{bio,lib}[GCCcore/14.2.0,foss/2025a] WhatsHap v2.6, python-isal v1.7.0 by JarneRenders · Pull Request #25892 · easybuilders/easybuild-easyconfigs

JarneRenders · 2026-04-30T08:58:05Z

(created using eb --new-pr)

…core-14.2.0.eb

github-actions · 2026-04-30T08:58:43Z

Updated software `python-isal-1.7.0-GCCcore-14.2.0.eb`

Diff against python-isal-1.7.0-GCCcore-14.3.0.eb

easybuild/easyconfigs/p/python-isal/python-isal-1.7.0-GCCcore-14.3.0.eb

diff --git a/easybuild/easyconfigs/p/python-isal/python-isal-1.7.0-GCCcore-14.3.0.eb b/easybuild/easyconfigs/p/python-isal/python-isal-1.7.0-GCCcore-14.2.0.eb
index af39ace8dc..1ca70d4f00 100644
--- a/easybuild/easyconfigs/p/python-isal/python-isal-1.7.0-GCCcore-14.3.0.eb
+++ b/easybuild/easyconfigs/p/python-isal/python-isal-1.7.0-GCCcore-14.2.0.eb
@@ -1,4 +1,4 @@
-easyblock = 'PythonPackage'
+easyblock = 'PythonBundle'
 
 name = 'python-isal'
 version = '1.7.0'
@@ -8,23 +8,23 @@ description = """Faster zlib and gzip compatible compression and decompression
  by providing python bindings for the isa-l library.
 """
 
-toolchain = {'name': 'GCCcore', 'version': '14.3.0'}
+toolchain = {'name': 'GCCcore', 'version': '14.2.0'}
 
 builddependencies = [
-    ('binutils', '2.44'),
-    ('versioningit', '3.3.0'),
+    ('binutils', '2.42'),
+    ('versioningit', '3.2.0'),
 ]
 dependencies = [
-    ('Python', '3.13.5'),
+    ('Python', '3.13.1'),
     ('ISA-L', '2.31.1'),
 ]
 
-source_urls = [PYPI_SOURCE.replace('%(name)s', 'isal')]
-sources = ['isal-%(version)s.tar.gz']
-checksums = ['9eb9457ed27fd0a8a7b403a5f4f9e6c8d1a44c2ca28ecd2f2bf3aed90b0a74bf']
-
-preinstallopts = 'PYTHON_ISAL_LINK_DYNAMIC=true'
-
-options = {'modulename': 'isal'}
+exts_list = [
+    ('isal', version, {
+        'sources': [SOURCE_TAR_GZ],
+        'preinstallopts': 'PYTHON_ISAL_LINK_DYNAMIC=true',
+        'checksums': ['9eb9457ed27fd0a8a7b403a5f4f9e6c8d1a44c2ca28ecd2f2bf3aed90b0a74bf'],
+    })
+]
 
 moduleclass = 'lib'

Diff against python-isal-1.8.0-GCCcore-14.3.0.eb

easybuild/easyconfigs/p/python-isal/python-isal-1.8.0-GCCcore-14.3.0.eb

diff --git a/easybuild/easyconfigs/p/python-isal/python-isal-1.8.0-GCCcore-14.3.0.eb b/easybuild/easyconfigs/p/python-isal/python-isal-1.7.0-GCCcore-14.2.0.eb
index abc1b801f9..1ca70d4f00 100644
--- a/easybuild/easyconfigs/p/python-isal/python-isal-1.8.0-GCCcore-14.3.0.eb
+++ b/easybuild/easyconfigs/p/python-isal/python-isal-1.7.0-GCCcore-14.2.0.eb
@@ -1,30 +1,30 @@
-easyblock = 'PythonPackage'
+easyblock = 'PythonBundle'
 
 name = 'python-isal'
-version = '1.8.0'
+version = '1.7.0'
 
 homepage = 'https://github.com/pycompression/python-isal'
 description = """Faster zlib and gzip compatible compression and decompression
  by providing python bindings for the isa-l library.
 """
 
-toolchain = {'name': 'GCCcore', 'version': '14.3.0'}
+toolchain = {'name': 'GCCcore', 'version': '14.2.0'}
 
 builddependencies = [
-    ('binutils', '2.44'),
-    ('versioningit', '3.3.0'),
+    ('binutils', '2.42'),
+    ('versioningit', '3.2.0'),
 ]
 dependencies = [
-    ('Python', '3.13.5'),
+    ('Python', '3.13.1'),
     ('ISA-L', '2.31.1'),
 ]
 
