{bio}[foss/2025b] nglview v4.0, MDTraj v1.11.0, PyTables v3.10.2, ...

easybuild/easyconfigs/b/Biopython/Biopython-1.86-gfbf-2025b.eb

@@ -0,0 +1,41 @@
+# Updated from previous easyconfig
+# Author: Robert Mijakovic <robert.mijakovic@lxp.lu>
+# Update: Pavel Tománek (INUITS)
+
+easyblock = 'PythonPackage'
+
+name = 'Biopython'
+version = '1.86'
+
+homepage = 'https://www.biopython.org'
+description = """Biopython is a set of freely available tools for biological
+ computation written in Python by an international team of developers. It is
+ a distributed collaborative effort to develop Python libraries and
+ applications which address the needs of current and future work in
+ bioinformatics. """
+
+toolchain = {'name': 'gfbf', 'version': '2025b'}
+
+source_urls = ['https://biopython.org/DIST']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['93a50b586a4d2cec68ab2f99d03ef583c5761d8fba5535cb8e81da781d0d92ff']
+
+dependencies = [
+    ('Python', '3.13.5'),
+    ('SciPy-bundle', '2025.07'),
+]
+
+# Run only tests that don't require internet connection
+runtest = 'python setup.py test --offline'
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['lib/python%(pyshortver)s/site-packages/Bio',
+             'lib/python%(pyshortver)s/site-packages/BioSQL']
+}
+
+sanity_check_commands = ["python -c 'import Bio.motifs'"]
+
+options = {'modulename': 'Bio'}
+
+moduleclass = 'bio'

easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-2.10.0-foss-2025b.eb

@@ -0,0 +1,73 @@
+easyblock = 'PythonBundle'
+
+name = 'MDAnalysis'
+version = '2.10.0'
+
+homepage = 'https://www.mdanalysis.org/'
+description = """MDAnalysis is an object-oriented Python library to analyze trajectories from molecular dynamics (MD)
+simulations in many popular formats."""
+
+toolchain = {'name': 'foss', 'version': '2025b'}
+
+builddependencies = [
+    ('Cython', '3.1.2'),
+]
+dependencies = [
+    ('Python', '3.13.5'),
+    ('Python-bundle-PyPI', '2025.07'),
+    ('SciPy-bundle', '2025.07'),
+    ('matplotlib', '3.10.5'),
+    ('tqdm', '4.67.1'),
+    ('mrcfile', '1.5.4'),  # needed by GridDataFormats
+    ('Biopython', '1.86'),  # optional
+    ('networkx', '3.5'),  # optional
+    ('Seaborn', '0.13.2'),  # optional
+    ('scikit-learn', '1.7.1'),  # optional
+    ('hypothesis', '6.136.6'),  # tests
+]
+
+exts_list = [
+    ('GridDataFormats', '1.0.2', {
+        'modulename': 'gridData',
+        'checksums': ['b93cf7f36fce33dbc428026f26dba560d5c7ba2387caca495bad920f90094502'],
+    }),
+    ('mmtf-python', '1.1.3', {
+        'modulename': 'mmtf',
+        'checksums': ['12a02fe1b7131f0a2b8ce45b46f1e0cdd28b9818fe4499554c26884987ea0c32'],
+    }),
+    ('mda_xdrlib', '0.2.0', {
+        'checksums': ['f26f7158a83c32b96d15b530fce2cbc1190c4b7024e41faa4ab3e3db74e272af'],
+    }),
+    ('tidynamics', '1.1.2', {
+        'checksums': ['103874edd79dc64a0c7b765f51200926822e74df63703acb6c630a8167dbcfa2'],
+    }),
+    ('waterdynamics', '1.2.0', {
+        'sources': ['%(name)s-%(version)s-py3-none-any.whl'],
+        'checksums': ['8a9eb7e7ad44e2abf9e2542661b2d7b371d8ab6474113a301968e4bf78d4432d'],
+    }),
+    ('pathsimanalysis', '1.2.0', {
+        'sources': ['%(name)s-%(version)s-py3-none-any.whl'],
+        'checksums': ['0edce2fd1a55a788ef80b3666f9704455c01f06719f516fec20215fb9e16e291'],
+    }),
+    ('mdahole2', '0.5.0', {
+        'sources': ['%(name)s-%(version)s-py3-none-any.whl'],
+        'checksums': ['6b7a9be247cd99331e8840c9012d0ed7a86874fe110983bbaed00eb39459e7a8'],
+    }),
+    ('mdanalysistests', version, {
+        'modulename': 'MDAnalysisTests',
+        'checksums': ['286b8678e19195093a19b57b26d76b8274415d33ac23fc872355639fcb49beef'],
+    }),
+    ('mdanalysis', version, {
+        'modulename': 'MDAnalysis',
+        'use_pip_extras': 'analysis',
+        'checksums': ['5cef1f1eba4b25cbf9dd4045f08eeab293bb9577b970aa96132f14491312d877'],
+    }),
+]
+
+sanity_check_commands = [
+    "export OMP_NUM_THREADS=1 OPENBLAS_NUM_THREADS=1 && "
+    "pytest --disable-pytest-warnings --numprocesses %(parallel)s "
+    "--pyargs MDAnalysisTests -p no:warnings --dist=loadscope"
+]
+
+moduleclass = 'bio'

