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RELEASE_NOTES
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This file contains a description of the major changes to the easybuild-easyconfigs EasyBuild package.
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 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)
---------------------
update/bugfix release
- added easyconfigs for foss/2024.05 toolchain (candidate for foss/2024a) (#20646)
- added example easyconfig files for 82 new software packages:
- AEDT (#20357), amdahl (#20346), AMGX (#20255), assembly-stats (#20281), Bio-FeatureIO (#20461),
bitshuffle (#20661), Cassiopeia (#20289), CCCL (#20255), charm-gems (#20327), CheckM2 (#20399),
chromVARmotifs (#20402), cmph (#20278), COMEBin (#20717), Compass (#20500), ctffind5 (#20669), currentNe (#20791),
CVX (#20231), deepfold (#20247), dotNET-Core (#20256), EasyMocap (#20446), ensmallen (#20485), EVcouplings (#20744),
Faiss (#19669), FDMNES (#20321), gnupg-bundle (#20406), grpcio (#20191), hatch-jupyter-builder (#20606),
hevea (#20597), HiGHS (#20186), hmmcopy_utils (#20472), HOMER (#20590), ICON (#20573), jiter (#20746),
LangChain (#20746), langchain-anthropic (#20746), libabigail (#20539), libbraiding (#20655), libhomfly (#20482),
libsupermesh (#20470), LIBSVM-MATLAB (#20752), Lightning (#19964), lil-aretomo (#20696), makefun (#20619),
MetalWalls (#20403), MICOM (#20186), ml-collections (#20247), ml_dtypes (#20707), mlpack (#20485), MOFA2 (#20538),
mumott (#20719), nvitop (#20512), ocamlbuild (#20552), optiSLang (#20320), orthAgogue (#20278), pdf2docx (#20416),
planarity (#20753), plantri (#20467), plmc (#20744), PortAudio (#20307), premailer (#20348), ProteinMPNN (#20705),
PRRTE (#20698), PSM2 (#20496), PyAEDT (#20357), pybind11-stubgen (#20518), PyEXR (#19983), pyGAM (#20385),
PyHMMER (#20544), pyseer (#20502), PyVista (#20649), qmflows (#20384), SciTools-Iris (#20767), SCReadCounts (#20455),
SDL2_gfx (#20466), subunit (#20412), TF-COMB (#20666), tiktoken (#20336), TorchIO (#20648), t-SNE-CUDA (#19669),
VAMPIRE-ASM (#20368), wfdb (#20521), WGDgc (#20367)
- added additional easyconfigs for various supported software packages, including:
- 4ti2 1.6.10, AFNI 24.0.02, Autoconf 2.72, Autotools 20231222, adjustText 1.1.1, aiohttp 3.9.5, alevin-fry 0.9.0,
alsa-lib 1.2.9, atropos 1.1.32, autopep8 2.2.0, BCFtools 1.19, BLIS 1.0, BWA 0.7.18, Boost 1.85.0, bcrypt 4.1.3,
binutils 2.42, bokeh 3.4.1, CGAL 5.6.1, CREST 3.0.1, CellRanger-ARC 2.0.2, CellRanger 8.0.1, CellRank 2.0.2,
Clang 17.0.6, CoCoALib 0.99850, Cython 3.0.10, cURL 8.7.1, cffi 1.16.0, code-server 4.89.1,
configurable-http-proxy 4.6.1, coverage 7.4.4, cpio 2.15, cppyy 3.1.2, cysignals 1.11.4, Doxygen 1.11.0,
dask-labextension 7.0.0, dask 2024.5.1, deal.II 9.5.2, dorado 0.5.3, dotNET-Core 8.0.203, E-ANTIC 2.0.2,
ECL 24.5.10, ESPResSo 4.2.2, eclib 20240408, expat 2.6.2, FLTK 1.3.9, FMM3D 1.0.4, FlexiBLAS 3.4.4, f90wrap 0.2.13,
fgbio 2.2.1, fontconfig 2.15.0, freetype-py 2.4.0, GAMESS-US 20220930-R2 + 20230930-R2, GCC 13.3.0 + 14.1.0,
GDB 14.2, GDRCopy 2.4.1, GOATOOLS 1.4.5, GTDB-Tk 2.4.0, Giza 1.4.1, gc 8.2.6, gcloud 472.0.0, gemmi 0.6.5,
gettext 0.22.5, giac 1.9.0-99, git 2.45.1, gmsh 4.12.2, gsutil 5.29, HDDM 0.9.9, HTSlib 1.19.1, HyPhy 2.5.60,
h5py 3.11.0, hwloc 2.10.0, ICU 75.1, IOR 4.0.0, imagecodecs 2024.1.1, imgaug 0.4.1, ipympl 0.9.4,
Jupyter-bundle 20240522, JupyterHub 4.1.5, JupyterLab 4.2.0, JupyterNotebook 7.2.0, jupyter-matlab-proxy 0.12.2,
jupyter-resource-usage 1.0.2, jupyter-rsession-proxy 2.2.0, jupyter-server-proxy 4.1.2, jupyter-server 2.14.0,
Kalign 3.4.0, KrakenUniq 1.0.4, kallisto 0.50.1, LAPACK 3.12.0, libarchive 3.7.4, libde265 1.0.15, libdeflate 1.20,
libdwarf 0.9.2, libfabric 1.21.0, libffi 3.4.5, libgcrypt 1.10.3, libgpg-error 1.48, libheif 1.17.6, libidn2 2.3.7,
libnsl 2.0.1, libpciaccess 0.18.1, libpng 1.6.43, libuv 1.48.0, libxml2 2.12.7, line_profiler 4.1.2, MATSim 15.0,
MDTraj 1.9.9, Mako 1.3.5, Meson 1.4.0, MetaMorpheus 1.0.5, Molpro 2024.1.0, MuJoCo 3.1.4, matlab-proxy 0.18.1,
mold 2.31.0, mpmath 1.3.0, NASM 2.16.03, NanoPlot 1.42.0, Nextflow 24.04.2, Ninja 1.12.1, nanoget 1.19.1,
napari 0.4.19.post1, nauty 2.8.8, ncurses 6.5, nghttp2 1.58.0, nghttp3 1.3.0, nglview 3.1.2, ngtcp2 1.2.0,
nodejs 20.13.1, numactl 2.0.18, nvtop 3.1.0, OCaml 5.1.1, OSU-Micro-Benchmarks 7.4, OpenBLAS 0.3.27, OpenMPI 5.0.3,
PARI-GP 2.15.5, PCRE2 10.43, PMIx 5.0.2, Perl 5.38.2, PhyML 3.3.20220408, PnetCDF 1.13.0, PyAMG 5.1.0,
PyQtGraph 0.13.7, PyTorch-Geometric 2.5.0, PyTorch-bundle 2.1.2, PycURL 7.45.3, Pysam 0.22.0, Python 3.12.3,
p11-kit 0.25.3, p4est 2.8.6, parallel 20240322, pauvre 0.2.3, petsc4py 3.20.3, pkgconf 2.2.0, plc 3.10, polars 0.20.2,
poppler 24.04.0, psutil 5.9.8, py3Dmol 2.1.0, pybedtools 0.9.1, pygame 2.5.2, pyiron 0.5.1, pyro-ppl 1.9.0,
python-mujoco 3.1.4, ROOT 6.30.06, RPostgreSQL 0.7-6, RStudio-Server 2023.12.1+402, Rtree 1.2.0, Rust 1.78.0,
SAMtools 1.19.2, SCOTCH 7.0.4, SDL2_image 2.8.2, SDL2_mixer 2.8.0, SDL2_ttf 2.22.0, SQLite 3.45.3, SWIG 4.2.1,
SentencePiece 0.2.0, Seurat 5.1.0, SeuratDisk 20231104, SimNIBS 4.0.1, Singular 4.4.0, Spack 0.21.2, Squidpy 1.4.1,
SymEngine-python 0.11.0, SymEngine 0.11.2, sbt 1.6.2, scikit-build-core 0.9.3, scikit-learn 1.4.2, TOBIAS 0.16.1,
Tcl 8.6.14, TensorFlow 2.15.1, Transformers 4.39.3, texlive 20230313, tmux 3.4, tokenizers 0.15.2, 0.2.5.20231120,
tornado 6.4, UCC 1.3.0, UCX 1.16.0, util-linux 2.40, VSCode 1.88.1, Valgrind 3.23.0, VisPy 0.14.1, wget 1.24.5,
XZ 5.4.5, xorg-macros 1.20.1, xprop 1.2.7, xtb 6.7.0, xxd 9.1.0307, yaml-cpp 0.8.0, zarr 2.17.1, zfp 1.0.1,
zlib-ng 2.1.6, zlib 1.3.1, zstd 1.5.6
- minor enhancements, including:
- add missing (optional) dependency pyproject-metadata to scikit-build-core (#20391)
- add hatch-requirements-txt extension to hatchling easyconfigs (#20389)
- install pkg-config files for ncurses 6.4 when using GCCcore toolchain (#20405)
- use regular 'configure' instead of wrapper script for recent UCX easyconfigs (#20428)
- add RISC-V support to UCX 1.15.0 (#20429), UCC 1.2.0 (#20432), BLIS 0.9.0 (#20468), PAPI 7.1.0 (20659)
- add extensions to R-bundle-CRAN v2023.12: cmna (#20445), rhandsontable (#20614), XBRL (#20506)
- add checksum for RISC-V version to easyconfig for Java 21.0.2 (#20495)
- remove 'TORCHVISION_INCLUDE' from PyTorch-bundle easyconfigs, now handled by custom easyblock for torchvision (#20504)
- add dependencies required for GUI in Cellpose 2.2.2 easyconfigs (#20620)
- add 'build_info_msg' about kernel modules to GDRCopy (#20641)
- build both static and shared libs for Brotli 1.1.0 (#20757)
- various bug fixes, including:
- add missing dependencies for funannotate (#17690)
- fix path to SuiteSparse include/lib in easyconfig for CVXopt v1.3.1 (#20232)
- fix Highway 1.0.3 on some systems by disabling 'AVX3_DL' (#20298)
- replace incorrect scikit-bio 0.5.9 with scikit-bio 0.6.0 as dependency for scCODA (#20300)
- add alternate checksum to OpenMolcas v23.06 (#20301)
- change arrow-R dependency of Bioconductor v3.18 to v14.0.1 (which depends on required matching Arrow v14.0.1) (#20324)
- fix hardcoded '/bin/mv' path in Rhdf5lib extension included in R-bundle-Bioconductor v3.16 + v3.18 (#20378)
- remove dependency on HDF5 in recent Bioconductor easyconfigs (#20379)
- make sure that libjpeg-turbo libraries are installed in 'lib' subdirectory (#20386)
- add patch for Libint 2.7.2 to fix compiler error with glibc >= 2.34 (#20396)
- use 'bash' rather than 'sh' to run PLINK-2.00a3.7 tests (#20404)
- add patch to fix 'UNPACK-OPAL-VALUE: UNSUPPORTED TYPE 33 FOR KEY' error in OpenMPI 4.1.5 (#20422)
- add patch to increase compatibility with AVX512 platforms for bwa-mem2 v2.2.1 (#20434)
- add patch for GROMACS 2024.1 to fix filesystem race in tests (#20439)
- demote poetry to build dependency for nanocompore (#20453)
- add patch to fix CVE-2024-27322 in R v3.6.x (#20464), v4.0.x (#20463), and v4.1.x + v4.2.x + v4.3.x (#20462)
- disable test that fetches from the web for torchtext extension in PyTorch-bundle v2.1.2 (#20484)
- fix sanity check paths for JupyterLab 4.0.5 (#20514)
- fix detection of CC/CXX compilers for 'wmake' in OpenFOAM v2306 + v2312 (#20517)
- use the included gmxapi for GROMACS 2024.1 (#20522)
- add new checksum for signal_1.8-0 to R-bundle-CRAN-2023.12 (#20527)
- fix test in Cwd extension of Perl-bundle-CPAN 5.36.1 (#20536)
- fix patch name in easyconfig for Perl-bundle-CPAN 5.36.1 + add also use it for Perl-bundle-CPAN 5.38.0 (#20540)
- fix cwd_enoent test in Perl (#20541)
- move dependency on BeasutifulSoup in IPython v8.14.0 to jupyter-server (#20547)
- remove dependency on BeasutifulSoup from IPython v8.17.2 (#20548)
- add alternative checksum for source tarball of MONAI 1.3.0 (#20618)
- add cpio as build dependency to recent BLAST+ versions (#20674)
- add --disable-htmlpages to recent FFmpeg easyconfigs (#20686)
- remove duplicate crates from easyconfig for timm-0.9.7 (#20687)
- add missing HDF5 dependency in recent Armadillo easyconfigs (>= 11.4.3) (#20710)
- add patches for failing LAPACK tests and RISC-V test segfaults to OpenBLAS 0.3.27 (#20745)
