{bio}[foss/2025a] Palantir v1.4.1, python-igraph v0.11.9, igraph v0.10.17, ... by pavelToman · Pull Request #24291 · easybuilders/easybuild-easyconfigs

pavelToman · 2025-10-17T12:59:05Z

(created using eb --new-pr)
resolves vscentrum/vsc-software-stack#606
requires:

…9-foss-2025a.eb, igraph-0.10.17-foss-2025a.eb, scanpy-1.11.4-foss-2025a.eb, umap-learn-0.5.9.post2-foss-2025a.eb, anndata-0.12.3-foss-2025a.eb

github-actions · 2025-10-17T12:59:47Z

Updated software `anndata-0.12.3-foss-2025a.eb`

Diff against anndata-0.10.9-foss-2024a.eb

easybuild/easyconfigs/a/anndata/anndata-0.10.9-foss-2024a.eb

diff --git a/easybuild/easyconfigs/a/anndata/anndata-0.10.9-foss-2024a.eb b/easybuild/easyconfigs/a/anndata/anndata-0.12.3-foss-2025a.eb
index a75a378f1d..c6a928e218 100644
--- a/easybuild/easyconfigs/a/anndata/anndata-0.10.9-foss-2024a.eb
+++ b/easybuild/easyconfigs/a/anndata/anndata-0.12.3-foss-2025a.eb
@@ -1,37 +1,38 @@
 easyblock = 'PythonBundle'
 
 name = 'anndata'
-version = '0.10.9'
+version = '0.12.3'
 
 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'}
+toolchain = {'name': 'foss', 'version': '2025a'}
 
 builddependencies = [
-    ('hatchling', '1.24.2'),
+    ('hatchling', '1.27.0'),
 ]
 
 dependencies = [
-    ('Python', '3.12.3'),
-    ('Python-bundle-PyPI', '2024.06'),
-    ('SciPy-bundle', '2024.05'),
-    ('h5py', '3.12.1'),
+    ('Python', '3.13.1'),
+    ('Python-bundle-PyPI', '2025.04'),
+    ('SciPy-bundle', '2025.06'),
+    ('h5py', '3.14.0'),
+    ('zarr', '3.1.1'),
 ]
 
 exts_list = [
-    ('array_api_compat', '1.11.2', {
-        'checksums': ['a3b7f7b6af18f4c42e79423b1b2479798998b6a74355069d77a01a5282755b5d'],
+    ('array_api_compat', '1.12.0', {
+        'checksums': ['585bc615f650de53ac24b7c012baecfcdd810f50df3573be47e6dd9fa20df974'],
+    }),
+    ('legacy_api_wrap', '1.4.1', {
+        'checksums': ['9c40d67aa8312fec8763e87cbf28fea4b67710c79ca7a18137b573d150f3b2b4'],
     }),
     ('natsort', '8.4.0', {
         'checksums': ['45312c4a0e5507593da193dedd04abb1469253b601ecaf63445ad80f0a1ea581'],
     }),
-    ('packaging', '25.0', {
-        'checksums': ['d443872c98d677bf60f6a1f2f8c1cb748e8fe762d2bf9d3148b5599295b0fc4f'],
-    }),
     (name, version, {
-        'checksums': ['fe36f2f3f8040ffed866c4932253407f594cfe34d420fe5b7854986cb6bb7178'],
+        'checksums': ['1ae821ae90d13b3aeedc9831b6ce4f6aa9d4cccf3dcbe398ae9424cf3df7bafd'],
     }),
 ]

Diff against anndata-0.11.1-foss-2023b.eb

easybuild/easyconfigs/a/anndata/anndata-0.11.1-foss-2023b.eb

diff --git a/easybuild/easyconfigs/a/anndata/anndata-0.11.1-foss-2023b.eb b/easybuild/easyconfigs/a/anndata/anndata-0.12.3-foss-2025a.eb
index c03367afd7..c6a928e218 100644
--- a/easybuild/easyconfigs/a/anndata/anndata-0.11.1-foss-2023b.eb
+++ b/easybuild/easyconfigs/a/anndata/anndata-0.12.3-foss-2025a.eb
@@ -1,34 +1,38 @@
 easyblock = 'PythonBundle'
 
 name = 'anndata'
-version = '0.11.1'
+version = '0.12.3'
 
 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': '2023b'}
+toolchain = {'name': 'foss', 'version': '2025a'}
 
 builddependencies = [
-    ('hatchling', '1.18.0'),
+    ('hatchling', '1.27.0'),
 ]
 
 dependencies = [
-    ('Python', '3.11.5'),
-    ('Python-bundle-PyPI', '2023.10'),
-    ('SciPy-bundle', '2023.11'),
-    ('h5py', '3.11.0'),
+    ('Python', '3.13.1'),
+    ('Python-bundle-PyPI', '2025.04'),
+    ('SciPy-bundle', '2025.06'),
+    ('h5py', '3.14.0'),
+    ('zarr', '3.1.1'),
 ]
 
 exts_list = [
-    ('array_api_compat', '1.9.1', {
-        'checksums': ['17bab828c93c79a5bb8b867145b71fcb889686607c5672b060aef437e0359ea8'],
+    ('array_api_compat', '1.12.0', {
+        'checksums': ['585bc615f650de53ac24b7c012baecfcdd810f50df3573be47e6dd9fa20df974'],
+    }),
+    ('legacy_api_wrap', '1.4.1', {
+        'checksums': ['9c40d67aa8312fec8763e87cbf28fea4b67710c79ca7a18137b573d150f3b2b4'],
     }),
     ('natsort', '8.4.0', {
         'checksums': ['45312c4a0e5507593da193dedd04abb1469253b601ecaf63445ad80f0a1ea581'],
     }),
     (name, version, {
-        'checksums': ['36bff9a85276fc5f1b9fd01f15aff9aa49408129985f42e0fca4e2c5b7fa909f'],
+        'checksums': ['1ae821ae90d13b3aeedc9831b6ce4f6aa9d4cccf3dcbe398ae9424cf3df7bafd'],
     }),
 ]