-source_urls = [PYPI_SOURCE.replace('%(name)s', 'isal')]
-sources = ['isal-%(version)s.tar.gz']
-checksums = ['124233e9a31a62030a07aafd48c26689561926f4e10417ed3ea46c211218f2b4']
-
-preinstallopts = 'PYTHON_ISAL_LINK_DYNAMIC=true'
-
-options = {'modulename': 'isal'}
+exts_list = [
+    ('isal', version, {
+        'sources': [SOURCE_TAR_GZ],
+        'preinstallopts': 'PYTHON_ISAL_LINK_DYNAMIC=true',
+        'checksums': ['9eb9457ed27fd0a8a7b403a5f4f9e6c8d1a44c2ca28ecd2f2bf3aed90b0a74bf'],
+    })
+]
 
 moduleclass = 'lib'

Diff against python-isal-1.6.1-GCCcore-12.3.0.eb

easybuild/easyconfigs/p/python-isal/python-isal-1.6.1-GCCcore-12.3.0.eb

diff --git a/easybuild/easyconfigs/p/python-isal/python-isal-1.6.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/python-isal/python-isal-1.7.0-GCCcore-14.2.0.eb
index fe09eeeaec..1ca70d4f00 100644
--- a/easybuild/easyconfigs/p/python-isal/python-isal-1.6.1-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/p/python-isal/python-isal-1.7.0-GCCcore-14.2.0.eb
@@ -1,29 +1,30 @@
-# Author: Jasper Grimm (UoY)
-
-easyblock = 'PythonPackage'
+easyblock = 'PythonBundle'
 
 name = 'python-isal'
-version = '1.6.1'
+version = '1.7.0'
 
 homepage = 'https://github.com/pycompression/python-isal'
 description = """Faster zlib and gzip compatible compression and decompression
  by providing python bindings for the isa-l library.
 """
 
-toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+toolchain = {'name': 'GCCcore', 'version': '14.2.0'}
 
-builddependencies = [('binutils', '2.40')]
+builddependencies = [
+    ('binutils', '2.42'),
+    ('versioningit', '3.2.0'),
+]
 dependencies = [
-    ('Python', '3.11.3'),
-    ('ISA-L', '2.30.0'),
+    ('Python', '3.13.1'),
+    ('ISA-L', '2.31.1'),
 ]
 
-source_urls = [PYPI_SOURCE.replace('%(name)s', 'isal')]
-sources = ['isal-%s.tar.gz' % version]
-checksums = ['7b64b75d260b544beea3f59cb25a6f520c04768818ef4ac316ee9a1f2ebf18f5']
-
-preinstallopts = 'PYTHON_ISAL_LINK_DYNAMIC=true'
-
-options = {'modulename': 'isal'}
+exts_list = [
+    ('isal', version, {
+        'sources': [SOURCE_TAR_GZ],
+        'preinstallopts': 'PYTHON_ISAL_LINK_DYNAMIC=true',
+        'checksums': ['9eb9457ed27fd0a8a7b403a5f4f9e6c8d1a44c2ca28ecd2f2bf3aed90b0a74bf'],
+    })
+]
 
 moduleclass = 'lib'

Updated software `WhatsHap-2.6-foss-2025a.eb`

Diff against WhatsHap-2.6-foss-2024a.eb

easybuild/easyconfigs/w/WhatsHap/WhatsHap-2.6-foss-2024a.eb

diff --git a/easybuild/easyconfigs/w/WhatsHap/WhatsHap-2.6-foss-2024a.eb b/easybuild/easyconfigs/w/WhatsHap/WhatsHap-2.6-foss-2025a.eb
index b4a69e99ea..ad3a2d856b 100644
--- a/easybuild/easyconfigs/w/WhatsHap/WhatsHap-2.6-foss-2024a.eb
+++ b/easybuild/easyconfigs/w/WhatsHap/WhatsHap-2.6-foss-2025a.eb
@@ -8,22 +8,25 @@ description = """WhatsHap is a software for phasing genomic variants using DNA
 sequencing reads, also called read-based phasing or haplotype assembly. It is
 especially suitable for long reads, but works also well with short reads."""
 
