{bio}[foss/2025b] scikit-bio v0.7.2, biom-format v2.1.17, statsmodels v0.14.6, Cython 3.2.4

easybuild/easyconfigs/b/biom-format/biom-format-2.1.17-foss-2025b.eb

@@ -0,0 +1,51 @@
+##
+# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia
+# Homepage:     https://staff.flinders.edu.au/research/deep-thought
+#
+# Authors::     Robert Qiao <rob.qiao@flinders.edu.au>
+# License::     Revised BSD
+#
+# Notes:: updated by Kenneth Hoste (HPC-UGent) for foss/2021b
+##
+# Updated: Petr Král (INUITS)
+#          Lara Peeters (Ghent University)
+#          Rafael Moretti (UiB)
+
+easyblock = 'PythonPackage'
+
+name = 'biom-format'
+version = '2.1.17'
+
+homepage = 'https://biom-format.org'
+description = """
+The BIOM file format (canonically pronounced biome) is designed to be
+ a general-use format for representing biological sample by observation
+ contingency tables. BIOM is a recognized standard for the Earth Microbiome
+ Project and is a Genomics Standards Consortium supported project.
+"""
+
+toolchain = {'name': 'foss', 'version': '2025b'}
+toolchainopts = {'usempi': True}
+
+source_urls = ['https://github.com/biocore/biom-format/archive/refs/tags']
+sources = ['%(version)s.tar.gz']
+checksums = ['70dc179472330e6cfb1b1e3483bcf3e17a9dedd91e7ee7c38b2906f1852cb042']
+
+builddependencies = [
+    ('Cython', '3.1.2'),
+]
+
+dependencies = [
+    ('Python', '3.13.5'),
+    ('SciPy-bundle', '2025.07'),
+    ('h5py', '3.14.0'),
+]
+
+sanity_check_paths = {
+    'files': ['bin/biom'],
+    'dirs': ['lib'],
+}
+
+options = {'modulename': 'biom'}
+
+moduleclass = 'bio'

easybuild/easyconfigs/c/Cython/Cython-3.2.4-GCCcore-14.3.0.eb

@@ -0,0 +1,36 @@
+easyblock = 'PythonPackage'
+
+name = 'Cython'
+version = '3.2.4'
+
+homepage = 'https://cython.org/'
+description = """
+Cython is an optimising static compiler for both the Python programming
+language and the extended Cython programming language (based on Pyrex).
+"""
+docurls = [
+    'https://cython.org/#documentation',
+    'https://github.com/cython/cython',
+]
+
+toolchain = {'name': 'GCCcore', 'version': '14.3.0'}
+
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['84226ecd313b233da27dc2eb3601b4f222b8209c3a7216d8733b031da1dc64e6']
+
+builddependencies = [
+    ('binutils', '2.44'),
+]
+
+dependencies = [
+    ('Python', '3.13.5'),
+]
+
+sanity_check_paths = {
+    'files': ['bin/cygdb', 'bin/cython', 'bin/cythonize'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = ["cython --version"]
+
+moduleclass = 'lang'

easybuild/easyconfigs/s/scikit-bio/scikit-bio-0.7.2-foss-2025b.eb

@@ -0,0 +1,43 @@
+easyblock = 'PythonBundle'
+
+name = 'scikit-bio'
+version = '0.7.2'
+
+homepage = 'http://scikit-bio.org'
+description = """scikit-bio is an open-source, BSD-licensed Python 3 package providing data structures, algorithms
+and educational resources for bioinformatics."""
+
+toolchain = {'name': 'foss', 'version': '2025b'}
+
+builddependencies = [
+    ('Cython', '3.2.4'),
+]
+
+dependencies = [
+    ('Python', '3.13.5'),
+    ('Python-bundle-PyPI', '2025.07'),
+    ('SciPy-bundle', '2025.07'),
+    ('matplotlib', '3.10.5'),
+    ('scikit-learn', '1.7.1'),
+    ('IPython', '9.4.0'),
+    ('h5py', '3.14.0'),
+    ('biom-format', '2.1.17'),
+    ('statsmodels', '0.14.6'),
+]
+
+exts_list = [
+    ('natsort', '8.4.0', {
+        'checksums': ['45312c4a0e5507593da193dedd04abb1469253b601ecaf63445ad80f0a1ea581'],
+    }),
+    ('array_api_compat', '1.13.0', {
+        'checksums': ['8b83a56aa8b9477472fee37f7731968dd213e20c198a05ac49caeff9b03f48a6'],
+    }),
+    (name, version, {
+        'modulename': 'skbio',
+        'checksums': ['d0a991818882c88ca47d9f6441321a440439e1a8a6716a101a931d590c395fe8'],
+    }),
+]
+
+sanity_check_commands = ['python -m skbio.test']
+
+moduleclass = 'bio'

easybuild/easyconfigs/s/statsmodels/statsmodels-0.14.6-gfbf-2025b.eb

@@ -0,0 +1,29 @@
+easyblock = 'PythonBundle'
+
+name = 'statsmodels'
+version = '0.14.6'
+
+homepage = 'https://www.statsmodels.org/'
+description = """Statsmodels is a Python module that allows users to explore data, estimate statistical models,
+and perform statistical tests."""
+
+toolchain = {'name': 'gfbf', 'version': '2025b'}
+
+builddependencies = [('Cython', '3.1.2')]
+
+dependencies = [
+    ('Python', '3.13.5'),
+    ('SciPy-bundle', '2025.07'),
+]
+
+exts_list = [
+    ('patsy', '1.0.1', {
+        'checksums': ['e786a9391eec818c054e359b737bbce692f051aee4c661f4141cc88fb459c0c4'],
+    }),
+    (name, version, {
+        'preinstallopts': """sed -i 's/url=URL,/url=URL, version="%(version)s",/g' setup.py && """,
+        'checksums': ['4d17873d3e607d398b85126cd4ed7aad89e4e9d89fc744cdab1af3189a996c2a'],
+    }),
+]
+
+moduleclass = 'math'