{bio}[foss/2025b] scikit-bio v0.7.2, biom-format v2.1.17, statsmodels v0.14.6, Cython 3.2.4 by boegel · Pull Request #25908 · easybuilders/easybuild-easyconfigs

boegel · 2026-05-04T10:56:06Z

(created using eb --new-pr)

… v0.14.6, Cython 3.2.4

github-actions · 2026-05-04T10:56:46Z

Updated software `biom-format-2.1.17-foss-2025b.eb`

Diff against biom-format-2.1.17-foss-2025a.eb

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

diff --git a/easybuild/easyconfigs/b/biom-format/biom-format-2.1.17-foss-2025a.eb b/easybuild/easyconfigs/b/biom-format/biom-format-2.1.17-foss-2025b.eb
index 03eba15f1f..b0f12430dd 100644
--- a/easybuild/easyconfigs/b/biom-format/biom-format-2.1.17-foss-2025a.eb
+++ b/easybuild/easyconfigs/b/biom-format/biom-format-2.1.17-foss-2025b.eb
@@ -24,7 +24,7 @@ The BIOM file format (canonically pronounced biome) is designed to be
  Project and is a Genomics Standards Consortium supported project.
 """
 
-toolchain = {'name': 'foss', 'version': '2025a'}
+toolchain = {'name': 'foss', 'version': '2025b'}
 toolchainopts = {'usempi': True}
 
 source_urls = ['https://github.com/biocore/biom-format/archive/refs/tags']
@@ -32,12 +32,12 @@ sources = ['%(version)s.tar.gz']
 checksums = ['70dc179472330e6cfb1b1e3483bcf3e17a9dedd91e7ee7c38b2906f1852cb042']
 
 builddependencies = [
-    ('Cython', '3.1.1'),
+    ('Cython', '3.1.2'),
 ]
 
 dependencies = [
-    ('Python', '3.13.1'),
-    ('SciPy-bundle', '2025.06'),
+    ('Python', '3.13.5'),
+    ('SciPy-bundle', '2025.07'),
     ('h5py', '3.14.0'),
 ]

Diff against biom-format-2.1.16-foss-2024a.eb

easybuild/easyconfigs/b/biom-format/biom-format-2.1.16-foss-2024a.eb

diff --git a/easybuild/easyconfigs/b/biom-format/biom-format-2.1.16-foss-2024a.eb b/easybuild/easyconfigs/b/biom-format/biom-format-2.1.17-foss-2025b.eb
index 56cd9e722d..b0f12430dd 100644
--- a/easybuild/easyconfigs/b/biom-format/biom-format-2.1.16-foss-2024a.eb
+++ b/easybuild/easyconfigs/b/biom-format/biom-format-2.1.17-foss-2025b.eb
@@ -8,12 +8,13 @@
 # Notes:: updated by Kenneth Hoste (HPC-UGent) for foss/2021b
 ##
 # Updated: Petr Král (INUITS)
-# Updated: Lara Peeters (Ghent University)
+#          Lara Peeters (Ghent University)
+#          Rafael Moretti (UiB)
 
 easyblock = 'PythonPackage'
 
 name = 'biom-format'
-version = '2.1.16'
+version = '2.1.17'
 
 homepage = 'https://biom-format.org'
 description = """
@@ -23,20 +24,21 @@ The BIOM file format (canonically pronounced biome) is designed to be
  Project and is a Genomics Standards Consortium supported project.
 """
 
-toolchain = {'name': 'foss', 'version': '2024a'}
+toolchain = {'name': 'foss', 'version': '2025b'}
 toolchainopts = {'usempi': True}
 
