{bio}[foss/2023a] AlphaPulldown v2.0.0 Uni-Core v0.0.3 w/ CUDA v12.1.1 by ThomasHoffmann77 · Pull Request #21204 · easybuilders/easybuild-easyconfigs

ThomasHoffmann77 · 2024-08-17T18:03:10Z

(created using eb --new-pr)
requires:

{bio}[foss/2023a] OpenMM v8.0.0 w/ CUDA 12.1.1 #20362

adapted from PR #21179

…sybuild/easyconfigs/t/tensorstore/tensorstore-0.1.53-foss-2023a.eb

boegel · 2024-08-21T14:24:28Z

@ThomasHoffmann77 Additional extensions are required for the convert_to_modelcif.py script, see 99abe91 (included in #21179)

ThomasHoffmann77 · 2024-10-10T08:07:52Z

switched to draft: expecting 2.0.0 final release soon with setup.cfg not using hardcoded lib/python3.10/site-packages (see KosinskiLab/AlphaPulldown@cc4b0af)

…DA-12.1.1.eb

….1.1.eb

…23a.eb

…ss-2023a-CUDA-12.1.1.eb

…2_biopython_IUPACData_as_SCOPData.patch

update TensorFlow dependency from 2.13.0 to 2.15.2-CUDA

AlphaPulldown TF2.15.1 multivariant dependency

…AlphaPulldown-2.0.0-foss-2023a-CUDA-12.1.1.eb update 2.0.0

github-actions · 2024-11-08T09:09:14Z

Updated software `AlphaPulldown-2.0.0-foss-2023a-CUDA-12.1.1.eb`

Diff against AlphaPulldown-2.0.0b4-foss-2022a-CUDA-11.7.0.eb

easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b4-foss-2022a-CUDA-11.7.0.eb

diff --git a/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b4-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0-foss-2023a-CUDA-12.1.1.eb
index 492a787c91..e1dd253f81 100644
--- a/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b4-foss-2022a-CUDA-11.7.0.eb
+++ b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0-foss-2023a-CUDA-12.1.1.eb
@@ -1,55 +1,59 @@
 # created by Denis Kristak (Inuits)
+# update: Thomas Hoffmann, EMBL
 easyblock = 'PythonBundle'
 
 name = 'AlphaPulldown'
-version = '2.0.0b4'
+version = '2.0.0'
 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'}
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+builddependencies = [
+    ('poetry', '1.5.1'),
+]
 
 dependencies = [
-    ('CUDA', '11.7.0', '', SYSTEM),
-    ('Python', '3.10.4'),
-    ('OpenMM', '8.0.0'),
-    ('Kalign', '3.3.5'),
+    ('CUDA', '12.1.1', '', SYSTEM),
+    ('Python', '3.11.3'),
+    ('OpenMM', '8.0.0', versionsuffix),
+    ('Kalign', '3.4.0'),
     ('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'),
+    ('jax', '0.4.25', versionsuffix),  # also provides absl-py
+    ('Biopython', '1.83'),
+    ('h5py', '3.9.0'),
+    ('IPython', '8.14.0'),
+    ('matplotlib', '3.7.2'),
+    # ('TensorFlow', '2.15.1', versionsuffix),
+    ('TensorFlow', '2.13.0'),  # to be consistent with AF2 ?
+    ('PyTorch', '2.1.2', versionsuffix),
+    ('tqdm', '4.66.1'),
     ('dm-tree', '0.1.8'),
-    ('py3Dmol', '2.0.1.post1'),
-    ('HMMER', '3.3.2'),
+    ('py3Dmol', '2.1.0'),
+    ('HMMER', '3.4'),
     ('HH-suite', '3.3.0'),
+    ('dm-haiku', '0.0.12', versionsuffix),
     ('Uni-Core', '0.0.3', versionsuffix),
+    ('JupyterLab', '4.0.5'),
 ]
-
+local_commit = 'cc4b0af60518c078305bbe4c584691d1ed9ade31'
 use_pip = True
 
