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Patch numpy so that f2py processes object files#25082

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jfgrimm merged 3 commits intoeasybuilders:developfrom
JarneRenders:20260116150952_new_pr_SciPy-bundle202506
Jan 19, 2026
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Patch numpy so that f2py processes object files#25082
jfgrimm merged 3 commits intoeasybuilders:developfrom
JarneRenders:20260116150952_new_pr_SciPy-bundle202506

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@JarneRenders JarneRenders commented Jan 16, 2026 •
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(created using eb --new-pr)

When using Python >= 3.12, f2py will use the meson backend rather than distutils. This introduced some issues, in particular, object files passed on the f2py command line were not passed to meson. This breaks for example the build of MOKIT, which used to build fine in 2023a and earlier.

This is fixed in numpy 2.4.0 in numpy/numpy#29572. This applies that patch to numpy 2.3.1.

@github-actions github-actions Bot added 2025a issues & PRs related to 2025a common toolchains change labels Jan 16, 2026
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Thyre commented Jan 16, 2026

We should add the patch to the 2025b EasyConfigs as well, since they're using NumPy 2.3.2.

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Thyre commented Jan 16, 2026

@boegelbot please test @ jsc-zen3
EB_ARGS="--installpath=/tmp/$USER/ecpr-25082"

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boegelbot commented Jan 16, 2026

@Thyre: 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=25082 EB_ARGS="--installpath=/tmp/$USER/ecpr-25082" EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_25082 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

  • exit code: 0
  • output:
Submitted batch job 9410

Test results coming soon (I hope)...

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@github-actions github-actions Bot added the 2025b issues & PRs related to 2025b common toolchains label Jan 16, 2026
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boegelbot commented Jan 16, 2026

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (total: 56 mins 14 secs) (1 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.7, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.23
See https://gist.github.com/boegelbot/3cb3cd568c69e79214e013b394c547b2 for a full test report.

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Thyre commented Jan 16, 2026

@boegelbot please test @ jsc-zen3
EB_ARGS="--installpath=/tmp/$USER/ecpr-25082"

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boegelbot commented Jan 16, 2026

@Thyre: 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=25082 EB_ARGS="--installpath=/tmp/$USER/ecpr-25082" EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_25082 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

  • exit code: 0
  • output:
Submitted batch job 9411

Test results coming soon (I hope)...

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boegelbot commented Jan 16, 2026

Test report by @boegelbot
SUCCESS
Build succeeded for 4 out of 4 (total: 3 hours 45 mins 47 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 3.9.23
See https://gist.github.com/boegelbot/29784616a17fba55c23a3f43d8351087 for a full test report.

@boegel boegel added this to the next release (5.2.1?) milestone Jan 18, 2026
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boegel commented Jan 18, 2026

@boegelbot please test @ jsc-zen3
CORE_CNT=16

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boegelbot commented Jan 18, 2026

@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=25082 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_25082 --ntasks="16" ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

  • exit code: 0
  • output:
Submitted batch job 9412

Test results coming soon (I hope)...

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boegelbot commented Jan 18, 2026

Test report by @boegelbot
SUCCESS
Build succeeded for 4 out of 4 (total: 3 hours 32 mins 3 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 3.9.23
See https://gist.github.com/boegelbot/22a4807879b19dd5205db4f6bbca5421 for a full test report.

boegel
boegel approved these changes Jan 18, 2026
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lgtm

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boegel commented Jan 18, 2026

Test report by @boegel
SUCCESS
Build succeeded for 4 out of 4 (total: 3 hours 26 mins 24 secs) (4 easyconfigs in total)
node4247.shinx.os - Linux RHEL 9.6, x86_64, AMD EPYC 9654 96-Core Processor (zen4), Python 3.9.21
See https://gist.github.com/boegel/e158222204eaaa7c2ef608c0a56ff88d for a full test report.

@JarneRenders JarneRenders mentioned this pull request Jan 19, 2026
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jfgrimm commented Jan 19, 2026

Test report by @jfgrimm
SUCCESS
Build succeeded for 13 out of 13 (total: 4 hours 51 mins 8 secs) (4 easyconfigs in total)
node090.viking2.yor.alces.network - Linux Rocky Linux 8.10, x86_64, AMD EPYC 7643 48-Core Processor, Python 3.6.8
See https://gist.github.com/jfgrimm/ade008990c58e78378e327f3c1c41d32 for a full test report.

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jfgrimm commented Jan 19, 2026

Going in, thanks @JarneRenders!

@jfgrimm jfgrimm merged commit 8e1d244 into easybuilders:develop Jan 19, 2026
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@JarneRenders JarneRenders deleted the 20260116150952_new_pr_SciPy-bundle202506 branch January 19, 2026 16:16
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