Diff against anndata-0.9.2-foss-2021b.eb

easybuild/easyconfigs/a/anndata/anndata-0.9.2-foss-2021b.eb

diff --git a/easybuild/easyconfigs/a/anndata/anndata-0.9.2-foss-2021b.eb b/easybuild/easyconfigs/a/anndata/anndata-0.12.3-foss-2025a.eb
index 9ad337b3bb..c6a928e218 100644
--- a/easybuild/easyconfigs/a/anndata/anndata-0.9.2-foss-2021b.eb
+++ b/easybuild/easyconfigs/a/anndata/anndata-0.12.3-foss-2025a.eb
@@ -1,26 +1,38 @@
 easyblock = 'PythonBundle'
 
 name = 'anndata'
-version = '0.9.2'
+version = '0.12.3'
 
 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': '2021b'}
+toolchain = {'name': 'foss', 'version': '2025a'}
+
+builddependencies = [
+    ('hatchling', '1.27.0'),
+]
 
 dependencies = [
-    ('Python', '3.9.6'),
-    ('SciPy-bundle', '2021.10'),
-    ('h5py', '3.6.0'),
+    ('Python', '3.13.1'),
+    ('Python-bundle-PyPI', '2025.04'),
+    ('SciPy-bundle', '2025.06'),
+    ('h5py', '3.14.0'),
+    ('zarr', '3.1.1'),
 ]
 
 exts_list = [
+    ('array_api_compat', '1.12.0', {
+        'checksums': ['585bc615f650de53ac24b7c012baecfcdd810f50df3573be47e6dd9fa20df974'],
+    }),
+    ('legacy_api_wrap', '1.4.1', {
+        'checksums': ['9c40d67aa8312fec8763e87cbf28fea4b67710c79ca7a18137b573d150f3b2b4'],
+    }),
     ('natsort', '8.4.0', {
         'checksums': ['45312c4a0e5507593da193dedd04abb1469253b601ecaf63445ad80f0a1ea581'],
     }),
     (name, version, {
-        'checksums': ['e5b8383d09723af674cae7ad0c2ef53eb1f8c73949b7f4c182a6e30f42196327'],
+        'checksums': ['1ae821ae90d13b3aeedc9831b6ce4f6aa9d4cccf3dcbe398ae9424cf3df7bafd'],
     }),
 ]

Updated software `igraph-0.10.17-foss-2025a.eb`

Diff against igraph-0.10.16-foss-2024a.eb

easybuild/easyconfigs/i/igraph/igraph-0.10.16-foss-2024a.eb

diff --git a/easybuild/easyconfigs/i/igraph/igraph-0.10.16-foss-2024a.eb b/easybuild/easyconfigs/i/igraph/igraph-0.10.17-foss-2025a.eb
index abe6b02ba9..c231c5ca71 100644
--- a/easybuild/easyconfigs/i/igraph/igraph-0.10.16-foss-2024a.eb
+++ b/easybuild/easyconfigs/i/igraph/igraph-0.10.17-foss-2025a.eb
@@ -1,32 +1,30 @@
 # Author: Denis Krišťák (INUITS)
 # Modified: Jasper Grimm (UoY)
-# Update: Pavel Tománek (INUITS)
 # Update: Petr Král (INUITS)
+# Update: Pavel Tománek (INUITS)
 
 easyblock = 'CMakeMake'
 
 name = 'igraph'
-version = '0.10.16'
+version = '0.10.17'
 
 homepage = 'https://igraph.org'
 description = """igraph is a collection of network analysis tools with the emphasis on
 efficiency, portability and ease of use. igraph is open source and free. igraph can be
 programmed in R, Python and C/C++."""
 
-toolchain = {'name': 'foss', 'version': '2024a'}
+toolchain = {'name': 'foss', 'version': '2025a'}
 toolchainopts = {'pic': True}
 
 source_urls = ['https://github.com/igraph/igraph/releases/download/%(version)s']
 sources = [SOURCE_TAR_GZ]
-checksums = ['15a1540a8d270232c9aa99adeeffb7787bea96289d6bef6646ec9c91a9a93992']
+checksums = ['21016ecf309a235f2bd9e208606d5a24c14a1f701dd7b2497e2e5f6bf2c5f848']
 
-builddependencies = [
-    ('CMake', '3.29.3'),
-]
+builddependencies = [('CMake', '3.31.3')]
 
 dependencies = [
     ('GLPK', '5.0'),
-    ('libxml2', '2.12.7'),
+    ('libxml2', '2.13.4'),
     ('zlib', '1.3.1'),
     ('arpack-ng', '3.9.1'),
 ]

Diff against igraph-0.10.12-foss-2023b.eb

easybuild/easyconfigs/i/igraph/igraph-0.10.12-foss-2023b.eb

diff --git a/easybuild/easyconfigs/i/igraph/igraph-0.10.12-foss-2023b.eb b/easybuild/easyconfigs/i/igraph/igraph-0.10.17-foss-2025a.eb
index 6e5f77cd3c..c231c5ca71 100644
--- a/easybuild/easyconfigs/i/igraph/igraph-0.10.12-foss-2023b.eb
+++ b/easybuild/easyconfigs/i/igraph/igraph-0.10.17-foss-2025a.eb
@@ -1,34 +1,32 @@
 # Author: Denis Krišťák (INUITS)
 # Modified: Jasper Grimm (UoY)
-# Update: Pavel Tománek (INUITS)
 # Update: Petr Král (INUITS)
+# Update: Pavel Tománek (INUITS)
 
 easyblock = 'CMakeMake'
 
 name = 'igraph'
-version = '0.10.12'
+version = '0.10.17'
 
 homepage = 'https://igraph.org'
 description = """igraph is a collection of network analysis tools with the emphasis on
 efficiency, portability and ease of use. igraph is open source and free. igraph can be
 programmed in R, Python and C/C++."""
 