+local_tests = [
+    'custom_db',
+    'remove_clashes_low_plddt',
+    'modelcif',
+    'features_with_templates',
+    'post_prediction',
+    # require pyrosetta, analysis aptainer image, and AlphaFold2 data:
+    # 'pdb_analyser',
+    # 'get_good_inter_pae',
+]
+local_testinstall_PATH = """ PATH=$(echo $PYTHONPATH|awk -F ':' '{print $1}')/../../../bin:$PATH """
 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'],
     }),
@@ -69,38 +73,49 @@ exts_list = [
     ('modelcif', '1.0', {
         'checksums': ['e8375bc502a73dcfab0b7fbdd454d67d393bbb8969981eb52199d77192a3de56'],
     }),
+    ('looseversion', '1.1.2', {
+        'checksums': ['94d80bdbd0b6d57c11b886147ba1601f7d1531571621b81933b34537cbe469ad'],
+    }),
+    ('mmtf-python', '1.1.3', {
+        'modulename': 'mmtf',
+        'checksums': ['12a02fe1b7131f0a2b8ce45b46f1e0cdd28b9818fe4499554c26884987ea0c32'],
+    }),
+    ('biopandas', '0.5.1.dev0', {
+        'checksums': ['6dc9de631babf8221c1ac60230133717039e08911f15e8ac48498c787022de12'],
+    }),
+    ('immutabledict', '4.1.0', {
+        'checksums': ['93d100ccd2cd09a1fd3f136b9328c6e59529ba341de8bb499437f6819159fe8a'],
+    }),
     (name, version, {
+        'preinstallopts': "sed -i 's/[>=]=.*//g;s/tensorflow-cpu/tensorflow/g' setup.cfg && ",
+        'runtest': '%s pytest -s %s ' % (local_testinstall_PATH, " ".join('test/test_%s.py' % x for x in local_tests)),
         'sources': [{
-            'filename': SOURCE_TAR_GZ,
+            'filename': '%(name)s-%(version)s.tar.gz',
             'git_config': {
                 'url': 'https://github.com/KosinskiLab',
                 'repo_name': 'AlphaPulldown',
-                'tag': version,
-                'recursive': True,
-            },
+                '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 && ",
+        'testinstall': True,
+        # This needs to be [None], at least until EB v5 is out
+        # 'checksums': ['e338195987e003f3caadb06bda0ca56dece87e358738143ea72662f9ad69b1d4'],
+        'checksums': [None],
     }),
 ]
 
 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'],
+    'files': ['bin/run_multimer_jobs.py', 'bin/rename_colab_search_a3m.py',
+              'lib/python%(pyshortver)s/site-packages/alphafold/common/stereo_chemical_props.txt'],
     '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'",
+    "create_individual_features.py --helpfull|grep 'Additional allowance for hydrogen bonding'",
 ]
 
 moduleclass = 'bio'

Diff against AlphaPulldown-2.0.0b4-foss-2022a.eb

easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b4-foss-2022a.eb

diff --git a/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b4-foss-2022a.eb b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0-foss-2023a-CUDA-12.1.1.eb
index f410c438e2..e1dd253f81 100644
--- a/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b4-foss-2022a.eb
+++ b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0-foss-2023a-CUDA-12.1.1.eb
@@ -1,53 +1,59 @@
 # created by Denis Kristak (Inuits)
+# update: Thomas Hoffmann, EMBL
 easyblock = 'PythonBundle'
 
 name = 'AlphaPulldown'
-version = '2.0.0b4'
+version = '2.0.0'
+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'}
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+builddependencies = [
+    ('poetry', '1.5.1'),
+]
 
