd = "make BGEN_PATH=$EBROOTBGENMINENKRE HAS_BOOST_IOSTREAM=1 " +build_cmd += "OPENBLAS_ROOT=$EBROOTOPENBLAS BOOST=$EBROOTBOOST STATIC=0" + +files_to_copy = [ + (['regenie'], 'bin'), + (['example/*'], 'example'), + (['docs/*'], 'docs'), +] + +sanity_check_commands = ['regenie --help'] + +sanity_check_paths = { + 'files': ['bin/regenie'], + 'dirs': ['bin', 'example', 'docs'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/Regenie/regenie-3.1.2_Makefile.patch b/easybuild/easyconfigs/r/Regenie/regenie-3.1.2_Makefile.patch new file mode 100644 index 000000000000..3fc4820cc4d3 --- /dev/null +++ b/easybuild/easyconfigs/r/Regenie/regenie-3.1.2_Makefile.patch @@ -0,0 +1,41 @@ +Patch to remove 3rd party software and replace lapack(e) with openblas and boost 1.55 +base on the work of Author: J. Sassmannshausen NHS/GSTT +diff -ruN regenie-3.1.1.orig/Makefile regenie-3.1.1/Makefile +--- regenie-3.1.1.orig/Makefile 2022-05-05 10:59:29.000000000 -0700 ++++ regenie-3.1.1/Makefile 2022-06-21 13:34:54.464076000 -0700 +@@ -44,7 +44,7 @@ + # detect OS architecture and add flags + UNAME_S := $(shell uname -s) + ifeq ($(UNAME_S),Linux) +- INC = -I${BGEN_PATH}/3rd_party/boost_1_55_0 ++ INC = -I${BOOST} + CFLAGS += -fopenmp + ifeq ($(strip $(STATIC)),1) + LPATHS = -static-libgcc -static-libstdc++ +@@ -103,10 +103,10 @@ + INC += -I${OPENBLAS_ROOT}/include/ + # static linking + ifeq ($(strip $(STATIC)),1) +- SLIBS += -Wl,-rpath=${OPENBLAS_ROOT}/lib/ -llapack -llapacke -lopenblas ++ SLIBS += -Wl,-rpath=${OPENBLAS_ROOT}/lib/ -lopenblas + # dynamic linking + else +- DLIBS += -Wl,-rpath=${OPENBLAS_ROOT}/lib/ -llapack -llapacke -lopenblas ++ DLIBS += -Wl,-rpath=${OPENBLAS_ROOT}/lib/ -lopenblas -lgfortran + endif + endif + endif +@@ -119,11 +119,10 @@ + OBJECTS = $(patsubst %.cpp,%.o,$(wildcard ./src/*.cpp)) + + PGEN_PATH = ./external_libs/pgenlib/ +-INC += -I${PGEN_PATH} -I${PGEN_PATH}/simde/ -I${PGEN_PATH}/include/ -I./external_libs/cxxopts/include/ -I./external_libs/LBFGSpp/include/ -I${BGEN_PATH} -I./external_libs/eigen-3.4.0/ -I${BGEN_PATH}/genfile/include/ -I${BGEN_PATH}/3rd_party/boost_1_55_0/ -I${BGEN_PATH}/3rd_party/zstd-1.1.0/lib -I${BGEN_PATH}/db/include/ -I${BGEN_PATH}/3rd_party/sqlite3 -I./external_libs/ ++INC += -I${PGEN_PATH} -I${PGEN_PATH}/simde/ -I${PGEN_PATH}/include/ -I./external_libs/cxxopts/include/ -I./external_libs/LBFGSpp/include/ -I./external_libs/eigen-3.4.0/ -I${BGEN_PATH}/include/ -I${BOOST}/include -I./external_libs/ + +-LPATHS += ${LIBMKL} -L${BGEN_PATH}/build/ -L${BGEN_PATH}/build/3rd_party/zstd-1.1.0/ -L${BGEN_PATH}/build/db/ -L${BGEN_PATH}/build/3rd_party/sqlite3/ -L${BGEN_PATH}/build/3rd_party/boost_1_55_0 -L/usr/lib/ + +-LIBS += ${SLIBS} -lbgen -lzstd -ldb -lsqlite3 -lboost ++LIBS += ${SLIBS} -lbgen -lzstd -ldb -lsqlite3 -lboost_system -lboost_filesystem -lboost_thread -lboost_timer + LIBS += -lz ${DLIBS} -lm -ldl -lgfortran + + diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.79.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/r/Rust/Rust-1.79.0-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..88962930f30e --- /dev/null +++ b/easybuild/easyconfigs/r/Rust/Rust-1.79.0-GCCcore-13.3.0.eb @@ -0,0 +1,31 @@ +name = 'Rust' +version = '1.79.0' + +homepage = 'https://www.rust-lang.org' +description = """Rust is a systems programming language that runs blazingly fast, prevents segfaults, + and guarantees thread safety.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://static.rust-lang.org/dist/'] +sources = ['rustc-%(version)s-src.tar.gz'] +patches = ['Rust-1.70_sysroot-fix-interpreter.patch'] +checksums = [ + {'rustc-1.79.0-src.tar.gz': '172ecf3c7d1f9d9fb16cd2a628869782670416ded0129e524a86751f961448c0'}, + {'Rust-1.70_sysroot-fix-interpreter.patch': '220129db55e022a98d25028da5dcc9f26b252dd995c3ac92f6312dbb1e362cb1'}, +] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), + ('Python', '3.12.3'), + ('Ninja', '1.12.1'), + ('pkgconf', '2.2.0'), + ('patchelf', '0.18.0'), # only required when RPATH linking is enabled +] + +dependencies = [ + ('OpenSSL', '3', '', SYSTEM), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/rMATS-long/rMATS-long-1.0.0-20240502-foss-2023a-R-4.3.2.eb b/easybuild/easyconfigs/r/rMATS-long/rMATS-long-1.0.0-20240502-foss-2023a-R-4.3.2.eb new file mode 100644 index 000000000000..6074c273fac8 --- /dev/null +++ b/easybuild/easyconfigs/r/rMATS-long/rMATS-long-1.0.0-20240502-foss-2023a-R-4.3.2.eb @@ -0,0 +1,44 @@ +easyblock = 'Tarball' + +name = 'rMATS-long' +local_commit = "592cb32" +version = '1.0.0-20240502' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/Xinglab/rMATS-long' +description = """rMATS-long is a collection of tools for analyzing long-read data.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/Xinglab/%(name)s/archive/'] +sources = [{ + 'download_filename': '%s.tar.gz' % local_commit, + 'filename': '%(name)s-%(version)s.tar.gz', +}] +checksums = ['9f4f859c05be5a274b8c0aaf79a18f8c02839f8e6d71330d07f77d027ddba003'] + +dependencies = [ + ('Python', '3.11.3'), + ('matplotlib', '3.7.2'), + ('networkx', '3.1'), + ('SciPy-bundle', '2023.07'), + ('R', '4.3.2'), + ('R-bundle-CRAN', '2023.12'), + ('R-bundle-Bioconductor', '3.18', '-R-%(rver)s'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['scripts'], +} + +sanity_check_commands = [ + 'cd %(installdir)s/scripts && python rmats_long.py -h', +] + +modloadmsg = """ +To run rMATS-long scripts first go to scripts directory: +$ cd $EBROOTRMATSMINLONG/scripts +""" + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/r/rankwidth/rankwidth-0.9-foss-2023b.eb b/easybuild/easyconfigs/r/rankwidth/rankwidth-0.9-foss-2023b.eb new file mode 100644 index 000000000000..090a4aaf87af --- /dev/null +++ b/easybuild/easyconfigs/r/rankwidth/rankwidth-0.9-foss-2023b.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'rankwidth' +version = '0.9' + +homepage = 'https://sourceforge.net/projects/rankwidth/' +description = """rw calculates rank-width and rank-decompositions. +It is based on ideas from "Computing rank-width exactly" by Sang-il Oum, +"Sopra una formula numerica" by Ernesto Pascal, "Generation of a Vector +from the Lexicographical Index" by B.P. Buckles and M. Lybanon and "Fast +additions on masked integers" by Michael D. Adams and David S. Wise.""" + +toolchain = {'name': 'foss', 'version': '2023b'} + +source_urls = ['https://master.dl.sourceforge.net/project/rankwidth'] +sources = ['rw-%(version)s.tar.gz'] +checksums = ['c1e03506fe25cdfcb428c051fc56b2d2affb5b06fba3f2ce756631466befb441'] + +dependencies = [('igraph', '0.10.12')] + +# fix `too few arguments to function igraph_get_adjacency` error +prebuildopts = 'sed -i "s/IGRAPH_GET_ADJACENCY_BOTH/IGRAPH_GET_ADJACENCY_BOTH, 0/g" simplerw.c && ' + +sanity_check_paths = { + 'files': [ + 'bin/rw', + 'include/rw.h', + 'lib/librw.%s' % SHLIB_EXT, + ], + 'dirs': ['share'], +} + +sanity_check_commands = ['rw --help | grep Usage:'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/r/rapidNJ/rapidNJ-2.3.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/r/rapidNJ/rapidNJ-2.3.3-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..b6fc9da5925c --- /dev/null +++ b/easybuild/easyconfigs/r/rapidNJ/rapidNJ-2.3.3-GCCcore-12.2.0.eb @@ -0,0 +1,41 @@ +# This seems to be actively maintained version of the code by the looks of it. +# See issue #5 +# https://github.com/somme89/rapidNJ/issues/5 +# why -march=native will not be used +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'MakeCp' + +name = 'rapidNJ' +version = '2.3.3' + +homepage = 'https://github.com/somme89/rapidNJ' +description = """RapidNJ is an algorithmic engineered implementation of canonical +neighbour-joining. It uses an efficient search heuristic to speed-up the core +computations of the neighbour-joining method that enables RapidNJ to +outperform other state-of-the-art neighbour-joining implementations.""" + +citing = """Rapid Neighbour Joining. Martin Simonsen, Thomas Mailund and Christian N. S. Pedersen. +In: Proceedings of the 8th Workshop in Algorithms in Bioinformatics (WABI), LNBI 5251, 113-122, +Springer Verlag, October 2008. +doi: 10.1007/978-3-540-87361-7_10""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/somme89/rapidNJ/archive/'] +sources = [{'filename': 'v%(version)s.tar.gz', 'download_filename': 'latest.tar.gz'}] +checksums = ['662f864cc3e5bc68aea23129f02e0062cac9ebd37e414b54c5c5e616ff4f245d'] + +builddependencies = [('binutils', '2.39')] + +files_to_copy = [(['bin/rapidnj'], 'bin')] + +# That is returning 1 instead of 0, so disabled for now +# sanity_check_commands = ['rapidnj --help'] + +sanity_check_paths = { + 'files': ['bin/rapidnj'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/redis-py/redis-py-5.0.9-GCCcore-13.2.0.eb b/easybuild/easyconfigs/r/redis-py/redis-py-5.0.9-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..b877029e19a3 --- /dev/null +++ b/easybuild/easyconfigs/r/redis-py/redis-py-5.0.9-GCCcore-13.2.0.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonBundle' + +name = 'redis-py' +version = '5.0.9' + +homepage = 'https://github.com/redis/redis-py' +description = "The Python interface to the Redis key-value store." + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('Python', '3.11.5'), + ('typing-extensions', '4.10.0'), + ('Redis', '7.2.4'), +] + +use_pip = True + +exts_list = [ + ('async-timeout', '4.0.3', { + 'checksums': ['4640d96be84d82d02ed59ea2b7105a0f7b33abe8703703cd0ab0bf87c427522f'], + }), + (name, version, { + 'modulename': 'redis', + 'source_urls': ['https://github.com/redis/redis-py/archive/refs/tags/'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['c107fddbaa40414559ddd21f0a78bc7d466cd6b20a800839ac18b9bb54e5c150'], + }), +] + +sanity_pip_check = True + +moduleclass = "data" diff --git a/easybuild/easyconfigs/r/regionmask/regionmask-0.12.1-foss-2023a.eb b/easybuild/easyconfigs/r/regionmask/regionmask-0.12.1-foss-2023a.eb new file mode 100644 index 000000000000..4172bf592e38 --- /dev/null +++ b/easybuild/easyconfigs/r/regionmask/regionmask-0.12.1-foss-2023a.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonBundle' + +name = 'regionmask' +version = '0.12.1' + +homepage = 'https://regionmask.readthedocs.io' +description = """regionmask creates masks of geographical regions. It determines to which +geographic region each grid point belongs.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('geopandas', '0.14.2'), + ('rasterio', '1.3.9'), + ('Shapely', '2.0.1'), + ('xarray', '2023.9.0'), +] + +use_pip = True + +exts_list = [ + (name, version, { + 'checksums': ['7ef1e70c6ebab7bfc6a80e13f6fe771945b8b6a31b7f8980fc88c8b8505bb854'], + }), +] + +sanity_pip_check = True + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/r/rjags/rjags-4-15-foss-2023a-R-4.3.2.eb b/easybuild/easyconfigs/r/rjags/rjags-4-15-foss-2023a-R-4.3.2.eb new file mode 100644 index 000000000000..f793f925da6c --- /dev/null +++ b/easybuild/easyconfigs/r/rjags/rjags-4-15-foss-2023a-R-4.3.2.eb @@ -0,0 +1,30 @@ +easyblock = 'RPackage' + +name = 'rjags' +version = '4-15' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://cran.r-project.org/web/packages/rjags' +description = """The rjags package is an interface to the JAGS library.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = [ + 'https://cran.r-project.org/src/contrib/', + 'https://cran.r-project.org/src/contrib/Archive/rjags/', +] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['35cd4c1faaaa8523b87ac053b881dccf29798f073f438459589e786b95ef18a1'] + +dependencies = [ + ('R', '4.3.2'), + ('R-bundle-CRAN', '2023.12'), + ('JAGS', '4.3.2'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['rjags'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/r/rpmrebuild/rpmrebuild-2.18.eb b/easybuild/easyconfigs/r/rpmrebuild/rpmrebuild-2.18.eb new file mode 100644 index 000000000000..64cae582362d --- /dev/null +++ b/easybuild/easyconfigs/r/rpmrebuild/rpmrebuild-2.18.eb @@ -0,0 +1,26 @@ +easyblock = "Tarball" + +name = "rpmrebuild" +version = "2.18" + +homepage = 'http://rpmrebuild.sourceforge.net/' +description = """rpmrebuild is a tool to build an RPM file from a package that has already been +installed in a basic use""" + +toolchain = SYSTEM + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['919ca6252eafbfb58dd54b0efa3ca4e6da293364937dcfe32c32a35b238a5837'] + +modextrapaths = {'PATH': ['']} +modextravars = {'RPMREBUILD_ROOT_DIR': '%(installdir)s'} + +sanity_check_paths = { + 'files': ["rpmrebuild"], + 'dirs': [] +} + +sanity_check_commands = ['rpmrebuild -h'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/r/ruamel.yaml/ruamel.yaml-0.18.6-GCCcore-13.3.0.eb b/easybuild/easyconfigs/r/ruamel.yaml/ruamel.yaml-0.18.6-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..48d0b0d8bb54 --- /dev/null +++ b/easybuild/easyconfigs/r/ruamel.yaml/ruamel.yaml-0.18.6-GCCcore-13.3.0.eb @@ -0,0 +1,60 @@ +easyblock = 'PythonBundle' + +name = 'ruamel.yaml' +version = '0.18.6' + +homepage = 'https://sourceforge.net/projects/ruamel-yaml' +description = "ruamel.yaml is a YAML 1.2 loader/dumper package for Python." + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('binutils', '2.42'), + ('poetry', '1.8.3'), +] + +dependencies = [ + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), +] + +use_pip = True + +exts_list = [ + ('ruamel.yaml.jinja2', '0.2.7', { + 'checksums': ['8449be29d9a157fa92d1648adc161d718e469f0d38a6b21e0eabb76fd5b3e663'], + }), + ('ruamel.yaml.clib', '0.2.8', { + 'modulename': False, + 'checksums': ['beb2e0404003de9a4cab9753a8805a8fe9320ee6673136ed7f04255fe60bb512'], + }), + (name, version, { + 'checksums': ['8b27e6a217e786c6fbe5634d8f3f11bc63e0f80f6a5890f28863d9c45aac311b'], + }), + ('configobj', '5.0.8', { + 'checksums': ['6f704434a07dc4f4dc7c9a745172c1cad449feb548febd9f7fe362629c627a97'], + }), + ('lz4', '4.3.3', { + 'checksums': ['01fe674ef2889dbb9899d8a67361e0c4a2c833af5aeb37dd505727cf5d2a131e'], + }), + ('ruamel.yaml.base', '0.3.2', { + 'checksums': ['88b6edc8ace60c12d98f05fda22e5d9d69ba9a4b531cf54783142151145b0372'], + }), + ('ruamel.yaml.convert', '0.3.2', { + 'checksums': ['065ed9492a3189291d5bc0256709afc0231b52e4a01376fc91cf1757560ac9c4'], + }), + ('ruamel.yaml.cmd', '0.6.5', { + 'checksums': ['49af59514cb87d7637d1186e31c9345c9947120a9ce49cf6975435aa7abd5aa8'], + }), +] + +sanity_check_paths = { + 'files': ['bin/yaml'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["yaml --help"] + +sanity_pip_check = True + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SCENICplus/SCENICplus-1.0a1-20240513-foss-2023a.eb b/easybuild/easyconfigs/s/SCENICplus/SCENICplus-1.0a1-20240513-foss-2023a.eb new file mode 100644 index 000000000000..796eb9a63b65 --- /dev/null +++ b/easybuild/easyconfigs/s/SCENICplus/SCENICplus-1.0a1-20240513-foss-2023a.eb @@ -0,0 +1,279 @@ +easyblock = 'PythonBundle' + +name = 'SCENICplus' +version = '1.0a1-20240513' +local_commit = "fa55dae" + +homepage = 'https://github.com/aertslab/scenicplus' +description = """SCENIC+ is a python package to build gene regulatory networks (GRNs) +using combined or separate single-cell gene expression (scRNA-seq) and single-cell +chromatin accessibility (scATAC-seq) data.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('poetry', '1.5.1'), + ('maturin', '1.4.0', '-Rust-1.75.0'), + ('CMake', '3.26.3'), +] +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('Single-cell-python-bundle', '2024.02'), + ('anndata', '0.10.5.post1'), + ('BeautifulSoup', '4.12.2'), + ('h5py', '3.9.0'), + ('python-igraph', '0.11.4'), + ('imageio', '2.33.1'), + ('leidenalg', '0.10.2'), + ('lxml', '4.9.2'), + ('MACS2', '2.2.9.1'), + ('numba', '0.58.1'), + ('polars', '0.20.2'), + ('Arrow', '14.0.1'), + ('plotly.py', '5.16.0'), + ('pybedtools', '0.9.1'), + ('pyBigWig', '0.3.22'), + ('pyGAM', '0.9.1'), + ('Pysam', '0.22.0'), + ('Ray-project', '2.9.1'), + ('scikit-image', '0.22.0'), + ('snakemake', '8.4.2'), + ('statsmodels', '0.14.1'), + ('IPython', '8.14.0'), + ('Pandoc', '3.1.2', '', SYSTEM), + ('ipympl', '0.9.3'), + ('PyTables', '3.8.0'), + ('Sphinx-RTD-Theme', '2.0.0'), + ('scrublet', '0.2.3'), + ('numexpr', '2.9.0'), + ('Kaleido', '0.2.1'), + ('pyfasta', '0.5.2'), + ('gensim', '4.3.2'), +] + +# fix requirements.txt of scenicplus +local_preinstallopts = ( + "sed -i" + " -e '/typing==3.7.4.3/d'" + " -e 's/==.*//g'" + " -e '/pyarrow-hotfix/d'" + " -e '/line-profiler/d'" + " -e '/ndindex/d'" + " -e '/sinfo/d'" + " requirements.txt && " +) +# unpin version restriction and delete typing requirement +local_pycistopic_preinstallopts = ( + "sed -i" + " -e 's/pyscenic>=0.12.0/pyscenic/'" + " -e 's/pandas==1.5/pandas/'" + " -e 's/python-Levenshtein/Levenshtein/'" + " -e 's/python-igraph/igraph/'" + " -e '/typing/d'" + # delete pyscenic and loomxpy req from commit - have versions now + " -e '/pyscenic@git/d'" + " -e '/loomxpy@git/d'" + " requirements.txt && " + "sed -i" + " -e 's/pandas == 1.5/pandas/'" + " -e 's/matplotlib < 3.7/matplotlib/'" + " pyproject.toml && " +) +# delete typing from requirements +local_pycistarget_preinstallopts = "sed -i '/typing/d' requirements.txt && " +# unpin version restriction and delete poetry.lock +local_loomxpy_preinstallopts = "sed -i 's/pyscenic>=0.12.0/pyscenic/' requirements.txt && " +local_loomxpy_preinstallopts += "sed -i 's/pyscenic = \">=0.12.0\"/pyscenic = \"*\"/' pyproject.toml && " +local_loomxpy_preinstallopts += "rm poetry.lock && " + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('bs4', '0.0.2', { + 'checksums': ['a48685c58f50fe127722417bae83fe6badf500d54b55f7e39ffe43b798653925'], + }), + ('attr', '0.3.2', { + 'checksums': ['1ceebca768181cdcce9827611b1d728e592be5d293911539ea3d0b0bfa1146f4'], + }), + ('attrs', '23.2.0', { + 'checksums': ['935dc3b529c262f6cf76e50877d35a4bd3c1de194fd41f47a2b7ae8f19971f30'], + }), + ('lda', '3.0.0', { + 'checksums': ['c9acbc1c55d2928f7e3e2336352b3382d78e43dbb0d12bf9ed97f87bce6d6708'], + }), + ('zope.interface', '6.2', { + 'checksums': ['3b6c62813c63c543a06394a636978b22dffa8c5410affc9331ce6cdb5bfa8565'], + }), + ('zope.event', '5.0', { + 'checksums': ['bac440d8d9891b4068e2b5a2c5e2c9765a9df762944bda6955f96bb9b91e67cd'], + }), + ('gevent', '24.2.1', { + 'checksums': ['432fc76f680acf7cf188c2ee0f5d3ab73b63c1f03114c7cd8a34cebbe5aa2056'], + }), + ('xmltodict', '0.13.0', { + 'checksums': ['341595a488e3e01a85a9d8911d8912fd922ede5fecc4dce437eb4b6c8d037e56'], + }), + ('suds-community', '1.1.2', { + 'modulename': 'suds', + 'checksums': ['883b4173ad23e7b20e9779ac7238b06140c50d7852afd5dc49dad1ea5f5a3d08'], + }), + ('grequests', '0.7.0', { + 'checksums': ['5c33f14268df5b8fa1107d8537815be6febbad6ec560524d6a404b7778cf6ba6'], + }), + ('pexpect', '4.9.0', { + 'checksums': ['ee7d41123f3c9911050ea2c2dac107568dc43b2d3b0c7557a33212c398ead30f'], + }), + ('colorlog', '6.8.2', { + 'checksums': ['3e3e079a41feb5a1b64f978b5ea4f46040a94f11f0e8bbb8261e3dbbeca64d44'], + }), + ('easydev', '0.12.1', { + 'checksums': ['b47b7e6f75316ac9045b46487930e16ddb567f3899310deee11d72d8e1f0a231'], + }), + ('bioservices', '1.11.2', { + 'checksums': ['31baaab4ab813b93f79995ba8cad431a16cbee99e1b0c6f9e419dd4be0c73a9e'], + }), + ('gseapy', '0.10.8', { + 'checksums': ['15be80bac73768501f5cecf6751aeb2e41416fd144bd6daa2ec453ad08a10ce0'], + }), + ('ncls', '0.0.68', { + 'checksums': ['81aaa5abb123bb21797ed2f8ef921e20222db14a3ecbc61ccf447532f2b7ba93'], + }), + ('pybigtools', '0.1.2', { + 'checksums': ['0f21bc8b4f2dce67c6e5287af895f5f28a8c6eb123d809e3ab5679e2131dbf58'], + }), + ('pybiomart', '0.2.0', { + 'checksums': ['e9eac20db921820670c646d99725b0ee279e407379e5e8c3ec7245a07425d8fe'], + }), + ('sorted_nearest', '0.0.39', { + 'checksums': ['16a51d5db87ae226b47ace43c176bb672477a1b7ba8052ea9291a6356c9c69b1'], + }), + ('pyranges', '0.0.111', { + 'checksums': ['d2cf3c31c1b9c6e1bf6e1e89254d8bd993bfb4401f2c4ede0ebc9c8e0678147d'], + }), + ('pyrle', '0.0.39', { + 'checksums': ['1be4be7814d3941db907aaf19f311bd46a407244316cadbf4b73109685c055c5'], + }), + ('pyvis', '0.3.2', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['5720c4ca8161dc5d9ab352015723abb7a8bb8fb443edeb07f7a322db34a97555'], + }), + ('url-normalize', '1.4.3', { + 'checksums': ['d23d3a070ac52a67b83a1c59a0e68f8608d1cd538783b401bc9de2c0fac999b2'], + }), + ('cattrs', '23.2.3', { + 'checksums': ['a934090d95abaa9e911dac357e3a8699e0b4b14f8529bcc7d2b1ad9d51672b9f'], + }), + ('requests_cache', '1.2.0', { + 'checksums': ['db1c709ca343cc1cd5b6c8b1a5387298eceed02306a6040760db538c885e3838'], + }), + ('scanorama', '1.7.4', { + 'checksums': ['67de100e63abc3028c7780d3a217e43e920a5781230bc6b6a51349d4605e005c'], + }), + ('rich_argparse', '1.4.0', { + 'checksums': ['c275f34ea3afe36aec6342c2a2298893104b5650528941fb53c21067276dba19'], + }), + ('scatac_fragment_tools', '0.1.0', { + 'checksums': ['e77a03ad1b7170c212f1ac672dad2c5d7e7f091b94e47b36a2ec2adc42051857'], + }), + ('snakemake_interface_common', '1.17.1', { + 'checksums': ['555c8218d9b68ddc1046f94a517e7d0f22e15bdc839d6ce149608d8ec137b9ae'], + }), + ('snakemake_interface_report_plugins', '1.0.0', { + 'checksums': ['02311cdc4bebab2a1c28469b5e6d5c6ac6e9c66998ad4e4b3229f1472127490f'], + }), + ('statistics', '1.0.3.5', { + 'checksums': ['2dc379b80b07bf2ddd5488cad06b2b9531da4dd31edb04dc9ec0dc226486c138'], + }), + ('globre', '0.1.5', { + 'checksums': ['ee214204f237e9114b8f61eeb61c2abd1e665ca3b59e5a6a0b070971c0bb12e2'], + }), + ('bidict', '0.23.1', { + 'checksums': ['03069d763bc387bbd20e7d49914e75fc4132a41937fa3405417e1a5a2d006d71'], + }), + ('tmtoolkit', '0.12.0', { + 'checksums': ['6df5429cd675989f21d9f075ddb11fe5ae273d6544fc337a2589bab2bc331909'], + }), + ('tspex', '0.6.3', { + 'checksums': ['315bfa1f60ea582777c549313cad9e9da0a4d11c5f69a6fc767bd0823dc46316'], + }), + ('plumbum', '1.8.3', { + 'checksums': ['6092c85ab970b7a7a9d5d85c75200bc93be82b33c9bdf640ffa87d2d7c8709f0'], + }), + ('pandoc', '2.3', { + 'checksums': ['e772c2c6d871146894579828dbaf1efd538eb64fc7e71d4a6b3a11a18baef90d'], + }), + ('nbsphinx', '0.9.4', { + 'checksums': ['042a60806fc23d519bc5bef59d95570713913fe442fda759d53e3aaf62104794'], + }), + ('nbsphinx-link', '1.3.0', { + 'checksums': ['fa3079a74c0dff1b2079e79a34babe770706ba8aa9cc0609c6dbfd593461a077'], + }), + ('numpydoc', '1.7.0', { + 'checksums': ['866e5ae5b6509dcf873fc6381120f5c31acf13b135636c1a81d68c166a95f921'], + }), + ('pyOpenSSL', '23.2.0', { + 'modulename': 'OpenSSL', + 'checksums': ['276f931f55a452e7dea69c7173e984eb2a4407ce413c918aa34b55f82f9b8bac'], + }), + ('entrypoints', '0.4', { + 'checksums': ['b706eddaa9218a19ebcd67b56818f05bb27589b1ca9e8d797b74affad4ccacd4'], + }), + ('ansicolors', '1.1.8', { + 'modulename': 'colors', + 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'checksums': ['00d2dde5a675579325902536738dd27e4fac1fd68f773fe36c21044eb559e187'], + }), + ('papermill', '2.6.0', { + 'checksums': ['9fe2a91912fd578f391b4cc8d6d105e73124dcd0cde2a43c3c4a1c77ac88ea24'], + }), + ('mypy_extensions', '1.0.0', { + 'checksums': ['75dbf8955dc00442a438fc4d0666508a9a97b6bd41aa2f0ffe9d2f2725af0782'], + }), + ('typing_inspect', '0.9.0', { + 'checksums': ['b23fc42ff6f6ef6954e4852c1fb512cdd18dbea03134f91f856a95ccc9461f78'], + }), + ('marshmallow', '3.21.1', { + 'checksums': ['4e65e9e0d80fc9e609574b9983cf32579f305c718afb30d7233ab818571768c3'], + }), + ('dataclasses_json', '0.6.4', { + 'checksums': ['73696ebf24936560cca79a2430cbc4f3dd23ac7bf46ed17f38e5e5e7657a6377'], + }), + ('loomxpy', '0.4.2', { + 'preinstallopts': local_loomxpy_preinstallopts, + 'checksums': ['188411b77e04fa8458c0a7f02cfb3f15b58410a020f81f522957e922e79cdd82'], + }), + ('pycisTopic', '2.0a-dca4bb6', { + 'modulename': 'pycisTopic', + 'preinstallopts': local_pycistopic_preinstallopts, + # download commit dca4bb6 to be compatible with pycistarget + 'source_urls': ['https://github.com/aertslab/pycisTopic/archive/'], + 'sources': [{'download_filename': 'dca4bb6.tar.gz', 'filename': '%(name)s-%(version)s-dca4bb6.tar.gz'}], + 'checksums': ['82edc9313bbb587aeb1540fd5b095b6eafb422fa12a5fc97ba090b99b684b240'], + }), + ('pycistarget', '1.0a1-16d14b9', { + 'preinstallopts': local_pycistarget_preinstallopts, + # download commit 16d14b9 to make '$ scenicplus' work + 'source_urls': ['https://github.com/aertslab/pycistarget/archive/'], + 'sources': [{'download_filename': '16d14b9.tar.gz', 'filename': '%(name)s-%(version)s-16d14b9.tar.gz'}], + 'checksums': ['7285ac03be9d148437442a726366d7c6f9f5f86bc6636369149a2bc2cd8e0e29'], + }), + ('scenicplus', version, { + 'preinstallopts': local_preinstallopts, + 'source_urls': ['https://github.com/aertslab/scenicplus/archive/'], + 'sources': [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}], + 'checksums': ['88cddec1ab2618861e5c93e8a0b17b8e9e2aa3a76410d882c35d472f98724e29'], + }), +] + +# copy files to let 'scenicplus init_snakemake' works +postinstallcmds = [ + "cp -r %%(builddir)s/scenicplus/scenicplus-%s*/src/scenicplus/snakemake " + "%%(installdir)s/lib/python%%(pyshortver)s/site-packages/scenicplus" % local_commit +] + +sanity_check_commands = ['scenicplus init_snakemake --help'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-7.0.4-iimpi-2023b.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-7.0.4-iimpi-2023b.eb new file mode 100644 index 000000000000..03292d904765 --- /dev/null +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-7.0.4-iimpi-2023b.eb @@ -0,0 +1,26 @@ +name = 'SCOTCH' +version = '7.0.4' + +homepage = 'https://www.labri.fr/perso/pelegrin/scotch/' +description = """Software package and libraries for sequential and parallel graph partitioning, +static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.""" + +toolchain = {'name': 'iimpi', 'version': '2023b'} +toolchainopts = {'pic': True} + +source_urls = ['https://gitlab.inria.fr/scotch/scotch/-/archive/v%(version)s/'] +sources = ['%(namelower)s-v%(version)s.tar.gz'] +checksums = ['8ef4719d6a3356e9c4ca7fefd7e2ac40deb69779a5c116f44da75d13b3d2c2c3'] + +threadedmpi = False + +builddependencies = [ + ('Bison', '3.8.2'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('zlib', '1.2.13'), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SDL2/SDL2-2.30.6-GCCcore-13.3.0.eb b/easybuild/easyconfigs/s/SDL2/SDL2-2.30.6-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..1c8130b397c6 --- /dev/null +++ b/easybuild/easyconfigs/s/SDL2/SDL2-2.30.6-GCCcore-13.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'SDL2' +version = '2.30.6' + +homepage = 'https://www.libsdl.org/' +description = "SDL: Simple DirectMedia Layer, a cross-platform multimedia library" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://www.libsdl.org/release/'] +sources = [SOURCE_TAR_GZ] +checksums = ['c6ef64ca18a19d13df6eb22df9aff19fb0db65610a74cc81dae33a82235cacd4'] + +builddependencies = [('binutils', '2.42')] + +dependencies = [ + ('X11', '20240607'), +] + +sanity_check_paths = { + 'files': ['bin/sdl2-config', 'lib/libSDL2.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/SHAP/SHAP-0.43.0-foss-2023a.eb b/easybuild/easyconfigs/s/SHAP/SHAP-0.43.0-foss-2023a.eb new file mode 100644 index 000000000000..6be374eb2136 --- /dev/null +++ b/easybuild/easyconfigs/s/SHAP/SHAP-0.43.0-foss-2023a.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonBundle' + +name = 'SHAP' +version = '0.43.0' + +homepage = "https://github.com/shap/shap" +description = """SHAP (SHapley Additive exPlanations) is a game theoretic approach to explain the output of any + machine learning model. It connects optimal credit allocation with local explanations using the classic Shapley + values from game theory and their related extensions.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('scikit-learn', '1.3.1'), + ('tqdm', '4.66.1'), + ('numba', '0.58.1'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('cloudpickle', '3.0.0', { + 'checksums': ['996d9a482c6fb4f33c1a35335cf8afd065d2a56e973270364840712d9131a882'], + }), + ('slicer', '0.0.7', { + 'checksums': ['f5d5f7b45f98d155b9c0ba6554fa9770c6b26d5793a3e77a1030fb56910ebeec'], + }), + (name, version, { + 'sources': ['%(namelower)s-%(version)s.tar.gz'], + 'checksums': ['1eabe01444a24e181ef6a7c9593b4d7c7143eefaeb1fa4d97bd5d9fdc96c4c1e'], + }), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-13.3.0-tools.eb b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-13.3.0-tools.eb new file mode 100644 index 000000000000..9d2584de1bbf --- /dev/null +++ b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-13.3.0-tools.eb @@ -0,0 +1,51 @@ +# # +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2016-2019 Juelich Supercomputing Centre, Germany +# Authors:: Markus Geimer +# Modified 2017 by Andreas Henkel +# License:: 3-clause BSD +# # + +easyblock = 'ConfigureMake' + +name = 'SIONlib' +version = '1.7.7' +# Provide a stripped-down version with renamed symbols for tools, +# see description for further details +versionsuffix = '-tools' + +homepage = 'https://www.fz-juelich.de/ias/jsc/EN/Expertise/Support/Software/SIONlib/_node.html' +description = """ + SIONlib is a scalable I/O library for parallel access to task-local files. + The library not only supports writing and reading binary data to or from + several thousands of processors into a single or a small number of physical + files, but also provides global open and close functions to access SIONlib + files in parallel. This package provides a stripped-down installation of + SIONlib for use with performance tools (e.g., Score-P), with renamed symbols + to avoid conflicts when an application using SIONlib itself is linked against + a tool requiring a different SIONlib version. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://apps.fz-juelich.de/jsc/%(namelower)s/download.php?version=%(version)sl'] +sources = ['%(namelower)s-%(version)sl.tar.gz'] +checksums = ['3b5072d8a32a9e9858d85dfe4dc01e7cfdbf54cdaa60660e760b634ee08d8a4c'] + +builddependencies = [ + ('binutils', '2.42'), +] + +configopts = '--disable-cxx --disable-fortran --disable-ompi ' + +# Comment it out if you have Xeon Phi: +configopts += '--disable-mic ' + +sanity_check_paths = { + 'files': ['bin/sionconfig'] + + ['lib/lib%s_64.a' % x for x in ['lsioncom', 'lsiongen', 'lsionser']], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/SIP/SIP-6.8.3-GCCcore-13.2.0.eb b/easybuild/easyconfigs/s/SIP/SIP-6.8.3-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..7e615a60c0ad --- /dev/null +++ b/easybuild/easyconfigs/s/SIP/SIP-6.8.3-GCCcore-13.2.0.eb @@ -0,0 +1,42 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Bart Verleye +# Center for eResearch, Auckland +# update 6.8.1: THEMBL +easyblock = 'PythonPackage' + +name = 'SIP' +version = '6.8.3' + +homepage = 'http://www.riverbankcomputing.com/software/sip/' +description = """SIP is a tool that makes it very easy to create Python bindings for C and C++ libraries.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['888547b018bb24c36aded519e93d3e513d4c6aa0ba55b7cc1affbd45cf10762c'] + +builddependencies = [ + ('binutils', '2.40'), +] +dependencies = [ + ('Python', '3.11.5'), + ('Python-bundle-PyPI', '2023.10'), + ('PLY', '3.11'), +] + +download_dep_fail = True +use_pip = True + +local_tools = ['build', 'distinfo', 'install', 'module', 'sdist', 'wheel'] +sanity_check_paths = { + 'files': ['bin/sip-%s' % x for x in local_tools], + 'dirs': ['lib/python%(pyshortver)s/site-packages/sipbuild'], +} + +sanity_pip_check = True + +sanity_check_commands = ['sip-%s --help' % x for x in local_tools] + +options = {'modulename': 'sipbuild'} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SIRIUS/SIRIUS-7.5.2-foss-2023a.eb b/easybuild/easyconfigs/s/SIRIUS/SIRIUS-7.5.2-foss-2023a.eb new file mode 100644 index 000000000000..5c7da32ecffc --- /dev/null +++ b/easybuild/easyconfigs/s/SIRIUS/SIRIUS-7.5.2-foss-2023a.eb @@ -0,0 +1,40 @@ +easyblock = 'CMakeMake' + +name = 'SIRIUS' +version = '7.5.2' + +homepage = 'https://github.com/electronic-structure/SIRIUS' +description = """SIRIUS is a domain specific library for electronic structure calculations. +It implements pseudopotential plane wave (PP-PW) and +full potential linearized augmented plane wave (FP-LAPW) methods.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/electronic-structure/SIRIUS/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['9ae01935578532c84f1d0d673dbbcdd490e26be22efa6c4acf7129f9dc1a0c60'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('pkgconf', '1.9.5'), +] +dependencies = [ + ('GSL', '2.7'), + ('libxc', '6.2.2'), + ('HDF5', '1.14.0'), + ('spglib', '2.5.0'), + ('SpFFT', '1.1.0'), + ('spla', '1.6.1'), + ('COSTA', '2.2.2'), + ('Umpire', '2024.02.1'), +] + +sanity_check_paths = { + 'files': [ + 'bin/sirius.scf', + 'lib/libsirius.%s' % SHLIB_EXT, + ], + 'dirs': ['bin', 'include/sirius'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/SKA2/SKA2-0.3.7-GCCcore-12.2.0.eb b/easybuild/easyconfigs/s/SKA2/SKA2-0.3.7-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..ec330ffc75da --- /dev/null +++ b/easybuild/easyconfigs/s/SKA2/SKA2-0.3.7-GCCcore-12.2.0.eb @@ -0,0 +1,395 @@ +easyblock = 'Cargo' + +name = 'SKA2' +version = 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'2b38e32f0abccf9987a4e3079dfb67dcd799fb61361e53e2882c3cbaf0d905d8'}, + {'windows_aarch64_gnullvm-0.52.4.tar.gz': 'bcf46cf4c365c6f2d1cc93ce535f2c8b244591df96ceee75d8e83deb70a9cac9'}, + {'windows_aarch64_msvc-0.48.5.tar.gz': 'dc35310971f3b2dbbf3f0690a219f40e2d9afcf64f9ab7cc1be722937c26b4bc'}, + {'windows_aarch64_msvc-0.52.4.tar.gz': 'da9f259dd3bcf6990b55bffd094c4f7235817ba4ceebde8e6d11cd0c5633b675'}, + {'windows_i686_gnu-0.48.5.tar.gz': 'a75915e7def60c94dcef72200b9a8e58e5091744960da64ec734a6c6e9b3743e'}, + {'windows_i686_gnu-0.52.4.tar.gz': 'b474d8268f99e0995f25b9f095bc7434632601028cf86590aea5c8a5cb7801d3'}, + {'windows_i686_msvc-0.48.5.tar.gz': '8f55c233f70c4b27f66c523580f78f1004e8b5a8b659e05a4eb49d4166cca406'}, + {'windows_i686_msvc-0.52.4.tar.gz': '1515e9a29e5bed743cb4415a9ecf5dfca648ce85ee42e15873c3cd8610ff8e02'}, + {'windows_x86_64_gnu-0.48.5.tar.gz': '53d40abd2583d23e4718fddf1ebec84dbff8381c07cae67ff7768bbf19c6718e'}, + {'windows_x86_64_gnu-0.52.4.tar.gz': '5eee091590e89cc02ad514ffe3ead9eb6b660aedca2183455434b93546371a03'}, + {'windows_x86_64_gnullvm-0.48.5.tar.gz': '0b7b52767868a23d5bab768e390dc5f5c55825b6d30b86c844ff2dc7414044cc'}, + {'windows_x86_64_gnullvm-0.52.4.tar.gz': '77ca79f2451b49fa9e2af39f0747fe999fcda4f5e241b2898624dca97a1f2177'}, + {'windows_x86_64_msvc-0.48.5.tar.gz': 'ed94fce61571a4006852b7389a063ab983c02eb1bb37b47f8272ce92d06d9538'}, + {'windows_x86_64_msvc-0.52.4.tar.gz': '32b752e52a2da0ddfbdbcc6fceadfeede4c939ed16d13e648833a61dfb611ed8'}, + {'xz2-0.1.7.tar.gz': '388c44dc09d76f1536602ead6d325eb532f5c122f17782bd57fb47baeeb767e2'}, + {'yansi-0.5.1.tar.gz': '09041cd90cf85f7f8b2df60c646f853b7f535ce68f85244eb6731cf89fa498ec'}, + {'zerocopy-0.7.32.tar.gz': '74d4d3961e53fa4c9a25a8637fc2bfaf2595b3d3ae34875568a5cf64787716be'}, + {'zerocopy-derive-0.7.32.tar.gz': '9ce1b18ccd8e73a9321186f97e46f9f04b778851177567b1975109d26a08d2a6'}, +] + +crates = [ + ('ska', version), + ('adler', '1.0.2'), + ('ahash', '0.8.11'), + ('aho-corasick', '1.1.2'), + ('allocator-api2', '0.2.16'), + ('anstream', '0.6.13'), + ('anstyle', '1.0.6'), + ('anstyle-parse', '0.2.3'), + ('anstyle-query', '1.0.2'), + ('anstyle-wincon', '3.0.2'), + ('anyhow', '1.0.81'), + ('argmin', '0.9.0'), + ('argmin-math', '0.3.0'), + ('assert_fs', '1.1.1'), + ('autocfg', '1.1.0'), + ('bincode', '1.3.3'), + ('bit-vec', '0.6.3'), + ('bitflags', '1.3.2'), + ('bitflags', '2.4.2'), + ('bstr', '1.9.1'), + ('buffer-redux', '1.0.1'), + ('bytecount', '0.6.7'), + ('byteorder', '1.5.0'), + ('bytes', '1.5.0'), + ('bzip2', '0.4.4'), + ('bzip2-sys', '0.1.11+1.0.8'), + ('cc', '1.0.90'), + ('cfg-if', '1.0.0'), + ('ciborium', '0.2.2'), + ('ciborium-io', '0.2.2'), + ('ciborium-ll', '0.2.2'), + ('clap', '4.5.2'), + ('clap_builder', '4.5.2'), + ('clap_derive', '4.5.0'), + ('clap_lex', '0.7.0'), + ('colorchoice', '1.0.0'), + ('colored', '2.1.0'), + ('console', '0.15.8'), + ('crc32fast', '1.4.0'), + ('crossbeam-channel', '0.5.12'), + ('crossbeam-deque', '0.8.5'), + ('crossbeam-epoch', '0.9.18'), + ('crossbeam-utils', '0.8.19'), + ('crunchy', '0.2.2'), + ('deranged', '0.3.11'), + ('diff', '0.1.13'), + ('difflib', '0.4.0'), + ('dirs-next', '2.0.0'), + ('dirs-sys-next', '0.1.2'), + ('doc-comment', '0.3.3'), + ('either', '1.10.0'), + ('encode_unicode', '0.3.6'), + ('equivalent', '1.0.1'), + ('errno', '0.3.8'), + ('fastrand', '2.0.1'), + ('flate2', '1.0.28'), + ('float-cmp', '0.9.0'), + ('getrandom', '0.2.12'), + ('globset', '0.4.14'), + ('globwalk', '0.9.1'), + ('half', '2.4.0'), + ('hashbrown', '0.14.3'), + ('heck', '0.4.1'), + ('hermit-abi', '0.3.9'), + ('ignore', '0.4.22'), + ('indexmap', '2.2.5'), + ('indicatif', '0.17.8'), + ('instant', '0.1.12'), + ('is-terminal', '0.4.12'), + ('itertools', '0.10.5'), + ('itoa', '1.0.10'), + ('lazy_static', '1.4.0'), + ('libc', '0.2.153'), + ('libm', '0.2.8'), + ('libredox', '0.0.1'), + ('linux-raw-sys', '0.4.13'), + ('log', '0.4.21'), + ('lzma-sys', '0.1.20'), + ('matrixmultiply', '0.3.8'), + ('memchr', '2.7.1'), + ('miniz_oxide', '0.7.2'), + ('ndarray', '0.15.6'), + ('needletail', '0.5.1'), + ('noodles-bgzf', '0.26.0'), + ('noodles-core', '0.14.0'), + ('noodles-csi', '0.30.0'), + ('noodles-tabix', '0.36.0'), + ('noodles-vcf', '0.49.0'), + ('normalize-line-endings', '0.3.0'), + ('num-complex', '0.4.5'), + ('num-conv', '0.1.0'), + ('num-integer', '0.1.46'), + ('num-traits', '0.2.18'), + ('num_cpus', '1.16.0'), + ('num_threads', '0.1.7'), + ('number_prefix', '0.4.0'), + ('once_cell', '1.19.0'), + ('paste', '1.0.14'), + ('percent-encoding', '2.3.1'), + ('pkg-config', '0.3.30'), + ('portable-atomic', '1.6.0'), + ('powerfmt', '0.2.0'), + ('ppv-lite86', '0.2.17'), + ('predicates', '2.1.5'), + ('predicates', '3.1.0'), + ('predicates-core', '1.0.6'), + ('predicates-tree', '1.0.9'), + ('pretty_assertions', '1.4.0'), + ('proc-macro2', '1.0.79'), + ('quote', '1.0.35'), + ('rand', '0.8.5'), + ('rand_chacha', '0.3.1'), + ('rand_core', '0.6.4'), + ('rand_xoshiro', '0.6.0'), + ('rawpointer', '0.2.1'), + ('rayon', '1.9.0'), + ('rayon-core', '1.12.1'), + ('redox_syscall', '0.4.1'), + ('redox_users', '0.4.4'), + ('regex', '1.10.3'), + ('regex-automata', '0.4.6'), + ('regex-syntax', '0.8.2'), + ('rustix', '0.38.31'), + ('rustversion', '1.0.14'), + ('ryu', '1.0.17'), + ('same-file', '1.0.6'), + ('serde', '1.0.197'), + ('serde_derive', '1.0.197'), + ('serde_json', '1.0.114'), + ('similar', '2.4.0'), + ('simple_logger', '4.3.3'), + ('slog', '2.7.0'), + ('slog-async', '2.8.0'), + ('slog-json', '2.6.1'), + ('slog-term', '2.9.1'), + ('snap', '1.1.1'), + ('snapbox', '0.4.17'), + ('snapbox-macros', '0.3.8'), + ('strsim', '0.11.0'), + ('syn', '2.0.52'), + ('take_mut', '0.2.2'), + ('tempfile', '3.10.1'), + ('term', '0.7.0'), + ('termtree', '0.4.1'), + ('thiserror', '1.0.58'), + ('thiserror-impl', '1.0.58'), + ('thread_local', '1.1.8'), + ('time', '0.3.34'), + ('time-core', '0.1.2'), + ('time-macros', '0.2.17'), + ('unicode-ident', '1.0.12'), + ('unicode-width', '0.1.11'), + ('utf8parse', '0.2.1'), + ('version_check', '0.9.4'), + ('walkdir', '2.5.0'), + ('wasi', '0.11.0+wasi-snapshot-preview1'), + ('winapi', '0.3.9'), + ('winapi-i686-pc-windows-gnu', '0.4.0'), + ('winapi-util', '0.1.6'), + ('winapi-x86_64-pc-windows-gnu', '0.4.0'), + ('windows-sys', '0.48.0'), + ('windows-sys', '0.52.0'), + ('windows-targets', '0.48.5'), + ('windows-targets', '0.52.4'), + ('windows_aarch64_gnullvm', '0.48.5'), + ('windows_aarch64_gnullvm', '0.52.4'), + ('windows_aarch64_msvc', '0.48.5'), + ('windows_aarch64_msvc', '0.52.4'), + ('windows_i686_gnu', '0.48.5'), + ('windows_i686_gnu', '0.52.4'), + ('windows_i686_msvc', '0.48.5'), + ('windows_i686_msvc', '0.52.4'), + ('windows_x86_64_gnu', '0.48.5'), + ('windows_x86_64_gnu', '0.52.4'), + ('windows_x86_64_gnullvm', '0.48.5'), + ('windows_x86_64_gnullvm', '0.52.4'), + ('windows_x86_64_msvc', '0.48.5'), + ('windows_x86_64_msvc', '0.52.4'), + ('xz2', '0.1.7'), + ('yansi', '0.5.1'), + ('zerocopy', '0.7.32'), + ('zerocopy-derive', '0.7.32'), +] + +builddependencies = [ + ('binutils', '2.39'), + ('Rust', '1.75.0'), +] + +sanity_check_paths = { + 'files': ['bin/ska'], + 'dirs': [], +} + +sanity_check_commands = ["ska --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SOCI/SOCI-4.0.3-GCC-12.3.0.eb b/easybuild/easyconfigs/s/SOCI/SOCI-4.0.3-GCC-12.3.0.eb new file mode 100644 index 000000000000..e100da22edbd --- /dev/null +++ b/easybuild/easyconfigs/s/SOCI/SOCI-4.0.3-GCC-12.3.0.eb @@ -0,0 +1,52 @@ +easyblock = 'CMakeMake' + +name = 'SOCI' +version = '4.0.3' + +homepage = 'http://soci.sourceforge.net/' +description = """SOCI is a database access library for C++ that makes the illusion of embedding SQL queries in the + regular C++ code, staying entirely within the Standard C++.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/SOCI/soci/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['4b1ff9c8545c5d802fbe06ee6cd2886630e5c03bf740e269bb625b45cf934928'] + +builddependencies = [ + ('CMake', '3.26.3'), +] + +dependencies = [ + ('Boost', '1.82.0'), + ('SQLite', '3.42.0'), + ('PostgreSQL', '16.1'), +] + +# Matches RStudio (1.4.1717) install options +# https://github.com/rstudio/rstudio/blob/ddcd7191ec89c4da00e77afae7e9f27e61e87c36/dependencies/common/install-soci +configopts = "-DCMAKE_POSITION_INDEPENDENT_CODE:BOOL=true " +configopts += "-DSOCI_TESTS=OFF " +configopts += "-DSOCI_CXX11=ON " +configopts += "-DSOCI_EMPTY=OFF " +configopts += '-DCMAKE_INCLUDE_PATH="$EBROOTBOOST/include" ' +configopts += "-DBoost_USE_STATIC_LIBS=ON " +configopts += '-DCMAKE_LIBRARY_PATH="$EBROOTBOOST/lib" ' +configopts += "-DWITH_BOOST=ON " +configopts += "-DWITH_POSTGRESQL=ON " +configopts += "-DWITH_SQLITE3=ON " +configopts += "-DWITH_DB2=OFF " +configopts += "-DWITH_MYSQL=OFF " +configopts += "-DWITH_ORACLE=OFF " +configopts += "-DWITH_FIREBIRD=OFF " +configopts += "-DWITH_ODBC=OFF " +configopts += "-DBoost_DEBUG=1 " + +local_dbs = ['postgresql', 'sqlite3'] + +sanity_check_paths = { + 'files': ['lib/libsoci_%s.%s' % (x, SHLIB_EXT) for x in local_dbs + ['core']], + 'dirs': ['include/soci/%s' % x for x in local_dbs], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.1.1-gompi-2023b.eb b/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.1.1-gompi-2023b.eb new file mode 100644 index 000000000000..624658d8e2be --- /dev/null +++ b/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.1.1-gompi-2023b.eb @@ -0,0 +1,76 @@ +# updated: Denis Kristak (INUITS) +# updated: Sebastien Moretti (SIB - Vital-IT) +# updated: Pavel Tománek (INUITS) +easyblock = 'CMakeMake' + +name = 'SRA-Toolkit' +version = '3.1.1' + +homepage = 'https://github.com/ncbi/sra-tools' +description = """The SRA Toolkit, and the source-code SRA System Development + Kit (SDK), will allow you to programmatically access data housed within SRA + and convert it from the SRA format""" +github_account = 'ncbi' + +toolchain = {'name': 'gompi', 'version': '2023b'} +toolchainopts = {'extra_cflags': '-DH5_USE_110_API'} + +source_urls = ['https://github.com/ncbi/sra-tools/archive/refs/tags/'] +sources = [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['96b110bd5a30ad312e2f02552062b48a77d40c763e6aba5bb84e83662a505cf1'] + +builddependencies = [ + ('CMake', '3.27.6'), + ('flex', '2.6.4'), + ('Bison', '3.8.2'), + ('Perl', '5.38.0'), +] + +dependencies = [ + ('Python', '3.11.5'), + ('Java', '11', '', SYSTEM), + ('OpenSSL', '1.1', '', SYSTEM), + ('ncbi-vdb', version), + ('bzip2', '1.0.8'), + ('file', '5.43'), + ('HDF5', '1.14.3'), + ('libxml2', '2.11.5'), + ('zlib', '1.2.13'), +] + +configopts = '-DVDB_INCDIR="$EBROOTNCBIMINVDB/include" -DVDB_LIBDIR="$EBROOTNCBIMINVDB/lib" ' +configopts += '-DBUILD_TOOLS_LOADERS=ON -DBUILD_TOOLS_INTERNAL=ON' + +postinstallcmds = [ + "cp -r %(start_dir)s/ngs/ngs-python/ %(installdir)s/", +] + +_sra_bin = [ + 'abi-dump', 'abi-load', 'align-info', 'bam-load', 'cache-mgr', 'cg-load', 'copycat', 'fasterq-dump', 'fastq-dump', + 'fastq-load', 'helicos-load', 'illumina-dump', 'illumina-load', 'kar', 'kdbmeta', 'latf-load', 'pacbio-load', + 'prefetch', 'rcexplain', 'sam-dump', 'sff-dump', 'sff-load', 'srapath', 'sra-pileup', 'sra-sort', 'sra-stat', + 'sratools', 'srf-load', 'test-sra', 'vdb-config', 'vdb-copy', 'vdb-decrypt', 'vdb-dump', 'vdb-encrypt', 'vdb-lock', + 'vdb-unlock', 'vdb-validate', +] + +_ngs_libs = ['libncbi-ngs.a', 'libncbi-ngs-c++.a', 'libncbi-ngs.%s' % SHLIB_EXT, + 'libngs-c++.a', 'libngs-c++.%s' % SHLIB_EXT] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in _sra_bin] + ['lib/%s' % y for y in _ngs_libs], + 'dirs': ['jar', 'include/ncbi-vdb', 'include/ngs'] +} + +sanity_check_commands = [ + "abi-dump --help", + "kar --help", + "sra-sort --help", + "python -c 'import ngs'", +] + +modextrapaths = { + 'CLASSPATH': 'jar/ngs-java.jar', + 'PYTHONPATH': 'ngs-python', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.7.11a-GCC-12.2.0.eb b/easybuild/easyconfigs/s/STAR/STAR-2.7.11a-GCC-12.2.0.eb index 42f094bb67b8..a61fe5e85bbc 100644 --- a/easybuild/easyconfigs/s/STAR/STAR-2.7.11a-GCC-12.2.0.eb +++ b/easybuild/easyconfigs/s/STAR/STAR-2.7.11a-GCC-12.2.0.eb @@ -24,6 +24,10 @@ checksums = [ {'STAR-%(version)s_use-external-htslib.patch': '2fdc3ed9372d983f77d861d6f16a60a553598358dce9ff8216f96eb20e63ce4e'}, ] +builddependencies = [ + ('xxd', '9.0.1696'), +] + dependencies = [ ('HTSlib', '1.17'), ('zlib', '1.2.12'), @@ -31,6 +35,9 @@ dependencies = [ start_dir = 'source' +# by default this is set to -mavx2 which makes it fail on non x86 systems +prebuildopts = 'CXXFLAGS_SIMD= ' + buildopts = ' STAR && make STARlong' files_to_copy = [ diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.7.11a-GCC-12.3.0.eb b/easybuild/easyconfigs/s/STAR/STAR-2.7.11a-GCC-12.3.0.eb index 1943af96d5ef..a017a2ba1094 100644 --- a/easybuild/easyconfigs/s/STAR/STAR-2.7.11a-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/s/STAR/STAR-2.7.11a-GCC-12.3.0.eb @@ -24,6 +24,10 @@ checksums = [ {'STAR-%(version)s_use-external-htslib.patch': '2fdc3ed9372d983f77d861d6f16a60a553598358dce9ff8216f96eb20e63ce4e'}, ] +builddependencies = [ + ('xxd', '9.0.2112'), +] + dependencies = [ ('HTSlib', '1.18'), ('zlib', '1.2.13'), @@ -31,6 +35,9 @@ dependencies = [ start_dir = 'source' +# by default this is set to -mavx2 which makes it fail on non x86 systems +prebuildopts = 'CXXFLAGS_SIMD= ' + buildopts = ' STAR && make STARlong' files_to_copy = [ diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.7.11b-GCC-12.3.0.eb b/easybuild/easyconfigs/s/STAR/STAR-2.7.11b-GCC-12.3.0.eb index cf16b5c2979e..67cac5d0f479 100644 --- a/easybuild/easyconfigs/s/STAR/STAR-2.7.11b-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/s/STAR/STAR-2.7.11b-GCC-12.3.0.eb @@ -24,6 +24,10 @@ checksums = [ {'STAR-2.7.11a_use-external-htslib.patch': '2fdc3ed9372d983f77d861d6f16a60a553598358dce9ff8216f96eb20e63ce4e'}, ] +builddependencies = [ + ('xxd', '9.0.2112'), +] + dependencies = [ ('HTSlib', '1.18'), ('zlib', '1.2.13'), @@ -31,6 +35,9 @@ dependencies = [ start_dir = 'source' +# by default this is set to -mavx2 which makes it fail on non x86 systems +prebuildopts = 'CXXFLAGS_SIMD= ' + buildopts = ' STAR && make STARlong' files_to_copy = [ diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.7.11b-GCC-13.2.0.eb b/easybuild/easyconfigs/s/STAR/STAR-2.7.11b-GCC-13.2.0.eb index a86f215d8dd3..886aa0a24c57 100644 --- a/easybuild/easyconfigs/s/STAR/STAR-2.7.11b-GCC-13.2.0.eb +++ b/easybuild/easyconfigs/s/STAR/STAR-2.7.11b-GCC-13.2.0.eb @@ -35,6 +35,9 @@ dependencies = [ start_dir = 'source' +# by default this is set to -mavx2 which makes it fail on non x86 systems +prebuildopts = 'CXXFLAGS_SIMD= ' + buildopts = ' STAR && make STARlong' files_to_copy = [ diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.7.11b_alpha_2024-02-09-GCC-12.3.0.eb b/easybuild/easyconfigs/s/STAR/STAR-2.7.11b_alpha_2024-02-09-GCC-12.3.0.eb new file mode 100644 index 000000000000..a0a119a428c7 --- /dev/null +++ b/easybuild/easyconfigs/s/STAR/STAR-2.7.11b_alpha_2024-02-09-GCC-12.3.0.eb @@ -0,0 +1,57 @@ +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# Based on STAR-2.7.7a-GCC-10.2.0.eb +# uploaded by J. Sassmannshausen +# modified by Thomas Eylenbosch + +easyblock = 'MakeCp' + +name = 'STAR' +version = '2.7.11b_alpha_2024-02-09' + +homepage = 'https://github.com/dobinlab/STAR_pre_releases' +description = "STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays." + +toolchain = {'name': 'GCC', 'version': '12.3.0'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/dobinlab/STAR_pre_releases/archive/'] +sources = ['%(version)s.tar.gz'] +patches = ['STAR-2.7.11a_use-external-htslib.patch'] +checksums = [ + {'2.7.11b_alpha_2024-02-09.tar.gz': '7a7bae1f802fc5bc5b270da89e66a824480fb33e21f7ebfbf7ed56e1d4907c1c'}, + {'STAR-2.7.11a_use-external-htslib.patch': '2fdc3ed9372d983f77d861d6f16a60a553598358dce9ff8216f96eb20e63ce4e'}, +] + +builddependencies = [ + ('xxd', '9.0.2112'), +] + +dependencies = [ + ('HTSlib', '1.18'), + ('zlib', '1.2.13'), +] + +start_dir = 'source' + +# by default this is set to -mavx2 which makes it fail on non x86 systems +prebuildopts = 'CXXFLAGS_SIMD= ' + +buildopts = ' STAR && make STARlong' + +files_to_copy = [ + (['source/%(name)s', 'source/%(name)slong'], 'bin'), + 'CHANGES.md', 'doc', 'extras', 'LICENSE', 'README.md', 'RELEASEnotes.md', +] + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'bin/%(name)slong'], + 'dirs': [], +} + +sanity_check_commands = [ + "STAR --help", + "STARlong --help", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/STREAM/STREAM-5.10-intel-compilers-2024.2.0.eb b/easybuild/easyconfigs/s/STREAM/STREAM-5.10-intel-compilers-2024.2.0.eb new file mode 100644 index 000000000000..17fdbcab3a4f --- /dev/null +++ b/easybuild/easyconfigs/s/STREAM/STREAM-5.10-intel-compilers-2024.