{bio}[foss/2024a] scvi-tools v1.4.1, scanpy v1.10.4, anndata v0.11.4, ...

easybuild/easyconfigs/a/anndata/anndata-0.11.4-foss-2024a.eb

@@ -0,0 +1,40 @@
+easyblock = 'PythonBundle'
+
+name = 'anndata'
+version = '0.11.4'
+
+homepage = 'https://github.com/scverse/anndata'
+description = """anndata is a Python package for handling annotated data matrices in memory and on disk,
+ positioned between pandas and xarray"""
+
+toolchain = {'name': 'foss', 'version': '2024a'}
+
+builddependencies = [('hatchling', '1.24.2')]
+dependencies = [
+    ('Python', '3.12.3'),
+    ('Python-bundle-PyPI', '2024.06'),
+    ('SciPy-bundle', '2024.05'),
+    ('h5py', '3.12.1'),
+    ('setuptools', '80.9.0'),
+]
+
+exts_list = [
+    ('array_api_compat', '1.12.0', {
+        'checksums': ['585bc615f650de53ac24b7c012baecfcdd810f50df3573be47e6dd9fa20df974'],
+    }),
+    ('natsort', '8.4.0', {
+        'checksums': ['45312c4a0e5507593da193dedd04abb1469253b601ecaf63445ad80f0a1ea581'],
+    }),
+    (name, version, {
+        'checksums': ['4ce08d09d2ccb5f37d32790363bbcc7fc1b79863842296ae4badfaf48c736e24'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/natsort'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = ["natsort --help"]
+
+moduleclass = 'bio'

easybuild/easyconfigs/l/Lightning/Lightning-2.5.2-foss-2024a.eb

@@ -0,0 +1,27 @@
+easyblock = 'PythonPackage'
+
+name = 'Lightning'
+version = '2.5.2'
+
+homepage = 'https://github.com/Lightning-AI/pytorch-lightning'
+description = """
+The deep learning framework to pretrain, finetune and deploy AI models.
+Lightning has 4 core packages:
+    PyTorch Lightning: Train and deploy PyTorch at scale.
+    Lightning Fabric: Expert control.
+    Lightning Data: Blazing fast, distributed streaming of training data from cloud storage.
+    Lightning Apps: Build AI products and ML workflows.
+"""
+
+toolchain = {'name': 'foss', 'version': '2024a'}
+
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['9550df613cfb22358ebf77b4a8ad45f3767cd7d26ba2d52b7f036bd3cdd701c4']
+
+dependencies = [
+    ('Python', '3.12.3'),
+    ('PyTorch', '2.6.0'),
+    ('PyTorch-Lightning', version),
+]
+
+moduleclass = 'tools'

easybuild/easyconfigs/m/ml-collections/ml-collections-1.1.0-foss-2024a.eb

@@ -0,0 +1,27 @@
+easyblock = 'PythonBundle'
+
+name = 'ml-collections'
+version = '1.1.0'
+
+homepage = 'https://github.com/google/ml_collections'
+description = """
+ML Collections is a library of Python Collections designed for ML use cases.
+"""
+
+toolchain = {'name': 'foss', 'version': '2024a'}
+
+builddependencies = [('hatchling', '1.24.2')]
+dependencies = [
+    ('Python', '3.12.3'),
+    ('SciPy-bundle', '2024.05'),
+    ('PyYAML', '6.0.2'),
+    ('absl-py', '2.1.0'),
+]
+
+exts_list = [
+    ('ml_collections', version, {
+        'checksums': ['0ac1ac6511b9f1566863e0bb0afad0c64e906ea278ad3f4d2144a55322671f6f'],
+    }),
+]
+
+moduleclass = 'vis'