- move all easyconfigs for libavif to GCCcore toolchain + fix dependencies (#20747)
- make sure mummerplot can use gnuplot if available for recent MUMmer (#20749)
- prevent configure script of recent BLAST+ versions from prepending system paths to $PATH (#20751)
- fix fastparquet v2023.4.0 using CargoPythonBundle easyblock (#20775)
- remove --with-64 from configopts for recent BLAST+ versions (#20784)
- add patch to fix build of pdsh 2.34 with Slurm 23.x (#20795)
- other changes:
- move 'build' from extensions to dependencies in easyconfig for napari 0.4.18 (#20433)
- update version of fsspec extension in easyconfig for Squidpy 1.4.1 to be compatible with s3fs provided via PyTorch-bundle (#20477)
- add commented out PSM2 dependency, relevant for x86_64 systems with OmniPath, to recent libfabric easyconfigs (#20501, #20585, #20794)
- replace SQLAlchemy extension with regular dependency in easyconfig for Optuna v3.5.0 (#20510)
- replace SQLAlchemy extension in JupyterHub v4.0.2 easyconfig with regular dependency (#20511)
- bump Cython to v3.0.8 in Cartopy v0.22.0 easyconfig for foss/2023a toolchain, to avoid dependency version conflict with sckit-learn v1.4.2, which requires Cython >= v3.0.8 (#20525)
- change dependency on hatchling of BeautifulSoup v4.12.2 to a build dependency (#20546)
- bump async-timeout to 4.0.3 in aiohttp 3.8.5 (#20553)
- stick to gfbf/2023a as toolchain for ipympl v0.9.3 (#20586)
- rename tornado-timeouts.patch to tornado-6.1_increase-default-timeouts.patch + add missing authorship (#20587)
- remove easyconfigs for CellBender v0.3.1, since this version has been redacted due to a serious bug (#20722)
v4.9.1 (5 April 2024)
---------------------
update/bugfix release
- added example easyconfig files for 101 new software packages:
- AMICA (#19842), AreTomo2 (#19681), btllib (#19779), bwa-mem2 (#20217), CENSO (#19826), Circlator (#19847), Clarabel.rs (#20149),
code-cli (#19645), Concorde (#19768), contextily (#19807), CUTLASS (#19304), DeepLoc (#19514), Delft3D (#19869), DeltaLake (#19758),
denseweight (#20139), desktop-file-utils (#19701), devbio-napari (#19586), DjVuLibre (#19701), Elmer (#19448),
EnergyPlus (#19565), EpiSCORE (#18618), evince (#19701), ExpressBetaDiversity (#19938), ExtremeLy (#19870), f90nml (#19171),
FFAVES (#19822), fugue (#19694), gcsfs (#20042), GenomeComb (#19749), GI-DocGen (#19701), GKlib-METIS (#20096), GRASP-suite (#19665),
gspell (#19701), GUIDANCE (#20063), hdWGCNA (#20124), HF-Datasets (#20166), IDG (#18924), igvShiny (#19714), inflection (#20036),
InterOp (#19303), IonQuant (#19812), Lab-Streaming-Layer (#19945), Levenshtein (#19771), libfyaml (#19856), libgxps (#19701),
libhandy (#19701), libspectre (#19701), lit (#20252), lmoments3 (#19870), Markdown (#20239), MetaDecoder (#20123), mfqe (#19781),
Miniforge3 (#20227), MLflow (#19893), MODFLOW (#20142), morphosamplers (#20000), MotionCor3 (#19681), MSFragger (#19811),
multiprocess (#19986), nf-core (#19107), noise (#20048), OpenMEEG (#19853), OpenSlide-Java (#19962), PAGAN2 (#19618), PASA (#19570),
pblat (#19570), PBZIP2 (#19677), PDM (#20012), Philosopher (#19383), phyluce (#19779), poppunk (#17402), PSASS (#20160), psycopg (#19107),
PyInstaller (#19519), PyQt-builder (#16703), pytest-workflow (#19107), python-casacore (#20089), pytorch-3dunet (#19290), pyXDF (#19916),
q2-krona (#19633), QuPath (#19962), radian (#19484), remake (#19581), rethinking (#19755), RHEIA (#19496), s3fs (#19576),
safestringlib (#20217), scikit-extremes (#19870), SemiBin (#19767), semla (#19747), Sentence-Transformers (#19509), sinto (#13846),
sktime (#19692), SQLAlchemy (#20242), tiny-cuda-nn (#19304), tox (#16178), Vamb (#17457), xpdf (#20024), yt (#20263), Zeo++ (#19555),
zUMIs (#19949)
- added additional easyconfigs for various supported software packages, including:
- Abseil 20240116.1, ABySS 2.3.7, AMS 2023.104, Anaconda3 2024.02, anndata 0.10.5.post1, anvio 8, ArchR 1.0.2,
archspec 0.2.2, Armadillo 12.8.0, arpack-ng 3.9.1, arrow-R 14.0.0.2, ASAP3 3.13.3, assimp 5.3.1, autopep8 2.0.4,
basemap 1.3.9, BerkeleyGW 3.1.0 + 4.0, BiG-SCAPE 1.1.5, Biopython 1.83, Blosc 1.21.5, Blosc2 2.13.2, Boost.MPI 1.82.0,
Boost.Python 1.83.0, Braindecode 0.8.1, Brotli-python 1.1.0, build 1.0.3, buildenv-default foss-2023b + intel-2023b,
bx-python 0.10.0, CapnProto 1.0.1.1, c-ares 1.27.0, Cartopy 0.22.0, casacore 3.5.0, Cbc 2.10.11, ccache 4.9, cclib 1.8,
CellBender 0.3.1, CellTypist 1.6.2, CFITSIO 4.3.1, Cgl 0.60.8, Clang-Python-bindings 16.0.6, Clp 1.17.9, CmdStanR 0.7.1,
COBRApy 0.29.0, code-server 4.22.1, CoinUtils 2.11.10, CoordgenLibs 3.0.2, CREST 2.12, cryoCARE 0.3.0, CSBLAST 2.2.4,
CUDA 12.3.2 + 12.4.0, cuDNN 8.9.7.29, CuPy 13.0.0, cuSPARSELt 0.6.0.6, cuTENSOR 2.0.1.2, CVXPY 1.4.2, Cython 3.0.8,
dask 2023.12.1, datalad 0.19.5, DB_File 1.859, deepdiff 6.7.1, DeepLabCut 2.3.6, DendroPy 4.6.1, Deprecated 1.2.14,
DFT-D4 3.6.0, DIAMOND 2.1.9, Dice 20240101, dlb 3.4, DLPack 0.8, dorado 0.5.1, EggLib 3.3.0, einops 0.7.0, ELPA 2023.11.001,
enchant-2 2.6.5, ESMF 8.4.2, eSpeak-NG 1.51, ETE 3.1.3, expecttest 0.2.1, fastjet 3.4.2, fastjet-contrib 1.053, FDS 6.8.0,
fineRADstructure 20210514, fio 3.36, Fiona 1.9.5, Flask 3.0.0, FLINT 3.1.1, Flye 2.9.3, fmt 10.2.0, freebayes 1.3.7,
GATK 4.5.0.0, gawk 5.3.0, geocube 0.4.3, geopandas 0.14.2, geopy 2.4.1, GHC 9.4.6, Ghostscript 10.02.1, GIMIC 2.2.1,
git-lfs 3.5.1, GitPython 3.1.42, GLFW 3.4, Go 1.22.1, GPAW 24.1.0, GPAW-setups 24.1.0, gperftools 2.14, Gradle 8.6,
graph-tool 2.55, Greenlet 3.0.3, GROMACS 2024.1, gRPC 1.62.1, GTK3 3.24.39, Gurobi 11.0.0, HDF5 1.14.3, HeFFTe 2.4.0,
HepMC3 3.2.6, hunspell 1.7.2, igraph 0.10.10, infercnvpy 0.4.3, iperf 3.16, IQ-TREE 2.2.2.7, ISA-L 2.31.0, Java/19 (19.0.2),
Java/21 (21.0.2), json-c 0.17, Julia 1.10.0, KaHIP 3.16, LAMMPS 2Aug2023_update2, LASTZ 1.04.22, LDC 1.36.0, leidenalg 0.10.2,
libcint 5.5.0, libgit2 1.7.2, librosa 0.10.1, librsvg 2.58.0, libSBML 5.19.7, libsigsegv 2.14, libtirpc 1.3.4,
libxml2-python 2.11.4, likwid 5.3.0, LLVM 14.0.6, MACS3 3.0.1, maeparser 1.3.1, Mamba 23.11.0-0, MATIO 1.5.26,
matplotlib 3.8.2, maturin 1.5.0, MCR R2023a, MDAnalysis 2.7.0, MDI 1.4.26, medaka 1.11.3, Meson 1.3.1, MiXCR 4.6.0,
MNE-Python-1.6., MOABB 1.0.0, molmod 1.4.8, MONAI 1.3.0, mpi4py 3.1.5, mrcfile 1.5.0, NCCL 2.20.5, NCO 5.1.9, NECI 20230620,
netcdf4-python-1.6.5, networkx 3.2.1, NGSpeciesID 0.3.0, NiBabel 5.2.0, nichenetr 2.0.4, Nilearn 0.10.3,
nlohmann_json 3.11.3, NLTK 3.8.1, ntCard 1.2.2, numba 0.58.1, NVHPC 24.1, OBITools3 3.0.1b26, OCaml 4.14.0, occt 7.8.0,
onedrive 2.4.25, ONNX 1.15.0, ONNX-Runtime 1.16.3, ont-fast5-api 4.1.2, OPARI2 2.0.8, OpenFOAM v2306 + v2312, OpenSSL/3,
Optuna 3.5.0, Osi 0.108.9, PAPI 7.1.0, Parallel-Hashmap 1.3.12, ParaView 5.12.0, PDT 3.25.2, PETSc 3.20.3, PGPLOT 5.2.2,
phonemizer 3.2.1, phono3py 2.7.0, Pillow 10.2.0, Pint 0.23, plotly.py 5.18.0, poetry 1.7.1, presto-1.0.0 20230501,
PROJ 9.3.1, prompt-toolkit 3.0.36, protobuf 25.3, protobuf-python 4.25.3, psmc 0.6.5_20221121, pstoedit 3.78,
psycopg2 2.9.9, PuLP 2.8.0, PyCheMPS2 1.8.12, pycodestyle 2.11.1, pydantic 1.10.13 + 2.5.3 2.6.4, pydicom 2.4.4, pydot 2.0.0,
pyfaidx 0.8.1.1, PyFrag 2023-dev.20240220, pymatgen 2023.12.18, PyOpenCL 2023.1.4, PyOpenGL 3.1.7, pyparsing 3.1.1,
PyQt5 5.15.10, Pysam 0.22.0, PySCF 2.4.0, pyspoa 0.2.1, PyTables 3.9.2, pytest-rerunfailures 14.0, python-igraph 0.11.4,
python-irodsclient 2.0.0, python-isal 1.6.1, python-libsbml 5.20.2, python-xxhash 3.4.1, PyTorch-Ignite 0.4.13,
PyTorch-Lightning 2.2.1, PyZMQ 25.1.2, QIIME2 2023.7.0, Qt5 5.15.13, Qt6 6.6.3, Qtconsole 5.5.1, QtPy 2.4.1,
QuantumESPRESSO 7.3, R 4.3.3, rasterio 1.3.9, R-bundle-Bioconductor 3.18, rclone 1.66.0, RE2 2024-03-01, Redis 7.2.4,
redis-py 5.0.1, rioxarray 0.15.0, Rivet 3.1.9, rMATS-turbo 4.2.0, RNA-Bloom 2.0.1, rocm-smi 5.6.0, rpy2 3.5.15,
ruamel.yaml 0.18.6, Ruby 3.3.0, Rust 1.75.0 + 1.76.0, Salmon 1.10.1, Sambamba 1.0.1, Saxon-HE 12.4, SBCL 2.4.1,
ScaFaCoS 1.0.4, Scalene 1.5.35, scanpy 1.9.8, scib 1.1.4, scikit-bio 0.5.9, scikit-learn 1.4.0, scikit-lego 0.7.4,
scikit-misc 0.3.1, SCons 4.6.0, Score-P 8.4, scVelo 0.3.1, Seaborn 0.13.2, SentencePiece 0.1.99, Seqmagick 0.8.6,
Seurat 5.0.1, SIP 6.8.1, siscone 3.0.6, skorch 0.15.0, SLEPc 3.20.1, snakemake 8.4.2, SNAPE-pooled 20150707,
SOAPdenovo-Trans 1.0.5, Spark 3.5.1, spdlog 1.12.0, spoa 4.1.0, SRA-Toolkit 3.0.10, Stack 2.13.1, STAR 2.7.11b,
statsmodels 0.14.1, tensorboard 2.15.1, tensorboardX 2.6.2.2, tensorflow-probability 0.20.0, texinfo 7.1, timm 0.9.7,
torchvision 0.16.0, tqdm 4.66.2, TRIQS 3.2.0, TRIQS-cthyb 3.2.1, TRIQS-dft_tools 3.2.0, TRIQS-tprf 3.2.1,
typing-extensions 4.9.0, UCX 1.16.0, UDUNITS 2.2.28, umap-learn 0.5.5, UMI-tools 1.1.4, Vala 0.56.14, VEP 111,
Vim 9.1.0004, vsc-mympirun 5.4.0, WFA2 2.3.4, wget 1.21.4, WhatsHap 2.2, WIEN2k 23.2, wrf-python 1.3.4.1,
Xerces-C++ 3.2.5, XlsxWriter 3.1.9, XML-LibXML v2.0209, xxHash 0.8.2, yaff 1.6.0, YAXT 0.10.0, Yices 2.6.4, YODA 1.9.9
- minor enhancements, including:
- add build info message to easyconfig for NLTK 3.7 (#18550)