-toolchain = {'name': 'foss', 'version': '2023b'}
+toolchain = {'name': 'foss', 'version': '2025a'}
 toolchainopts = {'pic': True}
 
 source_urls = ['https://github.com/igraph/igraph/releases/download/%(version)s']
 sources = [SOURCE_TAR_GZ]
-checksums = ['b011f7f9f38a3e59924cc9ff652e6d33105fa03fcaf3792f47d752626a0a4625']
+checksums = ['21016ecf309a235f2bd9e208606d5a24c14a1f701dd7b2497e2e5f6bf2c5f848']
 
-builddependencies = [
-    ('CMake', '3.27.6'),
-]
+builddependencies = [('CMake', '3.31.3')]
 
 dependencies = [
     ('GLPK', '5.0'),
-    ('libxml2', '2.11.5'),
-    ('zlib', '1.2.13'),
-    ('arpack-ng', '3.9.0'),
+    ('libxml2', '2.13.4'),
+    ('zlib', '1.3.1'),
+    ('arpack-ng', '3.9.1'),
 ]
 
 # Build static and shared libraries

Diff against igraph-0.10.10-foss-2023a.eb

easybuild/easyconfigs/i/igraph/igraph-0.10.10-foss-2023a.eb

diff --git a/easybuild/easyconfigs/i/igraph/igraph-0.10.10-foss-2023a.eb b/easybuild/easyconfigs/i/igraph/igraph-0.10.17-foss-2025a.eb
index 6ed3462390..c231c5ca71 100644
--- a/easybuild/easyconfigs/i/igraph/igraph-0.10.10-foss-2023a.eb
+++ b/easybuild/easyconfigs/i/igraph/igraph-0.10.17-foss-2025a.eb
@@ -1,33 +1,32 @@
 # Author: Denis Krišťák (INUITS)
 # Modified: Jasper Grimm (UoY)
+# Update: Petr Král (INUITS)
 # Update: Pavel Tománek (INUITS)
 
 easyblock = 'CMakeMake'
 
 name = 'igraph'
-version = '0.10.10'
+version = '0.10.17'
 
 homepage = 'https://igraph.org'
 description = """igraph is a collection of network analysis tools with the emphasis on
 efficiency, portability and ease of use. igraph is open source and free. igraph can be
 programmed in R, Python and C/C++."""
 
-toolchain = {'name': 'foss', 'version': '2023a'}
+toolchain = {'name': 'foss', 'version': '2025a'}
 toolchainopts = {'pic': True}
 
 source_urls = ['https://github.com/igraph/igraph/releases/download/%(version)s']
 sources = [SOURCE_TAR_GZ]
-checksums = ['6148f2e72a183ef5cd08324cccc73fa9eb8e54bb5a96c7f8f3c0465432ec2404']
+checksums = ['21016ecf309a235f2bd9e208606d5a24c14a1f701dd7b2497e2e5f6bf2c5f848']
 
-builddependencies = [
-    ('CMake', '3.26.3'),
-]
+builddependencies = [('CMake', '3.31.3')]
 
 dependencies = [
     ('GLPK', '5.0'),
-    ('libxml2', '2.11.4'),
-    ('zlib', '1.2.13'),
-    ('arpack-ng', '3.9.0'),
+    ('libxml2', '2.13.4'),
+    ('zlib', '1.3.1'),
+    ('arpack-ng', '3.9.1'),
 ]
 
 # Build static and shared libraries

Updated software `python-igraph-0.11.9-foss-2025a.eb`

Diff against python-igraph-0.11.9-foss-2024a.eb

easybuild/easyconfigs/p/python-igraph/python-igraph-0.11.9-foss-2024a.eb

diff --git a/easybuild/easyconfigs/p/python-igraph/python-igraph-0.11.9-foss-2024a.eb b/easybuild/easyconfigs/p/python-igraph/python-igraph-0.11.9-foss-2025a.eb
index e663f1b08f..048cd60fc1 100644
--- a/easybuild/easyconfigs/p/python-igraph/python-igraph-0.11.9-foss-2024a.eb
+++ b/easybuild/easyconfigs/p/python-igraph/python-igraph-0.11.9-foss-2025a.eb
@@ -7,21 +7,15 @@ homepage = 'https://igraph.org/python'
 description = """Python interface to the igraph high performance graph library, primarily aimed at complex network
  research and analysis."""
 
-toolchain = {'name': 'foss', 'version': '2024a'}
+toolchain = {'name': 'foss', 'version': '2025a'}
 
-builddependencies = [
-    ('pkgconf', '2.2.0'),
-    ('CMake', '3.29.3'),
-]
+builddependencies = [('pkgconf', '2.3.0')]
 
 dependencies = [
-    ('Python', '3.12.3'),
-    ('Python-bundle-PyPI', '2024.06'),
-    ('Clang', '18.1.8'),
-    ('libxml2', '2.12.7'),
-    ('zlib', '1.3.1'),
-    ('igraph', '0.10.16'),
-    ('cairo', '1.18.0'),
+    ('Python', '3.13.1'),
+    ('Python-bundle-PyPI', '2025.04'),
+    ('igraph', '0.10.17'),
+    ('cairo', '1.18.4'),
 ]
 
 exts_list = [
@@ -32,6 +26,8 @@ exts_list = [
         'checksums': ['2e48ee864884ec4a3a34bfa8c9ab9999f688286eb714a15a43ec9d068c36557b'],
     }),
     ('igraph', version, {
+        # tell python-igraph to use igraph's libigraph.so and do not build its own
+        'preinstallopts': 'export IGRAPH_USE_PKG_CONFIG=1 && ',
         'modulename': 'igraph',
         'checksums': ['c57ce44873abcfcfd1d61d7d261e416d352186958e7b5d299cf244efa6757816'],
     }),

Diff against python-igraph-0.11.8-foss-2023b.eb

easybuild/easyconfigs/p/python-igraph/python-igraph-0.11.8-foss-2023b.eb

diff --git a/easybuild/easyconfigs/p/python-igraph/python-igraph-0.11.8-foss-2023b.eb b/easybuild/easyconfigs/p/python-igraph/python-igraph-0.11.9-foss-2025a.eb
index 1bd68187f6..048cd60fc1 100644
--- a/easybuild/easyconfigs/p/python-igraph/python-igraph-0.11.8-foss-2023b.eb
+++ b/easybuild/easyconfigs/p/python-igraph/python-igraph-0.11.9-foss-2025a.eb
@@ -1,27 +1,21 @@
 easyblock = 'PythonBundle'
 
 name = 'python-igraph'
-version = '0.11.8'
+version = '0.11.9'
 
 homepage = 'https://igraph.org/python'
 description = """Python interface to the igraph high performance graph library, primarily aimed at complex network
  research and analysis."""
 