easybuild/easyconfigs/p/pyro-ppl/pyro-ppl-1.9.1-foss-2024a.eb

@@ -0,0 +1,39 @@
+easyblock = 'PythonBundle'
+
+name = 'pyro-ppl'
+version = '1.9.1'
+
+homepage = 'https://github.com/pyro-ppl/pyro'
+description = "Pyro is a flexible, scalable deep probabilistic programming library built on PyTorch."
+
+toolchain = {'name': 'foss', 'version': '2024a'}
+
+builddependencies = [('hatchling', '1.24.2')]
+dependencies = [
+    ('Python', '3.12.3'),
+    ('SciPy-bundle', '2024.05'),
+    ('PyTorch', '2.6.0'),
+    ('tqdm', '4.66.5'),
+]
+
+exts_list = [
+    ('opt_einsum', '3.4.0', {
+        'checksums': ['96ca72f1b886d148241348783498194c577fa30a8faac108586b14f1ba4473ac'],
+    }),
+    ('pyro-api', '0.1.2', {
+        'modulename': 'pyroapi',
+        'checksums': ['a1b900d9580aa1c2fab3b123ab7ff33413744da7c5f440bd4aadc4d40d14d920'],
+    }),
+    (name, version, {
+        'modulename': 'pyro',
+        'checksums': ['5e1596de276c038a3f77d2580a90d0a97126e0104900444a088eee620bb0d65e'],
+    }),
+]
+
+sanity_check_commands = [
+    "python -c 'from pyroapi import distributions as dist'",
+    "python -c 'from pyroapi import infer, ops, optim, pyro, pyro_backend'",
+    "python -c 'from pyro import infer, nn, distributions'",
+]
+
+moduleclass = 'tools'

easybuild/easyconfigs/s/scanpy/scanpy-1.10.4-foss-2024a.eb

@@ -0,0 +1,58 @@
+easyblock = 'PythonBundle'
+
+name = 'scanpy'
+version = '1.10.4'
+
+homepage = 'https://scanpy.readthedocs.io/en/stable/'
+description = """Scanpy is a scalable toolkit for analyzing single-cell gene expression data built
+ jointly with anndata. It includes preprocessing, visualization, clustering, trajectory inference
+ and differential expression testing. The Python-based implementation efficiently deals with
+ datasets of more than one million cells.
+"""
+
+toolchain = {'name': 'foss', 'version': '2024a'}
+toolchainopts = {'openmp': True}
+
+builddependencies = [('hatchling', '1.24.2')]
+dependencies = [
+    ('Python', '3.12.3'),
+    ('SciPy-bundle', '2024.05'),
+    ('matplotlib', '3.9.2'),
+    ('Seaborn', '0.13.2'),
+    ('h5py', '3.12.1'),
+    ('tqdm', '4.66.5'),
+    ('scikit-learn', '1.5.2'),
+    ('statsmodels', '0.14.4'),
+    ('networkx', '3.4.2'),
+    ('numba', '0.60.0'),
+    ('umap-learn', '0.5.7'),
+    ('anndata', '0.11.4'),
+]
+
+exts_list = [
+    ('stdlib_list', '0.11.0', {
+        'checksums': ['b74a7b643a77a12637e907f3f62f0ab9f67300bce4014f6b2d3c8b4c8fd63c66'],
+    }),
+    ('session-info', '1.0.0', {
+        'sources': ['session_info-%(version)s.tar.gz'],
+        'checksums': ['3cda5e03cca703f32ae2eadbd6bd80b6c21442cfb60e412c21cb8ad6d5cbb6b7'],
+    }),
+    ('legacy_api_wrap', '1.4.1', {
+        'checksums': ['9c40d67aa8312fec8763e87cbf28fea4b67710c79ca7a18137b573d150f3b2b4'],
+    }),
+    (name, version, {
+        'checksums': ['2682fbbe2e4106c349472feebef08e174062fb666db4c94123758c6a7a470396'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/scanpy'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = [
+    "natsort --help",
+    "scanpy --help",
+]
+
+moduleclass = 'bio'