-toolchain = {'name': 'foss', 'version': '2024a'}
+toolchain = {'name': 'foss', 'version': '2025a'}
 
 builddependencies = [
-    ('hatchling', '1.24.2'),
-    ('Cython', '3.0.10')]
+    ('hatchling', '1.27.0'),
+    ('Cython', '3.1.1'),
+    ('setuptools', '80.9.0'),
+]
 
 dependencies = [
-    ('Python', '3.12.3'),
-    ('Pysam', '0.22.1'),
-    ('networkx', '3.4.2'),
-    ('SciPy-bundle', '2024.05'),
-    ('Biopython', '1.84'),
+    ('Python', '3.13.1'),
+    ('Pysam', '0.23.3'),
+    ('networkx', '3.5'),
+    ('SciPy-bundle', '2025.06'),
+    ('Biopython', '1.85'),
     ('Yasm', '1.3.0'),
-    ('pyfaidx', '0.8.1.2'),
+    ('pyfaidx', '0.9.0.3'),
     ('python-isal', '1.7.0'),
-    ('zlib-ng', '2.2.1'),
+    ('zlib-ng', '2.2.4'),
+    ('PuLP', '3.3.0'),
 ]
 
 
@@ -32,17 +35,8 @@ exts_list = [
         'source_tmpl': SOURCE_PY3_WHL,
         'checksums': ['74e7f7fb7e7f42bd843c798595fa5a52086d7d1bf3de0e8513c6615516431313'],
     }),
-    ('PuLP', '3.1.1', {
-        'source_tmpl': SOURCELOWER_PY3_WHL,
-        'checksums': ['ad9d46afaf78a708270a2fa9b38e56536584c048dfbd7a6dbc719abee1051261'],
-    }),
     ('whatshap', version, {
-        'patches': ['remove_license_from_pythonproj.patch'],
-        'checksums': [
-            {'whatshap-2.6.tar.gz': 'd17f2840c51d11b2e40772805ecfb4bc611e4f0a0736c91bd5d66b694a6d116c'},
-            {'remove_license_from_pythonproj.patch':
-             '351fc96f6a71c6e72d5a17ac74244cc84282dea4763fd4383c6e06081904adf3'},
-        ],
+        'checksums': ['d17f2840c51d11b2e40772805ecfb4bc611e4f0a0736c91bd5d66b694a6d116c'],
     }),
 ]

Diff against WhatsHap-2.2-foss-2023a.eb

easybuild/easyconfigs/w/WhatsHap/WhatsHap-2.2-foss-2023a.eb

diff --git a/easybuild/easyconfigs/w/WhatsHap/WhatsHap-2.2-foss-2023a.eb b/easybuild/easyconfigs/w/WhatsHap/WhatsHap-2.6-foss-2025a.eb
index f912fbaa64..ad3a2d856b 100644
--- a/easybuild/easyconfigs/w/WhatsHap/WhatsHap-2.2-foss-2023a.eb
+++ b/easybuild/easyconfigs/w/WhatsHap/WhatsHap-2.6-foss-2025a.eb
@@ -1,40 +1,42 @@
 easyblock = 'PythonBundle'
 
 name = 'WhatsHap'
-version = '2.2'
+version = '2.6'
 
 homepage = 'https://whatshap.readthedocs.io'
 description = """WhatsHap is a software for phasing genomic variants using DNA
 sequencing reads, also called read-based phasing or haplotype assembly. It is
 especially suitable for long reads, but works also well with short reads."""
 
-toolchain = {'name': 'foss', 'version': '2023a'}
+toolchain = {'name': 'foss', 'version': '2025a'}
 