- enable KLU and CUDA solvers in SUNDIALS v6.6.0 (#19490)
- add extensions to R-bundle-CRAN v2023.12: tidybayes (#19712), spdep (#19729), fixest (#20055)
- add plyranges extension to R-bundle-Bioconductor (for zUMIs) (#19949)
- add PyOpenGL-accelerate extension to PyOpenGL v3.1.7 (#20007)
- use system architecture template in DB_File (#20014), GD (#20015), and GDGraph (#20016)
- add support for Vulkan software rendering in Mesa v23.1.9 by adding Wayland dependency (#20069)
- add MODIStsp extension (+ required dependencies) to R 4.2.2 (#20113)
- enable LittleCMS2 and WebP support in recent Pillow (#20195)
- improve test for validity of easyconfig files (#20205)
- add easyconfig test that checks if backdoored XZ versions are introduced (#20267)
- various bug fixes, including:
- add patch for Bison 3.7.1 to fix build error on old OS versions (#12291)
- add missing pkg-config build dependency for recent p11-kit easyconfigs (#16318)
- fix dependencies and configure flags of GnuTLS 3.7.x (#19070)
- remove numa configure option from hwloc 2.5+ (#19085)
- add patches for OpenBLAS v0.3.21 to disable -ftree-vectorize for netlib LAPACK (#19280)
- add patch to fix flaky scipy build in SciPy-bundle v2023.11 (#19481)
- add missing SciPy-bundle dependency to TensorRT easyconfig (#19486)
- fix lapack test failures in OpenBLAS 0.3.23/24 (#19495)
- add patch for Arrow v8.0.0 - v11.0.0 to add missing `__arrow_ext_class__` method to `BaseExtensionType` class (#19532)
- change homepage for argtable (#19551)
- add patches for PyTorch v2.1.2 with `foss/2022a` (#19571), `foss/2022b` (#19572), and `foss/2023a` (#19573) to fix test failures on non-x86 platforms
- use pocl with CUDA support as dependency for PyOpenCL v2023.1.4 (#19584)
- remove `osdependencies` from ccache easyconfigs using GCCcore toolchain (#19600)
- use https source URL for alsa-lib (#19628)
- add missing dm-tree dependency for dm-reverb 0.2.0 (#19653)
- add libyaml import check to PyYAML and fix builds since split to minimal Python (#19662)
- demote meson-python to a build dependency in recent matplotlib easyconfigs (#19670)
- add patch to fix upb CopyFrom error in protobuf-python 4.24.0 (#19671)
- demote poetry to build dep in expecttest (#19675)
- add zlib dependency to YODA and Rivet (#19679)
- fix missing spaces in Graphviz configure options (#19687)
- strip iconv from pkgconfig file for libarchive v3.6.2 (#19698)
- use separate bcrypt easyconfig (using CargoPythonPackage) as dependency for JupyterHub v4.0.2 (#19703)
- use maturin easyconfig using CargoPythonPackage as a dependency for fastparquet v2023.4.0 (#19704)
- add patches for Perl-bundle-CPAN v5.36.1 to fix installation of `Sys::Info::Driver::Linux*` extensions on Debian Bookworm (#19727)
- explicitly specify Fortran compiler for recent CDO versions to fix issues on non-x86_64 architectures (#19735)
- add patch for `jupyter_core` extension in `jupyter-server` to set jupyter path by `$EB_ENV_JUPYTER_ROOT` (#19737)
- add Python build dependency to 1.9.x Doxygen (#19743)
- fix Arrow v14.0.1 to install pyarrow as an extension (#19758)
- fix homepage + source URL for Gblocks 0.91b (#19797)
- make sure that Brunsli libraries are installed into `lib` (#19805)
- fix dependency with `libidn.so.11` in tbl2asn v20220427 and v20230713 easyconfigs (#19821)
- add missing dependencies for fslpy in easyconfig for FSL v6.0.5.1 (#19829)
- remove numa configure option from hwloc 2+ (#19833)
- avoid spurious test failure when enabling RPATH for Perl (#19835)
- add missing Python deps and packages in PSI4 1.7 (#19836)
- add patch to fix `MS_RDONLY` error in OpenMPI 3.1.x and 4.0.0 (#20140), 4.0.3 (#19944), and 4.0.5 (#19837)
- demote meson-python to build dependency for matplotlib v3.7.2 w/ `iimkl/2023a` (#19892)
- demote hatchling to build dependency in easyconfig for einops 0.7.0 (#19915)
- add patch for adding a write memory barrier to all OpenMPI 4.1.x easyconfigs (#19940)
- stop using non-existent `--disable-libdeflate` option for LibTIFF 4.1.0 (#19951)
- add patch to remove git version check and fix test command for molmod 1.4.8 (#19952)
- replace SYSTEM-level GCC dependency in git-annex with binutils (#19956)
- stop using non-existing `--with-doc` configure option for groff 1.23 (#19969)
- fix test failures of Perl-bundle-CPAN-5.38 in non-English locales (#19971)
- add patch to fix tree-optimization bug in GCC 12.3.0 + 13.1.0 + 13.2.0 for ARM architectures with SVE support (#19974, #20218)
- drop checksum from easyconfig for VSCode 1.85.0 since tarball are not stable (#19995)
- respect `sysroot` in recent Pillow-SIMD easyconfigs, when in use (#19996)
- remove `--disable-docs` configure option from FriBidi 1.0.5+ (#19998)
- fix geotiff configure option in GDAL (#19999)
- unpack SCG database to 'db' subdirectory for DAS_Tool (#20008)
- remove Jasper dependency and configure option from GDAL 3.5+ (#20009)
- update homepage and source URLs for SPAdes (#20018)
- fix GDAL 3.5.0 install on high-core-count machines (#20027)
- remove disable-visibility configure flag from GTK3 (#20028)
- remove mpi configure option from libfdf 0.2.2 (#20034)
- add patch to fix multiarch support for RISC-V to all GCCcore 12.x and 13.x easyconfigs (#20035)
- fix invocation typo and unneeded folder change on invocation in fgbio 1.3.0 easyconfig (#20039)
- remove hdf5 configure option from MDSplus 7.96.12 (#20041)
- fix python configure option of MEME (#20043)
- fix configure options of FFLAS-FFPACK (#20052)
- find the correct Python in xtensor (#20056)
- fix geotiff configure option in GDAL 2.2.3 (#20057)
- fix configure option and remove gperftools dependency for MIRA 5.0 (#20061)
- fix confgure options in GRASS (#20062)
- fix configure of LinBox 1.7.0 (#20064)
- remove unknown configure option from GnuTLS 3.7.2 (#20065)
- use 32-bit indexing for SUNDIALS 6.6.0 (with foss/2023a) to enable sunmatrix-cusparse (#20075)
- find correct Python for MDI (#20083)
- add `pixman` and `FriBidi` dependencies to recent ImageMagick easyconfigs (#20086)
- add patch to fix failing tests with OpenSSL 3.x for Net-SSLeay v1.92 extension in Perl-bundle-CPAN v5.36.1 (#20090) and v5.38.0 (#20118)
- add patches for minimus2 in AMOS-3.1.0 (#20114)
- fix download url for cuSPARSELt 0.3.0.3 (#20129)
- add patches to fix test issues for PyTorch 2.1.2 with `foss/2023a` + CUDA 12.1.1 (#20156)
- remove easyconfig for UCX-CUDA 1.15.0 using incompatible combo of CUDA 12.3.0 + GCC 13.2.0 (#20158)
- remove flake8 suppressions for invalid escape sequences (#20161)
- fix post-install command for SuperLU_DIST in case library prefix is `lib` instead of `lib64` (#20162)
- switch to gitlab source URL for libxc + add alternative checksum (#20163)
- enable `download_dep_fail` in Pythonpackage easyconfigs where it was wrongly disabled (#20174)
- add patch to fix PyTorch 1.12.x and 1.13.x for Linux 6+ (#20176, #20177, #20178, #20179, #20180, #20181, #20182)
- disable tests for `Time::HiRes` extension in Perl-bundle-CPAN v5.36.1 (#20187)
- fix several typos in GlobalArrays 5.8 configure step (#20188)
- fix broken homepage from older SCOTCH easyconfigs (#20192)
- remove dead URL for ISL from `source_urls` in easyconfigs for GCCcore 10.3.0, 11.1.0, 11.2.0 (#20193)
- fix package installation in easyconfigs for Python 2.7.15 and 3.7.2 (using `GCCcore/8.2.0`) (#20194)
- add missing zlib + OpenSSL deps to Ruby easyconfigs + promote binutils to runtime dependency (#20214)
- fix cuSPARSELt easyconfigs for aarch64 (#20216)
- fix python shebang in napari easyconfigs (#20219)
- add patch to fix scipy test failure for SciPy-bundle 2023.02 with `gfbf/2022b` (#20235)
- fix `incompatible types` errors when building the R extension `dbarts` on Arm (#20238)
- add patch to fix for libarchive to fix error reporting in tar (#20254)
- add patch for GCCcore 13.2.0 to fix unguarded use of is_convertible builtin (#20260)
- fix download for python-parasail 1.3.4 by adding missing source URL (#20263)
- other changes:
- update DualSPHysics easyconfig to use custom easyblock (#19400)
- fix name for DETONATE in existing easyconfig (was `detonate`) (#19569)
- rename `VSCode` to `code-cli` (to match with existing `code-server`) (#19585, #19645)
- remove urllib3 extension from wandb easyconfig, not neeed since Python-bundle-PyPI dependency already provides it (#19725)
- stop using custom easyblock for Doxygen (#19742)
- move `setuptools_scm` extension from hatchling to Python easyconfig (#19777, #20200)
- move xtb v6.6.1 to gfbf/2023a (#19826)
- unify Z3 4.12.2 easyconfigs into a single one with Python bindings (and fix Z3 dependency for PyTorch 2.1.2 accordingly) (#20050)
- use GPAW-setups v24.1.0 in existing GPAW easyconfigs (#20117)
- fix duplicate dict entries and enable fatal error checking for easyconfigs via `flake8` (#20173)
- move Greenlet 2.0.2 to GCCcore toolchain (#20241)
- update Java/8 wrapper to Java 8.402 (#20261)
- update copyright lines to 2024 (#20276)
v4.9.0 (30 December 2023)
-------------------------
feature release
- added easyconfigs for foss/2023b (#19449) and intel/2023b (#19450) common toolchains