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'CmdCp' + +name = 'STREAM' +version = '5.10' + +homepage = 'https://www.cs.virginia.edu/stream/' +description = """The STREAM benchmark is a simple synthetic benchmark program that measures sustainable + memory bandwidth (in MB/s) and the corresponding computation rate for simple vector kernels.""" + +toolchain = {'name': 'intel-compilers', 'version': '2024.2.0'} +toolchainopts = {'openmp': True} + +source_urls = ['https://www.cs.virginia.edu/stream/FTP/Code/'] +sources = [{'download_filename': '%(namelower)s.c', 'filename': 'stream-%(version)s.c', 'extract_cmd': "cp %s ."}] +checksums = ['a52bae5e175bea3f7832112af9c085adab47117f7d2ce219165379849231692b'] + +# 10 million array elements (1000 runs): requires ~224MB of memory +local_cmds = "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=10000000 -DNTIMES=1000 -o stream_1Kx10M; " +# 100 million array elements (1000 runs): requires ~2.2GiB of memory +local_cmds += "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=100000000 -DNTIMES=1000 -o stream_1Kx100M; " +# 1 billion array elements (1000 runs): requires ~22.4 GiB of memory +local_cmds += "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=1000000000 -DNTIMES=1000 -o stream_1Kx1B; " +# 2.5 billion array elements (1000 runs): requires ~56 GiB of memory +local_cmds += "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=2500000000 -DNTIMES=1000 -o stream_1Kx2.5B; " +# 5 billion array elements (1000 runs): requires ~111 GiB of memory +local_cmds += "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=5000000000 -DNTIMES=1000 -o stream_1Kx5B; " + +cmds_map = [('stream-%(version)s.c', local_cmds)] + +files_to_copy = [(['stream_1Kx10M', 'stream_1Kx100M', 'stream_1Kx1B', 'stream_1Kx2.5B', 'stream_1Kx5B'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/stream_1Kx10M', 'bin/stream_1Kx100M', 'bin/stream_1Kx1B', 'bin/stream_1Kx2.5B', 'bin/stream_1Kx5B'], + 'dirs': [], +} + +tests = ['%(installdir)s/bin/stream_1Kx10M'] + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-7.1.0-foss-2023b.eb b/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-7.1.0-foss-2023b.eb new file mode 100644 index 000000000000..dd1f8cff948a --- /dev/null +++ b/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-7.1.0-foss-2023b.eb @@ -0,0 +1,46 @@ +easyblock = 'CMakeMake' + +name = 'STRUMPACK' +version = '7.1.0' + +homepage = 'https://fastmath-scidac.llnl.gov/software/strumpack.html' +description = """STRUMPACK - STRUctured Matrix PACKage - Fast linear solvers and preconditioner + for both dense and sparse systems using low-rank structured factorization with randomized sampling.""" + +toolchain = {'name': 'foss', 'version': '2023b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/pghysels/%(name)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['a3e80e0530ea1cc6b62c22699cfe5f02f81794321f225440f0e08bceed69c241'] + +builddependencies = [ + ('CMake', '3.27.6'), +] + +dependencies = [ + ('zlib', '1.2.13'), + ('ParMETIS', '4.0.3'), + ('SCOTCH', '7.0.4'), +] + +configopts = '-DSTRUMPACK_USE_OPENMP=ON ' +configopts += '-DTPL_METIS_INCLUDE_DIRS=${EBROOTPARMETIS}/include ' +configopts += '-DTPL_METIS_LIBRARY_DIR=${EBROOTPARMETIS}/lib ' +configopts += '-DTPL_ENABLE_PARMETIS=ON ' +configopts += '-DTPL_PARMETIS_INCLUDE_DIRS=${EBROOTPARMETIS}/include ' +configopts += '-DTPL_PARMETIS_LIBRARY_DIR=${EBROOTPARMETIS}/lib ' +configopts += '-DTPL_ENABLE_SCOTCH=ON ' +configopts += '-DTPL_SCOTCH_INCLUDE_DIRS=${EBROOTSCOTCH}/include ' +configopts += '-DTPL_SCOTCH_LIBRARY_DIR=${EBROOTSCOTCH}/lib ' +configopts += '-DTPL_ENABLE_BPACK=OFF ' +configopts += '-DTPL_ENABLE_ZFP=OFF ' +configopts += '-DTPL_ENABLE_SLATE=OFF ' + +sanity_check_paths = { + 'files': ['lib/libstrumpack.a'], + 'dirs': ['include/%s' % x for x in ['BLR', 'clustering', 'dense', 'HSS', 'kernel', 'misc', 'python', 'sparse']] + + ['lib'], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-7.1.0-intel-2023b.eb b/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-7.1.0-intel-2023b.eb new file mode 100644 index 000000000000..b6ff89201c81 --- /dev/null +++ b/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-7.1.0-intel-2023b.eb @@ -0,0 +1,47 @@ +easyblock = 'CMakeMake' + +name = 'STRUMPACK' +version = '7.1.0' + +homepage = 'https://fastmath-scidac.llnl.gov/software/strumpack.html' +description = """STRUMPACK - STRUctured Matrix PACKage - Fast linear solvers and preconditioner + for both dense and sparse systems using low-rank structured factorization with randomized sampling.""" + +toolchain = {'name': 'intel', 'version': '2023b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/pghysels/%(name)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['a3e80e0530ea1cc6b62c22699cfe5f02f81794321f225440f0e08bceed69c241'] + +builddependencies = [ + ('CMake', '3.27.6'), +] + +dependencies = [ + ('zlib', '1.2.13'), + ('ParMETIS', '4.0.3'), + ('SCOTCH', '7.0.4'), +] + +configopts = '-DSTRUMPACK_USE_OPENMP=ON ' +configopts += '-DTPL_SCALAPACK_LIBRARIES="${LIBSCALAPACK_MT}" ' +configopts += '-DTPL_METIS_INCLUDE_DIRS=${EBROOTPARMETIS}/include ' +configopts += '-DTPL_METIS_LIBRARY_DIR=${EBROOTPARMETIS}/lib ' +configopts += '-DTPL_ENABLE_PARMETIS=ON ' +configopts += '-DTPL_PARMETIS_INCLUDE_DIRS=${EBROOTPARMETIS}/include ' +configopts += '-DTPL_PARMETIS_LIBRARY_DIR=${EBROOTPARMETIS}/lib ' +configopts += '-DTPL_ENABLE_SCOTCH=ON ' +configopts += '-DTPL_SCOTCH_INCLUDE_DIRS=${EBROOTSCOTCH}/include ' +configopts += '-DTPL_SCOTCH_LIBRARY_DIR=${EBROOTSCOTCH}/lib ' +configopts += '-DTPL_ENABLE_BPACK=OFF ' +configopts += '-DTPL_ENABLE_ZFP=OFF ' +configopts += '-DTPL_ENABLE_SLATE=OFF ' + +sanity_check_paths = { + 'files': ['lib/libstrumpack.a'], + 'dirs': ['include/%s' % x for x in ['BLR', 'clustering', 'dense', 'HSS', 'kernel', 'misc', 'python', 'sparse']] + + ['lib'], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/SVDSS2/SVDSS2-2.0.0-alpha.3-GCC-12.3.0.eb b/easybuild/easyconfigs/s/SVDSS2/SVDSS2-2.0.0-alpha.3-GCC-12.3.0.eb new file mode 100644 index 000000000000..404f2ce58f35 --- /dev/null +++ b/easybuild/easyconfigs/s/SVDSS2/SVDSS2-2.0.0-alpha.3-GCC-12.3.0.eb @@ -0,0 +1,56 @@ +easyblock = 'CMakeMakeCp' + +name = 'SVDSS2' +version = '2.0.0-alpha.3' + +homepage = 'https://github.com/Parsoa/SVDSS' +description = "Improved structural variant discovery in accurate long reads using sample-specific strings (SFS)." + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +sources = [{ + 'filename': 'v%(version)s.tar.gz', + 'git_config': { + 'url': 'https://github.com/Parsoa', + 'repo_name': 'SVDSS', + 'tag': 'v%(version)s', + 'recursive': True, + 'keep_git_dir': True, + } +}] +checksums = [None] + +builddependencies = [ + ('CMake', '3.26.3'), + ('make', '4.4.1'), + ('Autotools', '20220317'), + ('zlib', '1.2.13'), + ('bzip2', '1.0.8'), + ('XZ', '5.4.2'), + ('SAMtools', '1.18'), + ('BCFtools', '1.18'), +] +dependencies = [ + ('HTSlib', '1.18'), + ('libdeflate', '1.18'), + ('parasail', '2.6.2'), + ('spdlog', '1.11.0'), +] + +files_to_copy = [ + (['SVDSS'], 'bin'), + (['*'], 'lib'), +] + +separate_build_dir = False + +postinstallcmds = ["cd %(installdir)s/lib && rm SVDSS"] + +sanity_check_paths = { + 'files': ['bin/SVDSS'], + 'dirs': ['lib'], +} + +sanity_check_commands = ['SVDSS --version'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/Safetensors/Safetensors-0.4.3-gfbf-2023a.eb b/easybuild/easyconfigs/s/Safetensors/Safetensors-0.4.3-gfbf-2023a.eb new file mode 100644 index 000000000000..3c686b7380e4 --- /dev/null +++ b/easybuild/easyconfigs/s/Safetensors/Safetensors-0.4.3-gfbf-2023a.eb @@ -0,0 +1,295 @@ +easyblock = "CargoPythonBundle" + +name = 'Safetensors' +version = '0.4.3' +_rustver = '1.75.0' + +homepage = 'https://huggingface.co/docs/safetensors' +description = """Safetensors is a new simple format for storing tensors safely (as opposed to +pickle) and that is still fast (zero-copy). Safetensors is really fast. + +This variant of Safetensors is installed with support for numpy and PyTorch +""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +builddependencies = [ + ('Rust', _rustver), + ('maturin', '1.4.0', '-Rust-' + _rustver), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), +] + +# crates generated on 2024-05-24 from directories savetensors/ and bindings/python/ +crates = [ + ('aho-corasick', '1.1.3'), + ('anes', '0.1.6'), + ('anstyle', '1.0.7'), + ('autocfg', '1.2.0'), + ('autocfg', '1.3.0'), + ('bitflags', '1.3.2'), + ('bitflags', '2.5.0'), + ('bit-set', '0.5.3'), + ('bit-vec', '0.6.3'), + ('bumpalo', '3.16.0'), + ('cast', '0.3.0'), + ('cfg-if', '1.0.0'), + ('ciborium', '0.2.2'), + ('ciborium-io', '0.2.2'), + ('ciborium-ll', '0.2.2'), + ('clap', '4.5.4'), + ('clap_builder', '4.5.2'), + ('clap_lex', '0.7.0'), + ('criterion', '0.5.1'), + ('criterion-plot', '0.5.0'), + ('crossbeam-deque', '0.8.5'), + ('crossbeam-epoch', '0.9.18'), + ('crossbeam-utils', '0.8.20'), + ('crunchy', '0.2.2'), + ('either', '1.12.0'), + ('errno', '0.3.9'), + ('fastrand', '2.1.0'), + ('fnv', '1.0.7'), + ('getrandom', '0.2.15'), + ('half', '2.4.1'), + ('heck', '0.4.1'), + ('hermit-abi', '0.3.9'), + ('indoc', '2.0.5'), + ('is-terminal', '0.4.12'), + ('itertools', '0.10.5'), + ('itoa', '1.0.11'), + ('js-sys', '0.3.69'), + ('lazy_static', '1.4.0'), + ('libc', '0.2.153'), + ('libc', '0.2.155'), + ('libm', '0.2.8'), + ('linux-raw-sys', '0.4.14'), + ('lock_api', '0.4.11'), + ('log', '0.4.21'), + ('memchr', '2.7.2'), + ('memmap2', '0.9.4'), + ('memoffset', '0.9.1'), + ('num-traits', '0.2.19'), + ('once_cell', '1.19.0'), + ('oorandom', '11.1.3'), + ('parking_lot', '0.12.1'), + ('parking_lot_core', '0.9.9'), + ('plotters', '0.3.6'), + ('plotters-backend', '0.3.6'), + ('plotters-svg', '0.3.6'), + ('portable-atomic', '1.6.0'), + ('ppv-lite86', '0.2.17'), + ('proc-macro2', '1.0.80'), + ('proc-macro2', '1.0.83'), + ('proptest', '1.4.0'), + ('pyo3', '0.21.1'), + ('pyo3-build-config', '0.21.1'), + ('pyo3-ffi', '0.21.1'), + ('pyo3-macros', '0.21.1'), + ('pyo3-macros-backend', '0.21.1'), + ('quick-error', '1.2.3'), + ('quote', '1.0.36'), + ('rand', '0.8.5'), + ('rand_chacha', '0.3.1'), + ('rand_core', '0.6.4'), + ('rand_xorshift', '0.3.0'), + ('rayon', '1.10.0'), + ('rayon-core', '1.12.1'), + ('redox_syscall', '0.4.1'), + ('regex', '1.10.4'), + ('regex-automata', '0.4.6'), + ('regex-syntax', '0.8.3'), + ('rustix', '0.38.34'), + ('rusty-fork', '0.3.0'), + ('ryu', '1.0.17'), + ('ryu', '1.0.18'), + ('same-file', '1.0.6'), + ('scopeguard', '1.2.0'), + ('serde', '1.0.197'), + ('serde', '1.0.202'), + ('serde_derive', '1.0.197'), + ('serde_derive', '1.0.202'), + ('serde_json', '1.0.115'), + ('serde_json', '1.0.117'), + ('smallvec', '1.13.2'), + ('syn', '2.0.59'), + ('syn', '2.0.66'), + ('target-lexicon', '0.12.14'), + ('tempfile', '3.10.1'), + ('tinytemplate', '1.2.1'), + ('unarray', '0.1.4'), + ('unicode-ident', '1.0.12'), + ('unindent', '0.2.3'), + ('wait-timeout', '0.2.0'), + ('walkdir', '2.5.0'), + ('wasi', '0.11.0+wasi-snapshot-preview1'), + ('wasm-bindgen', '0.2.92'), + ('wasm-bindgen-backend', '0.2.92'), + ('wasm-bindgen-macro', '0.2.92'), + ('wasm-bindgen-macro-support', '0.2.92'), + ('wasm-bindgen-shared', '0.2.92'), + ('web-sys', '0.3.69'), + ('winapi-util', '0.1.8'), + ('windows_aarch64_gnullvm', '0.48.5'), + ('windows_aarch64_gnullvm', '0.52.5'), + ('windows_aarch64_msvc', '0.48.5'), + ('windows_aarch64_msvc', '0.52.5'), + ('windows_i686_gnu', '0.48.5'), + ('windows_i686_gnu', '0.52.5'), + ('windows_i686_gnullvm', '0.52.5'), + ('windows_i686_msvc', '0.48.5'), + ('windows_i686_msvc', '0.52.5'), + ('windows-sys', '0.52.0'), + ('windows-targets', '0.48.5'), + ('windows-targets', '0.52.5'), + ('windows_x86_64_gnu', '0.48.5'), + ('windows_x86_64_gnu', '0.52.5'), + ('windows_x86_64_gnullvm', '0.48.5'), + ('windows_x86_64_gnullvm', '0.52.5'), + ('windows_x86_64_msvc', '0.48.5'), + 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'2b38e32f0abccf9987a4e3079dfb67dcd799fb61361e53e2882c3cbaf0d905d8'}, + {'windows_aarch64_gnullvm-0.52.5.tar.gz': '7088eed71e8b8dda258ecc8bac5fb1153c5cffaf2578fc8ff5d61e23578d3263'}, + {'windows_aarch64_msvc-0.48.5.tar.gz': 'dc35310971f3b2dbbf3f0690a219f40e2d9afcf64f9ab7cc1be722937c26b4bc'}, + {'windows_aarch64_msvc-0.52.5.tar.gz': '9985fd1504e250c615ca5f281c3f7a6da76213ebd5ccc9561496568a2752afb6'}, + {'windows_i686_gnu-0.48.5.tar.gz': 'a75915e7def60c94dcef72200b9a8e58e5091744960da64ec734a6c6e9b3743e'}, + {'windows_i686_gnu-0.52.5.tar.gz': '88ba073cf16d5372720ec942a8ccbf61626074c6d4dd2e745299726ce8b89670'}, + {'windows_i686_gnullvm-0.52.5.tar.gz': '87f4261229030a858f36b459e748ae97545d6f1ec60e5e0d6a3d32e0dc232ee9'}, + {'windows_i686_msvc-0.48.5.tar.gz': '8f55c233f70c4b27f66c523580f78f1004e8b5a8b659e05a4eb49d4166cca406'}, + {'windows_i686_msvc-0.52.5.tar.gz': 'db3c2bf3d13d5b658be73463284eaf12830ac9a26a90c717b7f771dfe97487bf'}, + {'windows-sys-0.52.0.tar.gz': '282be5f36a8ce781fad8c8ae18fa3f9beff57ec1b52cb3de0789201425d9a33d'}, + {'windows-targets-0.48.5.tar.gz': '9a2fa6e2155d7247be68c096456083145c183cbbbc2764150dda45a87197940c'}, + {'windows-targets-0.52.5.tar.gz': '6f0713a46559409d202e70e28227288446bf7841d3211583a4b53e3f6d96e7eb'}, + {'windows_x86_64_gnu-0.48.5.tar.gz': '53d40abd2583d23e4718fddf1ebec84dbff8381c07cae67ff7768bbf19c6718e'}, + {'windows_x86_64_gnu-0.52.5.tar.gz': '4e4246f76bdeff09eb48875a0fd3e2af6aada79d409d33011886d3e1581517d9'}, + {'windows_x86_64_gnullvm-0.48.5.tar.gz': '0b7b52767868a23d5bab768e390dc5f5c55825b6d30b86c844ff2dc7414044cc'}, + {'windows_x86_64_gnullvm-0.52.5.tar.gz': '852298e482cd67c356ddd9570386e2862b5673c85bd5f88df9ab6802b334c596'}, + {'windows_x86_64_msvc-0.48.5.tar.gz': 'ed94fce61571a4006852b7389a063ab983c02eb1bb37b47f8272ce92d06d9538'}, + {'windows_x86_64_msvc-0.52.5.tar.gz': 'bec47e5bfd1bff0eeaf6d8b485cc1074891a197ab4225d504cb7a1ab88b02bf0'}, +] + +use_pip = True + +exts_list = [ + ('safetensors', version, { + 'checksums': ['2f85fc50c4e07a21e95c24e07460fe6f7e2859d0ce88092838352b798ce711c2'], + }), +] + +sanity_pip_check = True + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/s/Sagemath/Sagemath-10.4-foss-2023b.eb b/easybuild/easyconfigs/s/Sagemath/Sagemath-10.4-foss-2023b.eb new file mode 100644 index 000000000000..dcc9d919c130 --- /dev/null +++ b/easybuild/easyconfigs/s/Sagemath/Sagemath-10.4-foss-2023b.eb @@ -0,0 +1,158 @@ +easyblock = 'PythonBundle' + +name = 'Sagemath' +version = '10.4' + +homepage = 'https://doc.sagemath.org/html/en/index.html' +description = """Sage is open source mathematical software released under the GNU General Public Licence GPLv2+, + and includes packages that have compatible software licenses. + People all around the globe have contributed to the development of Sage. Full documentation is available online.""" + +toolchain = {'name': 'foss', 'version': '2023b'} + +builddependencies = [ + ('Cython', '3.0.10'), + ('Python-bundle-PyPI', '2023.10'), + ('Boost', '1.83.0'), +] + +dependencies = [ + ('Python', '3.11.5'), + ('SciPy-bundle', '2023.11'), + ('ECL', '24.5.10'), + ('FFLAS-FFPACK', '2.5.0'), + ('eclib', '20240408'), + ('GSL', '2.7'), + ('LinBox', '1.7.0'), + ('Singular', '4.4.0'), + ('libpng', '1.6.40'), + ('libgd', '2.3.3'), + ('m4ri', '20200125'), + ('cysignals', '1.11.4'), + ('gmpy2', '2.1.5'), + ('GMP-ECM', '7.0.5'), + ('MPFI', '1.5.4'), + ('cliquer', '1.21'), + ('nauty', '2.8.8'), + ('SYMMETRICA', '2.0'), + ('lcalc', '2.0.5'), + ('gap', '4.13.0'), + ('giac', '1.9.0-99'), + ('m4rie', '20200125'), + ('libhomfly', '1.02r6'), + ('libbraiding', '1.2'), + ('planarity', '3.0.2.0'), + ('rankwidth', '0.9'), + ('BRiAl', '1.2.12'), + ('bliss', '0.77'), + ('coxeter', '20180226'), + ('mcqd', '1.0.0'), + ('SharedMeatAxe', '1.0.1'), + ('sirocco', '2.1.0'), + ('tdlib', '0.9.3'), + ('pkgconfig', '1.5.5', '-python'), + ('matplotlib', '3.8.2'), + ('networkx', '3.2.1'), + ('sympy', '1.12'), + ('IPython', '8.17.2'), + ('Pillow', '10.2.0'), + ('fpylll', '0.6.1'), + ('primecountpy', '0.1.0'), + ('lrcalc', '2.1'), + ('PyZMQ', '25.1.2'), + ('tornado', '6.4'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('cypari2', '2.2.0', { + 'checksums': ['817606bf661b71d33e1d012421907a4f8fb09dd81b7d3e3ae179b3978020bbf1'], + }), + ('memory_allocator', '0.1.4', { + 'checksums': ['d609216b03031967e2b45a804b12ff9029578f4ec019fde42cf6aed6ca09efe4'], + }), + ('sage_setup', version, { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['4797ceae2f5f636a756f4121011246445611f7a56bced2df431328fe013c52c7'], + }), + ('conway_polynomials', '0.10', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['a354b4ac0a9985da75e2ac6ec6d7de2902396eff48913eeed86a962486171c28'], + }), + ('comm', '0.2.2', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['e6fb86cb70ff661ee8c9c14e7d36d6de3b4066f1441be4063df9c5009f0a64d3'], + }), + ('debugpy', '1.8.5', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['55919dce65b471eff25901acf82d328bbd5b833526b6c1364bd5133754777a44'], + }), + ('nest_asyncio', '1.6.0', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['87af6efd6b5e897c81050477ef65c62e2b2f35d51703cae01aff2905b1852e1c'], + }), + ('ipykernel', '6.29.5', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['afdb66ba5aa354b09b91379bac28ae4afebbb30e8b39510c9690afb7a10421b5'], + }), + ('jupyterlab_widgets', '3.0.13', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['e3cda2c233ce144192f1e29914ad522b2f4c40e77214b0cc97377ca3d323db54'], + }), + ('widgetsnbextension', '4.0.13', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['74b2692e8500525cc38c2b877236ba51d34541e6385eeed5aec15a70f88a6c71'], + }), + ('ipywidgets', '8.1.5', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['3290f526f87ae6e77655555baba4f36681c555b8bdbbff430b70e52c34c86245'], + }), + ('jupyter_core', '5.7.2', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['4f7315d2f6b4bcf2e3e7cb6e46772eba760ae459cd1f59d29eb57b0a01bd7409'], + }), + ('jupyter_client', '8.6.2', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['50cbc5c66fd1b8f65ecb66bc490ab73217993632809b6e505687de18e9dea39f'], + }), + ('lrcalc', '2.1', { + 'checksums': ['e3a0509aeda487b412b391a52e817ca36b5c063a8305e09fd54d53259dd6aaa9'], + }), + ('%(namelower)s_standard', version, { + 'modulename': 'sage', + 'checksums': ['f6579e85f33bd9bb6e9b991bfc4c49dab1e649858ed9ee41c7cec75cb92d4c62'], + }), + ('%(namelower)s_bliss', version, { + 'modulename': False, + 'checksums': ['70cccef849908436c2f9f1aabb3992a21c90d3ce99d1a965743f0fdec3735d32'], + }), + ('%(namelower)s_coxeter3', version, { + 'modulename': False, + 'checksums': ['c4f20204b91a696caeb7ad7cf33d2b0398d26d287085b2cb9434e8b067716fca'], + }), + ('%(namelower)s_mcqd', version, { + 'modulename': False, + 'checksums': ['6a140d8b3866ea27aa5966f3aab86a882785862fb00ae37087beb09105b94175'], + }), + ('%(namelower)s_meataxe', version, { + 'modulename': False, + 'checksums': ['5b625333c3168fc2ab55d32ad7e8c41912858bde8010b5aadc70c6450fa967e8'], + }), + ('%(namelower)s_sirocco', version, { + 'modulename': False, + 'checksums': ['499304b3331751d7b0f62de8379afb073d55f144c5f73775da0c5b92160e3a7c'], + }), + ('%(namelower)s_tdlib', version, { + 'modulename': False, + 'checksums': ['018497a1e220d3320a37d1acb3eee59ec820d167c7916e95f0508709a2e31703'], + }), +] + +sanity_check_commands = [ + "sage --help", + "python -c 'from sage.all import *'", +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/Salmon/Salmon-1.10.3-GCC-12.3.0.eb b/easybuild/easyconfigs/s/Salmon/Salmon-1.10.3-GCC-12.3.0.eb new file mode 100644 index 000000000000..9b52051eed3b --- /dev/null +++ b/easybuild/easyconfigs/s/Salmon/Salmon-1.10.3-GCC-12.3.0.eb @@ -0,0 +1,59 @@ +# # +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: GLPv2 +# +# Notes:: +# # +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen +# Thanks to people like Simon Brandord, Mikael Oehmann and Kenneth Hoste +# for their help with the ICE + +easyblock = 'CMakeMake' + +name = 'Salmon' +version = '1.10.3' + +homepage = 'https://github.com/COMBINE-lab/salmon' +description = """Salmon is a wicked-fast program to produce a highly-accurate, + transcript-level quantification estimate from RNA-seq data.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/COMBINE-lab/salmon/archive'] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['a053fba63598efc4ade3684aa2c8e8e2294186927d4fcdf1041c36edc2aa0871'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('pkgconf', '1.9.5'), + ('jemalloc', '5.3.0'), + ('Cereal', '1.3.2', '', SYSTEM), +] +dependencies = [ + ('Boost', '1.82.0'), + ('tbb', '2021.11.0'), + ('cURL', '8.0.1'), + ('libiconv', '1.17'), + ('bzip2', '1.0.8'), + ('XZ', '5.4.2'), + ('zlib', '1.2.13'), +] + +configopts = "-DJEMALLOC_ROOT=$EBROOTJEMALLOC" + +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/%(namelower)s', 'lib/libgraphdump.a', 'lib/libntcard.a', 'lib/libsalmon_core.a', 'lib/libtwopaco.a'], + 'dirs': [], +} + +sanity_check_commands = ['%(namelower)s --help'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/Satsuma2/Satsuma2-20220304-GCC-11.3.0.eb b/easybuild/easyconfigs/s/Satsuma2/Satsuma2-20220304-GCC-11.3.0.eb index e709378f6ea8..304dbf506697 100644 --- a/easybuild/easyconfigs/s/Satsuma2/Satsuma2-20220304-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/s/Satsuma2/Satsuma2-20220304-GCC-11.3.0.eb @@ -21,6 +21,12 @@ checksums = [ builddependencies = [('CMake', '3.23.1')] +# Define SATSUMA2_PATH as per: +# https://github.com/bioinfologics/satsuma2/blob/37c5f386819614cd3ce96016b423ddc4df1d86ec/README.md#running-satsuma2 +modextravars = { + 'SATSUMA2_PATH': '%(installdir)s/bin', +} + sanity_check_paths = { 'files': ['bin/ChromosomePaint', 'bin/MatchDump', 'bin/SatsumaSynteny2'], 'dirs': [], diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gmpich-2024.06-fb.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gmpich-2024.06-fb.eb new file mode 100644 index 000000000000..28d4f766d52e --- /dev/null +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gmpich-2024.06-fb.eb @@ -0,0 +1,40 @@ +name = 'ScaLAPACK' +version = '2.2.0' +versionsuffix = '-fb' + +homepage = 'https://www.netlib.org/scalapack/' +description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines + redesigned for distributed memory MIMD parallel computers.""" + +toolchain = {'name': 'gmpich', 'version': '2024.06'} +toolchainopts = {'extra_fflags': '-lpthread', 'openmp': True, 'pic': True, 'usempi': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TGZ] +patches = ['ScaLAPACK-%(version)s_fix-GCC-10.patch'] +checksums = [ + '40b9406c20735a9a3009d863318cb8d3e496fb073d201c5463df810e01ab2a57', # scalapack-2.2.0.tgz + 'f6bc3c6dee012ba4a696548a2e12b6aae932ce4fd5a142153b338839f52b5906', # ScaLAPACK-2.2.0_fix-GCC-10.patch +] + +builddependencies = [ + ('CMake', '3.26.3'), +] + +dependencies = [ + ('FlexiBLAS', '3.3.1'), +] + +# Config Opts based on AOCL User Guide: +# https://developer.amd.com/wp-content/resources/AOCL_User%20Guide_2.2.pdf + +configopts = '-DBUILD_SHARED_LIBS=ON ' +configopts += '-DBLAS_LIBRARIES="$EBROOTFLEXIBLAS/lib/libflexiblas.%s" ' % SHLIB_EXT +configopts += '-DLAPACK_LIBRARIES="$EBROOTFLEXIBLAS/lib/libflexiblas.%s" ' % SHLIB_EXT + +sanity_check_paths = { + 'files': ['lib/libscalapack.%s' % SHLIB_EXT, 'lib64/libscalapack.%s' % SHLIB_EXT], + 'dirs': ["lib", "lib64"], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2024a-fb.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2024a-fb.eb new file mode 100644 index 000000000000..1bccc16f38b3 --- /dev/null +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2024a-fb.eb @@ -0,0 +1,40 @@ +name = 'ScaLAPACK' +version = '2.2.0' +versionsuffix = '-fb' + +homepage = 'https://www.netlib.org/scalapack/' +description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines + redesigned for distributed memory MIMD parallel computers.""" + +toolchain = {'name': 'gompi', 'version': '2024a'} +toolchainopts = {'extra_fflags': '-lpthread', 'openmp': True, 'pic': True, 'usempi': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TGZ] +patches = ['ScaLAPACK-%(version)s_fix-GCC-10.patch'] +checksums = [ + '40b9406c20735a9a3009d863318cb8d3e496fb073d201c5463df810e01ab2a57', # scalapack-2.2.0.tgz + 'f6bc3c6dee012ba4a696548a2e12b6aae932ce4fd5a142153b338839f52b5906', # ScaLAPACK-2.2.0_fix-GCC-10.patch +] + +builddependencies = [ + ('CMake', '3.29.3'), +] + +dependencies = [ + ('FlexiBLAS', '3.4.4'), +] + +# Config Opts based on AOCL User Guide: +# https://developer.amd.com/wp-content/resources/AOCL_User%20Guide_2.2.pdf + +configopts = '-DBUILD_SHARED_LIBS=ON ' +configopts += '-DBLAS_LIBRARIES="$EBROOTFLEXIBLAS/lib/libflexiblas.%s" ' % SHLIB_EXT +configopts += '-DLAPACK_LIBRARIES="$EBROOTFLEXIBLAS/lib/libflexiblas.%s" ' % SHLIB_EXT + +sanity_check_paths = { + 'files': ['lib/libscalapack.%s' % SHLIB_EXT, 'lib64/libscalapack.%s' % SHLIB_EXT], + 'dirs': ["lib", "lib64"], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.05-foss-2021a.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.05-foss-2021a.eb index 2c0770da7e91..8d80f74fa667 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.05-foss-2021a.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.05-foss-2021a.eb @@ -23,12 +23,15 @@ exts_list = [ ('numpy', '1.20.3', { 'sources': [SOURCE_ZIP], 'patches': [ + 'numpy-1.20.3_fix-fortran-compiler-error.patch', 'numpy-1.20.3_skip-ppc-long-complex-test.patch', 'numpy-1.20.3_xfail-test-nan.patch', 'numpy-1.20.3_fix-target-test-ccompiler-opt.patch', ], 'checksums': [ 'e55185e51b18d788e49fe8305fd73ef4470596b33fc2c1ceb304566b99c71a69', # numpy-1.20.3.zip + {'numpy-1.20.3_fix-fortran-compiler-error.patch': + '016e0d02ffabe013248c4fd203a4456edee76839f747c05daf92ac1fe9925189'}, # numpy-1.20.3_skip-ppc-long-complex-test.patch '2f9a12e3a352b39076db84a7622fc8f4796abd3cb7f97f71958a495e864659a4', 'f0ce961f7d79551598e23050d92f46e827e300f6a7e5a6112e58efcc10385d4d', # numpy-1.20.3_xfail-test-nan.patch diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.05-gomkl-2021a.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.05-gomkl-2021a.eb index 3f0596710cc9..21890734ddf0 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.05-gomkl-2021a.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.05-gomkl-2021a.eb @@ -25,6 +25,7 @@ exts_list = [ 'numpy-1.18.2-mkl.patch', 'numpy-1.20.3_disable-broken-override-test.patch', 'numpy-1.20.3_fix-cpu-feature-detection-intel-compilers.patch', + 'numpy-1.20.3_fix-fortran-compiler-error.patch', 'numpy-1.20.3_fix-target-test-ccompiler-opt.patch', 'numpy-1.20.3_disable_fortran_callback_test.patch', ], @@ -36,6 +37,8 @@ exts_list = [ '43cc2e675c52db1776efcc6c84ebd5fc008b48e6355c81087420d5e790e4af9b', # numpy-1.20.3_fix-cpu-feature-detection-intel-compilers.patch '4c0b194c9d2e2c6b9798ebc271d4517f4c3cdbf2b3cbd68de16c7d4b068bb046', + {'numpy-1.20.3_fix-fortran-compiler-error.patch': + '016e0d02ffabe013248c4fd203a4456edee76839f747c05daf92ac1fe9925189'}, # numpy-1.20.3_fix-target-test-ccompiler-opt.patch '3d84e8b7d48387778974a5f6ae342a690ab5989547206b6add9d9667f8d7572a', # numpy-1.20.3_disable_fortran_callback_test.patch diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.05-intel-2021a.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.05-intel-2021a.eb index 3deadeac9d68..730ac590d33f 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.05-intel-2021a.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.05-intel-2021a.eb @@ -25,6 +25,7 @@ exts_list = [ 'numpy-1.18.2-mkl.patch', 'numpy-1.20.3_disable-broken-override-test.patch', 'numpy-1.20.3_fix-cpu-feature-detection-intel-compilers.patch', + 'numpy-1.20.3_fix-fortran-compiler-error.patch', 'numpy-1.20.3_fix-target-test-ccompiler-opt.patch', 'numpy-1.20.3_disable_fortran_callback_test.patch', ], @@ -36,6 +37,8 @@ exts_list = [ '43cc2e675c52db1776efcc6c84ebd5fc008b48e6355c81087420d5e790e4af9b', # numpy-1.20.3_fix-cpu-feature-detection-intel-compilers.patch '4c0b194c9d2e2c6b9798ebc271d4517f4c3cdbf2b3cbd68de16c7d4b068bb046', + {'numpy-1.20.3_fix-fortran-compiler-error.patch': + '016e0d02ffabe013248c4fd203a4456edee76839f747c05daf92ac1fe9925189'}, # numpy-1.20.3_fix-target-test-ccompiler-opt.patch '3d84e8b7d48387778974a5f6ae342a690ab5989547206b6add9d9667f8d7572a', # numpy-1.20.3_disable_fortran_callback_test.patch diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.10-foss-2021b-Python-2.7.18.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.10-foss-2021b-Python-2.7.18.eb index f806bd48d7ae..1bd36b39378b 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.10-foss-2021b-Python-2.7.18.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.10-foss-2021b-Python-2.7.18.eb @@ -29,6 +29,7 @@ exts_list = [ 'numpy-1.16.2_relax-long-complex-test.patch', 'numpy-1.16.6_add_flexiblas_detection.patch', 'numpy-1.16.6_handle_failing_linalg_test.patch', + 'numpy-1.20.3_fix-fortran-compiler-error.patch', ], 'sources': ['%(name)s-%(version)s.zip'], 'checksums': [ @@ -39,6 +40,8 @@ exts_list = [ '32ca32dd7ee8d6fcdce5875067acd50970c731cbb2603c6d1ad84ff81ff8c6d5', # numpy-1.16.6_handle_failing_linalg_test.patch 'be9dce98649626b7322ed8d1241b74a4e28c1d1de070a8072dc912cad3eb143d', + {'numpy-1.20.3_fix-fortran-compiler-error.patch': + '016e0d02ffabe013248c4fd203a4456edee76839f747c05daf92ac1fe9925189'}, ], }), ('ply', '3.11', { diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.10-foss-2021b.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.10-foss-2021b.eb index 46f9647ad263..3e1d85982cce 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.10-foss-2021b.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.10-foss-2021b.eb @@ -25,9 +25,14 @@ use_pip = True exts_list = [ ('numpy', '1.21.3', { 'sources': ['%(name)s-%(version)s.zip'], - 'patches': ['numpy-1.20.3_skip-ppc-long-complex-test.patch'], + 'patches': [ + 'numpy-1.20.3_fix-fortran-compiler-error.patch', + 'numpy-1.20.3_skip-ppc-long-complex-test.patch', + ], 'checksums': [ '63571bb7897a584ca3249c86dd01c10bcb5fe4296e3568b2e9c1a55356b6410e', # numpy-1.21.3.zip + {'numpy-1.20.3_fix-fortran-compiler-error.patch': + '016e0d02ffabe013248c4fd203a4456edee76839f747c05daf92ac1fe9925189'}, # numpy-1.20.3_skip-ppc-long-complex-test.patch '2f9a12e3a352b39076db84a7622fc8f4796abd3cb7f97f71958a495e864659a4', ], diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.10-intel-2021b.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.10-intel-2021b.eb index 87a1dfe31757..68420c452196 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.10-intel-2021b.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.10-intel-2021b.eb @@ -29,6 +29,7 @@ exts_list = [ 'numpy-1.18.2-mkl.patch', 'numpy-1.20.3_disable-broken-override-test.patch', 'numpy-1.20.3_disable_fortran_callback_test.patch', + 'numpy-1.20.3_fix-fortran-compiler-error.patch', ], 'checksums': [ '63571bb7897a584ca3249c86dd01c10bcb5fe4296e3568b2e9c1a55356b6410e', # numpy-1.21.3.zip @@ -37,6 +38,8 @@ exts_list = [ '43cc2e675c52db1776efcc6c84ebd5fc008b48e6355c81087420d5e790e4af9b', # numpy-1.20.3_disable_fortran_callback_test.patch '44975a944544fd0e771b7e63c32590d257a3713070f8f7fdf60105dc516f1d75', + {'numpy-1.20.3_fix-fortran-compiler-error.patch': + '016e0d02ffabe013248c4fd203a4456edee76839f747c05daf92ac1fe9925189'}, ], }), ('ply', '3.11', { diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-foss-2022.05.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-foss-2022.05.eb index e07fdee1c039..613b1853e884 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-foss-2022.05.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-foss-2022.05.eb @@ -26,6 +26,7 @@ exts_list = [ ('numpy', '1.22.3', { 'patches': [ 'numpy-1.20.3_disable_fortran_callback_test.patch', + 'numpy-1.20.3_fix-fortran-compiler-error.patch', 'numpy-1.22.3_disable-broken-override-test.patch', ], 'sources': ['%(name)s-%(version)s.zip'], @@ -33,6 +34,8 @@ exts_list = [ 'dbc7601a3b7472d559dc7b933b18b4b66f9aa7452c120e87dfb33d02008c8a18', # numpy-1.22.3.zip # numpy-1.20.3_disable_fortran_callback_test.patch '44975a944544fd0e771b7e63c32590d257a3713070f8f7fdf60105dc516f1d75', + {'numpy-1.20.3_fix-fortran-compiler-error.patch': + '016e0d02ffabe013248c4fd203a4456edee76839f747c05daf92ac1fe9925189'}, # numpy-1.22.3_disable-broken-override-test.patch '9c589bb073b28b25ff45eb3c63c57966aa508dd8b318d0b885b6295271e4983c', ], diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-foss-2022a.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-foss-2022a.eb index ce504e9607ab..21a801b8fb90 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-foss-2022a.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-foss-2022a.eb @@ -26,6 +26,7 @@ exts_list = [ ('numpy', '1.22.3', { 'patches': [ 'numpy-1.20.3_disable_fortran_callback_test.patch', + 'numpy-1.20.3_fix-fortran-compiler-error.patch', 'numpy-1.22.3_disable-broken-override-test.patch', '%(name)s-%(version)s_skip-ppc-long-complex-test.patch', ], @@ -34,6 +35,8 @@ exts_list = [ 'dbc7601a3b7472d559dc7b933b18b4b66f9aa7452c120e87dfb33d02008c8a18', # numpy-1.22.3.zip # numpy-1.20.3_disable_fortran_callback_test.patch '44975a944544fd0e771b7e63c32590d257a3713070f8f7fdf60105dc516f1d75', + {'numpy-1.20.3_fix-fortran-compiler-error.patch': + '016e0d02ffabe013248c4fd203a4456edee76839f747c05daf92ac1fe9925189'}, # numpy-1.22.3_disable-broken-override-test.patch '9c589bb073b28b25ff45eb3c63c57966aa508dd8b318d0b885b6295271e4983c', # numpy-1.22.3_skip-ppc-long-complex-test.patch diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-intel-2022.05.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-intel-2022.05.eb index 06ad5e918f63..979667121856 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-intel-2022.05.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-intel-2022.05.eb @@ -27,6 +27,7 @@ exts_list = [ 'patches': [ 'numpy-1.18.2-mkl.patch', 'numpy-1.20.3_disable_fortran_callback_test.patch', + 'numpy-1.20.3_fix-fortran-compiler-error.patch', 'numpy-1.22.3_disable-broken-override-test.patch', ], 'sources': ['%(name)s-%(version)s.zip'], @@ -35,6 +36,8 @@ exts_list = [ 'ea25ad5c0148c1398d282f0424e642fb9815a1a80f4512659b018e2adc378bcf', # numpy-1.18.2-mkl.patch # numpy-1.20.3_disable_fortran_callback_test.patch '44975a944544fd0e771b7e63c32590d257a3713070f8f7fdf60105dc516f1d75', + {'numpy-1.20.3_fix-fortran-compiler-error.patch': + '016e0d02ffabe013248c4fd203a4456edee76839f747c05daf92ac1fe9925189'}, # numpy-1.22.3_disable-broken-override-test.patch '9c589bb073b28b25ff45eb3c63c57966aa508dd8b318d0b885b6295271e4983c', ], diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-intel-2022a.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-intel-2022a.eb index a07d23a7f561..4e06a815c502 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-intel-2022a.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-intel-2022a.eb @@ -27,6 +27,7 @@ exts_list = [ 'patches': [ 'numpy-1.18.2-mkl.patch', 'numpy-1.20.3_disable_fortran_callback_test.patch', + 'numpy-1.20.3_fix-fortran-compiler-error.patch', 'numpy-1.22.3_disable-broken-override-test.patch', ], 'sources': ['%(name)s-%(version)s.zip'], @@ -35,6 +36,8 @@ exts_list = [ 'ea25ad5c0148c1398d282f0424e642fb9815a1a80f4512659b018e2adc378bcf', # numpy-1.18.2-mkl.patch # numpy-1.20.3_disable_fortran_callback_test.patch '44975a944544fd0e771b7e63c32590d257a3713070f8f7fdf60105dc516f1d75', + {'numpy-1.20.3_fix-fortran-compiler-error.patch': + '016e0d02ffabe013248c4fd203a4456edee76839f747c05daf92ac1fe9925189'}, # numpy-1.22.3_disable-broken-override-test.patch '9c589bb073b28b25ff45eb3c63c57966aa508dd8b318d0b885b6295271e4983c', ], diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.02-gfbf-2022b.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.02-gfbf-2022b.eb index e19bb6789f32..e9e059afe3a4 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.02-gfbf-2022b.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.02-gfbf-2022b.eb @@ -28,9 +28,14 @@ use_pip = True # order is important! exts_list = [ ('numpy', '1.24.2', { - 'patches': ['numpy-1.22.3_disable-broken-override-test.patch'], + 'patches': [ + 'numpy-1.20.3_fix-fortran-compiler-error.patch', + 'numpy-1.22.3_disable-broken-override-test.patch', + ], 'checksums': [ {'numpy-1.24.2.tar.gz': '003a9f530e880cb2cd177cba1af7220b9aa42def9c4afc2a2fc3ee6be7eb2b22'}, + {'numpy-1.20.3_fix-fortran-compiler-error.patch': + '016e0d02ffabe013248c4fd203a4456edee76839f747c05daf92ac1fe9925189'}, {'numpy-1.22.3_disable-broken-override-test.patch': '9c589bb073b28b25ff45eb3c63c57966aa508dd8b318d0b885b6295271e4983c'}, ], diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.07-gfbf-2023a.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.07-gfbf-2023a.eb index 44b5725fe7d1..9805854b0c33 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.07-gfbf-2023a.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.07-gfbf-2023a.eb @@ -30,6 +30,7 @@ use_pip = True exts_list = [ ('numpy', '1.25.1', { 'patches': [ + 'numpy-1.20.3_fix-fortran-compiler-error.patch', 'numpy-1.22.3_disable-broken-override-test.patch', ('numpy-1.25.1_fix-duplicate-avx512-symbols.patch', 'numpy/core/src/npysort/x86-simd-sort'), 'numpy-1.25.1_fix-undefined-avx512-reference.patch', @@ -38,6 +39,8 @@ exts_list = [ ], 'checksums': [ {'numpy-1.25.1.tar.gz': '9a3a9f3a61480cc086117b426a8bd86869c213fc4072e606f01c4e4b66eb92bf'}, + {'numpy-1.20.3_fix-fortran-compiler-error.patch': + '016e0d02ffabe013248c4fd203a4456edee76839f747c05daf92ac1fe9925189'}, {'numpy-1.22.3_disable-broken-override-test.patch': '9c589bb073b28b25ff45eb3c63c57966aa508dd8b318d0b885b6295271e4983c'}, {'numpy-1.25.1_fix-duplicate-avx512-symbols.patch': diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.07-iimkl-2023a.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.07-iimkl-2023a.eb index 95d1e9f41c41..25fa6ff36f77 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.07-iimkl-2023a.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.07-iimkl-2023a.eb @@ -31,6 +31,7 @@ exts_list = [ ('numpy', '1.25.1', { 'patches': [ 'numpy-1.18.2-mkl.patch', + 'numpy-1.20.3_fix-fortran-compiler-error.patch', 'numpy-1.25.1_disable_fortran_callback_test.patch', 'numpy-1.22.3_disable-broken-override-test.patch', 'numpy-1.25.1_disable-broken-test_long_long_map.patch', @@ -41,6 +42,8 @@ exts_list = [ 'checksums': [ {'numpy-1.25.1.tar.gz': '9a3a9f3a61480cc086117b426a8bd86869c213fc4072e606f01c4e4b66eb92bf'}, {'numpy-1.18.2-mkl.patch': 'ea25ad5c0148c1398d282f0424e642fb9815a1a80f4512659b018e2adc378bcf'}, + {'numpy-1.20.3_fix-fortran-compiler-error.patch': + '016e0d02ffabe013248c4fd203a4456edee76839f747c05daf92ac1fe9925189'}, {'numpy-1.25.1_disable_fortran_callback_test.patch': '3c02bd9973b7082fde9f9d18edfeb05798226ccb5731a56f5677269200c345cf'}, {'numpy-1.22.3_disable-broken-override-test.patch': diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2024.05-gfbf-2024.05.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2024.05-gfbf-2024.05.eb new file mode 100644 index 000000000000..99d61098d6b3 --- /dev/null +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2024.05-gfbf-2024.05.eb @@ -0,0 +1,103 @@ +easyblock = 'PythonBundle' + +name = 'SciPy-bundle' +version = '2024.05' + +homepage = 'https://python.org/' +description = "Bundle of Python packages for scientific software" + +toolchain = {'name': 'gfbf', 'version': '2024.05'} +toolchainopts = {'pic': True, 'lowopt': True} + +builddependencies = [ + ('hypothesis', '6.103.1'), + ('UnZip', '6.0'), + # scipy >= 1.9.0 uses Meson/Ninja + ('Meson', '1.4.0'), + ('meson-python', '0.16.0'), + ('Ninja', '1.12.1'), + ('pkgconf', '2.2.0'), # required by scipy + ('Cython', '3.0.10'), # required by numpy and scipy +] + +dependencies = [ + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), + ('pybind11', '2.12.0'), # required by scipy +] + +use_pip = True + +# order is important! +exts_list = [ + ('numpy', '1.26.4', { + 'patches': [ + 'numpy-1.22.3_disable-broken-override-test.patch', + 'numpy-1.26.4_fix-riscv64-test-failures.patch', + ], + 'checksums': [ + {'numpy-1.26.4.tar.gz': '2a02aba9ed12e4ac4eb3ea9421c420301a0c6460d9830d74a9df87efa4912010'}, + {'numpy-1.22.3_disable-broken-override-test.patch': + '9c589bb073b28b25ff45eb3c63c57966aa508dd8b318d0b885b6295271e4983c'}, + {'numpy-1.26.4_fix-riscv64-test-failures.patch': + '81bd487dbca6da8285971a16a2c7b488718a051d3cd66450277bed6ff21741de'}, + ], + }), + ('ply', '3.11', { + 'checksums': ['00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3'], + }), + ('gast', '0.5.4', { + 'checksums': ['9c270fe5f4b130969b54174de7db4e764b09b4f7f67ccfc32480e29f78348d97'], + }), + ('beniget', '0.4.1', { + 'checksums': ['75554b3b8ad0553ce2f607627dad3d95c60c441189875b98e097528f8e23ac0c'], + }), + ('pythran', '0.16.1', { + 'checksums': ['861748c0f9c7d422b32724b114b3817d818ed4eab86c09781aa0a3f7ceabb7f9'], + }), + ('versioneer', '0.29', { + 'checksums': ['5ab283b9857211d61b53318b7c792cf68e798e765ee17c27ade9f6c924235731'], + }), + ('scipy', '1.13.1', { + 'enable_slow_tests': True, + 'ignore_test_result': False, + 'patches': [ + 'scipy-1.11.1_disable-tests.patch', + 'scipy-1.11.1_xfail-aarch64_test_maxiter_worsening.patch', + ], + 'checksums': [ + {'scipy-1.13.1.tar.gz': '095a87a0312b08dfd6a6155cbbd310a8c51800fc931b8c0b84003014b874ed3c'}, + {'scipy-1.11.1_disable-tests.patch': '906bfb03397d94882ccdc1b93bc2c8e854e0e060c2d107c83042992394e6a4af'}, + {'scipy-1.11.1_xfail-aarch64_test_maxiter_worsening.patch': + '918c8e6fa8215d459126f267764c961bde729ea4a116c7f6287cddfdc58ffcea'}, + ], + }), + ('numexpr', '2.10.0', { + 'patches': ['numexpr-2.10.0_fix-numpy-1.x.patch'], + 'checksums': [ + {'numexpr-2.10.0.tar.gz': 'c89e930752639df040539160326d8f99a84159bbea41943ab8e960591edaaef0'}, + {'numexpr-2.10.0_fix-numpy-1.x.patch': '8d70b2e95579e6f0adc07bc615144f7657b3b607f9210ec328b6622458ca726d'}, + ], + }), + ('Bottleneck', '1.3.8', { + 'checksums': ['6780d896969ba7f53c8995ba90c87c548beb3db435dc90c60b9a10ed1ab4d868'], + }), + ('tzdata', '2024.1', { + 'checksums': ['2674120f8d891909751c38abcdfd386ac0a5a1127954fbc332af6b5ceae07efd'], + }), + ('pandas', '2.2.2', { + 'preinstallopts': "export PANDAS_CI=0 && ", + 'checksums': ['9e79019aba43cb4fda9e4d983f8e88ca0373adbb697ae9c6c43093218de28b54'], + }), + ('mpmath', '1.3.0', { + 'checksums': ['7a28eb2a9774d00c7bc92411c19a89209d5da7c4c9a9e227be8330a23a25b91f'], + }), + ('deap', '1.4.1', { + 'modulename': 'deap.base', + 'checksums': ['cc01de9892dfa7d1bc9803dab28892fead177f0182c81db47360a240ead778ff'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2024.05-gfbf-2024a.