 dependencies = [
-    ('Python', '3.10.4'),
-    ('OpenMM', '8.0.0'),
-    ('Kalign', '3.3.5'),
+    ('CUDA', '12.1.1', '', SYSTEM),
+    ('Python', '3.11.3'),
+    ('OpenMM', '8.0.0', versionsuffix),
+    ('Kalign', '3.4.0'),
     ('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'),
+    ('jax', '0.4.25', versionsuffix),  # also provides absl-py
+    ('Biopython', '1.83'),
+    ('h5py', '3.9.0'),
+    ('IPython', '8.14.0'),
+    ('matplotlib', '3.7.2'),
+    # ('TensorFlow', '2.15.1', versionsuffix),
+    ('TensorFlow', '2.13.0'),  # to be consistent with AF2 ?
+    ('PyTorch', '2.1.2', versionsuffix),
+    ('tqdm', '4.66.1'),
     ('dm-tree', '0.1.8'),
-    ('py3Dmol', '2.0.1.post1'),
-    ('HMMER', '3.3.2'),
+    ('py3Dmol', '2.1.0'),
+    ('HMMER', '3.4'),
     ('HH-suite', '3.3.0'),
-    ('Uni-Core', '0.0.3'),
+    ('dm-haiku', '0.0.12', versionsuffix),
+    ('Uni-Core', '0.0.3', versionsuffix),
+    ('JupyterLab', '4.0.5'),
 ]
-
+local_commit = 'cc4b0af60518c078305bbe4c584691d1ed9ade31'
 use_pip = True
 
+local_tests = [
+    'custom_db',
+    'remove_clashes_low_plddt',
+    'modelcif',
+    'features_with_templates',
+    'post_prediction',
+    # require pyrosetta, analysis aptainer image, and AlphaFold2 data:
+    # 'pdb_analyser',
+    # 'get_good_inter_pae',
+]
+local_testinstall_PATH = """ PATH=$(echo $PYTHONPATH|awk -F ':' '{print $1}')/../../../bin:$PATH """
 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'],
     }),
@@ -67,38 +73,49 @@ exts_list = [
     ('modelcif', '1.0', {
         'checksums': ['e8375bc502a73dcfab0b7fbdd454d67d393bbb8969981eb52199d77192a3de56'],
     }),
+    ('looseversion', '1.1.2', {
+        'checksums': ['94d80bdbd0b6d57c11b886147ba1601f7d1531571621b81933b34537cbe469ad'],
+    }),
+    ('mmtf-python', '1.1.3', {
+        'modulename': 'mmtf',
+        'checksums': ['12a02fe1b7131f0a2b8ce45b46f1e0cdd28b9818fe4499554c26884987ea0c32'],
+    }),
+    ('biopandas', '0.5.1.dev0', {
+        'checksums': ['6dc9de631babf8221c1ac60230133717039e08911f15e8ac48498c787022de12'],
+    }),
+    ('immutabledict', '4.1.0', {
+        'checksums': ['93d100ccd2cd09a1fd3f136b9328c6e59529ba341de8bb499437f6819159fe8a'],
+    }),
     (name, version, {
+        'preinstallopts': "sed -i 's/[>=]=.*//g;s/tensorflow-cpu/tensorflow/g' setup.cfg && ",
+        'runtest': '%s pytest -s %s ' % (local_testinstall_PATH, " ".join('test/test_%s.py' % x for x in local_tests)),
         'sources': [{
-            'filename': SOURCE_TAR_GZ,
+            'filename': '%(name)s-%(version)s.tar.gz',
             'git_config': {
                 'url': 'https://github.com/KosinskiLab',
                 'repo_name': 'AlphaPulldown',
-                'tag': version,
-                'recursive': True,
-            },
+                '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 && ",
+        'testinstall': True,
+        # This needs to be [None], at least until EB v5 is out
+        # 'checksums': ['e338195987e003f3caadb06bda0ca56dece87e358738143ea72662f9ad69b1d4'],
+        'checksums': [None],
     }),
 ]
 