- added example easyconfig files for 77 new software packages:
- AICSImageIO (#19315), ANTIC (#19203), BiasAdjustCXX (#19341), BOPTEST (#19295), BRiAl (#19208), castor (#19176),
CellBender (#19296), cliquer (#19210, #19323), CPMD (#19387), cppyy (#19204), CUDD (#19208), datalad (#18675),
Demystify (#17990), dftd4 (#19223), dialog (#17696), DIA-NN (#19454), dynesty (#19091), ebGSEA (#19447),
ECL (#19211), eclib (#19209), epct (#19298), EUKulele (#19217), FACE (#14840), fastml (#19357), forbear (#14840),
fplll (#19371), fpylll (#19371), ftfy (#19353), Gdspy (#19458), GFF3-toolkit (#19071), giac (#19323), GMP-ECM (#19323),
HepMC (#19139), hic-straw (#19309), HPCC (#18892), iced (#19309), IML (#19201), iperf (#19259), jedi (#19269),
jedi-language-server (#19269), jupyter-rsession-proxy (#19311), lcalc (#19329), libaed2 (#14840),
LoopTools (#19397), m4ri (#19208), m4rie (#19208), MDI (#19417), mdust (#19106), MitoHiFi (#19263), MPFI (#19323),
multicharge (#19221), OMERO.insight (#19337), OMERO.py (#19338), PFFT (#19255), primecount (#19370),
primecountpy (#19370), PyAV (#19359), pycubescd (#19302), pylipid (#19428), PySINDy (#19306),
pythermalcomfort (#19285), PyTorchVideo (#19359), R-bundle-CRAN (#19170), Restrander (#19232), scikit-lego (#19064),
scrublet (#19215), SEACells (#18724), simanneal (#19347), Simstrat (#14840), solo (#19216), SPEI (#19441),
SUPPA (#19181, #19275), SYMMETRICA (#19328), Triton (#19381), vaeda (#19214), VSCode (#19418), waLBerla (#18932)
- added additional easyconfigs for various supported software packages, including:
- ANTs 2.5.0, Arriba 2.4.0, Arrow 14.0.1, at-spi2-core 2.50.0, Autoconf-archive 2023.02.20, awscli 2.15.2,
Blender 3.6.5 + 4.0.1, Boost 1.83.0, boto3 1.28.70, Bracken 2.9, BUStools 0.43.1, cairo 1.18.0, cairomm 1.16.2,
CASTEP 23.1, cddlib 0.94m, cdo-bindings 1.6.0, CellRanger 7.2.0, CoCoALib 0.99818, COMSOL 6.2.0.290, Coreutils 9.1,
cryptography 41.0.5, CubeLib 4.8.2, CubeWriter 4.8.2, CUDA 12.3.0, CVXPY 1.3.0, cysignals 1.11.2, DBus 1.15.8,
dftd4 3.4.0, E-ANTIC 1.3.0, elfutils 0.190, f90wrap 0.2.11, FastQC 0.12.1, Ferret 7.6.0, FFLAS-FFPACK 2.5.0,
ffnvcodec 12.1.14.0, FPM 1.15.1, FriBidi 1.0.13, gap 4.12.2, git-lfs 3.4.0, GitPython 3.1.40, Givaro 4.2.0,
GLib 2.78.1, glog 0.6.0, GObject-Introspection 1.78.1, gperftools 2.13, GPyTorch 1.10, GROMACS 2023.3,
HarfBuzz 8.2.2, HiC-Pro 3.1.0, hifiasm 0.19.7, hypothesis 6.90.0, ICU 74.1, imageio 2.33.1, imkl 2024.0.0,
impi 2021.11.0, intel-compilers 2024.0.0, IPython 8.17.2, ITK 5.3.0, Kent_tools 457, KyotoCabinet 1.2.80,
LHAPDF 6.5.4, libfdf 0.5.0, libjxl 0.8.2, LinBox 1.7.0, lrslib 7.2, lxml 4.9.3, magma 2.7.2, maturin 1.3.1,
MEME 5.5.4, meson-python 0.15.0, Miniconda3 23.9.0, Mmg 5.7.2, Molden 7.3, mrcfile 1.4.3, nanoflann 1.5.0,
nauty 2.8.6, Nextflow 23.10.0, nodejs 20.9.0, Normaliz 3.10.1, NSS 3.94, NWChem 7.2.2, Oases 20180312, Pango 1.51.0,
Parallel-Hashmap 1.36, parameterized 0.9.0, phonopy 2.20.0, pigz 2.8, pmt 1.2.0, poetry 1.6.1, PostgreSQL 16.1,
pplpy 0.8.9, PyCairo 1.25.1, pypmt 1.2.0, PyQt5 5.15.7, pytest 7.4.2, pytest-xdist 3.3.1,
Python-bundle-PyPI 2023.10, PyTorch 2.1.2, R 4.3.2, RASPA2 2.0.47, SBCL 2.3.11, SCENIC 1.3.0, scikit-image 0.22.0,
SciPy-bundle 2023.11, SDL2 2.28.5, setuptools-rust 1.8.0, Seurat 4.4.0, SimpleITK 2.3.1, Singular 4.3.2p10,
Spark 3.5.0, STAR 2.7.11a, STAR-CCM+ 2310, strace 6.6, SuiteSparse 7.1.0, tbb 2021.11.0, TOML-Fortran 0.4.1,
TRAVIS-Analyzer 220729, UCX-CUDA 1.15.0, VirSorter 1.0.6, virtualenv 20.24.6, VSEARCH 2.25.0, VTK 9.3.0,
wandb 0.16.1, XGBoost 2.0.2, xprop 1.2.6, xtb 6.6.1, Xvfb 21.1.9, xxd 9.0.2112
- minor enhancements, including:
- add sanity check commands for recent GDB versions (#19102)
- add aarch64 and ppc64le checksums to NVHPC 23.7 (#19249)
- allow Python version of Z3 to be used as a dependency (#19354)
- various bug fixes, including:
- use `CargoPythonBundle` generic easyblock for timm to install required Rust packages in a controlled way (#18332)
- add alternate checksum for OpenImageIO v2.4.14.0 (#19090)
- only set flag `--enable-asmjit` for PLUMED when installing on `x86_64` (#19110)
- ensure right Python version is used in DP3, WSClean and dependencies by specifying `-DPython3_EXECUTABLE` CMake option (#19119)
- add patch to work around potential crash in PyTorch 1.13.1 caused by GCC 12 compiler bug (#19133)
- add patch to fix detection of newer Intel CPUs in OpenBLAS 0.3.20 through 0.3.23 (#19141)
- remove outdated `--disable-docs` configure option from FriBidi-1.0.12 (#19147)
- add libiconv dependency to gettext 0.22 (#19155)
- fix OpenBLAS 0.3.20+ on newer Intel CPUs (#19159)
- only use ScaFaCos as dependency for LAMMPS 23Jun2022 on `x86_64` (#19164)
- add patch to fix regression in GCC 12.x on AVX512 systems (#19180)
- add pkgconf build dependency to libGLU (#19186)
- sidestep some build issues with CUDA-Samples 12.1 (#19189)
- make Pillow easyconfigs aware of sysroot template (#19226, #19267)
- fix possible error/crash in NCCL on x86 due to cpuid (#19231)
- reduce timestep to fix sanity check commands in LAMMPS 23Jun2022 (#19246)
- add patch for GCC 12.x to fix miscompiling C++ code causing double-free in case of exceptions (#19253)
- replace format tag with explicit extension name in Optuna v3.0.3 (#19256)
- enhance easyconfigs for gnuplot 5.4.x to make sure that Lua dependency is always used (#19261)
- patch setup.py for grpcio extension in TensorFlow 2.13.0 easyconfigs to take into account alternate sysroot (#19268)
- avoid indirect dependency on old CMake version built with GCCcore/10.2.0 via Catch2 build dependency using system toolchain in recent pybind11 easyconfigs (#19270)
- use existing patch in pybind11 2.6.2 and 2.7.1 to fix failing test due to extra whitespace (#19279)
- change toolchain in `json-fortran` easyconfigs to `GCC`, since it includes Fortran modules (#19283)
- remove Unicode character in description of SMRT-Link easyconfigs (#19312)
- don't use `%(namelower)s` template in extension name in IPython v8.14.0 easyconfig (#19330)
- add patch to fix `[cz]asums` in OpenBLAS 0.3.24 (#19331)
- fix failing tokenizers with `CargoPythonPackage` easyblock (#19333)
- define `$GTKDOCIZE` as '`echo`' before generating configure script for new HarfBuzz versions (#19339)
- fix PAPI test step hanging on some systems (#19372)
- compile LERC test binary in `postinstallcmds` to fix sanity check error when RPATH linking is enabled (#19386)
- use `GCC` toolchain in `kim-api`, since it includes Fortran modules (#19399, #19401, #19402, #19403, #19404, #19405)
- fix wrong handling of floats in z3-solver (#19414)
- Fix numpy build on Sapphire Rapids CPUs in SciPy-bundle-2023.07-gfbf-2023a (#19419, #19425)
- allow ITK legacy code and Python wrappers in ITK v5.2.1 (#19431)
- link to xxHash library provided via EasyBuild in python-xxhash v3.2.0 (#19432)
- include MPFR 4.1.0 patch in MPFR 4.2.0 easyconfigs to fix failing tsprintf test with glibc >= 2.37 (#19438)
- skip `Test::Sys::Info` test that expects `/etc/fstab` in Perl-bundle-CPAN (#19440)
- exclude `cdp*` CUDA samples that fail to build on aarch64 in CUDA-Samples v12.1 (#19451)
- other changes:
- let SuiteSparse easyblock set `CMAKE_OPTIONS` for SuiteSparse v7.1.0 (#19177)
- add versionsuffix `-param` to easyconfig for ReaxFF 2.0 (#19307)
- use `LooseVersion` from `easybuild.tools` (#19376)
v4.8.2 (29 October 2023)
------------------------
update/bugfix release
- added example easyconfig files for 48 new software packages:
- ALL (#18971), anadama2 (#18688), AOFlagger (#19010), bases2fastq (#18866), BgeeCall (#18784),
biobakery-workflows (#18688), BMTK (#18863), CIRIquant (#18815), Clair3 (#18748), CLEAR (#16357),
cpio (#14728), DP3 (#19010), EveryBeam (#19010), fasta-reader (#18936), git-annex (#18673), GSD (#6453),
imutils (#18920), Jblob (#18478), Jmol (#18988), kneaddata (#18688), libbaseencode (#12319),
libcotp (#12319), MACS3 (#18354), Mashtree (#19019), mpath (#5029), MUSCLE3 (#18287), plotutils (#16196),
ProBiS (#18830), PyMC (#10399), PyPy (#18847), PyTensor (#18928), Qt6 (#18683), QuickTree (#19019),
Raptor (#18919), RCall (#18933), ResistanceGA (#18933), scCODA (#18949), scikit-build-core (#18777),
segmentation-models-pytorch (#18930), SNAP-ESA (#19031), SNAP-ESA-python (#19031), starparser (#18965),
synapseclient (#19016), uncertainties (#18923), WSClean (#19010), XBeach (#18849), XOOPIC (#15269),
zeus-mcmc (#19033)
- added additional easyconfigs for various supported software packages, including:
- alleleCount 4.3.0, Amber 22.4, ant 1.10.14, ArviZ 0.16.1, ASAP3 3.13.2, biobambam2 2.0.185, BLAST+ 2.14.1,
bokeh 3.2.2, Brotli 1.1.0, Cantera 3.0.0, CapnProto 1.0.1, casacore 3.5.0, Catch2 2.13.9, CGAL 5.6,
Chemaxon-Marvin 23.9, CMake 3.27.6, code-server 4.16.1, Coot 0.9.8.92, CSBDeep 0.7.4, CUDA-Samples 12.1.1,
CuPy 12.1.0, cURL 8.3.0, dask 2023.9.2, DL_POLY_4 5.1.0, DoubletFinder 2.0.3-20230131, Doxygen 1.9.8, dxpy 0.345.0,
EDirect 20.5.20231006, FastANI 1.34, FastME 2.1.6.3, Flask 2.3.3, Flye 2.9.2, fmt 10.1.0, foss/2023.09,
freetype 2.13.2, GDAL 3.7.1, GDRCopy 2.4, git 2.42.0, GMP 6.3.0, Go 1.21.1, googletest 1.14.0, GPAW 23.9.1,