-sources = [SOURCE_TAR_GZ]
-checksums = ['47f88d57a94ecaa4d06f3578ca394e78db6d12e46ab0886634743181e67dcfc9']
+source_urls = ['https://github.com/biocore/biom-format/archive/refs/tags']
+sources = ['%(version)s.tar.gz']
+checksums = ['70dc179472330e6cfb1b1e3483bcf3e17a9dedd91e7ee7c38b2906f1852cb042']
 
 builddependencies = [
-    ('Cython', '3.0.10'),
+    ('Cython', '3.1.2'),
 ]
 
 dependencies = [
-    ('Python', '3.12.3'),
-    ('SciPy-bundle', '2024.05'),
-    ('h5py', '3.12.1'),
+    ('Python', '3.13.5'),
+    ('SciPy-bundle', '2025.07'),
+    ('h5py', '3.14.0'),
 ]
 
 sanity_check_paths = {

Diff against biom-format-2.1.16-foss-2023b.eb

easybuild/easyconfigs/b/biom-format/biom-format-2.1.16-foss-2023b.eb

diff --git a/easybuild/easyconfigs/b/biom-format/biom-format-2.1.16-foss-2023b.eb b/easybuild/easyconfigs/b/biom-format/biom-format-2.1.17-foss-2025b.eb
index f70b9cff5f..b0f12430dd 100644
--- a/easybuild/easyconfigs/b/biom-format/biom-format-2.1.16-foss-2023b.eb
+++ b/easybuild/easyconfigs/b/biom-format/biom-format-2.1.17-foss-2025b.eb
@@ -8,12 +8,13 @@
 # Notes:: updated by Kenneth Hoste (HPC-UGent) for foss/2021b
 ##
 # Updated: Petr Král (INUITS)
-# Updated: Lara Peeters (Ghent University)
+#          Lara Peeters (Ghent University)
+#          Rafael Moretti (UiB)
 
 easyblock = 'PythonPackage'
 
 name = 'biom-format'
-version = '2.1.16'
+version = '2.1.17'
 
 homepage = 'https://biom-format.org'
 description = """
@@ -23,16 +24,21 @@ The BIOM file format (canonically pronounced biome) is designed to be
  Project and is a Genomics Standards Consortium supported project.
 """
 
-toolchain = {'name': 'foss', 'version': '2023b'}
+toolchain = {'name': 'foss', 'version': '2025b'}
 toolchainopts = {'usempi': True}
 
-sources = [SOURCE_TAR_GZ]
-checksums = ['47f88d57a94ecaa4d06f3578ca394e78db6d12e46ab0886634743181e67dcfc9']
+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', '3.11.5'),
-    ('SciPy-bundle', '2023.11'),
-    ('h5py', '3.11.0'),
+    ('Python', '3.13.5'),
+    ('SciPy-bundle', '2025.07'),
+    ('h5py', '3.14.0'),
 ]
 
 sanity_check_paths = {

Updated software `Cython-3.2.4-GCCcore-14.3.0.eb`

Diff against Cython-3.2.4-GCCcore-15.2.0.eb

easybuild/easyconfigs/c/Cython/Cython-3.2.4-GCCcore-15.2.0.eb

diff --git a/easybuild/easyconfigs/c/Cython/Cython-3.2.4-GCCcore-15.2.0.eb b/easybuild/easyconfigs/c/Cython/Cython-3.2.4-GCCcore-14.3.0.eb
index 82b127ac3a..a6ab92ad23 100644
--- a/easybuild/easyconfigs/c/Cython/Cython-3.2.4-GCCcore-15.2.0.eb
+++ b/easybuild/easyconfigs/c/Cython/Cython-3.2.4-GCCcore-14.3.0.eb
@@ -13,13 +13,18 @@ docurls = [
     'https://github.com/cython/cython',
 ]
 
-toolchain = {'name': 'GCCcore', 'version': '15.2.0'}
+toolchain = {'name': 'GCCcore', 'version': '14.3.0'}
 
 sources = [SOURCELOWER_TAR_GZ]
 checksums = ['84226ecd313b233da27dc2eb3601b4f222b8209c3a7216d8733b031da1dc64e6']
 
-builddependencies = [('binutils', '2.45')]
-dependencies = [('Python', '3.14.2')]
+builddependencies = [
+    ('binutils', '2.44'),
+]
+
+dependencies = [
+    ('Python', '3.13.5'),
+]
 
 sanity_check_paths = {
     'files': ['bin/cygdb', 'bin/cython', 'bin/cythonize'],