 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'],
+    'files': ['bin/run_multimer_jobs.py', 'bin/rename_colab_search_a3m.py',
+              'lib/python%(pyshortver)s/site-packages/alphafold/common/stereo_chemical_props.txt'],
     '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'",
+    "create_individual_features.py --helpfull|grep 'Additional allowance for hydrogen bonding'",
 ]
 
 moduleclass = 'bio'

Diff against AlphaPulldown-0.30.4-fosscuda-2020b.eb

easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-0.30.4-fosscuda-2020b.eb

diff --git a/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-0.30.4-fosscuda-2020b.eb b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0-foss-2023a-CUDA-12.1.1.eb
index fe9b546828..e1dd253f81 100644
--- a/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-0.30.4-fosscuda-2020b.eb
+++ b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0-foss-2023a-CUDA-12.1.1.eb
@@ -1,84 +1,121 @@
 # created by Denis Kristak (Inuits)
-easyblock = "PythonBundle"
+# update: Thomas Hoffmann, EMBL
+easyblock = 'PythonBundle'
 
-name = "AlphaPulldown"
-version = "0.30.4"
+name = 'AlphaPulldown'
+version = '2.0.0'
+versionsuffix = '-CUDA-%(cudaver)s'
 
-homepage = "https://github.com/KosinskiLab/AlphaPulldown"
+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': 'fosscuda', 'version': '2020b'}
+toolchain = {'name': 'foss', 'version': '2023a'}
 
-dependencies = [
-    ('Python', '3.8.6'),
-    ("OpenMM", "7.5.0"),
-    ("Kalign", "3.3.1"),
-    ('PyYAML', '5.3.1'),
-    ("cctbx-base", "2020.8"),
-    ('jax', '0.2.19'),  # also provides absl-py
-    ('Biopython', '1.78'),
-    ('h5py', '3.1.0'),
-    ('IPython', '7.18.1'),
-    ('JupyterLab', '2.2.8'),
-    ('matplotlib', '3.3.3'),
-    ('TensorFlow', '2.4.1'),
-    ('tqdm', '4.56.2'),
-    ('dm-tree', '0.1.5'),
+builddependencies = [
+    ('poetry', '1.5.1'),
 ]
 
+dependencies = [
+    ('CUDA', '12.1.1', '', SYSTEM),
+    ('Python', '3.11.3'),
+    ('OpenMM', '8.0.0', versionsuffix),
+    ('Kalign', '3.4.0'),
+    ('PyYAML', '6.0'),
+    ('jax', '0.4.25', versionsuffix),  # also provides absl-py
+    ('Biopython', '1.83'),
+    ('h5py', '3.9.0'),
+    ('IPython', '8.14.0'),
+    ('matplotlib', '3.7.2'),
+    # ('TensorFlow', '2.15.1', versionsuffix),
+    ('TensorFlow', '2.13.0'),  # to be consistent with AF2 ?
+    ('PyTorch', '2.1.2', versionsuffix),
+    ('tqdm', '4.66.1'),
+    ('dm-tree', '0.1.8'),
+    ('py3Dmol', '2.1.0'),
+    ('HMMER', '3.4'),
+    ('HH-suite', '3.3.0'),
+    ('dm-haiku', '0.0.12', versionsuffix),
+    ('Uni-Core', '0.0.3', versionsuffix),
+    ('JupyterLab', '4.0.5'),
+]
+local_commit = 'cc4b0af60518c078305bbe4c584691d1ed9ade31'
 use_pip = True
 
