update relion commits, use napari 0.4.19.post1, switch to mod*footers

easybuild/easyconfigs/r/RELION/RELION-5.0.0_beta.2024.02.01-foss-2023a-CUDA-12.1.1.eb → easybuild/easyconfigs/r/RELION/RELION-5.0.0_beta.2024.05.03-foss-2023a-CUDA-12.1.1.eb

@@ -2,8 +2,8 @@
 easyblock = 'CMakeMake'
 
 name = 'RELION'
-version = '5.0.0_beta.2024.02.01'
-_commit = 'b75b38c'
+version = '5.0.0_beta.2024.05.03'
+_commit = '6331fe6'
 versionsuffix = '-CUDA-%(cudaver)s'
 
 homepage = 'http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page'
@@ -35,7 +35,7 @@ build_info_msg = """To install RELION, it's recommended to change the defaults i
 
    * Set additional 'RELION_*' variables, such as 'RELION_SCRATCH_DIR'. See:
      https://relion.readthedocs.io/en/release-5.0/Installation.html#edit-the-environment-set-up
-     These variables should be added to 'modextrapaths'.
+     These variables should be added to 'modextrapaths' or 'mod{lua,tcl}footer' as appropriate.
 
    * Add a job submission template for queue submission. See:
      https://relion.readthedocs.io/en/release-5.0/Installation.html#set-up-queue-job-submission
@@ -75,6 +75,7 @@ dependencies = [
     ('LibTIFF', '4.5.0'),
     ('tbb', '2021.11.0'),
     ('libpng', '1.6.39'),
+    ('morphosamplers', '0.0.10'),   # required for: src/tomography_python_programs/get_particle_poses/filaments.py
 
     # optional dependencies #
     ('tcsh', '6.24.10'),
@@ -112,7 +113,7 @@ dependencies = [
     ('topaz', '0.2.5.20231120', versionsuffix),
     ('dask', '2023.9.2'),
     ('imageio', '2.33.1'),
-    ('napari', '0.4.18'),
+    ('napari', '0.4.19.post1'),
     ('tensorboard', '2.15.1'),
 ]
 
@@ -189,25 +190,25 @@ exts_list = [
         }],
         'checksums': [None],
     }),
-    ('DynaMight', '0.0.1_20231206', {
+    ('DynaMight', '0.0.1_20240319', {
         'sources': [{
              'filename': '%(name)s-%(version)s.tar.gz',
              'git_config': {
                  'url': 'https://github.com/3dem',
                  'repo_name': '%(name)s',
-                 'commit': '616360b790febf56edf08aef5d4c414058194376',
+                 'commit': 'eef4aa673af6cc908042b38646ae489ee8f2fde9',
                  'keep_git_dir': True,
              },
         }],
         'checksums': [None],
     }),
-    ('model-angelo', '1.0.12_20231207', {
+    ('model-angelo', '1.0.12_20240226', {
         'sources': [{
              'filename': '%(name)s-%(version)s.tar.gz',
              'git_config': {
                  'url': 'https://github.com/3dem',
                  'repo_name': '%(name)s',
-                 'commit': 'd4ecc968b37f0694c1216c052438dfaf1bf2d813',
+                 'commit': '6fdad9b47a0a2abb86990803f243ef028197a04d',
                  'keep_git_dir': True,
              },
         }],
@@ -228,10 +229,20 @@ modextrapaths = {
 
 modextravars = {
     'TORCH_HOME': _torch_home,
-    'RELION_PDFVIEWER_EXECUTABLE': '$EBROOTXPDF/bin/xpdf',
-    'RELION_SHELL': '$EBROOTTCSH/bin/tcsh',
 }
 
+# modextravars doesn't expand environment variables, so use mod*footer instead
+# see https://github.com/easybuilders/easybuild-framework/issues/2548
+modluafooter = """
+setenv("RELION_PDFVIEWER_EXECUTABLE", os.getenv("EBROOTXPDF") .. "/bin/xpdf")
+setenv("RELION_SHELL", os.getenv("EBROOTTCSH") .. "/bin/tcsh")
+"""
+
+modtclfooter = """
+setenv RELION_PDFVIEWER_EXECUTABLE $::env(EBROOTXPDF)/bin/xpdf
+setenv RELION_SHELL $::env(EBROOTTCSH)/bin/tcsh
+"""
+
 _version_maj = version.split('_')[0]
 modloadmsg = "Current version pulled from commit %s from https://github.com/3dem/relion ver%s branch" % (_commit,
                                                                                                          _version_maj)