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2024.05-gfbf-2024a.eb new file mode 100644 index 000000000000..2abab977addb --- /dev/null +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2024.05-gfbf-2024a.eb @@ -0,0 +1,103 @@ +easyblock = 'PythonBundle' + +name = 'SciPy-bundle' +version = '2024.05' + +homepage = 'https://python.org/' +description = "Bundle of Python packages for scientific software" + +toolchain = {'name': 'gfbf', 'version': '2024a'} +toolchainopts = {'pic': True, 'lowopt': True} + +builddependencies = [ + ('hypothesis', '6.103.1'), + ('UnZip', '6.0'), + # scipy >= 1.9.0 uses Meson/Ninja + ('Meson', '1.4.0'), + ('meson-python', '0.16.0'), + ('Ninja', '1.12.1'), + ('pkgconf', '2.2.0'), # required by scipy + ('Cython', '3.0.10'), # required by numpy and scipy +] + +dependencies = [ + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), + ('pybind11', '2.12.0'), # required by scipy +] + +use_pip = True + +# order is important! +exts_list = [ + ('numpy', '1.26.4', { + 'patches': [ + 'numpy-1.22.3_disable-broken-override-test.patch', + 'numpy-1.26.4_fix-riscv64-test-failures.patch', + ], + 'checksums': [ + {'numpy-1.26.4.tar.gz': '2a02aba9ed12e4ac4eb3ea9421c420301a0c6460d9830d74a9df87efa4912010'}, + {'numpy-1.22.3_disable-broken-override-test.patch': + '9c589bb073b28b25ff45eb3c63c57966aa508dd8b318d0b885b6295271e4983c'}, + {'numpy-1.26.4_fix-riscv64-test-failures.patch': + '81bd487dbca6da8285971a16a2c7b488718a051d3cd66450277bed6ff21741de'}, + ], + }), + ('ply', '3.11', { + 'checksums': ['00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3'], + }), + ('gast', '0.5.4', { + 'checksums': ['9c270fe5f4b130969b54174de7db4e764b09b4f7f67ccfc32480e29f78348d97'], + }), + ('beniget', '0.4.1', { + 'checksums': ['75554b3b8ad0553ce2f607627dad3d95c60c441189875b98e097528f8e23ac0c'], + }), + ('pythran', '0.16.1', { + 'checksums': ['861748c0f9c7d422b32724b114b3817d818ed4eab86c09781aa0a3f7ceabb7f9'], + }), + ('versioneer', '0.29', { + 'checksums': ['5ab283b9857211d61b53318b7c792cf68e798e765ee17c27ade9f6c924235731'], + }), + ('scipy', '1.13.1', { + 'enable_slow_tests': True, + 'ignore_test_result': False, + 'patches': [ + 'scipy-1.11.1_disable-tests.patch', + 'scipy-1.11.1_xfail-aarch64_test_maxiter_worsening.patch', + ], + 'checksums': [ + {'scipy-1.13.1.tar.gz': '095a87a0312b08dfd6a6155cbbd310a8c51800fc931b8c0b84003014b874ed3c'}, + {'scipy-1.11.1_disable-tests.patch': '906bfb03397d94882ccdc1b93bc2c8e854e0e060c2d107c83042992394e6a4af'}, + {'scipy-1.11.1_xfail-aarch64_test_maxiter_worsening.patch': + '918c8e6fa8215d459126f267764c961bde729ea4a116c7f6287cddfdc58ffcea'}, + ], + }), + ('numexpr', '2.10.0', { + 'patches': ['numexpr-2.10.0_fix-numpy-1.x.patch'], + 'checksums': [ + {'numexpr-2.10.0.tar.gz': 'c89e930752639df040539160326d8f99a84159bbea41943ab8e960591edaaef0'}, + {'numexpr-2.10.0_fix-numpy-1.x.patch': '8d70b2e95579e6f0adc07bc615144f7657b3b607f9210ec328b6622458ca726d'}, + ], + }), + ('Bottleneck', '1.3.8', { + 'checksums': ['6780d896969ba7f53c8995ba90c87c548beb3db435dc90c60b9a10ed1ab4d868'], + }), + ('tzdata', '2024.1', { + 'checksums': ['2674120f8d891909751c38abcdfd386ac0a5a1127954fbc332af6b5ceae07efd'], + }), + ('pandas', '2.2.2', { + 'preinstallopts': "export PANDAS_CI=0 && ", + 'checksums': ['9e79019aba43cb4fda9e4d983f8e88ca0373adbb697ae9c6c43093218de28b54'], + }), + ('mpmath', '1.3.0', { + 'checksums': ['7a28eb2a9774d00c7bc92411c19a89209d5da7c4c9a9e227be8330a23a25b91f'], + }), + ('deap', '1.4.1', { + 'modulename': 'deap.base', + 'checksums': ['cc01de9892dfa7d1bc9803dab28892fead177f0182c81db47360a240ead778ff'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SciPy-bundle/numexpr-2.10.0_fix-numpy-1.x.patch b/easybuild/easyconfigs/s/SciPy-bundle/numexpr-2.10.0_fix-numpy-1.x.patch new file mode 100644 index 000000000000..dff9bd069c91 --- /dev/null +++ b/easybuild/easyconfigs/s/SciPy-bundle/numexpr-2.10.0_fix-numpy-1.x.patch @@ -0,0 +1,18 @@ +fix for: error: PyDataType_SET_ELSIZE was not declared in this scope +see https://github.com/pydata/numexpr/pull/485 + +--- numexpr-2.10.0/numexpr/interpreter.cpp.orig 2024-06-14 21:47:27.999098607 +0200 ++++ numexpr-2.10.0/numexpr/interpreter.cpp 2024-06-14 21:49:53.403776961 +0200 +@@ -47,6 +47,12 @@ + #define AVAILABLE(Haystack, Haystack_Len, J, Needle_Len) \ + ((Haystack_Len) >= (J) + (Needle_Len)) + ++// To allow building with NumPy<2 locally define the new NumPy macros: ++#if NPY_ABI_VERSION < 0x02000000 ++ #define PyDataType_ELSIZE(descr) ((descr)->elsize) ++ #define PyDataType_SET_ELSIZE(descr, size) (descr)->elsize = size ++#endif ++ + #include "str-two-way.hpp" + + #ifdef DEBUG diff --git a/easybuild/easyconfigs/s/SciPy-bundle/numpy-1.20.3_fix-fortran-compiler-error.patch b/easybuild/easyconfigs/s/SciPy-bundle/numpy-1.20.3_fix-fortran-compiler-error.patch new file mode 100644 index 000000000000..32b41061f061 --- /dev/null +++ b/easybuild/easyconfigs/s/SciPy-bundle/numpy-1.20.3_fix-fortran-compiler-error.patch @@ -0,0 +1,43 @@ +Using Fortran compilers which differ "too much" from GCC fails building NumPy with something like +> A valid Fortran version was not found in this string: [...] + +See https://github.com/easybuilders/easybuild-easyblocks/issues/2518 and https://github.com/numpy/numpy/pull/26502 + +Fix by converting the hard error into a warning as the issue would be handled later if required. +E.g. for building NumPy we don't need a Fortran compiler at all. + +Author: Alexander Grund (TU Dresden) + +diff --git a/numpy/distutils/fcompiler/gnu.py b/numpy/distutils/fcompiler/gnu.py +index eac4cbb477..8a1043fe26 100644 +--- a/numpy/distutils/fcompiler/gnu.py ++++ b/numpy/distutils/fcompiler/gnu.py +@@ -8,6 +8,7 @@ import hashlib + import base64 + import subprocess + from subprocess import Popen, PIPE, STDOUT ++from distutils import log + from numpy.distutils.exec_command import filepath_from_subprocess_output + from numpy.distutils.fcompiler import FCompiler + from distutils.version import LooseVersion +@@ -69,9 +70,9 @@ class GnuFCompiler(FCompiler): + # from the version string + return ('gfortran', v) + +- # If still nothing, raise an error to make the problem easy to find. +- err = 'A valid Fortran version was not found in this string:\n' +- raise ValueError(err + version_string) ++ # If still nothing, warn to make the problem easy to find. ++ log.warn('A valid Fortran version was not found in this string:\n' ++ + version_string) + + def version_match(self, version_string): + v = self.gnu_version_match(version_string) +@@ -539,7 +540,6 @@ def _can_target(cmd, arch): + + + if __name__ == '__main__': +- from distutils import log + from numpy.distutils import customized_fcompiler + log.set_verbosity(2) + diff --git a/easybuild/easyconfigs/s/SciPy-bundle/numpy-1.26.4_fix-riscv64-test-failures.patch b/easybuild/easyconfigs/s/SciPy-bundle/numpy-1.26.4_fix-riscv64-test-failures.patch new file mode 100644 index 000000000000..ccc444e1f4d4 --- /dev/null +++ b/easybuild/easyconfigs/s/SciPy-bundle/numpy-1.26.4_fix-riscv64-test-failures.patch @@ -0,0 +1,156 @@ +From d9e88e32302b3842785a33d90cf22f8c1405cd05 Mon Sep 17 00:00:00 2001 +From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= +Date: Tue, 18 Jun 2024 13:28:35 +0200 +Subject: [PATCH 1/2] TST: Fix fp_noncontiguous and fpclass on riscv64 + +Modify fp_noncontiguous and fpclass so that they pass on riscv64. +The subtests that verify that the signs of negative NaNs are preserved +do not pass on riscv64 builds and are disabled. Many RISC-V +instructions that produce NaNs return a canonical NaN, as defined by +the RISC-V specification. The canonical NaNs are always positive. See +section 11.3 NaN Generation and Propagation of the RISC-V Unprivileged +ISA for more details. +--- + numpy/core/tests/test_umath.py | 44 +++++++++++++++++++++++++++++----- + 1 file changed, 38 insertions(+), 6 deletions(-) + +diff --git a/numpy/core/tests/test_umath.py b/numpy/core/tests/test_umath.py +index 963e740d8dcb..8444893c80c3 100644 +--- a/numpy/core/tests/test_umath.py ++++ b/numpy/core/tests/test_umath.py +@@ -1852,8 +1852,22 @@ def test_fpclass(self, stride): + assert_equal(np.isnan(arr_f64[::stride]), nan[::stride]) + assert_equal(np.isinf(arr_f32[::stride]), inf[::stride]) + assert_equal(np.isinf(arr_f64[::stride]), inf[::stride]) +- assert_equal(np.signbit(arr_f32[::stride]), sign[::stride]) +- assert_equal(np.signbit(arr_f64[::stride]), sign[::stride]) ++ if platform.processor() == 'riscv64': ++ # On RISC-V, many operations that produce NaNs, such as converting ++ # a -NaN from f64 to f32, return a canonical NaN. The canonical ++ # NaNs are always positive. See section 11.3 NaN Generation and ++ # Propagation of the RISC-V Unprivileged ISA for more details. ++ # We disable the sign test on riscv64 for -np.nan as we ++ # cannot assume that its sign will be honoured in these tests. ++ arr_f64_rv = np.copy(arr_f64) ++ arr_f32_rv = np.copy(arr_f32) ++ arr_f64_rv[1] = -1.0 ++ arr_f32_rv[1] = -1.0 ++ assert_equal(np.signbit(arr_f32_rv[::stride]), sign[::stride]) ++ assert_equal(np.signbit(arr_f64_rv[::stride]), sign[::stride]) ++ else: ++ assert_equal(np.signbit(arr_f32[::stride]), sign[::stride]) ++ assert_equal(np.signbit(arr_f64[::stride]), sign[::stride]) + assert_equal(np.isfinite(arr_f32[::stride]), finite[::stride]) + assert_equal(np.isfinite(arr_f64[::stride]), finite[::stride]) + +@@ -1874,23 +1888,37 @@ def test_fp_noncontiguous(self, dtype): + ncontig_in = data[1::3] + ncontig_out = out[1::3] + contig_in = np.array(ncontig_in) ++ ++ if platform.processor() == 'riscv64': ++ # Disable the -np.nan signbit tests on riscv64. See comments in ++ # test_fpclass for more details. ++ data_rv = np.copy(data) ++ data_rv[1] = -1.0 ++ ncontig_sign_in = data_rv[1::3] ++ contig_sign_in = np.array(ncontig_sign_in) ++ else: ++ ncontig_sign_in = ncontig_in ++ contig_sign_in = contig_in ++ + assert_equal(ncontig_in.flags.c_contiguous, False) + assert_equal(ncontig_out.flags.c_contiguous, False) + assert_equal(contig_in.flags.c_contiguous, True) ++ assert_equal(ncontig_sign_in.flags.c_contiguous, False) ++ assert_equal(contig_sign_in.flags.c_contiguous, True) + # ncontig in, ncontig out + assert_equal(np.isnan(ncontig_in, out=ncontig_out), nan[1::3]) + assert_equal(np.isinf(ncontig_in, out=ncontig_out), inf[1::3]) +- assert_equal(np.signbit(ncontig_in, out=ncontig_out), sign[1::3]) ++ assert_equal(np.signbit(ncontig_sign_in, out=ncontig_out), sign[1::3]) + assert_equal(np.isfinite(ncontig_in, out=ncontig_out), finite[1::3]) + # contig in, ncontig out + assert_equal(np.isnan(contig_in, out=ncontig_out), nan[1::3]) + assert_equal(np.isinf(contig_in, out=ncontig_out), inf[1::3]) +- assert_equal(np.signbit(contig_in, out=ncontig_out), sign[1::3]) ++ assert_equal(np.signbit(contig_sign_in, out=ncontig_out), sign[1::3]) + assert_equal(np.isfinite(contig_in, out=ncontig_out), finite[1::3]) + # ncontig in, contig out + assert_equal(np.isnan(ncontig_in), nan[1::3]) + assert_equal(np.isinf(ncontig_in), inf[1::3]) +- assert_equal(np.signbit(ncontig_in), sign[1::3]) ++ assert_equal(np.signbit(ncontig_sign_in), sign[1::3]) + assert_equal(np.isfinite(ncontig_in), finite[1::3]) + # contig in, contig out, nd stride + data_split = np.array(np.array_split(data, 2)) +@@ -1900,7 +1928,11 @@ def test_fp_noncontiguous(self, dtype): + finite_split = np.array(np.array_split(finite, 2)) + assert_equal(np.isnan(data_split), nan_split) + assert_equal(np.isinf(data_split), inf_split) +- assert_equal(np.signbit(data_split), sign_split) ++ if platform.processor() == 'riscv64': ++ data_split_rv = np.array(np.array_split(data_rv, 2)) ++ assert_equal(np.signbit(data_split_rv), sign_split) ++ else: ++ assert_equal(np.signbit(data_split), sign_split) + assert_equal(np.isfinite(data_split), finite_split) + + class TestLDExp: + +From ccb1d4adc01b49c7e900e5f532dc6361eac1362a Mon Sep 17 00:00:00 2001 +From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= +Date: Tue, 18 Jun 2024 13:30:00 +0200 +Subject: [PATCH 2/2] TST: Use platform.machine() for improved portability on + riscv64 + +Replace `platform.processor()` with `platform.machine()` considering the latter is more portable. More specifically, `platform.processor()` returns empty string on Arch Linux, and this PR fixes the corresponding test failure. +--- + numpy/core/tests/test_numeric.py | 2 +- + numpy/core/tests/test_umath.py | 6 +++--- + 2 files changed, 4 insertions(+), 4 deletions(-) + +diff --git a/numpy/core/tests/test_numeric.py b/numpy/core/tests/test_numeric.py +index e5edd3efce5a..ce5917a9b09f 100644 +--- a/numpy/core/tests/test_numeric.py ++++ b/numpy/core/tests/test_numeric.py +@@ -483,7 +483,7 @@ def setup_method(self): + # Propagation of the RISC-V Unprivileged ISA for more details. + # We disable the float32 sign test on riscv64 for -np.nan as the sign + # of the NaN will be lost when it's converted to a float32. +- if platform.processor() != 'riscv64': ++ if platform.machine() != 'riscv64': + self.signf[3::6][self.ef[3::6]] = -np.nan + self.signd[3::6][self.ed[3::6]] = -np.nan + self.signf[4::6][self.ef[4::6]] = -0. +diff --git a/numpy/core/tests/test_umath.py b/numpy/core/tests/test_umath.py +index 8444893c80c3..c5a3e2c81f83 100644 +--- a/numpy/core/tests/test_umath.py ++++ b/numpy/core/tests/test_umath.py +@@ -1852,7 +1852,7 @@ def test_fpclass(self, stride): + assert_equal(np.isnan(arr_f64[::stride]), nan[::stride]) + assert_equal(np.isinf(arr_f32[::stride]), inf[::stride]) + assert_equal(np.isinf(arr_f64[::stride]), inf[::stride]) +- if platform.processor() == 'riscv64': ++ if platform.machine() == 'riscv64': + # On RISC-V, many operations that produce NaNs, such as converting + # a -NaN from f64 to f32, return a canonical NaN. The canonical + # NaNs are always positive. See section 11.3 NaN Generation and +@@ -1889,7 +1889,7 @@ def test_fp_noncontiguous(self, dtype): + ncontig_out = out[1::3] + contig_in = np.array(ncontig_in) + +- if platform.processor() == 'riscv64': ++ if platform.machine() == 'riscv64': + # Disable the -np.nan signbit tests on riscv64. See comments in + # test_fpclass for more details. + data_rv = np.copy(data) +@@ -1928,7 +1928,7 @@ def test_fp_noncontiguous(self, dtype): + finite_split = np.array(np.array_split(finite, 2)) + assert_equal(np.isnan(data_split), nan_split) + assert_equal(np.isinf(data_split), inf_split) +- if platform.processor() == 'riscv64': ++ if platform.machine() == 'riscv64': + data_split_rv = np.array(np.array_split(data_rv, 2)) + assert_equal(np.signbit(data_split_rv), sign_split) + else: diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2024a-CUDA-12.6.0.eb b/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2024a-CUDA-12.6.0.eb new file mode 100644 index 000000000000..9d7b53221e92 --- /dev/null +++ b/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2024a-CUDA-12.6.0.eb @@ -0,0 +1,57 @@ +# Copyright 2013-2020 Juelich Supercomputing Centre, Germany +# Copyright 2020-2024 TU Dresden, Germany +# Authors:: +# * Bernd Mohr +# * Markus Geimer +# * Alexander Grund +# * Robert Mijakovic +# License:: 3-clause BSD + +name = 'Score-P' +version = '8.4' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://www.score-p.org' +description = """ + The Score-P measurement infrastructure is a highly scalable and easy-to-use + tool suite for profiling, event tracing, and online analysis of HPC + applications. +""" + +toolchain = {'name': 'gompi', 'version': '2024a'} + +source_urls = ['https://perftools.pages.jsc.fz-juelich.de/cicd/scorep/tags/scorep-%(version)s'] +sources = ['scorep-%(version)s.tar.gz'] +checksums = ['7bbde9a0721d27cc6205baf13c1626833bcfbabb1f33b325a2d67976290f7f8a'] + +dependencies = [ + ('CUDA', '12.6.0', '', SYSTEM), + ('UCX-CUDA', '1.16.0', versionsuffix), + ('CubeLib', '4.8.2'), + ('CubeWriter', '4.8.2'), + ('libunwind', '1.8.1'), + ('OPARI2', '2.0.8'), + ('OTF2', '3.0.3'), + # Hardware counter support (optional): + ('PAPI', '7.1.0'), + # PDT source-to-source instrumentation support (optional): + ('PDT', '3.25.2'), +] + +configopts = '--enable-shared' + +local_adapters = [ + 'compiler_event', 'cuda_mgmt', 'compiler_mgmt', 'mpi_event', 'mpi_mgmt', 'opari2_mgmt', 'user_event', 'user_mgmt' +] +sanity_check_paths = { + 'files': + ['bin/scorep', 'include/scorep/SCOREP_User.h'] + + ['lib/libscorep_adapter_%s.%s' % (a, e) for a in local_adapters for e in ('a', SHLIB_EXT)], + 'dirs': [], +} +sanity_check_commands = ['scorep-config --help'] + +# Ensure that local metric documentation is found by CubeGUI +modextrapaths = {'CUBE_DOCPATH': 'share/doc/scorep/profile'} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2024a.eb b/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2024a.eb new file mode 100644 index 000000000000..eda406cbe2a4 --- /dev/null +++ b/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2024a.eb @@ -0,0 +1,55 @@ +# Copyright 2013-2024 Juelich Supercomputing Centre, Germany +# Copyright 2020-2024 TU Dresden, Germany +# Authors:: +# * Bernd Mohr +# * Markus Geimer +# * Alexander Grund +# * Robert Mijakovic +# * Jan André Reuter +# License:: 3-clause BSD + +name = 'Score-P' +version = '8.4' + +homepage = 'https://www.score-p.org' +description = """ + The Score-P measurement infrastructure is a highly scalable and easy-to-use + tool suite for profiling, event tracing, and online analysis of HPC + applications. +""" + +toolchain = {'name': 'gompi', 'version': '2024a'} + +source_urls = ['https://perftools.pages.jsc.fz-juelich.de/cicd/scorep/tags/scorep-%(version)s'] +sources = ['scorep-%(version)s.tar.gz'] +checksums = ['7bbde9a0721d27cc6205baf13c1626833bcfbabb1f33b325a2d67976290f7f8a'] + +dependencies = [ + ('CubeLib', '4.8.2'), + ('CubeWriter', '4.8.2'), + ('libunwind', '1.8.1'), + ('OPARI2', '2.0.8'), + ('OTF2', '3.0.3'), + # Hardware counter support (optional): + ('PAPI', '7.1.0'), + # PDT source-to-source instrumentation support (optional): + ('PDT', '3.25.2'), +] + +configopts = '--enable-shared' + +local_adapters = [ + 'compiler_event', 'compiler_mgmt', 'mpi_event', 'mpi_mgmt', 'opari2_mgmt', 'user_event', 'user_mgmt' +] +sanity_check_paths = { + 'files': + ['bin/scorep', 'include/scorep/SCOREP_User.h'] + + ['lib/libscorep_adapter_%s.%s' % (a, e) for a in local_adapters for e in ('a', SHLIB_EXT)], + 'dirs': [], +} +sanity_check_commands = ['scorep-config --help'] + +# Ensure that local metric documentation is found by CubeGUI +modextrapaths = {'CUBE_DOCPATH': 'share/doc/scorep/profile'} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/s/SentencePiece/SentencePiece-0.2.0-GCC-13.2.0.eb b/easybuild/easyconfigs/s/SentencePiece/SentencePiece-0.2.0-GCC-13.2.0.eb new file mode 100644 index 000000000000..246989eefdcd --- /dev/null +++ b/easybuild/easyconfigs/s/SentencePiece/SentencePiece-0.2.0-GCC-13.2.0.eb @@ -0,0 +1,70 @@ +easyblock = 'Bundle' + +name = 'SentencePiece' +version = '0.2.0' + +homepage = 'https://github.com/google/sentencepiece' +description = "Unsupervised text tokenizer for Neural Network-based text generation." +github_account = 'google' + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +builddependencies = [ + ('CMake', '3.27.6'), + ('pkgconf', '2.0.3'), +] + +dependencies = [ + ('Python', '3.11.5'), + ('gperftools', '2.13'), +] + +default_component_specs = { + 'source_urls': [GITHUB_LOWER_SOURCE], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['9970f0a0afee1648890293321665e5b2efa04eaec9f1671fcf8048f456f5bb86'], +} + +local_external_absl = 'sed -i %(builddir)s/' + +components = [ + (name, version, { + 'easyblock': 'CMakeMake', + 'separate_build_dir': True, + 'start_dir': '%(namelower)s-%(version)s', + # using internal protobuf there is no matching pc file so requirement is removed: + 'preconfigopts': 'sed -i s/Requires.private.*// ../sentencepiece-%(version)s/sentencepiece.pc.in &&', + }), + ('sentencepiece', version, { + 'easyblock': 'PythonPackage', + 'start_dir': '%(namelower)s-%(version)s/python', + # Unpredicable where pc files end up; including both lib and lib64 + 'prebuildopts': 'export PKG_CONFIG_PATH=%(installdir)s/lib64/pkgconfig:%(installdir)s/lib/pkgconfig/:' + '$PKG_CONFIG_PATH && ', + 'preinstallopts': 'export PKG_CONFIG_PATH=%(installdir)s/lib64/pkgconfig:%(installdir)s/lib/pkgconfig/:' + '$PKG_CONFIG_PATH && ', + 'use_pip': True, + 'download_dep_fail': True, + 'sanity_pip_check': True, + }), +] + +postinstallcmds = ['cp -a %(builddir)s/%(namelower)s-%(version)s/{data,doc} %(installdir)s/'] + +sanity_check_paths = { + 'files': ['bin/spm_%s' % x for x in ['decode', 'encode', 'export_vocab', 'normalize', 'train']] + + ['lib/libsentencepiece.%s' % SHLIB_EXT, 'lib/libsentencepiece_train.%s' % SHLIB_EXT] + + ['include/sentencepiece_processor.h', 'include/sentencepiece_trainer.h'], + 'dirs': ['lib/python%(pyshortver)s/site-packages', 'data', 'doc'], +} + +sanity_check_commands = [ + 'spm_train --help | grep accept_language', # --help has exit code 1, so we check for output text + "python -c 'import sentencepiece'", +] + +modextrapaths = { + 'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/SeqKit/SeqKit-2.8.2.eb b/easybuild/easyconfigs/s/SeqKit/SeqKit-2.8.2.eb new file mode 100644 index 000000000000..820f9abf7192 --- /dev/null +++ b/easybuild/easyconfigs/s/SeqKit/SeqKit-2.8.2.eb @@ -0,0 +1,26 @@ +easyblock = 'GoPackage' + +name = 'SeqKit' +version = '2.8.2' + +homepage = 'https://bioinf.shenwei.me/seqkit/' +description = """SeqKit - a cross-platform and ultrafast toolkit for FASTA/Q file manipulation""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/shenwei356/seqkit/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['9cf1e744b785fa673af5a7a1ce2f96d52dc03e14b6537097df86aa6266204556'] + +builddependencies = [ + ('Go', '1.22.1'), +] + +installopts = './%(namelower)s' + +sanity_check_commands = [ + "seqkit version", + "seqkit genautocomplete" +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SharedMeatAxe/SharedMeatAxe-1.0.1-GCC-13.2.0.eb b/easybuild/easyconfigs/s/SharedMeatAxe/SharedMeatAxe-1.0.1-GCC-13.2.0.eb new file mode 100644 index 000000000000..36923c839cc4 --- /dev/null +++ b/easybuild/easyconfigs/s/SharedMeatAxe/SharedMeatAxe-1.0.1-GCC-13.2.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'SharedMeatAxe' +version = '1.0.1' + +homepage = 'https://github.com/simon-king-jena/SharedMeatAxe' +description = """This is an autotoolized shared library version of C MeatAxe 2.4.24, + a set of programs for computing with modular representations.""" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +source_urls = ['https://github.com/simon-king-jena/SharedMeatAxe/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['e1e802ef60f3280cdacb3de6d693ebd71b43af93e33c739de2697605c59b1a3b'] + +builddependencies = [ + ('Autotools', '20220317'), +] + +preconfigopts = 'autoreconf --install && ' + +runtest = 'check' + +local_bins = [ + 'cfcomp', 'genmod', 'mkgraph', 'mkinc', 'orbrep', 'pwkond', 'symnew', 'zad', 'zcl', 'zcv', 'zfr', 'zmo', 'znu', + 'zpr', 'zro', 'zsp', 'zte', 'zuk', 'chop', 'mkcycl', 'mkhom', 'mksub', 'precond', 'rad', 'tcond', 'zbl', 'zcp', + 'zef', 'ziv', 'zmu', 'zor', 'zpt', 'zsc', 'zsy', 'ztr', 'zvp', 'decomp', 'mkdotl', 'mkhom_old', 'mktree', + 'pseudochop', 'soc', 'tuc', 'zcf', 'zct', 'zev', 'zkd', 'zmw', 'zpo', 'zqt', 'zsi', 'ztc', 'zts', +] + +sanity_check_paths = { + 'files': ['bin/%s' % bin for bin in local_bins] + ['include/meataxe.h', 'lib/libmtx.%s' % SHLIB_EXT], + 'dirs': [] +} + +sanity_check_commands = ['mktree --help'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb b/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb new file mode 100644 index 000000000000..c0f6cb456313 --- /dev/null +++ b/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb @@ -0,0 +1,246 @@ +easyblock = 'PythonBundle' + +name = 'Single-cell-python-bundle' +version = '2024.02' + +homepage = (None) +description = """Bundle of tools for single-cell sequence analysis.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('poetry', '1.5.1'), + ('CMake', '3.26.3'), + ('hatchling', '1.18.0'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('matplotlib', '3.7.2'), + ('Seaborn', '0.13.2'), + ('PyTorch', '2.1.2'), + ('scanpy', '1.9.8'), + ('scib', '1.1.4'), + ('scVelo', '0.3.1'), + ('CellTypist', '1.6.2'), + ('epiScanpy', '0.4.0'), + ('scCODA', '0.1.9'), + ('infercnvpy', '0.4.3'), + ('pySCENIC', '0.12.1-20240311'), + ('CellRank', '2.0.2'), + ('Squidpy', '1.4.1'), + ('Cassiopeia', '2.0.0'), + ('scvi-tools', '1.1.2'), + ('scArches', '0.6.1'), + ('scib-metrics', '0.5.1'), + # deps of exts: + ('umap-learn', '0.5.5'), # bbknn + ('scikit-learn', '1.3.1'), # bbknn, sc_toolbox + ('PyYAML', '6.0'), # sc_toolbox + ('typing-extensions', '4.9.0'), # sc_toolbox + ('adjustText', '0.7.3'), # sc_toolbox + ('python-parasail', '1.3.4'), # scirpy + ('graph-tool', '2.59'), # schist + ('Pyomo', '6.7.3'), # pertpy + ('mpmath', '1.3.0'), # blitzgsea +] + +exts_list = [ + ('flit_core', '3.9.0', { + 'checksums': ['72ad266176c4a3fcfab5f2930d76896059851240570ce9a98733b658cb786eba'], + }), + ('annoy', '1.17.3', { + 'checksums': ['9cbfebefe0a5f843eba29c6be4c84d601f4f41ad4ded0486f1b88c3b07739c15'], + }), + ('pynndescent', '0.5.11', { + 'checksums': ['6f44ced9d5a9da2c87d9b2fff30bb5308540c0657605e4d5cde7ed3275bbad50'], + }), + ('bbknn', '1.6.0', { + 'checksums': ['1c01a9d6df2fc52a527de8a403617897a4b672724863299a7026f2132f1b041b'], + }), + ('tzlocal', '5.2', { + 'checksums': ['8d399205578f1a9342816409cc1e46a93ebd5755e39ea2d85334bea911bf0e6e'], + }), + ('anndata2ri', '1.3.1', { + 'checksums': ['0e3fa2f81789f682d19ef452fabdb401ec27899db9abe5a78e45e21dcc7caa42'], + }), + ('pypi-latest', '0.1.2', { + 'checksums': ['b195654567e6abaac6acfec37638d8e000838f419bc6b129962a896eedc4ed4e'], + }), + ('text-unidecode', '1.3', { + 'checksums': ['bad6603bb14d279193107714b288be206cac565dfa49aa5b105294dd5c4aab93'], + }), + ('python-slugify', '8.0.4', { + 'modulename': 'slugify', + 'checksums': ['59202371d1d05b54a9e7720c5e038f928f45daaffe41dd10822f3907b937c856'], + }), + ('prompt_toolkit', '3.0.36', { + 'checksums': ['3e163f254bef5a03b146397d7c1963bd3e2812f0964bb9a24e6ec761fd28db63'], + }), + ('binaryornot', '0.4.4', { + 'checksums': ['359501dfc9d40632edc9fac890e19542db1a287bbcfa58175b66658392018061'], + }), + ('types-python-dateutil', '2.9.0.20240316', { + 'modulename': False, + 'checksums': ['5d2f2e240b86905e40944dd787db6da9263f0deabef1076ddaed797351ec0202'], + }), + ('arrow', '1.3.0', { + 'checksums': ['d4540617648cb5f895730f1ad8c82a65f2dad0166f57b75f3ca54759c4d67a85'], + }), + ('cookiecutter', '2.6.0', { + 'checksums': ['db21f8169ea4f4fdc2408d48ca44859349de2647fbe494a9d6c3edfc0542c21c'], + }), + ('questionary', '2.0.1', { + 'checksums': ['bcce898bf3dbb446ff62830c86c5c6fb9a22a54146f0f5597d3da43b10d8fc8b'], + }), + ('rich', '13.7.1', { + 'checksums': ['9be308cb1fe2f1f57d67ce99e95af38a1e2bc71ad9813b0e247cf7ffbcc3a432'], + }), + ('sc_toolbox', '0.12.3', { + 'checksums': ['6ca22a364c269a095114e620eb3c6da8aac1950d8f43f58ceea08005a09cc2cb'], + }), + ('toolz', '0.12.1', { + 'checksums': ['ecca342664893f177a13dac0e6b41cbd8ac25a358e5f215316d43e2100224f4d'], + }), + ('altair', '5.2.0', { + 'checksums': ['2ad7f0c8010ebbc46319cc30febfb8e59ccf84969a201541c207bc3a4fa6cf81'], + }), + ('custom_inherit', '2.4.1', { + 'checksums': ['7052eb337bcce83551815264391cc4efc2bf70b295a3c52aba64f1ab57c3a8a2'], + }), + ('multipledispatch', '1.0.0', { + 'checksums': ['5c839915465c68206c3e9c473357908216c28383b425361e5d144594bf85a7e0'], + }), + ('pypng', '0.20220715.0', { + 'modulename': 'png', + 'checksums': ['739c433ba96f078315de54c0db975aee537cbc3e1d0ae4ed9aab0ca1e427e2c1'], + }), + ('reportlab', '4.1.0', { + 'checksums': ['3a99faf412691159c068b3ff01c15307ce2fd2cf6b860199434874e002040a84'], + }), + ('toyplot', '1.0.3', { + 'checksums': ['7b7b2bc5784fd75e5c695300bffc80d568c83bebef543bb54e6e6c2229912edd'], + }), + ('toytree', '2.0.5', { + 'checksums': ['7be04ca310067e0e9737449700d6ab1b68b4379b64e2d22f2f7697a70030ceb0'], + }), + ('tascCODA', '0.1.3', { + # strip out tensorflow-probability as required dependency, to ensure that 'pip check' passes + 'preinstallopts': "sed -i '/tensorflow-probability>=0.16/d' setup.py && ", + 'checksums': ['8c12ddccb72c41c96c6a5abceb52e7a76f439a9ab94fb092aa86ee3c1292383a'], + }), + ('harmonypy', '0.0.9', { + 'checksums': ['85bfdd4e6ec6e0fa8816a276639358d3598a40d60ba9f7a5d9dada8706be8c4d'], + }), + ('fbpca', '1.0', { + 'checksums': ['150677642479663f317fdbb5e06dab3f98721cf7031bb4a84113d7a631c472d1'], + }), + ('geosketch', '1.2', { + 'checksums': ['bbfe97366b91c5927b6076d5a6738d9cfbe094efb5ac1117aab7a30b6081cc4e'], + }), + ('python_circos', '0.3.0', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'modulename': 'pycircos', + 'checksums': ['410eaffc4eb2933cd688897356813da23310f5e2f14a8bceb003e9b96faa715b'], + }), + ('mizani', '0.9.3', { + 'checksums': ['fb61339e9e4711850e902ca286b1ae75255f483823d891aa0515b426d56c606d'], + }), + ('plotnine', '0.12.4', { + 'checksums': ['adc41a672503594445a8fa19872799253bd0784cdbd5a1cc16657a1dd20ba905'], + }), + ('ktplotspy', '0.2.3', { + 'checksums': ['9a1e3646217e6e99f59ab2258dfd76120cf1f50880c9cb2f9005de397c00f0a9'], + }), + ('cellphonedb', '5.0.0', { + 'checksums': ['1c96173d8527f1655216d265fc50a28ea3360d70486afa5050e3f5565fa3a8cd'], + }), + ('decoupler', '1.6.0', { + 'checksums': ['dde501f4d3e55a260f716e51b871bee403bc8aaa6b66799df0e42dee0787b98d'], + }), + ('mudata', '0.2.3', { + 'checksums': ['45288ac150bfc598d68acb7c2c1c43c38c5c39522107e04f7efbf3360c7f2035'], + }), + ('nodeenv', '1.9.0', { + 'checksums': ['07f144e90dae547bf0d4ee8da0ee42664a42a04e02ed68e06324348dafe4bdb1'], + }), + ('identify', '2.5.36', { + 'checksums': ['e5e00f54165f9047fbebeb4a560f9acfb8af4c88232be60a488e9b68d122745d'], + }), + ('cfgv', '3.4.0', { + 'checksums': ['e52591d4c5f5dead8e0f673fb16db7949d2cfb3f7da4582893288f0ded8fe560'], + }), + ('pre_commit', '3.7.1', { + 'checksums': ['8ca3ad567bc78a4972a3f1a477e94a79d4597e8140a6e0b651c5e33899c3654a'], + }), + ('muon', '0.1.6', { + 'checksums': ['762feeb6f52f865cf79d0d0332cc742fe91c1885f668ce15794b62b3952b02f9'], + }), + ('liana', '1.2.0', { + 'checksums': ['be899c69bfcbf3d0f8b61c04c35f225ac6b11fe1ea80e6ed4bdc0e6212cb2379'], + }), + ('squarify', '0.4.3', { + 'checksums': ['54091f6ad175f7f201f8934574e647ce1b50dedc478c5fd968688eb7d7469f95'], + }), + ('scikit_build_core', '0.9.3', { + 'checksums': ['341d113e473a5409dc62522e8b1b1b8b1647a0b95557ad15f6be2a36071fd390'], + }), + ('awkward-cpp', '33', { + 'checksums': ['550adebccd329d18d02e95226d0b89698188fd33e44f07450942c692881927d8'], + }), + ('awkward', '2.6.4', { + 'checksums': ['ee0cb27c64150f368749983dda499c108848c64dc830912480eb37b78c04300f'], + }), + ('yamlordereddictloader', '0.4.2', { + 'checksums': ['36af2f6210fcff5da4fc4c12e1d815f973dceb41044e795e1f06115d634bca13'], + }), + ('airr', '1.5.0', { + 'checksums': ['febc0a881bf46b1a9c29ac6a7089dd733ff9120d114585e75dede26403f68d42'], + }), + ('scirpy', '0.17.0', { + 'checksums': ['f61653a4f7387562ec89b00fbfd7cab762c0bf3320f21ccfc47df80a13cc5d41'], + }), + ('schist', '0.8.3', { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/dawe/schist/archive/'], + 'checksums': ['9b98ec9d85554573288c24f18c4791ba7c4d315397cbc422ea25d4a7cdd42e6d'], + }), + ('typeguard', '2.13.3', { + 'checksums': ['00edaa8da3a133674796cf5ea87d9f4b4c367d77476e185e80251cc13dfbb8c4'], + }), + ('jaxtyping', '0.2.29', { + 'checksums': ['e1cd916ed0196e40402b0638449e7d051571562b2cd68d8b94961a383faeb409'], + }), + ('equinox', '0.11.4', { + 'checksums': ['0033d9731083f402a855b12a0777a80aa8507651f7aa86d9f0f9503bcddfd320'], + }), + ('lineax', '0.0.4', { + 'checksums': ['e68f1eba2f352122fdce9adc0556684f31eb8364b1a00acee484dd6e44a34e5e'], + }), + ('jaxopt', '0.8.3', { + 'checksums': ['4b06dfa6f915a4f3291699606245af6069371a48dc5c92d4c507840d62990646'], + }), + ('ott_jax', '0.4.6', { + 'modulename': 'ott', + 'checksums': ['bc91f8d512cdb344439f5584712d76cd0650b6716b6686d53b828cc67abdbcba'], + }), + ('sparsecca', '0.3.1', { + 'checksums': ['be1526baebac5ce6efbc7190fd62a1cec13288c493f5d427024f66ca6afaec13'], + }), + ('PubChemPy', '1.0.4', { + 'checksums': ['24e9dc2fc90ab153b2764bf805e510b1410700884faf0510a9e7cf0d61d8ed0e'], + }), + ('blitzgsea', '1.3.42', { + 'checksums': ['dcc997b5d29d190d8632474f3bb57b5ead7fb1370b478c7f824b42782325a1ca'], + }), + ('pertpy', '0.7.0', { + 'checksums': ['273723b5b70f3cb714bb36d3234462014b72e133111eeaf08aa47153c9df14aa'], + }), +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SingleM/SingleM-0.16.0-foss-2023a.eb b/easybuild/easyconfigs/s/SingleM/SingleM-0.16.0-foss-2023a.eb new file mode 100644 index 000000000000..25fc18b7c631 --- /dev/null +++ b/easybuild/easyconfigs/s/SingleM/SingleM-0.16.0-foss-2023a.eb @@ -0,0 +1,107 @@ +easyblock = 'PythonBundle' + +name = 'SingleM' +version = '0.16.0' + +homepage = 'https://github.com/wwood/singlem' +description = """SingleM is a tool for profiling shotgun metagenomes. +It has a particular strength in detecting microbial lineages which are not in reference databases. +The method it uses also makes it suitable for some related tasks, such as assessing eukaryotic contamination, +finding bias in genome recovery, computing ecological diversity metrics, and lineage-targeted MAG recovery.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [('hatchling', '1.18.0')] +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('Biopython', '1.83'), + ('polars', '0.20.2'), + ('tqdm', '4.66.1'), + ('Arrow', '14.0.1'), + ('DIAMOND', '2.1.8'), + ('HMMER', '3.4'), + ('MAFFT', '7.520', '-with-extensions'), + ('OrfM', '0.7.1'), + ('mfqe', '0.5.0'), + ('KronaTools', '2.8.1'), + ('pplacer', '1.1.alpha19', '', SYSTEM), + ('SRA-Toolkit', '3.0.10'), + ('Seqmagick', '0.8.6'), + ('ExpressBetaDiversity', '1.0.10'), + ('FastTree', '2.1.11'), + ('SQLAlchemy', '2.0.25'), + ('CD-HIT', '4.8.1'), + ('smafa', '0.8.0'), + ('prodigal', '2.6.3'), + ('biom-format', '2.1.15'), + ('DendroPy', '4.6.1'), + ('PyYAML', '6.0'), + ('psycopg', '3.2.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('psycopg2-binary', '2.9.9', { + 'modulename': 'psycopg2', + 'checksums': ['7f01846810177d829c7692f1f5ada8096762d9172af1b1a28d4ab5b77c923c1c'], + }), + ('sqlparse', '0.5.1', { + 'checksums': ['bb6b4df465655ef332548e24f08e205afc81b9ab86cb1c45657a7ff173a3a00e'], + }), + ('sorted_nearest', '0.0.39', { + 'checksums': ['16a51d5db87ae226b47ace43c176bb672477a1b7ba8052ea9291a6356c9c69b1'], + }), + ('ncls', '0.0.68', { + 'checksums': ['81aaa5abb123bb21797ed2f8ef921e20222db14a3ecbc61ccf447532f2b7ba93'], + }), + ('natsort', '8.4.0', { + 'checksums': ['45312c4a0e5507593da193dedd04abb1469253b601ecaf63445ad80f0a1ea581'], + }), + ('argparse-manpage-birdtools', '1.7.0', { + 'modulename': 'build_manpages', + 'checksums': ['20eae3079a4a2dbe1a7557ef7276a4d8e5a44c7c4223afb50f4f1d0ae0e7d103'], + }), + ('taxtastic', '0.10.0', { + 'checksums': ['32db30aa2e499fbae913b991cd087fa69684ac4ff934b957c30b6085866f1748'], + }), + ('zenodo_backpack', '0.3.1', { + 'checksums': ['dc91f3c427f976465789746e94736abfa536cf42dc2e49b6d6067382a9a39b26'], + }), + ('bird_tool_utils', '0.4.1', { + 'checksums': ['6fe80f9608626427e8d382c5341c24088d61f17336fb6ce834d40aa4577499b5'], + }), + ('fastalite', '0.4.1', { + 'checksums': ['e85413ee22bdb3fe0f73f5226771cf71eb33074ccdf8bbefff3a1bc6242de37c'], + }), + ('squarify', '0.4.3', { + 'checksums': ['54091f6ad175f7f201f8934574e647ce1b50dedc478c5fd968688eb7d7469f95'], + }), + ('pyranges', '0.0.129', { + 'checksums': ['bee83b4fad0062be9586668c6b0fc4270d5e761951975e018202993680071fb3'], + }), + ('extern', '0.4.1', { + 'checksums': ['0ff01adc2ad423f3d1e31641024b3974569fb0127b4d925bc6bed1cb86b6b1e4'], + }), + ('graftm', '0.15.1', { + 'checksums': ['80d828c311d2d6067977cfad5b6bac7cbc5d223ef8ab770d676b39bf2bc75163'], + }), + ('singlem', version, { + 'checksums': ['64e43a6a40795d68ff5aed7dfff9a94532b862f25a28c27de7d588d64a8c7f79'], + }), +] + +sanity_check_paths = { + 'files': ['bin/graftM', 'bin/singlem'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "graftM --help", + "singlem --help", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SpFFT/SpFFT-1.1.0-foss-2023a.eb b/easybuild/easyconfigs/s/SpFFT/SpFFT-1.1.0-foss-2023a.eb new file mode 100644 index 000000000000..608918e373c1 --- /dev/null +++ b/easybuild/easyconfigs/s/SpFFT/SpFFT-1.1.0-foss-2023a.eb @@ -0,0 +1,30 @@ +easyblock = 'CMakeMake' + +name = 'SpFFT' +version = '1.1.0' + +homepage = 'https://github.com/eth-cscs/SpFFT/' +description = """Sparse 3D FFT library with MPI, OpenMP, CUDA and ROCm support.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/eth-cscs/SpFFT/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['d4673b3135aebfa1c440723226fe976d518ff881285b3d4787f1aa8210eac81e'] + +builddependencies = [ + ('CMake', '3.26.3'), +] + +configopts = "-DSPFFT_OMP=ON -DSPFFT_MPI=ON " + +sanity_check_paths = { + 'files': [ + 'include/spfft/spfft.h', + 'lib/libspfft.%s' % SHLIB_EXT, + ], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/Sphinx-RTD-Theme/Sphinx-RTD-Theme-2.0.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/s/Sphinx-RTD-Theme/Sphinx-RTD-Theme-2.0.0-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..c41639bc3ad5 --- /dev/null +++ b/easybuild/easyconfigs/s/Sphinx-RTD-Theme/Sphinx-RTD-Theme-2.0.0-GCCcore-12.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonBundle' + +name = 'Sphinx-RTD-Theme' +version = '2.0.0' + +homepage = 'https://sphinx-rtd-theme.readthedocs.io' +description = """Sphinx theme designed to provide a great reader experience + for documentation users on both desktop and mobile devices.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), +] + +use_pip = True + +exts_list = [ + ('sphinxcontrib-jquery', '4.1', { + 'modulename': 'sphinxcontrib.jquery', + 'checksums': ['1620739f04e36a2c779f1a131a2dfd49b2fd07351bf1968ced074365933abc7a'], + }), + ('sphinx_rtd_theme', version, { + 'checksums': ['bd5d7b80622406762073a04ef8fadc5f9151261563d47027de09910ce03afe6b'], + }), +] + +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/Sphinx-RTD-Theme/Sphinx-RTD-Theme-2.0.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/s/Sphinx-RTD-Theme/Sphinx-RTD-Theme-2.0.0-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..6642b38d8205 --- /dev/null +++ b/easybuild/easyconfigs/s/Sphinx-RTD-Theme/Sphinx-RTD-Theme-2.0.0-GCCcore-13.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonBundle' + +name = 'Sphinx-RTD-Theme' +version = '2.0.0' + +homepage = 'https://sphinx-rtd-theme.readthedocs.io' +description = """Sphinx theme designed to provide a great reader experience + for documentation users on both desktop and mobile devices.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('Python', '3.11.5'), + ('Python-bundle-PyPI', '2023.10'), +] + +use_pip = True + +exts_list = [ + ('sphinxcontrib-jquery', '4.1', { + 'modulename': 'sphinxcontrib.jquery', + 'checksums': ['1620739f04e36a2c779f1a131a2dfd49b2fd07351bf1968ced074365933abc7a'], + }), + ('sphinx_rtd_theme', version, { + 'checksums': ['bd5d7b80622406762073a04ef8fadc5f9151261563d47027de09910ce03afe6b'], + }), +] + +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/Stable-Baselines3/Stable-Baselines3-2.3.2-foss-2023a.eb b/easybuild/easyconfigs/s/Stable-Baselines3/Stable-Baselines3-2.3.2-foss-2023a.eb new file mode 100644 index 000000000000..24aee360a6e8 --- /dev/null +++ b/easybuild/easyconfigs/s/Stable-Baselines3/Stable-Baselines3-2.3.2-foss-2023a.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonBundle' + +name = 'Stable-Baselines3' +version = '2.3.2' + +homepage = 'https://github.com/DLR-RM/stable-baselines3' +description = """Stable Baselines3 (SB3) is a set of reliable implementations of +reinforcement learning algorithms in PyTorch.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('Gymnasium', '0.29.1'), + ('SciPy-bundle', '2023.07'), + ('PyTorch', '2.1.2'), + ('matplotlib', '3.7.2'), +] + +use_pip = True + +exts_list = [ + ('cloudpickle', '3.0.0', { + 'checksums': ['996d9a482c6fb4f33c1a35335cf8afd065d2a56e973270364840712d9131a882'], + }), + ('stable_baselines3', version, { + 'use_pip_extras': 'extra', + 'checksums': ['2f8188916e607571c4c24f88a9ff6f84edafb2cf22d5d24f9c199563c12ff168'], + }), +] + +sanity_pip_check = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/Stack/Stack-3.1.1-x86_64.eb b/easybuild/easyconfigs/s/Stack/Stack-3.1.1-x86_64.eb new file mode 100644 index 000000000000..0a822a69cbdd --- /dev/null +++ b/easybuild/easyconfigs/s/Stack/Stack-3.1.1-x86_64.eb @@ -0,0 +1,26 @@ +easyblock = 'Tarball' + +name = 'Stack' +version = '3.1.1' +versionsuffix = '-x86_64' + +homepage = 'https://docs.haskellstack.org' +description = """Stack is a cross-platform program for developing Haskell projects. +It is intended for Haskellers both new and experienced.""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/commercialhaskell/stack/releases/download/v%(version)s/'] +sources = ['%(namelower)s-%(version)s-linux-x86_64.tar.gz'] +checksums = ['d096125ea3d987a55d17f7d4f8599ee2fd96bd2d0f033566e28ddfe248f730f9'] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ['stack'], + 'dirs': ['doc'], +} + +sanity_check_commands = ['stack --help'] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-7.7.0-foss-2023b-METIS-5.1.0.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-7.7.0-foss-2023b-METIS-5.1.0.eb new file mode 100644 index 000000000000..260ca2793044 --- /dev/null +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-7.7.0-foss-2023b-METIS-5.1.0.eb @@ -0,0 +1,29 @@ +name = 'SuiteSparse' +version = '7.7.0' +local_metis_ver = '5.1.0' +versionsuffix = '-METIS-%s' % local_metis_ver + +homepage = 'https://faculty.cse.tamu.edu/davis/suitesparse.html' +description = """SuiteSparse is a collection of libraries to manipulate sparse matrices.""" + +toolchain = {'name': 'foss', 'version': '2023b'} +toolchainopts = {'unroll': True, 'pic': True} + +source_urls = ['https://github.com/DrTimothyAldenDavis/SuiteSparse/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['529b067f5d80981f45ddf6766627b8fc5af619822f068f342aab776e683df4f3'] + +builddependencies = [ + ('CMake', '3.27.6'), + ('M4', '1.4.19'), +] + +dependencies = [ + ('METIS', local_metis_ver), + ('MPFR', '4.2.1'), +] + +# make sure that bin/demo can find libsuitesparseconfig.so.5 during build +prebuildopts = "export LD_LIBRARY_PATH=%(builddir)s/SuiteSparse-%(version)s/lib:$LD_LIBRARY_PATH && " + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/SuperLU/SuperLU-6.0.1-foss-2023b.eb b/easybuild/easyconfigs/s/SuperLU/SuperLU-6.0.1-foss-2023b.eb new file mode 100644 index 000000000000..fb80e7ab219b --- /dev/null +++ b/easybuild/easyconfigs/s/SuperLU/SuperLU-6.0.1-foss-2023b.eb @@ -0,0 +1,21 @@ +name = 'SuperLU' +version = '6.0.1' + +homepage = 'https://crd-legacy.lbl.gov/~xiaoye/SuperLU/' +description = """SuperLU is a general purpose library for the +direct solution of large, sparse, nonsymmetric systems + of linear equations on high performance machines.""" + +toolchain = {'name': 'foss', 'version': '2023b'} +toolchainopts = {'pic': True, 'openmp': True} + +github_account = 'xiaoyeli' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ["v%(version)s.tar.gz"] +checksums = ['6c5a3a9a224cb2658e9da15a6034eed44e45f6963f5a771a6b4562f7afb8f549'] + +builddependencies = [('CMake', '3.27.6')] + +runtest = " test" + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/SuperLU_DIST/SuperLU_DIST-8.2.1-foss-2023b.eb b/easybuild/easyconfigs/s/SuperLU_DIST/SuperLU_DIST-8.2.1-foss-2023b.eb new file mode 100644 index 000000000000..a113fb7ef50b --- /dev/null +++ b/easybuild/easyconfigs/s/SuperLU_DIST/SuperLU_DIST-8.2.1-foss-2023b.eb @@ -0,0 +1,44 @@ +easyblock = "EB_SuperLU" + +name = 'SuperLU_DIST' +version = '8.2.1' + +homepage = 'https://crd-legacy.lbl.gov/~xiaoye/SuperLU/' +description = """SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems + of linear equations on high performance machines.""" + +toolchain = {'name': 'foss', 'version': '2023b'} +toolchainopts = {'pic': True, 'openmp': True} + +github_account = 'xiaoyeli' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ["v%(version)s.tar.gz"] +checksums = ['b77d065cafa6bc1a1dcc15bf23fd854f54b05762b165badcffc195835ad2bddf'] + +builddependencies = [('CMake', '3.27.6')] + +dependencies = [ + ('ParMETIS', '4.0.3'), +] + +configopts = '-DTPL_PARMETIS_INCLUDE_DIRS="${EBROOTPARMETIS}/include" ' +configopts += '-DTPL_PARMETIS_LIBRARIES="${EBROOTPARMETIS}/lib/libparmetis.a;${EBROOTPARMETIS}/lib/libmetis.a" ' + +# Some tests run longer than default 1500s timeout on fairly big machine (36 cores). +# Include only first four tests, which should be fairly small to run +pretestopts = 'export ARGS="$ARGS --tests-regex pdtest_[21]x1_[13]_2_8_20_SP" && ' + +# remove broken symlink to libsuperlu.a +postinstallcmds = [ + "if [ -f %(installdir)s/lib64/libsuperlu.a ]; then rm %(installdir)s/lib64/libsuperlu.a; fi", + # This second one can be removed when https://github.com/easybuilders/easybuild-framework/pull/4435 is merged + # (i.e. in EasyBuild 5.0) + "if [ -f %(installdir)s/lib/libsuperlu.a ]; then rm %(installdir)s/lib/libsuperlu.a; fi" +] + +sanity_check_paths = { + 'files': ['lib64/libsuperlu_dist.a'], + 'dirs': ['include'] +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-10.2.0.eb index 88e067c36e80..576e48c80b4e 100644 --- a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-10.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Szip' version = '2.1.1' -homepage = 'https://www.hdfgroup.org/doc_resource/SZIP/' +homepage = 'https://support.hdfgroup.org/doc_resource/SZIP/' description = """ Szip compression software, providing lossless compression of scientific data @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} toolchainopts = {'pic': True} -source_urls = ['https://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] checksums = ['21ee958b4f2d4be2c9cabfa5e1a94877043609ce86fde5f286f105f7ff84d412'] diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-10.3.0.eb index 10b926a9b61a..5cc6a3396822 100644 --- a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-10.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Szip' version = '2.1.1' -homepage = 'https://www.hdfgroup.org/doc_resource/SZIP/' +homepage = 'https://support.hdfgroup.org/doc_resource/SZIP/' description = """ Szip compression software, providing lossless compression of scientific data @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '10.3.0'} toolchainopts = {'pic': True} -source_urls = ['https://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] checksums = ['21ee958b4f2d4be2c9cabfa5e1a94877043609ce86fde5f286f105f7ff84d412'] diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-11.2.0.eb index b2d223898c77..70a9918dc8ed 100644 --- a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-11.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Szip' version = '2.1.1' -homepage = 'https://www.hdfgroup.org/doc_resource/SZIP/' +homepage = 'https://support.hdfgroup.org/doc_resource/SZIP/' description = """ Szip compression software, providing lossless compression of scientific data @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '11.2.0'} toolchainopts = {'pic': True} -source_urls = ['https://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] checksums = ['21ee958b4f2d4be2c9cabfa5e1a94877043609ce86fde5f286f105f7ff84d412'] diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-11.3.0.eb index 3dc0b200849d..6d34fd7a4765 100644 --- a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-11.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Szip' version = '2.1.1' -homepage = 'https://www.hdfgroup.org/doc_resource/SZIP/' +homepage = 'https://support.hdfgroup.org/doc_resource/SZIP/' description = """ Szip compression software, providing lossless compression of scientific data @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '11.3.0'} toolchainopts = {'pic': True} -source_urls = ['https://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] checksums = ['21ee958b4f2d4be2c9cabfa5e1a94877043609ce86fde5f286f105f7ff84d412'] diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-12.2.0.eb index 6f536c566dda..e58b9c3ffefc 100644 --- a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-12.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Szip' version = '2.1.1' -homepage = 'https://www.hdfgroup.org/doc_resource/SZIP/' +homepage = 'https://support.hdfgroup.org/doc_resource/SZIP/' description = """ Szip compression software, providing lossless compression of scientific data @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '12.2.0'} toolchainopts = {'pic': True} -source_urls = ['https://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] checksums = ['21ee958b4f2d4be2c9cabfa5e1a94877043609ce86fde5f286f105f7ff84d412'] diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-12.3.0.eb index e0a01221b9d0..ee9fd884627c 100644 --- a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-12.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Szip' version = '2.1.1' -homepage = 'https://www.hdfgroup.org/doc_resource/SZIP/' +homepage = 'https://support.hdfgroup.org/doc_resource/SZIP/' description = """ Szip compression software, providing lossless compression of scientific data @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} toolchainopts = {'pic': True} -source_urls = ['https://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] checksums = ['21ee958b4f2d4be2c9cabfa5e1a94877043609ce86fde5f286f105f7ff84d412'] diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-13.2.0.eb index 8eb126706529..5fcc21050e54 100644 --- a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-13.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Szip' version = '2.1.1' -homepage = 'https://www.hdfgroup.org/doc_resource/SZIP/' +homepage = 'https://support.hdfgroup.org/doc_resource/SZIP/' description = """ Szip compression software, providing lossless compression of scientific data @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '13.2.0'} toolchainopts = {'pic': True} -source_urls = ['https://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] checksums = ['21ee958b4f2d4be2c9cabfa5e1a94877043609ce86fde5f286f105f7ff84d412'] diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-6.3.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-6.3.0.eb index f614a665648b..5cebe3f7c68e 100644 --- a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-6.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Szip' version = '2.1.1' -homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/' +homepage = 'http://support.hdfgroup.org/doc_resource/SZIP/' description = """ Szip compression software, providing lossless compression of scientific data @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '6.3.0'} toolchainopts = {'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +source_urls = ['http://support.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] checksums = ['21ee958b4f2d4be2c9cabfa5e1a94877043609ce86fde5f286f105f7ff84d412'] diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-6.4.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-6.4.0.eb index 924f439ed4eb..8edba3b1aa27 100644 --- a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-6.4.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Szip' version = '2.1.1' -homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/' +homepage = 'http://support.hdfgroup.org/doc_resource/SZIP/' description = """ Szip compression software, providing lossless compression of scientific data @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '6.4.0'} toolchainopts = {'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +source_urls = ['http://support.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] checksums = ['21ee958b4f2d4be2c9cabfa5e1a94877043609ce86fde5f286f105f7ff84d412'] diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-7.3.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-7.3.0.eb index 4b9a4923df9d..a9926ab81d10 100644 --- a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-7.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Szip' version = '2.1.1' -homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/' +homepage = 'http://support.hdfgroup.org/doc_resource/SZIP/' description = """ Szip compression software, providing lossless compression of scientific data @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '7.3.0'} toolchainopts = {'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +source_urls = ['http://support.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] checksums = ['21ee958b4f2d4be2c9cabfa5e1a94877043609ce86fde5f286f105f7ff84d412'] diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-8.2.0.eb index 7f564c5a0fab..0d07710e2382 100644 --- a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-8.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Szip' version = '2.1.1' -homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/' +homepage = 'http://support.hdfgroup.org/doc_resource/SZIP/' description = """ Szip compression software, providing lossless compression of scientific data @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '8.2.0'} toolchainopts = {'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +source_urls = ['http://support.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] checksums = ['21ee958b4f2d4be2c9cabfa5e1a94877043609ce86fde5f286f105f7ff84d412'] diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-8.3.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-8.3.0.eb index 69db79f2d43e..e522a3ac747b 100644 --- a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-8.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Szip' version = '2.1.1' -homepage = 'https://www.hdfgroup.org/doc_resource/SZIP/' +homepage = 'https://support.hdfgroup.org/doc_resource/SZIP/' description = """ Szip compression software, providing lossless compression of scientific data @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '8.3.0'} toolchainopts = {'pic': True} -source_urls = ['https://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] checksums = ['21ee958b4f2d4be2c9cabfa5e1a94877043609ce86fde5f286f105f7ff84d412'] diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-9.3.0.eb index 242c281b919b..822080c60fed 100644 --- a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-9.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Szip' version = '2.1.1' -homepage = 'https://www.hdfgroup.org/doc_resource/SZIP/' +homepage = 'https://support.hdfgroup.org/doc_resource/SZIP/' description = """ Szip compression software, providing lossless compression of scientific data @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '9.3.0'} toolchainopts = {'pic': True} -source_urls = ['https://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] checksums = ['21ee958b4f2d4be2c9cabfa5e1a94877043609ce86fde5f286f105f7ff84d412'] diff --git a/easybuild/easyconfigs/s/scArches/scArches-0.6.1-foss-2023a.eb b/easybuild/easyconfigs/s/scArches/scArches-0.6.1-foss-2023a.eb new file mode 100644 index 000000000000..bdcb1ab880cd --- /dev/null +++ b/easybuild/easyconfigs/s/scArches/scArches-0.6.1-foss-2023a.eb @@ -0,0 +1,52 @@ +easyblock = 'PythonBundle' + +name = 'scArches' +version = '0.6.1' + +homepage = 'https://github.com/theislab/scarches' +description = """Single-cell architecture surgery (scArches) is a package for reference-based analysis of single-cell + data.