Diff against Cython-0.29.37-GCCcore-13.3.0.eb

easybuild/easyconfigs/c/Cython/Cython-0.29.37-GCCcore-13.3.0.eb

diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.29.37-GCCcore-13.3.0.eb b/easybuild/easyconfigs/c/Cython/Cython-3.2.4-GCCcore-14.3.0.eb
index 8665d066e9..a6ab92ad23 100644
--- a/easybuild/easyconfigs/c/Cython/Cython-0.29.37-GCCcore-13.3.0.eb
+++ b/easybuild/easyconfigs/c/Cython/Cython-3.2.4-GCCcore-14.3.0.eb
@@ -1,7 +1,7 @@
 easyblock = 'PythonPackage'
 
 name = 'Cython'
-version = '0.29.37'
+version = '3.2.4'
 
 homepage = 'https://cython.org/'
 description = """
@@ -13,17 +13,17 @@ docurls = [
     'https://github.com/cython/cython',
 ]
 
-toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+toolchain = {'name': 'GCCcore', 'version': '14.3.0'}
 
-sources = [SOURCE_TAR_GZ]
-checksums = ['f813d4a6dd94adee5d4ff266191d1d95bf6d4164a4facc535422c021b2504cfb']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['84226ecd313b233da27dc2eb3601b4f222b8209c3a7216d8733b031da1dc64e6']
 
 builddependencies = [
-    ('binutils', '2.42'),
+    ('binutils', '2.44'),
 ]
 
 dependencies = [
-    ('Python', '3.12.3'),
+    ('Python', '3.13.5'),
 ]
 
 sanity_check_paths = {

Diff against Cython-3.1.2-GCCcore-14.3.0.eb

easybuild/easyconfigs/c/Cython/Cython-3.1.2-GCCcore-14.3.0.eb

diff --git a/easybuild/easyconfigs/c/Cython/Cython-3.1.2-GCCcore-14.3.0.eb b/easybuild/easyconfigs/c/Cython/Cython-3.2.4-GCCcore-14.3.0.eb
index 3b88ae00ab..a6ab92ad23 100644
--- a/easybuild/easyconfigs/c/Cython/Cython-3.1.2-GCCcore-14.3.0.eb
+++ b/easybuild/easyconfigs/c/Cython/Cython-3.2.4-GCCcore-14.3.0.eb
@@ -1,7 +1,7 @@
 easyblock = 'PythonPackage'
 
 name = 'Cython'
-version = '3.1.2'
+version = '3.2.4'
 
 homepage = 'https://cython.org/'
 description = """
@@ -16,7 +16,7 @@ docurls = [
 toolchain = {'name': 'GCCcore', 'version': '14.3.0'}
 
 sources = [SOURCELOWER_TAR_GZ]
-checksums = ['6bbf7a953fa6762dfecdec015e3b054ba51c0121a45ad851fa130f63f5331381']
+checksums = ['84226ecd313b233da27dc2eb3601b4f222b8209c3a7216d8733b031da1dc64e6']
 
 builddependencies = [
     ('binutils', '2.44'),

Updated software `scikit-bio-0.7.2-foss-2025b.eb`

Diff against scikit-bio-0.6.3-foss-2024a.eb

easybuild/easyconfigs/s/scikit-bio/scikit-bio-0.6.3-foss-2024a.eb

diff --git a/easybuild/easyconfigs/s/scikit-bio/scikit-bio-0.6.3-foss-2024a.eb b/easybuild/easyconfigs/s/scikit-bio/scikit-bio-0.7.2-foss-2025b.eb
index 61583c79c9..728473a840 100644
--- a/easybuild/easyconfigs/s/scikit-bio/scikit-bio-0.6.3-foss-2024a.eb
+++ b/easybuild/easyconfigs/s/scikit-bio/scikit-bio-0.7.2-foss-2025b.eb
@@ -1,42 +1,43 @@
 easyblock = 'PythonBundle'
 
 name = 'scikit-bio'
-version = '0.6.3'
+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': '2024a'}
+toolchain = {'name': 'foss', 'version': '2025b'}
+
+builddependencies = [
+    ('Cython', '3.2.4'),
+]
 