groff 1.23.0, GTDB-Tk 2.3.2, GTK4 4.13.1, gzip 1.13, harmony 0.1.0, HDF 4.2.16, HighFive 2.7.1, Highway 1.0.7,
HMMER 3.4, hmmlearn 0.3.0, Imath 3.1.9, Inspector 2023.2.0, intel/2023.07, IsoSeq 4.0.0, itac 2021.10.0,
JupyterNotebook 7.0.3, libarchive 3.7.2, libcint 5.4.0, libdeflate 1.19, libdrm 2.4.117, libglvnd 1.7.0,
libjpeg-turbo 3.0.1, libmaus2 2.0.813, libpng 1.6.40, libsigc++ 2.12.1, libsodium 1.0.19, LibTIFF 4.6.0,
libwebp 1.3.2, libxc 6.2.2, line_profiler 4.1.1, LMDB 0.9.31, MAFFT 7.520, makeinfo 7.1, MATLAB 2023b,
MEGAN 6.25.3, Mesa 23.1.9, Meson 1.2.3, mold 2.3.1, MPFR 4.2.1, msgpack-c 6.0.0, nanopolish 0.14.0,
NBO 7.0.10, netcdf4-python 1.6.4, OpenBLAS 0.3.24, OpenCV 4.8.1, OpenEXR 3.2.0, OpenMolcas 23.06, OpenMPI 4.1.6,
openslide-python 1.3.1, OrthoFinder 2.5.5, OSU-Micro-Benchmarks 7.2, ParaView 5.11.2, Perl-bundle-CPAN 5.38.0,
PETSc 3.19.2, PMIx 4.2.6, poppler 23.09.0, preCICE 2.5.0, pretty-yaml 23.9.5, PyCairo 1.25.0, pyEGA3 5.0.2,
PyGObject 3.46.0, pygraphviz 1.11, pytest-rerunfailures 12.0, Python 3.11.5, PyTorch 2.0.1, PyTorch-bundle 1.13.1,
PyTorch-Ignite 0.4.12, PyYAML 6.0.1, RagTag 2.1.0, rapidcsv 8.62, rasterstats 0.19.0, RAxML-NG 1.2.0,
RDFlib 7.0.0, RDKit 2023.03.3, ReFrame 4.3.3, RMBlast 2.14.0, ruamel.yaml 0.17.32, Rust 1.73.0, scikit-learn 1.3.1,
SCons 4.5.2, SHAP 0.42.1, SignalP 6.0h, SMRT-Link 12.0.0.177059, spglib-python 2.1.0, SQLite 3.43.1,
TensorRT 8.6.1, texlive 20230313, Tkinter 3.11.5, UCX 1.15.0, VBZ-Compression 1.0.3, VCFtools 0.1.16,
VTune 2023.2.0, X11 20231019, x264 20231019, xarray 2023.9.0, XlsxWriter 3.1.3, xtb 6.6.0, ZeroMQ 4.3.5
- minor enhancements, including:
- also run easyconfigs test suite with Python 3.11 (#18009)
- don't disable building of third and fourth derivates in libxc 6.1.0 (#18467)
- add easyconfigs cache file to `.gitignore` (#18797)
- add patch to improve CUDA 11 compatibility of `GCCcore/12.2.0` and `GCCcore/12.3.0` (#18854)
- also build Python bindings for ITK 5.2.1 with `foss/2022a` (#18922)
- add ridge extension to R 4.2.2 (#18924)
- add MSstatsLiP (#19009)and escape (#19027) to Bioconductor 3.16 bundle
- add patches to build Qt5 5.15.10 with Python 3 instead of Python 2.7 (#19045)
- various bug fixes, including:
- rename ACT to Artemis (#18382)
- backport lchown patch to PMIx 3.1.x + 3.2.x (#18759)
- also copy scripts directory for Clair3 (#18783)
- rename isoseq3 after download for IsoSeq 3.8.2 + fix permissions (#18785)
- add missing required extensions + fix wrong version of extensions in recent Perl easyconfigs (#18789)
- add patch for OpenBLAS 0.3.23 to fix hanging tests (#18790)
- add patch to fix Open MPI 4.1.5 with PMIx >= 4.2.3 (#18833)
- fix permission issues when copying xvfb-run script in Xvfb easyconfigs (#18834)
- statically link Boost 1.75 in Cufflinks v20190706 installed with `GCC/11.2.0`, so Boost can be changed to build dependency (#18843)
- add missing required PyPy dependency for Clair3, also copy preprocess and shared subdirectories, and enhance sanity check for provided libclair3 Python package (#18847)
- add patch to fix build of util-linux 2.39 on CentOS 7 (#18855)
- add patch to fix finding of tk.tcl for Tk 8.6.13 (#18864)
- add patch to fix issue with automatic detection of NeoverseV1 CPU architecture in OpenBLAS v0.3.20 (#18870)
- fix source URL for segemehl 0.3.4 (#18878)
- avoid use of hardcoded paths for Pillow by using `--disable-platform-guessing` option (#18881)
- add patch to disable flaky DDRGES3 LAPACK test in OpenBLAS 0.3.23 + 0.3.24 (#18887)
- add alternate checksum for NCCL v2.18.3 (#18906)
- add missing dependencies for MONAI to support extras required by MONAI-Label (#18921)
- make sure Python dependency included for ESPResSo is actually used by specifying `-DPYTHON_EXECUTABLE` (#18963)
- only add tbb as dependency in recent LAMMPS easyconfigs when installing on x86_64 (#19000)
- detect the correct Python for vcflib (#19001)
- fix invalid pointer access in UCX 1.11-1.14 (#19023)
- disable threadedmpi in recent SCOTCH easyconfigs using gompi toolchain (#19024)
- add missing GSL dependency for casacore 3.4.0 (#19042)
- fix pybind11 incompatibility with some CUDA versions and add Catch2 dependency for tests (#19047)
- enable `-fPIC` in easyconfig for libwebp 1.3.2 (#19098)
- other changes:
- remove 'cstd': 'c++17' as that's the default in GCC 11 (#18941, #18942, #18943, #18944, #18945, #18946)
- rename CVS to ConcurrentVersionsSystem, to avoid problems with recent setuptools versions (#18985)
- use sysroot template in wget easyconfigs to define PKG_CONFIG_PATH (#19080)
v4.8.1 (11 September 2023)
--------------------------
update/bugfix release
- added example easyconfig files for 83 new software packages:
- ALAMODE (#18733), AMRFinderPlus (#18559), Ax (#68), bcrypt (#18208), bench (#18656), BgeeDB (#18743),
Boost.Python-NumPy (#18505), CatBoost (#18591), centerline (#18273), cffi (#7105), ChIPseeker (#18662),
connected-components-3d (#18289), cryptography (#8495), CVglasso (#18657), DiffBind (#18663), drmaa-python (#18614),
e3nn (#18304), flit (#18208), GAPPadder (#18692), GenerativeModels (#18451), geosphere (#18659), gffutils (#18331),
gkmSVM (#18660), hampel (#18409), hatchling (#18208), HDF-EOS2 (#18297), Hybpiper (#18414), inih (#18516),
IsoformSwitchAnalyzeR (#18664), IsoQuant (#18331), Jupyter-bundle (#18634), JupyterNotebook (#18735, #18735),
leafcutter (#18615), libleidenalg (#18548), LIBSVM-Python (#18455), libvori (#18379), maturin (#18405),
meboot (#18658), mgen (#18402), Mikado (#18614), NanoCaller (#18726), nbclassic (#18617), ncolor (#7146),
nose3 (#18234), novaSTA (#18601), Omnipose (#18402), Optax (#18610), paramiko (#1504), Parsl (#18408),
peakdetect (#18402), PICRUSt2 (#18333, #18459), Platypus-Opt (#18291), PortMidi (#18252), pv (#16439),
py-c3d (#18409), pygame (#18252), pyodbc (#18334), Python-bundle-PyPI (#18208), qforce (#18456),
RFdiffusion (#18304), Rhodium (#18291), ruptures (#18306), Sabre (#18342), scGSVA (#18401), scib-metrics (#18734),
scikit-plot (#18377), SDL2_mixer (#18252), SDL2_ttf (#18252), segment-anything (#18290), sentinelsat (#18367),
setuptools-rust (#18208), slurm-drmaa (#18614), SuAVE-biomat (#18678), T-Coffee (#17916),
tensorflow-compression (#18676), torchvf (#18637), tornado (#18511), tseriesEntropy (#18661), TXR (#18665),
unifdef (#18427), UniFrac (#18407), virtualenv (#2660), WFA2 (#18636)
- added additional easyconfigs for various supported software packages, including:
- ABINIT 9.10.3, Advisor 2023.2.0, aiohttp 3.8.5, AMD-uProf 4.1.424, Anaconda3 2023.07-2, anndata 0.9.2,
APR 1.7.4, APR-util 1.6.3, Arcade-Learning-Envionment 0.8.1, archspec 0.2.1, Armadillo 12.6.2, arpack-ng 3.9.0,
assimp 5.2.5, BAGEL 1.2.2, bam-readcount 1.0.1, Bazel 6.3.1, BCFtools 1.18, BeautifulSoup 4.12.2, BEDTools 2.31.0,
biom-format 2.1.15, bokeh 3.2.1, Boost 1.82.0, cairo 1.17.8, c-ares 1.19.1, ccache 4.8.3, CDO 2.2.2, CFITSIO 4.3.0,
Cgl 0.60.7, CharLS 2.4.2, cicero 1.3.8, Clang 16.0.6, Clp 1.17.8, Cluster-Buster 20200507, CoinUtils 2.11.9,
conan 1.60.2, configurable-http-proxy 4.5.5, coverage 7.2.7, CP2K 2023.1, CubeLib 4.8.1, CubeWriter 4.8.1,
CUDA 12.2.2, dask 2023.7.1, dcm2niix 1.0.20230411, Delly 1.1.6, dill 0.3.7, ecBuild 3.8.0, ecCodes 2.31.0,
ELPA 2023.05.001, exiv2 0.28.0, expecttest 0.1.5, fastparquet 2023.4.0, FFmpeg 6.0, ffnvcodec 12.0.16.0,
flatbuffers 23.5.26, flatbuffers-python 23.5.26, FreeSurfer 7.4.1, fsom 20151117, gc 8.2.4, GCC 13.2.0, GDB 13.2,
GEOS 3.12.0, gettext 0.22, GHC 9.2.2, Ghostscript 10.01.2, GLib 2.77.1, gmpy2 2.1.5, gnuplot 5.4.8,
GObject-Introspection 1.76.1, gperftools 2.12, Graphviz 8.1.0, gRPC 1.57.0, GST-plugins-base 1.22.5,
GStreamer 1.22.5, GTK3 3.24.37, GTK4 4.11.3, h4toh5 2.2.5, h5netcdf 1.2.0, h5py 3.9.0, hiredis 1.2.0,
Horovod 0.28.1, htop 3.2.2, HTSlib 1.18, hwloc 2.9.2, Hydra 1.3.2, hypothesis 6.82.0, Hypre 2.29.0, ICU 73.2,
igraph 0.10.6, iimkl/2023a, imageio 2.31.1, ImageMagick 7.1.1-15, inferCNV 1.14.2, IPython 8.14.0, ISL 0.26,
Julia 1.9.3, JupyterLab 4.0.5, jupyter-resource-usage 1.0.0, kma 1.4.12a, KMC 3.2.2, leidenalg 0.10.1,
libdrm 2.4.115, libdwarf 0.7.0, libfabric 1.19.0, libgit2 1.7.1, libGLU 9.0.3, libsndfile 1.2.2, libwpe 1.14.1,
libxml2 2.11.5, LittleCMS 2.15, LLVM 16.0.6, Lua 5.4.6, MACS2 2.2.9.1, magma 2.7.1, mahotas 1.4.13, makeinfo 7.0.3,
Mamba 23.1.0, matplotlib 3.7.2, medaka 1.8.1 + 1.9.1, Mercurial 6.4.5, Mesa 23.1.4, meson-python 0.13.2,
Miniconda3 23.5.2, Monocle3 1.3.1, MPC 1.3.1, MRtrix 3.0.4, MUMPS 5.6.1, MXNet 1.9.1, napari 0.4.18, ncdu 1.18,
netCDF 4.9.2, netCDF-Fortran 4.6.1, nettle 3.9.1, networkx 3.1, nodejs 18.17.1, nsync 1.26.0, NVHPC 23.7,
OpenAI-Gym 0.26.2, OpenCV 4.8.0, OpenFOAM 11, OpenImageIO 2.4.14.0, Osi 0.108.8, OTF2 3.0.3, Pango 1.50.14,
PAPI 7.0.1, parallel 20230722, Perl 5.38.0, Pillow 10.0.0, Pillow-SIMD 9.5.0, Pint 0.22, pkgconf 2.0.3,
plotly.py 5.16.0, PLUMED 2.9.0, pocl 4.0, poetry 1.5.1, protobuf 24.0, protobuf-python 4.24.0, psutil 5.9.5,
PuLP 2.7.0, pyBigWig 0.3.22, pybind11 2.11.1, PyCairo 1.24.0, PyGObject 3.44.1, Pylint 2.17.4, pyproj 3.6.0,