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('Python-bundle-PyPI', '2023.06'), + ('matplotlib', '3.7.2'), + ('anndata', '0.10.5.post1'), + ('h5py', '3.9.0'), + ('leidenalg', '0.10.2'), + ('scanpy', '1.9.8'), + ('scikit-learn', '1.3.1'), + ('scvi-tools', '1.1.2'), + ('PyTorch', '2.1.2'), + ('tqdm', '4.66.1'), +] + +use_pip = True + +exts_list = [ + ('gdown', '5.1.0', { + 'checksums': ['550a72dc5ca2819fe4bcc15d80d05d7c98c0b90e57256254b77d0256b9df4683'], + }), + ('muon', '0.1.6', { + 'checksums': ['762feeb6f52f865cf79d0d0332cc742fe91c1885f668ce15794b62b3952b02f9'], + }), + ('newick', '1.9.0', { + 'checksums': ['9f81be96ec86aefca74d920fc0d6962d89a3156547003ca6915c2e6e31ad3ddf'], + }), + ('scHPL', '1.0.5', { + 'modulename': 'scHPL', + # unpin pandas and newick versions to be compatible with foss/2023a versions + 'preinstallopts': "sed -i 's/~=/>=/g' setup.py && sed -i 's/pandas>=1.1.2,<2/pandas/g' setup.py && ", + 'checksums': ['3eb62b2e65b1faba04b7bcb86f7bf6967a6301866a605551211b8f14fd27eced'], + }), + (name, version, { + 'checksums': ['187463c25781d5c5586c129ad137d96327a9f8604d530a696d5f568a9225d77c'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/scCustomize/scCustomize-2.1.2-foss-2023a-R-4.3.2.eb b/easybuild/easyconfigs/s/scCustomize/scCustomize-2.1.2-foss-2023a-R-4.3.2.eb new file mode 100644 index 000000000000..2f94ec912065 --- /dev/null +++ b/easybuild/easyconfigs/s/scCustomize/scCustomize-2.1.2-foss-2023a-R-4.3.2.eb @@ -0,0 +1,65 @@ +easyblock = 'Bundle' + +name = 'scCustomize' +version = '2.1.2' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://cran.r-project.org/web/packages/scCustomize/index.html' +description = """ +Collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using 'R'. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + # Seurat has its own module, but is either in R-bundle-Bioconductor + ('R', '4.3.2'), + ('R-bundle-CRAN', '2023.12'), + ('R-bundle-Bioconductor', '3.18', '-R-%(rver)s'), +] + +exts_default_options = { + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'sources': ['%(name)s_%(version)s.tar.gz'], +} + +exts_defaultclass = 'RPackage' + +exts_list = [ + ('rlang', '1.1.3', { + 'checksums': ['24a3424b5dc2c4bd3e5f7c0b54fbe1355028e329181b2d41f4464c8ade28bf0a'], + }), + ('prismatic', '1.1.2', { + 'checksums': ['babf5b7ad4c9b52921c619de66f93936755dc385b2b69c6504d87c7d5a71e261'], + }), + ('paletteer', '1.6.0', { + 'checksums': ['b5de20300c93df203ddc4f3bfeb0a825ef2745c22d66590b33cef9e7448d92d8'], + }), + ('snakecase', '0.11.1', { + 'checksums': ['2a5f9791337ca42e392f23fb873eb44f74810583e9aa7c62fda2f28f9e750821'], + }), + ('janitor', '2.2.0', { + 'checksums': ['29d5d0185e4e824bb38f905b158162a12f52dc01c2e8a487fc730ce46bf6baae'], + }), + ('ggprism', '1.0.5', { + 'checksums': ['7f35eeb010ef3cb47f23cb23b0b084156c56af02cff534c217652ea38cdb5171'], + }), + (name, version, { + 'checksums': ['2b569a145fe6dd888ac72ced424352b100b7acc913d6027ddae7799ca4421094'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +sanity_check_commands = ['Rscript -e "library(%(name)s)"'] + +modextrapaths = {'R_LIBS_SITE': ''} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/scFEA/scFEA-1.1-20221109-foss-2023a.eb b/easybuild/easyconfigs/s/scFEA/scFEA-1.1-20221109-foss-2023a.eb new file mode 100644 index 000000000000..3e1d61330154 --- /dev/null +++ b/easybuild/easyconfigs/s/scFEA/scFEA-1.1-20221109-foss-2023a.eb @@ -0,0 +1,32 @@ +easyblock = 'Tarball' + +name = 'scFEA' +local_commit = '4c1fb76' +version = '1.1-20221109' + +homepage = 'https://github.com/changwn/scFEA' +description = """scFEA: A graph neural network model to estimate cell-wise metabolic using single cell RNA-seq data""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/changwn/scFEA/archive'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['79774974964fed427dd67ba1d51c202a5ff90418fd84f74ebd9b478113ff50f6'] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('matplotlib', '3.7.2'), + ('tqdm', '4.66.1'), + ('PyTorch', '2.1.2'), + ('MAGIC', '3.0.0'), +] + +sanity_check_paths = { + 'files': ['src/scFEA.py'], + 'dirs': [], +} + +sanity_check_commands = ["python %(installdir)s/src/scFEA.py --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/scib-metrics/scib-metrics-0.5.1-foss-2023a.eb b/easybuild/easyconfigs/s/scib-metrics/scib-metrics-0.5.1-foss-2023a.eb new file mode 100644 index 000000000000..68ef32b71ad9 --- /dev/null +++ b/easybuild/easyconfigs/s/scib-metrics/scib-metrics-0.5.1-foss-2023a.eb @@ -0,0 +1,54 @@ +easyblock = 'PythonBundle' + +name = 'scib-metrics' +version = '0.5.1' + +homepage = 'https://scib-metrics.readthedocs.io' +description = "Accelerated and Python-only metrics for benchmarking single-cell integration outputs" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('hatchling', '1.18.0'), + ('poetry', '1.5.1'), +] +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('anndata', '0.10.5.post1'), + ('jax', '0.4.25'), + ('scikit-learn', '1.3.1'), + ('scanpy', '1.9.8'), + ('python-igraph', '0.11.4'), + ('matplotlib', '3.7.2'), + ('tqdm', '4.66.1'), + ('umap-learn', '0.5.5'), +] + +use_pip = True + +exts_list = [ + ('toolz', '0.12.1', { + 'checksums': ['ecca342664893f177a13dac0e6b41cbd8ac25a358e5f215316d43e2100224f4d'], + }), + ('plottable', '0.1.5', { + 'checksums': ['235d762a31c82129dc5bf74205c103a14b1e4393d0f921cc0231be5de884041d'], + }), + ('pynndescent', '0.5.11', { + 'checksums': ['6f44ced9d5a9da2c87d9b2fff30bb5308540c0657605e4d5cde7ed3275bbad50'], + }), + ('rich', '13.7.1', { + 'checksums': ['9be308cb1fe2f1f57d67ce99e95af38a1e2bc71ad9813b0e247cf7ffbcc3a432'], + }), + ('chex', '0.1.86', { + 'checksums': ['e8b0f96330eba4144659e1617c0f7a57b161e8cbb021e55c6d5056c7378091d1'], + }), + (name, version, { + 'sources': ['scib_metrics-%(version)s.tar.gz'], + 'checksums': ['74d10251acf1c11402b994faf063e55317881d7950fb78f6cef011d232a1e266'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/scikit-build/scikit-build-0.17.6-GCCcore-13.3.0.eb b/easybuild/easyconfigs/s/scikit-build/scikit-build-0.17.6-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..2d799810ee18 --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-build/scikit-build-0.17.6-GCCcore-13.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonBundle' + +name = 'scikit-build' +version = '0.17.6' + +homepage = 'https://scikit-build.readthedocs.io/en/latest' +description = """Scikit-Build, or skbuild, is an improved build system generator +for CPython C/C++/Fortran/Cython extensions.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('binutils', '2.42'), + ('hatchling', '1.24.2'), +] + +dependencies = [ + ('Python', '3.12.3'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('packaging', '23.1', { + 'checksums': ['a392980d2b6cffa644431898be54b0045151319d1e7ec34f0cfed48767dd334f'], + }), + ('distro', '1.8.0', { + 'checksums': ['02e111d1dc6a50abb8eed6bf31c3e48ed8b0830d1ea2a1b78c61765c2513fdd8'], + }), + (name, version, { + 'modulename': 'skbuild', + 'sources': ['scikit_build-%(version)s.tar.gz'], + 'checksums': ['b51a51a36b37c42650994b5047912f59b22e3210b23e321f287611f9ef6e5c9d'], + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/scikit-misc/scikit-misc-0.3.1-foss-2023a.eb b/easybuild/easyconfigs/s/scikit-misc/scikit-misc-0.3.1-foss-2023a.eb index e355180eb496..dda0a838bf3b 100644 --- a/easybuild/easyconfigs/s/scikit-misc/scikit-misc-0.3.1-foss-2023a.eb +++ b/easybuild/easyconfigs/s/scikit-misc/scikit-misc-0.3.1-foss-2023a.eb @@ -9,6 +9,10 @@ description = "Miscellaneous tools for data analysis and scientific computing" toolchain = {'name': 'foss', 'version': '2023a'} +builddependencies = [ + ('pkgconf', '1.9.5'), +] + dependencies = [ ('Python', '3.11.3'), ('SciPy-bundle', '2023.07'), diff --git a/easybuild/easyconfigs/s/scrublet/scrublet-0.2.3-foss-2023a.eb b/easybuild/easyconfigs/s/scrublet/scrublet-0.2.3-foss-2023a.eb new file mode 100644 index 000000000000..5b6d65b6bb42 --- /dev/null +++ b/easybuild/easyconfigs/s/scrublet/scrublet-0.2.3-foss-2023a.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonBundle' + +name = 'scrublet' +version = '0.2.3' + +homepage = 'https://github.com/swolock/scrublet' +description = "Single-Cell Remover of Doublets - Python code for identifying doublets in single-cell RNA-seq data" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('scikit-learn', '1.3.1'), + ('scikit-image', '0.22.0'), + ('matplotlib', '3.7.2'), + ('numba', '0.58.1'), + ('tqdm', '4.66.1'), + ('umap-learn', '0.5.5'), +] + +use_pip = True + +exts_list = [ + ('annoy', '1.17.3', { + 'checksums': ['9cbfebefe0a5f843eba29c6be4c84d601f4f41ad4ded0486f1b88c3b07739c15'], + }), + (name, version, { + 'checksums': ['2185f63070290267f82a36e5b4cae8c321f10415d2d0c9f7e5e97b1126bf653a'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/scvi-tools/scvi-tools-1.1.2-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/s/scvi-tools/scvi-tools-1.1.2-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 000000000000..c434f381cfd9 --- /dev/null +++ b/easybuild/easyconfigs/s/scvi-tools/scvi-tools-1.1.2-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,57 @@ +easyblock = 'PythonBundle' + +name = 'scvi-tools' +version = '1.1.2' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/scverse/scvi-tools' +description = """scvi-tools (single-cell variational inference tools) is a package for probabilistic modeling and +analysis of single-cell omics data, built on top of PyTorch and AnnData.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [('hatchling', '1.18.0')] +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('anndata', '0.10.5.post1'), + ('matplotlib', '3.7.2'), + ('scikit-learn', '1.3.1'), + ('tqdm', '4.66.1'), + ('h5py', '3.9.0'), + ('jax', '0.4.25', versionsuffix), + ('Flax', '0.8.4', versionsuffix), + ('PyTorch-Lightning', '2.2.1', versionsuffix), + ('pyro-ppl', '1.9.0', versionsuffix), + ('ml-collections', '0.1.1'), +] + +use_pip = True + +exts_list = [ + ('mudata', '0.2.3', { + 'checksums': ['45288ac150bfc598d68acb7c2c1c43c38c5c39522107e04f7efbf3360c7f2035'], + }), + ('multipledispatch', '1.0.0', { + 'checksums': ['5c839915465c68206c3e9c473357908216c28383b425361e5d144594bf85a7e0'], + }), + ('numpyro', '0.15.0', { + 'checksums': ['e16c9f47cc31e2aa259584a0b6c944312081d33ca92406022632ad584b0e600d'], + }), + ('docrep', '0.3.2', { + 'checksums': ['ed8a17e201abd829ef8da78a0b6f4d51fb99a4cbd0554adbed3309297f964314'], + }), + ('lightning', '2.1.4', { + 'checksums': ['0e45098c700fa28c604a11ae233ce181b44aeffce2404debebc2616118431d9f'], + }), + (name, version, { + 'modulename': 'scvi', + 'sources': ['scvi_tools-%(version)s.tar.gz'], + 'checksums': ['104a11a30e8996f5ceaa907b8c81b48b1f4b380d492ef2dd9b9a5577ed81b0f9'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/scvi-tools/scvi-tools-1.1.2-foss-2023a.eb b/easybuild/easyconfigs/s/scvi-tools/scvi-tools-1.1.2-foss-2023a.eb new file mode 100644 index 000000000000..be427d2af9ee --- /dev/null +++ b/easybuild/easyconfigs/s/scvi-tools/scvi-tools-1.1.2-foss-2023a.eb @@ -0,0 +1,55 @@ +easyblock = 'PythonBundle' + +name = 'scvi-tools' +version = '1.1.2' + +homepage = 'https://github.com/scverse/scvi-tools' +description = """scvi-tools (single-cell variational inference tools) is a package for probabilistic modeling and +analysis of single-cell omics data, built on top of PyTorch and AnnData.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [('hatchling', '1.18.0')] +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('anndata', '0.10.5.post1'), + ('matplotlib', '3.7.2'), + ('scikit-learn', '1.3.1'), + ('tqdm', '4.66.1'), + ('jax', '0.4.25'), + ('h5py', '3.9.0'), + ('PyTorch-Lightning', '2.2.1'), + ('pyro-ppl', '1.9.0'), + ('ml-collections', '0.1.1'), + ('Flax', '0.8.4'), +] + +use_pip = True + +exts_list = [ + ('mudata', '0.2.3', { + 'checksums': ['45288ac150bfc598d68acb7c2c1c43c38c5c39522107e04f7efbf3360c7f2035'], + }), + ('multipledispatch', '1.0.0', { + 'checksums': ['5c839915465c68206c3e9c473357908216c28383b425361e5d144594bf85a7e0'], + }), + ('numpyro', '0.15.0', { + 'checksums': ['e16c9f47cc31e2aa259584a0b6c944312081d33ca92406022632ad584b0e600d'], + }), + ('docrep', '0.3.2', { + 'checksums': ['ed8a17e201abd829ef8da78a0b6f4d51fb99a4cbd0554adbed3309297f964314'], + }), + ('lightning', '2.1.4', { + 'checksums': ['0e45098c700fa28c604a11ae233ce181b44aeffce2404debebc2616118431d9f'], + }), + (name, version, { + 'modulename': 'scvi', + 'sources': ['scvi_tools-%(version)s.tar.gz'], + 'checksums': ['104a11a30e8996f5ceaa907b8c81b48b1f4b380d492ef2dd9b9a5577ed81b0f9'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/sdsl-lite/sdsl-lite-2.0.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/s/sdsl-lite/sdsl-lite-2.0.3-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..d4bda3a4a9e9 --- /dev/null +++ b/easybuild/easyconfigs/s/sdsl-lite/sdsl-lite-2.0.3-GCCcore-12.2.0.eb @@ -0,0 +1,31 @@ +# This easyconfig was created by the BEAR Software team at the University of Birmingham. +easyblock = "CMakeMake" + +name = 'sdsl-lite' +version = '2.0.3' + +homepage = "https://github.com/simongog/sdsl-lite" +description = """The Succinct Data Structure Library (SDSL) is a powerful and flexible C++11 library implementing + succinct data structures. In total, the library contains the highlights of 40 research publications. Succinct + data structures can represent an object (such as a bitvector or a tree) in space close to the information-theoretic + lower bound of the object while supporting operations of the original object efficiently. The theoretical time + complexity of an operation performed on the classical data structure and the equivalent succinct data structure + are (most of the time) identical.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/simongog/%(name)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['08ece40ce44041906bfa425af81a20a8071d187285f674debd8816c2e3113c2f'] + +builddependencies = [ + ('CMake', '3.24.3'), + ('binutils', '2.39'), +] + +sanity_check_paths = { + 'files': ['lib/libdivsufsort64.a', 'lib/libdivsufsort.a', 'lib/libsdsl.a', 'include/divsufsort64.h'], + 'dirs': ['include/sdsl'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/segment-anything/segment-anything-1.0-foss-2023a.eb b/easybuild/easyconfigs/s/segment-anything/segment-anything-1.0-foss-2023a.eb new file mode 100644 index 000000000000..23c6de38a670 --- /dev/null +++ b/easybuild/easyconfigs/s/segment-anything/segment-anything-1.0-foss-2023a.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'segment-anything' +version = '1.0' + +homepage = 'https://github.com/facebookresearch/segment-anything' +description = """The Segment Anything Model (SAM) produces high quality object masks from input prompts + such as points or boxes, and it can be used to generate masks for all objects in an image. + It has been trained on a dataset of 11 million images and 1.1 billion masks, and has strong zero-shot + performance on a variety of segmentation tasks.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +sources = ['segment_anything-%(version)s.tar.gz'] +checksums = ['ed0c9f6fb07bbef9c6238a7028a13c8272f1ba6b6305ca73e3e064266503736b'] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('torchvision', '0.16.0'), + ('OpenCV', '4.8.1', '-contrib'), + ('pycocotools', '2.0.7'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/s/setuptools-rust/setuptools-rust-1.6.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/s/setuptools-rust/setuptools-rust-1.6.0-GCCcore-12.3.0.eb index 8cbf2db9fe75..b2517ef684cc 100644 --- a/easybuild/easyconfigs/s/setuptools-rust/setuptools-rust-1.6.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/s/setuptools-rust/setuptools-rust-1.6.0-GCCcore-12.3.0.eb @@ -18,11 +18,8 @@ dependencies = [ ('Python', '3.11.3'), ] -exts_default_options = { - 'download_dep_fail': True, - 'sanity_pip_check': True, - 'use_pip': True, -} +sanity_pip_check = True +use_pip = True exts_list = [ ('typing_extensions', '4.6.3', { diff --git a/easybuild/easyconfigs/s/setuptools-rust/setuptools-rust-1.8.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/s/setuptools-rust/setuptools-rust-1.8.0-GCCcore-13.2.0.eb index 669229c8f11d..044d56266ae0 100644 --- a/easybuild/easyconfigs/s/setuptools-rust/setuptools-rust-1.8.0-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/s/setuptools-rust/setuptools-rust-1.8.0-GCCcore-13.2.0.eb @@ -18,11 +18,8 @@ dependencies = [ ('Python', '3.11.5'), ] -exts_default_options = { - 'download_dep_fail': True, - 'sanity_pip_check': True, - 'use_pip': True, -} +sanity_pip_check = True +use_pip = True exts_list = [ ('typing_extensions', '4.8.0', { diff --git a/easybuild/easyconfigs/s/setuptools-rust/setuptools-rust-1.9.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/s/setuptools-rust/setuptools-rust-1.9.0-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..b763364ba26d --- /dev/null +++ b/easybuild/easyconfigs/s/setuptools-rust/setuptools-rust-1.9.0-GCCcore-13.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonBundle' + +name = 'setuptools-rust' +version = '1.9.0' + +homepage = 'https://github.com/PyO3/setuptools-rust' +description = """setuptools-rust is a plugin for setuptools to build Rust Python extensions +implemented with PyO3 or rust-cpython.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +builddependencies = [ + ('binutils', '2.42'), +] + +dependencies = [ + ('Python', '3.12.3'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('typing-extensions', '4.12.2', { + 'sources': ['typing_extensions-%(version)s.tar.gz'], + 'checksums': ['1a7ead55c7e559dd4dee8856e3a88b41225abfe1ce8df57b7c13915fe121ffb8'], + }), + ('semantic-version', '2.10.0', { + 'sources': ['semantic_version-%(version)s.tar.gz'], + 'checksums': ['bdabb6d336998cbb378d4b9db3a4b56a1e3235701dc05ea2690d9a997ed5041c'], + }), + (name, version, { + 'checksums': ['704df0948f2e4cc60c2596ad6e840ea679f4f43e58ed4ad0c1857807240eab96'], + }), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/sirocco/sirocco-2.1.0-GCC-13.2.0.eb b/easybuild/easyconfigs/s/sirocco/sirocco-2.1.0-GCC-13.2.0.eb new file mode 100644 index 000000000000..3819e493fe2e --- /dev/null +++ b/easybuild/easyconfigs/s/sirocco/sirocco-2.1.0-GCC-13.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'sirocco' +version = '2.1.0' + +homepage = 'https://github.com/miguelmarco/SIROCCO2/' +description = """C++ library that allows to compute piecewise linear + approximations of the path followed by the root of a complex polynomial""" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +source_urls = ['https://github.com/miguelmarco/SIROCCO2/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['1fd66ae94d73095f1355389c1d3d94222437bed87579d77667f50548bdd9fa9a'] + +builddependencies = [ + ('Autotools', '20220317'), +] + +dependencies = [ + ('MPFR', '4.2.1'), +] + +preconfigopts = 'autoreconf --install && ' + +sanity_check_paths = { + 'files': [ + 'include/sirocco.h', + 'lib/libsirocco.%s' % SHLIB_EXT, + ], + 'dirs': [] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/slepc4py/slepc4py-3.20.2-foss-2023a.eb b/easybuild/easyconfigs/s/slepc4py/slepc4py-3.20.2-foss-2023a.eb new file mode 100644 index 000000000000..c161116802d1 --- /dev/null +++ b/easybuild/easyconfigs/s/slepc4py/slepc4py-3.20.2-foss-2023a.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'slepc4py' +version = '3.20.2' + +homepage = 'https://bitbucket.org/slepc/slepc4py' +description = "Python bindings for SLEPc, the Scalable Library for Eigenvalue Problem Computations." + +toolchain = {'name': 'foss', 'version': '2023a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['89ebd1964edd0eb63d4dbfa977d6f35408f4e19a3da290696fd1197901544bd8'] + +dependencies = [ + ('Python', '3.11.3'), + ('SLEPc', '3.20.1'), + ('petsc4py', '3.20.3'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_commands = ["python -c 'from slepc4py import SLEPc'"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/smafa/smafa-0.8.0-GCC-12.3.0.eb b/easybuild/easyconfigs/s/smafa/smafa-0.8.0-GCC-12.3.0.eb new file mode 100644 index 000000000000..342d27e7548f --- /dev/null +++ b/easybuild/easyconfigs/s/smafa/smafa-0.8.0-GCC-12.3.0.eb @@ -0,0 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+crates = [ + ('addr2line', '0.22.0'), + ('adler', '1.0.2'), + ('aho-corasick', '1.1.3'), + ('anstream', '0.6.14'), + ('anstyle', '1.0.7'), + ('anstyle-parse', '0.2.4'), + ('anstyle-query', '1.1.0'), + ('anstyle-wincon', '3.0.3'), + ('assert_cli', '0.6.3'), + ('atomic-polyfill', '1.0.3'), + ('autocfg', '1.3.0'), + ('backtrace', '0.3.73'), + ('bird_tool_utils', '0.4.1'), + ('bird_tool_utils-man', '0.4.0'), + ('bitflags', '2.6.0'), + ('buffer-redux', '1.0.1'), + ('bytecount', '0.6.8'), + ('byteorder', '1.5.0'), + ('bzip2', '0.4.4'), + ('bzip2-sys', '0.1.11+1.0.8'), + ('cargo-husky', '1.5.0'), + ('cc', '1.1.5'), + ('cfg-if', '1.0.0'), + ('clap', '4.5.9'), + ('clap_builder', '4.5.9'), + ('clap_lex', '0.7.1'), + ('cobs', '0.2.3'), + ('colorchoice', '1.0.1'), + ('colored', '1.9.4'), + ('crc32fast', '1.4.2'), + ('critical-section', '1.1.2'), + ('difference', '2.0.0'), + ('embedded-io', '0.4.0'), + ('env_logger', '0.10.2'), + ('environment', '0.1.1'), + ('errno', '0.3.9'), + ('failure', '0.1.8'), + ('failure_derive', '0.1.8'), + ('fastrand', '2.1.0'), + ('flate2', '1.0.30'), + ('gimli', '0.29.0'), + ('hash32', '0.2.1'), + ('heapless', '0.7.17'), + ('hermit-abi', '0.3.9'), + ('humantime', '2.1.0'), + ('is-terminal', '0.4.12'), + ('is_terminal_polyfill', '1.70.0'), + ('itoa', '1.0.11'), + ('lazy_static', '1.5.0'), + ('libc', '0.2.155'), + ('linux-raw-sys', '0.4.14'), + ('lock_api', '0.4.12'), + ('log', '0.4.22'), + ('lzma-sys', '0.1.20'), + ('memchr', '2.7.4'), + ('miniz_oxide', '0.7.4'), + ('needletail', '0.5.1'), + ('object', '0.36.1'), + ('pkg-config', '0.3.30'), + ('postcard', '1.0.8'), + ('proc-macro2', '1.0.86'), + ('quote', '1.0.36'), + ('regex', '1.10.5'), + ('regex-automata', '0.4.7'), + ('regex-syntax', '0.8.4'), + ('roff', '0.1.0'), + ('rustc-demangle', '0.1.24'), + ('rustc_version', '0.4.0'), + ('rustix', '0.38.34'), + ('ryu', '1.0.18'), + ('scopeguard', '1.2.0'), + ('semver', '1.0.23'), + ('serde', '1.0.204'), + ('serde_derive', '1.0.204'), + ('serde_json', '1.0.120'), + ('spin', '0.9.8'), + ('stable_deref_trait', '1.2.0'), + ('strsim', '0.11.1'), + ('syn', '1.0.109'), + ('syn', '2.0.71'), + ('synstructure', '0.12.6'), + ('tempfile', '3.10.1'), + ('termcolor', '1.4.1'), + ('unicode-ident', '1.0.12'), + ('unicode-xid', '0.2.4'), + ('utf8parse', '0.2.2'), + ('version-compare', '0.1.1'), + ('winapi', '0.3.9'), + ('winapi-i686-pc-windows-gnu', '0.4.0'), + ('winapi-util', '0.1.8'), + ('winapi-x86_64-pc-windows-gnu', '0.4.0'), + ('windows-sys', '0.52.0'), + ('windows-targets', '0.52.6'), + ('windows_aarch64_gnullvm', '0.52.6'), + ('windows_aarch64_msvc', '0.52.6'), + ('windows_i686_gnu', '0.52.6'), + ('windows_i686_gnullvm', '0.52.6'), + ('windows_i686_msvc', '0.52.6'), + ('windows_x86_64_gnu', '0.52.6'), + ('windows_x86_64_gnullvm', '0.52.6'), + ('windows_x86_64_msvc', '0.52.6'), + ('xz2', '0.1.7'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/smithwaterman/smithwaterman-20160702-GCCcore-12.2.0.eb b/easybuild/easyconfigs/s/smithwaterman/smithwaterman-20160702-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..d546525a5c91 --- /dev/null +++ b/easybuild/easyconfigs/s/smithwaterman/smithwaterman-20160702-GCCcore-12.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'smithwaterman' +version = '20160702' +local_commit = '2610e25' + +homepage = 'https://github.com/ekg/smithwaterman' +description = """smith-waterman-gotoh alignment algorithm.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +github_account = 'ekg' +source_urls = [GITHUB_SOURCE] +sources = ['%s.tar.gz' % local_commit] +patches = ['%(name)s-%(version)s_build-shared-lib.patch'] +checksums = [ + '8e1b37ab0e8cd9d3d5cbfdba80258c0ebd0862749b531e213f44cdfe2fc541d8', # 2610e25.tar.gz + '2aa63ec5cd0260efcab002eaf4bbf62497b91afc0e3f82d8290496803c35e582', # smithwaterman-20160702_build-shared-lib.patch +] + +builddependencies = [('binutils', '2.39')] + +skipsteps = ['configure'] + +installopts = 'PREFIX=%(installdir)s ' + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'lib/libsw.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ["%(name)s --help"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/snpEff/snpEff-5.2c-GCCcore-12.2.0-Java-11.eb b/easybuild/easyconfigs/s/snpEff/snpEff-5.2c-GCCcore-12.2.0-Java-11.eb new file mode 100644 index 000000000000..3b25c1e949f9 --- /dev/null +++ b/easybuild/easyconfigs/s/snpEff/snpEff-5.2c-GCCcore-12.2.0-Java-11.eb @@ -0,0 +1,37 @@ +easyblock = 'Tarball' + +name = 'snpEff' +version = '5.2c' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://pcingola.github.io/SnpEff/' +description = """SnpEff is a variant annotation and effect prediction tool. + It annotates and predicts the effects of genetic variants (such as amino acid changes).""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://snpeff.blob.core.windows.net/versions/'] +sources = ['%%(name)s_v%s_core.zip' % version.replace('.', '_')] +checksums = ['9926f600662707e85478940abc283ef120a909f1d41c32a036f01d958cd51232'] + +dependencies = [ + # ignore website claim that Java 12+ is required, nothing is compiled for + # anything newer than Java 11 + ('Java', '11', '', SYSTEM), + ('Python', '3.10.8'), + ('Perl', '5.36.0'), +] + +fix_perl_shebang_for = ['scripts/*.pl'] +fix_python_shebang_for = ['scripts/*.py'] + +sanity_check_paths = { + 'files': ['%(name)s.jar', 'SnpSift.jar', 'scripts/%(name)s'], + 'dirs': [], +} + +sanity_check_commands = ["%(name)s -version"] + +modextrapaths = {'PATH': 'scripts'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/spaCy/spaCy-3.7.4-foss-2023a.eb b/easybuild/easyconfigs/s/spaCy/spaCy-3.7.4-foss-2023a.eb new file mode 100644 index 000000000000..e8c79ceb6bf1 --- /dev/null +++ b/easybuild/easyconfigs/s/spaCy/spaCy-3.7.4-foss-2023a.eb @@ -0,0 +1,86 @@ +easyblock = 'PythonBundle' + +name = 'spaCy' +version = '3.7.4' + +homepage = 'https://spacy.io/' +description = "Industrial-strength Natural Language Processing (NLP) in Python." + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('poetry', '1.7.1'), + ('hatchling', '1.18.0'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('tqdm', '4.66.1'), + ('pydantic', '2.5.3'), +] + +use_pip = True + +exts_list = [ + ('spacy-legacy', '3.0.12', { + 'checksums': ['b37d6e0c9b6e1d7ca1cf5bc7152ab64a4c4671f59c85adaf7a3fcb870357a774'], + }), + ('spacy-loggers', '1.0.5', { + 'checksums': ['d60b0bdbf915a60e516cc2e653baeff946f0cfc461b452d11a4d5458c6fe5f24'], + }), + ('cymem', '2.0.8', { + 'checksums': ['8fb09d222e21dcf1c7e907dc85cf74501d4cea6c4ed4ac6c9e016f98fb59cbbf'], + }), + ('murmurhash', '1.0.10', { + 'checksums': ['5282aab1317804c6ebd6dd7f69f15ba9075aee671c44a34be2bde0f1b11ef88a'], + }), + ('preshed', '3.0.9', { + 'checksums': ['721863c5244ffcd2651ad0928951a2c7c77b102f4e11a251ad85d37ee7621660'], + }), + ('blis', '0.7.11', { + 'checksums': ['cec6d48f75f7ac328ae1b6fbb372dde8c8a57c89559172277f66e01ff08d4d42'], + }), + ('confection', '0.1.4', { + 'checksums': ['e80f22fd008b5231a2e8852fac6de9e28f2276a04031d0536cff74fe4a990c8f'], + }), + ('thinc', '8.2.3', { + 'checksums': ['f5afc5222912a80bda8bdcec958362a2ba538d7027dc8db6154845d2859dca76'], + }), + ('ml_datasets', '0.2.0', { + 'checksums': ['3f9c8901f8d6be3dab5b23ec3a6c01e619a60d0184696b1030cde2e3086943f1'], + }), + ('wasabi', '1.1.2', { + 'checksums': ['1aaef3aceaa32edb9c91330d29d3936c0c39fdb965743549c173cb54b16c30b5'], + }), + ('srsly', '2.4.8', { + 'checksums': ['b24d95a65009c2447e0b49cda043ac53fecf4f09e358d87a57446458f91b8a91'], + }), + ('catalogue', '2.0.10', { + 'checksums': ['4f56daa940913d3f09d589c191c74e5a6d51762b3a9e37dd53b7437afd6cda15'], + }), + ('typer', '0.9.0', { + 'checksums': ['50922fd79aea2f4751a8e0408ff10d2662bd0c8bbfa84755a699f3bada2978b2'], + }), + ('smart-open', '6.4.0', { + 'source_tmpl': 'smart_open-%(version)s.tar.gz', + 'checksums': ['be3c92c246fbe80ebce8fbacb180494a481a77fcdcb7c1aadb2ea5b9c2bee8b9'], + }), + ('langcodes', '3.3.0', { + 'checksums': ['794d07d5a28781231ac335a1561b8442f8648ca07cd518310aeb45d6f0807ef6'], + }), + ('weasel', '0.3.4', { + 'checksums': ['eb16f92dc9f1a3ffa89c165e3a9acd28018ebb656e0da4da02c0d7d8ae3f6178'], + }), + ('cloudpathlib', '0.16.0', { + 'checksums': ['cdfcd35d46d529587d744154a0bdf962aca953b725c8784cd2ec478354ea63a3'], + }), + (name, version, { + 'sources': ['%(namelower)s-%(version)s.tar.gz'], + 'checksums': ['525f2ced2e40761562c8cace93ef6a1e6e8c483f27bd564bc1b15f608efbe85b'], + }), +] + +sanity_pip_check = True + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/spektral/spektral-1.2.0-fosscuda-2020b-TensorFlow-2.5.0.eb b/easybuild/easyconfigs/s/spektral/spektral-1.2.0-fosscuda-2020b-TensorFlow-2.5.0.eb new file mode 100644 index 000000000000..75446a8cbffe --- /dev/null +++ b/easybuild/easyconfigs/s/spektral/spektral-1.2.0-fosscuda-2020b-TensorFlow-2.5.0.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonBundle' + +name = 'spektral' +version = '1.2.0' +local_tf_version = '2.5.0' +versionsuffix = '-TensorFlow-%s' % local_tf_version + +homepage = 'https://graphneural.network' +description = "Spektral is a Python library for graph deep learning, based on the Keras API and TensorFlow 2" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('lxml', '4.6.2'), + ('networkx', '2.5'), + ('scikit-learn', '0.23.2'), + ('tqdm', '4.56.2'), + ('TensorFlow', local_tf_version), +] + +use_pip = True + +exts_list = [ + (name, version, { + 'checksums': ['215f148e5d5067081bc28abe282bfd0942ed8be6d68f128fd7786006a884abf7'], + }), +] + +sanity_pip_check = True + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/s/spglib-python/spglib-python-2.5.0-gfbf-2023b.eb b/easybuild/easyconfigs/s/spglib-python/spglib-python-2.5.0-gfbf-2023b.eb new file mode 100644 index 000000000000..9f26cade5d34 --- /dev/null +++ b/easybuild/easyconfigs/s/spglib-python/spglib-python-2.5.0-gfbf-2023b.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonBundle' + +name = 'spglib-python' +version = '2.5.0' + +homepage = 'https://pypi.python.org/pypi/spglib' +description = """Spglib for Python. + +Spglib is a library for finding and handling crystal symmetries written in C. +""" + +toolchain = {'name': 'gfbf', 'version': '2023b'} + +builddependencies = [ + ('scikit-build-core', '0.9.3') +] + +dependencies = [ + ('Python', '3.11.5'), + ('Python-bundle-PyPI', '2023.10'), + ('SciPy-bundle', '2023.11'), +] + +use_pip = True + +sanity_pip_check = True + +exts_list = [ + ('pyproject_metadata', '0.8.0', { + 'checksums': ['376d5a00764ac29440a54579f88e66b7d9cb7e629d35c35a1c7248bfebc9b455'], + }), + ('spglib', version, { + 'checksums': ['f8bb638897be91b9dbd4c085d9fde1f69048f5949e20f3832cb9438e57418d4b'], + }), +] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/s/spglib/spglib-2.5.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/s/spglib/spglib-2.5.0-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..a7e62a33f217 --- /dev/null +++ b/easybuild/easyconfigs/s/spglib/spglib-2.5.0-GCCcore-12.3.0.eb @@ -0,0 +1,34 @@ +# with thanks to akesandgren for the easyconfig for 2022a +# updated for 2022b by BEAR Software team at University of Birmingham +# update to v2.5.0 for GCC/12.3.0 by Pavel Tománek (Inuits) + +easyblock = 'CMakeMake' + +name = 'spglib' +version = '2.5.0' + +homepage = 'https://spglib.github.io/spglib/' +description = """Spglib is a C library for finding and handling crystal symmetries.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/spglib/spglib/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['b6026f5e85106c0c9ee57e54b9399890d0f29982e20e96ede0428b3efbe6b914'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), +] + +postinstallcmds = ["cd %(installdir)s/include && mkdir spglib && ln -s ../spglib.h spglib/"] + +sanity_check_paths = { + 'files': [ + 'include/spglib.h', + 'lib/libsymspg.%s' % SHLIB_EXT + ], + 'dirs': [], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/s/spla/spla-1.6.1-foss-2023a.eb b/easybuild/easyconfigs/s/spla/spla-1.6.1-foss-2023a.eb new file mode 100644 index 000000000000..983086996789 --- /dev/null +++ b/easybuild/easyconfigs/s/spla/spla-1.6.1-foss-2023a.eb @@ -0,0 +1,31 @@ +easyblock = 'CMakeMake' + +name = 'spla' +version = '1.6.1' + +homepage = 'https://github.com/eth-cscs/spla/' +description = """SPLA provides specialized functions for linear algebra computations with a C++ and C interface, +which are inspired by requirements in computational material science codes.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/eth-cscs/spla/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['62b51e6ce05c41cfc1c6f6600410f9549a209c50f0331e1db41047f94493e02f'] + +builddependencies = [ + ('CMake', '3.26.3'), +] + +configopts = '-DBLA_VENDOR=FlexiBLAS' + +sanity_check_paths = { + 'files': [ + 'include/spla/spla.h', + 'lib/libspla.%s' % SHLIB_EXT, + ], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/spoa/spoa-4.1.0-GCC-13.2.0.eb b/easybuild/easyconfigs/s/spoa/spoa-4.1.0-GCC-13.2.0.eb new file mode 100644 index 000000000000..16062a7636e8 --- /dev/null +++ b/easybuild/easyconfigs/s/spoa/spoa-4.1.0-GCC-13.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'CMakeMake' + +name = 'spoa' +version = '4.1.0' + +homepage = 'https://github.com/rvaser/spoa' +description = """Spoa (SIMD POA) is a c++ implementation of the partial order alignment (POA) algorithm + which is used to generate consensus sequences""" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/rvaser/spoa/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['43238356f00bce2ad9698fc18b3e320024172a82182dcff24d57c5cf19e342c8'] + +builddependencies = [('CMake', '3.27.6')] + +configopts = "-Dspoa_build_executable=ON" + +sanity_check_paths = { + 'files': ['bin/spoa'] + ['include/spoa/%s' % x for x in ['alignment_engine.hpp', 'graph.hpp', 'spoa.hpp']] + + ['lib/libspoa.a'], + 'dirs': [], +} + +sanity_check_commands = ["spoa --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/submitit/submitit-1.2.0-foss-2023a.eb b/easybuild/easyconfigs/s/submitit/submitit-1.2.0-foss-2023a.eb new file mode 100644 index 000000000000..0ce1edf27663 --- /dev/null +++ b/easybuild/easyconfigs/s/submitit/submitit-1.2.0-foss-2023a.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonBundle' + +name = 'submitit' +version = '1.2.0' + +homepage = 'https://github.com/facebookincubator/submitit' +description = """ +Submitit is a lightweight tool for submitting Python functions +for computation within a Slurm cluster. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), +] + +use_pip = True + +exts_list = [ + ('cloudpickle', '3.0.0', { + 'checksums': ['996d9a482c6fb4f33c1a35335cf8afd065d2a56e973270364840712d9131a882'], + }), + ('typing_extensions', '4.12.2', { + 'checksums': ['1a7ead55c7e559dd4dee8856e3a88b41225abfe1ce8df57b7c13915fe121ffb8'], + }), + (name, version, { + 'checksums': ['16c099ed80943fbf942a7a37c6356a598b1f2b9d7ce40dd5fe058a6c7827e600'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2022b.eb b/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2022b.eb new file mode 100644 index 000000000000..72d977763e95 --- /dev/null +++ b/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2022b.eb @@ -0,0 +1,61 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) +# Update: Pavel Tománek (Inuits) + +easyblock = 'PythonBundle' + +name = 'svist4get' +version = '1.3.1' + +homepage = 'https://github.com/art-egorov/svist4get' +description = """Svist4get is a simple bioinformatics tool for visualization of +genomic signal tracks in user-defined genomic windows, either arbitrary selected +by genomic coordinates or anchored to particular transcripts or genes.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), + ('pybedtools', '0.9.0'), + ('Biopython', '1.81'), + ('Pillow', '9.4.0'), + ('ImageMagick', '7.1.0-53'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('reportlab', '3.6.9', { + 'patches': ['reportlab-3.6.12-fontconfig.patch'], + 'checksums': ['5d0cc3682456ad213150f6dbffe7d47eab737d809e517c316103376be548fb84', + # reportlab-3.6.12-fontconfig.patch: + '2cc9b40e09650b7404ee9c4d72b134739acc89bacac3da58131cef2308726297'], + }), + ('configs', '3.0.3', { + 'sources': ['%(name)s-%(version)s.zip'], + 'checksums': ['a5ab09e04e441dac6aa856a71fbf5ffc62954352630f79d311b8f8a31d9ce19c'], + }), + ('argparse', '1.4.0', { + 'checksums': ['62b089a55be1d8949cd2bc7e0df0bddb9e028faefc8c32038cc84862aefdd6e4'], + }), + ('Wand', '0.6.10', { + 'checksums': ['373f4a7f2866c868c31ce910e1f9b36a92d132640a20068ec17cea3284fedc57'], + }), + (name, version, { + # unpin statistics dependency - it is old package and interfering with python lib statistics + 'preinstallopts': "sed -i 's/statistics//' setup.py && ", + 'checksums': ['22311fdc956cca531dac7ba924744e8f870a57bc6f27cbe4e8ba9854117e720c'], + }), +] + +sanity_check_paths = { + 'files': ['bin/svist4get', 'bin/svist4get_copier'], + 'dirs': ['lib'], +} + +sanity_check_commands = [ + "svist4get --help", + "svist4get -v", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2022a.eb b/easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2022a.eb new file mode 100644 index 000000000000..c672ef52e800 --- /dev/null +++ b/easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2022a.eb @@ -0,0 +1,46 @@ +easyblock = 'PythonPackage' + +name = 'TAMkin' +version = '1.2.6' + +homepage = 'https://molmod.github.io/tamkin/' +description = """TAMkin is a post-processing toolkit for normal mode analysis, + thermochemistry and reaction kinetics. It uses a Hessian computation from a + standard computational chemistry program as its input.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://github.com/molmod/tamkin/releases/download/%(version)s'] +sources = [SOURCE_TAR_GZ] +patches = [ + 'TAMkin-1.2.6_fix-python38.patch', + 'TAMkin-1.2.6_fix-test_vsa_no_mass.patch', +] +checksums = [ + {'TAMkin-1.2.6.tar.gz': '1bde275a09be91e5241616aaa9fedc60cb359a263f5c5909bb14431c3a4ed5fd'}, + {'TAMkin-1.2.6_fix-python38.patch': '1633d5b24b012f8c4b6731491e4072c819ebbba65574966b7185ecca52eeac9b'}, + {'TAMkin-1.2.6_fix-test_vsa_no_mass.patch': '67d8b8671d7c71123e8ee9a7b9ebea6562e9711edb41555d1926b1b51d549066'}, +] + +builddependencies = [('nose3', '1.3.8')] +dependencies = [ + ('Python', '3.10.4'), + ('matplotlib', '3.5.2'), + ('molmod', '1.4.8'), +] + +download_dep_fail = True +use_pip = True + +# disable tests that require X11 by specifying "backend: agg" in matplotlibrc +runtest = 'export MATPLOTLIBRC=$PWD; echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc; ' +runtest += 'export OMP_NUM_THREADS=1; nosetests -v tamkin' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_pip_check = True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2022b.eb b/easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2022b.eb new file mode 100644 index 000000000000..f0ac1c8820c5 --- /dev/null +++ b/easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2022b.eb @@ -0,0 +1,46 @@ +easyblock = 'PythonPackage' + +name = 'TAMkin' +version = '1.2.6' + +homepage = 'https://molmod.github.io/tamkin/' +description = """TAMkin is a post-processing toolkit for normal mode analysis, + thermochemistry and reaction kinetics. It uses a Hessian computation from a + standard computational chemistry program as its input.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +source_urls = ['https://github.com/molmod/tamkin/releases/download/%(version)s'] +sources = [SOURCE_TAR_GZ] +patches = [ + 'TAMkin-1.2.6_fix-python38.patch', + 'TAMkin-1.2.6_fix-test_vsa_no_mass.patch', +] +checksums = [ + {'TAMkin-1.2.6.tar.gz': '1bde275a09be91e5241616aaa9fedc60cb359a263f5c5909bb14431c3a4ed5fd'}, + {'TAMkin-1.2.6_fix-python38.patch': '1633d5b24b012f8c4b6731491e4072c819ebbba65574966b7185ecca52eeac9b'}, + {'TAMkin-1.2.6_fix-test_vsa_no_mass.patch': '67d8b8671d7c71123e8ee9a7b9ebea6562e9711edb41555d1926b1b51d549066'}, +] + +builddependencies = [('nose3', '1.3.8')] +dependencies = [ + ('Python', '3.10.8'), + ('matplotlib', '3.7.0'), + ('molmod', '1.4.8'), +] + +download_dep_fail = True +use_pip = True + +# disable tests that require X11 by specifying "backend: agg" in matplotlibrc +runtest = 'export MATPLOTLIBRC=$PWD; echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc; ' +runtest += 'export OMP_NUM_THREADS=1; nosetests -v tamkin' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_pip_check = True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/t/TELEMAC-MASCARET/TELEMAC-MASCARET-8p5r0-foss-2023a.eb b/easybuild/easyconfigs/t/TELEMAC-MASCARET/TELEMAC-MASCARET-8p5r0-foss-2023a.eb new file mode 100644 index 000000000000..ab96be492309 --- /dev/null +++ b/easybuild/easyconfigs/t/TELEMAC-MASCARET/TELEMAC-MASCARET-8p5r0-foss-2023a.eb @@ -0,0 +1,90 @@ +easyblock = 'Binary' + +name = 'TELEMAC-MASCARET' +version = '8p5r0' + +homepage = 'http://www.opentelemac.org' +description = """TELEMAC-MASCARET is an integrated suite of solvers for use in the field of free-surface flow. Having +been used in the context of many studies throughout the world, it has become one of the major standards in its field.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'extra_fcflags': "-fallow-invalid-boz"} + +source_urls = ['https://gitlab.pam-retd.fr/otm/telemac-mascaret/-/archive/v%(version)s/'] +sources = ['telemac-mascaret-v%(version)s.tar.gz'] +checksums = ['2beb9793fb83d17de31b17f001f985fc30702c151e2ced614f5e0117e8e34aa0'] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), # provides numpy, scipy + ('matplotlib', '3.7.2'), + ('HDF5', '1.14.0'), + ('METIS', '5.1.0'), + ('SCOTCH', '7.0.3'), + ('MUMPS', '5.6.1', '-metis'), +] + +extract_sources = True +unpack_options = '--strip-components=1' + +buildininstalldir = True + +local_tweak_cfg_cmd = ' '.join([ + "sed -i -e 's/S10.gfortran/easybuild/g'", + # strip out use of AED, GOTM, MED (optional dependencies) + r"-e 's/\(^[a-z]*_aed:\).*/\1/g' -e 's/\(^[a-z]*_gotm:\).*/\1/g' -e 's/\(^[a-z]*_med:\).*/\1/g'", + # replace -O2 with desired compiler options + '-e "s/-O2/$F90FLAGS/g"', + # fix linker option for BLAS + '-e "s/ -lblas/ $LIBBLAS/g"', + # downgrade Fortran compiler error to warning + "-e 's/^fflags_gfo:/fflags_gfo: -fallow-invalid-boz/g'", + # Disable hyperthreading option + "-e 's/--use-hwthread-cpus//'", + "$HOMETEL/configs/systel.easybuild.cfg", +]) + +install_cmd = ' && '.join([ + "export HOMETEL=$PWD", + # add Python scripts to $PATH and $PYTHONPATH + "export PATH=$HOMETEL/scripts/python3/:$PATH", + "export PYTHONPATH=$HOMETEL/scripts/python3:$PYTHONPATH", + # force python to flush its output + "export PYTHONUNBUFFERED=1", + "cp $HOMETEL/configs/systel.edf.cfg $HOMETEL/configs/systel.easybuild.cfg", + local_tweak_cfg_cmd, + "export SYSTELCFG=$HOMETEL/configs/systel.easybuild.cfg", + "export USETELCFG=easybuild.dyn", + "export SCALAPACKHOME=$EBROOTSCALAPACK", + "export METISHOME=$EBROOTMETIS", + "export SCOTCHHOME=$EBROOTSCOTCH", + "export MUMPSHOME=$EBROOTMUMPS", + "export HDF5HOME=$EBROOTHDF5", + "config.py", + "compile_telemac.py -j %(parallel)s", +]) + +sanity_check_paths = { + 'files': ['builds/easybuild.dyn/bin/telemac2d', 'builds/easybuild.dyn/bin/telemac3d', + 'builds/easybuild.dyn/lib/libtelemac2d.%s' % SHLIB_EXT, + 'builds/easybuild.dyn/lib/libtelemac3d.%s' % SHLIB_EXT], + 'dirs': ['scripts/python3'], +} + +sanity_check_commands = [ + "tmpdir=$(mktemp -d) && cp -a %(installdir)s/examples/telemac2d/gouttedo $tmpdir/ && chmod -R u+w $tmpdir && " + "cd $tmpdir/gouttedo && telemac2d.py t2d_gouttedo.cas", +] + +modextrapaths = { + 'LD_LIBRARY_PATH': 'builds/easybuild.dyn/lib', + 'PATH': 'scripts/python3', + 'PYTHONPATH': 'scripts/python3', +} + +modextravars = { + 'SYSTELCFG': '%(installdir)s/configs/systel.easybuild.cfg', + 'USETELCFG': 'easybuild.dyn', +} + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/t/TF-COMB/TF-COMB-1.1-foss-2022b.eb b/easybuild/easyconfigs/t/TF-COMB/TF-COMB-1.1-foss-2022b.eb new file mode 100644 index 000000000000..2c06e8c9c8fd --- /dev/null +++ b/easybuild/easyconfigs/t/TF-COMB/TF-COMB-1.1-foss-2022b.eb @@ -0,0 +1,48 @@ +easyblock = 'PythonBundle' + +name = 'TF-COMB' +version = '1.1' + +homepage = 'https://github.com/loosolab/TF-COMB' +description = """Transcription Factor Co-Occurrence using Market Basket analysis.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('tqdm', '4.64.1'), + ('Pysam', '0.21.0'), + ('matplotlib', '3.7.0'), + ('networkx', '3.0'), + ('Graphviz', '8.1.0'), + ('statsmodels', '0.14.0'), + ('dill', '0.3.7'), + ('Seaborn', '0.12.2'), + ('IPython', '8.14.0'), + ('TOBIAS', '0.16.1'), + ('python-louvain', '0.16'), + ('GOATOOLS', '1.4.5'), + ('qnorm', '0.8.1'), +] + +use_pip = True +sanity_pip_check = True + +# remove graphviz from deps - the pip check failing, should be "import gv" +local_tfcomb_preinstallopts = "sed -i '70d' setup.py && " +# fix "import graphviz" to "import gv" +local_tfcomb_preinstallopts += "sed -i 's/import graphviz/import gv as graphviz/' tfcomb/plotting.py && " + +exts_list = [ + ('uropa', '4.0.3', { + 'checksums': ['e0b648881b95f301e3f3ecc924314995312f10b0cbabf96d5a5ce2fb18c53a59'], + }), + (name, version, { + 'preinstallopts': local_tfcomb_preinstallopts, + 'modulename': 'tfcomb', + 'checksums': ['5b718061660e0f9f94d86459eb742ca81de5851b0defd8b08c8a7a7e3370c253'], + }), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/TOBIAS/TOBIAS-0.16.1-foss-2022b.eb b/easybuild/easyconfigs/t/TOBIAS/TOBIAS-0.16.1-foss-2022b.eb new file mode 100644 index 000000000000..9150965319e7 --- /dev/null +++ b/easybuild/easyconfigs/t/TOBIAS/TOBIAS-0.16.1-foss-2022b.eb @@ -0,0 +1,55 @@ +easyblock = 'PythonBundle' + +name = 'TOBIAS' +version = '0.16.1' + +homepage = 'https://github.com/loosolab/TOBIAS' +description = """TOBIAS is a collection of command-line bioinformatics tools +for performing footprinting analysis on ATAC-seq data.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('matplotlib', '3.7.0'), + ('Seaborn', '0.12.2'), + ('Pysam', '0.21.0'), + ('pybedtools', '0.9.0'), + ('boto3', '1.26.163'), + ('pyBigWig', '0.3.22'), + ('scikit-learn', '1.2.1'), + ('PyYAML', '6.0'), + ('XlsxWriter', '3.1.2'), + ('svist4get', '1.3.1'), + ('adjustText', '0.7.3'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('kneed', '0.8.5', { + 'checksums': ['a4847ac4f1d04852fea278d5de7aa8bfdc3beb7fbca4a182fec0f0efee43f4b1'], + }), + ('logomaker', '0.8', { + 'checksums': ['d8c7501a7d6d7961cd68e5a44e939000ebf1b0c4197a0c9198351e1d681d3f6d'], + }), + ('MOODS-python', '1.9.4.1', { + 'modulename': 'MOODS', + 'checksums': ['b3b5e080cb0cd13c0fd175d0ee0d453fde3e42794fa7ac39a4f6db1ac5ddb4cc'], + }), + ('PyPDF2', '3.0.1', { + 'modulename': 'PyPDF2', + 'checksums': ['a74408f69ba6271f71b9352ef4ed03dc53a31aa404d29b5d31f53bfecfee1440'], + }), + ('tobias', version, { + # remove pyBigWig dependency - pip_check fails with "import pybigwig" + 'preinstallopts': "sed -i '81d' setup.py && ", + 'checksums': ['c46267c01287be06201b3e6f7a36daad1ad86d6c578f96e878501be7da7fd109'], + }), +] + +sanity_check_commands = ["python -c 'import pyBigWig'"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/TOBIAS/TOBIAS-0.16.1-foss-2023a.eb b/easybuild/easyconfigs/t/TOBIAS/TOBIAS-0.16.1-foss-2023a.eb index 186556eb374d..0404ad39d858 100644 --- a/easybuild/easyconfigs/t/TOBIAS/TOBIAS-0.16.1-foss-2023a.eb +++ b/easybuild/easyconfigs/t/TOBIAS/TOBIAS-0.16.1-foss-2023a.eb @@ -46,8 +46,6 @@ exts_list = [ 'checksums': ['a74408f69ba6271f71b9352ef4ed03dc53a31aa404d29b5d31f53bfecfee1440'], }), ('tobias', version, { - # remove pyBigWig dependency - pip_check fails with "import pybigwig" - 'preinstallopts': "sed -i '81d' setup.py && ", 'checksums': ['c46267c01287be06201b3e6f7a36daad1ad86d6c578f96e878501be7da7fd109'], }), ] diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 000000000000..1d1c871f3d5d --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,238 @@ +easyblock = 'PythonBundle' + +name = 'TensorFlow' +version = '2.15.