easybuild/easyconfigs/s/scvi-tools/scvi-tools-1.4.1-foss-2024a.eb

@@ -0,0 +1,77 @@
+easyblock = 'PythonBundle'
+
+name = 'scvi-tools'
+version = '1.4.1'
+
+homepage = 'https://github.com/scverse/scvi-tools'
+description = """scvi-tools (single-cell variational inference tools) is a package for probabilistic modeling and
+analysis of single-cell omics data, built on top of PyTorch and AnnData."""
+
+toolchain = {'name': 'foss', 'version': '2024a'}
+
+builddependencies = [
+    ('hatchling', '1.27.0'),
+    ('coverage', '7.9.2'),
+    ('captum', '0.8.0'),
+]
+dependencies = [
+    ('Python', '3.12.3'),
+    ('SciPy-bundle', '2024.05'),
+    ('PyTorch', '2.6.0'),
+    ('PyTorch-Lightning', '2.5.2'),
+    ('Lightning', '2.5.2'),
+    ('anndata', '0.11.4'),
+    ('matplotlib', '3.9.2'),
+    ('scikit-learn', '1.5.2'),
+    ('tqdm', '4.66.5'),
+    ('h5py', '3.12.1'),
+    ('pyro-ppl', '1.9.1'),
+    ('ml-collections', '1.1.0'),
+    ('numba', '0.60.0'),
+    ('scanpy', '1.10.4'),
+    ('tensorboard', '2.18.0'),
+    ('xarray', '2024.11.0'),
+]
+
+# avoid srun problem
+# https://github.com/easybuilders/easybuild-easyconfigs/pull/25021#issuecomment-3744728157
+local_test_command = 'export SLURM_NTASKS_PER_NODE=$SLURM_NTASKS && '
+local_test_command += 'pytest -vs tests '
+# skip tests required optional dependencies
+local_test_command += (
+    '--ignore=tests/external/mrvi_jax '
+    '--ignore=tests/external/tangram '
+    '--ignore=tests/model/test_jaxscvi.py '
+    '--ignore=tests/hub '
+    '--ignore=tests/criticism '
+    '--ignore=tests/external/cytovi '
+    '--deselect=tests/data/test_anndata.py::test_anntorchdataset_dask '
+    '--deselect tests/model/test_multivi.py::test_multivi_mudata_rna_atac '
+)
+
+exts_list = [
+    ('packaging', '25.0', {
+        'checksums': ['d443872c98d677bf60f6a1f2f8c1cb748e8fe762d2bf9d3148b5599295b0fc4f'],
+    }),
+    ('pytest_pretty', '1.3.0', {
+        'checksums': ['97e9921be40f003e40ae78db078d4a0c1ea42bf73418097b5077970c2cc43bf3'],
+    }),
+    ('mudata', '0.3.2', {
+        'checksums': ['c9b24f2429f369512f38e48599e341e7684abcf769df277e473700d4f1212740'],
+    }),
+    ('sparse', '0.17.0', {
+        'checksums': ['6b1ad51a810c5be40b6f95e28513ec810fe1c785923bd83b2e4839a751df4bf7'],
+    }),
+    ('docrep', '0.3.2', {
+        'checksums': ['ed8a17e201abd829ef8da78a0b6f4d51fb99a4cbd0554adbed3309297f964314'],
+    }),
+    (name, version, {
+        'modulename': 'scvi',
+        'runtest': local_test_command,
+        'sources': ['scvi_tools-%(version)s.tar.gz'],
+        'testinstall': True,
+        'checksums': ['ee75eaac665618b9ee6fa466f6353ef68eb33cd3d7e2c77069e743471ca2103a'],
+    }),
+]
+
+moduleclass = 'bio'

test/easyconfigs/easyconfigs.py

@@ -553,6 +553,8 @@ def check_dep_vars(self, gen, dep, dep_vars):
 
         # some software packages require a specific (older/newer) version of a particular dependency
         alt_dep_versions = {
+            # scanpy-1.10.4 and scvi-tools-1.4.1 requires anndata >= 0.11
+            'anndata': [(r'0\.11\.4', [r'scvi-tools-1.4.1-', r'scanpy-1.10.4-'])],
             # arrow-R 6.0.0.2 is used for two R/R-bundle-Bioconductor sets (4.1.2/3.14 and 4.2.0/3.15)
             'arrow-R': [('6.0.0.2', [r'R-bundle-Bioconductor-'])],
             # BRAKER 3.0.8 depends on AUGUSTUS 3.5.0-20240612