-toolchain = {'name': 'foss', 'version': '2023b'}
+toolchain = {'name': 'foss', 'version': '2025a'}
 
-builddependencies = [
-    ('pkgconf', '2.0.3'),
-    ('CMake', '3.27.6'),
-]
+builddependencies = [('pkgconf', '2.3.0')]
 
 dependencies = [
-    ('Python', '3.11.5'),
-    ('Python-bundle-PyPI', '2023.10'),
-    ('Clang', '17.0.6'),
-    ('libxml2', '2.11.5'),
-    ('zlib', '1.2.13'),
-    ('igraph', '0.10.12'),
-    ('cairo', '1.18.0'),
+    ('Python', '3.13.1'),
+    ('Python-bundle-PyPI', '2025.04'),
+    ('igraph', '0.10.17'),
+    ('cairo', '1.18.4'),
 ]
 
 exts_list = [
@@ -32,8 +26,10 @@ exts_list = [
         'checksums': ['2e48ee864884ec4a3a34bfa8c9ab9999f688286eb714a15a43ec9d068c36557b'],
     }),
     ('igraph', version, {
+        # tell python-igraph to use igraph's libigraph.so and do not build its own
+        'preinstallopts': 'export IGRAPH_USE_PKG_CONFIG=1 && ',
         'modulename': 'igraph',
-        'checksums': ['d7dc1404567ba3b0ea1bf8b5fa6e101617915c8ad11ea5a9f925a40bf4adad7d'],
+        'checksums': ['c57ce44873abcfcfd1d61d7d261e416d352186958e7b5d299cf244efa6757816'],
     }),
 ]

Diff against python-igraph-0.11.4-foss-2023a.eb

easybuild/easyconfigs/p/python-igraph/python-igraph-0.11.4-foss-2023a.eb

diff --git a/easybuild/easyconfigs/p/python-igraph/python-igraph-0.11.4-foss-2023a.eb b/easybuild/easyconfigs/p/python-igraph/python-igraph-0.11.9-foss-2025a.eb
index 22fbd94f2b..048cd60fc1 100644
--- a/easybuild/easyconfigs/p/python-igraph/python-igraph-0.11.4-foss-2023a.eb
+++ b/easybuild/easyconfigs/p/python-igraph/python-igraph-0.11.9-foss-2025a.eb
@@ -1,43 +1,38 @@
 easyblock = 'PythonBundle'
 
 name = 'python-igraph'
-version = '0.11.4'
+version = '0.11.9'
 
 homepage = 'https://igraph.org/python'
 description = """Python interface to the igraph high performance graph library, primarily aimed at complex network
  research and analysis."""
 
-toolchain = {'name': 'foss', 'version': '2023a'}
+toolchain = {'name': 'foss', 'version': '2025a'}
 
-builddependencies = [
-    ('pkgconf', '1.9.5'),
-    ('CMake', '3.26.3'),
-]
+builddependencies = [('pkgconf', '2.3.0')]
 
 dependencies = [
-    ('Python', '3.11.3'),
-    ('Python-bundle-PyPI', '2023.06'),
-    ('Clang', '16.0.6'),
-    ('libxml2', '2.11.4'),
-    ('zlib', '1.2.13'),
-    ('igraph', '0.10.10'),
-    ('cairo', '1.17.8'),
+    ('Python', '3.13.1'),
+    ('Python-bundle-PyPI', '2025.04'),
+    ('igraph', '0.10.17'),
+    ('cairo', '1.18.4'),
 ]
 
 exts_list = [
     ('texttable', '1.7.0', {
         'checksums': ['2d2068fb55115807d3ac77a4ca68fa48803e84ebb0ee2340f858107a36522638'],
     }),
-    ('cairocffi', '1.6.1', {
-        'checksums': ['78e6bbe47357640c453d0be929fa49cd05cce2e1286f3d2a1ca9cbda7efdb8b7'],
+    ('cairocffi', '1.7.1', {
+        'checksums': ['2e48ee864884ec4a3a34bfa8c9ab9999f688286eb714a15a43ec9d068c36557b'],
     }),
     ('igraph', version, {
+        # tell python-igraph to use igraph's libigraph.so and do not build its own
+        'preinstallopts': 'export IGRAPH_USE_PKG_CONFIG=1 && ',
         'modulename': 'igraph',
-        'checksums': ['2437ae0157af6824e2e65a23f7a1fa4fbf0f3664333c72aeca4fc01b83e18483'],
+        'checksums': ['c57ce44873abcfcfd1d61d7d261e416d352186958e7b5d299cf244efa6757816'],
     }),
 ]
 
-
 # cairo must be available for proper plotting support
 sanity_check_commands = [
     "python -c 'from igraph.drawing.cairo.utils import find_cairo; "

Updated software `scanpy-1.11.4-foss-2025a.eb`

Diff against scanpy-1.9.8-foss-2023a.eb

easybuild/easyconfigs/s/scanpy/scanpy-1.9.8-foss-2023a.eb

diff --git a/easybuild/easyconfigs/s/scanpy/scanpy-1.9.8-foss-2023a.eb b/easybuild/easyconfigs/s/scanpy/scanpy-1.11.4-foss-2025a.eb
index 8f2a7e6444..afa4b41c75 100644
--- a/easybuild/easyconfigs/s/scanpy/scanpy-1.9.8-foss-2023a.eb
+++ b/easybuild/easyconfigs/s/scanpy/scanpy-1.11.4-foss-2025a.eb
@@ -1,7 +1,7 @@
 easyblock = 'PythonBundle'
 
 name = 'scanpy'
-version = '1.9.8'
+version = '1.11.4'
 
 homepage = 'https://scanpy.readthedocs.io/en/stable/'
 description = """Scanpy is a scalable toolkit for analyzing single-cell gene expression data built
@@ -10,60 +10,43 @@ description = """Scanpy is a scalable toolkit for analyzing single-cell gene exp
  datasets of more than one million cells.
 """
 
-toolchain = {'name': 'foss', 'version': '2023a'}
+toolchain = {'name': 'foss', 'version': '2025a'}
 toolchainopts = {'openmp': True}
 