pyro-ppl 1.8.4, python-igraph 0.10.6, PyZMQ 25.1.1, QIIME2 2023.5.1, Qt5 5.15.10, QuantumESPRESSO 7.2,
rclone 1.63.1, RE2 2023-08-01, re2c 3.1, RegTools 1.0.0, RnBeads 2.14.0, RTG-Tools 3.12.1, SAMtools 1.18,
Scalene 1.5.26, scikit-build 0.17.6, scikit-image 0.21.0, SciPy-bundle 2023.07, Score-P 8.1, SCOTCH 7.0.3,
SDL2 2.28.2, SDL2_image 2.6.3, setuptools 64.0.3, SeuratWrappers 20221022, snakemake 7.32.3, SpaceRanger 2.1.0,
SpiecEasi 1.1.1, Stack 2.11.1, STAR 2.7.11a, SUNDIALS 6.6.0, SWIG 4.1.1, sympy 1.12, tabixpp 1.1.2, tbb 2021.10.0,
tbl2asn 20230713, tcsh 6.24.10, TensorFlow 2.13.0, tensorflow-probability 0.19.0, Tk 8.6.13, Tkinter 3.11.3,
tqdm 4.66.1, unixODBC 2.3.11, Valgrind 3.21.0, vcflib 1.0.9, VirtualGL 3.1, VisPy 0.12.2, Wayland 1.22.0,
WebKitGTK+ 2.40.4, wpebackend-fdo 1.14.1, wxPython 4.2.1, Xvfb 21.1.8, xxd 9.0.1696, XZ 5.4.4, Yambo 5.1.2,
Z3 4.12.2, zarr 2.16.0
- minor enhancements, including:
- add extensions to recent R-bundle-Bioconductors easyconfigs: UCell (#18281), decoupleR (#18399, #18552), RnBeads (#18682)
- add extensions to recent R easyconfigs: tabletools (#18510), flextables (#18719)
- add test for easyconfig file permissions (#18647)
- simplify build and install options for Ghostscript (#18750)
- various bug fixes, including:
- set `$JULIA_DEPOT_PATH` in Julia easyconfigs with default value (#17976)
- remove superflous dependencies from Horovod easyconfig on top of PyTorch (#18262)
- disable building documentation for libsigc++ 2.10.x (#18301)
- use MCR dependency in FreeSurfer 7.3.2 and 7.4.0 (#18303)
- add `hpctestlib` to the `$PYTHONPATH` in ReFrame 4.2.0 easyconfig (#18320)
- fix installation of Python bindings for recent Arrow easyconfigs by adding `--no-build-isolation` to `pip install` command (#18348, #18432, #18440, #18441)
- add/fix patches for PyTorch 1.13.1 w/ foss/2022a (#18371)
- add missing nbclassic extension to jupyter-server 1.21.0 (#18389)
- Fix batchspawner for JupyterHub 3.0 (#18390)
- fix compiler flags and toolchain options for ScaLAPACK 2.1.0 + 2.2.0 (#18396, #18397)
- add patch to fix CUDA race condition problem for Score-P v8.0 (#18411)
- add `-DABSL_PROPAGATE_CXX_STD=ON` to recent Abseil easyconfigs (required for PyTorch) (#18413)
- add missing patches for PyTorch 1.12.0 w/ foss/2022a (#18430)
- fix regression in GCC 12.1 + 12.2 with wrong warnings (#18434)
- add patch for LIBSVM 3.30 to pass `$CFLAGS` + `$LDFLAGS` and run tests (#18454)
- add patch for Automake 1.16.5 to fix help2man error (#18468)
- consistently use ON/OFF for -DBUILD_SHARED_LIBS (#18484)
- add missing patches for PyTorch 1.12.0 w/ `foss/2022a` + CUDA 11.7.0 (#18491)
- add patches to fix PyTorch 1.12.1 + 1.13.1 on POWER on POWER (#18489, #18490, #18492, #18493, #18494, #18500)
- add patch to fix flaky `test_jit_legacy` test for PyTorch 1.13.1 (#18500)
- add alternative checksum for Extrae v4.0.4 (#18564)
- remove appending of `$__EGL_VENDOR_LIBRARY_DIRS` in recent Mesa easyconfigs, since Mesa easyblock now appends to it (#18630)
- correct `dirs` in `sanity_check_paths` in template easyconfig (#18635)
- set `$MUJOCO_PY_FORCE_CPU` to avoid that mujoco-py checks for nvidia-smi and aborts installation because `/usr/lib/nvidia` is not in `$LD_LIBRARY_PATH` (#18641)
- fix sanity check for ccache by setting `LC_ALL=C` (#18677)
- make Autoconf a build dep for tRNAscan-SE + add missing Perl dependency (#18680)
- strip out hardcoded `-march=native` used by RapidJSON 1.1.0 (#18725)
- disable detection of Dbus broker for `at-spi2-core` (#18727)
- make sure that 'moduleclass' is set in all easyconfig files (and is not set to default `base` moduleclass) (#18739)
- add patch for MPFR 4.1.0 to fix failing tsprintf test with glibc >= 2.37 (#18746)
- add patch for PMIx 4.x to use `lchown` so links are not followed (#18755)
- other changes:
- update Java/11 wrapper to Java/11.0.20 (#18435)
- use custom easyblock for recent sympy easyconfigs to prevent test failures (#18428)
- use GCC/12.2.0 toolchain for GSL 2.7, remove easyconfig for GSL 2.7 with GCCcore/12.2.0 (#18501)
- disable wx support in gnuplot 5.4.6 (#18648, #18691)
- filter out template + archived easyconfigs when determining changed easyconfigs in PRs (#18753)
v4.8.0 (7 Jul 2023)
--------------------
feature release
- added easyconfigs for foss/2023a (#18264) and intel/2023a (#18275) common toolchains
- added example easyconfig files for 76 new software packages:
- 3d-dna (#9258), affinity (#18051), AIMAll (#13153), alleleIntegrator (#17923), AlphaPulldown (#17774),
ASCAT (#17923), ASF-SearchAPI (#18179), ATAT (#18213), AutoDockSuite (#9678), axel (#10961), BayesPrism (#17885),
BGC-Bayesian-genomic-clines (#18005), CalculiX-CrunchiX (#16805), CASA (#18055), cctbx-base (#17774),
Circuitscape (#16720), CppHeaderParser (#18272), CuCLARK (#9482), cuteSV (#18077), DALI (#18204), DaliLite (#17989),
DEICODE (#18181), dm-haiku (#18013), dominate (#18086), dx-toolkit (#18232), easel (#18156), ecFlow (#15719),
EDirect (#17479), FragPipe (#18161), GEM (#18120), gemelli (#18120), GLIMPSE (#18163), GRIDSS (#18170),
HOOMD-blue (#18224), KerasTuner (#18197), LayoutParser (#18220), LISFLOOD-FP (#18194), LuaRocks (#18073),
mannkendall (#18043), MOB-suite (#16798), molecularGSM (#13150), MONAI-Label (#18180), MView (#18198),
NanoStat (#18201), oxDNA (#18175 + #18214), pastml (#15336), pbipa (#18229), Perl-bundle-CPAN (#17970), PheWeb (#10951),
plinkliftover (#18136), pmt (#18052), PyBioLib (#18124), Pychopper (#10344), pydicom-seg (#18180),
pyMannKendall (#18044), pypmt (#18045), python-mujoco (#18253), pytorch-CycleGAN-pix2pix (#18086),
PyTorch-Image-Models (#18220), PyWBGT (#17980), Safetensors (#18220), Sniffles (#18048), strace (#14381),
Structure_threader (#18219), subset-bam (#18032), SVclone (#18084), SVIM (#18071), Tapenade (#18109),
TensorFlow-Graphics (#17465), timm (#17787), Trinotate (#18124), Ultralytics (#17894), visdom (#18086),
wrapt (#18125), xclip (#17055), xdotool (#17055)
- added additional easyconfigs for various supported software packages, including:
- AGAT 1.1.0, alleleCount 4.2.1, AMS 2023.101, ANSYS 2023R1, BayesTraits 3.0.2, Bismark 0.24.1, BLAST+ 2.14.0,
boto3 1.26.163, Bowtie2 2.5.1, BUSCO 5.4.7, Cellpose 2.2.2, CHERAB 1.4.0, CmdStanR 0.5.2, CNVkit 0.9.10,
corner 2.2.2, CUDA 12.1.1 + 12.2.0, cuDNN 8.9.2.26, cutadapt 4.4, cuTENSOR 1.7.0.1, CVXOPT 1.3.1, Dalton 2020.1,
datamash 1.8, deepTools 3.5.2, DIAMOND 2.1.8, DMTCP 3.0.0, dorado 0.3.0 + 0.3.1, dtcmp 1.1.4, duplex-tools 0.3.3,
elastix 5.0.0, Emacs 28.2, emcee 3.1.4, Extrae 4.0.4, fastp 0.23.4, FlexiBLAS 3.3.1, fontconfig 2.14.2,
FreeSurfer 7.4.0, freetype 2.13.0, GATK 4.4.0.0, GBprocesS 4.0.0.post1, GCC 11.4.0, GCTA 1.94.1, GDRCopy 2.3.1,
Geant4 11.1.2, Geant4-data 11.1, GetOrganelle 1.7.7.0, git 2.41.0, GMAP-GSNAP 2023-04-20, GROMACS 2023.1,
hifiasm 0.19.5, Horovod 0.25.0, hwloc 2.9.1, InterProScan 5.62, IQ-TREE 2.2.2.3, ITSTool 2.0.7, JAGS 4.3.2,
Julia 1.9.0, libfabric 1.18.0, libheif 1.16.2, libjxl 0.8.1, LibLZF 3.6, LMfit 1.2.1, LSD2 2.4.1, LuaJIT 2.1.0,
lwgrp 1.0.5, MAGeCK 0.5.9.5, MATLAB 2023a, MaxQuant 2.4.2.0.eb, MCR R2022a.5, meshio 5.3.4, Meson 1.1.1,
minimap2 2.26, MMseqs2 14-7e284, mpifileutils 0.11.1, MuJoCo 2.2.2, nanomath 1.3.0, ncbi-vdb 3.0.5, NCCL 2.18.3,
Nextflow 23.04.2, ngspice 39, ont-fast5-api 4.1.1, OpenBLAS 0.3.23, OpenMPI 4.1.5, openpyxl 3.1.2,
OSU-Micro-Benchmarks 7.1-1, parasail 2.6.2, Paraver 4.11.1, ParaView 5.11.1, patchelf 0.18.0, Perl 5.36.1,
PMIx 4.2.4, POT 0.9.0, PSI4 1.7, psutil 5.9.4, psycopg2 2.9.6, PyCalib 20230531, pycocotools 2.0.6,
pyfaidx 0.7.2.1, pyiron 0.3.0, PyQtGraph 0.13.3, Pysam 0.21.0, pySCENIC 0.12.1, pyspoa 0.0.9, Python 3.11.3,
python-parasail 1.3.4, PyTorch 1.13.1, rasterio 1.3.8, regionmask 0.10.0, Ruby 3.2.2, Rust 1.70.0, ScaFaCoS 1.0.4,
seqtk 1.4, SRA-Toolkit 3.0.5, statsmodels 0.14.0, strace 5.14, Subversion 1.14.2, SUNDIALS 6.5.1, tidymodels 1.1.0,
tokenizers 0.13.3, torchaudio 0.12.0, TransDecoder 5.5.0, Transformers 4.29.2 + 4.30.2, UCC 1.2.0, UCC-CUDA 1.2.0,
UCX 1.14.1, UCX-CUDA 1.14.1, util-linux 2.39, VASP 6.3.2, VTK 9.2.6, WhatsHap 1.7, X11 20230603, xarray 2023.4.2,
XlsxWriter 3.1.2, XML-LibXML 2.0208, xorg-macros 1.20.0, zlib-ng 2.0.7
- minor enhancements, including:
- add CI check for -DCMAKE_BUILD_TYPE, should use build_type instead (#14008)
- enhance sanity check for recent LibTIFF easyconfigs (#17975)
- update JupyterLab v3.5.0 to set `$JUPYTERLAB_SETTINGS_DIR` and `$JUPYTERLAB_WORKSPACES_DIR` on loading of module (#17982)
- use custom easyblock for Rust 1.65.0 (#18174) and Rust 1.70.0 (#18167)
- update easyconfig for Nextflow 23.04.2 to use `install_cmds` (#18173)
- add extra packages to recent R easyconfigs (#18029, #18063, #18122, #18195, #18245)
- add extra packages to recent R-bundle-Bioconductor easyconfigs (#18196, #18246)
- various bug fixes, including:
- add patches to fix TensorFlow 2.7.1 on POWER (#16795)
- fix patches + extensions in easyconfig for TensorFlow 2.8.4 w/ foss/2021b (#17058)
- stick to FFmpeg 4.4.2 as dependency for SoX 14.4.2 (#17998)
- add pkgconfig as build dependency for nodejs , required for finding ICU dependency (#18007)