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://www.tensorflow.org/' +description = "An open-source software library for Machine Intelligence" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'pic': True} + +use_pip = True +sanity_pip_check = True + +builddependencies = [ + ('Bazel', '6.1.0'), + # git 2.x required, see also https://github.com/tensorflow/tensorflow/issues/29053 + ('git', '2.41.0', '-nodocs'), + ('pybind11', '2.11.1'), + ('UnZip', '6.0'), + # Required to build some of the extensions + ('poetry', '1.5.1'), + # Protobuf disabled since 2.13.0 easyconfigs: + # Compiling with system protobuf don't seem to work, see: + # https://github.com/tensorflow/tensorflow/issues/61593 + # ('protobuf', '24.0'), +] + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('cuDNN', '8.9.2.26', versionsuffix, SYSTEM), + ('NCCL', '2.18.3', versionsuffix), + ('Python', '3.11.3'), + ('h5py', '3.9.0'), + ('cURL', '8.0.1'), + ('dill', '0.3.7'), + ('double-conversion', '3.3.0'), + ('flatbuffers', '23.5.26'), + ('flatbuffers-python', '23.5.26'), + ('giflib', '5.2.1'), + ('hwloc', '2.9.1'), + ('ICU', '73.2'), + ('JsonCpp', '1.9.5'), + ('libjpeg-turbo', '2.1.5.1'), + ('ml_dtypes', '0.3.2'), + ('NASM', '2.16.01'), + ('nsync', '1.26.0'), + ('SQLite', '3.42.0'), + ('patchelf', '0.18.0'), + ('libpng', '1.6.39'), + ('snappy', '1.1.10'), + ('zlib', '1.2.13'), + ('grpcio', '1.57.0'), +] + +# Dependencies created and updated using findPythonDeps, see: +# https://docs.easybuild.io/api/easybuild/scripts/findPythonDeps +# Notable changes since 2.13.0-foss-2023a +# - tensoboard-wit deprecated as of tensorboard 2.13.0 (tensorboard@33abcb54d7) +# - portpicker for tests no longer needed (TF@e85860e838) +# - opt_einsum now comes from ml_dtypes +exts_list = [ + ('wrapt', '1.14.1', { + 'checksums': ['380a85cf89e0e69b7cfbe2ea9f765f004ff419f34194018a6827ac0e3edfed4d'], + }), + ('termcolor', '2.3.0', { + 'checksums': ['b5b08f68937f138fe92f6c089b99f1e2da0ae56c52b78bf7075fd95420fd9a5a'], + }), + ('tensorflow-estimator', '2.15.0', { + 'source_tmpl': 'tensorflow_estimator-%(version)s-py2.py3-none-any.whl', + 'checksums': ['aedf21eec7fb2dc91150fc91a1ce12bc44dbb72278a08b58e79ff87c9e28f153'], + }), + ('Werkzeug', '3.0.2', { + 'source_tmpl': SOURCELOWER_TAR_GZ, + 'checksums': ['e39b645a6ac92822588e7b39a692e7828724ceae0b0d702ef96701f90e70128d'], + }), + ('tensorboard-data-server', '0.7.2', { + 'source_tmpl': 'tensorboard_data_server-%(version)s-py3-none-any.whl', + 'checksums': ['7e0610d205889588983836ec05dc098e80f97b7e7bbff7e994ebb78f578d0ddb'], + }), + ('Markdown', '3.6', { + 'checksums': ['ed4f41f6daecbeeb96e576ce414c41d2d876daa9a16cb35fa8ed8c2ddfad0224'], + }), + ('oauthlib', '3.2.2', { + 'checksums': ['9859c40929662bec5d64f34d01c99e093149682a3f38915dc0655d5a633dd918'], + }), + ('requests-oauthlib', '2.0.0', { + 'checksums': ['b3dffaebd884d8cd778494369603a9e7b58d29111bf6b41bdc2dcd87203af4e9'], + }), + ('rsa', '4.9', { + 'checksums': ['e38464a49c6c85d7f1351b0126661487a7e0a14a50f1675ec50eb34d4f20ef21'], + }), + ('pyasn1-modules', '0.4.0', { + 'source_tmpl': 'pyasn1_modules-%(version)s.tar.gz', + 'checksums': ['831dbcea1b177b28c9baddf4c6d1013c24c3accd14a1873fffaa6a2e905f17b6'], + }), + ('cachetools', '5.3.3', { + 'checksums': ['ba29e2dfa0b8b556606f097407ed1aa62080ee108ab0dc5ec9d6a723a007d105'], + }), + ('google-auth', '2.29.0', { + 'modulename': 'google.auth', + 'checksums': ['672dff332d073227550ffc7457868ac4218d6c500b155fe6cc17d2b13602c360'], + }), + ('google-auth-oauthlib', '1.2.0', { + 'checksums': ['292d2d3783349f2b0734a0a0207b1e1e322ac193c2c09d8f7c613fb7cc501ea8'], + }), + ('absl-py', '2.1.0', { + 'modulename': 'absl', + 'checksums': ['7820790efbb316739cde8b4e19357243fc3608a152024288513dd968d7d959ff'], + }), + ('tensorboard', '2.15.2', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['a6f6443728064d962caea6d34653e220e34ef8df764cb06a8212c17e1a8f0622'], + }), + ('keras', '2.15.0', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['2dcc6d2e30cf9c951064b63c1f4c404b966c59caf09e01f3549138ec8ee0dd1f'], + }), + ('google-pasta', '0.2.0', { + 'modulename': 'pasta', + 'checksums': ['c9f2c8dfc8f96d0d5808299920721be30c9eec37f2389f28904f454565c8a16e'], + }), + ('astunparse', '1.6.3', { + 'checksums': ['5ad93a8456f0d084c3456d059fd9a92cce667963232cbf763eac3bc5b7940872'], + }), + # Required by tests + ('tblib', '3.0.0', { + 'checksums': ['93622790a0a29e04f0346458face1e144dc4d32f493714c6c3dff82a4adb77e6'], + }), + ('astor', '0.8.1', { + 'checksums': ['6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e'], + }), + # Optional profile plugin + dependency + ('gviz-api', '1.10.0', { + 'source_tmpl': 'gviz_api-%(version)s.tar.gz', + 'checksums': ['846692dd8cc73224fc31b18e41589bd934e1cc05090c6576af4b4b26c2e71b90'], + }), + ('tensorboard-plugin-profile', '2.15.1', { + 'source_tmpl': 'tensorboard_plugin_profile-%(version)s.tar.gz', + 'checksums': ['84bb33e446eb4a9c0616f669fc6a42cdd40eadd9ae1d74bf756f4f0479993273'], + }), + (name, version, { + 'patches': [ + 'TensorFlow-2.1.0_fix-cuda-build.patch', + 'TensorFlow-2.4.0_dont-use-var-lock.patch', + 'TensorFlow-2.13.0_add-missing-system-protobuf-targets.patch', + 'TensorFlow-2.13.0_exclude-xnnpack-on-ppc.patch', + 'TensorFlow-2.15.1_remove-duplicate-gpu-tests.patch', + 'TensorFlow-2.15.1_remove-libclang-dep.patch', + 'TensorFlow-2.15.1_remove-io-gcs-filesystem-dep.patch', + 'TensorFlow-2.15.1_add-default-shell-env.patch', + 'TensorFlow-2.15.1_fix-AVX512-eigen-compilation.patch', + 'TensorFlow-2.15.1_fix-flatbuffer-license.patch', + 'TensorFlow-2.15.1_fix-pybind11-build.patch', + 'TensorFlow-2.15.1_fix-cuda_build_defs.patch', + 'TensorFlow-2.15.1_disable-avx512-extensions.patch', + 'TensorFlow-2.15.1_disable-tf32-in-fused-matmul-tests.patch' + ], + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], + 'test_script': 'TensorFlow-2.x_mnist-test.py', + 'test_tag_filters_cpu': ( + '-gpu,-tpu,-no_cuda_on_cpu_tap,' + '-no_pip,-no_oss,-oss_serial,-benchmark-test,-v1only' + ), + 'test_tag_filters_gpu': ( + 'gpu,-no_gpu,-nogpu,-gpu_cupti,-no_cuda11,' + '-no_pip,-no_oss,-oss_serial,-benchmark-test,-v1only' + ), + 'test_targets': [ + '//tensorflow/core/...', + '-//tensorflow/core:example_java_proto', + '-//tensorflow/core/example:example_protos_closure', + '//tensorflow/cc/...', + '//tensorflow/c/...', + '//tensorflow/python/...', + '-//tensorflow/c/eager:c_api_test_gpu', + '-//tensorflow/c/eager:c_api_distributed_test', + '-//tensorflow/c/eager:c_api_distributed_test_gpu', + '-//tensorflow/c/eager:c_api_cluster_test_gpu', + '-//tensorflow/c/eager:c_api_remote_function_test_gpu', + '-//tensorflow/c/eager:c_api_remote_test_gpu', + '-//tensorflow/core/common_runtime:collective_param_resolver_local_test', + '-//tensorflow/core/kernels/mkl:mkl_fused_ops_test', + '-//tensorflow/core/kernels/mkl:mkl_fused_batch_norm_op_test', + '-//tensorflow/core/ir/importexport/tests/roundtrip/...', + ], + 'testopts': '--test_env=HOME=/tmp --test_timeout=3600 --test_size_filters=small ', + 'testopts_gpu': ( + '--test_env=HOME=/tmp --test_timeout=3600 --test_size_filters=small ' + '--run_under=//tensorflow/tools/ci_build/gpu_build:parallel_gpu_execute ' + ), + 'with_xla': True, + 'checksums': [ + {'v2.15.1.tar.gz': 'f36416d831f06fe866e149c7cd752da410a11178b01ff5620e9f265511ed57cf'}, + {'TensorFlow-2.1.0_fix-cuda-build.patch': + '78c20aeaa7784b8ceb46238a81e8c2461137d28e0b576deeba8357d23fbe1f5a'}, + {'TensorFlow-2.4.0_dont-use-var-lock.patch': + 'b14f2493fd2edf79abd1c4f2dde6c98a3e7d5cb9c25ab9386df874d5f072d6b5'}, + {'TensorFlow-2.13.0_add-missing-system-protobuf-targets.patch': + '77d8c8a5627493fc7c38b4de79d49e60ff6628b05ff969f4cd3ff9857176c459'}, + {'TensorFlow-2.13.0_exclude-xnnpack-on-ppc.patch': + 'd0818206846911d946666ded7d3216c0546e37cee1890a2f48dc1a9d71047cad'}, + {'TensorFlow-2.15.1_remove-duplicate-gpu-tests.patch': + 'd8810d5b875de5be8603afd743774ce9dd8c0d4a82314c7fe2f284a080be7498'}, + {'TensorFlow-2.15.1_remove-libclang-dep.patch': + '871b2f0221b7a150ac9f563ffad7187e052a7eedd95c20fb4524987d7edb6f21'}, + {'TensorFlow-2.15.1_remove-io-gcs-filesystem-dep.patch': + 'eba7351a4b0696c589b9c507bacb0257ebce8c39fde39ab72d5d6a69deaaec02'}, + {'TensorFlow-2.15.1_add-default-shell-env.patch': + '3d5196b4bf2e91048dc8a18f9e8f487a223fcd973d6302e80b0d4000ea3d652b'}, + {'TensorFlow-2.15.1_fix-AVX512-eigen-compilation.patch': + '761059e5f5f5eeeef8aed5517a7685a0eb0a9193d4afe8d45237527681c9c0a3'}, + {'TensorFlow-2.15.1_fix-flatbuffer-license.patch': + '2c04d5095977a628a238dbf93c5fada7159c86752a7183e64e0cf7c7ab00caf4'}, + {'TensorFlow-2.15.1_fix-pybind11-build.patch': + '3bb350ac92ab99c63c951c96b3b0160699f5f16822b64f72111ebfd2275cafce'}, + {'TensorFlow-2.15.1_fix-cuda_build_defs.patch': + '091581a7c4fc2fc7af282cab6661632c29029d2f36eccb6695ffa5783e065f88'}, + {'TensorFlow-2.15.1_disable-avx512-extensions.patch': + '506ceecff67237eed9cd9e9e114bc1461f35a343f77f83cb3dab710aa701dc0f'}, + {'TensorFlow-2.15.1_disable-tf32-in-fused-matmul-tests.patch': + 'f78aa0e8f814a57e8d2e6b24ff095df49e8654aadb797393fa95a9378d0aa662'}, + ], + }), +] + +# Taken from tensorboard-2.15.1-gfbf-2023a.eb: +# Relax restriction on protobuf dependency as issue was fixed +# in https://github.com/protocolbuffers/upb/pull/1514 +# see also: https://github.com/easybuilders/easybuild-easyconfigs/pull/19671 +postinstallcmds = [ + 'sed -i "s/Requires-Dist: protobuf.*/Requires-Dist: protobuf >=3.19.6/g" ' + + '%(installdir)s/lib/python%(pyshortver)s/site-packages/tensorboard-2.15.2.dist-info/METADATA', +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a.eb index 014f3bbd7a5e..506cbafd52b9 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a.eb @@ -140,11 +140,14 @@ exts_list = [ (name, version, { 'patches': [ 'TensorFlow-2.13.0_add-missing-system-protobuf-targets.patch', + 'TensorFlow-2.13.0_exclude-xnnpack-on-ppc.patch', 'TensorFlow-2.15.1_remove-libclang-dep.patch', 'TensorFlow-2.15.1_remove-io-gcs-filesystem-dep.patch', 'TensorFlow-2.15.1_add-default-shell-env.patch', + 'TensorFlow-2.15.1_fix-AVX512-eigen-compilation.patch', 'TensorFlow-2.15.1_fix-flatbuffer-license.patch', 'TensorFlow-2.15.1_fix-pybind11-build.patch', + 'TensorFlow-2.15.1_disable-avx512-extensions.patch', ], 'source_tmpl': 'v%(version)s.tar.gz', 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], @@ -185,16 +188,22 @@ exts_list = [ {'v2.15.1.tar.gz': 'f36416d831f06fe866e149c7cd752da410a11178b01ff5620e9f265511ed57cf'}, {'TensorFlow-2.13.0_add-missing-system-protobuf-targets.patch': '77d8c8a5627493fc7c38b4de79d49e60ff6628b05ff969f4cd3ff9857176c459'}, + {'TensorFlow-2.13.0_exclude-xnnpack-on-ppc.patch': + 'd0818206846911d946666ded7d3216c0546e37cee1890a2f48dc1a9d71047cad'}, {'TensorFlow-2.15.1_remove-libclang-dep.patch': '871b2f0221b7a150ac9f563ffad7187e052a7eedd95c20fb4524987d7edb6f21'}, {'TensorFlow-2.15.1_remove-io-gcs-filesystem-dep.patch': 'eba7351a4b0696c589b9c507bacb0257ebce8c39fde39ab72d5d6a69deaaec02'}, {'TensorFlow-2.15.1_add-default-shell-env.patch': '3d5196b4bf2e91048dc8a18f9e8f487a223fcd973d6302e80b0d4000ea3d652b'}, + {'TensorFlow-2.15.1_fix-AVX512-eigen-compilation.patch': + '761059e5f5f5eeeef8aed5517a7685a0eb0a9193d4afe8d45237527681c9c0a3'}, {'TensorFlow-2.15.1_fix-flatbuffer-license.patch': '2c04d5095977a628a238dbf93c5fada7159c86752a7183e64e0cf7c7ab00caf4'}, {'TensorFlow-2.15.1_fix-pybind11-build.patch': '3bb350ac92ab99c63c951c96b3b0160699f5f16822b64f72111ebfd2275cafce'}, + {'TensorFlow-2.15.1_disable-avx512-extensions.patch': + '506ceecff67237eed9cd9e9e114bc1461f35a343f77f83cb3dab710aa701dc0f'}, ], }), ] diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_disable-avx512-extensions.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_disable-avx512-extensions.patch new file mode 100644 index 000000000000..7778d2b4a91e --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_disable-avx512-extensions.patch @@ -0,0 +1,19 @@ +(Some of the) AVX512 extensions to Eigen introduced by TensorFlow are broken and return wrong values. +So disable them for now to keep AVX512 in the other code parts working. +See https://github.com/tensorflow/tensorflow/issues/49944 + +Author: Alexander Grund (TU Dresden) + +diff --git a/third_party/xla/third_party/tsl/tsl/framework/fixedpoint/FixedPoint.h b/third_party/xla/third_party/tsl/tsl/framework/fixedpoint/FixedPoint.h +index 5301914ad37..8923bfed7bf 100644 +--- a/third_party/xla/third_party/tsl/tsl/framework/fixedpoint/FixedPoint.h ++++ b/third_party/xla/third_party/tsl/tsl/framework/fixedpoint/FixedPoint.h +@@ -20,7 +20,7 @@ limitations under the License. + #include "tsl/framework/fixedpoint_types.h" + + // Use optimized implementations whenever available +-#if defined(EIGEN_VECTORIZE_AVX512DQ) || defined(EIGEN_VECTORIZE_AVX512BW) ++#if 0 + #include "tsl/framework/fixedpoint/PacketMathAVX512.h" + #include "tsl/framework/fixedpoint/TypeCastingAVX512.h" + diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_disable-tf32-in-fused-matmul-tests.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_disable-tf32-in-fused-matmul-tests.patch new file mode 100644 index 000000000000..9cc742e53d0f --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_disable-tf32-in-fused-matmul-tests.patch @@ -0,0 +1,46 @@ +Fixes failing FusedMatMul test on certain GPU models + +diff --git a/tensorflow/core/kernels/matmul_op_test.cc b/tensorflow/core/kernels/matmul_op_test.cc +index 8d81d4c796e..2de0365f067 100644 +--- a/tensorflow/core/kernels/matmul_op_test.cc ++++ b/tensorflow/core/kernels/matmul_op_test.cc +@@ -21,6 +21,7 @@ limitations under the License. + #include "tensorflow/core/framework/tensor.h" + #include "tensorflow/core/kernels/ops_testutil.h" + #include "tensorflow/core/lib/core/status_test_util.h" ++#include "tensorflow/core/platform/tensor_float_32_utils.h" + #include "tensorflow/core/platform/test.h" + #include "tensorflow/core/platform/test_benchmark.h" + #include "tensorflow/core/protobuf/rewriter_config.pb.h" +@@ -287,6 +288,7 @@ TYPED_TEST_SUITE_P(FusedMatMulWithBiasOpTest); + // -------------------------------------------------------------------------- // + + TYPED_TEST_P(FusedMatMulWithBiasOpTest, MatMul256x128x64) { ++ tensorflow::enable_tensor_float_32_execution(false); + this->VerifyMatMulWithBias(256, 128, 64, false, false); + this->VerifyMatMulWithBias(256, 128, 64, true, false); + this->VerifyMatMulWithBias(256, 128, 64, false, true); +@@ -294,6 +296,7 @@ TYPED_TEST_P(FusedMatMulWithBiasOpTest, MatMul256x128x64) { + } + + TYPED_TEST_P(FusedMatMulWithBiasOpTest, MatMul1x256x256) { ++ tensorflow::enable_tensor_float_32_execution(false); + this->VerifyMatMulWithBias(1, 256, 256, false, false); + this->VerifyMatMulWithBias(4, 128, 256, false, false); + this->VerifyMatMulWithBias(1, 256, 256, true, false); +@@ -302,6 +305,7 @@ TYPED_TEST_P(FusedMatMulWithBiasOpTest, MatMul1x256x256) { + } + + TYPED_TEST_P(FusedMatMulWithBiasOpTest, MatMul256x256x1) { ++ tensorflow::enable_tensor_float_32_execution(false); + this->VerifyMatMulWithBias(256, 256, 1, false, false); + this->VerifyMatMulWithBias(256, 128, 4, false, false); + this->VerifyMatMulWithBias(256, 256, 1, true, false); +@@ -314,6 +318,7 @@ TYPED_TEST_P(FusedMatMulWithBiasOpTest, MatMul1x256x1) { + } + + TYPED_TEST_P(FusedMatMulWithBiasOpTest, MatMul256x128x64WithActivation) { ++ tensorflow::enable_tensor_float_32_execution(false); + for (const string& activation : {"Relu", "Relu6", "Elu", "LeakyRelu"}) { + this->VerifyConv2DWithBiasAndActivation(256, 128, 64, false, false, + activation); diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_fix-AVX512-eigen-compilation.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_fix-AVX512-eigen-compilation.patch new file mode 100644 index 000000000000..514f215cde9a --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_fix-AVX512-eigen-compilation.patch @@ -0,0 +1,47 @@ +Fix a compilation error for CPUs with AVX512 features where an issue in Eigen leads to +> invalid 'static_cast' from type 'const Eigen::internal::eigen_packet_wrapper<__vector(4) long long int, 1>' to type '__vector(16) float' + +See https://gitlab.com/libeigen/eigen/-/issues/2829 + +Author: Alexander Grund (TU Dresden) + +diff --git a/third_party/eigen3/fix-avx512.patch b/third_party/eigen3/fix-avx512.patch +new file mode 100644 +index 00000000000..0650d52a0c9 +--- /dev/null ++++ b/third_party/eigen3/fix-avx512.patch +@@ -0,0 +1,22 @@ ++diff --git a/Eigen/src/Core/arch/AVX512/TypeCasting.h b/Eigen/src/Core/arch/AVX512/TypeCasting.h ++index 02c56282f..e253e6b49 100644 ++--- a/Eigen/src/Core/arch/AVX512/TypeCasting.h +++++ b/Eigen/src/Core/arch/AVX512/TypeCasting.h ++@@ -145,8 +145,6 @@ template<> EIGEN_STRONG_INLINE Packet8bf preinterpret(con ++ return _mm256_castsi256_si128(a); ++ } ++ ++-#ifndef EIGEN_VECTORIZE_AVX512FP16 ++- ++ template<> EIGEN_STRONG_INLINE Packet16f pcast(const Packet16h& a) { ++ return half2float(a); ++ } ++@@ -155,8 +153,6 @@ template<> EIGEN_STRONG_INLINE Packet16h pcast(const Packe ++ return float2half(a); ++ } ++ ++-#endif ++- ++ template<> EIGEN_STRONG_INLINE Packet16f pcast(const Packet16bf& a) { ++ return Bf16ToF32(a); ++ } +diff --git a/third_party/eigen3/workspace.bzl b/third_party/eigen3/workspace.bzl +index d1d8d4ac486..da549e37432 100644 +--- a/third_party/eigen3/workspace.bzl ++++ b/third_party/eigen3/workspace.bzl +@@ -14,6 +14,7 @@ def repo(): + tf_http_archive( + name = "eigen_archive", + build_file = "//third_party/eigen3:eigen_archive.BUILD", ++ patch_file = ["//third_party/eigen3:fix-avx512.patch"], + sha256 = EIGEN_SHA256, + strip_prefix = "eigen-{commit}".format(commit = EIGEN_COMMIT), + urls = tf_mirror_urls("https://gitlab.com/libeigen/eigen/-/archive/{commit}/eigen-{commit}.tar.gz".format(commit = EIGEN_COMMIT)), diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_fix-cuda_build_defs.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_fix-cuda_build_defs.patch new file mode 100644 index 000000000000..0982df21bb9c --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_fix-cuda_build_defs.patch @@ -0,0 +1,40 @@ +Backport cuda_build_defs path fix for TF 2.15, see: + +https://github.com/tensorflow/tensorflow/commit/1536f2ca228099f0cf7793d3031d9b9bebbf03ed + +diff --git a/third_party/nccl/system.BUILD.tpl b/third_party/nccl/system.BUILD.tpl +index 405d1e7298b..6e2a22a950b 100644 +--- a/third_party/nccl/system.BUILD.tpl ++++ b/third_party/nccl/system.BUILD.tpl +@@ -1,6 +1,6 @@ + load("@bazel_skylib//rules:write_file.bzl", "write_file") + load( +- "@org_tensorflow//tensorflow/platform/default:cuda_build_defs.bzl", ++ "@local_tsl//tsl/platform/default:cuda_build_defs.bzl", + "cuda_rpath_flags" + ) + +diff --git a/third_party/xla/third_party/nccl/system.BUILD.tpl b/third_party/xla/third_party/nccl/system.BUILD.tpl +index 13328fdeeac..6e2a22a950b 100644 +--- a/third_party/xla/third_party/nccl/system.BUILD.tpl ++++ b/third_party/xla/third_party/nccl/system.BUILD.tpl +@@ -1,6 +1,6 @@ + load("@bazel_skylib//rules:write_file.bzl", "write_file") + load( +- "@local_xla//tensorflow/platform/default:cuda_build_defs.bzl", ++ "@local_tsl//tsl/platform/default:cuda_build_defs.bzl", + "cuda_rpath_flags" + ) + +diff --git a/third_party/xla/third_party/tsl/third_party/nccl/system.BUILD.tpl b/third_party/xla/third_party/tsl/third_party/nccl/system.BUILD.tpl +index b45138eaa79..6e2a22a950b 100644 +--- a/third_party/xla/third_party/tsl/third_party/nccl/system.BUILD.tpl ++++ b/third_party/xla/third_party/tsl/third_party/nccl/system.BUILD.tpl +@@ -1,6 +1,6 @@ + load("@bazel_skylib//rules:write_file.bzl", "write_file") + load( +- "@local_tsl//tensorflow/platform/default:cuda_build_defs.bzl", ++ "@local_tsl//tsl/platform/default:cuda_build_defs.bzl", + "cuda_rpath_flags" + ) + diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_remove-duplicate-gpu-tests.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_remove-duplicate-gpu-tests.patch new file mode 100644 index 000000000000..7c6d72c89c97 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_remove-duplicate-gpu-tests.patch @@ -0,0 +1,55 @@ +TensorFlow adds some GPU tests twice increasing the runtime of the test suite. +This filters out the test part meant for CPU. + +See https://github.com/tensorflow/tensorflow/issues/47081 +From https://github.com/tensorflow/tensorflow/pull/59129 + +Author: Alexander Grund (TU Dresden) +--- + tensorflow/tensorflow.bzl | 33 +++++++++++++++++---------------- + 1 file changed, 17 insertions(+), 16 deletions(-) + +diff --git a/tensorflow/tensorflow.bzl b/tensorflow/tensorflow.bzl +index a1531f55cca..3b9c977dcc4 100644 +--- a/tensorflow/tensorflow.bzl ++++ b/tensorflow/tensorflow.bzl +@@ -1626,22 +1626,23 @@ def tf_gpu_cc_test( + linkopts = [], + **kwargs): + targets = [] +- tf_cc_test( +- name = name, +- size = size, +- srcs = srcs, +- args = args, +- data = data, +- extra_copts = extra_copts + if_cuda(["-DNV_CUDNN_DISABLE_EXCEPTION"]), +- kernels = kernels, +- linkopts = linkopts, +- linkstatic = linkstatic, +- suffix = "_cpu", +- tags = tags, +- deps = deps, +- **kwargs +- ) +- targets.append(name + "_cpu") ++ if 'gpu' not in tags: ++ tf_cc_test( ++ name = name, ++ size = size, ++ srcs = srcs, ++ args = args, ++ data = data, ++ extra_copts = extra_copts + if_cuda(["-DNV_CUDNN_DISABLE_EXCEPTION"]), ++ kernels = kernels, ++ linkopts = linkopts, ++ linkstatic = linkstatic, ++ suffix = "_cpu", ++ tags = tags, ++ deps = deps, ++ **kwargs ++ ) ++ targets.append(name + "_cpu") + tf_cc_test( + name = name, + size = size, diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.14-GCCcore-13.3.0.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.14-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..4069dc5a0489 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.14-GCCcore-13.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.14' + +homepage = 'https://www.tcl.tk/' +description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for + building a graphical user interface (GUI) in many different programming languages.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ["https://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] +checksums = ['8ffdb720f47a6ca6107eac2dd877e30b0ef7fac14f3a84ebbd0b3612cee41a94'] + +builddependencies = [('binutils', '2.42')] +dependencies = [ + ('Tcl', version), + ('X11', '20240607'), + ('zlib', '1.3.1'), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib CFLAGS="-I$EBROOTTCL/include"' + +installopts = "&& make install-private-headers" + +postinstallcmds = ["ln -s wish%(version_major_minor)s %(installdir)s/bin/wish"] + +sanity_check_paths = { + 'files': ["bin/wish", "lib/tkConfig.sh", "include/tkInt.h"], + 'dirs': [], +} + +start_dir = 'unix' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/Tkinter/Tkinter-3.12.3-GCCcore-13.3.0.eb b/easybuild/easyconfigs/t/Tkinter/Tkinter-3.12.3-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..00f02ee64243 --- /dev/null +++ b/easybuild/easyconfigs/t/Tkinter/Tkinter-3.12.3-GCCcore-13.3.0.eb @@ -0,0 +1,25 @@ +name = 'Tkinter' +version = '3.12.3' + +homepage = 'https://python.org/' +description = "Tkinter module, built with the Python buildsystem" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.python.org/ftp/python/%(version)s/'] +sources = ['Python-%(version)s.tgz'] +checksums = ['a6b9459f45a6ebbbc1af44f5762623fa355a0c87208ed417628b379d762dddb0'] + +builddependencies = [ + ('binutils', '2.42'), + ('libffi', '3.4.5'), +] + +dependencies = [ + ('Python', '3.12.3'), + ('Tk', '8.6.14'), + ('zlib', '1.3.1'), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/Transformers/Transformers-4.39.3-gfbf-2023a.eb b/easybuild/easyconfigs/t/Transformers/Transformers-4.39.3-gfbf-2023a.eb index cef130c99472..421741f88324 100644 --- a/easybuild/easyconfigs/t/Transformers/Transformers-4.39.3-gfbf-2023a.eb +++ b/easybuild/easyconfigs/t/Transformers/Transformers-4.39.3-gfbf-2023a.eb @@ -8,27 +8,19 @@ description = """State-of-the-art Natural Language Processing for PyTorch and Te toolchain = {'name': 'gfbf', 'version': '2023a'} -_rust_ver = '1.75.0' -builddependencies = [ - ('Rust', _rust_ver), - ('maturin', '1.4.0', '-Rust-%s' % _rust_ver), -] - dependencies = [ ('Python', '3.11.3'), ('SciPy-bundle', '2023.07'), ('PyYAML', '6.0'), ('tqdm', '4.66.1'), ('tokenizers', '0.15.2'), + ('Safetensors', '0.4.3'), ] use_pip = True sanity_pip_check = True exts_list = [ - ('safetensors', '0.4.2', { - 'checksums': ['acc85dcb09ec5e8aa787f588d7ad4d55c103f31e4ff060e17d92cc0e8b8cac73'], - }), ('regex', '2023.12.25', { 'checksums': ['29171aa128da69afdf4bde412d5bedc335f2ca8fcfe4489038577d05f16181e5'], }), diff --git a/easybuild/easyconfigs/t/Transrate/Transrate-1.0.3-GCC-12.3.0.eb b/easybuild/easyconfigs/t/Transrate/Transrate-1.0.3-GCC-12.3.0.eb new file mode 100644 index 000000000000..a70ecf2a9013 --- /dev/null +++ b/easybuild/easyconfigs/t/Transrate/Transrate-1.0.3-GCC-12.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'RubyGem' + +name = 'Transrate' +version = '1.0.3' + +homepage = 'https://hibberdlab.com/transrate' +description = """Transrate is software for de-novo transcriptome assembly quality analysis. + It examines your assembly in detail and compares it to experimental evidence such as the sequencing reads, + reporting quality scores for contigs and assemblies. This allows you to choose between assemblers and parameters, + filter out the bad contigs from an assembly, and help decide when to stop trying to improve the assembly.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/blahah/transrate/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['Transrate-1.0.3_undefined_method_fix.patch'] +checksums = [ + {'v1.0.3.tar.gz': '2ccb101cfab5a33586ea9e62af2b2f14caf6bc016724d1fef796b427e39fe100'}, + {'Transrate-1.0.3_undefined_method_fix.patch': 'ead5e51318d6d810fb11b783d517ea38648f62ae2bdd5f3f4dac7baa9ae94d95'}, +] + +dependencies = [ + ('Ruby', '3.3.0'), + ('crb-blast', '0.6.9'), + ('colorize', '0.7.7'), + ('yell', '2.2.2'), +] + +# requirement is too strict +preinstallopts = """sed -i "s/'yell', '~> 2.0',/'yell',/g" transrate.gemspec && """ + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['gems/%(namelower)s-%(version)s'], +} + +sanity_check_commands = ["%(namelower)s --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/Transrate/Transrate-1.0.3_undefined_method_fix.patch b/easybuild/easyconfigs/t/Transrate/Transrate-1.0.3_undefined_method_fix.patch new file mode 100644 index 000000000000..47526bd2242a --- /dev/null +++ b/easybuild/easyconfigs/t/Transrate/Transrate-1.0.3_undefined_method_fix.patch @@ -0,0 +1,42 @@ +to avoid the `terminal_columns': undefined method `winsize' for nil (NoMethodError)` error +Author: Petr Král (INUITS) +--- lib/transrate/cmdline.rb.orig 2016-06-06 15:10:26.000000000 +0200 ++++ lib/transrate/cmdline.rb 2024-07-25 11:23:20.250369056 +0200 +@@ -87,11 +87,6 @@ + end + end + +- def terminal_columns +- require 'io/console' +- IO.console.winsize.last +- end +- + def help_message + <<-EOS + +@@ -117,19 +112,17 @@ + end + + def transrate_banner +- if terminal_columns > 70 +- txp = '░▓▓▓^▓▓▓░' +- toptxp = txp.green +- midtxp = txp.yellow +- bottxp = txp.red +- puts <<-EOS ++ txp = '░▓▓▓^▓▓▓░' ++ toptxp = txp.green ++ midtxp = txp.yellow ++ bottxp = txp.red ++ puts <<-EOS + _ _ + | |_ _ __ __ _ _ __ ___ _ __ __ _ | |_ ___ + #{toptxp} | __|| '__|/ _` || '_ \\ / __|| '__|/ _` || __|/ _ \\ #{toptxp} + #{midtxp} | |_ | | | (_| || | | |\\__ \\| | | (_| || |_| __/ #{midtxp} + #{bottxp} \\__||_| \\__,_||_| |_||___/|_| \\__,_| \\__|\\___| #{bottxp} +- EOS +- end ++ EOS + "" + end + diff --git a/easybuild/easyconfigs/t/Triangle/Triangle-1.6-GCCcore-13.2.0.eb b/easybuild/easyconfigs/t/Triangle/Triangle-1.6-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..12d41a6857eb --- /dev/null +++ b/easybuild/easyconfigs/t/Triangle/Triangle-1.6-GCCcore-13.2.0.eb @@ -0,0 +1,44 @@ +easyblock = 'MakeCp' + +name = 'Triangle' +version = '1.6' + +homepage = 'https://www.cs.cmu.edu/~quake/triangle.html' +description = """Triangle generates exact Delaunay triangulations, constrained Delaunay triangulations, + conforming Delaunay triangulations, Voronoi diagrams, and high-quality triangular meshes. + The latter can be generated with no small or large angles, + and are thus suitable for finite element analysis.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.netlib.org/voronoi/'] +sources = ['%(namelower)s.zip'] +checksums = [ + '1766327add038495fa3499e9b7cc642179229750f7201b94f8e1b7bee76f8480', # triangle.zip + '38fc1395c2392f627068b669275c30da0c25b1a6db8ed8b80d6bf05a98971568', # Triangle-1.6_makefile.patch +] + +patches = ['%(name)s-%(version)s_makefile.patch'] + +builddependencies = [('binutils', '2.40')] + +buildopts = 'triangle trilibrary' + +files_to_copy = [ + (['triangle', 'tricall'], 'bin'), + (['triangle.h'], 'include'), + (['libtriangle.a'], 'lib'), +] + +sanity_check_paths = { + 'files': ['bin/triangle', 'bin/tricall', 'include/triangle.h', 'lib/libtriangle.a'], + 'dirs': [] +} + +sanity_check_commands = [ + 'triangle -h', + 'tricall', +] + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/t/Trycycler/Trycycler-0.5.5-foss-2023a-R-4.3.2.eb b/easybuild/easyconfigs/t/Trycycler/Trycycler-0.5.5-foss-2023a-R-4.3.2.eb new file mode 100644 index 000000000000..00aa967bdc2c --- /dev/null +++ b/easybuild/easyconfigs/t/Trycycler/Trycycler-0.5.5-foss-2023a-R-4.3.2.eb @@ -0,0 +1,46 @@ +easyblock = 'PythonBundle' + +name = 'Trycycler' +version = '0.5.5' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/rrwick/Trycycler' +description = """A tool for generating consensus long-read assemblies for bacterial genomes.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('R', '4.3.2'), + ('R-bundle-CRAN', '2023.12'), + ('edlib', '1.3.9'), + ('Pillow', '10.0.0'), + ('pytest', '7.4.2'), + ('minimap2', '2.26'), + ('miniasm', '0.3-20191007'), + ('Mash', '2.3'), + ('MUSCLE', '5.1.0'), +] + +use_pip = True + +exts_list = [ + (name, version, { + 'source_urls': ['https://github.com/rrwick/Trycycler/archive/'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['5794a4520c3b8673adc69c975cee06d7658cd74ac6d9378d1fc7af860bec1a89'], + 'runtest': 'pytest', + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/trycycler'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["trycycler --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/tabixpp/tabixpp-1.1.2-GCC-12.2.0.eb b/easybuild/easyconfigs/t/tabixpp/tabixpp-1.1.2-GCC-12.2.0.eb new file mode 100644 index 000000000000..452f3caa3fa4 --- /dev/null +++ b/easybuild/easyconfigs/t/tabixpp/tabixpp-1.1.2-GCC-12.2.0.eb @@ -0,0 +1,41 @@ +# Author: Jasper Grimm (UoY) +# Updated: Petr Král (INUITS) + +easyblock = 'ConfigureMake' + +name = 'tabixpp' +version = '1.1.2' + +homepage = 'https://github.com/ekg/tabixpp' +description = """C++ wrapper to tabix indexer""" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} + +github_account = 'ekg' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_use-external-HTSlib.patch'] + +checksums = [ + 'c850299c3c495221818a85c9205c60185c8ed9468d5ec2ed034470bb852229dc', # v1.1.2.tar.gz + 'a4684b6c3a69258d0686f601564b635ae3dc098e712783b46d9ca5b7ff996906', # tabixpp-1.1.2_use-external-HTSlib.patch +] + +dependencies = [ + ('zlib', '1.2.12'), + ('bzip2', '1.0.8'), + ('XZ', '5.2.7'), + ('HTSlib', '1.17'), + ('PCRE', '8.45'), +] + +skipsteps = ['configure'] + +preinstallopts = 'PREFIX=%(installdir)s' + +sanity_check_paths = { + 'files': ['bin/tabix++', 'lib/libtabixpp.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/tbb/tbb-2021.9.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/t/tbb/tbb-2021.9.0-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..d0173aab4eaa --- /dev/null +++ b/easybuild/easyconfigs/t/tbb/tbb-2021.9.0-GCCcore-12.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'CMakeMake' + +name = 'tbb' +version = '2021.9.0' + +homepage = 'https://github.com/oneapi-src/oneTBB' +description = """Intel(R) Threading Building Blocks (Intel(R) TBB) lets you easily write parallel C++ programs that + take full advantage of multicore performance, that are portable, composable and have future-proof scalability.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/oneapi-src/oneTBB/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['1ce48f34dada7837f510735ff1172f6e2c261b09460e3bf773b49791d247d24e'] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), +] + +dependencies = [('hwloc', '2.8.0')] + +# use -Wno-error as workaround for compiler error when building the tests +preconfigopts = 'export CXXFLAGS="$CXXFLAGS -Wno-stringop-overflow" && ' + +sanity_check_paths = { + 'files': ['lib/libtbb.%s' % SHLIB_EXT, 'lib/libtbbmalloc.%s' % SHLIB_EXT], + 'dirs': ['lib', 'include', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/tdlib/tdlib-0.9.3-GCC-13.2.0.eb b/easybuild/easyconfigs/t/tdlib/tdlib-0.9.3-GCC-13.2.0.eb new file mode 100644 index 000000000000..63408d65ee73 --- /dev/null +++ b/easybuild/easyconfigs/t/tdlib/tdlib-0.9.3-GCC-13.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'tdlib' +version = '0.9.3' + +homepage = 'https://github.com/freetdi/tdlib/' +description = """treedec provides tree decomposition algorithms.""" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +source_urls = ['https://github.com/freetdi/tdlib/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['d1730c98f41dcb23bbd0bd8de9dbec51df015304f28a38935848925901594ae8'] + +builddependencies = [ + ('Autotools', '20220317'), + ('Boost', '1.83.0'), + ('Python', '3.11.5'), +] + +preconfigopts = 'autoreconf --install && ' + +sanity_check_paths = { + 'files': [ + 'include/treedec/combinations.hpp', + ], + 'dirs': [] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/t/tensorboard/tensorboard-2.10.0-foss-2022a.eb b/easybuild/easyconfigs/t/tensorboard/tensorboard-2.10.0-foss-2022a.eb index 4cf2f36f1d5c..83fc611834b1 100644 --- a/easybuild/easyconfigs/t/tensorboard/tensorboard-2.10.0-foss-2022a.eb +++ b/easybuild/easyconfigs/t/tensorboard/tensorboard-2.10.0-foss-2022a.eb @@ -9,6 +9,14 @@ and graphs.""" toolchain = {'name': 'foss', 'version': '2022a'} +postinstallpatches = [ + ('tensorboard-2.10_jupyterhub-support.patch', 'lib/python%(pyshortver)s/site-packages'), +] +checksums = [ + {'tensorboard-2.10_jupyterhub-support.patch': + '50a292e6ee518aecb5644595e0f3db4867be4f82e328e008e5a3f6a1f19baf87'}, +] + dependencies = [ ('Python', '3.10.4'), ('SciPy-bundle', '2022.05'), diff --git a/easybuild/easyconfigs/t/tensorboard/tensorboard-2.10_jupyterhub-support.patch b/easybuild/easyconfigs/t/tensorboard/tensorboard-2.10_jupyterhub-support.patch new file mode 100644 index 000000000000..211bf6862568 --- /dev/null +++ b/easybuild/easyconfigs/t/tensorboard/tensorboard-2.10_jupyterhub-support.patch @@ -0,0 +1,103 @@ +From: qzchenwl +Date: Tue, 14 Jan 2020 15:22:27 +0800 +Subject: support jupyterhub with jupyter-server-proxy +Issue: https://github.com/tensorflow/tensorboard/pull/3142 + +--- a/tensorboard/notebook.py 2024-06-13 16:04:51.656772000 +0200 ++++ b/tensorboard/notebook.py 2024-06-13 16:06:38.749780722 +0200 +@@ -34,6 +34,7 @@ + # details). + _CONTEXT_COLAB = "_CONTEXT_COLAB" + _CONTEXT_IPYTHON = "_CONTEXT_IPYTHON" ++_CONTEXT_JUPYTERHUB = "_CONTEXT_JUPYTERHUB" + _CONTEXT_NONE = "_CONTEXT_NONE" + + +@@ -70,12 +71,31 @@ + else: + ipython = IPython.get_ipython() + if ipython is not None and ipython.has_trait("kernel"): ++ if os.environ.get("JUPYTERHUB_SERVICE_PREFIX") is not None: ++ return _CONTEXT_JUPYTERHUB + return _CONTEXT_IPYTHON + + # Otherwise, we're not in a known notebook context. + return _CONTEXT_NONE + + ++def _prefix_jupyterhub(port): ++ prefix = os.path.join( ++ os.environ["JUPYTERHUB_SERVICE_PREFIX"], "proxy/absolute" ++ ) ++ return "%s/%d/" % (prefix, port) ++ ++ ++def _patch_args_jupyterhub(parsed_args): ++ if "--port" in parsed_args: ++ arg_idx = parsed_args.index("--port") ++ port = int(parsed_args[arg_idx + 1]) ++ else: ++ port = 6006 ++ parsed_args += ["--port", str(port)] ++ return parsed_args + ["--path_prefix", _prefix_jupyterhub(port)] ++ ++ + def load_ipython_extension(ipython): + """Deprecated: use `%load_ext tensorboard` instead. + +@@ -149,6 +169,9 @@ + handle.update(IPython.display.Pretty(message)) + + parsed_args = shlex.split(args_string, comments=True, posix=True) ++ if context == _CONTEXT_JUPYTERHUB: ++ parsed_args = _patch_args_jupyterhub(parsed_args) ++ + start_result = manager.start(parsed_args) + + if isinstance(start_result, manager.StartLaunched): +@@ -305,6 +328,7 @@ + fn = { + _CONTEXT_COLAB: _display_colab, + _CONTEXT_IPYTHON: _display_ipython, ++ _CONTEXT_JUPYTERHUB: _display_jupyterhub, + _CONTEXT_NONE: _display_cli, + }[_get_context()] + return fn(port=port, height=height, display_handle=display_handle) +@@ -401,6 +425,36 @@ + for (k, v) in replacements: + shell = shell.replace(k, v) + iframe = IPython.display.HTML(shell) ++ if display_handle: ++ display_handle.update(iframe) ++ else: ++ IPython.display.display(iframe) ++ ++ ++def _display_jupyterhub(port, height, display_handle): ++ import IPython.display ++ ++ frame_id = "tensorboard-frame-{:08x}".format(random.getrandbits(64)) ++ shell = """ ++ ++ ++ """ ++ replacements = [ ++ ("%HTML_ID%", html.escape(frame_id, quote=True)), ++ ("%JSON_ID%", json.dumps(frame_id)), ++ ("%PREFIX%", _prefix_jupyterhub(port)), ++ ("%HEIGHT%", "%d" % height), ++ ] ++ for (k, v) in replacements: ++ shell = shell.replace(k, v) ++ iframe = IPython.display.HTML(shell) + if display_handle: + display_handle.update(iframe) + else: +From 5615204ba44a6b8718e58c9b4b875fef5027baaf Mon Sep 17 00:00:00 2001 diff --git a/easybuild/easyconfigs/t/tensorboard/tensorboard-2.15.1-gfbf-2022b.eb b/easybuild/easyconfigs/t/tensorboard/tensorboard-2.15.1-gfbf-2022b.eb new file mode 100644 index 000000000000..304e56b390fa --- /dev/null +++ b/easybuild/easyconfigs/t/tensorboard/tensorboard-2.15.1-gfbf-2022b.eb @@ -0,0 +1,90 @@ +easyblock = 'PythonBundle' + +name = 'tensorboard' +version = '2.15.1' + +homepage = 'https://github.com/tensorflow/tensorboard' +description = """TensorBoard is a suite of web applications for inspecting and +understanding your TensorFlow runs and graphs.""" + +toolchain = {'name': 'gfbf', 'version': '2022b'} + +postinstallpatches = [ + ('tensorboard-2.10_jupyterhub-support.patch', 'lib/python%(pyshortver)s/site-packages'), +] +checksums = [ + {'tensorboard-2.10_jupyterhub-support.patch': + '50a292e6ee518aecb5644595e0f3db4867be4f82e328e008e5a3f6a1f19baf87'}, +] + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('protobuf-python', '4.23.0'), + ('grpcio', '1.57.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('absl-py', '2.1.0', { + 'modulename': 'absl', + 'checksums': ['7820790efbb316739cde8b4e19357243fc3608a152024288513dd968d7d959ff'], + }), + ('cachetools', '5.3.2', { + 'checksums': ['086ee420196f7b2ab9ca2db2520aca326318b68fe5ba8bc4d49cca91add450f2'], + }), + ('pyasn1_modules', '0.3.0', { + 'checksums': ['5bd01446b736eb9d31512a30d46c1ac3395d676c6f3cafa4c03eb54b9925631c'], + }), + ('rsa', '4.9', { + 'checksums': ['e38464a49c6c85d7f1351b0126661487a7e0a14a50f1675ec50eb34d4f20ef21'], + }), + ('google-auth', '2.26.2', { + 'modulename': 'google.auth', + 'checksums': ['97327dbbf58cccb58fc5a1712bba403ae76668e64814eb30f7316f7e27126b81'], + }), + ('oauthlib', '3.2.2', { + 'checksums': ['9859c40929662bec5d64f34d01c99e093149682a3f38915dc0655d5a633dd918'], + }), + ('requests-oauthlib', '1.3.1', { + 'checksums': ['75beac4a47881eeb94d5ea5d6ad31ef88856affe2332b9aafb52c6452ccf0d7a'], + }), + ('google-auth-oauthlib', '1.2.0', { + 'checksums': ['292d2d3783349f2b0734a0a0207b1e1e322ac193c2c09d8f7c613fb7cc501ea8'], + }), + ('Markdown', '3.5.2', { + 'checksums': ['e1ac7b3dc550ee80e602e71c1d168002f062e49f1b11e26a36264dafd4df2ef8'], + }), + ('tensorboard_data_server', '0.7.2', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['7e0610d205889588983836ec05dc098e80f97b7e7bbff7e994ebb78f578d0ddb'], + }), + ('gviz-api', '1.10.0', { + 'source_tmpl': 'gviz_api-%(version)s.tar.gz', + 'checksums': ['846692dd8cc73224fc31b18e41589bd934e1cc05090c6576af4b4b26c2e71b90'], + }), + ('tensorboard-plugin-profile', '2.15.1', { + 'source_tmpl': 'tensorboard_plugin_profile-%(version)s.tar.gz', + 'checksums': ['84bb33e446eb4a9c0616f669fc6a42cdd40eadd9ae1d74bf756f4f0479993273'], + }), + ('Werkzeug', '3.0.1', { + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'checksums': ['507e811ecea72b18a404947aded4b3390e1db8f826b494d76550ef45bb3b1dcc'], + }), + (name, version, { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['c46c1d1cf13a458c429868a78b2531d8ff5f682058d69ec0840b0bc7a38f1c0f'], + }), +] + +# Relax restriction on protobuf dependency as issue was fixed +# in https://github.com/protocolbuffers/upb/pull/1514 +# see also: https://github.com/easybuilders/easybuild-easyconfigs/pull/19671 +postinstallcmds = [ + 'sed -i "s/Requires-Dist: protobuf.*/Requires-Dist: protobuf >=3.19.6/g" ' + + '%(installdir)s/lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s.dist-info/METADATA', +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/tensorboard/tensorboard-2.15.1-gfbf-2023a.eb b/easybuild/easyconfigs/t/tensorboard/tensorboard-2.15.1-gfbf-2023a.eb index 9c74e1a8f87d..ab4999088318 100644 --- a/easybuild/easyconfigs/t/tensorboard/tensorboard-2.15.1-gfbf-2023a.eb +++ b/easybuild/easyconfigs/t/tensorboard/tensorboard-2.15.1-gfbf-2023a.eb @@ -9,6 +9,14 @@ understanding your TensorFlow runs and graphs.""" toolchain = {'name': 'gfbf', 'version': '2023a'} +postinstallpatches = [ + ('tensorboard-2.10_jupyterhub-support.patch', 'lib/python%(pyshortver)s/site-packages'), +] +checksums = [ + {'tensorboard-2.10_jupyterhub-support.patch': + '50a292e6ee518aecb5644595e0f3db4867be4f82e328e008e5a3f6a1f19baf87'}, +] + builddependencies = [ ('poetry', '1.5.1'), ] @@ -17,8 +25,12 @@ dependencies = [ ('Python', '3.11.3'), ('SciPy-bundle', '2023.07'), ('protobuf-python', '4.24.0'), + ('grpcio', '1.57.0'), ] +use_pip = True +sanity_pip_check = True + exts_list = [ ('absl-py', '2.1.0', { 'modulename': 'absl', @@ -46,11 +58,6 @@ exts_list = [ ('google-auth-oauthlib', '1.2.0', { 'checksums': ['292d2d3783349f2b0734a0a0207b1e1e322ac193c2c09d8f7c613fb7cc501ea8'], }), - ('grpcio', '1.60.0', { - 'modulename': 'grpc', - 'preinstallopts': "export GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS=%(parallel)s && ", - 'checksums': ['2199165a1affb666aa24adf0c97436686d0a61bc5fc113c037701fb7c7fceb96'], - }), ('Markdown', '3.5.2', { 'checksums': ['e1ac7b3dc550ee80e602e71c1d168002f062e49f1b11e26a36264dafd4df2ef8'], }), @@ -58,9 +65,13 @@ exts_list = [ 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', 'checksums': ['7e0610d205889588983836ec05dc098e80f97b7e7bbff7e994ebb78f578d0ddb'], }), - ('tensorboard_plugin_wit', '1.8.1', { - 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', - 'checksums': ['ff26bdd583d155aa951ee3b152b3d0cffae8005dc697f72b44a8e8c2a77a8cbe'], + ('gviz-api', '1.10.0', { + 'source_tmpl': 'gviz_api-%(version)s.tar.gz', + 'checksums': ['846692dd8cc73224fc31b18e41589bd934e1cc05090c6576af4b4b26c2e71b90'], + }), + ('tensorboard-plugin-profile', '2.15.1', { + 'source_tmpl': 'tensorboard_plugin_profile-%(version)s.tar.gz', + 'checksums': ['84bb33e446eb4a9c0616f669fc6a42cdd40eadd9ae1d74bf756f4f0479993273'], }), ('Werkzeug', '3.0.1', { 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', @@ -80,7 +91,4 @@ postinstallcmds = [ '%(installdir)s/lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s.dist-info/METADATA', ] -use_pip = True -sanity_pip_check = True - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.20.0-foss-2023a.eb b/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.20.0-foss-2023a.eb index c86b16b035f4..efede874267f 100644 --- a/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.20.0-foss-2023a.eb +++ b/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.20.0-foss-2023a.eb @@ -28,6 +28,12 @@ dependencies = [ use_pip = True +# avoid pip check fail when tensorflow-probability is a dependency +local_postinstallcmds = "cd %(installdir)s/lib/python%(pyshortver)s/site-packages && " +local_postinstallcmds += "mv tfp_nightly-%(version)s.dist-info tensorflow_probability-%(version)s.dist-info && " +local_postinstallcmds += "sed -i 's/Name: tfp-nightly/Name: %(name)s/' " +local_postinstallcmds += "tensorflow_probability-%(version)s.dist-info/METADATA" + exts_list = [ ('cloudpickle', '3.0.0', { 'checksums': ['996d9a482c6fb4f33c1a35335cf8afd065d2a56e973270364840712d9131a882'], @@ -37,6 +43,7 @@ exts_list = [ 'source_tmpl': 'v%(version)s.tar.gz', 'source_urls': ['https://github.com/tensorflow/probability/archive/'], 'checksums': ['f0fb9a1f88a36a8f57d4d9cce4f9bf8dfacb6fc7778751729fe3c3067e5a1363'], + 'postinstallcmds': [local_postinstallcmds], }), ] diff --git a/easybuild/easyconfigs/t/tiktoken/tiktoken-0.7.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/t/tiktoken/tiktoken-0.7.0-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..3dc06c7edcb6 --- /dev/null +++ b/easybuild/easyconfigs/t/tiktoken/tiktoken-0.7.0-GCCcore-12.3.0.eb @@ -0,0 +1,135 @@ +easyblock = 'CargoPythonPackage' + +name = 'tiktoken' +version = '0.7.0' +_rust_ver = '1.75.0' + +homepage = 'https://github.com/openai/tiktoken' +description = "tiktoken is a fast BPE tokeniser for use with OpenAI's models" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('Rust', _rust_ver), + ('maturin', '1.4.0', '-Rust-%s' % _rust_ver), + ('hypothesis', '6.82.0') +] + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), # regex (and pytest for tests) +] + +crates = [ + ('aho-corasick', '1.1.3'), + ('autocfg', '1.2.0'), + ('bit-set', '0.5.3'), + ('bit-vec', '0.6.3'), + ('bitflags', '1.3.2'), + ('bstr', '1.9.1'), + ('cfg-if', '1.0.0'), + ('fancy-regex', '0.11.0'), + ('heck', '0.4.1'), + ('indoc', '2.0.5'), + ('libc', '0.2.153'), + ('lock_api', '0.4.11'), + ('memchr', '2.7.2'), + ('memoffset', '0.9.1'), + ('once_cell', '1.19.0'), + ('parking_lot', '0.12.1'), + ('parking_lot_core', '0.9.9'), + ('portable-atomic', '1.6.0'), + ('proc-macro2', '1.0.79'), + ('pyo3', '0.20.3'), + ('pyo3-build-config', '0.20.3'), + ('pyo3-ffi', '0.20.3'), + ('pyo3-macros', '0.20.3'), + ('pyo3-macros-backend', '0.20.3'), + ('quote', '1.0.36'), + ('redox_syscall', '0.4.1'), + ('regex', '1.10.4'), + ('regex-automata', '0.4.6'), + ('regex-syntax', '0.8.3'), + ('rustc-hash', '1.1.0'), + ('scopeguard', '1.2.0'), + ('serde', '1.0.197'), + ('serde_derive', '1.0.197'), + ('smallvec', '1.13.2'), + ('syn', '2.0.58'), + ('target-lexicon', '0.12.14'), + ('unicode-ident', '1.0.12'), + ('unindent', '0.2.3'), + ('windows-targets', '0.48.5'), + ('windows_aarch64_gnullvm', '0.48.5'), + ('windows_aarch64_msvc', '0.48.5'), + ('windows_i686_gnu', '0.48.5'), + ('windows_i686_msvc', '0.48.5'), + ('windows_x86_64_gnu', '0.48.5'), + ('windows_x86_64_gnullvm', '0.48.5'), + ('windows_x86_64_msvc', '0.48.5'), +] +sources = [SOURCE_TAR_GZ] +checksums = [ + {'tiktoken-0.7.0.tar.gz': '1077266e949c24e0291f6c350433c6f0971365ece2b173a23bc3b9f9defef6b6'}, + {'aho-corasick-1.1.3.tar.gz': '8e60d3430d3a69478ad0993f19238d2df97c507009a52b3c10addcd7f6bcb916'}, + {'autocfg-1.2.0.tar.gz': 'f1fdabc7756949593fe60f30ec81974b613357de856987752631dea1e3394c80'}, + {'bit-set-0.5.3.tar.gz': '0700ddab506f33b20a03b13996eccd309a48e5ff77d0d95926aa0210fb4e95f1'}, + {'bit-vec-0.6.3.tar.gz': '349f9b6a179ed607305526ca489b34ad0a41aed5f7980fa90eb03160b69598fb'}, + {'bitflags-1.3.2.tar.gz': 'bef38d45163c2f1dde094a7dfd33ccf595c92905c8f8f4fdc18d06fb1037718a'}, + {'bstr-1.9.1.tar.gz': '05efc5cfd9110c8416e471df0e96702d58690178e206e61b7173706673c93706'}, + {'cfg-if-1.0.0.tar.gz': 'baf1de4339761588bc0619e3cbc0120ee582ebb74b53b4efbf79117bd2da40fd'}, + {'fancy-regex-0.11.0.tar.gz': 'b95f7c0680e4142284cf8b22c14a476e87d61b004a3a0861872b32ef7ead40a2'}, + {'heck-0.4.1.tar.gz': '95505c38b4572b2d910cecb0281560f54b440a19336cbbcb27bf6ce6adc6f5a8'}, + {'indoc-2.0.5.tar.gz': 'b248f5224d1d606005e02c97f5aa4e88eeb230488bcc03bc9ca4d7991399f2b5'}, + {'libc-0.2.153.tar.gz': '9c198f91728a82281a64e1f4f9eeb25d82cb32a5de251c6bd1b5154d63a8e7bd'}, + {'lock_api-0.4.11.tar.gz': '3c168f8615b12bc01f9c17e2eb0cc07dcae1940121185446edc3744920e8ef45'}, + {'memchr-2.7.2.tar.gz': '6c8640c5d730cb13ebd907d8d04b52f55ac9a2eec55b440c8892f40d56c76c1d'}, + {'memoffset-0.9.1.tar.gz': '488016bfae457b036d996092f6cb448677611ce4449e970ceaf42695203f218a'}, + {'once_cell-1.19.0.tar.gz': '3fdb12b2476b595f9358c5161aa467c2438859caa136dec86c26fdd2efe17b92'}, + {'parking_lot-0.12.1.tar.gz': '3742b2c103b9f06bc9fff0a37ff4912935851bee6d36f3c02bcc755bcfec228f'}, + {'parking_lot_core-0.9.9.tar.gz': '4c42a9226546d68acdd9c0a280d17ce19bfe27a46bf68784e4066115788d008e'}, + {'portable-atomic-1.6.0.tar.gz': '7170ef9988bc169ba16dd36a7fa041e5c4cbeb6a35b76d4c03daded371eae7c0'}, + {'proc-macro2-1.0.79.tar.gz': 'e835ff2298f5721608eb1a980ecaee1aef2c132bf95ecc026a11b7bf3c01c02e'}, + {'pyo3-0.20.3.tar.gz': '53bdbb96d49157e65d45cc287af5f32ffadd5f4761438b527b055fb0d4bb8233'}, + {'pyo3-build-config-0.20.3.tar.gz': 'deaa5745de3f5231ce10517a1f5dd97d53e5a2fd77aa6b5842292085831d48d7'}, + {'pyo3-ffi-0.20.3.tar.gz': '62b42531d03e08d4ef1f6e85a2ed422eb678b8cd62b762e53891c05faf0d4afa'}, + {'pyo3-macros-0.20.3.tar.gz': '7305c720fa01b8055ec95e484a6eca7a83c841267f0dd5280f0c8b8551d2c158'}, + {'pyo3-macros-backend-0.20.3.tar.gz': '7c7e9b68bb9c3149c5b0cade5d07f953d6d125eb4337723c4ccdb665f1f96185'}, + {'quote-1.0.36.tar.gz': '0fa76aaf39101c457836aec0ce2316dbdc3ab723cdda1c6bd4e6ad4208acaca7'}, + {'redox_syscall-0.4.1.tar.gz': '4722d768eff46b75989dd134e5c353f0d6296e5aaa3132e776cbdb56be7731aa'}, + {'regex-1.10.4.tar.gz': 'c117dbdfde9c8308975b6a18d71f3f385c89461f7b3fb054288ecf2a2058ba4c'}, + {'regex-automata-0.4.6.tar.gz': '86b83b8b9847f9bf95ef68afb0b8e6cdb80f498442f5179a29fad448fcc1eaea'}, + {'regex-syntax-0.8.3.tar.gz': 'adad44e29e4c806119491a7f06f03de4d1af22c3a680dd47f1e6e179439d1f56'}, + {'rustc-hash-1.1.0.tar.gz': '08d43f7aa6b08d49f382cde6a7982047c3426db949b1424bc4b7ec9ae12c6ce2'}, + {'scopeguard-1.2.0.tar.gz': '94143f37725109f92c262ed2cf5e59bce7498c01bcc1502d7b9afe439a4e9f49'}, + {'serde-1.0.197.tar.gz': '3fb1c873e1b9b056a4dc4c0c198b24c3ffa059243875552b2bd0933b1aee4ce2'}, + {'serde_derive-1.0.197.tar.gz': '7eb0b34b42edc17f6b7cac84a52a1c5f0e1bb2227e997ca9011ea3dd34e8610b'}, + {'smallvec-1.13.2.tar.gz': '3c5e1a9a646d36c3599cd173a41282daf47c44583ad367b8e6837255952e5c67'}, + {'syn-2.0.58.tar.gz': '44cfb93f38070beee36b3fef7d4f5a16f27751d94b187b666a5cc5e9b0d30687'}, + {'target-lexicon-0.12.14.tar.gz': 'e1fc403891a21bcfb7c37834ba66a547a8f402146eba7265b5a6d88059c9ff2f'}, + {'unicode-ident-1.0.12.tar.gz': '3354b9ac3fae1ff6755cb6db53683adb661634f67557942dea4facebec0fee4b'}, + {'unindent-0.2.3.tar.gz': 'c7de7d73e1754487cb58364ee906a499937a0dfabd86bcb980fa99ec8c8fa2ce'}, + {'windows-targets-0.48.5.tar.gz': '9a2fa6e2155d7247be68c096456083145c183cbbbc2764150dda45a87197940c'}, + {'windows_aarch64_gnullvm-0.48.5.tar.gz': '2b38e32f0abccf9987a4e3079dfb67dcd799fb61361e53e2882c3cbaf0d905d8'}, + {'windows_aarch64_msvc-0.48.5.tar.gz': 'dc35310971f3b2dbbf3f0690a219f40e2d9afcf64f9ab7cc1be722937c26b4bc'}, + {'windows_i686_gnu-0.48.5.tar.gz': 'a75915e7def60c94dcef72200b9a8e58e5091744960da64ec734a6c6e9b3743e'}, + {'windows_i686_msvc-0.48.5.tar.gz': '8f55c233f70c4b27f66c523580f78f1004e8b5a8b659e05a4eb49d4166cca406'}, + {'windows_x86_64_gnu-0.48.5.tar.gz': '53d40abd2583d23e4718fddf1ebec84dbff8381c07cae67ff7768bbf19c6718e'}, + {'windows_x86_64_gnullvm-0.48.5.tar.gz': '0b7b52767868a23d5bab768e390dc5f5c55825b6d30b86c844ff2dc7414044cc'}, + {'windows_x86_64_msvc-0.48.5.tar.gz': 'ed94fce61571a4006852b7389a063ab983c02eb1bb37b47f8272ce92d06d9538'}, +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +# https://github.com/openai/tiktoken/issues/194 +runtest = ( + 'ln -s $PWD/tests ../tests_%(name)s' + ' && cd ..' + ' && pytest tests_%(name)s/' +) +testinstall = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/timm/timm-1.0.8-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/t/timm/timm-1.0.8-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 000000000000..aadc225d0fa0 --- /dev/null +++ b/easybuild/easyconfigs/t/timm/timm-1.0.8-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,44 @@ +easyblock = 'PythonBundle' + +name = 'timm' +version = '1.0.8' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://huggingface.co/docs/timm' +description = """ +timm is a library containing SOTA computer vision models, layers, utilities, +optimizers, schedulers, data-loaders, augmentations, and training/evaluation +scripts. It comes packaged with >700 pretrained models, and is designed to be +flexible and easy to use. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('CUDA', '12.1.1', '', SYSTEM), + ('PyTorch', '2.1.2', versionsuffix), + ('PyYAML', '6.0'), + ('tqdm', '4.66.1'), + ('torchvision', '0.16.0', versionsuffix), + ('Safetensors', '0.4.3'), +] + +builddependencies = [ + ('PDM', '2.12.4'), +] + +use_pip = True + +exts_list = [ + ('huggingface_hub', '0.24.5', { + 'checksums': ['7b45d6744dd53ce9cbf9880957de00e9d10a9ae837f1c9b7255fc8fa4e8264f3'], + }), + (name, version, { + 'checksums': ['f54a579f1cc39c43d99a4b03603e39c4cee87d4f0a08aba9c22e19064b30bf95'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/torch-em/torch-em-0.7.1-foss-2023a.eb b/easybuild/easyconfigs/t/torch-em/torch-em-0.7.1-foss-2023a.eb new file mode 100644 index 000000000000..425ec7e35af7 --- /dev/null +++ b/easybuild/easyconfigs/t/torch-em/torch-em-0.7.1-foss-2023a.eb @@ -0,0 +1,104 @@ +easyblock = 'PythonBundle' + +name = 'torch-em' +version = '0.7.1' + +homepage = 'https://github.com/constantinpape/torch-em/' +description = """Deep-learning based semantic and instance segmentation for 3D Electron Microscopy and +other bioimage analysis problems based on pytorch.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('maturin', '1.1.0'), + ('CMake', '3.26.3'), + ('hatchling', '1.18.0'), +] +dependencies = [ + ('Python', '3.11.3'), + ('torchvision', '0.16.0'), + ('h5py', '3.9.0'), + ('imagecodecs', '2024.1.1'), + ('tensorboard', '2.15.1'), + ('tqdm', '4.66.1'), + ('napari', '0.4.18'), + ('vigra', '1.11.2'), + ('python-elf', '0.5.1'), + ('z5py', '2.0.17'), + ('pydantic', '2.5.3'), + ('xarray', '2023.9.0'), + ('affogato', '0.3.3'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('termcolor', '2.3.0', { + 'checksums': ['b5b08f68937f138fe92f6c089b99f1e2da0ae56c52b78bf7075fd95420fd9a5a'], + }), + ('dnspython', '2.6.1', { + 'modulename': False, + 'checksums': ['e8f0f9c23a7b7cb99ded64e6c3a6f3e701d78f50c55e002b839dea7225cff7cc'], + }), + ('kornia_rs', '0.1.3', { + 'checksums': ['e299d110774fc10f82c547fb04b1b8bf450a0514010324e7be06206d2179ceaf'], + }), + ('email_validator', '2.1.1', { + 'checksums': ['200a70680ba08904be6d1eef729205cc0d687634399a5924d842533efb824b84'], + }), + ('annotated_types', '0.7.0', { + 'checksums': ['aff07c09a53a08bc8cfccb9c85b05f1aa9a2a6f23728d790723543408344ce89'], + }), + ('ruyaml', '0.91.0', { + 'checksums': ['6ce9de9f4d082d696d3bde264664d1bcdca8f5a9dff9d1a1f1a127969ab871ab'], + }), + ('python-dotenv', '1.0.1', { + 'modulename': 'dotenv', + 'checksums': ['e324ee90a023d808f1959c46bcbc04446a10ced277783dc6ee09987c37ec10ca'], + }), + ('pydantic_settings', '2.2.1', { + 'checksums': ['00b9f6a5e95553590434c0fa01ead0b216c3e10bc54ae02e37f359948643c5ed'], + }), + ('loguru', '0.7.2', { + 'checksums': ['e671a53522515f34fd406340ee968cb9ecafbc4b36c679da03c18fd8d0bd51ac'], + }), + ('fire', '0.6.0', { + 'checksums': ['54ec5b996ecdd3c0309c800324a0703d6da512241bc73b553db959d98de0aa66'], + }), + ('kornia', '0.7.2', { + 'checksums': ['f834ccd51188d071ed286a6727471c94344ea2a718903cc6f0e56a92f9c66ac5'], + }), + ('tifffile', '2024.5.10', { + 'checksums': ['aa1e1b12be952ab20717d6848bd6d4a5ee88d2aa319f1152bff4354ad728ec86'], + }), + ('bioimageio.core', '0.6.5', { + 'checksums': ['3b2851e44a2b074536c36fe3bb05b28dc1413ed358d3edd0eb272b75e6c9ca2b'], + }), + ('bioimageio.spec', '0.5.2.post5', { + # delete pin of pydantic version + 'preinstallopts': "sed -i 's/pydantic>=2.6.3,<3/pydantic/' setup.py && ", + 'checksums': ['3007aedc4da9f77f4fb46f72c134c8367bd469f05f6dd275db1a93f0fff48e97'], + }), + (name, version, { + 'source_urls': ['https://github.com/constantinpape/torch-em/archive/'], + 'sources': ['%(version)s.tar.gz'], + 'checksums': ['201aae9af1e698b5a0d8e878def4538b00b0cd8ab9165b71194a6c978ae50931'], + }), +] + +sanity_check_commands = [ + "python -c 'import torch_em.data.datasets.util'", + "python -c 'import torch_em.transform.label'", + "python -c 'import torch_em.data.sampler'", + "python -c 'import torch_em.segmentation'", + "python -c 'import torch_em.data.datasets.neurips_cell_seg'", + "python -c 'import torch_em.model'", + "python -c 'import torch_em.loss'", + "python -c 'import torch_em.trainer'", + # check if unpined pydantic version is woking + "python -c 'import bioimageio.spec.model.v0_5'", + "python -c 'from bioimageio.spec import save_bioimageio_package'", +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.15.0-GCCcore-13.2.0-CUDA-12.5.0.eb b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.15.0-GCCcore-13.2.0-CUDA-12.5.0.eb new file mode 100644 index 000000000000..5c88f6a5c5de --- /dev/null +++ b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.15.0-GCCcore-13.2.0-CUDA-12.5.0.eb @@ -0,0 +1,41 @@ +easyblock = 'EB_UCX_Plugins' + +name = 'UCX-CUDA' +version = '1.15.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'http://www.openucx.org/' +description = """Unified Communication X +An open-source production grade communication framework for data centric +and high-performance applications + +This module adds the UCX CUDA support. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s'] +sources = [{'filename': 'ucx-%(version)s.tar.gz', 'alt_location': 'UCX'}] +patches = ['%(name)s-1.11.0_link_against_existing_UCX_libs.patch'] +checksums = [ + {'ucx-1.15.0.tar.gz': '4b202087076bc1c98f9249144f0c277a8ea88ad4ca6f404f94baa9cb3aebda6d'}, + {'UCX-CUDA-1.11.0_link_against_existing_UCX_libs.patch': + '457187fa020e526609ba91e7750c9941d57bd57d60d6eed317b40ad8824aca93'}, +] + +builddependencies = [ + ('binutils', '2.40'), + ('Autotools', '20220317'), + ('pkgconf', '2.0.3'), +] + +dependencies = [ + ('zlib', '1.2.13'), + ('UCX', version), + ('CUDA', '12.5.0', '', SYSTEM), + ('GDRCopy', '2.4'), +] + + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.16.0-GCCcore-13.3.0-CUDA-12.6.0.eb b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.16.0-GCCcore-13.3.0-CUDA-12.6.0.eb new file mode 100644 index 000000000000..34271e18021b --- /dev/null +++ b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.16.0-GCCcore-13.3.0-CUDA-12.6.0.eb @@ -0,0 +1,41 @@ +easyblock = 'EB_UCX_Plugins' + +name = 'UCX-CUDA' +version = '1.16.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'http://www.openucx.org/' +description = """Unified Communication X +An open-source production grade communication framework for data centric +and high-performance applications + +This module adds the UCX CUDA support. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s'] +sources = [{'filename': 'ucx-%(version)s.tar.gz', 'alt_location': 'UCX'}] +patches = ['%(name)s-1.16.0_link_against_existing_UCX_libs.patch'] +checksums = [ + {'ucx-1.16.0.tar.gz': 'f73770d3b583c91aba5fb07557e655ead0786e057018bfe42f0ebe8716e9d28c'}, + {'UCX-CUDA-1.16.0_link_against_existing_UCX_libs.patch': + 'aa5bab38c188276958dd6829da4929ed9ff0b67cd55665b4459521cf3fbbe46d'}, +] + +builddependencies = [ + ('binutils', '2.42'), + ('Autotools', '20231222'), + ('pkgconf', '2.2.0'), +] + +dependencies = [ + ('zlib', '1.3.1'), + ('UCX', version), + ('CUDA', '12.6.0', '', SYSTEM), + ('GDRCopy', '2.4.1'), +] + + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.16.0_link_against_existing_UCX_libs.patch b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.16.0_link_against_existing_UCX_libs.patch new file mode 100644 index 000000000000..92973cd7f802 --- /dev/null +++ b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.16.0_link_against_existing_UCX_libs.patch @@ -0,0 +1,93 @@ +diff --git a/configure.ac b/configure.ac +index 8d8da54..2765fe0 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -30,13 +30,13 @@ valgrind_libpath="" + AC_USE_SYSTEM_EXTENSIONS + AC_CONFIG_HEADERS([config.h]) + +-AC_CHECK_PROG(GITBIN, git, yes) +-AS_IF([test x"${GITBIN}" = x"yes"], +- [# remove preceding "refs/heads/" (11 characters) for symbolic ref +- AC_SUBST(SCM_BRANCH, esyscmd([sh -c 'git symbolic-ref --quiet HEAD | sed "s/^.\{11\}//"'])) +- AC_SUBST(SCM_VERSION, esyscmd([sh -c 'git rev-parse --short=7 HEAD']))], +- [AC_SUBST(SCM_BRANCH, "") +- AC_SUBST(SCM_VERSION, "0000000")]) ++#AC_CHECK_PROG(GITBIN, git, yes) ++#AS_IF([test x"${GITBIN}" = x"yes"], ++# [# remove preceding "refs/heads/" (11 characters) for symbolic ref ++# AC_SUBST(SCM_BRANCH, esyscmd([sh -c 'git symbolic-ref --quiet HEAD | sed "s/^.\{11\}//"'])) ++# AC_SUBST(SCM_VERSION, esyscmd([sh -c 'git rev-parse --short=7 HEAD']))], ++# [AC_SUBST(SCM_BRANCH, "") ++# AC_SUBST(SCM_VERSION, "0000000")]) + + AH_TOP([ + #ifndef UCX_CONFIG_H +diff --git a/src/ucm/cuda/Makefile.am b/src/ucm/cuda/Makefile.am +index 00bd224..22e719f 100644 +--- a/src/ucm/cuda/Makefile.am ++++ b/src/ucm/cuda/Makefile.am +@@ -9,7 +9,7 @@ if HAVE_CUDA + module_LTLIBRARIES = libucm_cuda.la + libucm_cuda_la_CPPFLAGS = $(BASE_CPPFLAGS) $(CUDA_CPPFLAGS) + libucm_cuda_la_CFLAGS = $(BASE_CFLAGS) $(CUDA_CFLAGS) +-libucm_cuda_la_LIBADD = ../libucm.la $(CUDA_LIBS) $(CUDART_LIBS) ++libucm_cuda_la_LIBADD = -lucm $(CUDA_LIBS) $(CUDART_LIBS) + libucm_cuda_la_LDFLAGS = $(UCM_MODULE_LDFLAGS) \ + $(patsubst %, -Xlinker %, $(CUDA_LDFLAGS)) \ + -version-info $(SOVERSION) +diff --git a/src/ucm/rocm/Makefile.am b/src/ucm/rocm/Makefile.am +index f9e183f..dcd1587 100644 +--- a/src/ucm/rocm/Makefile.am ++++ b/src/ucm/rocm/Makefile.am +@@ -10,7 +10,7 @@ if HAVE_ROCM + module_LTLIBRARIES = libucm_rocm.la + libucm_rocm_la_CPPFLAGS = $(BASE_CPPFLAGS) $(ROCM_CPPFLAGS) + libucm_rocm_la_CFLAGS = $(BASE_CFLAGS) $(ROCM_CFLAGS) +-libucm_rocm_la_LIBADD = ../libucm.la ++libucm_rocm_la_LIBADD = -lucm + libucm_rocm_la_LDFLAGS = $(UCM_MODULE_LDFLAGS) \ + $(ROCM_LDFLAGS) $(ROCM_LIBS) -version-info $(SOVERSION) \ + $(patsubst %, -Xlinker %, -L$(ROCM_ROOT)/lib -rpath $(ROCM_ROOT)/hip/lib -rpath $(ROCM_ROOT)/lib) \ +diff --git a/src/uct/cuda/Makefile.am b/src/uct/cuda/Makefile.am +index 00899ab..dcee6b0 100644 +--- a/src/uct/cuda/Makefile.am ++++ b/src/uct/cuda/Makefile.am +@@ -11,8 +11,8 @@ module_LTLIBRARIES = libuct_cuda.la + libuct_cuda_la_CPPFLAGS = $(BASE_CPPFLAGS) $(CUDA_CPPFLAGS) + libuct_cuda_la_CFLAGS = $(BASE_CFLAGS) $(CUDA_CFLAGS) + libuct_cuda_la_LDFLAGS = $(CUDA_LDFLAGS) -version-info $(SOVERSION) +-libuct_cuda_la_LIBADD = $(top_builddir)/src/ucs/libucs.la \ +- $(top_builddir)/src/uct/libuct.la \ ++libuct_cuda_la_LIBADD = -lucs \ ++ -luct \ + $(CUDA_LIBS) $(CUDART_LIBS) $(NVML_LIBS) + + noinst_HEADERS = \ +diff --git a/src/uct/cuda/gdr_copy/Makefile.am b/src/uct/cuda/gdr_copy/Makefile.am +index 47602c7..601cb9f 100644 +--- a/src/uct/cuda/gdr_copy/Makefile.am ++++ b/src/uct/cuda/gdr_copy/Makefile.am +@@ -9,7 +9,7 @@ module_LTLIBRARIES = libuct_cuda_gdrcopy.la + libuct_cuda_gdrcopy_la_CPPFLAGS = $(BASE_CPPFLAGS) $(GDR_COPY_CPPFLAGS) + libuct_cuda_gdrcopy_la_CFLAGS = $(BASE_CFLAGS) + libuct_cuda_gdrcopy_la_LDFLAGS = $(GDR_COPY_LDFLAGS) -version-info $(SOVERSION) +-libuct_cuda_gdrcopy_la_LIBADD = $(top_builddir)/src/ucs/libucs.la \ ++libuct_cuda_gdrcopy_la_LIBADD = -lucs \ + $(top_builddir)/src/uct/cuda/libuct_cuda.la \ + $(GDR_COPY_LIBS) + +diff --git a/src/uct/rocm/Makefile.am b/src/uct/rocm/Makefile.am +index c7abce1..257e33f 100644 +--- a/src/uct/rocm/Makefile.am ++++ b/src/uct/rocm/Makefile.am +@@ -8,8 +8,7 @@ if HAVE_ROCM + module_LTLIBRARIES = libuct_rocm.la + libuct_rocm_la_CPPFLAGS = $(BASE_CPPFLAGS) $(ROCM_CPPFLAGS) + libuct_rocm_la_CFLAGS = $(BASE_CFLAGS) +-libuct_rocm_la_LIBADD = $(top_builddir)/src/ucs/libucs.la \ +- $(top_builddir)/src/uct/libuct.la ++libuct_rocm_la_LIBADD = -lucs -luct + libuct_rocm_la_LDFLAGS = $(ROCM_LDFLAGS) $(ROCM_LIBS) -version-info $(SOVERSION) \ + $(patsubst %, -Xlinker %, -L$(ROCM_ROOT)/lib -rpath $(ROCM_ROOT)/hip/lib -rpath $(ROCM_ROOT)/lib) \ + $(patsubst %, -Xlinker %, --enable-new-dtags) \ diff --git a/easybuild/easyconfigs/u/Umpire/Umpire-2024.02.1-foss-2023a.eb b/easybuild/easyconfigs/u/Umpire/Umpire-2024.02.1-foss-2023a.eb new file mode 100644 index 000000000000..fddfdf851cf4 --- /dev/null +++ b/easybuild/easyconfigs/u/Umpire/Umpire-2024.02.1-foss-2023a.eb @@ -0,0 +1,33 @@ +easyblock = 'CMakeMake' + +name = 'Umpire' +version = '2024.02.1' + +homepage = 'https://github.com/LLNL/Umpire' +description = """Umpire is a resource management library that allows the discovery, provision, +and management of memory on machines with multiple memory devices like NUMA and GPUs.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +sources = [{ + 'filename': 'v%(version)s.tar.gz', + 'git_config': { + 'url': 'https://github.com/LLNL', + 'repo_name': 'Umpire', + 'tag': 'v%(version)s', + 'recursive': True, + 'keep_git_dir': True, + } +}] +checksums = [None] + +builddependencies = [ + ('CMake', '3.26.3'), +] + +sanity_check_paths = { + 'files': ['lib/libcamp.a', 'include/umpire/Umpire.hpp'], + 'dirs': ['bin', 'include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/u/Uni-Core/Uni-Core-0.0.3-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/u/Uni-Core/Uni-Core-0.0.3-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 000000000000..2ca769764aa2 --- /dev/null +++ b/easybuild/easyconfigs/u/Uni-Core/Uni-Core-0.0.3-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,55 @@ +easyblock = 'PythonBundle' + +name = 'Uni-Core' +version = '0.0.3' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/dptech-corp/Uni-Core' +description = "An efficient distributed PyTorch framework" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('Python', '3.10.4'), + ('PyTorch', '1.12.0', versionsuffix), + ('jax', '0.3.25', versionsuffix), # provides absl-py + ('tensorboardX', '2.5.1'), + ('tqdm', '4.64.0'), + ('wandb', '0.13.4'), +] + +use_pip = True + +exts_list = [ + ('lmdb', '1.4.1', { + 'checksums': ['1f4c76af24e907593487c904ef5eba1993beb38ed385af82adb25a858f2d658d'], + }), + ('contextlib2', '21.6.0', { + 'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'], + }), + ('ml-collections', '0.1.1', { + 'sources': ['ml_collections-%(version)s.tar.gz'], + 'checksums': ['3fefcc72ec433aa1e5d32307a3e474bbb67f405be814ea52a2166bfc9dbe68cc'], + 'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ", + }), + ('huggingface-hub', '0.17.3', { + 'source_tmpl': 'huggingface_hub-%(version)s.tar.gz', + 'checksums': ['40439632b211311f788964602bf8b0d9d6b7a2314fba4e8d67b2ce3ecea0e3fd'], + }), + ('tokenizers', '0.19.1', { + 'sources': ['tokenizers-%(version)s-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl'], + 'checksums': ['8b01afb7193d47439f091cd8f070a1ced347ad0f9144952a30a41836902fe09e'], + }), + (name, version, { + 'source_urls': ['https://github.com/dptech-corp/Uni-Core/archive/'], + 'sources': ['%(version)s.tar.gz'], + 'checksums': ['e7a1e938d7d340d7aa483a05ed5ecf715bfa22f5f32a92e46d096da5b9a08043'], + 'preinstallopts': "sed -i 's/torch>=[0-9.]*/torch/g' setup.py && ", + 'modulename': 'unicore', + }), +] + +sanity_pip_check = True + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/u/Uni-Core/Uni-Core-0.0.3-foss-2022a.eb b/easybuild/easyconfigs/u/Uni-Core/Uni-Core-0.0.3-foss-2022a.eb new file mode 100644 index 000000000000..d82f94349bc9 --- /dev/null +++ b/easybuild/easyconfigs/u/Uni-Core/Uni-Core-0.0.3-foss-2022a.eb @@ -0,0 +1,56 @@ +easyblock = 'PythonBundle' + +name = 'Uni-Core' +version = '0.0.3' + +homepage = 'https://github.com/dptech-corp/Uni-Core' +description = "An efficient distributed PyTorch framework" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('PyTorch', '1.12.0'), + ('jax', '0.3.25'), # provides absl-py + ('tensorboardX', '2.5.1'), + ('tqdm', '4.64.0'), + ('wandb', '0.13.4'), +] + +use_pip = True + +local_preinstallopts = "sed -i -e 's/DISABLE_CUDA_EXTENSION = False/DISABLE_CUDA_EXTENSION = True/g' " +local_preinstallopts += "-e 's/torch>=[0-9.]*/torch/g' setup.py && " + +exts_list = [ + ('lmdb', '1.4.1', { + 'checksums': ['1f4c76af24e907593487c904ef5eba1993beb38ed385af82adb25a858f2d658d'], + }), + ('contextlib2', '21.6.0', { + 'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'], + }), + ('ml-collections', '0.1.1', { + 'sources': ['ml_collections-%(version)s.tar.gz'], + 'checksums': ['3fefcc72ec433aa1e5d32307a3e474bbb67f405be814ea52a2166bfc9dbe68cc'], + 'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ", + }), + ('huggingface-hub', '0.17.3', { + 'source_tmpl': 'huggingface_hub-%(version)s.tar.gz', + 'checksums': ['40439632b211311f788964602bf8b0d9d6b7a2314fba4e8d67b2ce3ecea0e3fd'], + }), + ('tokenizers', '0.19.1', { + 'sources': ['tokenizers-%(version)s-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl'], + 'checksums': ['8b01afb7193d47439f091cd8f070a1ced347ad0f9144952a30a41836902fe09e'], + }), + (name, version, { + 'source_urls': ['https://github.com/dptech-corp/Uni-Core/archive/'], + 'sources': ['%(version)s.tar.gz'], + 'checksums': ['e7a1e938d7d340d7aa483a05ed5ecf715bfa22f5f32a92e46d096da5b9a08043'], + 'preinstallopts': local_preinstallopts, + 'modulename': 'unicore', + }), +] + +sanity_pip_check = True + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/u/unixODBC/unixODBC-2.3.12-GCCcore-12.3.0.eb b/easybuild/easyconfigs/u/unixODBC/unixODBC-2.3.12-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..7e5cec281f29 --- /dev/null +++ b/easybuild/easyconfigs/u/unixODBC/unixODBC-2.3.12-GCCcore-12.3.0.eb @@ -0,0 +1,32 @@ +# Easyconfig for unixODBC +# Author: Lykle Voort +# SURFsara, Amsterdam, The Netherlands +# Updated: Petr Král (INUITS) + +easyblock = 'ConfigureMake' + +name = 'unixODBC' +version = '2.3.12' + +homepage = "https://www.unixodbc.org" +description = """unixODBC provides a uniform interface between +application and database driver""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['https://www.unixodbc.org/'] +checksums = ['f210501445ce21bf607ba51ef8c125e10e22dffdffec377646462df5f01915ec'] + +builddependencies = [('binutils', '2.40')] + +sanity_check_paths = { + 'files': [ + 'lib/libodbc.%s' % SHLIB_EXT, + 'lib/libodbccr.%s' % SHLIB_EXT, + 'lib/libodbcinst.%s' % SHLIB_EXT, + ], + 'dirs': [] +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/u/utf8proc/utf8proc-2.9.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/u/utf8proc/utf8proc-2.9.0-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..3ae6a55c2053 --- /dev/null +++ b/easybuild/easyconfigs/u/utf8proc/utf8proc-2.9.0-GCCcore-13.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'CMakeMake' + +name = 'utf8proc' +version = '2.9.0' + +homepage = 'https://github.com/JuliaStrings/utf8proc' +description = """utf8proc is a small, clean C library that provides Unicode normalization, case-folding, +and other operations for data in the UTF-8 encoding.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://github.com/JuliaStrings/utf8proc/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['18c1626e9fc5a2e192311e36b3010bfc698078f692888940f1fa150547abb0c1'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.27.6'), +] + +separate_build_dir = True + +configopts = ['-DBUILD_SHARED_LIBS=OFF', '-DBUILD_SHARED_LIBS=ON'] + +sanity_check_paths = { + 'files': ['include/utf8proc.h', 'lib/libutf8proc.a', 'lib/libutf8proc.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/v/VBZ-Compression/VBZ-Compression-1.0.3-gompi-2023a.eb b/easybuild/easyconfigs/v/VBZ-Compression/VBZ-Compression-1.0.3-gompi-2023a.eb new file mode 100644 index 000000000000..3a3c79f38758 --- /dev/null +++ b/easybuild/easyconfigs/v/VBZ-Compression/VBZ-Compression-1.0.3-gompi-2023a.eb @@ -0,0 +1,43 @@ +easyblock = 'CMakeMake' + +name = 'VBZ-Compression' +version = '1.0.3' + +homepage = 'https://github.com/nanoporetech/vbz_compression' +description = "VBZ compression HDF5 plugin for nanopolish" + +toolchain = {'name': 'gompi', 'version': '2023a'} + +source_urls = [ + 'https://github.com/nanoporetech/vbz_compression/archive', + 'https://github.com/lemire/streamvbyte/archive', +] +sources = [ + {'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}, + {'download_filename': 'v0.4.1.tar.gz', 'filename': 'streamvbyte-v0.4.1.tar.gz'}, +] +checksums = [ + {'VBZ-Compression-1.0.3.tar.gz': 'a7450e076db628681bbc0e2b3f941c6c21cc2981a7e1c78628807ffdf1b34f31'}, + {'streamvbyte-v0.4.1.tar.gz': '4c4e53134a60b0b06816d3faa7dcde28c3e5e8a656dd415d16d80ae6e3d39fcc'}, +] + +builddependencies = [('CMake', '3.26.3')] + +dependencies = [ + ('HDF5', '1.14.0'), + ('zstd', '1.5.5'), +] + +preconfigopts = "rmdir %(builddir)s/vbz_compression*/third_party/streamvbyte && " +preconfigopts += "mv %(builddir)s/streamvbyte-* %(builddir)s/streamvbyte && " +preconfigopts += "mv %(builddir)s/streamvbyte %(builddir)s/vbz_compression*/third_party/. && " +configopts = "-DENABLE_CONAN=OFF -DENABLE_PERF_TESTING=OFF -DENABLE_PYTHON=OFF " + +sanity_check_paths = { + 'files': ['hdf5/lib/plugin/libvbz_hdf_plugin.%s' % SHLIB_EXT], + 'dirs': [], +} + +modextrapaths = {'HDF5_PLUGIN_PATH': 'hdf5/lib/plugin/'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/v/VSEARCH/VSEARCH-2.28.1-GCC-10.2.0.eb b/easybuild/easyconfigs/v/VSEARCH/VSEARCH-2.28.1-GCC-10.2.0.eb new file mode 100644 index 000000000000..14ed6e6d975b --- /dev/null +++ b/easybuild/easyconfigs/v/VSEARCH/VSEARCH-2.28.1-GCC-10.2.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'VSEARCH' +version = '2.28.1' + +homepage = 'https://github.com/torognes/vsearch' +description = """VSEARCH supports de novo and reference based chimera detection, + clustering, full-length and prefix dereplication, rereplication, + reverse complementation, masking, all-vs-all pairwise global alignment, + exact and global alignment searching, shuffling, subsampling and sorting. + It also supports FASTQ file analysis, filtering, + conversion and merging of paired-end reads.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://github.com/torognes/vsearch/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['4f8bf0ad43fef77e573d152b59f55a1f81eb84c22d6545911757e6108f8de21c'] + +builddependencies = [ + ('Autotools', '20200321'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), +] + +preconfigopts = './autogen.sh &&' + +configopts = '--disable-pdfman ' + +sanity_check_paths = { + 'files': ['bin/vsearch'], + 'dirs': [], +} + +sanity_check_commands = ['vsearch --help'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/v/VTK/VTK-9.2.6-foss-2023a.eb b/easybuild/easyconfigs/v/VTK/VTK-9.2.6-foss-2023a.eb new file mode 100644 index 000000000000..5c6c6f7a1229 --- /dev/null +++ b/easybuild/easyconfigs/v/VTK/VTK-9.2.6-foss-2023a.eb @@ -0,0 +1,98 @@ +## +# Authors:: +# * Fotis Georgatos +# * Robert Mijakovic +# Update: Pavel Tománek (Inuits) +## + +easyblock = 'CMakeNinja' + +name = 'VTK' +version = '9.2.6' + +homepage = 'https://www.vtk.org' +description = """The Visualization Toolkit (VTK) is an open-source, freely available software system for + 3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several + interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization + algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques + such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://www.vtk.org/files/release/%(version_major_minor)s'] +sources = [ + SOURCE_TAR_GZ, + '%(name)sData-%(version)s.tar.gz', +] +patches = [('vtk-version.egg-info', '.')] +checksums = [ + {'VTK-9.2.6.tar.gz': '06fc8d49c4e56f498c40fcb38a563ed8d4ec31358d0101e8988f0bb4d539dd12'}, + {'VTKData-9.2.6.tar.gz': '032c4b827173f859c898403d25360dc99409a4674559ad58f48828f23a6258b8'}, + {'vtk-version.egg-info': '787b82415ae7a4a1f815b4db0e25f7abc809a05fc85d7d219627f3a7e5d3867b'}, +] + +builddependencies = [ + ('CMake', '3.26.3'), + ('Ninja', '1.11.1'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('XZ', '5.4.2'), + ('libGLU', '9.0.3'), + ('X11', '20230603'), + ('Qt5', '5.15.10'), +] + +separate_build_dir = True + +# OpenGL +configopts = "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT +configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT +configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include " +# Python +configopts += "-DVTK_WRAP_PYTHON=ON -DVTK_PYTHON_VERSION=3 -DVTK_PYTHON_OPTIONAL_LINK=OFF " +configopts += "-DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python3 " +configopts += "-DPython3_INCLUDE_DIR=$EBROOTPYTHON/include/python%(pyshortver)s " +configopts += "-DPython3_LIBRARY=$EBROOTPYTHON/lib/libpython%(pyshortver)s.so " +# Other +configopts += "-DVTK_USE_MPI=ON " +configopts += "-DCMAKE_INSTALL_LIBDIR=lib " +configopts += "-DVTK_QT_VERSION=5 " +configopts += "-DQt5_DIR=$EBROOTQT5 " +configopts += "-DVTK_MODULE_ENABLE_VTK_GuiSupportQt=YES " +configopts += "-DVTK_MODULE_ENABLE_VTK_ViewsQt=YES" + +preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " + +# Install a egg-info file so VTK is more python friendly, required for mayavi +local_egg_info_src = '%(builddir)s/VTK-%(version)s/vtk-version.egg-info' +local_egg_info_dest = '%(installdir)s/lib/python%(pyshortver)s/site-packages/vtk-%(version)s.egg-info' +postinstallcmds = [ + 'sed "s/#VTK_VERSION#/%%(version)s/" %s > %s' % (local_egg_info_src, local_egg_info_dest), +] + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +local_vtk_exec = ['vtk%s-%%(version_major_minor)s' % x + for x in ['WrapJava', 'ParseJava', 'WrapPythonInit', 'WrapPython', 'WrapHierarchy']] +local_vtk_exec += ['vtkpython'] +local_vtk_libs = ['CommonCore', 'IONetCDF', 'ParallelCore', 'RenderingOpenGL2'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_vtk_exec] + ['include/vtk-%(version_major_minor)s/vtkMPI.h'] + + ['lib/libvtk%s-%%(version_major_minor)s.%s' % (l, SHLIB_EXT) for l in local_vtk_libs], + 'dirs': ['lib/python%(pyshortver)s/site-packages/', 'include/vtk-%(version_major_minor)s'], +} + +sanity_check_commands = [ + "python -c 'import %(namelower)s'", + "python -c 'import pkg_resources; pkg_resources.get_distribution(\"vtk\")'", + # make sure that VTK Python libraries link to libpython (controlled via DVTK_PYTHON_OPTIONAL_LINK=OFF), + # see https://gitlab.kitware.com/vtk/vtk/-/issues/17881 + "ldd $EBROOTVTK/lib/libvtkPythonContext2D-%%(version_major_minor)s.%s | grep /libpython" % SHLIB_EXT, +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/v/VTK/VTK-9.3.0-foss-2023a.eb b/easybuild/easyconfigs/v/VTK/VTK-9.3.0-foss-2023a.eb index 9278837da13e..740fd888dfb2 100644 --- a/easybuild/easyconfigs/v/VTK/VTK-9.3.0-foss-2023a.eb +++ b/easybuild/easyconfigs/v/VTK/VTK-9.3.0-foss-2023a.eb @@ -2,6 +2,7 @@ # Authors:: # * Fotis Georgatos # * Robert Mijakovic +# Update: Pavel Tománek (Inuits) ## easyblock = 'CMakeNinja' @@ -42,6 +43,7 @@ dependencies = [ ('XZ', '5.4.2'), ('libGLU', '9.0.3'), ('X11', '20230603'), + ('Qt5', '5.15.10'), ] separate_build_dir = True @@ -57,7 +59,11 @@ configopts += "-DPython3_INCLUDE_DIR=$EBROOTPYTHON/include/python%(pyshortver)s configopts += "-DPython3_LIBRARY=$EBROOTPYTHON/lib/libpython%(pyshortver)s.so " # Other configopts += "-DVTK_USE_MPI=ON " -configopts += "-DCMAKE_INSTALL_LIBDIR=lib" +configopts += "-DCMAKE_INSTALL_LIBDIR=lib " +configopts += "-DVTK_QT_VERSION=5 " +configopts += "-DQt5_DIR=$EBROOTQT5 " +configopts += "-DVTK_MODULE_ENABLE_VTK_GuiSupportQt=YES " +configopts += "-DVTK_MODULE_ENABLE_VTK_ViewsQt=YES" preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " diff --git a/easybuild/easyconfigs/v/VTK/VTK-9.3.0-foss-2023b.eb b/easybuild/easyconfigs/v/VTK/VTK-9.3.0-foss-2023b.eb index 8a0452f863f8..3be42a90bacc 100644 --- a/easybuild/easyconfigs/v/VTK/VTK-9.3.0-foss-2023b.eb +++ b/easybuild/easyconfigs/v/VTK/VTK-9.3.0-foss-2023b.eb @@ -42,6 +42,7 @@ dependencies = [ ('XZ', '5.4.4'), ('libGLU', '9.0.3'), ('X11', '20231019'), + ('Qt5', '5.15.13'), ] separate_build_dir = True @@ -57,7 +58,11 @@ configopts += "-DPython3_INCLUDE_DIR=$EBROOTPYTHON/include/python%(pyshortver)s configopts += "-DPython3_LIBRARY=$EBROOTPYTHON/lib/libpython%(pyshortver)s.so " # Other configopts += "-DVTK_USE_MPI=ON " -configopts += "-DCMAKE_INSTALL_LIBDIR=lib" +configopts += "-DCMAKE_INSTALL_LIBDIR=lib " +configopts += "-DVTK_QT_VERSION=5 " +configopts += "-DQt5_DIR=$EBROOTQT5 " +configopts += "-DVTK_MODULE_ENABLE_VTK_GuiSupportQt=YES " +configopts += "-DVTK_MODULE_ENABLE_VTK_ViewsQt=YES" preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " diff --git a/easybuild/easyconfigs/v/VTune/VTune-2018_update3.eb b/easybuild/easyconfigs/v/VTune/VTune-2018_update3.eb index 0938ca5f98f1..8f1db4ac7254 100644 --- a/easybuild/easyconfigs/v/VTune/VTune-2018_update3.eb +++ b/easybuild/easyconfigs/v/VTune/VTune-2018_update3.eb @@ -7,7 +7,7 @@ description = """Intel VTune Amplifier XE is the premier performance profiler fo toolchain = SYSTEM -source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13079/'] +source_urls = ['http://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13079/'] sources = ['vtune_amplifier_%(version)s.tar.gz'] checksums = ['a47e3b304b993bc28190d7efaac29dcb4a9b533837f2fe4cd9d5617c537f568a'] diff --git a/easybuild/easyconfigs/v/VTune/VTune-2019_update3.eb b/easybuild/easyconfigs/v/VTune/VTune-2019_update3.eb index bd9fed83da99..50053de39257 100644 --- a/easybuild/easyconfigs/v/VTune/VTune-2019_update3.eb +++ b/easybuild/easyconfigs/v/VTune/VTune-2019_update3.eb @@ -7,7 +7,7 @@ description = """Intel VTune Amplifier XE is the premier performance profiler fo toolchain = SYSTEM -source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15214/'] +source_urls = ['http://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15214/'] sources = ['vtune_amplifier_%(version)s.tar.gz'] checksums = ['d873abd0e98b477056030f3520fc8dfb1521dbb4dfaa6d20d830af02ec12a12d'] diff --git a/easybuild/easyconfigs/v/VTune/VTune-2019_update5.eb b/easybuild/easyconfigs/v/VTune/VTune-2019_update5.eb index 09f9e6b61208..1390fece3776 100644 --- a/easybuild/easyconfigs/v/VTune/VTune-2019_update5.eb +++ b/easybuild/easyconfigs/v/VTune/VTune-2019_update5.eb @@ -7,7 +7,7 @@ description = """Intel VTune Amplifier XE is the premier performance profiler fo toolchain = SYSTEM -source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15703/'] +source_urls = ['http://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15703/'] sources = ['vtune_amplifier_%(version)s.tar.gz'] checksums = ['7b2124123347bbb593d1b8f8cf858d88829a05605769cba5c39444b0aa545473'] diff --git a/easybuild/easyconfigs/v/VTune/VTune-2020_update3.eb b/easybuild/easyconfigs/v/VTune/VTune-2020_update3.eb index b4c024b03be1..ab1cb7c1ebca 100644 --- a/easybuild/easyconfigs/v/VTune/VTune-2020_update3.eb +++ b/easybuild/easyconfigs/v/VTune/VTune-2020_update3.eb @@ -7,7 +7,7 @@ description = """Intel VTune Amplifier XE is the premier performance profiler fo toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/17095/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/17095/'] sources = [{'download_filename': 'vtune_profiler_2020.tar.gz', 'filename': 'vtune_profiler_%(version)s.tar.gz'}] checksums = ['b22dd61d3931ca6ab7d96df2cf8648e5e1061ab2db13b8d42e3c87586b07c974'] diff --git a/easybuild/easyconfigs/v/VTune/VTune-2021.6.0.eb b/easybuild/easyconfigs/v/VTune/VTune-2021.6.0.eb index 9b6582a6610e..d33e54a78185 100644 --- a/easybuild/easyconfigs/v/VTune/VTune-2021.6.0.eb +++ b/easybuild/easyconfigs/v/VTune/VTune-2021.6.0.eb @@ -13,7 +13,7 @@ toolchain = SYSTEM # By downloading, you accept the Intel End User License Agreement # (https://software.intel.com/content/www/us/en/develop/articles/end-user-license-agreement.html) # accept_eula = True -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18012/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18012/'] sources = ['l_oneapi_vtune_p_%(version)s.411_offline.sh'] checksums = ['6b1df7da713337aa665bcc6ff23e4a006695b5bfaf71dffd305cbadca2e5560c'] diff --git a/easybuild/easyconfigs/v/VTune/VTune-2021.9.0.eb b/easybuild/easyconfigs/v/VTune/VTune-2021.9.0.eb index cd2356a18bb2..b0f65557f626 100644 --- a/easybuild/easyconfigs/v/VTune/VTune-2021.9.0.eb +++ b/easybuild/easyconfigs/v/VTune/VTune-2021.9.0.eb @@ -13,7 +13,7 @@ toolchain = SYSTEM # By downloading, you accept the Intel End User License Agreement # (https://software.intel.com/content/www/us/en/develop/articles/end-user-license-agreement.html) # accept_eula = True -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18302/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18302/'] sources = ['l_oneapi_vtune_p_%(version)s.545_offline.sh'] checksums = ['55c8ac25e685f03c849bb5383da249c7caaf2138a2b57a10c8975a38fa3828bc'] diff --git a/easybuild/easyconfigs/v/VTune/VTune-2022.0.0.eb b/easybuild/easyconfigs/v/VTune/VTune-2022.0.0.eb index e205471e1e54..16f445c0f644 100644 --- a/easybuild/easyconfigs/v/VTune/VTune-2022.0.0.eb +++ b/easybuild/easyconfigs/v/VTune/VTune-2022.0.0.eb @@ -13,7 +13,7 @@ toolchain = SYSTEM # By downloading, you accept the Intel End User License Agreement # (https://software.intel.com/content/www/us/en/develop/articles/end-user-license-agreement.html) # accept_eula = True -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18406/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18406/'] sources = ['l_oneapi_vtune_p_%(version)s.94_offline.sh'] checksums = ['aa4d575c22e7be0c950b87d67d9e371f470f682906864c4f9b68e530ecd22bd7'] diff --git a/easybuild/easyconfigs/v/VTune/VTune-2022.2.0.eb b/easybuild/easyconfigs/v/VTune/VTune-2022.2.0.eb index 773718fc4420..458b8143c022 100644 --- a/easybuild/easyconfigs/v/VTune/VTune-2022.2.0.eb +++ b/easybuild/easyconfigs/v/VTune/VTune-2022.2.0.eb @@ -13,7 +13,7 @@ toolchain = SYSTEM # By downloading, you accept the Intel End User License Agreement # (https://software.intel.com/content/www/us/en/develop/articles/end-user-license-agreement.html) # accept_eula = True -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18602/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18602/'] sources = ['l_oneapi_vtune_p_%(version)s.172_offline.sh'] checksums = ['d9f92ab6486a02c8ba226c98893492a54eda706d9edd3206a6b6143bfbc97195'] diff --git a/easybuild/easyconfigs/v/VTune/VTune-2022.3.0.eb b/easybuild/easyconfigs/v/VTune/VTune-2022.3.0.eb index b8a718b77b0d..e2fea76fc3af 100644 --- a/easybuild/easyconfigs/v/VTune/VTune-2022.3.0.eb +++ b/easybuild/easyconfigs/v/VTune/VTune-2022.3.0.eb @@ -13,7 +13,7 @@ toolchain = SYSTEM # By downloading, you accept the Intel End User License Agreement # (https://software.intel.com/content/www/us/en/develop/articles/end-user-license-agreement.html) # accept_eula = True -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18656/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18656/'] sources = ['l_oneapi_vtune_p_%(version)s.195_offline.sh'] checksums = ['7921fce7fcc3b82575be22d9c36beec961ba2a9fb5262ba16a04090bcbd2e1a6'] diff --git a/easybuild/easyconfigs/v/Visit/Visit-3.4.1-foss-2023a.eb b/easybuild/easyconfigs/v/Visit/Visit-3.4.1-foss-2023a.eb new file mode 100644 index 000000000000..406d78fa3128 --- /dev/null +++ b/easybuild/easyconfigs/v/Visit/Visit-3.4.1-foss-2023a.eb @@ -0,0 +1,64 @@ +easyblock = 'CMakeMake' + +name = 'Visit' +version = '3.4.1' + +homepage = 'https://github.com/visit-dav/visit' +description = """ +VisIt is an Open Source, interactive, scalable, visualization, animation +and analysis tool. From Unix, Windows or Mac workstations, users can +interactively visualize and analyze data ranging in scale from small +(<101 core) desktop-sized projects to large (>105 core) leadership-class +computing facility simulation campaigns. Users can quickly generate +visualizations, animate them through time, manipulate them with a +variety of operators and mathematical expressions, and save the +resulting images and animations for presentations. VisIt contains a rich +set of visualization features to enable users to view a wide variety of +data including scalar and vector fields defined on two- and +three-dimensional (2D and 3D) structured, adaptive and unstructured +meshes. Owing to its customizeable plugin design, VisIt is capabable of +visualizing data from over 120 different scientific data formats. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/visit-dav/visit/releases/download/v%(version)s/'] +sources = ['%(namelower)s%(version)s.tar.gz'] +checksums = ['942108cb294f4c9584a1628225b0be39c114c7e9e01805fb335d9c0b507689f5'] + +builddependencies = [('CMake', '3.26.3')] +dependencies = [ + ('zlib', '1.2.13'), + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('X11', '20230603'), + ('Mesa', '23.1.4'), + ('libglvnd', '1.6.0'), + ('Qt5', '5.15.10'), + ('Qwt', '6.3.0'), + # Visit-3.4.1 needs VTK-9.2.x (not 9.3.x) - https://github.com/visit-dav/visit/issues/19547 + ('VTK', '9.2.6'), + ('FFmpeg', '6.0'), +] + +configopts = "-DVISIT_ZLIB_DIR=$EBROOTZLIB " +configopts += "-DVISIT_VTK_DIR=$EBROOTVTK -DVISIT_VTK_VERSION=$EBVERSIONVTK " +configopts += "-DVISIT_QWT_DIR=$EBROOTQWT " +configopts += "-DVISIT_QT_VERSION=$EBVERSIONQT5 -DVISIT_QT_DIR=$EBROOTQT5 " +configopts += "-DVISIT_OSMESA_DIR=$EBROOTMESA " +configopts += "-DVISIT_MESAGL_DIR=$EBROOTLIBGLVND " +configopts += "-DPYTHON_DIR=$EBROOTPYTHON " +configopts += "-DVISIT_PYTHON_SKIP_INSTALL=ON " +configopts += "-DVISIT_PARALLEL=ON -DVISIT_MPI_COMPILER=$MPICC -DVISIT_MPI_COMPILER_CXX=$MPICXX " +configopts += "-DOpenGL_GL_PREFERENCE=GLVND " + +# add missing include to fix make step +prebuildopts = "sed -i '23 a #include ' %(builddir)s/%(namelower)s%(version)s/src/gui/QvisStripChart.C && " + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['frontendlauncher', 'frontendlauncher.py', 'visit']], + 'dirs': ['%(version)s/bin'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/v/vcflib/vcflib-1.0.9-foss-2022b-R-4.2.2.eb b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.9-foss-2022b-R-4.2.2.eb new file mode 100644 index 000000000000..d22ff1aee079 --- /dev/null +++ b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.9-foss-2022b-R-4.2.2.eb @@ -0,0 +1,81 @@ +# Author: Jasper Grimm (UoY) +# Updated: Denis Kristak (INUITS) +# Updated: Petr Král (INUITS) +easyblock = 'CMakeMake' + +name = 'vcflib' +version = '1.0.9' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/vcflib/vcflib' +description = """vcflib provides methods to manipulate and interpret sequence variation as it can be + described by VCF. The Variant Call Format (VCF) is a flat-file, tab-delimited textual format intended + to concisely describe reference-indexed genetic variations between individuals.""" + +toolchain = {'name': 'foss', 'version': '2022b'} +toolchainopts = {'openmp': True} + +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'vcflib-1.0.9_use-external-deps_and_fix_shared_lib.patch', +] +checksums = [ + {'v1.0.9.tar.gz': 'd17fcf8a34d65f1dfecf4b4290d058be744422b6baf34ecdef8ea912d59a4569'}, + {'vcflib-1.0.9_use-external-deps_and_fix_shared_lib.patch': + '82f622a6b4bac1501b10bbc82c4e6567e095869c17b7d34d92b8c4836816b5a1'}, +] + +builddependencies = [ + ('CMake', '3.24.3'), + ('pkgconf', '1.9.3'), + ('pybind11', '2.10.3'), +] + +dependencies = [ + ('Python', '3.10.8'), + ('Perl', '5.36.0'), + ('R', '4.2.2'), + ('XZ', '5.2.7'), + ('zlib', '1.2.12'), + ('bzip2', '1.0.8'), + ('HTSlib', '1.17'), + ('tabixpp', '1.1.2'), + ('intervaltree', '0.1'), + ('fastahack', '1.0.0'), + ('filevercmp', '20191210'), + ('fsom', '20151117'), + ('multichoose', '1.0.3'), + ('smithwaterman', '20160702'), + ('WFA2', '2.3.4'), +] + +preconfigopts = "find %(builddir)s/%(name)s-%(version)s/src -type f " +preconfigopts += r"-regextype egrep -regex '.*\.(h|cpp)' -exec sed -i" +preconfigopts += " -e 's|SmithWatermanGotoh.h|smithwaterman/SmithWatermanGotoh.h|g'" +preconfigopts += " -e 's|IntervalTree.h|intervaltree/IntervalTree.h|g'" +preconfigopts += " -e 's|multichoose.h|multichoose/multichoose.h|g' -e 's|filevercmp.h|filevercmp/filevercmp.h|g'" +preconfigopts += " -e 's|tabix.hpp|tabixpp/tabix.hpp|g' -e 's|Fasta.h|fastahack/Fasta.h|g'" +preconfigopts += r" -e 's|disorder.h|smithwaterman/disorder.h|g' {} \; && " + +configopts = "-DZIG=OFF -DWFA_GITMODULE=OFF -DWFA_INCLUDE_DIRS=$EBROOTWFA2/include/wfa2lib " +configopts += "-DPYTHON_EXECUTABLE=$EBROOTPYTHON/bin/python" + +postinstallcmds = ["cp -r %(builddir)s/%(name)s-%(version)s/scripts %(installdir)s"] + +modextrapaths = { + 'PATH': 'scripts', + 'PYTHONPATH': 'lib', +} + +sanity_check_paths = { + 'files': ['bin/vcffilter', 'bin/vcfcombine', 'lib/libvcflib.a', 'lib/libvcflib.%s' % SHLIB_EXT], + 'dirs': ['scripts', 'include'], +} + +sanity_check_commands = [ + "python -c 'import pyvcflib'", + "vcfwave --help", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/v/velocyto/velocyto-0.17.17-foss-2023a.eb b/easybuild/easyconfigs/v/velocyto/velocyto-0.17.17-foss-2023a.eb new file mode 100644 index 000000000000..344d3ab38958 --- /dev/null +++ b/easybuild/easyconfigs/v/velocyto/velocyto-0.17.17-foss-2023a.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonBundle' + +name = 'velocyto' +version = '0.17.17' + +homepage = 'https://velocyto.org/velocyto.py/' +description = "Velocyto is a library for the analysis of RNA velocity." + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('matplotlib', '3.7.2'), + ('numba', '0.58.1'), + ('scikit-learn', '1.3.1'), + ('h5py', '3.9.0'), + ('Pysam', '0.22.0'), + ('loompy', '3.0.7'), +] + +use_pip = True + +exts_list = [ + (name, version, { + 'checksums': ['1ad65fc53292ce1970a70bc742d73491b370038e0b0065761303e787bf7ffe39'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/velocyto'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['velocyto'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/v/vigra/vigra-1.11.2-foss-2023a.eb b/easybuild/easyconfigs/v/vigra/vigra-1.11.2-foss-2023a.eb new file mode 100644 index 000000000000..6df5b9c0895d --- /dev/null +++ b/easybuild/easyconfigs/v/vigra/vigra-1.11.2-foss-2023a.eb @@ -0,0 +1,48 @@ +easyblock = 'CMakePythonPackage' + +name = 'vigra' +version = '1.11.2' + +homepage = 'https://ukoethe.github.io/vigra/' +description = """Vision with Generic Algorithms is an image processing and analysis library +that puts its main emphasis on customizable algorithms and data structures.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/ukoethe/vigra/archive/'] +sources = ['Version-1-11-2.tar.gz'] +checksums = ['4841936f5c3c137611ec782e293d961df29d3b5b70ade8cb711374de0f4cb5d3'] + +builddependencies = [ + ('CMake', '3.26.3'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('Boost.Python', '1.82.0'), + ('libjpeg-turbo', '2.1.5.1'), + ('OpenJPEG', '2.5.0'), + ('LibTIFF', '4.5.0'), + ('libpng', '1.6.39'), + ('OpenEXR', '3.1.7'), + ('HDF5', '1.14.0'), + ('FFTW', '3.3.10'), + ('nose3', '1.3.8'), +] + +# Fix python files path in make install step +_py_path = "%(builddir)s/%(name)s-Version-1-11-2/config/FindVIGRANUMPY_DEPENDENCIES.cmake" +_py_add = "SET(VIGRANUMPY_INSTALL_DIR ${CMAKE_INSTALL_PREFIX}/lib/python%(pyshortver)s/site-packages)" +preinstallopts = "sed -i '90,91d' %s && " % _py_path +preinstallopts += "sed -i '94d' %s && " % _py_path +preinstallopts += r"sed -i '89 a\%s' %s && " % (_py_add, _py_path) + +sanity_check_paths = { + 'files': ['bin/vigra-config'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/vigra'], +} + +sanity_check_commands = ["vigra-config --version", "python -c 'import vigra'"] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/v/virtualenv/virtualenv-20.23.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/v/virtualenv/virtualenv-20.23.1-GCCcore-12.3.0.eb index 122f3d8d6c83..c36c435d1da7 100644 --- a/easybuild/easyconfigs/v/virtualenv/virtualenv-20.23.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/v/virtualenv/virtualenv-20.23.1-GCCcore-12.3.0.eb @@ -18,11 +18,8 @@ dependencies = [ ('Python', '3.11.3'), ] -exts_default_options = { - 'download_dep_fail': True, - 'sanity_pip_check': True, - 'use_pip': True, -} +sanity_pip_check = True +use_pip = True exts_list = [ ('distlib', '0.3.6', { diff --git a/easybuild/easyconfigs/v/virtualenv/virtualenv-20.24.6-GCCcore-13.2.0.eb b/easybuild/easyconfigs/v/virtualenv/virtualenv-20.24.6-GCCcore-13.2.0.eb index a0b9921fb5cc..2820042ba9de 100644 --- a/easybuild/easyconfigs/v/virtualenv/virtualenv-20.24.6-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/v/virtualenv/virtualenv-20.24.6-GCCcore-13.2.0.eb @@ -18,11 +18,8 @@ dependencies = [ ('Python', '3.11.5'), ] -exts_default_options = { - 'download_dep_fail': True, - 'sanity_pip_check': True, - 'use_pip': True, -} +sanity_pip_check = True +use_pip = True exts_list = [ ('distlib', '0.3.7', { diff --git a/easybuild/easyconfigs/v/virtualenv/virtualenv-20.26.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/v/virtualenv/virtualenv-20.26.2-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..65f1ced6caeb --- /dev/null +++ b/easybuild/easyconfigs/v/virtualenv/virtualenv-20.26.2-GCCcore-13.3.0.eb @@ -0,0 +1,46 @@ +easyblock = 'PythonBundle' + +name = 'virtualenv' +version = '20.26.2' + +homepage = 'https://github.com/pypa/virtualenv' +description = "A tool for creating isolated virtual python environments." + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +builddependencies = [ + ('binutils', '2.42'), + ('hatchling', '1.24.2'), +] + +dependencies = [ + ('Python', '3.12.3'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('distlib', '0.3.8', { + 'checksums': ['1530ea13e350031b6312d8580ddb6b27a104275a31106523b8f123787f494f64'], + }), + ('filelock', '3.15.1', { + 'checksums': ['58a2549afdf9e02e10720eaa4d4470f56386d7a6f72edd7d0596337af8ed7ad8'], + }), + ('platformdirs', '4.2.2', { + 'checksums': ['38b7b51f512eed9e84a22788b4bce1de17c0adb134d6becb09836e37d8654cd3'], + }), + (name, version, { + 'checksums': ['82bf0f4eebbb78d36ddaee0283d43fe5736b53880b8a8cdcd37390a07ac3741c'], + }), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], +} + +sanity_check_commands = ["virtualenv --help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/w/WFA2/WFA2-2.3.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/w/WFA2/WFA2-2.3.4-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..cef70fe1233c --- /dev/null +++ b/easybuild/easyconfigs/w/WFA2/WFA2-2.3.4-GCCcore-12.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'CMakeMake' + +name = 'WFA2' +version = '2.3.4' + +homepage = 'https://github.com/smarco/WFA2-lib' +description = """The wavefront alignment (WFA) algorithm is an exact + gap-affine algorithm that takes advantage of homologous regions + between the sequences to accelerate the alignment process.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/smarco/WFA2-lib/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['3a02d19b45c7efcdcabdd956421b1e449e771fca0b0f072e02d7aa65ebb29f23'] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), + ('pkgconf', '1.9.3'), +] + +configopts = "-DOPENMP=ON" + +sanity_check_paths = { + 'files': ['lib/libwfa2.a'], + 'dirs': ['include/wfa2lib'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-23.2-intel-2021b.eb b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-23.2-intel-2021b.eb index a8881dbe1180..0dd0b641cebf 100644 --- a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-23.2-intel-2021b.eb +++ b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-23.2-intel-2021b.eb @@ -61,6 +61,10 @@ fix_perl_shebang_for = [ 'bashtime2csh.pl_lapw', ] +# skip running of serial/parallel benchmark, because links to download test_case.tar.gz and mpi-benchmark.tar.gz +# from http://www.wien2k.at/reg_user/benchmark/ that are used by WIEN2k easyblock are broken... +runtest = False + tests = [ # test case 1: NaCl ('NaCl', '-b', '-i 100', [r'^:DIS.*0.1', r'^:ENE.*-1248.1']), diff --git a/easybuild/easyconfigs/w/WRF/WRF-4.5.1-foss-2023a-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-4.5.1-foss-2023a-dmpar.eb new file mode 100644 index 000000000000..5b7d53ec8377 --- /dev/null +++ b/easybuild/easyconfigs/w/WRF/WRF-4.5.1-foss-2023a-dmpar.eb @@ -0,0 +1,45 @@ +name = 'WRF' +version = '4.5.1' +buildtype = 'dmpar' +versionsuffix = '-%s' % buildtype + +homepage = 'https://www.wrf-model.org' +description = """The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale + numerical weather prediction system designed to serve both operational forecasting and atmospheric + research needs.