+local_tests = [
+    'custom_db',
+    'remove_clashes_low_plddt',
+    'modelcif',
+    'features_with_templates',
+    'post_prediction',
+    # require pyrosetta, analysis aptainer image, and AlphaFold2 data:
+    # 'pdb_analyser',
+    # 'get_good_inter_pae',
+]
+local_testinstall_PATH = """ PATH=$(echo $PYTHONPATH|awk -F ':' '{print $1}')/../../../bin:$PATH """
 exts_list = [
-    ('py3Dmol', '2.0.1.post1', {
-        'modulename': 'py3Dmol',
-        'checksums': ['add70ecf8f647970925eb8c1043c5c1343813fa49e613b77f0628e522c4148ac'],
-    }),
-    ('PDBFixer', '1.7', {
-        'source_urls': ['https://github.com/openmm/pdbfixer/archive/refs/tags/'],
-        'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],
-        'checksums': ['a0bef3c52a7bbe69a6aea5333f51f3e7d158339be5829aed19b0344bd66d4eea'],
-    }),
-    ('dm-haiku', '0.0.4', {
-        'modulename': 'haiku',
-        'patches': ['%(name)s-%(version)s_fix-deps.patch'],
-        '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': [
-            {'dm-haiku-0.0.4.tar.gz': 'e9896d161938b53f869fde207f3f6fca496d09b2a47d21dd9b6b65e897ad6aab'},
-            {'dm-haiku-0.0.4_fix-deps.patch': 'c509e0aa049401f340234b0a5eba59c9e8af8eff94b9e92f0693aeadfa4c5aa8'},
-        ],
-    }),
-    ('toolz', '0.11.1', {
-        'checksums': ['c7a47921f07822fe534fb1c01c9931ab335a4390c782bd28c6bcc7c2f71f3fbf'],
-    }),
-    ('importlib-resources', '5.12.0', {
-        'modulename': 'importlib_resources',
-        'source_tmpl': 'importlib_resources-%(version)s.tar.gz',
-        'checksums': ['4be82589bf5c1d7999aedf2a45159d10cb3ca4f19b2271f8792bc8e6da7b22f6'],
-    }),
     ('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'],
+    }),
+    ('looseversion', '1.1.2', {
+        'checksums': ['94d80bdbd0b6d57c11b886147ba1601f7d1531571621b81933b34537cbe469ad'],
+    }),
+    ('mmtf-python', '1.1.3', {
+        'modulename': 'mmtf',
+        'checksums': ['12a02fe1b7131f0a2b8ce45b46f1e0cdd28b9818fe4499554c26884987ea0c32'],
+    }),
+    ('biopandas', '0.5.1.dev0', {
+        'checksums': ['6dc9de631babf8221c1ac60230133717039e08911f15e8ac48498c787022de12'],
+    }),
+    ('immutabledict', '4.1.0', {
+        'checksums': ['93d100ccd2cd09a1fd3f136b9328c6e59529ba341de8bb499437f6819159fe8a'],
+    }),
     (name, version, {
-        'patches': ['%(name)s-%(version)s_fix-deps.patch'],
-        'sources': ['%(namelower)s-%(version)s.tar.gz'],
-        'checksums': [
-            {'alphapulldown-0.30.4.tar.gz': '7797500abaee2e92d28034dc97844bca8c8d7281817e29dc110220824e9d1b5b'},
-            {'AlphaPulldown-0.30.4_fix-deps.patch': 'fc5bf395cb36d02efa6d538df49749e722b2d2c257197e3dac83a81c9405c0c9'},
-        ],
+        'preinstallopts': "sed -i 's/[>=]=.*//g;s/tensorflow-cpu/tensorflow/g' setup.cfg && ",
+        'runtest': '%s pytest -s %s ' % (local_testinstall_PATH, " ".join('test/test_%s.py' % x for x in local_tests)),
+        'sources': [{
+            'filename': '%(name)s-%(version)s.tar.gz',
+            'git_config': {
+                'url': 'https://github.com/KosinskiLab',
+                'repo_name': 'AlphaPulldown',
+                'tag': version, 'recursive': True
+            }
+        }],
+        'testinstall': True,
+        # This needs to be [None], at least until EB v5 is out
+        # 'checksums': ['e338195987e003f3caadb06bda0ca56dece87e358738143ea72662f9ad69b1d4'],
+        'checksums': [None],
     }),
 ]
 