-builddependencies = [
-    ('hatchling', '1.18.0'),
-]
+builddependencies = [('hatchling', '1.27.0')]
 
 dependencies = [
-    ('Python', '3.11.3'),
-    ('SciPy-bundle', '2023.07'),
-    ('matplotlib', '3.7.2'),
+    ('Python', '3.13.1'),
+    ('Python-bundle-PyPI', '2025.04'),
+    ('SciPy-bundle', '2025.06'),
+    ('networkx', '3.5'),
+    ('anndata', '0.12.3'),
+    ('matplotlib', '3.10.3'),
     ('Seaborn', '0.13.2'),
-    ('h5py', '3.9.0'),
-    ('tqdm', '4.66.1'),
-    ('scikit-learn', '1.3.1'),
-    ('statsmodels', '0.14.1'),
-    ('networkx', '3.1'),
-    ('numba', '0.58.1'),
-    ('umap-learn', '0.5.5'),
-    ('anndata', '0.10.5.post1'),
+    ('h5py', '3.14.0'),
+    ('tqdm', '4.67.1'),
+    ('scikit-learn', '1.7.0'),
+    ('statsmodels', '0.14.5'),
+    ('numba', '0.62.0'),
+    ('umap-learn', '0.5.9.post2'),
 ]
 
 exts_list = [
-    ('stdlib_list', '0.10.0', {
-        'checksums': ['6519c50d645513ed287657bfe856d527f277331540691ddeaf77b25459964a14'],
-    }),
-    ('packaging', '23.2', {
-        'checksums': ['048fb0e9405036518eaaf48a55953c750c11e1a1b68e0dd1a9d62ed0c092cfc5'],
-    }),
-    ('natsort', '8.4.0', {
-        'checksums': ['45312c4a0e5507593da193dedd04abb1469253b601ecaf63445ad80f0a1ea581'],
-    }),
-    ('joblib', '1.3.2', {
-        'checksums': ['92f865e621e17784e7955080b6d042489e3b8e294949cc44c6eac304f59772b1'],
+    ('joblib', '1.5.2', {
+        'checksums': ['3faa5c39054b2f03ca547da9b2f52fde67c06240c31853f306aea97f13647b55'],
     }),
-    ('session-info', '1.0.0', {
-        'sources': ['session_info-%(version)s.tar.gz'],
-        'checksums': ['3cda5e03cca703f32ae2eadbd6bd80b6c21442cfb60e412c21cb8ad6d5cbb6b7'],
-    }),
-    ('legacy_api_wrap', '1.4', {
-        'checksums': ['92dfa274cedb26d6e6f70fac85c856fbdcc05058066656d76a665fb4bf11b785'],
+    ('session-info2', '0.2.3', {
+        'sources': ['session_info2-%(version)s.tar.gz'],
+        'checksums': ['6d16e3c6bb72ea52e589da4d722d24798aa3511c34ab8446a131d655cba2e2c9'],
     }),
     (name, version, {
-        'checksums': ['2ab1790d2b82eadb0cf8d487f468beac7a8f6a3a8fd7112d1ae989f8c52a4353'],
+        'checksums': ['333189ecac9c7009bf55d416ee2e272e1c490d54c719478f7b4dd1fc294d2f95'],
     }),
 ]
 
 sanity_check_paths = {
-    'files': ['bin/%s' % x for x in ['natsort', 'scanpy']],
+    'files': ['bin/scanpy'],
     'dirs': ['lib/python%(pyshortver)s/site-packages/'],
 }
 
-sanity_check_commands = [
-    "natsort --help",
-]
-
 moduleclass = 'bio'

Diff against scanpy-1.9.1-foss-2022a.eb

easybuild/easyconfigs/s/scanpy/scanpy-1.9.1-foss-2022a.eb

diff --git a/easybuild/easyconfigs/s/scanpy/scanpy-1.9.1-foss-2022a.eb b/easybuild/easyconfigs/s/scanpy/scanpy-1.11.4-foss-2025a.eb
index 03389a60d2..afa4b41c75 100644
--- a/easybuild/easyconfigs/s/scanpy/scanpy-1.9.1-foss-2022a.eb
+++ b/easybuild/easyconfigs/s/scanpy/scanpy-1.11.4-foss-2025a.eb
@@ -1,7 +1,7 @@
 easyblock = 'PythonBundle'
 
 name = 'scanpy'
-version = '1.9.1'
+version = '1.11.4'
 
 homepage = 'https://scanpy.readthedocs.io/en/stable/'
 description = """Scanpy is a scalable toolkit for analyzing single-cell gene expression data built
@@ -10,56 +10,43 @@ description = """Scanpy is a scalable toolkit for analyzing single-cell gene exp
  datasets of more than one million cells.
 """
 
-toolchain = {'name': 'foss', 'version': '2022a'}
+toolchain = {'name': 'foss', 'version': '2025a'}
 toolchainopts = {'openmp': True}
 
+builddependencies = [('hatchling', '1.27.0')]
+
 dependencies = [
-    ('Python', '3.10.4'),
-    ('SciPy-bundle', '2022.05'),
-    ('h5py', '3.7.0'),
-    ('networkx', '2.8.4'),
-    ('numba', '0.56.4'),
-    ('PyTables', '3.8.0'),
-    ('statsmodels', '0.13.1'),
-    ('scikit-learn', '1.1.2'),
-    ('Seaborn', '0.12.1'),
-    ('tqdm', '4.64.0'),
-    ('leidenalg', '0.9.1'),
-    ('umap-learn', '0.5.3'),
+    ('Python', '3.13.1'),
+    ('Python-bundle-PyPI', '2025.04'),
+    ('SciPy-bundle', '2025.06'),
+    ('networkx', '3.5'),
+    ('anndata', '0.12.3'),
+    ('matplotlib', '3.10.3'),
+    ('Seaborn', '0.13.2'),
+    ('h5py', '3.14.0'),
+    ('tqdm', '4.67.1'),
+    ('scikit-learn', '1.7.0'),
+    ('statsmodels', '0.14.5'),
+    ('numba', '0.62.0'),
+    ('umap-learn', '0.5.9.post2'),
 ]
 