- fix exec permissions for all binaries & scripts of L_RNA_scaffolder 20190530 (#18030)
- update SUNDIALS dependency for Cantera v2.6.0 to v6.5.1 + add missing dependencies (#18041)
- fix --sanity-check-only for MAGeCK v0.5.9.4 (#18047)
- enable building static libs and check for libexslt.* in libxslt (#18064)
- add -pthread flag for dorado (#18072)
- add missing patch files for Qt5 5.15.2 to fix build problems with glibc 2.34 (#18087)
- add missing pkgconf build dependency for XML-LibXML v2.0208 (#18159)
- update homepage for NWChem 7.x (#18184)
- update homepage for SUNDIALS 5.x and 6.x (#18186)
- add missing source_urls for SimpleITK (#18212)
- use patch files for Qt5 v5.17.7 to fix compatiblity with glibc 2.34 (#18230)
- fix incorrect version for GMAP-GSNAP 2021-12-17 (was 2021-21-17) (#18231)
- fix CUDA build of recent TensorFlow easyconfigs when using compiler symlinks (#18235)
- use patch to make ncbi-vdb 2.11.2 compatible with HDF5 1.12.2 (#18236)
- update source_urls for Velvet 1.2.10 (#18237)
- use upstream patch for symbol compatibility in XZ 5.2.5 (#18250)
- update source url for pkgconf (#18271)
- other changes:
- stop running easyconfig unit tests with Python 2.7 (#18006)
- fix toolchain for networkx-3.0 (foss/2022b -> gfbf/2022b) (#18061)
- remove unused PyTorch patch (#18062)
- allow multiple dependency variants of ncbi-vdb for SRA-TOolkit per easyconfigs generation, as long as versions match (#18098)
- bump OpenSSL 1.1 wrapper fallback to 1.1.1u (#18188)
- remove default `separate_build_dir = True` and `build_type = 'Release'` from double-conversion (#18222)
- remove default `separate_build_dir = True` and `CMAKE_BUILD_TYPE=Release` from MariaDB (#18223)
- remove incorrect '-Dgallium-drivers=swrast' configure option in ROOT easyconfigs (#18260)
- change base compiler for intel/2023.03 to GCCcore/12.3.0 (required to use it as intel/2023a) (#18263)
v4.7.2 (27 May 2023)
--------------------
update/bugfix release
- added easyconfigs for intel/2023.03 (#17676)
- added example easyconfig files for 89 new software packages:
- AGeNT (#17864), anndata (#17677), Annocript (#17910), avro-cpp (#17527), batchgenerators (#17833),
BoltzTraP2 (#17742), Braindecode (#17913), build (#17776), casacore (#15499), Casanovo (#17735, #17736),
CASPR (#17606), CellChat (#17856), CellOracle (#17507), CLIP (#17782), CodingQuarry (#17682), ColabFold (#17751),
CopyKAT (#17646), CPC2 (#17849), cppzmq (#17601), dask-labextension (#17882), DIALOGUE (#17696), DiCE-ML (#17591),
ESPResSo (#17709), Evcxr-REPL (#17831), EZC3D (#17832), funannotate (#17588), FunGAP (#17652), GATB-Core (#17635),
GenMap (#17746), GimmeMotifs (#17507), GLI (#17793), GOBNILP (#17639), h5netcdf (#17835), HD-BET (#17833),
HTSplotter (#17369, #17586), ipympl (#17613), IsoSeq (#17791), KrakenUniq (#17569), LIANA (#17928),
libWallModelledLES (#17480), LoRDEC (#17635), M3GNet (#17555), mandrake (#17394), mctc-lib (#16760), MOABB (#17913),
MRPRESSO (#17925), ont-guppy (#17477, #17828), OptaDOS (#17777), PALEOMIX (#17912), PGPLOT (#15496),
PICI-LIGGGHTS (#17710), pod5-file-format (#17776), powerlaw (#17647), pp-sketchlib (#17397),
py3Dmol (#17752), pytesseract (#17898), pytest-cpp (#17966), pytest-flakefinder (#17966), Python-bundle (#17626),
python-xxhash (#17844), PyTorch-bundle (#17540), qnorm (#17507), R-MXM (#17667), R-transport (#17642, #17968),
Raven (#15833), ReaxFF (#17780), ripunzip (#17959), RPostgreSQL (#17739), rustworkx (#17857), Scalene (#16472),
sceasy (#17677), SCIP (#17639), Simple-DFTD3 (#16760), SMAP (#17672), SoPlex (#17639), SoupX (#17851),
spektral (#15551), synthcity (#17623), sysbench (#17643), tantan (#17681), thirdorder (#17703), TOPAS (#17553),
Triplexator (#17866), tRNAscan-SE (#17680, #17800), turbinesFoam (#17917), unicore-uftp (#17665), vispr (#17606),
WCSLIB (#15497), ZIMPL (#17639)
- added additional easyconfigs for various supported software packages, including:
- Abseil v20230125.2, AlphaFold v2.3.1 + v2.3.4, Arrow v11.0.0, arrow-R v11.0.0.3, astropy v5.2.2, awscli v2.11.21,
Bismark v0.24.0, biom-format v2.1.14, Blender v3.5.0, Blosc2 v2.8.0, Bottleneck v1.3.7, breseq v0.38.1,
bwa-meth v0.2.6, buildenv default for foss/2022b + CUDA 12.0.0, Cantera v2.6.0, CapnProto v0.10.3, CASTEP v22.11,
Clang v15.0.5, CLHEP v2.4.6.4, CMake v3.26.3, CMSeq v1.0.4, coverage v7.2.3, CP2K v9.1 + v2022.1, CPLEX v22.1.1,
CREST v2.11.2, cURL v8.0.1, CuPy v11.4.0, DBus v1.15.4, DBG2OLC v20200724, dlb v3.3.1, double-conversion v3.3.0,
Doxygen v1.9.7, expat v2.5.0, FASTA v36.3.8i, FHI-aims v221103, fio v3.34, Fiona v1.9.2, Flask v2.2.3, fmt v10.0.0,
freeglut v3.4.0, FUSE v3.14.1, GapFiller v2.1.2, GCC 12.3.0 + 13.1.0, GDCM v3.0.21, GitPython v3.1.31, Go v1.20.4,
googletest v1.13.0, gpustat v1.1, Guile v3.0.9, Gurobi v10.0.1, Harminv v1.4.2, Highway v1.0.4, IgBlast v1.21.0,
Imath v3.1.7, infercnvpy v0.4.2, IQ-TREE v2.2.2.3, jax v0.3.25, jupyterlmod v4.0.3, Kalign v3.3.5,
L_RNA_scaffolder v20190530, libaio v0.3.113, libarchive v3.6.2, libctl v4.5.1, libdeflate v1.8, libgcrypt v1.10.1,
libGridXC v1.1.0, libjpeg-turbo v2.1.5.1, libmaus2 v2.0.499, libopus v1.4, libpng v1.6.39, libPSML v1.1.12,
libRmath v4.2.1, libsigc++ v3.4.0, LibTIFF v4.5.0, libunistring v1.1, libxc v6.1.0, libxml2 v2.11.4,
libxslt v1.1.38, lifelines v0.27.4, lxml v4.9.2, make v4.4.1, MariaDB v10.11.2, Meep v1.26.0, MetaPhlAn v4.0.6,
mold v1.11.0, MPB v1.11.1, muParser v2.3.4, NAG v7.1, NAGfor v7.1, nano v7.2, NASM v2.16.01, ncurses v6.4,
netcdf4-python v1.6.3, networkx v2.8.8, NSS v3.89.1, numexpr v2.8.4, nvtop v3.0.1, OpenEXR v3.1.7, OpenMM v8.0.0,
Pandoc v3.1.2, ParaView v5.11.0, PCRE2 v10.42, PhyloPhlAn v3.0.3, phyx v1.3, picard v3.0.0, Pint v0.20.1,
pkgconf v1.9.5, PostgreSQL v15.2, PROJ v9.2.0, Proteinortho v6.2.3, protobuf v23.0, protobuf-python v4.23.0,
pydantic v1.10.4, pyFFTW v0.13.1, PyGEOS v0.14, Pyomo v6.5.0, pyparsing v3.0.9, pyperf v2.6.0, pyproj v3.5.0,
pytest v7.2.2, PYTHIA v8.309, Qtconsole v5.4.0, R-bundle-Bioconductor v3.16, R-tesseract v5.1.0, RE2 v2023-03-01,
ReFrame v4.2.0, RepeatMasker v4.1.5, RevBayes v1.2.1, rgdal v1.6-6, rioxarray v0.14.0, rocm-smi v5.4.4,
ROOT v6.26.10, Rtree v1.0.1, scib v1.1.3, scikit-build v0.17.2, Seaborn v0.12.2, SHAP v0.41.0, Shapely v2.0.1,
ShengBTE v1.5.0, SLiM v4.0.1, snappy v1.1.10, spdlog v1.11.0, spglib v2.0.2, spglib-python v2.0.2, SQLite v3.42.0,
Subread v2.0.4, Tcl v8.6.13, tcsh v6.24.05, torchtext v0.14.1, trimesh v3.21.5, UCC-CUDA v1.1.0, utf8proc v2.8.0,
Vim v9.0.1434, vsc-mympirun v5.3.1, WRF v4.4.1, xmlf90 v1.5.6, xxHash v0.8.1, XZ v5.4.2, zsh v5.9, zstd v1.5.5
- minor enhancements, including:
- add local::lib extension to Perl 5.34.0 (#17679)
- install shared libraries for tesseract (#17721)
- add additional extensions to recent R easyconfigs: word2vec, tau, quanteda, ... (#17738)
- add extensions to R-bundle-Bioconductor 3.15: deepSNV (#17852)
- add extensions to R 4.2.x: dlm (#17640), PMA + unikn + ppcor (#17695), tvem (#17729), epitools (#17852)
- various bug fixes, including:
- add patch for UCC 1.1.0 for multiple component paths (#17255)
- fix configure step for ELSI 2.5.0+ (#17288)
- switch bamtofastq to Cargo easyblock (#17595)
- add missing OpenJPEG dependency for recent GDAL versions (#17599)
- fix CodAn bin/* executable permissions for all users #(#17607)
- upgrade traitlets, ipywidgets, and widgetsnbextension + downgrade jupyterlab_widgets extensions in IPython v8.5.0 to fix known issues (#17612)
- add patch for GPAW-22.8.0 with 2022a toolchain to make test tolerance a bit less strict (#17618)
- add alternative checksum for MONAI 1.0.1 (#17628)
- fix paths to Perl modules in MAKER v3.01.04 (#17629)
- add missing dependencies and add patch for fix incorrect ids for BRAKER v2.1.6 (#17631)
- explicitely disable mpi/python in Boost (intel-compilers/2021.4.0) (#17638)
- remove LLVM build dependency from TensorFlow easyconfigs (#17641)
- update easyconfig for Longshot 0.4.5 to use Cargo easyblock (#17666)
- fix homepage in ELPA easyconfigs (due to switch to new domain) (#17697)
- add patch for scipy 1.10.1 extension in SciPy-bundle 2023.02 to fix broken test (#17713)
- use CUDA variant of OpenMM 7.5.1 as dependency for AlphaFold 2.3.0 (#17717)
- exclude flaky test_optim for PyTorch 1.12.1 + make excluded tests for PyTorch 1.12.1 consistent (#17726, #17730, #17731, #17737)
- add missing PCRE dependency for InterProScan 5.55-88.0 (#17762)
- fix building Python bindings of DGL, requires static libs (#17764)
- only use QEF gitlab source url for QuantumESPRESSO itself (#17766)
- add egg file to OpenCV 4.6.0 python package for pip + pkgconfig file (#17779)
- fix broken source URL for AOCC 4.0.0 (#17794)
- specify source_urls inside exts_default_options in Seurat easyconfigs to ensure correct name expansion for the archived packages (#17830)
- add Doxygen build dependency to X11 (#17842)
- FLINT needs BLAS so move it up from GCC level (#17868)
- fix broken tarball links for ispc 1.6, 1.10, and 1.12 easyconfigs (#17875)
- add dependency on PycURL to JupyterHub-3.0.0-GCCcore-11.3.0.eb (#17887)
