{data}[foss/2025a] netcdf4-python v1.7.2 by pavelToman · Pull Request #23350 · easybuilders/easybuild-easyconfigs

pavelToman · 2025-07-08T14:29:13Z

(created using eb --new-pr)
resolves vscentrum/vsc-software-stack#578
requires:

netCDF from: {lib}[GCCcore/14.2.0] GDAL v3.11.1, LERC v4.0.0, Brunsli v0.1, ... #23349

github-actions · 2025-07-08T14:29:45Z

Updated software `netcdf4-python-1.7.2-foss-2025a.eb`

Diff against netcdf4-python-1.7.1.post2-foss-2023b.eb

easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.7.1.post2-foss-2023b.eb

diff --git a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.7.1.post2-foss-2023b.eb b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.7.2-foss-2025a.eb
index fb452757a0..cc29eb5cf5 100644
--- a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.7.1.post2-foss-2023b.eb
+++ b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.7.2-foss-2025a.eb
@@ -1,35 +1,39 @@
 easyblock = 'PythonBundle'
 
 name = 'netcdf4-python'
-version = '1.7.1.post2'
+version = '1.7.2'
 
 homepage = 'https://unidata.github.io/netcdf4-python/'
-description = """Python/numpy interface to netCDF."""
+description = "Python/numpy interface to netCDF."
 
-toolchain = {'name': 'foss', 'version': '2023b'}
+toolchain = {'name': 'foss', 'version': '2025a'}
 toolchainopts = {'usempi': True}
 
+builddependencies = [
+    ('Cython', '3.1.1'),
+]
+
 dependencies = [
-    ('Python', '3.11.5'),
-    ('SciPy-bundle', '2023.11'),
-    ('netCDF', '4.9.2'),
-    ('cURL', '8.3.0'),
-    ('mpi4py', '3.1.5'),
+    ('Python', '3.13.1'),
+    ('SciPy-bundle', '2025.06'),
+    ('netCDF', '4.9.3'),
+    ('cURL', '8.11.1'),
+    ('mpi4py', '4.1.0'),
 ]
 
+fix_python_shebang_for = ['bin/*']
+
 exts_list = [
-    ('cftime', '1.6.4', {
-        'checksums': ['e325406193758a7ed67308deb52e727782a19e384e183378e7ff62098be0aedc'],
+    ('cftime', '1.6.4.post1', {
+        'checksums': ['50ac76cc9f10ab7bd46e44a71c51a6927051b499b4407df4f29ab13d741b942f'],
     }),
     (name, version, {
         'source_tmpl': 'netcdf4-%(version)s.tar.gz',
         'source_urls': ['https://pypi.python.org/packages/source/n/netCDF4'],
-        'checksums': ['37d557e36654889d7020192bfb56f9d5f93894cb32997eb837ae586c538fd7b6'],
+        'checksums': ['a4c6375540b19989896136943abb6d44850ff6f1fa7d3f063253b1ad3f8b7fce'],
     }),
 ]
 
-fix_python_shebang_for = ['bin/*']
-
 sanity_check_paths = {
     'files': ['bin/nc3tonc4', 'bin/nc4tonc3', 'bin/ncinfo'],
     'dirs': ['lib/python%(pyshortver)s/site-packages'],

Diff against netcdf4-python-1.7.1.post2-foss-2024a.eb

easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.7.1.post2-foss-2024a.eb

diff --git a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.7.1.post2-foss-2024a.eb b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.7.2-foss-2025a.eb
index 344d1e0852..cc29eb5cf5 100644
--- a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.7.1.post2-foss-2024a.eb
+++ b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.7.2-foss-2025a.eb
@@ -1,43 +1,36 @@
 easyblock = 'PythonBundle'
 
 name = 'netcdf4-python'
-version = '1.7.1.post2'
+version = '1.7.2'
 
 homepage = 'https://unidata.github.io/netcdf4-python/'
 description = "Python/numpy interface to netCDF."
 