+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"],
+    'files': ['bin/run_multimer_jobs.py', 'bin/rename_colab_search_a3m.py',
+              'lib/python%(pyshortver)s/site-packages/alphafold/common/stereo_chemical_props.txt'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages/alphapulldown'],
 }
 
-moduleclass = "data"
+sanity_check_commands = [
+    "run_multimer_jobs.py --help | grep 'A script to perform structure prediction'",
+    "create_individual_features.py --helpfull|grep 'Additional allowance for hydrogen bonding'",
+]
+
+moduleclass = 'bio'

Updated software `Uni-Core-0.0.3-foss-2023a-CUDA-12.1.1.eb`

Diff against Uni-Core-0.0.3-foss-2022a-CUDA-11.7.0.eb

easybuild/easyconfigs/u/Uni-Core/Uni-Core-0.0.3-foss-2022a-CUDA-11.7.0.eb

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-2023a-CUDA-12.1.1.eb
index 2ca769764a..24fb0a0d2e 100644
--- 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-2023a-CUDA-12.1.1.eb
@@ -7,46 +7,51 @@ versionsuffix = '-CUDA-%(cudaver)s'
 homepage = 'https://github.com/dptech-corp/Uni-Core'
 description = "An efficient distributed PyTorch framework"
 
-toolchain = {'name': 'foss', 'version': '2022a'}
+toolchain = {'name': 'foss', 'version': '2023a'}
 
+builddependencies = [
+    ('maturin', '1.4.0', '-Rust-1.75.0')
+]
 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'),
+    ('CUDA', '12.1.1', '', SYSTEM),
+    ('Python', '3.11.3'),
+    ('PyTorch', '2.1.2', versionsuffix),
+    ('jax', '0.4.25', versionsuffix),  # provides absl-py
+    ('tensorboardX', '2.6.2.2'),
+    ('tqdm', '4.66.1'),
+    ('wandb', '0.16.1'),
 ]
 
 use_pip = True
+local_preinstallopts = "sed -i "
+# local_preinstallopts += "-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'],
+    ('lmdb', '1.5.1', {
+        'checksums': ['717c255827d331e02f7242b44051aa06466c90f6d732ecb07b31edfb1e06c67a'],
     }),
     ('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'],
-        'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ",
     }),
-    ('huggingface-hub', '0.17.3', {
+    ('huggingface-hub', '0.24.5', {
         'source_tmpl': 'huggingface_hub-%(version)s.tar.gz',
-        'checksums': ['40439632b211311f788964602bf8b0d9d6b7a2314fba4e8d67b2ce3ecea0e3fd'],
+        'checksums': ['7b45d6744dd53ce9cbf9880957de00e9d10a9ae837f1c9b7255fc8fa4e8264f3'],
     }),
-    ('tokenizers', '0.19.1', {
-        'sources': ['tokenizers-%(version)s-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl'],
-        'checksums': ['8b01afb7193d47439f091cd8f070a1ced347ad0f9144952a30a41836902fe09e'],
+    ('tokenizers', '0.20.0', {
+        'checksums': ['39d7acc43f564c274085cafcd1dae9d36f332456de1a31970296a6b8da4eac8d'],
     }),
     (name, version, {
+        'modulename': 'unicore',
+        'preinstallopts': local_preinstallopts,
         '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',
     }),
 ]

Diff against Uni-Core-0.0.3-foss-2022a.eb

easybuild/easyconfigs/u/Uni-Core/Uni-Core-0.0.3-foss-2022a.eb

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-2023a-CUDA-12.1.1.eb
index d82f94349b..24fb0a0d2e 100644
--- 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-2023a-CUDA-12.1.1.eb
@@ -2,52 +2,56 @@ 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'}
+toolchain = {'name': 'foss', 'version': '2023a'}
 