-builddependencies = [('Cython', '3.0.10')]
 dependencies = [
-    ('Python', '3.12.3'),
-    ('Python-bundle-PyPI', '2024.06'),
-    ('SciPy-bundle', '2024.05'),
-    ('matplotlib', '3.9.2'),
-    ('scikit-learn', '1.5.2'),
-    ('IPython', '8.28.0'),
-    ('h5py', '3.12.1'),
-    ('biom-format', '2.1.16'),
-    ('statsmodels', '0.14.4'),
+    ('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 = [
-    ('hdmedians', '0.14.2', {
-        # removes cython from runtime dependencies
-        'preinstallopts': """sed -i "18s/, 'Cython>=0.23'//" setup.py && """,
-        'checksums': ['b47aecb16771e1ba0736557255d80ae0240b09156bff434321de559b359ac2d6'],
-    }),
     ('natsort', '8.4.0', {
         'checksums': ['45312c4a0e5507593da193dedd04abb1469253b601ecaf63445ad80f0a1ea581'],
     }),
+    ('array_api_compat', '1.13.0', {
+        'checksums': ['8b83a56aa8b9477472fee37f7731968dd213e20c198a05ac49caeff9b03f48a6'],
+    }),
     (name, version, {
         'modulename': 'skbio',
-        'testinstall': True,
-        'runtest': 'cd /tmp && python -m skbio.test --pyargs skbio',
-        'checksums': ['f06cc87a1823902906821819e66f7cd704563a9f8cdf6720296a42dcbc2fe1c2'],
+        'checksums': ['d0a991818882c88ca47d9f6441321a440439e1a8a6716a101a931d590c395fe8'],
     }),
 ]
 
+sanity_check_commands = ['python -m skbio.test']
+
 moduleclass = 'bio'

Diff against scikit-bio-0.7.1.post1-foss-2025a.eb

easybuild/easyconfigs/s/scikit-bio/scikit-bio-0.7.1.post1-foss-2025a.eb

diff --git a/easybuild/easyconfigs/s/scikit-bio/scikit-bio-0.7.1.post1-foss-2025a.eb b/easybuild/easyconfigs/s/scikit-bio/scikit-bio-0.7.2-foss-2025b.eb
index fb08b89455..728473a840 100644
--- a/easybuild/easyconfigs/s/scikit-bio/scikit-bio-0.7.1.post1-foss-2025a.eb
+++ b/easybuild/easyconfigs/s/scikit-bio/scikit-bio-0.7.2-foss-2025b.eb
@@ -1,32 +1,31 @@
 easyblock = 'PythonBundle'
 
 name = 'scikit-bio'
-version = '0.7.1.post1'
+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': '2025a'}
+toolchain = {'name': 'foss', 'version': '2025b'}
+
+builddependencies = [
+    ('Cython', '3.2.4'),
+]
 
 dependencies = [
-    ('Python', '3.13.1'),
-    ('Python-bundle-PyPI', '2025.04'),
-    ('SciPy-bundle', '2025.06'),
-    ('matplotlib', '3.10.3'),
-    ('scikit-learn', '1.7.0'),
-    ('IPython', '9.3.0'),
+    ('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', '0.14.5'),
-    ('setuptools', '80.9.0'),
-    ('Cython', '3.1.1'),
+    ('statsmodels', '0.14.6'),
 ]
 
 exts_list = [
-    ('packaging', '25.0', {
-        'checksums': ['d443872c98d677bf60f6a1f2f8c1cb748e8fe762d2bf9d3148b5599295b0fc4f'],
-    }),
     ('natsort', '8.4.0', {
         'checksums': ['45312c4a0e5507593da193dedd04abb1469253b601ecaf63445ad80f0a1ea581'],
     }),
@@ -35,12 +34,7 @@ exts_list = [
     }),
     (name, version, {
         'modulename': 'skbio',
-        'patches': ['scikit-bio-0.7.1.post1_ignore_dirmult_lme_test.patch'],
-        'checksums': [
-            {'scikit-bio-0.7.1.post1.tar.gz': 'cbd92418b711492837ea5ca3a088b540e725bea53a45bc2332b2631afd539f95'},
-            {'scikit-bio-0.7.1.post1_ignore_dirmult_lme_test.patch':
-             '6c03405349f7a9cc0a3b5c0ddf08bd277075a14403bd2ec166a1581aa6b37bc3'},
-        ],
+        'checksums': ['d0a991818882c88ca47d9f6441321a440439e1a8a6716a101a931d590c395fe8'],
     }),
 ]