-toolchain = {'name': 'foss', 'version': '2024a'}
+toolchain = {'name': 'foss', 'version': '2025a'}
 toolchainopts = {'usempi': True}
 
 builddependencies = [
-    ('Cython', '3.0.10'),
+    ('Cython', '3.1.1'),
 ]
 
 dependencies = [
-    ('Python', '3.12.3'),
-    ('SciPy-bundle', '2024.05'),
-    ('netCDF', '4.9.2'),
-    ('cURL', '8.7.1'),
-    ('mpi4py', '4.0.1'),
+    ('Python', '3.13.1'),
+    ('SciPy-bundle', '2025.06'),
+    ('netCDF', '4.9.3'),
+    ('cURL', '8.11.1'),
+    ('mpi4py', '4.1.0'),
 ]
 
 fix_python_shebang_for = ['bin/*']
 
 exts_list = [
-    ('cftime', '1.6.4', {
-        'checksums': ['e325406193758a7ed67308deb52e727782a19e384e183378e7ff62098be0aedc'],
+    ('cftime', '1.6.4.post1', {
+        'checksums': ['50ac76cc9f10ab7bd46e44a71c51a6927051b499b4407df4f29ab13d741b942f'],
     }),
     (name, version, {
-        'patches': [
-            'netcdf4-python-1.7.1.post2_relax_tolerance_compression_test.patch',
-        ],
         'source_tmpl': 'netcdf4-%(version)s.tar.gz',
         'source_urls': ['https://pypi.python.org/packages/source/n/netCDF4'],
-        'checksums': [
-            {'netcdf4-1.7.1.post2.tar.gz': '37d557e36654889d7020192bfb56f9d5f93894cb32997eb837ae586c538fd7b6'},
-            {'netcdf4-python-1.7.1.post2_relax_tolerance_compression_test.patch':
-             '7faa7e839ad1e816ffd0153e4b76b43ebce3e14d35f0534f812168dfaa78316c'},
-        ],
+        'checksums': ['a4c6375540b19989896136943abb6d44850ff6f1fa7d3f063253b1ad3f8b7fce'],
     }),
 ]

Diff against netcdf4-python-1.6.5-foss-2023b.eb

easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.6.5-foss-2023b.eb

diff --git a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.6.5-foss-2023b.eb b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.7.2-foss-2025a.eb
index 895ea1f59d..cc29eb5cf5 100644
--- a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.6.5-foss-2023b.eb
+++ b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.7.2-foss-2025a.eb
@@ -1,45 +1,39 @@
 easyblock = 'PythonBundle'
 
 name = 'netcdf4-python'
-version = '1.6.5'
+version = '1.7.2'
 
 homepage = 'https://unidata.github.io/netcdf4-python/'
-description = """Python/numpy interface to netCDF."""
+description = "Python/numpy interface to netCDF."
 
-toolchain = {'name': 'foss', 'version': '2023b'}
+toolchain = {'name': 'foss', 'version': '2025a'}
 toolchainopts = {'usempi': True}
 
+builddependencies = [
+    ('Cython', '3.1.1'),
+]
+
 dependencies = [
-    ('Python', '3.11.5'),
-    ('SciPy-bundle', '2023.11'),
-    ('netCDF', '4.9.2'),
-    ('cURL', '8.3.0'),
-    ('mpi4py', '3.1.5'),
+    ('Python', '3.13.1'),
+    ('SciPy-bundle', '2025.06'),
+    ('netCDF', '4.9.3'),
+    ('cURL', '8.11.1'),
+    ('mpi4py', '4.1.0'),
 ]
 
+fix_python_shebang_for = ['bin/*']
+
 exts_list = [
-    ('cftime', '1.6.2', {
-        'checksums': ['8614c00fb8a5046de304fdd86dbd224f99408185d7b245ac6628d0276596e6d2'],
+    ('cftime', '1.6.4.post1', {
+        'checksums': ['50ac76cc9f10ab7bd46e44a71c51a6927051b499b4407df4f29ab13d741b942f'],
     }),
     (name, version, {
-        'patches': [
-            'netcdf4-python-1.1.8-avoid-diskless-test.patch',
-            'netcdf4-python-1.6.1_relax_tolerance_compression_test.patch',
-        ],
-        'source_tmpl': 'netCDF4-%(version)s.tar.gz',
+        'source_tmpl': 'netcdf4-%(version)s.tar.gz',
         'source_urls': ['https://pypi.python.org/packages/source/n/netCDF4'],
-        'checksums': [
-            {'netCDF4-1.6.5.tar.gz': '824881d0aacfde5bd982d6adedd8574259c85553781e7b83e0ce82b890bfa0ef'},
-            {'netcdf4-python-1.1.8-avoid-diskless-test.patch':
-             'a8b262fa201d55f59015e1bc14466c1d113f807543bc1e05a22481ab0d216d72'},
-            {'netcdf4-python-1.6.1_relax_tolerance_compression_test.patch':
-             '64d192a5d1e3e00af78f053da78f5a35015fa713c7f97b10b622be6a44347166'},
-        ],
+        'checksums': ['a4c6375540b19989896136943abb6d44850ff6f1fa7d3f063253b1ad3f8b7fce'],
     }),
 ]
 