-builddependencies = [('hatchling', '1.18.0')]
+builddependencies = [
+    ('hatchling', '1.27.0'),
+    ('Cython', '3.1.1'),
+    ('setuptools', '80.9.0'),
+]
 
 dependencies = [
-    ('Python', '3.11.3'),
-    ('Pysam', '0.22.0'),
-    ('networkx', '3.1'),
-    ('SciPy-bundle', '2023.07'),
-    ('Biopython', '1.83'),
+    ('Python', '3.13.1'),
+    ('Pysam', '0.23.3'),
+    ('networkx', '3.5'),
+    ('SciPy-bundle', '2025.06'),
+    ('Biopython', '1.85'),
     ('Yasm', '1.3.0'),
-    ('pyfaidx', '0.8.1.1'),
-    ('python-isal', '1.1.0'),
+    ('pyfaidx', '0.9.0.3'),
+    ('python-isal', '1.7.0'),
+    ('zlib-ng', '2.2.4'),
+    ('PuLP', '3.3.0'),
 ]
 
 
 exts_list = [
-    ('xopen', '1.7.0', {
-        'source_tmpl': SOURCE_PY3_WHL,
-        'checksums': ['c4c6c978bb5f6f2a4364438da09f4f8fde078b6df4de18e3f72fccc472d1ee33'],
-    }),
-    ('PuLP', '2.8.0', {
+    ('xopen', '2.0.2', {
         'source_tmpl': SOURCE_PY3_WHL,
-        'checksums': ['4a19814a5b0a4392d788ac2315263435293579b0583c3469943fe0c6a586f263'],
+        'checksums': ['74e7f7fb7e7f42bd843c798595fa5a52086d7d1bf3de0e8513c6615516431313'],
     }),
     ('whatshap', version, {
-        'checksums': ['4cd34e9b82930c4f42e9e6b7dce2e321e4c81f934fdb980b6093ad91a06ae30a'],
+        'checksums': ['d17f2840c51d11b2e40772805ecfb4bc611e4f0a0736c91bd5d66b694a6d116c'],
     }),
 ]

Diff against WhatsHap-2.1-foss-2022b.eb

easybuild/easyconfigs/w/WhatsHap/WhatsHap-2.1-foss-2022b.eb

diff --git a/easybuild/easyconfigs/w/WhatsHap/WhatsHap-2.1-foss-2022b.eb b/easybuild/easyconfigs/w/WhatsHap/WhatsHap-2.6-foss-2025a.eb
index 071c16ba06..ad3a2d856b 100644
--- a/easybuild/easyconfigs/w/WhatsHap/WhatsHap-2.1-foss-2022b.eb
+++ b/easybuild/easyconfigs/w/WhatsHap/WhatsHap-2.6-foss-2025a.eb
@@ -1,43 +1,42 @@
-# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
-
 easyblock = 'PythonBundle'
 
 name = 'WhatsHap'
-version = '2.1'
+version = '2.6'
 
 homepage = 'https://whatshap.readthedocs.io'
 description = """WhatsHap is a software for phasing genomic variants using DNA
 sequencing reads, also called read-based phasing or haplotype assembly. It is
 especially suitable for long reads, but works also well with short reads."""
 
-toolchain = {'name': 'foss', 'version': '2022b'}
+toolchain = {'name': 'foss', 'version': '2025a'}
+
+builddependencies = [
+    ('hatchling', '1.27.0'),
+    ('Cython', '3.1.1'),
+    ('setuptools', '80.9.0'),
+]
 
 dependencies = [
-    ('Python', '3.10.8'),
-    ('Pysam', '0.21.0'),
-    ('networkx', '3.0'),
-    ('SciPy-bundle', '2023.02'),
-    ('Biopython', '1.81'),
+    ('Python', '3.13.1'),
+    ('Pysam', '0.23.3'),
+    ('networkx', '3.5'),
+    ('SciPy-bundle', '2025.06'),
+    ('Biopython', '1.85'),
     ('Yasm', '1.3.0'),
-    ('pyfaidx', '0.7.2.1'),
-    ('python-isal', '1.1.0'),
+    ('pyfaidx', '0.9.0.3'),
+    ('python-isal', '1.7.0'),
+    ('zlib-ng', '2.2.4'),
+    ('PuLP', '3.3.0'),
 ]
 