 exts_list = [
-    ('natsort', '8.2.0', {
-        'checksums': ['57f85b72c688b09e053cdac302dd5b5b53df5f73ae20b4874fcbffd8bf783d11'],
-    }),
-    ('xlrd', '2.0.1', {
-        'checksums': ['f72f148f54442c6b056bf931dbc34f986fd0c3b0b6b5a58d013c9aef274d0c88'],
-    }),
-    ('anndata', '0.8.0', {
-        'checksums': ['94d2cc6f76c0317c0ac28564e3092b313b7ad19c737d66701961f3e620b9066e'],
-    }),
-    ('stdlib-list', '0.8.0', {
-        'checksums': ['a1e503719720d71e2ed70ed809b385c60cd3fb555ba7ec046b96360d30b16d9f'],
+    ('joblib', '1.5.2', {
+        'checksums': ['3faa5c39054b2f03ca547da9b2f52fde67c06240c31853f306aea97f13647b55'],
     }),
-    ('sinfo', '0.3.4', {
-        'checksums': ['81ea91c69a875de178e10bada9476d7300a1f712e1823dbd7714f43a10baba4d'],
-    }),
-    ('session_info', '1.0.0', {
-        'checksums': ['3cda5e03cca703f32ae2eadbd6bd80b6c21442cfb60e412c21cb8ad6d5cbb6b7'],
+    ('session-info2', '0.2.3', {
+        'sources': ['session_info2-%(version)s.tar.gz'],
+        'checksums': ['6d16e3c6bb72ea52e589da4d722d24798aa3511c34ab8446a131d655cba2e2c9'],
     }),
     (name, version, {
-        'checksums': ['00c9a83b649da7e0171c91e9a08cff632102faa760614fd05cd4d1dbba4eb541'],
+        'checksums': ['333189ecac9c7009bf55d416ee2e272e1c490d54c719478f7b4dd1fc294d2f95'],
     }),
 ]
 
 sanity_check_paths = {
-    'files': ['bin/%s' % x for x in ['natsort', 'scanpy']],
+    'files': ['bin/scanpy'],
     'dirs': ['lib/python%(pyshortver)s/site-packages/'],
 }
 
-sanity_check_commands = [
-    "natsort --help",
-    "scanpy --help",
-]
-
 moduleclass = 'bio'

Diff against scanpy-1.9.1-foss-2021b.eb

easybuild/easyconfigs/s/scanpy/scanpy-1.9.1-foss-2021b.eb

diff --git a/easybuild/easyconfigs/s/scanpy/scanpy-1.9.1-foss-2021b.eb b/easybuild/easyconfigs/s/scanpy/scanpy-1.11.4-foss-2025a.eb
index a172ab4637..afa4b41c75 100644
--- a/easybuild/easyconfigs/s/scanpy/scanpy-1.9.1-foss-2021b.eb
+++ b/easybuild/easyconfigs/s/scanpy/scanpy-1.11.4-foss-2025a.eb
@@ -1,7 +1,7 @@
 easyblock = 'PythonBundle'
 
 name = 'scanpy'
-version = '1.9.1'
+version = '1.11.4'
 
 homepage = 'https://scanpy.readthedocs.io/en/stable/'
 description = """Scanpy is a scalable toolkit for analyzing single-cell gene expression data built
@@ -10,62 +10,43 @@ description = """Scanpy is a scalable toolkit for analyzing single-cell gene exp
  datasets of more than one million cells.
 """
 
-toolchain = {'name': 'foss', 'version': '2021b'}
+toolchain = {'name': 'foss', 'version': '2025a'}
 toolchainopts = {'openmp': True}
 
+builddependencies = [('hatchling', '1.27.0')]
+
 dependencies = [
-    ('Python', '3.9.6'),
-    ('SciPy-bundle', '2021.10'),
-    ('h5py', '3.6.0'),
-    ('networkx', '2.6.3'),
-    ('numba', '0.54.1'),
-    ('PyTables', '3.6.1'),
-    ('statsmodels', '0.13.1'),
-    ('scikit-learn', '1.0.1'),
-    ('Seaborn', '0.11.2'),
-    ('tqdm', '4.62.3'),
-    ('leidenalg', '0.8.8'),
+    ('Python', '3.13.1'),
+    ('Python-bundle-PyPI', '2025.04'),
+    ('SciPy-bundle', '2025.06'),
+    ('networkx', '3.5'),
+    ('anndata', '0.12.3'),
+    ('matplotlib', '3.10.3'),
+    ('Seaborn', '0.13.2'),
+    ('h5py', '3.14.0'),
+    ('tqdm', '4.67.1'),
+    ('scikit-learn', '1.7.0'),
+    ('statsmodels', '0.14.5'),
+    ('numba', '0.62.0'),
+    ('umap-learn', '0.5.9.post2'),
 ]
 
 exts_list = [
-    ('natsort', '8.2.0', {
-        'checksums': ['57f85b72c688b09e053cdac302dd5b5b53df5f73ae20b4874fcbffd8bf783d11'],
-    }),
-    ('xlrd', '2.0.1', {
-        'checksums': ['f72f148f54442c6b056bf931dbc34f986fd0c3b0b6b5a58d013c9aef274d0c88'],
-    }),
-    ('anndata', '0.8.0', {
-        'checksums': ['94d2cc6f76c0317c0ac28564e3092b313b7ad19c737d66701961f3e620b9066e'],
-    }),
-    ('pynndescent', '0.5.8', {
-        'checksums': ['a7c552569bf604a101fd54bba1d27c12389e065945dee3a6777a518c63a46f2b'],
-    }),
-    ('umap-learn', '0.5.3', {
-        'modulename': 'umap',
-        'checksums': ['dbd57cb181c2b66d238acb5635697526bf24c798082daed0cf9b87f6a3a6c0c7'],
+    ('joblib', '1.5.2', {
+        'checksums': ['3faa5c39054b2f03ca547da9b2f52fde67c06240c31853f306aea97f13647b55'],
     }),
-    ('stdlib-list', '0.8.0', {
-        'checksums': ['a1e503719720d71e2ed70ed809b385c60cd3fb555ba7ec046b96360d30b16d9f'],
-    }),
-    ('sinfo', '0.3.4', {
-        'checksums': ['81ea91c69a875de178e10bada9476d7300a1f712e1823dbd7714f43a10baba4d'],
-    }),
-    ('session_info', '1.0.0', {
-        'checksums': ['3cda5e03cca703f32ae2eadbd6bd80b6c21442cfb60e412c21cb8ad6d5cbb6b7'],
+    ('session-info2', '0.2.3', {
+        'sources': ['session_info2-%(version)s.tar.gz'],
+        'checksums': ['6d16e3c6bb72ea52e589da4d722d24798aa3511c34ab8446a131d655cba2e2c9'],
     }),
     (name, version, {
-        'checksums': ['00c9a83b649da7e0171c91e9a08cff632102faa760614fd05cd4d1dbba4eb541'],
+        'checksums': ['333189ecac9c7009bf55d416ee2e272e1c490d54c719478f7b4dd1fc294d2f95'],
     }),
 ]
 
 sanity_check_paths = {
-    'files': ['bin/%s' % x for x in ['natsort', 'scanpy']],
+    'files': ['bin/scanpy'],
     'dirs': ['lib/python%(pyshortver)s/site-packages/'],
 }
 