easybuild/easyconfigs/m/MDTraj/MDTraj-1.11.0-foss-2025b.eb

@@ -0,0 +1,44 @@
+easyblock = 'PythonBundle'
+
+name = 'MDTraj'
+version = '1.11.0'
+
+homepage = 'https://mdtraj.org'
+description = "Read, write and analyze MD trajectories with only a few lines of Python code."
+
+toolchain = {'name': 'foss', 'version': '2025b'}
+toolchainopts = {'openmp': True}
+
+builddependencies = [('Cython', '3.1.2')]
+
+dependencies = [
+    ('zlib', '1.3.1'),
+    ('Python', '3.13.5'),
+    ('Python-bundle-PyPI', '2025.07'),
+    ('SciPy-bundle', '2025.07'),
+    ('netcdf4-python', '1.7.2'),  # optional+tests
+    ('networkx', '3.5'),  # optional+tests
+    ('PyTables', '3.10.2'),  # optional+tests
+]
+
+exts_list = [
+    ('pyparsing', '3.2.5', {
+        'checksums': ['2df8d5b7b2802ef88e8d016a2eb9c7aeaa923529cd251ed0fe4608275d4105b6'],
+    }),
+    ('gsd', '4.2.0', {
+        'checksums': ['eb197abd735e98817bcdc1ee34e4968231d572da48c097b3ccf316be828cf86a'],
+    }),
+    ('pytest_rerunfailures', '16.1', {
+        'checksums': ['c38b266db8a808953ebd71ac25c381cb1981a78ff9340a14bcb9f1b9bff1899e'],
+    }),
+    ('mdtraj', version, {
+        'runtest': "cd tests && pytest -v --numprocesses %(parallel)s",
+        'source_urls': ['https://github.com/mdtraj/mdtraj/archive/'],
+        'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s-github.tar.gz'}],
+        'testinstall': True,
+        'use_pip_extras': 'optional',
+        'checksums': ['fefca787f882d0716a7aeb01b4d8e30caddbd2be0b2893acfa7201c31d13c786'],
+    }),
+]
+
+moduleclass = 'chem'

easybuild/easyconfigs/m/mrcfile/mrcfile-1.5.4-gfbf-2025b.eb

@@ -0,0 +1,39 @@
+# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2025/03
+easyblock = 'PythonPackage'
+
+name = 'mrcfile'
+version = '1.5.4'
+
+homepage = 'https://github.com/ccpem/mrcfile'
+description = """mrcfile is a Python implementation of the MRC2014 file format, which is used in
+structural biology to store image and volume data.
+
+It allows MRC files to be created and opened easily using a very simple API,
+which exposes the file’s header and data as numpy arrays. The code runs in
+Python 2 and 3 and is fully unit-tested.
+
+This library aims to allow users and developers to read and write standard-
+compliant MRC files in Python as easily as possible, and with no dependencies on
+any compiled libraries except numpy. You can use it interactively to inspect
+files, correct headers and so on, or in scripts and larger software packages to
+provide basic MRC file I/O functions. """
+
+toolchain = {'name': 'gfbf', 'version': '2025b'}
+
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['8fa9eb2e237d87d99b301c61bf02854dd85a451db25eefcbe142c09b36d8d601']
+
+dependencies = [
+    ('Python', '3.13.5'),
+    ('SciPy-bundle', '2025.07'),
+]
+
+testinstall = True
+runtest = 'pytest -vvvs tests'
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s']
+}
+
+moduleclass = 'bio'