+
 exts_list = [
-    ('xopen', '1.7.0', {
-        'preinstallopts': """sed -i -e 's/^dynamic = \\["version"\\]/version = "%(version)s"/' """ +
-                          "%(start_dir)s/pyproject.toml && ",
-        'checksums': ['901f9c8298e95ed74767a4bd76d9f4cf71d8de27b8cf296ac3e7bc1c11520d9f'],
-    }),
-    ('pulp', '2.8.0', {
-        'source_tmpl': 'PuLP-%(version)s.tar.gz',
-        'checksums': ['4903bf96110bbab8ed2c68533f90565ebb76aa367d9e4df38e51bf727927c125'],
+    ('xopen', '2.0.2', {
+        'source_tmpl': SOURCE_PY3_WHL,
+        'checksums': ['74e7f7fb7e7f42bd843c798595fa5a52086d7d1bf3de0e8513c6615516431313'],
     }),
-    (name, version, {
-        'preinstallopts': """sed -i -e 's/^dynamic = \\["version",/version = "%(version)s"\\ndynamic = \\[/' """ +
-                          "%(start_dir)s/pyproject.toml && ",
-        'source_tmpl': '%(namelower)s-%(version)s.tar.gz',
-        'checksums': ['9b61812eda1dd5251ba8d02db16d7ddda152ccc813cb3db6a1ec796f1865fe8d'],
+    ('whatshap', version, {
+        'checksums': ['d17f2840c51d11b2e40772805ecfb4bc611e4f0a0736c91bd5d66b694a6d116c'],
     }),
 ]

JarneRenders · 2026-04-30T11:46:21Z

Pip list check failing cause python-isal != isal.

Test report by @JarneRenders
FAILED
Build succeeded for 0 out of 2 (total: 1 min 35 secs) (2 easyconfigs in total)
node511.anansi.os - Linux Rocky Linux 9.7 (Blue Onyx), x86_64, AMD EPYC 9335 32-Core Processor, Python 3.9.25
See https://gist.github.com/JarneRenders/1d71719d9ed20b1cd9b47dfb86e0fb4f for a full test report.

JarneRenders · 2026-04-30T12:32:32Z

Test report by @JarneRenders
SUCCESS
Build succeeded for 2 out of 2 (total: 2 mins 31 secs) (2 easyconfigs in total)
node511.anansi.os - Linux Rocky Linux 9.7 (Blue Onyx), x86_64, AMD EPYC 9335 32-Core Processor, Python 3.9.25
See https://gist.github.com/JarneRenders/f34f173f10c5e6f4ddd4dba68c9f7184 for a full test report.

verdurin · 2026-05-01T17:23:01Z

Test report by @verdurin
SUCCESS
Build succeeded for 16 out of 16 (total: 25 mins 24 secs) (2 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/5b1d4bed8a9bebbceb60f8887d2d66bf for a full test report.

verdurin · 2026-05-05T07:48:11Z

@boegelbot please test @ jsc-zen3

boegelbot · 2026-05-05T07:50:09Z

@verdurin: 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=25892 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_25892 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 10349

Test results coming soon (I hope)...

Details

- notification for comment with ID 4377420479 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 · 2026-05-05T07:55:48Z

Test report by @boegelbot
SUCCESS
Build succeeded for 2 out of 2 (total: 5 mins 24 secs) (2 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/da07e139a0cfdfa7d500db38c5b75a40 for a full test report.

verdurin · 2026-05-05T09:21:28Z

@JarneRenders could you put a comment here explaining the removal of the patch in WhatsHap?

JarneRenders · 2026-05-05T14:52:16Z

That patch was used to fix the "project.license must be valid exactly by one definition" error when using an older setuptools. Since a newer setuptools is added as a build dependency here the pyproject.toml file gets parsed correctly in this form.

adding easyconfigs: WhatsHap-2.6-foss-2025a.eb, python-isal-1.7.0-GCC…

388fb74

…core-14.2.0.eb

github-actions Bot added 2025a issues & PRs related to 2025a common toolchains update labels Apr 30, 2026

JarneRenders mentioned this pull request Apr 30, 2026

{bio}[foss/2025a] medaka v2.2.1 w/ CUDA 12.8.0 #25895

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{bio,lib}[GCCcore/14.2.0,foss/2025a] WhatsHap v2.6, python-isal v1.7.0#25892

{bio,lib}[GCCcore/14.2.0,foss/2025a] WhatsHap v2.6, python-isal v1.7.0#25892
JarneRenders wants to merge 2 commits intoeasybuilders:developfrom
JarneRenders:20260430105800_new_pr_WhatsHap26

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Updated software python-isal-1.7.0-GCCcore-14.2.0.eb

Updated software WhatsHap-2.6-foss-2025a.eb

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Updated software `python-isal-1.7.0-GCCcore-14.2.0.eb`

Updated software `WhatsHap-2.6-foss-2025a.eb`

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