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'opt': False} # don't use agressive optimization, stick to -O2 + +github_account = 'wrf-model' +source_urls = [GITHUB_RELEASE] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'WRF-4.5.1_netCDF-Fortran_separate_path.patch', # note: no longer required for version 4.5.2 +] +checksums = [ + {'v4.5.1.tar.gz': '9d557c34c105db4d41e727843ecb19199233c7cf82c5369b34a2ce8efe65e2d1'}, + {'WRF-4.5.1_netCDF-Fortran_separate_path.patch': + '951bff9a3fc651482b287cc03a9f3197979b7800d515fe61cc9c932d9e0dc62e'}, +] + +# csh is used by WRF install scripts +builddependencies = [ + ('Autotools', '20220317'), + ('tcsh', '6.24.10'), + ('time', '1.9'), + ('Perl', '5.36.1'), +] + +dependencies = [ + ('JasPer', '4.0.0'), + ('netCDF', '4.9.2'), + ('netCDF-Fortran', '4.6.1'), +] + +runtest = True + +# limit parallel build to 20 +maxparallel = 20 + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/w/WRF/WRF-4.5.1_netCDF-Fortran_separate_path.patch b/easybuild/easyconfigs/w/WRF/WRF-4.5.1_netCDF-Fortran_separate_path.patch new file mode 100644 index 000000000000..2e35f0dbb86a --- /dev/null +++ b/easybuild/easyconfigs/w/WRF/WRF-4.5.1_netCDF-Fortran_separate_path.patch @@ -0,0 +1,300 @@ +# Allow netCDF library with separate directories for C and Fortran +# ============================================================================ +# This patch has been around in EasyBuild since WRF3.5; it was committed by +# @boegel then. Adapted by @andreas-h to accomodate WRFv4 and foss toolchain +# +# updated for WPS v4.4 by Maxim Masterov (SURF) +# updated for WRF v4.5.1 by Stefan Wolfsheimer (SURF) + + +diff -Nru WRFV4.5.1.orig/arch/Config.pl WRFV4.5.1/arch/Config.pl +--- WRFV4.5.1.orig/arch/Config.pl 2023-07-25 23:14:55.214200451 +0200 ++++ WRFV4.5.1/arch/Config.pl 2023-09-07 18:29:05.423831752 +0200 +@@ -11,6 +11,7 @@ + select((select(STDOUT), $|=1)[0]); + $sw_perl_path = perl ; + $sw_netcdf_path = "" ; ++$sw_netcdff_path = "" ; + $sw_pnetcdf_path = "" ; + $sw_netcdfpar_path = "" ; + $sw_adios2_path = "" ; +@@ -96,6 +97,10 @@ + } + } + } ++ if ( substr( $ARGV[0], 1, 8 ) eq "netcdff=" ) ++ { ++ $sw_netcdff_path = substr( $ARGV[0], 9 ) ; ++ } + if ( substr( $ARGV[0], 1, 8 ) eq "pnetcdf=" ) + { + $sw_pnetcdf_path = substr( $ARGV[0], 9 ) ; +@@ -130,7 +135,8 @@ + } + if ( substr( $ARGV[0], 1, 11 ) eq "USENETCDFF=" ) + { +- $sw_usenetcdff = substr( $ARGV[0], 12 ) ; ++ $sw_usenetcdff = substr( $ARGV[0], 12 ) ; ++ $sw_usenetcdff =~ s/!/ /g ; + } + if ( substr( $ARGV[0], 1, 10 ) eq "USENETCDF=" ) + { +@@ -615,6 +621,7 @@ + { + $_ =~ s/CONFIGURE_PERL_PATH/$sw_perl_path/g ; + $_ =~ s/CONFIGURE_NETCDF_PATH/$sw_netcdf_path/g ; ++ $_ =~ s/CONFIGURE_NETCDFF_PATH/$sw_netcdff_path/g ; + $_ =~ s/CONFIGURE_PNETCDF_PATH/$sw_pnetcdf_path/g ; + $_ =~ s/CONFIGURE_NETCDFPAR_PATH/$sw_netcdfpar_path/g ; + $_ =~ s/CONFIGURE_ADIOS2_PATH/$sw_adios2_path/g ; +@@ -666,7 +673,7 @@ + } elsif ( $sw_os eq "Interix" ) { + $_ =~ s:CONFIGURE_NETCDFPAR_LIB_PATH:\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdfpar/libwrfio_nfpar.a -L$sw_netcdfpar_path/lib $sw_usenetcdff $sw_usenetcdf : ; + } else { +- $_ =~ s:CONFIGURE_NETCDFPAR_LIB_PATH:-L\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdfpar -lwrfio_nfpar -L$sw_netcdfpar_path/lib $sw_usenetcdff $sw_usenetcdf : ; ++ $_ =~ s:CONFIGURE_NETCDFPAR_LIB_PATH:-L\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdfpar -lwrfio_nfpar -L$sw_netcdfpar_path/lib $sw_usenetcdff $sw_usenetcdf : ; + } + } + else +@@ -684,7 +691,7 @@ + } elsif ( $sw_os eq "Interix" ) { + $_ =~ s:CONFIGURE_NETCDF_LIB_PATH:\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdf/libwrfio_nf.a -L$sw_netcdf_path/lib $sw_usenetcdff $sw_usenetcdf : ; + } else { +- $_ =~ s:CONFIGURE_NETCDF_LIB_PATH:-L\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdf -lwrfio_nf -L$sw_netcdf_path/lib $sw_usenetcdff $sw_usenetcdf : ; ++ $_ =~ s:CONFIGURE_NETCDF_LIB_PATH:-L\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdf -lwrfio_nf -L$sw_netcdff_path/lib -L$sw_netcdf_path/lib64 $sw_usenetcdff $sw_usenetcdf : ; + } + } + else +@@ -1072,7 +1079,7 @@ + } elsif ( $sw_os eq "Interix" ) { + $_ =~ s:CONFIGURE_NETCDF_LIB_PATH:\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdf/libwrfio_nf.a -L$sw_netcdf_path/lib $sw_usenetcdff $sw_usenetcdf : ; + } else { +- $_ =~ s:CONFIGURE_NETCDF_LIB_PATH:-L\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdf -lwrfio_nf -L$sw_netcdf_path/lib $sw_usenetcdff $sw_usenetcdf : ; ++ $_ =~ s:CONFIGURE_NETCDF_LIB_PATH:-L\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdf -lwrfio_nf -L$sw_netcdff_path/lib -L$sw_netcdf_path/lib $sw_usenetcdff $sw_usenetcdf : ; + } + } + else +diff -Nru WRFV4.5.1.orig/arch/configure.defaults WRFV4.5.1/arch/configure.defaults +--- WRFV4.5.1.orig/arch/configure.defaults 2023-07-25 23:14:55.215890637 +0200 ++++ WRFV4.5.1/arch/configure.defaults 2023-09-07 14:20:06.651406753 +0200 +@@ -1638,6 +1638,7 @@ + + LIB_EXTERNAL = \ + ../external/io_netcdf/libwrfio_nf.a CONFIGURE_NETCDF_PATH/lib/libnetcdf.lib \ ++ CONFIGURE_NETCDFF_PATH/lib/libnetcdff.lib \ + ../external/wavelet/libWavelet.a ../external/wavelet/lib_wavelet.a + ESMF_IO_LIB = ../external/esmf_time_f90/libesmf_time.a + LIB_BUNDLED = \ +diff -Nru WRFV4.5.1.orig/arch/conf_tokens WRFV4.5.1/arch/conf_tokens +--- WRFV4.5.1.orig/arch/conf_tokens 2023-07-25 23:14:55.215165000 +0200 ++++ WRFV4.5.1/arch/conf_tokens 2023-09-07 14:20:50.194754577 +0200 +@@ -5,6 +5,7 @@ + CONFIGURE_DMPARALLEL + CONFIGURE_RWORDSIZE + CONFIGURE_NETCDF_FLAG ++CONFIGURE_NETCDFF_FLAG + CONFIGURE_GRIB2_FLAG + CONFIGURE_NETCDF_LIB_PATH + CONFIGURE_GRIB2_LIB +@@ -13,4 +14,5 @@ + CONFIGURE_WRFIO_NF + CONFIGURE_WRFIO_GRIB2 + CONFIGURE_NETCDF_PATH ++CONFIGURE_NETCDFF_PATH + CONFIGURE_GRIB2_INC +diff -Nru WRFV4.5.1.orig/arch/postamble WRFV4.5.1/arch/postamble +--- WRFV4.5.1.orig/arch/postamble 2023-07-25 23:14:55.219090000 +0200 ++++ WRFV4.5.1/arch/postamble 2023-09-07 16:01:17.500706228 +0200 +@@ -54,6 +54,7 @@ + -I$(WRF_SRC_ROOT_DIR)/phys \ + -I$(WRF_SRC_ROOT_DIR)/wrftladj \ + -I$(WRF_SRC_ROOT_DIR)/chem -I$(WRF_SRC_ROOT_DIR)/inc \ ++ -I$(NETCDFPATH)/include -I$(NETCDFFPATH)/include \ + -I$(NETCDFPATH)/include \ + CONFIGURE_RTTOV_INC CONFIGURE_CTSM_INC + REGISTRY = Registry +@@ -64,6 +65,7 @@ + ENVCOMPDEFS = CONFIGURE_COMPILEFLAGS + CPPFLAGS = $(ARCHFLAGS) $(ENVCOMPDEFS) -I$(LIBINCLUDE) $(TRADFLAG) CONFIGURE_COMMS_INCLUDE + NETCDFPATH = CONFIGURE_NETCDF_PATH ++NETCDFFPATH = CONFIGURE_NETCDFF_PATH + HDF5PATH = CONFIGURE_HDF5_PATH + WRFPLUSPATH = CONFIGURE_WRFPLUS_PATH + RTTOVPATH = CONFIGURE_RTTOV_PATH +@@ -96,18 +98,18 @@ + + wrfio_nf : + ( cd $(WRF_SRC_ROOT_DIR)/external/io_netcdf ; \ +- make $(J) NETCDFPATH="$(NETCDFPATH)" RANLIB="$(RANLIB)" CPP="$(CPP)" \ ++ make $(J) NETCDFPATH="$(NETCDFPATH)" NETCDFFPATH="$(NETCDFFPATH)" RANLIB="$(RANLIB)" CPP="$(CPP)" \ + CC="$(SCC)" CFLAGS="$(CFLAGS)" \ + FC="$(SFC) $(PROMOTION) $(OMP) $(FCFLAGS)" TRADFLAG="$(TRADFLAG)" AR="$(AR)" ARFLAGS="$(ARFLAGS)" ) + + wrfio_nfpar : + ( cd $(WRF_SRC_ROOT_DIR)/external/io_netcdfpar ; \ +- make $(J) NETCDFPARPATH="$(NETCDFPATH)" RANLIB="$(RANLIB)" CPP="$(CPP) $(ARCHFLAGS)" \ ++ make $(J) NETCDFPARPATH="$(NETCDFPATH)" NETCDFFPATH="$(NETCDFFPATH)" RANLIB="$(RANLIB)" CPP="$(CPP) $(ARCHFLAGS)" \ + FC="$(FC) $(PROMOTION) $(OMP) $(FCFLAGS)" TRADFLAG="$(TRADFLAG)" AR="$(AR)" ARFLAGS="$(ARFLAGS)" ) + + wrfio_pnf : + ( cd $(WRF_SRC_ROOT_DIR)/external/io_pnetcdf ; \ +- make $(J) NETCDFPATH="$(PNETCDFPATH)" RANLIB="$(RANLIB)" CPP="$(CPP) $(ARCHFLAGS)" \ ++ make $(J) NETCDFPATH="$(PNETCDFPATH)" NETCDFFPATH="$(PNETCDFPATH)" RANLIB="$(RANLIB)" CPP="$(CPP) $(ARCHFLAGS)" \ + FC="$(FC) $(PROMOTION) $(OMP) $(FCFLAGS)" TRADFLAG="$(TRADFLAG)" AR="$(AR)" ARFLAGS="$(ARFLAGS)" ) + + wrfio_adios2 : +diff -Nru WRFV4.5.1.orig/configure WRFV4.5.1/configure +--- WRFV4.5.1.orig/configure 2023-07-25 23:14:55.692864209 +0200 ++++ WRFV4.5.1/configure 2023-09-08 11:40:15.875789587 +0200 +@@ -214,17 +214,19 @@ + unset NETCDF4 + fi + +-USENETCDFF="" ++if [ -f "$NETCDFF/lib/libnetcdff.a" -o -f "$NETCDFF/lib/libnetcdff.so" -o -f "$NETCDFF/lib64/libnetcdff.so" -o -f "$NETCDFF/lib64/libnetcdff.so" ] ; then ++ USENETCDFF="-L$NETCDFF/lib!-L$NETCDFF/lib64!-lnetcdff" # ! will be replaced with space ++else ++ USENETCDFF=" " ++fi + USENETCDF="" + if [ -n "$NETCDF" ] ; then + echo "Will use NETCDF in dir: $NETCDF" + # Oh UNIDATA, why make it so hard ... + if [ -f "$NETCDF/lib/libnetcdff.a" -o -f "$NETCDF/lib/libnetcdff.so" -o -f "$NETCDF/lib/libnetcdff.dll.a" ] ; then + USENETCDFF="-lnetcdff" +- else +- USENETCDFF=" " + fi +- if [ -f "$NETCDF/lib/libnetcdf.a" -o -f "$NETCDF/lib/libnetcdf.so" -o -f "$NETCDF/lib/libnetcdf.dll.a" ] ; then ++ if [ -f "$NETCDF/lib/libnetcdf.a" -o -f "$NETCDF/lib/libnetcdf.so" -o -f "$NETCDF/lib64/libnetcdf.a" -o -f "$NETCDF/lib64/libnetcdf.so" ] ; then + USENETCDF="-lnetcdf" + else + USENETCDF=" " +@@ -572,7 +574,7 @@ + srch=`grep -i "^#ARCH.*$os" arch/configure.defaults | grep -i "$mach"` + if [ -n "$srch" ] ; then + $PERL arch/Config.pl -dmparallel=$COMMLIB -ompparallel=$OMP -perl=$PERL \ +- -netcdf=$NETCDF -pnetcdf=$PNETCDF -netcdfpar=$NETCDFPAR -adios2=$ADIOS2 -hdf5=$HDF5 -phdf5=$PHDF5 -os=$os -mach=$mach -ldflags=$ldflags \ ++ -netcdf=$NETCDF -netcdff=$NETCDFF -pnetcdf=$PNETCDF -netcdfpar=$NETCDFPAR -hdf5=$HDF5 -phdf5=$PHDF5 -os=$os -mach=$mach -ldflags=$ldflags \ + -compileflags=$compileflags -opt_level=$opt_level -USENETCDFF=$USENETCDFF -USENETCDF=$USENETCDF \ + -time=$FORTRAN_COMPILER_TIMER -tfl="$TFL" -cfl="$CFL" -config_line="$config_line" \ + -wrf_core=$wrf_core -gpfs=$GPFS_PATH -curl=$CURL_PATH -dep_lib_path="$DEP_LIB_PATH" +@@ -654,14 +656,14 @@ + echo "If you wish to change the default options, edit the file:" + echo " arch/configure.defaults" + +-if test -n "$NETCDF" ; then +- if [ ! -f $NETCDF/include/netcdf.inc ] ; then ++if test -n "$NETCDFF" ; then ++ if [ ! -f $NETCDFF/include/netcdf.inc ] ; then + echo +- echo "Error : Not found $NETCDF/include/netcdf.inc" ++ echo "Error : Not found $NETCDFF/include/netcdf.inc" + echo " Please check this installation of NetCDF and re-run this configure script" + exit -1 + fi +- grep nf_format_64bit $NETCDF/include/netcdf.inc > /dev/null ++ grep nf_format_64bit $NETCDFF/include/netcdf.inc > /dev/null + configure_aaaa=$? ; export configure_aaaa + if [ $configure_aaaa -a -z "$WRFIO_NCD_NO_LARGE_FILE_SUPPORT" ] ; then + echo "NetCDF users note:" +diff -Nru WRFV4.5.1.orig/external/io_netcdf/makefile WRFV4.5.1/external/io_netcdf/makefile +--- WRFV4.5.1.orig/external/io_netcdf/makefile 2023-07-25 23:14:55.935985000 +0200 ++++ WRFV4.5.1/external/io_netcdf/makefile 2023-09-07 14:33:23.630405047 +0200 +@@ -3,9 +3,9 @@ + OBJSL = wrf_io.o field_routines.o module_wrfsi_static.o + OBJS = $(OBJSL) + CODE = ext_ncd_get_dom_ti.code ext_ncd_get_var_td.code ext_ncd_get_var_ti.code ext_ncd_put_dom_ti.code ext_ncd_put_var_td.code ext_ncd_put_var_ti.code transpose.code +-FFLAGS = $(FCFLAGS) -I$(NETCDFPATH)/include -I../ioapi_share +-LIBS = $(LIB_LOCAL) -L$(NETCDFPATH)/lib -lnetcdf +-LIBFFS = $(LIB_LOCAL) -L$(NETCDFPATH)/lib -lnetcdff -lnetcdf $(NETCDF4_DEP_LIB) ++FFLAGS = $(FCFLAGS) -I$(NETCDFFPATH)/include -I../ioapi_share ++LIBS = $(LIB_LOCAL) -L$(NETCDFPATH)/lib -L$(NETCDFPATH)/lib64 -lnetcdf ++LIBFFS = $(LIB_LOCAL) -L$(NETCDFPATH)/lib -L$(NETCDFPATH)/lib64 -L$(NETCDFFPATH)/lib -L$(NETCDFFPATH)/lib64 -lnetcdff -lnetcdf $(NETCDF4_DEP_LIB) + CPP1 = $(CPP) -P $(TRADFLAG) + M4 = m4 -Uinclude -Uindex -Ulen + AR = ar +@@ -24,7 +24,7 @@ + $(RANLIB) $@ + + wrf_io.o: wrf_io.F90 $(CODE) +- grep nf_format_64bit $(NETCDFPATH)/include/netcdf.inc ;\ ++ grep nf_format_64bit $(NETCDFFPATH)/include/netcdf.inc ;\ + a=$$? ; export a ; \ + if [ $$a -a "$$WRFIO_NCD_LARGE_FILE_SUPPORT" = "1" ] ; then \ + $(CPP1) -DWRFIO_NCD_LARGE_FILE_SUPPORT -I../ioapi_share wrf_io.F90 | $(M4) - > wrf_io.f ; \ +@@ -43,14 +43,14 @@ + x=`echo "$(FC)" | awk '{print $$1}'` ; export x ; \ + if [ $$x = "gfortran" ] ; then \ + echo removing external declaration of iargc for gfortran ; \ +- $(CPP1) -I$(NETCDFPATH)/include -I../ioapi_share diffwrf.F90 | sed '/integer *, *external.*iargc/d' > diffwrf.f ;\ ++ $(CPP1) -I$(NETCDFFPATH)/include -I../ioapi_share diffwrf.F90 | sed '/integer *, *external.*iargc/d' > diffwrf.f ;\ + else \ +- $(CPP1) -I$(NETCDFPATH)/include -I../ioapi_share diffwrf.F90 > diffwrf.f ; \ ++ $(CPP1) -I$(NETCDFFPATH)/include -I../ioapi_share diffwrf.F90 > diffwrf.f ; \ + fi + $(FC) -c $(FFLAGS) diffwrf.f + @if [ \( -f ../../frame/wrf_debug.o \) -a \( -f ../../frame/module_wrf_error.o \) -a \( -f $(ESMF_MOD_DEPENDENCE) \) -a \( -f ../../frame/clog.o \) ] ; then \ + echo "diffwrf io_netcdf is being built now. " ; \ +- if [ \( -f $(NETCDFPATH)/lib/libnetcdff.a -o -f $(NETCDFPATH)/lib/libnetcdff.so -o -f $(NETCDFPATH)/lib/libnetcdff.dll.a \) ] ; then \ ++ if [ \( -f $(NETCDFFPATH)/lib/libnetcdff.a -o -f $(NETCDFFPATH)/lib/libnetcdff.so -o -f $(NETCDFFPATH)/lib/libnetcdff.dll.a \) ] ; then \ + $(FC) $(FFLAGS) $(LDFLAGS) -o diffwrf diffwrf.o $(OBJSL) ../../frame/wrf_debug.o ../../frame/module_wrf_error.o ../../frame/clog.o $(ESMF_IO_LIB_EXT) $(LIBFFS) ;\ + else \ + $(FC) $(FFLAGS) $(LDFLAGS) -o diffwrf diffwrf.o $(OBJSL) ../../frame/wrf_debug.o ../../frame/module_wrf_error.o ../../frame/clog.o $(ESMF_IO_LIB_EXT) $(LIBS) ;\ +diff -Nru WRFV4.5.1.orig/external/io_pnetcdf/Makefile WRFV4.5.1/external/io_pnetcdf/Makefile +--- WRFV4.5.1.orig/external/io_pnetcdf/Makefile 2023-07-25 23:14:55.952757000 +0200 ++++ WRFV4.5.1/external/io_pnetcdf/Makefile 2023-09-07 14:34:31.077960575 +0200 +@@ -9,8 +9,8 @@ + ext_pnc_put_var_td.code \ + ext_pnc_put_var_ti.code \ + transpose.code +-FFLAGS = $(FCFLAGS) -I$(NETCDFPATH)/include -I../ioapi_share +-LIBS = -L$(NETCDFPATH)/lib -lpnetcdf ++FFLAGS = $(FCFLAGS) -I$(NETCDFFPATH)/include -I../ioapi_share ++LIBS = -L$(NETCDFFPATH)/lib -lpnetcdf + CPP1 = $(CPP) -P $(TRADFLAG) + M4 = m4 -Uinclude -Uindex -Ulen + AR = ar +@@ -25,15 +25,15 @@ + $(RANLIB) libwrfio_pnf.a + + wrf_io.o: wrf_io.F90 $(CODE) +- $(CPP1) -I$(NETCDFPATH)/include -I../ioapi_share wrf_io.F90 | $(M4) - > wrf_io.f ++ $(CPP1) -I$(NETCDFFPATH)/include -I../ioapi_share wrf_io.F90 | $(M4) - > wrf_io.f + $(FC) $(FFLAGS) -c wrf_io.f + + module_wrfsi_static.o: module_wrfsi_static.F90 +- $(CPP1) -I$(NETCDFPATH)/include -I../ioapi_share module_wrfsi_static.F90 > module_wrfsi_static.f ++ $(CPP1) -I$(NETCDFFPATH)/include -I../ioapi_share module_wrfsi_static.F90 > module_wrfsi_static.f + $(FC) $(FFLAGS) -c module_wrfsi_static.f + + field_routines.o: field_routines.F90 wrf_io.o +- $(CPP1) -I$(NETCDFPATH)/include -I../ioapi_share field_routines.F90 > field_routines.f ++ $(CPP1) -I$(NETCDFFPATH)/include -I../ioapi_share field_routines.F90 > field_routines.f + $(FC) $(FFLAGS) -c field_routines.f + + superclean: +diff -Nru WRFV4.5.1.orig/Makefile WRFV4.5.1/Makefile +--- WRFV4.5.1.orig/Makefile 2023-07-25 23:14:55.185289891 +0200 ++++ WRFV4.5.1/Makefile 2023-09-07 14:36:58.707252929 +0200 +@@ -923,7 +923,7 @@ + @ echo '--------------------------------------' + ( cd frame ; $(MAKE) $(J) LLIST="$(LINKLIST)" framework ; \ + cd ../external/io_netcdf ; \ +- $(MAKE) NETCDFPATH="$(NETCDFPATH)" \ ++ $(MAKE) NETCDFPATH="$(NETCDFPATH)" NETCDFFPATH="$(NETCDFFPATH)" \ + FC="$(FC) $(FCBASEOPTS) $(PROMOTION) $(FCDEBUG) $(OMP)" RANLIB="$(RANLIB)" \ + CPP="$(CPP)" LDFLAGS="$(LDFLAGS)" TRADFLAG="$(TRADFLAG)" ESMF_IO_LIB_EXT="$(ESMF_IO_LIB_EXT)" \ + LIB_LOCAL="$(LIB_LOCAL)" \ +@@ -1070,9 +1070,9 @@ + # rule used by configure to test if this will compile with netcdf4 + nc4_test: + if [ $(USENETCDFPAR) -eq 0 ] ; then \ +- ( cd tools ; /bin/rm -f nc4_test.{exe,nc,o} ; $(SCC) -o nc4_test.exe nc4_test.c -I$(NETCDF)/include -L$(NETCDF)/lib -lnetcdf $(NETCDF4_DEP_LIB) ; cd .. ) ; \ ++ ( cd tools ; /bin/rm -f nc4_test.{exe,nc,o} ; $(SCC) -o nc4_test.exe nc4_test.c -I$(NETCDF)/include -L$(NETCDF)/lib64 -lnetcdf $(NETCDF4_DEP_LIB) ; cd .. ) ; \ + else \ +- ( cd tools ; /bin/rm -f nc4_test.{exe,nc,o} ; $(DM_CC) -o nc4_test.exe nc4_test.c -I$(NETCDF)/include -L$(NETCDF)/lib -lnetcdf $(NETCDF4_DEP_LIB) ; cd .. ) ; \ ++ ( cd tools ; /bin/rm -f nc4_test.{exe,nc,o} ; $(DM_CC) -o nc4_test.exe nc4_test.c -I$(NETCDF)/include -L$(NETCDF)/lib64 -lnetcdf $(NETCDF4_DEP_LIB) ; cd .. ) ; \ + fi + + # rule used by configure to test if Fortran 2003 IEEE signaling is available diff --git a/easybuild/easyconfigs/w/Wayland/Wayland-1.23.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/w/Wayland/Wayland-1.23.0-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..b774886e5cb2 --- /dev/null +++ b/easybuild/easyconfigs/w/Wayland/Wayland-1.23.0-GCCcore-13.3.0.eb @@ -0,0 +1,63 @@ +# Author: Jasper Grimm (UoY) +# URL of Wayland download changed to GitLab due to changes upstream +# Author: J. Sassmannshausen (Imperial College London/UK) +easyblock = 'Bundle' + +name = 'Wayland' +version = '1.23.0' + +homepage = 'https://wayland.freedesktop.org/' +description = """ +Wayland is a project to define a protocol for a compositor to talk to + its clients as well as a library implementation of the protocol. The + compositor can be a standalone display server running on Linux kernel + modesetting and evdev input devices, an X application, or a wayland + client itself. The clients can be traditional applications, X servers + (rootless or fullscreen) or other display servers. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('CMake', '3.29.3'), + ('Meson', '1.4.0'), + ('Ninja', '1.12.1'), + ('pkgconf', '2.2.0'), + ('binutils', '2.42'), +] + +dependencies = [ + ('libffi', '3.4.5'), + ('expat', '2.6.2'), + ('libxml2', '2.12.7'), +] + +default_easyblock = 'MesonNinja' +default_component_specs = { + 'start_dir': '%(namelower)s-%(version)s', +} + +components = [ + ('wayland', version, { + 'source_urls': ['https://gitlab.freedesktop.org/wayland/%(namelower)s/-/releases/%(version)s/downloads'], + 'checksums': ['05b3e1574d3e67626b5974f862f36b5b427c7ceeb965cb36a4e6c2d342e45ab2'], + 'sources': [SOURCE_TAR_XZ], + 'configopts': "-Ddocumentation=false", + }), + ('wayland-protocols', '1.36', { + 'source_urls': ['https://gitlab.freedesktop.org/wayland/%(namelower)s/-/releases/%(version)s/downloads'], + 'checksums': ['71fd4de05e79f9a1ca559fac30c1f8365fa10346422f9fe795f74d77b9ef7e92'], + 'sources': [SOURCE_TAR_XZ], + 'preconfigopts': "PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH " + }), +] + +_libs = ['lib/libwayland-%s.%s' % (x, SHLIB_EXT) for x in ['client', 'cursor', 'egl', 'server']] +sanity_check_paths = { + 'files': ['bin/wayland-scanner'] + _libs, + 'dirs': ['lib'], +} + +sanity_check_commands = ["wayland-scanner --help", "wayland-scanner --version"] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/w/weblogo/weblogo-2.8.2-foss-2022b.eb b/easybuild/easyconfigs/w/weblogo/weblogo-2.8.2-foss-2022b.eb new file mode 100644 index 000000000000..809231835148 --- /dev/null +++ b/easybuild/easyconfigs/w/weblogo/weblogo-2.8.2-foss-2022b.eb @@ -0,0 +1,45 @@ +easyblock = 'Tarball' + +name = 'weblogo' +version = '2.8.2' + +homepage = "https://weblogo.berkeley.edu" +description = """WebLogo is a web based application designed to make the generation of sequence logos as easy +and painless as possible.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +source_urls = ['https://weblogo.berkeley.edu/release'] +sources = ['weblogo.%(version)s.tar.gz'] +checksums = ['2d3e0040c0c1e363c1dfd57f8b585387eb682ed08b2cc2fe2e4cc2a33ac52266'] + +dependencies = [ + ('Perl', '5.36.0'), + ('Ghostscript', '10.0.0'), + ('ImageMagick', '7.1.0-53'), +] + +postinstallcmds = [ + 'mkdir %(installdir)s/bin', + 'mkdir -p %(installdir)s/lib', + 'mv %(installdir)s/seqlogo %(installdir)s/bin/', + 'cp %(installdir)s/template.eps %(installdir)s/bin/', + 'mv %(installdir)s/*.pm %(installdir)s/lib/', # Move all Perl modules to the lib directory + 'mv %(installdir)s/logo.cgi %(installdir)s/lib/', + 'chmod +x %(installdir)s/bin/seqlogo', +] + +modextrapaths = { + 'PERL5LIB': 'lib', # Use relative path +} + +sanity_check_paths = { + 'files': ['bin/seqlogo', 'lib/logo.pm', 'lib/template.pm'], + 'dirs': [], +} + +sanity_check_commands = [ + "seqlogo -f %(installdir)s/globin.fasta" +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/w/wget/wget-1.21.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/w/wget/wget-1.21.4-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..7dae35b8d9f5 --- /dev/null +++ b/easybuild/easyconfigs/w/wget/wget-1.21.4-GCCcore-12.2.0.eb @@ -0,0 +1,50 @@ +easyblock = 'ConfigureMake' + +name = 'wget' +version = '1.21.4' + +homepage = 'https://www.gnu.org/software/wget' +description = """GNU Wget is a free software package for retrieving files using HTTP, HTTPS and FTP, + the most widely-used Internet protocols. It is a non-interactive commandline tool, + so it may easily be called from scripts, cron jobs, terminals without X-Windows support, etc.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = [ + {SOURCE_TAR_GZ: '81542f5cefb8faacc39bbbc6c82ded80e3e4a88505ae72ea51df27525bcde04c'}, +] + +builddependencies = [ + ('binutils', '2.39'), + ('pkgconf', '1.9.3'), + ('Perl', '5.36.0'), +] +dependencies = [ + ('PCRE', '8.45'), + ('libidn2', '2.3.4'), + ('zlib', '1.2.12'), + ('OpenSSL', '1.1', '', SYSTEM), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date gnutls for security reasons + # ('GnuTLS', '3.7.1'), +] + +# make sure pkgconfig picks up system packages (OpenSSL & co) +local_pc = "%(sysroot)s/usr/lib64/pkgconfig:" +local_pc += "%(sysroot)s/usr/lib/pkgconfig:" +local_pc += "%(sysroot)s/usr/lib/x86_64-linux-gnu/pkgconfig" +preconfigopts = "export PKG_CONFIG_PATH=%s && " % local_pc +configopts = '--with-ssl=openssl ' + +# Optionally, you can use gnutls (default) instead of OpenSSL. +# Do not forget to comment out configopts in that case. +# osdependencies = [('gnutls-devel', 'gnutls-dev', 'libgnutls-devel')] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/w/wradlib/wradlib-2.0.3-foss-2022a.eb b/easybuild/easyconfigs/w/wradlib/wradlib-2.0.3-foss-2022a.eb new file mode 100644 index 000000000000..010b73f371bf --- /dev/null +++ b/easybuild/easyconfigs/w/wradlib/wradlib-2.0.3-foss-2022a.eb @@ -0,0 +1,57 @@ +easyblock = 'PythonBundle' + +name = 'wradlib' +version = '2.0.3' + +homepage = 'https://docs.wradlib.org/' +description = """ +The wradlib project has been initiated in order to facilitate the use of weather +radar data as well as to provide a common platform for research on new +algorithms.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('xarray', '2022.6.0'), + ('Cartopy', '0.20.3'), + ('dask', '2022.10.0'), + ('matplotlib', '3.5.2'), + ('netcdf4-python', '1.6.1'), + ('h5netcdf', '1.2.0'), + ('geopandas', '0.12.2'), +] + +use_pip = True + +exts_list = [ + ('deprecation', '2.1.0', { + 'checksums': ['72b3bde64e5d778694b0cf68178aed03d15e15477116add3fb773e581f9518ff'], + }), + ('cmweather', '0.3.2', { + 'checksums': ['d374b068fcbfeed87bc511f1f77a6047ae752f4a175a852587414b615b4baa5a'], + }), + ('lat_lon_parser', '1.3.0', { + 'checksums': ['e3a65dacd5b25a18c56e3ae31b11cd724480be7fe8db2df1c46ed0dd322a1fca'], + }), + ('xarray-datatree', '0.0.13', { + 'modulename': 'datatree', + 'checksums': ['f42bd519cab8754eb8a98749464846893b59560318520c45212e85c46af692c9'], + }), + ('xmltodict', '0.13.0', { + 'checksums': ['341595a488e3e01a85a9d8911d8912fd922ede5fecc4dce437eb4b6c8d037e56'], + }), + ('xradar', '0.5.1', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['0337b4a0798ded019b26e0746b7b7baeb6f21344a2a2e3704965049972ccbf51'], + }), + (name, version, { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['e2b625d10bc9b3ea2f33356fe467683b474c0a5410ff10ea6a708238d9172a10'], + }), +] + +sanity_pip_check = True + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/w/wradlib/wradlib-2.0.3-foss-2023a.eb b/easybuild/easyconfigs/w/wradlib/wradlib-2.0.3-foss-2023a.eb new file mode 100644 index 000000000000..d53e56422bcc --- /dev/null +++ b/easybuild/easyconfigs/w/wradlib/wradlib-2.0.3-foss-2023a.eb @@ -0,0 +1,59 @@ +easyblock = 'PythonBundle' + +name = 'wradlib' +version = '2.0.3' + +homepage = 'https://docs.wradlib.org/' +description = """ +The wradlib project has been initiated in order to facilitate the use of weather +radar data as well as to provide a common platform for research on new +algorithms.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('hatchling', '1.18.0'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('xarray', '2023.9.0'), + ('Cartopy', '0.22.0'), + ('dask', '2023.9.2'), + ('matplotlib', '3.7.2'), + ('netcdf4-python', '1.6.4'), + ('h5netcdf', '1.2.0'), + ('geopandas', '0.14.2'), +] + +use_pip = True + +exts_list = [ + ('deprecation', '2.1.0', { + 'checksums': ['72b3bde64e5d778694b0cf68178aed03d15e15477116add3fb773e581f9518ff'], + }), + ('cmweather', '0.3.2', { + 'checksums': ['d374b068fcbfeed87bc511f1f77a6047ae752f4a175a852587414b615b4baa5a'], + }), + ('lat_lon_parser', '1.3.0', { + 'checksums': ['e3a65dacd5b25a18c56e3ae31b11cd724480be7fe8db2df1c46ed0dd322a1fca'], + }), + ('xarray-datatree', '0.0.13', { + 'modulename': 'datatree', + 'checksums': ['f42bd519cab8754eb8a98749464846893b59560318520c45212e85c46af692c9'], + }), + ('xmltodict', '0.13.0', { + 'checksums': ['341595a488e3e01a85a9d8911d8912fd922ede5fecc4dce437eb4b6c8d037e56'], + }), + ('xradar', '0.5.1', { + 'checksums': ['b71021164b005f3270afd2079b8ed831a01ed43accbb7fc42c79e31a342546c5'], + }), + (name, version, { + 'checksums': ['0d5448a1dd0e030bdd36f7bbc69fa50aee7fb74dbc7b6407d2dc52d18ea40c49'], + }), +] + +sanity_pip_check = True + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/x/X11/X11-20240607-GCCcore-13.3.0.eb b/easybuild/easyconfigs/x/X11/X11-20240607-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..64a4416b30ef --- /dev/null +++ b/easybuild/easyconfigs/x/X11/X11-20240607-GCCcore-13.3.0.eb @@ -0,0 +1,214 @@ +easyblock = 'Bundle' + +name = 'X11' +version = '20240607' + +homepage = 'https://www.x.org' +description = "The X Window System (X11) is a windowing system for bitmap displays" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('binutils', '2.42'), + ('Autotools', '20231222'), + ('Bison', '3.8.2'), + ('gettext', '0.22.5'), + ('pkgconf', '2.2.0'), + ('intltool', '0.51.0'), + ('Meson', '1.4.0'), + ('Ninja', '1.12.1'), + ('Doxygen', '1.11.0'), +] + +dependencies = [ + ('bzip2', '1.0.8'), + ('fontconfig', '2.15.0'), + ('freetype', '2.13.2'), + ('zlib', '1.3.1'), + ('xorg-macros', '1.20.1'), + ('libpciaccess', '0.18.1'), +] + +source_urls = [ + XORG_LIB_SOURCE, + XORG_PROTO_SOURCE, + 'https://xcb.freedesktop.org/dist/', + 'https://xkbcommon.org/download/', + XORG_DATA_SOURCE + '/xkeyboard-config', + XORG_DATA_SOURCE, +] + +default_easyblock = 'ConfigureMake' + +default_component_specs = { + 'sources': [SOURCE_TAR_GZ], + 'start_dir': '%(name)s-%(version)s', +} + +components = [ + ('libpthread-stubs', '0.5', { # 2023-07-18 + 'checksums': ['593196cc746173d1e25cb54a93a87fd749952df68699aab7e02c085530e87747'], + }), + ('xorgproto', '2024.1', { # 2024-03-26 + 'checksums': ['4f6b9b4faf91e5df8265b71843a91fc73dc895be6210c84117a996545df296ce'], + }), + ('libXau', '1.0.11', { # 2022-12-08 + 'checksums': ['3a321aaceb803577a4776a5efe78836eb095a9e44bbc7a465d29463e1a14f189'], + }), + ('libXdmcp', '1.1.5', { # 2024-03-02 + 'checksums': ['31a7abc4f129dcf6f27ae912c3eedcb94d25ad2e8f317f69df6eda0bc4e4f2f3'], + }), + ('xcb-proto', '1.17.0', { # 2024-04-15 + 'checksums': ['392d3c9690f8c8202a68fdb89c16fd55159ab8d65000a6da213f4a1576e97a16'], + }), + ('libxcb', '1.17.0', { # 2024-04-15 + 'checksums': ['2c69287424c9e2128cb47ffe92171e10417041ec2963bceafb65cb3fcf8f0b85'], + }), + ('xtrans', '1.5.0', { # 2023-06-03 + 'checksums': ['a806f8a92f879dcd0146f3f1153fdffe845f2fc0df9b1a26c19312b7b0a29c86'], + }), + ('libxkbcommon', '1.7.0', { # 2024-03-23 + 'easyblock': 'MesonNinja', + 'sources': [SOURCE_TAR_XZ], + 'checksums': ['65782f0a10a4b455af9c6baab7040e2f537520caa2ec2092805cdfd36863b247'], + 'preconfigopts': '', + 'configopts': '-Denable-wayland=false -Denable-docs=false ', + }), + ('libX11', '1.8.9', { # 2024-04-05 + 'checksums': ['57ca5f07d263788ad661a86f4139412e8b699662e6b60c20f1f028c25a935e48'], + }), + ('libXext', '1.3.6', { # 2024-02-04 + 'checksums': ['1a0ac5cd792a55d5d465ced8dbf403ed016c8e6d14380c0ea3646c4415496e3d'], + }), + ('libFS', '1.0.9', { # 2022-08-26 + 'checksums': ['8bc2762f63178905228a28670539badcfa2c8793f7b6ce3f597b7741b932054a'], + }), + ('libICE', '1.1.1', { # 2022-12-08 + 'checksums': ['04fbd34a11ba08b9df2e3cdb2055c2e3c1c51b3257f683d7fcf42dabcf8e1210'], + }), + ('libSM', '1.2.4', { # 2022-12-20 + 'checksums': ['51464ce1abce323d5b6707ceecf8468617106e1a8a98522f8342db06fd024c15'], + }), + ('libXScrnSaver', '1.2.4', { # 2022-12-05 + 'checksums': ['0656b2630475104d6df75d91ebb8e0153e61d14e9871ef1f403bcda4a62a838a'], + }), + ('libXt', '1.3.0', { # 2023-05-09 + 'checksums': ['de4a80c4cc7785b9620e572de71026805f68e85a2bf16c386009ef0e50be3f77'], + }), + ('libXmu', '1.2.1', { # 2024-04-16 + 'checksums': ['bf0902583dd1123856c11e0a5085bd3c6e9886fbbd44954464975fd7d52eb599'], + }), + ('libXpm', '3.5.17', { # 2023-10-03 + 'checksums': ['959466c7dfcfcaa8a65055bfc311f74d4c43d9257900f85ab042604d286df0c6'], + }), + ('libXaw', '1.0.16', { # 2024-03-10 + 'checksums': ['012f90adf8739f2f023d63a5fee1528949cf2aba92ef7ac1abcfc2ae9cf28798'], + }), + ('libXfixes', '6.0.1', { # 2023-04-09 + 'checksums': ['e69eaa321173c748ba6e2f15c7cf8da87f911d3ea1b6af4b547974aef6366bec'], + }), + ('libXcomposite', '0.4.6', { # 2022-12-04 + 'checksums': ['3599dfcd96cd48d45e6aeb08578aa27636fa903f480f880c863622c2b352d076'], + }), + ('libXrender', '0.9.11', { # 2022-10-22 + 'checksums': ['6aec3ca02e4273a8cbabf811ff22106f641438eb194a12c0ae93c7e08474b667'], + }), + ('libXcursor', '1.2.2', { # 2024-03-02 + 'checksums': ['98c3a30a3f85274c167d1ac5419d681ce41f14e27bfa5fe3003c8172cd8af104'], + }), + ('libXdamage', '1.1.6', { # 2022-12-04 + 'checksums': ['2afcc139eb6eb926ffe344494b1fc023da25def42874496e6e6d3aa8acef8595'], + }), + ('libfontenc', '1.1.8', { # 2024-03-02 + 'checksums': ['b55039f70959a1b2f02f4ec8db071e5170528d2c9180b30575dccf7510d7fb9f'], + }), + ('libXfont', '1.5.4', { # 2017-11-28 + 'checksums': ['59be6eab53f7b0feb6b7933c11d67d076ae2c0fd8921229c703fc7a4e9a80d6e'], + }), + ('libXfont2', '2.0.6', { # 2022-08-26 + 'checksums': ['a944df7b6837c8fa2067f6a5fc25d89b0acc4011cd0bc085106a03557fb502fc'], + }), + ('libXft', '2.3.8', { # 2023-04-17 + 'checksums': ['32e48fe2d844422e64809e4e99b9d8aed26c1b541a5acf837c5037b8d9f278a8'], + }), + ('libXi', '1.8.1', { # 2023-05-04 + 'checksums': ['3b5f47c223e4b63d7f7fe758886b8bf665b20a7edb6962c423892fd150e326ea'], + }), + ('libXinerama', '1.1.5', { # 2022-10-29 + 'checksums': ['2efa855cb42dc620eff3b77700d8655695e09aaa318f791f201fa60afa72b95c'], + }), + ('libXrandr', '1.5.4', { # 2023-10-04 + 'checksums': ['c72c94dc3373512ceb67f578952c5d10915b38cc9ebb0fd176a49857b8048e22'], + }), + ('libXres', '1.2.2', { # 2022-12-05 + 'checksums': ['8abce597ced4a7ab89032aee91f6f784d9960adc772b2b59f17e515cd4127950'], + }), + ('libXtst', '1.2.4', { # 2022-09-27 + 'checksums': ['01366506aeb033f6dffca5326af85f670746b0cabbfd092aabefb046cf48c445'], + }), + ('libXv', '1.0.12', { # 2022-12-05 + 'checksums': ['ce706619a970a580a0e35e9b5c98bdd2af243ac6494c65f44608a89a86100126'], + }), + ('libXvMC', '1.0.14', { # 2024-02-04 + 'checksums': ['3ad5d2b991219e2bf9b2f85d40b12c16f1afec038715e462f6058af73a9b5ef8'], + }), + ('libXxf86dga', '1.1.6', { # 2022-12-05 + 'checksums': ['87c7482b1e29b4eeb415815641c4f69c00545a8138e1b73ff1f361f7d9c22ac4'], + }), + ('libXxf86vm', '1.1.5', { # 2022-09-27 + 'checksums': ['f3f1c29fef8accb0adbd854900c03c6c42f1804f2bc1e4f3ad7b2e1f3b878128'], + }), + ('libdmx', '1.1.5', { # 2023-06-03 + 'checksums': ['070e82cc1daa1b21ee1339aef56a909eab04cbe7d430fabfbb01ecd21b2dd9f3'], + }), + ('libxkbfile', '1.1.3', { # 2024-02-04 + 'checksums': ['c4c2687729d1f920f165ebb96557a1ead2ef655809ab5eaa66a1ad36dc31050d'], + }), + ('libxshmfence', '1.3.2', { # 2022-12-08 + 'checksums': ['e93a85099604beb244ee756dcaf70e18b08701c1ca84c4de0126cd71bd6c8181'], + }), + ('xcb-util', '0.4.1', { # 2022-12-20 + 'checksums': ['21c6e720162858f15fe686cef833cf96a3e2a79875f84007d76f6d00417f593a'], + }), + ('xcb-util-image', '0.4.1', { # 2022-10-18 + 'checksums': ['0ebd4cf809043fdeb4f980d58cdcf2b527035018924f8c14da76d1c81001293b'], + }), + ('xcb-util-keysyms', '0.4.1', { # 2022-10-19 + 'checksums': ['1fa21c0cea3060caee7612b6577c1730da470b88cbdf846fa4e3e0ff78948e54'], + }), + ('xcb-util-renderutil', '0.3.10', { # 2022-10-19 + 'checksums': ['e04143c48e1644c5e074243fa293d88f99005b3c50d1d54358954404e635128a'], + }), + ('xcb-util-wm', '0.4.2', { # 2022-10-19 + 'checksums': ['dcecaaa535802fd57c84cceeff50c64efe7f2326bf752e16d2b77945649c8cd7'], + }), + ('xcb-util-cursor', '0.1.5', { # 2023-10-19 + 'checksums': ['0e9c5446dc6f3beb8af6ebfcc9e27bcc6da6fe2860f7fc07b99144dfa568e93b'], + }), + ('xkeyboard-config', '2.42', { # 2024-06-07 + 'easyblock': 'MesonNinja', + 'sources': [SOURCE_TAR_XZ], + 'checksums': ['a6b06ebfc1f01fc505f2f05f265f95f67cc8873a54dd247e3c2d754b8f7e0807'], + # required to overrule parent preconfigopts that runs autogen.sh if configure script is missing + 'preconfigopts': '', + }), + ('printproto', '1.0.5', { # 2011-01-06 + 'checksums': ['e8b6f405fd865f0ea7a3a2908dfbf06622f57f2f91359ec65d13b955e49843fc'], + }), + ('libXp', '1.0.4', { # 2022-09-12 + 'checksums': ['05e46af1ccb68f1752cca5879774a4fb9bf3b19fe088eb745034956e0c6fadba'], + }), + ('xbitmaps', '1.1.3', { # 2023-02-23 + 'checksums': ['93b433b7ff223c4685fdba583b4bd30f2706be2413a670021084422d85b0269d'], + }), +] + +preconfigopts = "if [ ! -f configure ]; then ./autogen.sh; fi && " + +sanity_check_paths = { + 'files': ['include/X11/Xlib.h', 'include/X11/Xutil.h'], + 'dirs': ['include/GL', 'include/X11', 'include/X11/extensions', 'lib/pkgconfig', + 'share/pkgconfig', 'share/X11/xkb'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/XGBoost/XGBoost-2.1.1-gfbf-2023b.eb b/easybuild/easyconfigs/x/XGBoost/XGBoost-2.1.1-gfbf-2023b.eb new file mode 100644 index 000000000000..91e9be0529c6 --- /dev/null +++ b/easybuild/easyconfigs/x/XGBoost/XGBoost-2.1.1-gfbf-2023b.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'XGBoost' +version = '2.1.1' + +homepage = 'https://github.com/dmlc/xgboost' +description = """XGBoost is an optimized distributed gradient boosting library designed to be highly efficient, + flexible and portable.""" + +toolchain = {'name': 'gfbf', 'version': '2023b'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['4b1729837f9f1ba88a32ef1be3f8efb860fee6454a68719b196dc88032c23d97'] + +builddependencies = [ + ('CMake', '3.27.6'), + ('hatchling', '1.18.0'), +] + +dependencies = [ + ('Python', '3.11.5'), + ('SciPy-bundle', '2023.11'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0210-GCCcore-13.3.0.eb b/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0210-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..1d4cbe245434 --- /dev/null +++ b/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0210-GCCcore-13.3.0.eb @@ -0,0 +1,65 @@ +# updated toolchain, version, and dependency versions +# Thomas Eylenbosch 5-Jun-23 + +easyblock = 'Bundle' + +name = 'XML-LibXML' +version = '2.0210' + +homepage = 'https://metacpan.org/pod/distribution/XML-LibXML/LibXML.pod' +description = "Perl binding for libxml2" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), +] + +dependencies = [ + ('Perl', '5.38.2'), + ('Perl-bundle-CPAN', '5.38.2'), + ('libxml2', '2.12.7'), +] + +exts_defaultclass = 'PerlModule' +exts_filter = ("perldoc -lm %(ext_name)s ", "") + +exts_list = [ + ('File::chdir', '0.1011', { + 'source_tmpl': 'File-chdir-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + 'checksums': ['31ebf912df48d5d681def74b9880d78b1f3aca4351a0ed1fe3570b8e03af6c79'], + }), + ('Alien::Base', '2.83', { + 'source_tmpl': 'Alien-Build-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE/'], + 'checksums': ['4817270314431350ff397125547f55641dcff98bdde213b9e5efc613f7c8b85a'], + }), + ('Alien::Build::Plugin::Download::GitLab', '0.01', { + 'source_tmpl': 'Alien-Build-Plugin-Download-GitLab-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + 'checksums': ['c1f089c8ea152a789909d48a83dbfcf2626f773daf30431c8622582b26aba902'], + }), + ('Alien::Libxml2', '0.19', { + 'source_tmpl': 'Alien-Libxml2-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + 'checksums': ['f4a674099bbd5747c0c3b75ead841f3b244935d9ef42ba35368024bd611174c9'], + }), + ('XML::LibXML', version, { + 'source_tmpl': 'XML-LibXML-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF/'], + 'checksums': ['a29bf3f00ab9c9ee04218154e0afc8f799bf23674eb99c1a9ed4de1f4059a48d'], + }), +] + +modextrapaths = { + 'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/', +} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/%(arch)s-linux-thread-multi/XML/LibXML'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/x/x264/x264-20231019-GCCcore-13.2.0.eb b/easybuild/easyconfigs/x/x264/x264-20231019-GCCcore-13.2.0.eb index a1d60486ce0b..3a5bb6947d87 100644 --- a/easybuild/easyconfigs/x/x264/x264-20231019-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/x/x264/x264-20231019-GCCcore-13.2.0.eb @@ -14,7 +14,11 @@ toolchain = {'name': 'GCCcore', 'version': '13.2.0'} source_urls = ['https://code.videolan.org/videolan/%(name)s/-/archive/baee400f/'] sources = [{'download_filename': '%(name)s-9c3c7168.tar.gz', 'filename': SOURCE_TAR_GZ}] -checksums = ['bf6a61dcc7e1f4e623a44f09de02e843f06e7ec14f807557b43130fc84287f29'] +patches = ['x264-20231019_add-riscv-support.patch'] +checksums = [ + {'x264-20231019.tar.gz': 'bf6a61dcc7e1f4e623a44f09de02e843f06e7ec14f807557b43130fc84287f29'}, + {'x264-20231019_add-riscv-support.patch': 'd4455f3f643f255d4e907cf8a7bd803a3184ab2b6cc3445298bd2986fbb976f6'}, +] builddependencies = [ ('binutils', '2.40'), diff --git a/easybuild/easyconfigs/x/x264/x264-20231019_add-riscv-support.patch b/easybuild/easyconfigs/x/x264/x264-20231019_add-riscv-support.patch new file mode 100644 index 000000000000..b522010af86a --- /dev/null +++ b/easybuild/easyconfigs/x/x264/x264-20231019_add-riscv-support.patch @@ -0,0 +1,29 @@ +Add Risc-V 64 bit to config.guess +https://code.videolan.org/videolan/x264/-/merge_requests/121 + +From 941cae6d1d6d6344c9a1d27440eaf2872b18ca9a Mon Sep 17 00:00:00 2001 +From: Roger Hardiman +Date: Fri, 18 Nov 2022 20:15:40 +0000 +Subject: [PATCH] Add Risc-V 64 bit + +--- + config.guess | 3 +++ + 1 file changed, 3 insertions(+) + +diff --git a/config.guess b/config.guess +index d437be00..14c12963 100755 +--- a/config.guess ++++ b/config.guess +@@ -985,6 +985,9 @@ EOF + ppc:Linux:*:*) + echo powerpc-unknown-linux-gnu + exit ;; ++ riscv64:Linux:*:*) ++ echo ${UNAME_MACHINE}-unknown-linux-gnu ++ exit ;; + s390:Linux:*:* | s390x:Linux:*:*) + echo ${UNAME_MACHINE}-ibm-linux + exit ;; +-- +GitLab + diff --git a/easybuild/easyconfigs/x/x264/x264-20240513-GCCcore-13.3.0.eb b/easybuild/easyconfigs/x/x264/x264-20240513-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..a2a4cccf4212 --- /dev/null +++ b/easybuild/easyconfigs/x/x264/x264-20240513-GCCcore-13.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'x264' +version = '20240513' + +homepage = 'https://www.videolan.org/developers/x264.html' +description = """ + x264 is a free software library and application for encoding video streams + into the H.264/MPEG-4 AVC compression format, and is released under the + terms of the GNU GPL. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://code.videolan.org/videolan/%(name)s/-/archive/31e19f92/'] +sources = [{'download_filename': '%(name)s-4613ac3c.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['cf7e66bd0a75f3baba3502b58c80ee388b3d80a9a01be806337dd2214b8a290e'] + +builddependencies = [ + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), + ('NASM', '2.16.03'), +] + +configopts = " --enable-shared --enable-static --disable-bashcompletion" + + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'include/x264_config.h', 'include/%(name)s.h', 'lib/libx264.a', 'lib/libx264.so'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-11.2.0.eb b/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-11.2.0.eb index 0732a992f17f..e053931ce573 100644 --- a/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-11.2.0.eb @@ -25,7 +25,7 @@ builddependencies = [ start_dir = 'source' -configopts = '-DGIT_ARCHETYPE=1' +configopts = '-DGIT_ARCHETYPE=1 -DENABLE_PIC=ON' sanity_check_paths = { 'files': ['bin/x265', 'include/x265_config.h', 'include/x265.h', 'lib/libx265.a', 'lib/libx265.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-11.3.0.eb index 281db53772bf..1544a97d4b60 100644 --- a/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-11.3.0.eb @@ -22,7 +22,7 @@ builddependencies = [ ('Yasm', '1.3.0'), ] -configopts = '-DGIT_ARCHETYPE=1' +configopts = '-DGIT_ARCHETYPE=1 -DENABLE_PIC=ON' start_dir = 'source' diff --git a/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-12.2.0.eb b/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-12.2.0.eb index 27b2b0662962..d31e45da4777 100644 --- a/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-12.2.0.eb @@ -22,7 +22,7 @@ builddependencies = [ ('Yasm', '1.3.0'), ] -configopts = '-DGIT_ARCHETYPE=1' +configopts = '-DGIT_ARCHETYPE=1 -DENABLE_PIC=ON' start_dir = 'source' diff --git a/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-12.3.0.eb b/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-12.3.0.eb index 4c754f3021d6..4bd77d7f07e4 100644 --- a/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-12.3.0.eb @@ -22,7 +22,7 @@ builddependencies = [ ('Yasm', '1.3.0'), ] -configopts = '-DGIT_ARCHETYPE=1' +configopts = '-DGIT_ARCHETYPE=1 -DENABLE_PIC=ON' start_dir = 'source' diff --git a/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-13.2.0.eb b/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-13.2.0.eb index d1bca35c8d77..1466e0c5f3cd 100644 --- a/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-13.2.0.eb @@ -22,7 +22,7 @@ builddependencies = [ ('Yasm', '1.3.0'), ] -configopts = '-DGIT_ARCHETYPE=1' +configopts = '-DGIT_ARCHETYPE=1 -DENABLE_PIC=ON' start_dir = 'source' diff --git a/easybuild/easyconfigs/x/x265/x265-3.6-GCCcore-13.3.0.eb b/easybuild/easyconfigs/x/x265/x265-3.6-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..fc9ad81c0cb5 --- /dev/null +++ b/easybuild/easyconfigs/x/x265/x265-3.6-GCCcore-13.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'CMakeMake' + +name = 'x265' +version = '3.6' + +homepage = 'https://x265.org/' +description = """ + x265 is a free software library and application for encoding video streams + into the H.265 AVC compression format, and is released under the terms of + the GNU GPL. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://bitbucket.org/multicoreware/x265_git/downloads/'] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['663531f341c5389f460d730e62e10a4fcca3428ca2ca109693867bc5fe2e2807'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), + ('Yasm', '1.3.0'), +] + +configopts = '-DGIT_ARCHETYPE=1 -DENABLE_PIC=ON' + +start_dir = 'source' + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'include/x265_config.h', 'include/%(name)s.h', 'lib/libx265.a', 'lib/libx265.so'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/xarray/xarray-2024.5.0-gfbf-2023b.eb b/easybuild/easyconfigs/x/xarray/xarray-2024.5.0-gfbf-2023b.eb new file mode 100644 index 000000000000..09e903222930 --- /dev/null +++ b/easybuild/easyconfigs/x/xarray/xarray-2024.5.0-gfbf-2023b.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonBundle' + +name = 'xarray' +version = '2024.5.0' + +homepage = 'https://github.com/pydata/xarray' +description = """xarray (formerly xray) is an open source project and Python package that aims to bring + the labeled data power of pandas to the physical sciences, by providing N-dimensional variants of the + core pandas data structures.""" + +toolchain = {'name': 'gfbf', 'version': '2023b'} + +dependencies = [ + ('Python', '3.11.5'), + ('SciPy-bundle', '2023.11'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'preinstallopts': """sed -i 's/^dynamic = .*version.*/version = "%(version)s"/g' pyproject.toml && """, + 'checksums': ['e0eb1cb265f265126795f388ed9591f3c752f2aca491f6c0576711fd15b708f2'], + }), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/x/xtb-IFF/xtb-IFF-1.1.eb b/easybuild/easyconfigs/x/xtb-IFF/xtb-IFF-1.1.eb new file mode 100644 index 000000000000..ca25542f582c --- /dev/null +++ b/easybuild/easyconfigs/x/xtb-IFF/xtb-IFF-1.1.eb @@ -0,0 +1,26 @@ +easyblock = 'Tarball' + +name = 'xtb-IFF' +version = '1.1' + +homepage = 'https://github.com/grimme-lab/xtbiff' +description = """ +General Intermolecular Force Field based on Tight-Binding Quantum Chemical Calculations. +""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/grimme-lab/xtbiff/releases/download/v1.1'] +sources = ['xtbiff.tar.xz'] +checksums = ['6d5dee10ba39ecb1e26374b7bf82e2364d8ebed5b6f35cdce4ced73245c296f5'] + +sanity_check_paths = { + 'files': ['xtbiff'], + 'dirs': [], +} + +sanity_check_commands = ["xtbiff --help"] + +modextrapaths = {'PATH': ''} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/x/xtb/xtb-6.7.0-gfbf-2023a.eb b/easybuild/easyconfigs/x/xtb/xtb-6.7.0-gfbf-2023a.eb index 97ce290bfe0b..81ee768fed0f 100644 --- a/easybuild/easyconfigs/x/xtb/xtb-6.7.0-gfbf-2023a.eb +++ b/easybuild/easyconfigs/x/xtb/xtb-6.7.0-gfbf-2023a.eb @@ -11,7 +11,13 @@ toolchain = {'name': 'gfbf', 'version': '2023a'} github_account = 'grimme-lab' source_urls = [GITHUB_LOWER_SOURCE] sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] -checksums = ['9cf1997064d2d5bde7fae4cec6f873469602e6554872ad79de4079f022855ae2'] +patches = [ + 'xtb-6.7.0_fix-tblite-pr1072.patch' +] +checksums = [ + {'xtb-6.7.0.tar.gz': '9cf1997064d2d5bde7fae4cec6f873469602e6554872ad79de4079f022855ae2'}, + {'xtb-6.7.0_fix-tblite-pr1072.patch': 'cb8de869fc4a7c6bde44c61a479fc9edb3ccdc47c2a71f15ef124326f8a117e6'}, +] builddependencies = [ ('Meson', '1.1.1'), diff --git a/easybuild/easyconfigs/x/xtb/xtb-6.7.0_fix-tblite-pr1072.patch b/easybuild/easyconfigs/x/xtb/xtb-6.7.0_fix-tblite-pr1072.patch new file mode 100644 index 000000000000..74e2ea4950ef --- /dev/null +++ b/easybuild/easyconfigs/x/xtb/xtb-6.7.0_fix-tblite-pr1072.patch @@ -0,0 +1,487 @@ +see https://github.com/grimme-lab/xtb/pull/1072 + https://github.com/grimme-lab/xtb/issues/1091 +diff -Naur xtb-6.7.0.orig/src/dipro/xtb.F90 xtb-6.7.0/src/dipro/xtb.F90 +--- xtb-6.7.0.orig/src/dipro/xtb.F90 2024-08-23 13:50:09.000345982 +0200 ++++ xtb-6.7.0/src/dipro/xtb.F90 2024-08-23 14:14:49.499145489 +0200 +@@ -50,11 +50,11 @@ + call fatal_error(error, "Unknown method '"//method//"' requested") + ! error stop + case("gfn2") +- call new_gfn2_calculator(xcalc, mol) ++ call new_gfn2_calculator(xcalc, mol, error) + case("gfn1") +- call new_gfn1_calculator(xcalc, mol) ++ call new_gfn1_calculator(xcalc, mol, error) + case("ipea1") +- call new_ipea1_calculator(xcalc, mol) ++ call new_ipea1_calculator(xcalc, mol, error) + end select + end subroutine get_calculator + #endif +diff -Naur xtb-6.7.0.orig/src/dipro.F90 xtb-6.7.0/src/dipro.F90 +--- xtb-6.7.0.orig/src/dipro.F90 2024-08-23 13:50:08.996896000 +0200 ++++ xtb-6.7.0/src/dipro.F90 2024-08-23 13:55:44.571958738 +0200 +@@ -130,6 +130,10 @@ + !=========================set up calculator=========================================== + + call get_calculator(xcalc, struc, tblite%method, error) ++ if (allocated(error)) then ++ call env%error(error%message, source) ++ return ++ end if + call new_wavefunction(wfn, struc%nat, xcalc%bas%nsh, xcalc%bas%nao, & + & 1, set%etemp * ktoau) + wfn%nspin=1 +@@ -258,6 +262,10 @@ + write(*,'(A,I2)') "unpaired e- of fragment : ", mfrag(ifr)%uhf + + call get_calculator(fcalc(ifr), mfrag(ifr), tblite%method, error) ++ if (allocated(error)) then ++ call env%error(error%message, source) ++ return ++ end if + !> mol%charge is updated automatically from wfn by tblite library + call new_wavefunction(wfx(ifr), mfrag(ifr)%nat, fcalc(ifr)%bas%nsh, fcalc(ifr)%bas%nao, & + & 1, set%etemp * ktoau) +diff -Naur xtb-6.7.0.orig/src/tblite/calculator.F90 xtb-6.7.0/src/tblite/calculator.F90 +--- xtb-6.7.0.orig/src/tblite/calculator.F90 2024-08-23 13:50:09.192101000 +0200 ++++ xtb-6.7.0/src/tblite/calculator.F90 2024-08-23 14:18:13.034251635 +0200 +@@ -144,11 +144,11 @@ + case default + call fatal_error(error, "Unknown method '"//method//"' requested") + case("gfn2") +- call new_gfn2_calculator(calc%tblite, struc) ++ call new_gfn2_calculator(calc%tblite, struc, error) + case("gfn1") +- call new_gfn1_calculator(calc%tblite, struc) ++ call new_gfn1_calculator(calc%tblite, struc, error) + case("ipea1") +- call new_ipea1_calculator(calc%tblite, struc) ++ call new_ipea1_calculator(calc%tblite, struc, error) + end select + end if + if (allocated(error)) then +diff -Naur xtb-6.7.0.orig/subprojects/mstore.wrap xtb-6.7.0/subprojects/mstore.wrap +--- xtb-6.7.0.orig/subprojects/mstore.wrap 2024-08-23 13:50:09.235197230 +0200 ++++ xtb-6.7.0/subprojects/mstore.wrap 2024-08-23 14:18:50.314014066 +0200 +@@ -1,4 +1,4 @@ + [wrap-git] + directory = mstore + url = https://github.com/grimme-lab/mstore +-revision = v0.2.0 ++revision = v0.3.0 +diff -Naur xtb-6.7.0.orig/test/unit/test_ptb.F90 xtb-6.7.0/test/unit/test_ptb.F90 +--- xtb-6.7.0.orig/test/unit/test_ptb.F90 2024-08-23 13:50:09.260760000 +0200 ++++ xtb-6.7.0/test/unit/test_ptb.F90 2024-08-23 14:34:18.302090669 +0200 +@@ -186,12 +186,37 @@ + !> (Scaled) overlap matrix + character(len=:), allocatable :: message + real(wp), parameter :: overlap_exp(6) = [ & +- & 0.93209460_wp, & ! 1,2 +- & 0.35489609_wp, & ! 1,3 +- & 0.65682608_wp, & ! 2,3 +- & 0.05627743_wp, & ! 1,15 +- & -0.14217162_wp, & ! 1,24; diffferent because of tblite ordering +- & 0.41844087_wp] ! 