{bio,tools}[foss/2025b] CellBender v0.4.0, pyro-ppl v1.9.1 w/ CUDA 12.9.1

easybuild/easyconfigs/c/CellBender/CellBender-0.4.0-foss-2025b-CUDA-12.9.1.eb

@@ -0,0 +1,56 @@
+easyblock = 'PythonBundle'
+
+name = 'CellBender'
+version = '0.4.0'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'http://github.com/broadinstitute/CellBender'
+description = """
+CellBender is a software package for eliminating technical artifacts from
+high-throughput single-cell RNA sequencing (scRNA-seq) data.
+"""
+
+toolchain = {'name': 'foss', 'version': '2025b'}
+
+builddependencies = [
+    ('hatchling', '1.27.0'),
+    ('scikit-learn', '1.7.1'),  # tests
+]
+dependencies = [
+    ('CUDA', '12.9.1', '', SYSTEM),
+    ('Python', '3.13.5'),
+    ('SciPy-bundle', '2025.07'),
+    ('PyTorch', '2.9.1', versionsuffix),
+    ('pyro-ppl', '1.9.1', versionsuffix),
+    ('matplotlib', '3.10.5'),
+    ('IPython', '9.4.0'),
+    ('anndata', '0.12.16'),
+    ('jupyter-server', '2.17.0'),
+    ('PyTables', '3.10.2'),
+    ('dill', '0.4.1'),
+    ('lxml', '6.0.0'),
+]
+
+exts_list = [
+    ('lxml_html_clean', '0.4.4', {
+        'checksums': ['58f39a9d632711202ed1d6d0b9b47a904e306c85de5761543b90e3e3f736acfb'],
+    }),
+    ('cellbender', version, {
+        'runtest': 'pytest -v tests',
+        'testinstall': True,
+        'source_urls': ['https://github.com/broadinstitute/%(name)s/archive/'],
+        'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],
+        'patches': ['CellBender-0.4.0_fix-version.patch'],
+        'checksums': [
+            {'cellbender-0.4.0.tar.gz': '4e25735f04047fffee68e7082c0471f89ffe0ac28a9f2a90481098503e07b40a'},
+            {'CellBender-0.4.0_fix-version.patch': 'd19ed8202ebcde6a17f6b57da544d81aad24133b92c319b99b9247fa1ce6fdbd'},
+        ],
+    }),
+]
+
+sanity_check_commands = [
+    "cellbender --help",
+    "cellbender remove-background --help",
+]
+
+moduleclass = 'bio'

easybuild/easyconfigs/c/CellBender/CellBender-0.4.0_fix-version.patch

@@ -0,0 +1,37 @@
+Use a static version instead of deriving the CellBender version from Git metadata.
+
+The GitHub release archive does not contain the .git directory required by
+setuptools-git-versioning, which causes the installed package version to be
+reported incorrectly. Set the release version explicitly in pyproject.toml
+and remove setuptools-git-versioning from the build requirements.
+
+Author: Pavel Tomanek (Inuits/UGent) with help from ChatGPT5.6
+--- CellBender-0.4.0.orig/pyproject.toml
++++ CellBender-0.4.0/pyproject.toml
+@@ -1,5 +1,5 @@
+ [build-system]
+-requires = ["setuptools>=61.2", "setuptools-git-versioning>=2.0"]
++requires = ["setuptools>=61.2"]
+ build-backend = "setuptools.build_meta"
+
+ [project]
+@@ -19,7 +19,8 @@
+     "Programming Language :: Python :: 3.12",
+     "Topic :: Scientific/Engineering :: Bio-Informatics",
+ ]
+-dynamic = ["version", "dependencies", "optional-dependencies"]
++version = "0.4.0"
++dynamic = ["dependencies", "optional-dependencies"]
+
+ [project.readme]
+ file = "README.rst"
+@@ -48,10 +49,6 @@
+ [tool.setuptools.package-data]
+ "*" = ["cellbender.remove_background.report.ipynb"]
+
+-[tool.setuptools-git-versioning]
+-enabled = true
+-starting_version = "0.3.2"
+-
+ [tool.pytest.ini_options]
+ testpaths = ["tests"]

easybuild/easyconfigs/p/pyro-ppl/pyro-ppl-1.9.1-foss-2025b-CUDA-12.9.1.eb

@@ -0,0 +1,39 @@
+easyblock = 'PythonBundle'
+
+name = 'pyro-ppl'
+version = '1.9.1'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'https://github.com/pyro-ppl/pyro'
+description = "Pyro is a flexible, scalable deep probabilistic programming library built on PyTorch."
+
+toolchain = {'name': 'foss', 'version': '2025b'}
+
+builddependencies = [('hatchling', '1.27.0')]
+dependencies = [
+    ('CUDA', '12.9.1', '', SYSTEM),
+    ('Python', '3.13.5'),
+    ('SciPy-bundle', '2025.07'),
+    ('PyTorch', '2.9.1', versionsuffix),
+    ('tqdm', '4.67.1'),
+    ('opt-einsum', '3.4.0'),
+]
+
+exts_list = [
+    ('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'