-sanity_check_commands = [
-    "natsort --help",
-    "scanpy --help",
-]
-
 moduleclass = 'bio'

Updated software `umap-learn-0.5.9.post2-foss-2025a.eb`

Diff against umap-learn-0.5.7-foss-2024a.eb

easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.7-foss-2024a.eb

diff --git a/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.7-foss-2024a.eb b/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.9.post2-foss-2025a.eb
index 6ea82e0e49..1eeb905f39 100644
--- a/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.7-foss-2024a.eb
+++ b/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.9.post2-foss-2025a.eb
@@ -1,12 +1,12 @@
 # Author: Denis Krišťák (INUITS)
 # This is a contribution from HPCNow! (http://hpcnow.com)
 # Update: Erica Bianco <[email protected]>
-# Update: Petr Král (INUITS)
+# Update: Petr Král, Pavel Tomanek (INUITS)
 # License::     GPL-v3.0
 easyblock = "PythonBundle"
 
 name = 'umap-learn'
-version = '0.5.7'
+version = '0.5.9.post2'
 
 homepage = 'https://umap-learn.readthedocs.io/en/latest/'
 description = """
@@ -15,15 +15,16 @@ that can be used for visualisation similarly to t-SNE, but also for general non-
 dimension reduction.
 """
 
-toolchain = {'name': 'foss', 'version': '2024a'}
+toolchain = {'name': 'foss', 'version': '2025a'}
 
 dependencies = [
-    ('Python', '3.12.3'),
-    ('SciPy-bundle', '2024.05'),
-    ('scikit-learn', '1.5.2'),
-    ('numba', '0.60.0'),
-    ('LLVM', '18.1.8'),
-    ('tqdm', '4.66.5'),
+    ('Python', '3.13.1'),
+    ('Python-bundle-PyPI', '2025.04'),
+    ('SciPy-bundle', '2025.06'),
+    ('scikit-learn', '1.7.0'),
+    ('numba', '0.62.0'),
+    ('LLVM', '20.1.7'),
+    ('tqdm', '4.67.1'),
 ]
 
 exts_list = [
@@ -32,7 +33,8 @@ exts_list = [
     }),
     (name, version, {
         'modulename': 'umap',
-        'checksums': ['b2a97973e4c6ffcebf241100a8de589a4c84126a832ab40f296c6d9fcc5eb19e'],
+        'sources': ['umap_learn-%(version)s.tar.gz'],
+        'checksums': ['bdf60462d779bd074ce177a0714ced17e6d161285590fa487f3f9548dd3c31c9'],
     }),
 ]

Diff against umap-learn-0.5.7-foss-2023b.eb

easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.7-foss-2023b.eb

diff --git a/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.7-foss-2023b.eb b/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.9.post2-foss-2025a.eb
index 0a526feb43..1eeb905f39 100644
--- a/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.7-foss-2023b.eb
+++ b/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.9.post2-foss-2025a.eb
@@ -1,11 +1,12 @@
 # Author: Denis Krišťák (INUITS)
 # This is a contribution from HPCNow! (http://hpcnow.com)
-# Update: Erica Bianco <[email protected]>, Pavel Tomanek (INUITS)
+# Update: Erica Bianco <[email protected]>
+# Update: Petr Král, Pavel Tomanek (INUITS)
 # License::     GPL-v3.0
 easyblock = "PythonBundle"
 
 name = 'umap-learn'
-version = '0.5.7'
+version = '0.5.9.post2'
 
 homepage = 'https://umap-learn.readthedocs.io/en/latest/'
 description = """
@@ -14,15 +15,16 @@ that can be used for visualisation similarly to t-SNE, but also for general non-
 dimension reduction.
 """
 
-toolchain = {'name': 'foss', 'version': '2023b'}
+toolchain = {'name': 'foss', 'version': '2025a'}
 
 dependencies = [
-    ('Python', '3.11.5'),
-    ('SciPy-bundle', '2023.11'),
-    ('scikit-learn', '1.4.0'),
-    ('numba', '0.60.0'),
-    ('LLVM', '16.0.6'),
-    ('tqdm', '4.66.2'),
+    ('Python', '3.13.1'),
+    ('Python-bundle-PyPI', '2025.04'),
+    ('SciPy-bundle', '2025.06'),
+    ('scikit-learn', '1.7.0'),
+    ('numba', '0.62.0'),
+    ('LLVM', '20.1.7'),
+    ('tqdm', '4.67.1'),
 ]
 
 exts_list = [
@@ -31,7 +33,8 @@ exts_list = [
     }),
     (name, version, {
         'modulename': 'umap',
-        'checksums': ['b2a97973e4c6ffcebf241100a8de589a4c84126a832ab40f296c6d9fcc5eb19e'],
+        'sources': ['umap_learn-%(version)s.tar.gz'],
+        'checksums': ['bdf60462d779bd074ce177a0714ced17e6d161285590fa487f3f9548dd3c31c9'],
     }),
 ]

Diff against umap-learn-0.5.5-foss-2023a.eb

easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.5-foss-2023a.eb

diff --git a/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.5-foss-2023a.eb b/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.9.post2-foss-2025a.eb
index b79a615cb4..1eeb905f39 100644
--- a/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.5-foss-2023a.eb
+++ b/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.9.post2-foss-2025a.eb
@@ -1,11 +1,12 @@
 # Author: Denis Krišťák (INUITS)
 # This is a contribution from HPCNow! (http://hpcnow.com)
 # Update: Erica Bianco <[email protected]>
+# Update: Petr Král, Pavel Tomanek (INUITS)
 # License::     GPL-v3.0
 easyblock = "PythonBundle"
 
 name = 'umap-learn'
-version = '0.5.5'
+version = '0.5.9.post2'
 
 homepage = 'https://umap-learn.readthedocs.io/en/latest/'
 description = """
@@ -14,24 +15,26 @@ that can be used for visualisation similarly to t-SNE, but also for general non-
 dimension reduction.
 """
 