14,23; diffferent because of tblite ordering ++ & 0.93209460_wp, & ! s(Mg)-s(Mg) ++ & 0.35489609_wp, & ! s(Mg)-s(Mg) ++ & 0.65682608_wp, & ! s(Mg)-s(Mg) ++ & 0.05627743_wp, & ! s(Mg)-s(H) ++ & -0.14217162_wp, & ! s(Mg)-pz(H) ++ & 0.41844087_wp] ! dyz(Mg)-py(H) ++ ! 1: s(Mg) ++ ! 2: s(Mg) ++ ! 3: s(Mg) ++ ! 4: py(Mg) ++ ! 5: pz(Mg) ++ ! 6: px(Mg) ++ ! 7: py(Mg) ++ ! 8: pz(Mg) ++ ! 9: px(Mg) ++ ! 10: dxy(Mg) ++ ! 11: dyz(Mg) ++ ! 12: dz2(Mg) ++ ! 13: dxz(Mg) ++ ! 14: dx2-y2(Mg) ++ ! 15: s(H) ++ ! 16: s(H) ++ ! 17: py(H) ++ ! 18: pz(H) ++ ! 19: px(H) ++ ! 20: s(H) ++ ! 21: s(H) ++ ! 22: py(H) ++ ! 23: pz(H) ++ ! 24: px(H) ++ + real(wp), allocatable :: lattr(:, :) + real(wp) :: cutoff + +@@ -215,7 +240,7 @@ + call check_(error, ints%overlap(2, 3), overlap_exp(3), thr=thr) + call check_(error, ints%overlap(1, 15), overlap_exp(4), thr=thr) + call check_(error, ints%overlap(1, 23), overlap_exp(5), thr=thr) +- call check_(error, ints%overlap(12, 22), overlap_exp(6), thr=thr) ++ call check_(error, ints%overlap(11, 22), overlap_exp(6), thr=thr) + + end subroutine test_ptb_overlap + +@@ -249,12 +274,37 @@ + type(error_type), allocatable, intent(out) :: error + character(len=:), allocatable :: message + real(wp), parameter :: overlap_exp(6) = [ & +- & 0.95689468_wp, & ! 1,2 +- & 0.39195790_wp, & ! 1,3 +- & 0.62961212_wp, & ! 2,3 +- & 0.03782850_wp, & ! 1,15 +- &-0.13826216_wp, & ! 1,24; diffferent because of tblite ordering +- & 0.43334922_wp] ! 14,23; diffferent because of tblite ordering ++ & 0.95689468_wp, & ! s(Mg)-s(Mg) ++ & 0.39195790_wp, & ! s(Mg)-s(Mg) ++ & 0.62961212_wp, & ! s(Mg)-s(Mg) ++ & 0.03782850_wp, & ! s(Mg)-s(H) ++ &-0.13826216_wp, & ! s(Mg)-pz(H) ++ & 0.43334922_wp] ! dyz(Mg)-py(H) ++ ! 1: s(Mg) ++ ! 2: s(Mg) ++ ! 3: s(Mg) ++ ! 4: py(Mg) ++ ! 5: pz(Mg) ++ ! 6: px(Mg) ++ ! 7: py(Mg) ++ ! 8: pz(Mg) ++ ! 9: px(Mg) ++ ! 10: dxy(Mg) ++ ! 11: dyz(Mg) ++ ! 12: dz2(Mg) ++ ! 13: dxz(Mg) ++ ! 14: dx2-y2(Mg) ++ ! 15: s(H) ++ ! 16: s(H) ++ ! 17: py(H) ++ ! 18: pz(H) ++ ! 19: px(H) ++ ! 20: s(H) ++ ! 21: s(H) ++ ! 22: py(H) ++ ! 23: pz(H) ++ ! 24: px(H) ++ + real(wp), allocatable :: lattr(:, :) + real(wp) :: cutoff + +@@ -286,7 +336,7 @@ + & message=message) + call check_(error, auxints%overlap_h0_1(1, 23), overlap_exp(5), thr=thr, & + & message=message) +- call check_(error, auxints%overlap_h0_1(12, 22), overlap_exp(6), thr=thr, & ++ call check_(error, auxints%overlap_h0_1(11, 22), overlap_exp(6), thr=thr, & + & message=message) + + end subroutine test_ptb_overlap_h0 +@@ -319,12 +369,37 @@ + real(wp), allocatable :: overlap_sx(:, :), overlap_oneminusx(:, :) + character(len=:), allocatable :: message + real(wp), parameter :: overlap_oneminusx_exp(6) = [ & +- & 0.70788_wp, & ! 1,2 +- & 0.16203_wp, & ! 1,3 +- & 0.41532_wp, & ! 2,3 +- & 0.01449_wp, & ! 1,15 +- &-0.07203_wp, & ! 1,24; diffferent because of tblite ordering +- & 0.28751_wp] ! 14,23; diffferent because of tblite ordering ++ & 0.70788_wp, & ! s(Mg)-s(Mg) ++ & 0.16203_wp, & ! s(Mg)-s(Mg) ++ & 0.41532_wp, & ! s(Mg)-s(Mg) ++ & 0.01449_wp, & ! s(Mg)-s(H) ++ &-0.07203_wp, & ! s(Mg)-pz(H) ++ & 0.28751_wp] ! dyz(Mg)-py(H) ++ ! 1: s(Mg) ++ ! 2: s(Mg) ++ ! 3: s(Mg) ++ ! 4: py(Mg) ++ ! 5: pz(Mg) ++ ! 6: px(Mg) ++ ! 7: py(Mg) ++ ! 8: pz(Mg) ++ ! 9: px(Mg) ++ ! 10: dxy(Mg) ++ ! 11: dyz(Mg) ++ ! 12: dz2(Mg) ++ ! 13: dxz(Mg) ++ ! 14: dx2-y2(Mg) ++ ! 15: s(H) ++ ! 16: s(H) ++ ! 17: py(H) ++ ! 18: pz(H) ++ ! 19: px(H) ++ ! 20: s(H) ++ ! 21: s(H) ++ ! 22: py(H) ++ ! 23: pz(H) ++ ! 24: px(H) ++ + real(wp), allocatable :: lattr(:, :) + real(wp) :: cutoff + +@@ -356,7 +431,7 @@ + & message=message) + call check_(error, overlap_oneminusx(1, 23), overlap_oneminusx_exp(5), thr=thr2, & + & message=message) +- call check_(error, overlap_oneminusx(12, 22), overlap_oneminusx_exp(6), thr=thr2, & ++ call check_(error, overlap_oneminusx(11, 22), overlap_oneminusx_exp(6), thr=thr2, & + & message=message) + + end subroutine test_ptb_overlap_SX +@@ -392,10 +467,37 @@ + type(error_type), allocatable, intent(out) :: error + character(len=:), allocatable :: message + real(wp), parameter :: vecp_ref(4) = [ & +- & 0.077719_wp, & ! 1,1 ; diffferent because of tblite ordering +- & -0.059122_wp, & ! 1,3 ; diffferent because of tblite ordering +- & 0.052775_wp, & ! 3,5 ; diffferent because of tblite ordering +- & 0.117176_wp] ! 9,9 ; diffferent because of tblite ordering ++ & 0.077719_wp, & ! s(B)-s(B) ++ & -0.059122_wp, & ! s(B)-px(B) ++ & 0.052775_wp, & ! px(B)-px(B) ++ & 0.117176_wp] ! dx2-y2(B)-dx2-y2(B) ++ ! 1: s(B) ++ ! 2: s(B) ++ ! 3: py(B) ++ ! 4: pz(B) ++ ! 5: px(B) ++ ! 6: py(B) ++ ! 7: pz(B) ++ ! 8: px(B) ++ ! 9: dxy(B) ++ ! 10: dyz(B) ++ ! 11: dz2(B) ++ ! 12: dxz(B) ++ ! 13: dx2-y2(B) ++ ! 14: s(Cl) ++ ! 15: s(Cl) ++ ! 16: py(Cl) ++ ! 17: pz(Cl) ++ ! 18: px(Cl) ++ ! 19: py(Cl) ++ ! 20: pz(Cl) ++ ! 21: px(Cl) ++ ! 22: dxy(Cl) ++ ! 23: dyz(Cl) ++ ! 24: dz2(Cl) ++ ! 25: dxz(Cl) ++ ! 26: dx2-y2(Cl) ++ + real(wp), parameter :: xyz(3, 2) = reshape([ & + & 2.0_wp, 0.0_wp, 0.0_wp, & + & 0.0_wp, 0.0_wp, 0.0_wp], [3, 2]) +@@ -434,7 +536,7 @@ + & message=message) + call check_(error, vecp(5, 8), vecp_ref(3), thr=thr2, & + & message=message) +- call check_(error, vecp(12, 12), vecp_ref(4), thr=thr2, & ++ call check_(error, vecp(13, 13), vecp_ref(4), thr=thr2, & + & message=message) + end subroutine test_ptb_V_ECP + +@@ -629,12 +731,39 @@ + real(wp), allocatable :: vecp(:, :) + + real(wp), parameter :: h0_ref(6) = [ & +- & -1.59330281_wp, & ! 1,1 +- & -2.24996207_wp, & ! 1,2 +- & 0.34974782_wp, & ! 1,23 ; diffferent because of tblite ordering +- & 0.0_wp, & ! 7,11 ; different because of tblite ordering +- & -1.17757007_wp, & ! 3,6 ; different because of tblite ordering +- & 0.48301561_wp] ! 11,24 ; diffferent because of tblite ordering ++ & -1.59330281_wp, & ! s(B)-s(B) ++ & -2.24996207_wp, & ! s(B)-s(B) ++ & 0.34974782_wp, & ! s(B)-py(Cl) ++ & 0.0_wp, & ! dx2-y2(B)-py(B) ++ & -1.17757007_wp, & ! px(B)-px(B) ++ & 0.48301561_wp] ! dxy(B)-dxy(Cl) ++ ! 1: s(B) ++ ! 2: s(B) ++ ! 3: py(B) ++ ! 4: pz(B) ++ ! 5: px(B) ++ ! 6: py(B) ++ ! 7: pz(B) ++ ! 8: px(B) ++ ! 9: dxy(B) ++ ! 10: dyz(B) ++ ! 11: dz2(B) ++ ! 12: dxz(B) ++ ! 13: dx2-y2(B) ++ ! 14: s(Cl) ++ ! 15: s(Cl) ++ ! 16: py(Cl) ++ ! 17: pz(Cl) ++ ! 18: px(Cl) ++ ! 19: py(Cl) ++ ! 20: pz(Cl) ++ ! 21: px(Cl) ++ ! 22: dxy(Cl) ++ ! 23: dyz(Cl) ++ ! 24: dz2(Cl) ++ ! 25: dxz(Cl) ++ ! 26: dx2-y2(Cl) ++ + real(wp), parameter :: levels(10) = [ & + & -0.796651404_wp, & + & -0.269771638_wp, & +@@ -670,10 +799,10 @@ + message = "H0 matrix element not matching to expected value." + call check_(error, ints%hamiltonian(1, 1), h0_ref(1), thr=thr) + call check_(error, ints%hamiltonian(1, 2), h0_ref(2), thr=thr) +- call check_(error, ints%hamiltonian(1, 22), h0_ref(3), thr=thr) ++ call check_(error, ints%hamiltonian(1, 24), h0_ref(3), thr=thr) + call check_(error, ints%hamiltonian(13, 6), h0_ref(4), thr=thr) + call check_(error, ints%hamiltonian(8, 5), h0_ref(5), thr=thr) +- call check_(error, ints%hamiltonian(13, 26), h0_ref(6), thr=thr) ++ call check_(error, ints%hamiltonian(9, 22), h0_ref(6), thr=thr) + end subroutine test_ptb_hamiltonian_h0 + + subroutine test_ptb_V_XC(error) +@@ -708,10 +837,37 @@ + type(error_type), allocatable, intent(out) :: error + character(len=:), allocatable :: message + real(wp), parameter :: Vxc_ref(4) = [ & +- & -0.92793357_wp, & ! 1,1 +- & -0.85981333_wp, & ! 1,2 +- & 0.06632750_wp, & ! 1,23 ; diffferent because of tblite ordering +- & 0.00151880_wp] ! 11,24 ; diffferent because of tblite ordering ++ & -0.92793357_wp, & ! s(B)-s(B) ++ & -0.85981333_wp, & ! s(B)-s(B) ++ & 0.06632750_wp, & ! s(B)-dz2(Cl) ++ & 0.00151880_wp] ! dxy(B)-dxy(Cl) ++ ! 1: s(B) ++ ! 2: s(B) ++ ! 3: py(B) ++ ! 4: pz(B) ++ ! 5: px(B) ++ ! 6: py(B) ++ ! 7: pz(B) ++ ! 8: px(B) ++ ! 9: dxy(B) ++ ! 10: dyz(B) ++ ! 11: dz2(B) ++ ! 12: dxz(B) ++ ! 13: dx2-y2(B) ++ ! 14: s(Cl) ++ ! 15: s(Cl) ++ ! 16: py(Cl) ++ ! 17: pz(Cl) ++ ! 18: px(Cl) ++ ! 19: py(Cl) ++ ! 20: pz(Cl) ++ ! 21: px(Cl) ++ ! 22: dxy(Cl) ++ ! 23: dyz(Cl) ++ ! 24: dz2(Cl) ++ ! 25: dxz(Cl) ++ ! 26: dx2-y2(Cl) ++ + real(wp), parameter :: xyz(3, 2) = reshape([ & + & 2.0_wp, 0.0_wp, 0.0_wp, & + & 0.0_wp, 0.0_wp, 0.0_wp], [3, 2]) +@@ -769,9 +925,9 @@ + & message=message) + call check_(error, Vxc(1, 2), Vxc_ref(2), thr=thr, & + & message=message) +- call check_(error, Vxc(1, 22), Vxc_ref(3), thr=thr, & ++ call check_(error, Vxc(1, 24), Vxc_ref(3), thr=thr, & + & message=message) +- call check_(error, Vxc(13, 26), Vxc_ref(4), thr=thr, & ++ call check_(error, Vxc(9, 22), Vxc_ref(4), thr=thr, & + & message=message) + + end subroutine test_ptb_V_XC +@@ -957,10 +1113,35 @@ + !> Conversion factor from temperature to energy + real(wp), parameter :: kt = 3.166808578545117e-06_wp + real(wp), parameter :: coulomb_pot_ref(4) = [ & +- & -0.05693153_wp, & ! 1,1 +- & -0.33917531_wp, & ! 1,2 +- & -0.00539212_wp, & ! 1,21 ; diffferent because of tblite ordering +- & 0.01305793_wp] ! 6,24 ; diffferent because of tblite ordering ++ & -0.05693153_wp, & ! s(Mg)-s(Mg) ++ & -0.33917531_wp, & ! s(Mg)-s(Mg) ++ & -0.00539212_wp, & ! s(Mg)-s(H) ++ & 0.01305793_wp] ! pz(Mg)-pz(H) ++ ! 1: s(Mg) ++ ! 2: s(Mg) ++ ! 3: s(Mg) ++ ! 4: py(Mg) ++ ! 5: pz(Mg) ++ ! 6: px(Mg) ++ ! 7: py(Mg) ++ ! 8: pz(Mg) ++ ! 9: px(Mg) ++ ! 10: dxy(Mg) ++ ! 11: dyz(Mg) ++ ! 12: dz2(Mg) ++ ! 13: dxz(Mg) ++ ! 14: dx2-y2(Mg) ++ ! 15: s(H) ++ ! 16: s(H) ++ ! 17: py(H) ++ ! 18: pz(H) ++ ! 19: px(H) ++ ! 20: s(H) ++ ! 21: s(H) ++ ! 22: py(H) ++ ! 23: pz(H) ++ ! 24: px(H) ++ + real(wp), allocatable :: lattr(:, :) + real(wp) :: cutoff + +@@ -1044,10 +1225,36 @@ + integer, parameter :: nat = 2 + integer, parameter :: at(nat) = [5, 17] + real(wp), parameter :: plusU_pot_ref(4) = [ & +- & -0.0023185_wp, & ! 1,1 +- & -0.0018289_wp, & ! 1,2 +- & -0.5266562_wp, & ! 1,21 ; diffferent because of tblite ordering +- & -1.6745659_wp] ! 6,24 ; diffferent because of tblite ordering ++ & -0.0023185_wp, & ! s(B)-s(B) ++ & -0.0018289_wp, & ! s(B)-s(B) ++ & -0.5266562_wp, & ! s(B)-pz(Cl) ++ & -1.6745659_wp] ! px(B)-dxy(Cl) ++ ! 1: s(B) ++ ! 2: s(B) ++ ! 3: py(B) ++ ! 4: pz(B) ++ ! 5: px(B) ++ ! 6: py(B) ++ ! 7: pz(B) ++ ! 8: px(B) ++ ! 9: dxy(B) ++ ! 10: dyz(B) ++ ! 11: dz2(B) ++ ! 12: dxz(B) ++ ! 13: dx2-y2(B) ++ ! 14: s(Cl) ++ ! 15: s(Cl) ++ ! 16: py(Cl) ++ ! 17: pz(Cl) ++ ! 18: px(Cl) ++ ! 19: py(Cl) ++ ! 20: pz(Cl) ++ ! 21: px(Cl) ++ ! 22: dxy(Cl) ++ ! 23: dyz(Cl) ++ ! 24: dz2(Cl) ++ ! 25: dxz(Cl) ++ ! 26: dx2-y2(Cl) + + call new(mol, at, xyz) + allocate (ptbData) +@@ -1067,7 +1274,7 @@ + call check_(error, wfn%coeff(1, 1, 1), plusU_pot_ref(1), thr=thr) + call check_(error, wfn%coeff(1, 2, 1), plusU_pot_ref(2), thr=thr) + call check_(error, wfn%coeff(1, 20, 1), plusU_pot_ref(3), thr=thr) +- call check_(error, wfn%coeff(8, 26, 1), plusU_pot_ref(4), thr=thr) ++ call check_(error, wfn%coeff(8, 22, 1), plusU_pot_ref(4), thr=thr) + + end subroutine test_ptb_plus_U_potential + diff --git a/easybuild/easyconfigs/x/xtb/xtb-6.7.1-gfbf-2023b.eb b/easybuild/easyconfigs/x/xtb/xtb-6.7.1-gfbf-2023b.eb new file mode 100644 index 000000000000..09d459d356b7 --- /dev/null +++ b/easybuild/easyconfigs/x/xtb/xtb-6.7.1-gfbf-2023b.eb @@ -0,0 +1,50 @@ +easyblock = 'MesonNinja' + +name = 'xtb' +version = '6.7.1' + +homepage = 'https://xtb-docs.readthedocs.io' +description = """ xtb - An extended tight-binding semi-empirical program package. """ + +toolchain = {'name': 'gfbf', 'version': '2023b'} + +github_account = 'grimme-lab' +source_urls = [GITHUB_LOWER_SOURCE] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +patches = [ + 'xtb-6.7.1_fix-tblite-pr1072.patch', + 'xtb-6.7.1_fix-dftd4-test.patch', +] +checksums = [ + {'xtb-6.7.1.tar.gz': '52506a689147cdb4695bf1c666158b6d6d6b31726fecaa5bf53af7f4e3f3d20d'}, + {'xtb-6.7.1_fix-tblite-pr1072.patch': '1f10fef3e94c29926b1f632acc94c3ec92be861ee5c5139104194172726ffe68'}, + {'xtb-6.7.1_fix-dftd4-test.patch': '340e7d5cbc6bbaf0c53d4d292f3624cd67455b7a817818fe2cc8d26f5c34864b'}, +] + +builddependencies = [ + ('Meson', '1.2.3'), + ('Ninja', '1.11.1'), + ('pkgconf', '2.0.3'), +] + +configopts = "-Dlapack='custom' " +configopts += "-Dcustom_libraries='flexiblas' " +configopts += "--buildtype release " + +runtest = 'meson' +pretestopts = 'export OMP_NUM_THREADS=2 && ' +testopts = 'test -C %(builddir)s/easybuild_obj -t 60' # Ensure test don't timeout + +sanity_check_paths = { + 'files': ['bin/xtb', 'include/xtb.h'] + ['lib/libxtb.%s' % e for e in ('a', SHLIB_EXT)], + 'dirs': ['share'], +} + +sanity_check_commands = ["xtb --help"] + +modextravars = { + 'XTBHOME': '%(installdir)s', + 'XTBPATH': '%(installdir)s', +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/x/xtb/xtb-6.7.1_fix-dftd4-test.patch b/easybuild/easyconfigs/x/xtb/xtb-6.7.1_fix-dftd4-test.patch new file mode 100644 index 000000000000..0405b372a8a6 --- /dev/null +++ b/easybuild/easyconfigs/x/xtb/xtb-6.7.1_fix-dftd4-test.patch @@ -0,0 +1,20 @@ +fix for failing xtb test: + 72/148 dftd4 / param FAIL 1.85s exit status 1 + +from meson-logs/testlog.txt: +# Testing: param + Starting rational-damping ... (1/1) + ... rational-damping [FAILED] + Message: Condition not fullfilled + +see https://github.com/grimme-lab/xtb/pull/1085 +diff --git a/subprojects/dftd4.wrap b/subprojects/dftd4.wrap +index 46dc07ad9..e3e93f459 100644 +--- a/subprojects/dftd4.wrap ++++ b/subprojects/dftd4.wrap +@@ -1,4 +1,4 @@ + [wrap-git] + directory = dftd4 + url = https://github.com/dftd4/dftd4 +-revision = v3.5.0 ++revision = v3.6.0 diff --git a/easybuild/easyconfigs/x/xtb/xtb-6.7.1_fix-tblite-pr1072.patch b/easybuild/easyconfigs/x/xtb/xtb-6.7.1_fix-tblite-pr1072.patch new file mode 100644 index 000000000000..0684569d3e43 --- /dev/null +++ b/easybuild/easyconfigs/x/xtb/xtb-6.7.1_fix-tblite-pr1072.patch @@ -0,0 +1,528 @@ +see https://github.com/grimme-lab/xtb/pull/1072 + https://github.com/grimme-lab/xtb/issues/1091 +diff --git a/src/dipro.F90 b/src/dipro.F90 +index 42a136364..ab64e0710 100644 +--- a/src/dipro.F90 ++++ b/src/dipro.F90 +@@ -130,6 +130,10 @@ subroutine get_jab(env, tblite, mol, fragment, dipro) + !=========================set up calculator=========================================== + + call get_calculator(xcalc, struc, tblite%method, error) ++ if (allocated(error)) then ++ call env%error(error%message, source) ++ return ++ end if + call new_wavefunction(wfn, struc%nat, xcalc%bas%nsh, xcalc%bas%nao, & + & 1, set%etemp * ktoau) + wfn%nspin=1 +@@ -258,6 +262,10 @@ subroutine get_jab(env, tblite, mol, fragment, dipro) + write(*,'(A,I2)') "unpaired e- of fragment : ", mfrag(ifr)%uhf + + call get_calculator(fcalc(ifr), mfrag(ifr), tblite%method, error) ++ if (allocated(error)) then ++ call env%error(error%message, source) ++ return ++ end if + !> mol%charge is updated automatically from wfn by tblite library + call new_wavefunction(wfx(ifr), mfrag(ifr)%nat, fcalc(ifr)%bas%nsh, fcalc(ifr)%bas%nao, & + & 1, set%etemp * ktoau) +diff --git a/src/dipro/xtb.F90 b/src/dipro/xtb.F90 +index 95aff7848..4db948a3e 100644 +--- a/src/dipro/xtb.F90 ++++ b/src/dipro/xtb.F90 +@@ -50,11 +50,11 @@ subroutine get_calculator(xcalc, mol, method, error) + call fatal_error(error, "Unknown method '"//method//"' requested") + ! error stop + case("gfn2") +- call new_gfn2_calculator(xcalc, mol) ++ call new_gfn2_calculator(xcalc, mol, error) + case("gfn1") +- call new_gfn1_calculator(xcalc, mol) ++ call new_gfn1_calculator(xcalc, mol, error) + case("ipea1") +- call new_ipea1_calculator(xcalc, mol) ++ call new_ipea1_calculator(xcalc, mol, error) + end select + end subroutine get_calculator + #endif +diff --git a/src/tblite/calculator.F90 b/src/tblite/calculator.F90 +index 653e6b285..f05087414 100644 +--- a/src/tblite/calculator.F90 ++++ b/src/tblite/calculator.F90 +@@ -150,16 +150,16 @@ subroutine newTBLiteCalculator(env, mol, calc, input) + case default + call fatal_error(error, "Unknown method '"//method//"' requested") + case("gfn2") +- call new_gfn2_calculator(calc%tblite, struc) ++ call new_gfn2_calculator(calc%tblite, struc, error) + case("gfn1") +- call new_gfn1_calculator(calc%tblite, struc) ++ call new_gfn1_calculator(calc%tblite, struc, error) + case("ipea1") +- call new_ipea1_calculator(calc%tblite, struc) ++ call new_ipea1_calculator(calc%tblite, struc, error) + case("ceh") + calc%guess = method + calc%nspin = 1 +- calc%etemp = 5000.0_wp * kt +- call new_ceh_calculator(calc%tblite, struc) ++ calc%etemp = 4000.0_wp * kt ++ call new_ceh_calculator(calc%tblite, struc, error) + end select + end if + if (allocated(error)) then +@@ -244,18 +244,18 @@ subroutine newTBLiteWavefunction(env, mol, calc, chk) + block + use tblite_context, only : context_type, context_terminal + use tblite_context_terminal, only : escape +- use tblite_ceh_singlepoint, only : ceh_guess ++ use tblite_ceh_singlepoint, only : ceh_singlepoint + use tblite_lapack_solver, only : lapack_solver + use tblite_lapack_solver, only : lapack_algorithm + type(context_type) :: ctx +- ++ + ctx%solver = lapack_solver(lapack_algorithm%gvd) + ctx%terminal = context_terminal(calc%color) + + write (env%unit, '(1x,a)') escape(ctx%terminal%cyan) // "Calculation of CEH charges" // & + & escape(ctx%terminal%reset) +- +- call ceh_guess(ctx, calc%tblite, struc, error, wfn, calc%accuracy, 1) ++ ++ call ceh_singlepoint(ctx, calc%tblite, struc, wfn, calc%accuracy, 1) + end block + end select + end associate +diff --git a/subprojects/mstore.wrap b/subprojects/mstore.wrap +index acf5df9de..0dfe716c0 100644 +--- a/subprojects/mstore.wrap ++++ b/subprojects/mstore.wrap +@@ -1,4 +1,4 @@ + [wrap-git] + directory = mstore + url = https://github.com/grimme-lab/mstore +-revision = v0.2.0 ++revision = v0.3.0 +diff --git a/test/unit/test_ptb.F90 b/test/unit/test_ptb.F90 +index 16c14cbe4..5e585f90d 100644 +--- a/test/unit/test_ptb.F90 ++++ b/test/unit/test_ptb.F90 +@@ -186,12 +186,37 @@ subroutine test_ptb_overlap(error) + !> (Scaled) overlap matrix + character(len=:), allocatable :: message + real(wp), parameter :: overlap_exp(6) = [ & +- & 0.93209460_wp, & ! 1,2 +- & 0.35489609_wp, & ! 1,3 +- & 0.65682608_wp, & ! 2,3 +- & 0.05627743_wp, & ! 1,15 +- & -0.14217162_wp, & ! 1,24; diffferent because of tblite ordering +- & 0.41844087_wp] ! 14,23; diffferent because of tblite ordering ++ & 0.93209460_wp, & ! s(Mg)-s(Mg) ++ & 0.35489609_wp, & ! s(Mg)-s(Mg) ++ & 0.65682608_wp, & ! s(Mg)-s(Mg) ++ & 0.05627743_wp, & ! s(Mg)-s(H) ++ & -0.14217162_wp, & ! s(Mg)-pz(H) ++ & 0.41844087_wp] ! dyz(Mg)-py(H) ++ ! 1: s(Mg) ++ ! 2: s(Mg) ++ ! 3: s(Mg) ++ ! 4: py(Mg) ++ ! 5: pz(Mg) ++ ! 6: px(Mg) ++ ! 7: py(Mg) ++ ! 8: pz(Mg) ++ ! 9: px(Mg) ++ ! 10: dxy(Mg) ++ ! 11: dyz(Mg) ++ ! 12: dz2(Mg) ++ ! 13: dxz(Mg) ++ ! 14: dx2-y2(Mg) ++ ! 15: s(H) ++ ! 16: s(H) ++ ! 17: py(H) ++ ! 18: pz(H) ++ ! 19: px(H) ++ ! 20: s(H) ++ ! 21: s(H) ++ ! 22: py(H) ++ ! 23: pz(H) ++ ! 24: px(H) ++ + real(wp), allocatable :: lattr(:, :) + real(wp) :: cutoff + +@@ -215,7 +240,7 @@ subroutine test_ptb_overlap(error) + call check_(error, ints%overlap(2, 3), overlap_exp(3), thr=thr) + call check_(error, ints%overlap(1, 15), overlap_exp(4), thr=thr) + call check_(error, ints%overlap(1, 23), overlap_exp(5), thr=thr) +- call check_(error, ints%overlap(12, 22), overlap_exp(6), thr=thr) ++ call check_(error, ints%overlap(11, 22), overlap_exp(6), thr=thr) + + end subroutine test_ptb_overlap + +@@ -249,12 +274,37 @@ subroutine test_ptb_overlap_h0(error) + type(error_type), allocatable, intent(out) :: error + character(len=:), allocatable :: message + real(wp), parameter :: overlap_exp(6) = [ & +- & 0.95689468_wp, & ! 1,2 +- & 0.39195790_wp, & ! 1,3 +- & 0.62961212_wp, & ! 2,3 +- & 0.03782850_wp, & ! 1,15 +- &-0.13826216_wp, & ! 1,24; diffferent because of tblite ordering +- & 0.43334922_wp] ! 14,23; diffferent because of tblite ordering ++ & 0.95689468_wp, & ! s(Mg)-s(Mg) ++ & 0.39195790_wp, & ! s(Mg)-s(Mg) ++ & 0.62961212_wp, & ! s(Mg)-s(Mg) ++ & 0.03782850_wp, & ! s(Mg)-s(H) ++ &-0.13826216_wp, & ! s(Mg)-pz(H) ++ & 0.43334922_wp] ! dyz(Mg)-py(H) ++ ! 1: s(Mg) ++ ! 2: s(Mg) ++ ! 3: s(Mg) ++ ! 4: py(Mg) ++ ! 5: pz(Mg) ++ ! 6: px(Mg) ++ ! 7: py(Mg) ++ ! 8: pz(Mg) ++ ! 9: px(Mg) ++ ! 10: dxy(Mg) ++ ! 11: dyz(Mg) ++ ! 12: dz2(Mg) ++ ! 13: dxz(Mg) ++ ! 14: dx2-y2(Mg) ++ ! 15: s(H) ++ ! 16: s(H) ++ ! 17: py(H) ++ ! 18: pz(H) ++ ! 19: px(H) ++ ! 20: s(H) ++ ! 21: s(H) ++ ! 22: py(H) ++ ! 23: pz(H) ++ ! 24: px(H) ++ + real(wp), allocatable :: lattr(:, :) + real(wp) :: cutoff + +@@ -286,7 +336,7 @@ subroutine test_ptb_overlap_h0(error) + & message=message) + call check_(error, auxints%overlap_h0_1(1, 23), overlap_exp(5), thr=thr, & + & message=message) +- call check_(error, auxints%overlap_h0_1(12, 22), overlap_exp(6), thr=thr, & ++ call check_(error, auxints%overlap_h0_1(11, 22), overlap_exp(6), thr=thr, & + & message=message) + + end subroutine test_ptb_overlap_h0 +@@ -319,12 +369,37 @@ subroutine test_ptb_overlap_SX(error) + real(wp), allocatable :: overlap_sx(:, :), overlap_oneminusx(:, :) + character(len=:), allocatable :: message + real(wp), parameter :: overlap_oneminusx_exp(6) = [ & +- & 0.70788_wp, & ! 1,2 +- & 0.16203_wp, & ! 1,3 +- & 0.41532_wp, & ! 2,3 +- & 0.01449_wp, & ! 1,15 +- &-0.07203_wp, & ! 1,24; diffferent because of tblite ordering +- & 0.28751_wp] ! 14,23; diffferent because of tblite ordering ++ & 0.70788_wp, & ! s(Mg)-s(Mg) ++ & 0.16203_wp, & ! s(Mg)-s(Mg) ++ & 0.41532_wp, & ! s(Mg)-s(Mg) ++ & 0.01449_wp, & ! s(Mg)-s(H) ++ &-0.07203_wp, & ! s(Mg)-pz(H) ++ & 0.28751_wp] ! dyz(Mg)-py(H) ++ ! 1: s(Mg) ++ ! 2: s(Mg) ++ ! 3: s(Mg) ++ ! 4: py(Mg) ++ ! 5: pz(Mg) ++ ! 6: px(Mg) ++ ! 7: py(Mg) ++ ! 8: pz(Mg) ++ ! 9: px(Mg) ++ ! 10: dxy(Mg) ++ ! 11: dyz(Mg) ++ ! 12: dz2(Mg) ++ ! 13: dxz(Mg) ++ ! 14: dx2-y2(Mg) ++ ! 15: s(H) ++ ! 16: s(H) ++ ! 17: py(H) ++ ! 18: pz(H) ++ ! 19: px(H) ++ ! 20: s(H) ++ ! 21: s(H) ++ ! 22: py(H) ++ ! 23: pz(H) ++ ! 24: px(H) ++ + real(wp), allocatable :: lattr(:, :) + real(wp) :: cutoff + +@@ -356,7 +431,7 @@ subroutine test_ptb_overlap_SX(error) + & message=message) + call check_(error, overlap_oneminusx(1, 23), overlap_oneminusx_exp(5), thr=thr2, & + & message=message) +- call check_(error, overlap_oneminusx(12, 22), overlap_oneminusx_exp(6), thr=thr2, & ++ call check_(error, overlap_oneminusx(11, 22), overlap_oneminusx_exp(6), thr=thr2, & + & message=message) + + end subroutine test_ptb_overlap_SX +@@ -392,10 +467,37 @@ subroutine test_ptb_V_ECP(error) + type(error_type), allocatable, intent(out) :: error + character(len=:), allocatable :: message + real(wp), parameter :: vecp_ref(4) = [ & +- & 0.077719_wp, & ! 1,1 ; diffferent because of tblite ordering +- & -0.059122_wp, & ! 1,3 ; diffferent because of tblite ordering +- & 0.052775_wp, & ! 3,5 ; diffferent because of tblite ordering +- & 0.117176_wp] ! 9,9 ; diffferent because of tblite ordering ++ & 0.077719_wp, & ! s(B)-s(B) ++ & -0.059122_wp, & ! s(B)-px(B) ++ & 0.052775_wp, & ! px(B)-px(B) ++ & 0.117176_wp] ! dx2-y2(B)-dx2-y2(B) ++ ! 1: s(B) ++ ! 2: s(B) ++ ! 3: py(B) ++ ! 4: pz(B) ++ ! 5: px(B) ++ ! 6: py(B) ++ ! 7: pz(B) ++ ! 8: px(B) ++ ! 9: dxy(B) ++ ! 10: dyz(B) ++ ! 11: dz2(B) ++ ! 12: dxz(B) ++ ! 13: dx2-y2(B) ++ ! 14: s(Cl) ++ ! 15: s(Cl) ++ ! 16: py(Cl) ++ ! 17: pz(Cl) ++ ! 18: px(Cl) ++ ! 19: py(Cl) ++ ! 20: pz(Cl) ++ ! 21: px(Cl) ++ ! 22: dxy(Cl) ++ ! 23: dyz(Cl) ++ ! 24: dz2(Cl) ++ ! 25: dxz(Cl) ++ ! 26: dx2-y2(Cl) ++ + real(wp), parameter :: xyz(3, 2) = reshape([ & + & 2.0_wp, 0.0_wp, 0.0_wp, & + & 0.0_wp, 0.0_wp, 0.0_wp], [3, 2]) +@@ -434,7 +536,7 @@ subroutine test_ptb_V_ECP(error) + & message=message) + call check_(error, vecp(5, 8), vecp_ref(3), thr=thr2, & + & message=message) +- call check_(error, vecp(12, 12), vecp_ref(4), thr=thr2, & ++ call check_(error, vecp(13, 13), vecp_ref(4), thr=thr2, & + & message=message) + end subroutine test_ptb_V_ECP + +@@ -629,12 +731,39 @@ subroutine test_ptb_hamiltonian_h0(error) + real(wp), allocatable :: vecp(:, :) + + real(wp), parameter :: h0_ref(6) = [ & +- & -1.59330281_wp, & ! 1,1 +- & -2.24996207_wp, & ! 1,2 +- & 0.34974782_wp, & ! 1,23 ; diffferent because of tblite ordering +- & 0.0_wp, & ! 7,11 ; different because of tblite ordering +- & -1.17757007_wp, & ! 3,6 ; different because of tblite ordering +- & 0.48301561_wp] ! 11,24 ; diffferent because of tblite ordering ++ & -1.59330281_wp, & ! s(B)-s(B) ++ & -2.24996207_wp, & ! s(B)-s(B) ++ & 0.34974782_wp, & ! s(B)-py(Cl) ++ & 0.0_wp, & ! dx2-y2(B)-py(B) ++ & -1.17757007_wp, & ! px(B)-px(B) ++ & 0.48301561_wp] ! dxy(B)-dxy(Cl) ++ ! 1: s(B) ++ ! 2: s(B) ++ ! 3: py(B) ++ ! 4: pz(B) ++ ! 5: px(B) ++ ! 6: py(B) ++ ! 7: pz(B) ++ ! 8: px(B) ++ ! 9: dxy(B) ++ ! 10: dyz(B) ++ ! 11: dz2(B) ++ ! 12: dxz(B) ++ ! 13: dx2-y2(B) ++ ! 14: s(Cl) ++ ! 15: s(Cl) ++ ! 16: py(Cl) ++ ! 17: pz(Cl) ++ ! 18: px(Cl) ++ ! 19: py(Cl) ++ ! 20: pz(Cl) ++ ! 21: px(Cl) ++ ! 22: dxy(Cl) ++ ! 23: dyz(Cl) ++ ! 24: dz2(Cl) ++ ! 25: dxz(Cl) ++ ! 26: dx2-y2(Cl) ++ + real(wp), parameter :: levels(10) = [ & + & -0.796651404_wp, & + & -0.269771638_wp, & +@@ -665,15 +794,16 @@ subroutine test_ptb_hamiltonian_h0(error) + & alpha_scal=id_to_atom(mol, ptbData%hamiltonian%kalphah0l)) + allocate (vecp(bas%nao, bas%nao), source=0.0_wp) + ++ ints%hamiltonian = 0.0_wp + call get_hamiltonian(mol, list, bas, ptbData%hamiltonian, ptbData%hamiltonian%kla, auxints%overlap_h0_1, & + & levels, ints%hamiltonian, ptbGlobals%kpol, ptbGlobals%kitr, ptbGlobals%kitocod) + message = "H0 matrix element not matching to expected value." + call check_(error, ints%hamiltonian(1, 1), h0_ref(1), thr=thr) + call check_(error, ints%hamiltonian(1, 2), h0_ref(2), thr=thr) +- call check_(error, ints%hamiltonian(1, 22), h0_ref(3), thr=thr) ++ call check_(error, ints%hamiltonian(1, 24), h0_ref(3), thr=thr) + call check_(error, ints%hamiltonian(13, 6), h0_ref(4), thr=thr) + call check_(error, ints%hamiltonian(8, 5), h0_ref(5), thr=thr) +- call check_(error, ints%hamiltonian(13, 26), h0_ref(6), thr=thr) ++ call check_(error, ints%hamiltonian(9, 22), h0_ref(6), thr=thr) + end subroutine test_ptb_hamiltonian_h0 + + subroutine test_ptb_V_XC(error) +@@ -708,10 +838,37 @@ subroutine test_ptb_V_XC(error) + type(error_type), allocatable, intent(out) :: error + character(len=:), allocatable :: message + real(wp), parameter :: Vxc_ref(4) = [ & +- & -0.92793357_wp, & ! 1,1 +- & -0.85981333_wp, & ! 1,2 +- & 0.06632750_wp, & ! 1,23 ; diffferent because of tblite ordering +- & 0.00151880_wp] ! 11,24 ; diffferent because of tblite ordering ++ & -0.92793357_wp, & ! s(B)-s(B) ++ & -0.85981333_wp, & ! s(B)-s(B) ++ & 0.06632750_wp, & ! s(B)-dz2(Cl) ++ & 0.00151880_wp] ! dxy(B)-dxy(Cl) ++ ! 1: s(B) ++ ! 2: s(B) ++ ! 3: py(B) ++ ! 4: pz(B) ++ ! 5: px(B) ++ ! 6: py(B) ++ ! 7: pz(B) ++ ! 8: px(B) ++ ! 9: dxy(B) ++ ! 10: dyz(B) ++ ! 11: dz2(B) ++ ! 12: dxz(B) ++ ! 13: dx2-y2(B) ++ ! 14: s(Cl) ++ ! 15: s(Cl) ++ ! 16: py(Cl) ++ ! 17: pz(Cl) ++ ! 18: px(Cl) ++ ! 19: py(Cl) ++ ! 20: pz(Cl) ++ ! 21: px(Cl) ++ ! 22: dxy(Cl) ++ ! 23: dyz(Cl) ++ ! 24: dz2(Cl) ++ ! 25: dxz(Cl) ++ ! 26: dx2-y2(Cl) ++ + real(wp), parameter :: xyz(3, 2) = reshape([ & + & 2.0_wp, 0.0_wp, 0.0_wp, & + & 0.0_wp, 0.0_wp, 0.0_wp], [3, 2]) +@@ -769,9 +926,9 @@ subroutine test_ptb_V_XC(error) + & message=message) + call check_(error, Vxc(1, 2), Vxc_ref(2), thr=thr, & + & message=message) +- call check_(error, Vxc(1, 22), Vxc_ref(3), thr=thr, & ++ call check_(error, Vxc(1, 24), Vxc_ref(3), thr=thr, & + & message=message) +- call check_(error, Vxc(13, 26), Vxc_ref(4), thr=thr, & ++ call check_(error, Vxc(9, 22), Vxc_ref(4), thr=thr, & + & message=message) + + end subroutine test_ptb_V_XC +@@ -957,10 +1114,35 @@ subroutine test_ptb_coulomb_potential(error) + !> Conversion factor from temperature to energy + real(wp), parameter :: kt = 3.166808578545117e-06_wp + real(wp), parameter :: coulomb_pot_ref(4) = [ & +- & -0.05693153_wp, & ! 1,1 +- & -0.33917531_wp, & ! 1,2 +- & -0.00539212_wp, & ! 1,21 ; diffferent because of tblite ordering +- & 0.01305793_wp] ! 6,24 ; diffferent because of tblite ordering ++ & -0.05693153_wp, & ! s(Mg)-s(Mg) ++ & -0.33917531_wp, & ! s(Mg)-s(Mg) ++ & -0.00539212_wp, & ! s(Mg)-s(H) ++ & 0.01305793_wp] ! pz(Mg)-pz(H) ++ ! 1: s(Mg) ++ ! 2: s(Mg) ++ ! 3: s(Mg) ++ ! 4: py(Mg) ++ ! 5: pz(Mg) ++ ! 6: px(Mg) ++ ! 7: py(Mg) ++ ! 8: pz(Mg) ++ ! 9: px(Mg) ++ ! 10: dxy(Mg) ++ ! 11: dyz(Mg) ++ ! 12: dz2(Mg) ++ ! 13: dxz(Mg) ++ ! 14: dx2-y2(Mg) ++ ! 15: s(H) ++ ! 16: s(H) ++ ! 17: py(H) ++ ! 18: pz(H) ++ ! 19: px(H) ++ ! 20: s(H) ++ ! 21: s(H) ++ ! 22: py(H) ++ ! 23: pz(H) ++ ! 24: px(H) ++ + real(wp), allocatable :: lattr(:, :) + real(wp) :: cutoff + +@@ -1044,10 +1226,36 @@ subroutine test_ptb_plus_U_potential(error) + integer, parameter :: nat = 2 + integer, parameter :: at(nat) = [5, 17] + real(wp), parameter :: plusU_pot_ref(4) = [ & +- & -0.0023185_wp, & ! 1,1 +- & -0.0018289_wp, & ! 1,2 +- & -0.5266562_wp, & ! 1,21 ; diffferent because of tblite ordering +- & -1.6745659_wp] ! 6,24 ; diffferent because of tblite ordering ++ & -0.0023185_wp, & ! s(B)-s(B) ++ & -0.0018289_wp, & ! s(B)-s(B) ++ & -0.5266562_wp, & ! s(B)-pz(Cl) ++ & -1.6745659_wp] ! px(B)-dxy(Cl) ++ ! 1: s(B) ++ ! 2: s(B) ++ ! 3: py(B) ++ ! 4: pz(B) ++ ! 5: px(B) ++ ! 6: py(B) ++ ! 7: pz(B) ++ ! 8: px(B) ++ ! 9: dxy(B) ++ ! 10: dyz(B) ++ ! 11: dz2(B) ++ ! 12: dxz(B) ++ ! 13: dx2-y2(B) ++ ! 14: s(Cl) ++ ! 15: s(Cl) ++ ! 16: py(Cl) ++ ! 17: pz(Cl) ++ ! 18: px(Cl) ++ ! 19: py(Cl) ++ ! 20: pz(Cl) ++ ! 21: px(Cl) ++ ! 22: dxy(Cl) ++ ! 23: dyz(Cl) ++ ! 24: dz2(Cl) ++ ! 25: dxz(Cl) ++ ! 26: dx2-y2(Cl) + + call new(mol, at, xyz) + allocate (ptbData) +@@ -1067,7 +1275,7 @@ subroutine test_ptb_plus_U_potential(error) + call check_(error, wfn%coeff(1, 1, 1), plusU_pot_ref(1), thr=thr) + call check_(error, wfn%coeff(1, 2, 1), plusU_pot_ref(2), thr=thr) + call check_(error, wfn%coeff(1, 20, 1), plusU_pot_ref(3), thr=thr) +- call check_(error, wfn%coeff(8, 26, 1), plusU_pot_ref(4), thr=thr) ++ call check_(error, wfn%coeff(8, 22, 1), plusU_pot_ref(4), thr=thr) + + end subroutine test_ptb_plus_U_potential + diff --git a/easybuild/easyconfigs/x/xtensor/xtensor-0.24.7-foss-2023a.eb b/easybuild/easyconfigs/x/xtensor/xtensor-0.24.7-foss-2023a.eb new file mode 100644 index 000000000000..8b30ddf8a2f1 --- /dev/null +++ b/easybuild/easyconfigs/x/xtensor/xtensor-0.24.7-foss-2023a.eb @@ -0,0 +1,49 @@ +easyblock = 'Bundle' + +name = 'xtensor' +version = '0.24.7' + +homepage = 'https://github.com/xtensor-stack/xtensor' +description = "xtensor is a C++ library meant for numerical analysis with multi-dimensional array expressions." + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('CMake', '3.26.3'), + ('pybind11', '2.11.1'), +] +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), +] + +default_easyblock = 'CMakeMake' + +default_component_specs = { + 'source_urls': ['https://github.com/xtensor-stack/%(name)s/archive/'], + 'sources': ['%(version)s.tar.gz'], + 'start_dir': '%(name)s-%(version)s', +} + +components = [ + ('xtl', '0.7.5', { + 'checksums': ['3286fef5fee5d58f82f7b91375cd449c819848584bae9367893501114d923cbe'], + }), + ('xsimd', '8.0.5', { + 'checksums': ['0e1b5d973b63009f06a3885931a37452580dbc8d7ca8ad40d4b8c80d2a0f84d7'], + }), + ('xtensor', version, { + 'checksums': ['0fbbd524dde2199b731b6af99b16063780de6cf1d0d6cb1f3f4d4ceb318f3106'], + }), + ('xtensor-python', '0.26.1', { + 'checksums': ['eb64155c6824be471decf93927beedae3645714c8ce92f38e037434db2c2454a'], + 'configopts': '-DPYTHON_EXECUTABLE=$EBROOTPYTHON/bin/python', + }), +] + +sanity_check_paths = { + 'files': ['include/xtensor.hpp', 'lib/pkgconfig/xsimd.pc'], + 'dirs': ['include/xsimd', 'include/xtensor', 'include/xtensor-python', 'include/xtl', 'lib/cmake'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/y/YACS/YACS-0.1.8-GCCcore-13.3.0.eb b/easybuild/easyconfigs/y/YACS/YACS-0.1.8-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..2ab12a60fcae --- /dev/null +++ b/easybuild/easyconfigs/y/YACS/YACS-0.1.8-GCCcore-13.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'YACS' +version = '0.1.8' + +homepage = "https://github.com/rbgirshick/yacs" +description = """YACS was created as a lightweight library to define and +manage system configurations, such as those commonly found in software +designed for scientific experimentation. These "configurations" +typically cover concepts like hyperparameters used in training a machine +learning model or configurable model hyperparameters, such as the depth +of a convolutional neural network.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['efc4c732942b3103bea904ee89af98bcd27d01f0ac12d8d4d369f1e7a2914384'] + +builddependencies = [('binutils', '2.42')] + +dependencies = [ + ('Python', '3.12.3'), + ('PyYAML', '6.0.2'), +] + +use_pip = True +download_dep_fail = True + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..5ac8fd8176fd --- /dev/null +++ b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-13.3.0.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'Yasm' +version = '1.3.0' + +homepage = 'https://www.tortall.net/projects/yasm/' +description = "Yasm: Complete rewrite of the NASM assembler with BSD license" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/%(namelower)s/%(namelower)s/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3dce6601b495f5b3d45b59f7d2492a340ee7e84b5beca17e48f862502bd5603f'] + +builddependencies = [ + ('binutils', '2.42'), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/y/yell/yell-2.2.2-GCC-12.3.0.eb b/easybuild/easyconfigs/y/yell/yell-2.2.2-GCC-12.3.0.eb new file mode 100644 index 000000000000..48cc38e0d7c1 --- /dev/null +++ b/easybuild/easyconfigs/y/yell/yell-2.2.2-GCC-12.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'RubyGem' + +name = 'yell' +version = '2.2.2' + +homepage = 'https://github.com/rudionrails/yell' +description = """Yell - Your Extensible Logging Library is a comprehensive logging replacement for Ruby.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://rubygems.org/downloads/'] +sources = ['%(name)s-%(version)s.gem'] +checksums = ['1d166f3cc3b6dc49a59778ea7156ed6d8de794c15106d48ffd6cbb061b9b26bc'] + +gem_file = '%(name)s-%(version)s.gem' + +dependencies = [ + ('Ruby', '3.3.0'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['gems/%(namelower)s-%(version)s'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/y/yelp-tools/yelp-tools-42.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/y/yelp-tools/yelp-tools-42.1-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..bbf260ff417e --- /dev/null +++ b/easybuild/easyconfigs/y/yelp-tools/yelp-tools-42.1-GCCcore-12.3.0.eb @@ -0,0 +1,50 @@ +easyblock = 'MesonNinja' + +name = 'yelp-tools' +version = '42.1' + +homepage = 'https://gitlab.gnome.org/GNOME/yelp-tools' +description = """yelp-tools is a collection of scripts and build utilities to help create, +manage, and publish documentation for Yelp and the web. Most of the heavy +lifting is done by packages like yelp-xsl and itstool. This package just +wraps things up in a developer-friendly way.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://gitlab.gnome.org/GNOME/yelp-tools/-/archive/%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['4776766816aaa4fff5a9be7229d03e2444fca2f60a11f645c6171abe8bb73925'] + +builddependencies = [ + ('binutils', '2.40'), + ('Meson', '1.1.1'), + ('Ninja', '1.11.1'), + ('CMake', '3.26.3'), + ('Autotools', '20220317'), +] + +dependencies = [ + ('yelp-xsl', '42.1'), + ('ITSTool', '2.0.7'), + ('libxml2', '2.11.4'), + ('mallard-ducktype', '1.0.2'), + ('lxml', '4.9.2'), +] + +fix_python_shebang_for = ['bin/*'] + +sanity_check_paths = { + 'files': [ + 'bin/yelp-build', + 'bin/yelp-check', + 'bin/yelp-new', + ], + 'dirs': ['share/%(name)s'], +} + +sanity_check_commands = [ + 'yelp-build cache -h', + 'yelp-check hrefs -h', +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/y/yelp-xsl/yelp-xsl-42.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/y/yelp-xsl/yelp-xsl-42.1-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..ad7d8eddb4ec --- /dev/null +++ b/easybuild/easyconfigs/y/yelp-xsl/yelp-xsl-42.1-GCCcore-12.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'yelp-xsl' +version = '42.1' + +homepage = "https://gitlab.gnome.org/GNOME/yelp-xslg" +description = """yelp-xsl is a collection of programs and data files to help you build, maintain, + and distribute documentation. It provides XSLT stylesheets that can be built upon for help + viewers and publishing systems. These stylesheets output JavaScript and CSS content, + and reference images provided by yelp-xsl. This package also redistributes copies + of the jQuery and jQuery.Syntax JavaScript libraries. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://gitlab.gnome.org/GNOME/yelp-xsl/-/archive/%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['00f3ee8d9fa048d80063cc09477d24a09349e35c58ffdf9ecea253a4ca882068'] + +builddependencies = [ + ('binutils', '2.40'), + ('ITSTool', '2.0.7'), + ('gettext', '0.21.1'), + ('Autotools', '20220317'), +] + +preconfigopts = 'NOCONFIGURE=1 ./autogen.sh && ' + +sanity_check_paths = { + 'files': [], + 'dirs': [ + 'share/pkgconfig', + 'share/%(name)s', + ] +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/z/Z3/Z3-4.13.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/z/Z3/Z3-4.13.0-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..a925168f1478 --- /dev/null +++ b/easybuild/easyconfigs/z/Z3/Z3-4.13.0-GCCcore-13.3.0.eb @@ -0,0 +1,50 @@ +easyblock = 'PythonBundle' + +name = 'Z3' +version = '4.13.0' + +homepage = 'https://github.com/Z3Prover/z3' +description = """Z3 is a theorem prover from Microsoft Research with support for bitvectors, +booleans, arrays, floating point numbers, strings, and other data types. This +module includes z3-solver, the Python interface of Z3. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('CMake', '3.29.3'), + ('binutils', '2.42'), +] +dependencies = [ + ('Python', '3.12.3'), + ('GMP', '6.3.0'), +] + +use_pip = True + +_fix_parallelism = """sed -i 's/str(multiprocessing.cpu_count())/"%(parallel)s"/' setup.py && """ +_enable_gmp = """sed -i "s/Z3_USE_LIB_GMP.*/Z3_USE_LIB_GMP' : True,/" setup.py && """ + +exts_list = [ + ('z3-solver', version + '.0', { + 'modulename': 'z3', + 'checksums': ['52588e92aec7cb338fd6288ce93758ae01770f62ca0c80e8f4f2b2333feaf51b'], + 'preinstallopts': _fix_parallelism + _enable_gmp, + }), +] + +# make Z3 headers and libraries accessible in their usual location +local_z3_site_path = "lib/python%(pyshortver)s/site-packages/%(namelower)s" +postinstallcmds = [ + 'ln -s %s/include "%%(installdir)s/include"' % local_z3_site_path, + 'cd "%%(installdir)s"; for lib in %s/lib/*; do ln -s ../$lib lib/$(basename $lib); done' % local_z3_site_path +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/z3', 'include/z3_api.h', 'lib/libz3.' + SHLIB_EXT], + 'dirs': ['include', 'lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.5-GCCcore-13.3.0.eb b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.5-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..98db227b9aa2 --- /dev/null +++ b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.5-GCCcore-13.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'ZeroMQ' +version = '4.3.5' + +homepage = 'https://www.zeromq.org/' +description = """ZeroMQ looks like an embeddable networking library but acts like a concurrency framework. + It gives you sockets that carry atomic messages across various transports like in-process, + inter-process, TCP, and multicast. You can connect sockets N-to-N with patterns like fanout, + pub-sub, task distribution, and request-reply. It's fast enough to be the fabric for clustered + products. Its asynchronous I/O model gives you scalable multicore applications, built as asynchronous + message-processing tasks. It has a score of language APIs and runs on most operating systems.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/%(namelower)s/libzmq/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['6653ef5910f17954861fe72332e68b03ca6e4d9c7160eb3a8de5a5a913bfab43'] + +builddependencies = [ + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), +] +dependencies = [ + ('OpenPGM', '5.2.122'), + ('libsodium', '1.0.20'), + ('util-linux', '2.40'), +] + +# Compialtion warnings in GCC 11, cf. https://github.com/zeromq/libzmq/issues/4178 +# Needto disable warnings as errors. +configopts = "--with-pic --with-pgm --with-libsodium --disable-Werror" + + +sanity_check_paths = { + 'files': ['lib/libzmq.%s' % SHLIB_EXT, 'lib/libzmq.a'], + 'dirs': ['include', 'lib'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/z/Zoltan/Zoltan-3.901-foss-2023a.eb b/easybuild/easyconfigs/z/Zoltan/Zoltan-3.901-foss-2023a.eb new file mode 100644 index 000000000000..57432d0e0ced --- /dev/null +++ b/easybuild/easyconfigs/z/Zoltan/Zoltan-3.901-foss-2023a.eb @@ -0,0 +1,46 @@ +# This easyconfig was created by the BEAR Software team at the University of Birmingham. +easyblock = 'ConfigureMake' + +name = 'Zoltan' +version = '3.901' + +homepage = "https://sandialabs.github.io/Zoltan/" +description = """Zoltan Dynamic Load Balancing and Graph Algorithm Toolkit""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'pic': True} + +github_account = 'sandialabs' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['030c22d9f7532d3076e40cba1f03a63b2ee961d8cc9a35149af4a3684922a910'] + +dependencies = [ + ('gzip', '1.12'), + ('SCOTCH', '7.0.3'), + ('ParMETIS', '4.0.3'), +] + +preconfigopts = 'mkdir build && cd build &&' +configure_cmd = '../configure' +configopts = ' '.join([ + '--enable-gzip', + '--with-scotch', + '--with-scotch-incdir=$EBROOTSCOTCH/include', + '--with-scotch-libdir=$EBROOTSCOTCH/lib', + '--with-parmetis', + '--with-parmetis-incdir=$EBROOTPARMETIS/include', + '--with-parmetis-libdir=$EBROOTPARMETIS/lib', + '--disable-examples', + '--disable-tests', +]) +prebuildopts = 'cd build &&' +buildopts = 'everything' +preinstallopts = 'cd build &&' + +sanity_check_paths = { + 'files': ['lib/libzoltan.a', 'include/zoltan.h'], + 'dirs': [], +} + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/z/z5py/z5py-2.0.17-foss-2023a.eb b/easybuild/easyconfigs/z/z5py/z5py-2.0.17-foss-2023a.eb new file mode 100644 index 000000000000..3f3c87147716 --- /dev/null +++ b/easybuild/easyconfigs/z/z5py/z5py-2.0.17-foss-2023a.eb @@ -0,0 +1,50 @@ +easyblock = 'CMakeMakeCp' + +name = 'z5py' +version = '2.0.17' + +homepage = 'https://github.com/constantinpape/z5/' +description = """Lightweight C++ and Python interface for datasets in zarr and N5 format.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/constantinpape/z5/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['76acaeec7203b8d3baec45ccce82cd260dc1893f1516640acec5de6d74c078ef'] + +builddependencies = [('CMake', '3.26.3')] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('bzip2', '1.0.8'), + ('lz4', '1.9.4'), + ('XZ', '5.4.2'), + ('zlib', '1.2.13'), + ('xtensor', '0.24.7'), + ('python-blosc', '1.11.0'), + ('imageio', '2.33.1'), + ('h5py', '3.9.0'), + ('nlohmann_json', '3.11.2'), + ('zarr', '2.17.1'), + ('pybind11', '2.11.1'), +] + +configopts = '-DWITH_ZLIB=ON -DWITH_BZIP2=ON ' +# Fix path to python executable - it finds v3.6.8 from /usr/bin/ without this fix +configopts += '-DPYTHON_EXECUTABLE="$EBROOTPYTHON/bin/python" ' + +# export PYTHON_MODULE_INSTALL_DIR to fix make install +preinstallopts = 'export PYTHON_MODULE_INSTALL_DIR="%(builddir)s/easybuild_obj/python/" && ' + +files_to_copy = [(['python/z5py'], 'lib/python%(pyshortver)s/site-packages'), 'z5-config.cmake'] + +sanity_check_paths = { + 'files': ['z5-config.cmake'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/z5py'], +} +sanity_check_commands = ["python -c 'import z5py'"] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.3.1-GCCcore-14.2.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.3.1-GCCcore-14.2.0.eb new file mode 100644 index 000000000000..187f8da34f7d --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.3.1-GCCcore-14.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.3.1' + +homepage = 'https://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'GCCcore', 'version': '14.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://zlib.net/fossils'] +sources = [SOURCELOWER_TAR_GZ] +# patches = ['zlib-%(version)s_fix-CC-logic-in-configure.patch'] +checksums = ['9a93b2b7dfdac77ceba5a558a580e74667dd6fede4585b91eefb60f03b72df23'] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.42', '', SYSTEM)] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/setup.py b/setup.py index 3aa9a8222085..ae4897821b1f 100644 --- a/setup.py +++ b/setup.py @@ -44,7 +44,7 @@ # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '4.9.2' +VERSION = '4.9.3' MAJ_VER = VERSION.split('.')[0] MAJMIN_VER = '.'.join(VERSION.split('.')[0:2]) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index ceae4c5bef92..dc24739ec012 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -614,6 +614,7 @@ def check_dep_vars(self, gen, dep, dep_vars): 'pydantic': [ # GTDB-Tk v2.3.2 requires pydantic 1.x (see https://github.com/Ecogenomics/GTDBTk/pull/530) ('1.10.13;', ['GTDB-Tk-2.3.2-', 'GTDB-Tk-2.4.0-']), + ('2.7.4;', ['MultiQC-1.22.3-']), ], # medaka 1.1.*, 1.2.*, 1.4.* requires Pysam 0.16.0.1, # which is newer than what others use as dependency w.r.t. Pysam version in 2019b generation; @@ -662,6 +663,8 @@ def check_dep_vars(self, gen, dep, dep_vars): 'UCX': [('1.11.0;', ['UCX-CUDA-1.11.0-'])], # Napari 0.4.19post1 requires VisPy >=0.14.1 <0.15 'VisPy': [('0.14.1;', ['napari-0.4.19.post1-'])], + # Visit-3.4.1 requires VTK 9.2.x + 'VTK': [('9.2.6;', ['Visit-3.4.1-'])], # WPS 3.9.1 requires WRF 3.9.1.1 'WRF': [(r'3\.9\.1\.1', [r'WPS-3\.9\.1'])], # wxPython 4.2.0 depends on wxWidgets 3.2.0 @@ -1044,25 +1047,19 @@ def test_pr_sha256_checksums(self): 'R-bundle-Bioconductor-3.[2-5]', ] - # the check_sha256_checksums function (again) creates an EasyBlock instance - # for easyconfigs using the Bundle easyblock, this is a problem because the 'sources' easyconfig parameter - # is updated in place (sources for components are added to the 'parent' sources) in Bundle's __init__; - # therefore, we need to reset 'sources' to an empty list here if Bundle is used... - # likewise for 'patches' and 'checksums' - bundle_easyblocks = ['Bundle', 'CargoPythonBundle', 'PythonBundle', 'EB_OpenSSL_wrapper'] - for ec in self.changed_ecs: - if ec['easyblock'] in bundle_easyblocks or ec['name'] in ['Clang-AOMP']: - ec['sources'] = [] - ec['patches'] = [] - ec['checksums'] = [] - # filter out deprecated easyconfigs - retained_changed_ecs = [] - for ec in self.changed_ecs: - if not ec['deprecated']: - retained_changed_ecs.append(ec) - - checksum_issues = check_sha256_checksums(retained_changed_ecs, whitelist=whitelist) + retained_changed_ecs = [ec for ec in self.changed_ecs if not ec['deprecated']] + + # The check_sha256_checksums function creates an EasyBlock instance. + # For easyconfigs using the Bundle easyblock, this is a problem because the 'sources' easyconfig parameter + # is updated in place (sources for components are added to the 'parent' sources) in Bundle's __init__. + # Therefore, we need to a operate on a copy of those easyconfigs. + bundle_easyblocks = {'Bundle', 'CargoPythonBundle', 'PythonBundle', 'EB_OpenSSL_wrapper'} + + def is_bundle(ec): + return ec['easyblock'] in bundle_easyblocks or ec['name'] == 'Clang-AOMP' + ecs = [ec.copy() if is_bundle(ec) else ec for ec in retained_changed_ecs] + checksum_issues = check_sha256_checksums(ecs, whitelist=whitelist) self.assertTrue(len(checksum_issues) == 0, "No checksum issues:\n%s" % '\n'.join(checksum_issues)) @skip_if_not_pr_to_non_main_branch() @@ -1079,10 +1076,15 @@ def test_pr_python_packages(self): whitelist_pip_check = [ r'Mako-1.0.4.*Python-2.7.12.*', - # no pip 9.x or newer for configparser easyconfigs using a 2016a or 2016b toolchain - r'configparser-3.5.0.*-2016[ab].*', + # no pip 9.x or newer for easyconfigs using a 2016a or 2016b toolchain + r'.*-2016[ab]-Python-.*', # mympirun is installed with system Python, pip may not be installed for system Python r'vsc-mympirun.*', + # ReFrame intentionally installs its deps in a %(installdir)s/external subdir, which is added + # to sys.path by the ReFrame command, and is intentionally NOT on the PYTHONPATH. + # Thus, a pip check fails, but this is expected and ok, it is still a working ReFrame installation + # See https://github.com/easybuilders/easybuild-easyconfigs/pull/21269 for more info + r'ReFrame.*', ] failing_checks = [] @@ -1212,8 +1214,9 @@ def test_pr_sanity_check_paths(self): # including CargoPythonPackage, CMakePythonPackage, GoPackage, JuliaBundle, PerlBundle, # PythonBundle & PythonPackage; # BuildEnv, ModuleRC and Toolchain easyblocks doesn't install anything so there is nothing to check. - whitelist = ['BuildEnv', 'CargoPythonBundle', 'CargoPythonPackage', 'CMakePythonPackage', 'CrayToolchain', - 'GoPackage', 'JuliaBundle', 'ModuleRC', 'PerlBundle', 'PythonBundle', 'PythonPackage', 'Toolchain'] + whitelist = ['BuildEnv', 'CargoPythonBundle', 'CargoPythonPackage', 'CMakePythonPackage', + 'ConfigureMakePythonPackage', 'CrayToolchain', 'GoPackage', 'JuliaBundle', 'ModuleRC', + 'PerlBundle', 'PythonBundle', 'PythonPackage', 'Toolchain'] # Bundles of dependencies without files of their own # Autotools: Autoconf + Automake + libtool, (recent) GCC: GCCcore + binutils, CUDA: GCC + CUDAcore, # CESM-deps: Python + Perl + netCDF + ESMF + git, FEniCS: DOLFIN and co,