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{bio}[foss/2023a] Cellformer v20240917 w/ R 4.3.2#21621

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PetrKralCZ:20241011161625_new_pr_Cellformer20240917
Oct 17, 2024
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{bio}[foss/2023a] Cellformer v20240917 w/ R 4.3.2#21621
boegel merged 4 commits intoeasybuilders:developfrom
PetrKralCZ:20241011161625_new_pr_Cellformer20240917

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@PetrKralCZ PetrKralCZ commented Oct 11, 2024 •
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(created using eb --new-pr)
resolves vscentrum/vsc-software-stack#395

@PetrKralCZ PetrKralCZ added the new label Oct 11, 2024
@PetrKralCZ PetrKralCZ mentioned this pull request Oct 11, 2024
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PetrKralCZ commented Oct 11, 2024

@boegelbot please test @ generoso

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boegelbot commented Oct 11, 2024

@PetrKralCZ: Request for testing this PR well received on login1

PR test command 'EB_PR=21621 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_21621 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

  • exit code: 0
  • output:
Submitted batch job 14455

Test results coming soon (I hope)...

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boegelbot commented Oct 11, 2024

Test report by @boegelbot
FAILED
Build succeeded for 0 out of 1 (1 easyconfigs in total)
cns1 - Linux Rocky Linux 8.9, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/boegelbot/4c8956e308320b6a0c7bdf14a30cc6b1 for a full test report.

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PetrKralCZ commented Oct 11, 2024

@boegelbot please test @ generoso

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boegelbot commented Oct 11, 2024

@PetrKralCZ: Request for testing this PR well received on login1

PR test command 'EB_PR=21621 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_21621 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

  • exit code: 0
  • output:
Submitted batch job 14458

Test results coming soon (I hope)...

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boegelbot commented Oct 11, 2024

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
cns1 - Linux Rocky Linux 8.9, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/boegelbot/803b0289e87750fadc8592cc827a268d for a full test report.

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PetrKralCZ commented Oct 11, 2024

@boegelbot please test @ jsc-zen3

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boegelbot commented Oct 11, 2024

@PetrKralCZ: 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=21621 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_21621 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

  • exit code: 0
  • output:
Submitted batch job 5067

Test results coming soon (I hope)...

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boegelbot commented Oct 11, 2024

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 9.4, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.18
See https://gist.github.com/boegelbot/c79d62dfea4ebb00842203032e5f3011 for a full test report.

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boegel approved these changes Oct 15, 2024
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lgtm

@boegel boegel added this to the release after 4.9.4 milestone Oct 15, 2024
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Comment thread easybuild/easyconfigs/c/Cellformer/Cellformer-20240917-foss-2023a-R-4.3.2.eb Outdated
}

exts_list = [
('typing_extensions', '4.12.2', {
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There should be no need for this, since typing-extensions is already a dependency?

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@PetrKralCZ Just for sanity's sake: in your test environment, the scanpy/1.9.8-foss-2023a module is still loading hatchling/1.18.0-GCCcore-12.3.0 as a runtime dependency, which includes typing-extensions 4.6.3 as an extension. That's wrong, hatchling should only ever be a build dependency...

The same goes for the scanpy module in my test environment, but there's another difference that affects the order of $PYTHONPATH: in my test environment the pydantic/1.10.13-GCCcore-12.3.0 module is old, it was not rebuilt after the changes in 479ecec.

If pydantic/1.10.13-GCCcore-12.3.0 loads typing-extensions/4.9.0-GCCcore-12.3.0 (like it is in your case), then it gets superseded by the older typing-extensions that is included in the hatchling installation that gets loaded as a dependency of scanpy.

Long story short: we should make hatchling a build dependency of scanpy, and then the problem should be resolved... => being fixed via #21657

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Other then scanpy I also had to rebuild anndata on Donphan to pass the pip checks without typing-extensions in exts_list.

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boegel commented Oct 16, 2024

Test report by @boegel
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
node3124.skitty.os - Linux RHEL 9.4, x86_64, Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz (skylake_avx512), Python 3.9.18
See https://gist.github.com/boegel/a7d0a9f5cce726297ead73100889299c for a full test report.

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PetrKralCZ commented Oct 16, 2024

Test report by @PetrKralCZ
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
node4003.donphan.os - Linux RHEL 8.8, x86_64, Intel(R) Xeon(R) Gold 6240 CPU @ 2.60GHz, 1 x NVIDIA NVIDIA A2, 545.23.08, Python 3.6.8
See https://gist.github.com/PetrKralCZ/56cb1f671f8f6992af74385c1b34a734 for a full test report.

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boegel commented Oct 17, 2024

Going in, thanks @PetrKralCZ!

@boegel boegel merged commit bfdd8f2 into easybuilders:develop Oct 17, 2024
@boegel boegel modified the milestones: release after 4.9.4, 5.0.0 Mar 18, 2025
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