+builddependencies = [
+    ('maturin', '1.4.0', '-Rust-1.75.0')
+]
 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'),
+    ('CUDA', '12.1.1', '', SYSTEM),
+    ('Python', '3.11.3'),
+    ('PyTorch', '2.1.2', versionsuffix),
+    ('jax', '0.4.25', versionsuffix),  # provides absl-py
+    ('tensorboardX', '2.6.2.2'),
+    ('tqdm', '4.66.1'),
+    ('wandb', '0.16.1'),
 ]
 
 use_pip = True
-
-local_preinstallopts = "sed -i -e 's/DISABLE_CUDA_EXTENSION = False/DISABLE_CUDA_EXTENSION = True/g' "
+local_preinstallopts = "sed -i "
+# local_preinstallopts += "-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'],
+    ('lmdb', '1.5.1', {
+        'checksums': ['717c255827d331e02f7242b44051aa06466c90f6d732ecb07b31edfb1e06c67a'],
     }),
     ('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'],
-        'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ",
     }),
-    ('huggingface-hub', '0.17.3', {
+    ('huggingface-hub', '0.24.5', {
         'source_tmpl': 'huggingface_hub-%(version)s.tar.gz',
-        'checksums': ['40439632b211311f788964602bf8b0d9d6b7a2314fba4e8d67b2ce3ecea0e3fd'],
+        'checksums': ['7b45d6744dd53ce9cbf9880957de00e9d10a9ae837f1c9b7255fc8fa4e8264f3'],
     }),
-    ('tokenizers', '0.19.1', {
-        'sources': ['tokenizers-%(version)s-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl'],
-        'checksums': ['8b01afb7193d47439f091cd8f070a1ced347ad0f9144952a30a41836902fe09e'],
+    ('tokenizers', '0.20.0', {
+        'checksums': ['39d7acc43f564c274085cafcd1dae9d36f332456de1a31970296a6b8da4eac8d'],
     }),
     (name, version, {
+        'modulename': 'unicore',
+        'preinstallopts': local_preinstallopts,
         'source_urls': ['https://github.com/dptech-corp/Uni-Core/archive/'],
         'sources': ['%(version)s.tar.gz'],
         'checksums': ['e7a1e938d7d340d7aa483a05ed5ecf715bfa22f5f32a92e46d096da5b9a08043'],
-        'preinstallopts': local_preinstallopts,
-        'modulename': 'unicore',
     }),
 ]

add ext. immutabledict; fix tensorflow-cpu requirement

fix typo

test/easyconfigs/easyconfigs.py

…ulldown200b4

easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0-foss-2023a-CUDA-12.1.1.eb

move Jupyterlab dependency to end of list

akesandgren

LGTM

akesandgren · 2024-12-11T09:46:43Z

Test report by @akesandgren
FAILED
Build succeeded for 1 out of 2 (2 easyconfigs in total)
b-cn1611.hpc2n.umu.se - Linux Ubuntu 22.04, x86_64, AMD EPYC 7313 16-Core Processor, 1 x NVIDIA NVIDIA A100 80GB PCIe, 555.58.02, Python 3.10.12
See https://gist.github.com/akesandgren/56aea3df4b4f9d09c1011edb6e7d97b3 for a full test report.

easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0-foss-2023a-CUDA-12.1.1.eb

akesandgren · 2024-12-13T09:33:26Z

Test report by @akesandgren
SUCCESS
Build succeeded for 2 out of 2 (2 easyconfigs in total)
b-cn1611.hpc2n.umu.se - Linux Ubuntu 22.04, x86_64, AMD EPYC 7313 16-Core Processor, 1 x NVIDIA NVIDIA A100 80GB PCIe, 555.58.02, Python 3.10.12
See https://gist.github.com/akesandgren/48ee3cf53275a000291a44b6c8a8e5e2 for a full test report.

akesandgren

LGTM

akesandgren · 2024-12-13T09:55:26Z

Going in, thanks @ThomasHoffmann77!