Diff against scikit-bio-0.6.2-foss-2023b.eb

easybuild/easyconfigs/s/scikit-bio/scikit-bio-0.6.2-foss-2023b.eb

diff --git a/easybuild/easyconfigs/s/scikit-bio/scikit-bio-0.6.2-foss-2023b.eb b/easybuild/easyconfigs/s/scikit-bio/scikit-bio-0.7.2-foss-2025b.eb
index 07dc1e444e..728473a840 100644
--- a/easybuild/easyconfigs/s/scikit-bio/scikit-bio-0.6.2-foss-2023b.eb
+++ b/easybuild/easyconfigs/s/scikit-bio/scikit-bio-0.7.2-foss-2025b.eb
@@ -1,41 +1,40 @@
 easyblock = 'PythonBundle'
 
 name = 'scikit-bio'
-version = '0.6.2'
+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': '2023b'}
+toolchain = {'name': 'foss', 'version': '2025b'}
+
+builddependencies = [
+    ('Cython', '3.2.4'),
+]
 
 dependencies = [
-    ('Python', '3.11.5'),
-    ('Python-bundle-PyPI', '2023.10'),
-    ('SciPy-bundle', '2023.11'),
-    ('matplotlib', '3.8.2'),
-    ('scikit-learn', '1.4.0'),
-    ('IPython', '8.17.2'),
-    ('h5py', '3.11.0'),
-    ('biom-format', '2.1.16'),
-    ('statsmodels', '0.14.1'),
+    ('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 = [
-    ('hdmedians', '0.14.2', {
-        'checksums': ['b47aecb16771e1ba0736557255d80ae0240b09156bff434321de559b359ac2d6'],
-    }),
     ('natsort', '8.4.0', {
         'checksums': ['45312c4a0e5507593da193dedd04abb1469253b601ecaf63445ad80f0a1ea581'],
     }),
+    ('array_api_compat', '1.13.0', {
+        'checksums': ['8b83a56aa8b9477472fee37f7731968dd213e20c198a05ac49caeff9b03f48a6'],
+    }),
     (name, version, {
         'modulename': 'skbio',
-        'patches': ['fix-cython-segmentation-error_scikit-bio-0.6.2.patch'],
-        'checksums': [
-            {'scikit-bio-0.6.2.tar.gz': 'af217ad12243cdaeef74a8f3bebe0d04aefda2a22d963d634201a36318b1a404'},
-            {'fix-cython-segmentation-error_scikit-bio-0.6.2.patch':
-             'd5e7f2266eb2f19905c5ff4b56e691c42ea0372c8c85a08791074ecf28aced51'},
-        ],
+        'checksums': ['d0a991818882c88ca47d9f6441321a440439e1a8a6716a101a931d590c395fe8'],
     }),
 ]

Updated software `statsmodels-0.14.6-gfbf-2025b.eb`

Diff against statsmodels-0.14.5-gfbf-2025a.eb

easybuild/easyconfigs/s/statsmodels/statsmodels-0.14.5-gfbf-2025a.eb

diff --git a/easybuild/easyconfigs/s/statsmodels/statsmodels-0.14.5-gfbf-2025a.eb b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.14.6-gfbf-2025b.eb
index 048cd12582..2c50f1a69b 100644
--- a/easybuild/easyconfigs/s/statsmodels/statsmodels-0.14.5-gfbf-2025a.eb
+++ b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.14.6-gfbf-2025b.eb
@@ -1,19 +1,19 @@
 easyblock = 'PythonBundle'
 
 name = 'statsmodels'
-version = '0.14.5'
+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': '2025a'}
+toolchain = {'name': 'gfbf', 'version': '2025b'}
 