-toolchain = {'name': 'foss', 'version': '2023a'}
+toolchain = {'name': 'foss', 'version': '2025a'}
 
 dependencies = [
-    ('Python', '3.11.3'),
-    ('SciPy-bundle', '2023.07'),
-    ('scikit-learn', '1.3.1'),
-    ('numba', '0.58.1'),
-    ('LLVM', '16.0.6'),
-    ('tqdm', '4.66.1'),
+    ('Python', '3.13.1'),
+    ('Python-bundle-PyPI', '2025.04'),
+    ('SciPy-bundle', '2025.06'),
+    ('scikit-learn', '1.7.0'),
+    ('numba', '0.62.0'),
+    ('LLVM', '20.1.7'),
+    ('tqdm', '4.67.1'),
 ]
 
 exts_list = [
-    ('pynndescent', '0.5.11', {
-        'checksums': ['6f44ced9d5a9da2c87d9b2fff30bb5308540c0657605e4d5cde7ed3275bbad50'],
+    ('pynndescent', '0.5.13', {
+        'checksums': ['d74254c0ee0a1eeec84597d5fe89fedcf778593eeabe32c2f97412934a9800fb'],
     }),
     (name, version, {
         'modulename': 'umap',
-        'checksums': ['c54d607364413eade968b73ba07c8b3ea14412817f53cd07b6f720ac957293c4'],
+        'sources': ['umap_learn-%(version)s.tar.gz'],
+        'checksums': ['bdf60462d779bd074ce177a0714ced17e6d161285590fa487f3f9548dd3c31c9'],
     }),
 ]

pavelToman · 2025-10-17T13:21:52Z

Test report by @pavelToman
SUCCESS
Build succeeded for 7 out of 7 (6 easyconfigs in total)
node4002.donphan.os - Linux RHEL 9.6, x86_64, Intel(R) Xeon(R) Gold 6240 CPU @ 2.60GHz, 1 x NVIDIA NVIDIA A2, 580.82.07, Python 3.9.21
See https://gist.github.com/pavelToman/eb401736926a85b961f772943fcc8072 for a full test report.

pavelToman · 2025-10-17T13:38:12Z

@boegelbot please test @ jsc-zen3

boegelbot · 2025-10-17T13:40:10Z

@pavelToman: 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=24291 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_24291 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 8460

Test results coming soon (I hope)...

Details

- notification for comment with ID 3415664962 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 · 2025-10-17T13:56:43Z

Test report by @boegelbot
SUCCESS
Build succeeded for 6 out of 6 (6 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.6, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.21
See https://gist.github.com/boegelbot/9f639daba9859e3961ee76f3a5d42775 for a full test report.

boegel · 2025-10-20T08:42:46Z

@pavelToman Looks like #23729 will need a fair amount of work to get it merged, maybe it's better to flesh out the statsmodels easyconfig to a separate PR, so this PR can be unblocked?

pavelToman · 2025-10-20T09:56:39Z

@pavelToman Looks like #23729 will need a fair amount of work to get it merged, maybe it's better to flesh out the statsmodels easyconfig to a separate PR, so this PR can be unblocked?

It is ready:

{math}[gfbf/2025a] statsmodels v0.14.5 #24306

pavelToman · 2025-10-20T11:14:48Z

@boegelbot please test @ jsc-zen3

boegelbot · 2025-10-20T11:20:13Z

@pavelToman: 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=24291 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_24291 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 8487

Test results coming soon (I hope)...

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boegelbot · 2025-10-20T11:36:00Z

Test report by @boegelbot
SUCCESS
Build succeeded for 6 out of 6 (6 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.6, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.21
See https://gist.github.com/boegelbot/2735926f970c14bbb9c40af0ed5f55c7 for a full test report.

…asyconfigs into 20251017145902_new_pr_Palantir141

pavelToman · 2025-10-22T17:02:00Z

Test report by @pavelToman
SUCCESS
Build succeeded for 6 out of 6 (6 easyconfigs in total)
node4221.shinx.os - Linux RHEL 9.6, x86_64, AMD EPYC 9654 96-Core Processor, Python 3.9.21
See https://gist.github.com/pavelToman/b5e1a4076b55a6c3832defc86e73edbb for a full test report.

smoors

lgtm

smoors · 2025-12-11T21:55:19Z

Going in, thanks @pavelToman!

adding easyconfigs: Palantir-1.4.1-foss-2025a.eb, python-igraph-0.11.…

0e5b831

…9-foss-2025a.eb, igraph-0.10.17-foss-2025a.eb, scanpy-1.11.4-foss-2025a.eb, umap-learn-0.5.9.post2-foss-2025a.eb, anndata-0.12.3-foss-2025a.eb

pavelToman added new update labels Oct 17, 2025

pavelToman mentioned this pull request Oct 17, 2025

Palantir vscentrum/vsc-software-stack#606

Closed

pavelToman added the 2025a issues & PRs related to 2025a common toolchains label Oct 17, 2025

Merge branch 'develop' of https://github.com/easybuilders/easybuild-e…

faa2040

…asyconfigs into 20251017145902_new_pr_Palantir141

boegel added this to the next release (5.2.0?) milestone Nov 19, 2025

smoors approved these changes Dec 11, 2025

View reviewed changes

smoors merged commit 385b755 into easybuilders:develop Dec 11, 2025
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Updated software anndata-0.12.3-foss-2025a.eb

Updated software igraph-0.10.17-foss-2025a.eb

Updated software python-igraph-0.11.9-foss-2025a.eb

Updated software scanpy-1.11.4-foss-2025a.eb

Updated software umap-learn-0.5.9.post2-foss-2025a.eb

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Updated software `anndata-0.12.3-foss-2025a.eb`

Updated software `igraph-0.10.17-foss-2025a.eb`

Updated software `python-igraph-0.11.9-foss-2025a.eb`

Updated software `scanpy-1.11.4-foss-2025a.eb`

Updated software `umap-learn-0.5.9.post2-foss-2025a.eb`