- add historical repo paths to install cmd for old versions of texlive (#17893)
- add missing FastTreeMP binary for FastTree (#17897)
- add checksum for arm64 source tarball for Go 1.18.3 (#17903)
- add patch to fix test_quantization in PyTorch 1.12.1 (#17908)
- add make 4.3 as build dependency for recent OpenBLAS versions (#17924)
- other changes:
- bump versions in Java wrappers to latest builds that include ppc64le: Java/8.362, Java/11.0.8, Java/17.0.6 (#17775)
- move Arb and polymake to gfbf/foss since FLINT is now at gfbf/foss (#17869)
v4.7.1 (March 20th 2023)
------------------------
update/bugfix release
- added example easyconfig files for 99 new software packages:
- astro-tulips (#17263), BA3-SNPS-autotune (#17248), BayesAss3-SNPs (#17247), Block (#27), CatLearn (#14940),
CDFlib (#17133), Cellpose (#13703), CheckM-Database (#17462), chemprop (#17261), cimfomfa (#17268), conan (#17326),
cooler (#17328), crossguid (#16207), cuSPARSELt (#17141), cython-blis (#17544), DBCSR (#17170), dclone (#17225),
DensPart (#17473), Deprecated (#1248), DLPack (#17311), DMLC-Core (#17311), dorado (#17195), duplex-tools (#17497),
eQuilibrator (#16812), fastai (#16985), fastjet (#17367), fastjet-contrib (#17377), ffnvcodec (#17271),
finder (#1917), flowFDA (#17495), gbasis (#17473), genomepy (#17506), Giotto-Suite (#17207), GKeyll (#16044),
GraphDB (#17280), graphviz-python (#17352), grid (#17473), GUSHR (#16905), Health-GPS (#17434), HepMC3 (#17341),
HiCMatrix (#17330), Inferelator (#17223), iodata (#17473), irodsfs (#17486), jupyter-contrib-nbextensions (#17270),
jupyterlab-lmod (#16563), jupyterlmod (#16563), kb-python (#17260), kineto (#17194), KMCP (#17267),
krbalancing (#17325), Lace (#954), LASSO-Python (#17510), libemf (#16188), loomR (#14518), MAKER (#17345),
methylartist (#17264), nanoflann (#17311), netMHCII (#9741), NEXUS-CL (#17350), nichenetr (#17524),
Parallel-Hashmap (#17311), pdsh (#17139), Perseus (#17210), PfamScan (#17530), Phenoflow (#17495), PIRATE (#17275),
PLAMS (#17473), plot1cell (#17498), pybinding (#17137), pyperf (#17063), pyslim (#17150),
pytest-rerunfailures (#17295), pytest-shard (#17295), python-louvain (#17207), PyTorch-Ignite (#15491),
PyVCF3 (#17519), R2jags (#17226), rapidcsv (#16211), rapidNJ (#17399), Rivet (#17380), rmarkdown (#17189),
scArches (#17069), scHiCExplorer (#17334), scib (#17142), SeaView (#17385), silhouetteRank (#17207),
siscone (#17342), smfishHmrf (#17207), sparse-neighbors-search (#17329), SpatialDE (#17207), sradownloader (#17188),
stardist (#17215), Strainberry (#17522), toil (#17098), vConTACT2 (#17372), VirSorter2 (#17371),
vitessce-python (#17472), vitessceR (#17525), YODA (#17343)
- added additional easyconfigs for various supported software packages, including:
- AlphaFold 2.3.0, Anaconda3 2022.10, angsd 0.940, archspec 0.2.0, Armadillo 11.4.3, AUGUSTUS 3.5.0, bcbio-gff 0.7.0,
BCFtools 1.17, beagle-lib 4.0.0, Beast 2.7.3, BeautifulSoup 4.11.1, Biopython 1.81, BLAT 3.7, Blender 3.4.1,
Blosc2 2.6.1, Boost 1.81.0, Bottleneck 1.3.6, BUSCO 5.4.5, bx-python 0.9.0, CatMAP 20220519, CellRanger 7.1.0,
Cereal 1.3.2, CFITSIO 4.2.0, CheckM 1.2.2, code-server 4.9.1, configurable-http-proxy 4.5.3, csvkit 1.1.0, 4.8,
CUDA 12.1.0, cuDNN 8.8.0.121, cwltool 3.1.20221008225030, Cython 0.29.33, DGL 0.9.1, DIAMOND 2.1.0, dill 0.3.6,
DIRAC 23.0, dm-tree 0.1.8, dRep 3.4.2, eggnog-mapper 2.1.10, elfutils 0.189, ELPA 2022.05.001, epiScanpy 0.4.0,
FabIO 0.14.0, FastQ_Screen 0.14.0, FFmpeg 5.1.2, FLAC 1.4.2, flatbuffers 23.1.4, FLINT 2.9.0, GDAL 2.4.4,
GDAL 3.6.2, GDGraph 1.56, GEOS 3.11.1, GMAP-GSNAP 2023-02-17, gmsh 4.11.1, gnuplot 5.4.6, GOATOOLS 1.3.1,
googletest 1.12.1, GPyTorch 1.9.1, Greenlet 2.0.2, GST-plugins-base 1.22.1, GStreamer 1.22.1, GTDB-Tk 2.1.1,
h5py 3.8.0, HDBSCAN 0.8.29, HDF5 1.14.0, HiCExplorer 3.7.2, Highway 1.0.3, HTSlib 1.17, hypothesis 6.68.2,
Hypre 2.27.0, igraph 0.10.3, IGV 2.16.0, IJulia 1.24.0, Imath 3.1.6, imbalanced-learn 0.10.1, imkl 2023.0.0,
imkl-FFTW 2023.0.0, impi 2021.8.0, intel-compilers 2023.0.0, IRkernel 1.3.2, JAGS 4.3.1, jax 0.4.4, Julia 1.8.5,
JupyterHub 3.0.0, jupyter-matlab-proxy 0.5.0, jupyter-resource-usage 0.6.3, jupyter-server-proxy 3.2.2,
Kent_tools 442, leidenalg 0.9.1, LERC 4.0.0, libcerf 2.3, libgit2 1.5.0, libnsl 2.0.0, libsndfile 1.2.0,
libtirpc 1.3.3, libxslt 1.1.37, Longshot 0.4.5, MAFFT 7.505, Maple 2022.1, MaSuRCA 4.1.0, Mathematica 13.1.0,
MATIO 1.5.23, MATLAB 2022a + 2022a-r3 + 2022b, matplotlib 3.7.0, MaxQuant 2.2.0.0, MCL 22.282, MDAnalysis 2.4.2,
Miniconda3 22.11.1, mm-common 1.0.5, MPFR 4.2.0, mpi4py 3.1.4, mpmath 1.2.1, msprime 1.2.0, MultiQC 1.14,
mygene 3.2.2, nano 7.1, nanomax-analysis-utils 0.4.4, ncbi-vdb 3.0.2, NetLogo 6.2.2 + 6.3.0, nettle 3.8.1,
networkx 3.0, Nextflow 22.10.6, nlohmann_json 3.11.2, numba 0.56.4, NVHPC 22.9 + 22.11 + 23.1, NVSHMEM 2.8.0,
OpenMPI 4.1.5, Optuna 3.1.0, ORCA 5.0.4, PAML 4.10.5, panaroo 1.3.2, ParallelIO 2.5.10, parasail 2.6, Pillow 9.4.0,
PIPITS 3.0, PLINK 2.00a3.7, plotly.py 5.12.0 + 5.13.1, PLUMED 2.8.1, poetry 1.2.2, polymake 4.8, preseq 3.2.0,
presto 1.0.0-20230113, PROJ 9.1.1, protobuf 3.21.9, psycopg2 2.9.5, pybind11 2.10.3, PyCharm 2022.3.2,
py-cpuinfo 9.0.0, pyFAI 0.21.3, pyfaidx 0.7.1, pyGenomeTracks 3.8, pygraphviz 1.10, pymca 5.7.6, Pysam 0.20.0,
PySCF 2.1.1, PyTables 3.8.0, Python 3.11.2, python-parasail 1.3.3, PyZMQ 24.0.1, QCG-PilotJob 0.13.1,
QIIME2 2022.11, QtPy 2.3.0, QUAST 5.2.0, R 4.2.2, Ray-project 2.2.0, RDKit 2022.09.4, Redis 7.0.8, redis-py 4.5.1,
ReFrame 4.0.5, RepeatMasker 4.1.4, RepeatModeler 2.0.4, rjags 4-13, RMBlast 2.13.0, ROOT 6.22.08, Salmon 1.9.0,
SAMtools 1.17, Scalasca 2.6.1, scikit-learn 1.2.1, SciPy-bundle 2023.02, SDL2 2.26.3, SeqKit 2.3.1, silx 1.0.0,
snakemake 7.22.0, SNAP-HMM 20221022, SpaceRanger 2.0.1, SPAdes 3.15.5, spaln 2.4.13f, Spark 3.3.1,
SRA-Toolkit 3.0.3, SSW 1.2.4, STAR 2.7.10b, STAR-CCM+ 18.02.008, SVG 2.87, TensorFlow-Datasets 4.8.3,
Tkinter 3.10.8, tqdm 4.64.1, Trilinos 13.4.1, Trim_Galore 0.6.10, Trinity 2.15.1, TWL-NINJA 0.98-cluster_only,
Unidecode 1.3.6, vsc-mympirun 5.3.0, VSEARCH 2.22.1, wget 1.21.3, wxWidgets 3.2.2.1, x264 20230226,
Xerces-C++ 3.2.4, XlsxWriter 3.0.8, xtb 6.5.1, Xvfb 21.1.6
- minor enhancements, including:
- add additional extensions to R 4.2.1 (#17043, #17125, #17224, #17493, #17523)
- add additional extensions to Bioconductor 3.15 (#17126, #17315, #17494)
- add sanity check command to OpenMolcas v22.10 (#17128)
- add Set::Object and Heap::Fibonacci extensions to Perl 5.32.1 (#17151)
- add additional extensions to Python 3.10.8 (required for scipy test suite) (#17159)
- enhance OpenFold 1.0.1 for standalone usage (#17206)
- add SDL2 dependency for FFmpeg 5.0.1 to build ffplay (#17213)
- set $JULIA_DEPOT_PATH and $JULIA_HISTORY in Julia easyconfigs (#17216)
- add Devel::Size + Math::Utils extension to recent Perl easyconfigs (#17246, #17466)
- combine errors of extension patch check into a single failure (#17286)
- add case-insensitive name clash test (#17303)
- add ffnvcodec build dependency to all recent FFmpeg easyconfigs (#17316)
- use 'import deap.base' in sanity check for deap extension in SciPy-bundle 2022.05 (#17429)
- add source URL to cuDNN 8.8 easyconfig (#17439)
- add missing zstd dep to Boost (#17482)
- various bug fixes, including:
- fix postinstallcmds and clarify download instructions for netMHC + netMHCpan 4.0a (#9739, #9740)
- fix OpenBLAS 0.3.15 patch to correctly set the CPU core type for Tiger Lake (#15845)
- add alternative checksum for UCX 1.13.1 after source tarball was changed in-place (without actual code changes) (#17077)
- fix build of TensorFlow 2.5+ on aarch64 (#17101)
- explictely download qe-gipaw source tarball from qe-gipaw GitHub repository in QuantumESPRESSO 7.1 easyconfigs (#17129)
- add patch for GCCcore 11.1.0 + 11.2.0 to fix AVX2 bug (#17135)
- add patch to make ncbi-vdb 3.0.0 compatible with HDF5 1.12.2 (#17140)
- fix source URL for p7zip v17.x (#17144)
- add patches for Qt5 5.15.5 to fix compilation failures in abseil and breakpad with glibc 2.34 (#17165)
- remove dependency on Pillow from scikit-bio v0.5.7 (#17178)
- correctly specify path to libfabric installation prefix in PMIx 4.1.0 easyconfig (#17204)
- use GCC as toolchain for serial variants of HDF5, since it has a FORTRAN API (#17221)
- fix CMake print summary for long hostnames for NECI (#17230)
- add missing pmix patch to OpenMPI 4.1.1 easyconfig used in iomkl/2021a and iomkl/2021b (#17240)
- include required stereo_chemical_props.txt for OpenFold 1.0.1 (#17242)
- add patch for PAPI 7.0.0 to fix compilation error (#17244)
- also update $PERL5LIB for RepeatMasker v4.1.4 (#17245)
- add alternative source_url for MariaDB > 10.4 (#17250)
- remove use of rysnc in building Kent_tools (#17252)
- add missing pkgconf build dependency in recent libxslt easyconfigs (#17254)
- add psycopg2, PyYAML, and Cartopy dependencies to QGIS 3.28.1 (#17257)
- fix postinstallcmds in shovill easyconfigs (#17279)
- allow multiple easyconfigs with same name if they differ by CUDA version included in versionsuffix (#17289)