easybuild/easyconfigs/n/nglview/nglview-4.0-foss-2025b.eb

@@ -0,0 +1,48 @@
+easyblock = 'PythonBundle'
+
+name = 'nglview'
+version = '4.0'
+
+homepage = 'https://github.com/arose/nglview'
+description = "IPython widget to interactively view molecular structures and trajectories."
+
+toolchain = {'name': 'foss', 'version': '2025b'}
+
+builddependencies = [
+    ('nodejs', '22.17.1'),
+]
+
+dependencies = [
+    ('Python', '3.13.5'),
+    ('Python-bundle-PyPI', '2025.07'),
+    ('SciPy-bundle', '2025.07'),
+    ('JupyterLab', '4.4.9'),
+    ('JupyterNotebook', '7.4.7'),
+    ('ASE', '3.26.0'),  # optional
+    ('MDAnalysis', '2.10.0'),  # optional
+    ('MDTraj', '1.11.0'),  # optional
+]
+
+local_pytest_cmd = (
+    "pytest -v "
+    "--deselect tests/test_show.py::test_show_schrodinger "
+    "--deselect tests/test_widget.py::test_existing_js_files "
+    "--deselect tests/test_movie_maker.py::test_movie_maker "
+    "tests"
+)
+
+exts_list = [
+    (name, version, {
+        'use_pip_extras': 'ase,MDAnalysis,mdtraj',
+        # unpin numpy - pinned due to ParmEd
+        # https://github.com/ParmEd/ParmEd/issues/1406
+        'preinstallopts': "sed -i 's/numpy<2.3/numpy/' setup.py && ",
+        'testinstall': True,
+        'runtest': local_pytest_cmd,
+        'checksums': ['2c0cff2c5b1e2a0a72e3393087ce44ae0308524c5aa5f95357812d3edbc26e83'],
+    }),
+]
+
+modextrapaths = {'EB_ENV_JUPYTER_ROOT': ''}
+
+moduleclass = 'chem'

easybuild/easyconfigs/p/PyTables/PyTables-3.10.2-foss-2025b.eb

@@ -0,0 +1,72 @@
+easyblock = 'PythonBundle'
+
+name = 'PyTables'
+version = '3.10.2'
+
+homepage = 'https://www.pytables.org'
+description = """PyTables is a package for managing hierarchical datasets and designed to efficiently and easily cope
+ with extremely large amounts of data. PyTables is built on top of the HDF5 library, using the Python language and the
+ NumPy package. It features an object-oriented interface that, combined with C extensions for the performance-critical
+ parts of the code (generated using Cython), makes it a fast, yet extremely easy to use tool for interactively browsing,
+ processing and searching very large amounts of data. One important feature of PyTables is that it optimizes memory and
+ disk resources so that data takes much less space (specially if on-flight compression is used) than other solutions
+ such as relational or object oriented databases."""
+
+toolchain = {'name': 'foss', 'version': '2025b'}
+toolchainopts = {'usempi': True}
+
+builddependencies = [
+    ('pkgconf', '2.4.3'),
+    ('CMake', '4.0.3'),
+    ('Cython', '3.1.2'),
+    ('scikit-build-core', '0.11.5'),
+]
+
+dependencies = [
+    ('Python', '3.13.5'),
+    ('Python-bundle-PyPI', '2025.07'),
+    ('SciPy-bundle', '2025.07'),
+    ('HDF5', '1.14.6'),
+    ('LZO', '2.10'),
+    ('Blosc', '1.21.6'),
+    ('Blosc2', '2.19.0'),
+    ('py-cpuinfo', '9.0.0'),
+]
+
+exts_list = [
+    ('ndindex', '1.10.0', {
+        'checksums': ['20e3a2f0a8ed4646abf0f13296aab0b5b9cc8c5bc182b71b5945e76eb6f558bb'],
+    }),
+    ('blosc2', '3.6.1', {
+        'preinstallopts': "USE_SYSTEM_BLOSC2=ON ",
+        'runtest': "pytest -v",
+        'testinstall': True,
+        'checksums': ['0b6f05311fbee9e9dc23bd7f53a8690af3b60eef640a059f1eb624ca6699cc59'],
+    }),
+    ('tables', version, {
+        'patches': [
+            'PyTables-3.8.0_fix-libs.patch',
+            'PyTables-3.9.2_fix-find-blosc2-dep.patch',
+        ],
+        'runtest': "cd .. && python -m tables.tests.test_all",
+        'testinstall': True,
+        'checksums': [
+            {'tables-3.10.2.tar.gz': '2544812a7186fadba831d6dd34eb49ccd788d6a83f4e4c2b431b835b6796c910'},
+            {'PyTables-3.8.0_fix-libs.patch': '7a1e6fa1f9169e52293e2b433a4302fa13c5d31e7709cd4fe0e087199b9e3f8a'},
+            {'PyTables-3.9.2_fix-find-blosc2-dep.patch':
+             'e2149f43da12d9ba26cca4c838f6e8a4694adab75c0f055b186674a017e41a55'},
+        ],
+    }),
+]
+
+local_bins = ['pt2to3', 'ptdump', 'ptrepack', 'pttree']
+sanity_check_paths = {
+    'files': ['bin/%s' % x for x in local_bins],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+options = {'modulename': 'tables'}
+
+sanity_check_commands = ["%s --help" % x for x in local_bins]
+
+moduleclass = 'data'