-builddependencies = [('Cython', '3.1.1')]
+builddependencies = [('Cython', '3.1.2')]
 
 dependencies = [
-    ('Python', '3.13.1'),
-    ('SciPy-bundle', '2025.06'),
+    ('Python', '3.13.5'),
+    ('SciPy-bundle', '2025.07'),
 ]
 
 exts_list = [
@@ -22,7 +22,7 @@ exts_list = [
     }),
     (name, version, {
         'preinstallopts': """sed -i 's/url=URL,/url=URL, version="%(version)s",/g' setup.py && """,
-        'checksums': ['de260e58cccfd2ceddf835b55a357233d6ca853a1aa4f90f7553a52cc71c6ddf'],
+        'checksums': ['4d17873d3e607d398b85126cd4ed7aad89e4e9d89fc744cdab1af3189a996c2a'],
     }),
 ]

Diff against statsmodels-0.14.4-gfbf-2024a.eb

easybuild/easyconfigs/s/statsmodels/statsmodels-0.14.4-gfbf-2024a.eb

diff --git a/easybuild/easyconfigs/s/statsmodels/statsmodels-0.14.4-gfbf-2024a.eb b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.14.6-gfbf-2025b.eb
index 7701590d16..2c50f1a69b 100644
--- a/easybuild/easyconfigs/s/statsmodels/statsmodels-0.14.4-gfbf-2024a.eb
+++ b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.14.6-gfbf-2025b.eb
@@ -1,28 +1,28 @@
 easyblock = 'PythonBundle'
 
 name = 'statsmodels'
-version = '0.14.4'
+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': '2024a'}
+toolchain = {'name': 'gfbf', 'version': '2025b'}
 
-builddependencies = [('Cython', '3.0.10')]
+builddependencies = [('Cython', '3.1.2')]
 
 dependencies = [
-    ('Python', '3.12.3'),
-    ('SciPy-bundle', '2024.05'),
+    ('Python', '3.13.5'),
+    ('SciPy-bundle', '2025.07'),
 ]
 
 exts_list = [
-    ('patsy', '0.5.6', {
-        'checksums': ['95c6d47a7222535f84bff7f63d7303f2e297747a598db89cf5c67f0c0c7d2cdb'],
+    ('patsy', '1.0.1', {
+        'checksums': ['e786a9391eec818c054e359b737bbce692f051aee4c661f4141cc88fb459c0c4'],
     }),
     (name, version, {
         'preinstallopts': """sed -i 's/url=URL,/url=URL, version="%(version)s",/g' setup.py && """,
-        'checksums': ['5d69e0f39060dc72c067f9bb6e8033b6dccdb0bae101d76a7ef0bcc94e898b67'],
+        'checksums': ['4d17873d3e607d398b85126cd4ed7aad89e4e9d89fc744cdab1af3189a996c2a'],
     }),
 ]

Diff against statsmodels-0.14.1-gfbf-2023a.eb

easybuild/easyconfigs/s/statsmodels/statsmodels-0.14.1-gfbf-2023a.eb

diff --git a/easybuild/easyconfigs/s/statsmodels/statsmodels-0.14.1-gfbf-2023a.eb b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.14.6-gfbf-2025b.eb
index 85487c26f7..2c50f1a69b 100644
--- a/easybuild/easyconfigs/s/statsmodels/statsmodels-0.14.1-gfbf-2023a.eb
+++ b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.14.6-gfbf-2025b.eb
@@ -1,26 +1,28 @@
 easyblock = 'PythonBundle'
 
 name = 'statsmodels'
-version = '0.14.1'
+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': '2023a'}
+toolchain = {'name': 'gfbf', 'version': '2025b'}
+
+builddependencies = [('Cython', '3.1.2')]
 
 dependencies = [
-    ('Python', '3.11.3'),
-    ('SciPy-bundle', '2023.07'),
+    ('Python', '3.13.5'),
+    ('SciPy-bundle', '2025.07'),
 ]
 