-fix_python_shebang_for = ['bin/*']
-
 sanity_check_paths = {
     'files': ['bin/nc3tonc4', 'bin/nc4tonc3', 'bin/ncinfo'],
     'dirs': ['lib/python%(pyshortver)s/site-packages'],

pavelToman · 2025-07-08T14:36:32Z

Test report by @pavelToman
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
node4201.shinx.os - Linux RHEL 9.4, x86_64, AMD EPYC 9654 96-Core Processor, Python 3.9.18
See https://gist.github.com/pavelToman/b0fd54dd5b1d6ef5f2c47c3391920044 for a full test report.

pavelToman · 2025-07-09T08:08:33Z

Test report by @pavelToman
SUCCESS
Build succeeded for 2 out of 2 (1 easyconfigs in total)
node4010.donphan.os - Linux RHEL 9.4, x86_64, Intel(R) Xeon(R) Gold 6240 CPU @ 2.60GHz, 1 x NVIDIA NVIDIA A2, 570.133.20, Python 3.9.18
See https://gist.github.com/pavelToman/81bc1ff866c2d1769e7c5e3513c9619c for a full test report.

…asyconfigs into 20250708162910_new_pr_netcdf4-python172

branfosj · 2025-07-18T13:33:26Z

@boegelbot please test @ jsc-zen3

laraPPr · 2025-07-18T13:35:00Z

Test report by @laraPPr
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
node3537.doduo.os - Linux RHEL 9.4 (Plow), x86_64, AMD EPYC 7552 48-Core Processor, Python 3.9.18
See https://gist.github.com/laraPPr/f202347e6cc649e94751daf348bae387 for a full test report.

laraPPr

lgtm

boegelbot · 2025-07-18T13:40:10Z

@branfosj: 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=23350 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_23350 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 7289

Test results coming soon (I hope)...

Details

- notification for comment with ID 3089501479 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 · 2025-07-18T13:44:58Z

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.5, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.21
See https://gist.github.com/boegelbot/65fea0f7903972f2870b71c25fb36444 for a full test report.

laraPPr · 2025-07-18T14:02:31Z

Going in, thanks @pavelToman!

adding easyconfigs: netcdf4-python-1.7.2-foss-2025a.eb

fc1c46b

pavelToman added the update label Jul 8, 2025

pavelToman mentioned this pull request Jul 8, 2025

updated of Python packages on top of Python 3.13 for courses (Py4Sci) vscentrum/vsc-software-stack#578

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pavelToman mentioned this pull request Jul 10, 2025

{lib}[GCCcore/14.2.0] MDTraj v1.11.0 #23381

Merged

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

af170be

…asyconfigs into 20250708162910_new_pr_netcdf4-python172

laraPPr approved these changes Jul 18, 2025

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laraPPr added this to the 5.x milestone Jul 18, 2025

laraPPr merged commit 8e74f89 into easybuilders:develop Jul 18, 2025
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laraPPr modified the milestones: 5.x, release after 5.1.1 Jul 18, 2025

pavelToman mentioned this pull request Jul 21, 2025

{chem}[foss/2025a] AmberTools v25.2 #23420

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{vis}[foss/2025b] yt v4.4.1 #24134

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{data}[foss/2025a] netcdf4-python v1.7.2#23350

{data}[foss/2025a] netcdf4-python v1.7.2#23350
laraPPr merged 2 commits intoeasybuilders:developfrom
pavelToman:20250708162910_new_pr_netcdf4-python172

pavelToman commented Jul 8, 2025 •

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Updated software netcdf4-python-1.7.2-foss-2025a.eb

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pavelToman commented Jul 8, 2025 •

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Updated software `netcdf4-python-1.7.2-foss-2025a.eb`