ThomasHoffmann77 and others added 3 commits August 17, 2024 20:03

{bio}[foss/2023a] AlphaPulldown v2.0.0b4 Uni-Core v0.0.3 w/ CUDA v12.1.1

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Add files via upload

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Rename easybuild/easyconfigs/t/tensorstore-0.1.53-foss-2023a.eb to ea…

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…sybuild/easyconfigs/t/tensorstore/tensorstore-0.1.53-foss-2023a.eb

boegel added the update label Aug 21, 2024

boegel added this to the 4.x milestone Aug 21, 2024

boegel mentioned this pull request Aug 22, 2024

AlphaPullDown vscentrum/vsc-software-stack#39

Closed

ThomasHoffmann77 marked this pull request as draft October 10, 2024 08:00

ThomasHoffmann77 and others added 7 commits October 14, 2024 12:32

update 2.0.0b6

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Delete easybuild/easyconfigs/d/dm-haiku/dm-haiku-0.0.11-foss-2023a-CU…

6e3c92d

…DA-12.1.1.eb

Delete easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2023a-CUDA-12…

1900069

….1.1.eb

Delete easybuild/easyconfigs/t/tensorstore/tensorstore-0.1.53-foss-20…

d36e3ed

…23a.eb

Delete easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b4-fo…

c9b0f98

…ss-2023a-CUDA-12.1.1.eb

Delete easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b4_af…

b656747

…2_biopython_IUPACData_as_SCOPData.patch

Update AlphaPulldown-2.0.0b6-foss-2023a-CUDA-12.1.1.eb

d96e84f

update TensorFlow dependency from 2.13.0 to 2.15.2-CUDA

ThomasHoffmann77 changed the title ~~{bio}[foss/2023a] AlphaPulldown v2.0.0b4 Uni-Core v0.0.3 w/ CUDA v12.1.1~~ {bio}[foss/2023a] AlphaPulldown v2.0.0b6 Uni-Core v0.0.3 w/ CUDA v12.1.1 Oct 14, 2024

ThomasHoffmann77 and others added 2 commits October 14, 2024 14:58

Update easyconfigs.py

cbc778d

AlphaPulldown TF2.15.1 multivariant dependency

add missing checksums; use TF-CPU 2.13.0

1eaea1a

ThomasHoffmann77 marked this pull request as ready for review October 15, 2024 07:49

Update and rename AlphaPulldown-2.0.0b6-foss-2023a-CUDA-12.1.1.eb to …

0126a76

…AlphaPulldown-2.0.0-foss-2023a-CUDA-12.1.1.eb update 2.0.0

ThomasHoffmann77 changed the title ~~{bio}[foss/2023a] AlphaPulldown v2.0.0b6 Uni-Core v0.0.3 w/ CUDA v12.1.1~~ {bio}[foss/2023a] AlphaPulldown v2.0.0 Uni-Core v0.0.3 w/ CUDA v12.1.1 Nov 8, 2024

ThomasHoffmann77 added 2 commits November 8, 2024 10:34

Update AlphaPulldown-2.0.0-foss-2023a-CUDA-12.1.1.eb

b3c9399

add ext. immutabledict; fix tensorflow-cpu requirement

Update AlphaPulldown-2.0.0-foss-2023a-CUDA-12.1.1.eb

95d4237

fix typo

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ThomasHoffmann77 added 2 commits December 6, 2024 14:14

Merge branch 'easybuilders:develop' into 20240817200306_new_pr_AlphaP…

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…ulldown200b4

Update easyconfigs.py

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move Jupyterlab dependency to end of list

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{bio}[foss/2023a] AlphaPulldown v2.0.0 Uni-Core v0.0.3 w/ CUDA v12.1.1#21204

{bio}[foss/2023a] AlphaPulldown v2.0.0 Uni-Core v0.0.3 w/ CUDA v12.1.1#21204
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ThomasHoffmann77:20240817200306_new_pr_AlphaPulldown200b4

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Updated software `AlphaPulldown-2.0.0-foss-2023a-CUDA-12.1.1.eb`

Updated software `Uni-Core-0.0.3-foss-2023a-CUDA-12.1.1.eb`