 exts_list = [
-    ('patsy', '0.5.6', {
-        'checksums': ['95c6d47a7222535f84bff7f63d7303f2e297747a598db89cf5c67f0c0c7d2cdb'],
+    ('patsy', '1.0.1', {
+        'checksums': ['e786a9391eec818c054e359b737bbce692f051aee4c661f4141cc88fb459c0c4'],
     }),
     (name, version, {
-        'checksums': ['2260efdc1ef89f39c670a0bd8151b1d0843567781bcafec6cda0534eb47a94f6'],
-        'preinstallopts': """sed -i 's/name=DISTNAME/name=DISTNAME, version = "%(version)s"/g' setup.py && """,
+        'preinstallopts': """sed -i 's/url=URL,/url=URL, version="%(version)s",/g' setup.py && """,
+        'checksums': ['4d17873d3e607d398b85126cd4ed7aad89e4e9d89fc744cdab1af3189a996c2a'],
     }),
 ]

boegel · 2026-05-04T11:38:39Z

@boegelbot please test @ jsc-zen3
CORE_CNT=16

boegelbot · 2026-05-04T11:40:08Z

@boegel: Request for testing this PR well received on jsczen3l1.int.jsc-zen3.fz-juelich.de

PR test command 'if [[ develop != 'develop' ]]; then EB_BRANCH=develop ./easybuild_develop.sh 2> /dev/null 1>&2; EB_PREFIX=/home/boegelbot/easybuild/develop source init_env_easybuild_develop.sh; fi; EB_PR=25908 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_25908 --ntasks="16" ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 10346

Test results coming soon (I hope)...

Details

- notification for comment with ID 4370712673 processed

Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

boegelbot · 2026-05-04T11:54:27Z

Test report by @boegelbot
SUCCESS
Build succeeded for 4 out of 4 (total: 14 mins 0 secs) (4 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.7, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.25
See https://gist.github.com/boegelbot/918eb0c6fa5af908048fa24a45f2b740 for a full test report.

boegel · 2026-05-04T14:55:01Z

Test report by @boegel
SUCCESS
Build succeeded for 4 out of 4 (total: 58 mins 41 secs) (4 easyconfigs in total)
node4414.skiddo.os - Linux RHEL 9.6, x86_64, AMD EPYC 9755 128-Core Processor (zen5), Python 3.9.21
See https://gist.github.com/boegel/4c82b5d96a1164203db04a7da8bfe9f1 for a full test report.

verdurin · 2026-05-05T10:26:30Z

Test report by @verdurin
SUCCESS
Build succeeded for 29 out of 29 (total: 2 hours 36 mins 35 secs) (4 easyconfigs in total)
centos-stream-9 - Linux CentOS Stream 9, x86_64, Intel Core Processor (Skylake, IBRS), Python 3.12.12
See https://gist.github.com/verdurin/2113fa05e00c00aec1f117b4733c57be for a full test report.

verdurin · 2026-05-05T10:39:10Z

@boegel could you add a comment here about the removal of hdmedians?

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

d046904

… v0.14.6, Cython 3.2.4

boegel added the update label May 4, 2026

github-actions Bot added the 2025b issues & PRs related to 2025b common toolchains label May 4, 2026

boegel added this to the 5.x milestone May 4, 2026

boegel mentioned this pull request May 4, 2026

{2025.06}[foss/2025b] scikit-bio 0.7.2 EESSI/software-layer#1494

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{bio}[foss/2025b] scikit-bio v0.7.2, biom-format v2.1.17, statsmodels v0.14.6, Cython 3.2.4#25908

{bio}[foss/2025b] scikit-bio v0.7.2, biom-format v2.1.17, statsmodels v0.14.6, Cython 3.2.4#25908
boegel wants to merge 1 commit intoeasybuilders:developfrom
boegel:20260504125602_new_pr_scikit-bio072

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boegel commented May 4, 2026

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github-actions Bot commented May 4, 2026

Updated software biom-format-2.1.17-foss-2025b.eb

Updated software Cython-3.2.4-GCCcore-14.3.0.eb

Updated software scikit-bio-0.7.2-foss-2025b.eb

Updated software statsmodels-0.14.6-gfbf-2025b.eb

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Updated software `biom-format-2.1.17-foss-2025b.eb`

Updated software `Cython-3.2.4-GCCcore-14.3.0.eb`

Updated software `scikit-bio-0.7.2-foss-2025b.eb`

Updated software `statsmodels-0.14.6-gfbf-2025b.eb`