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add missing required PyPy dependency for Clair3, also copy preprocess and shared subdirectories, and enhance sanity check for provided libclair3 Python package#18847

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verdurin merged 1 commit intoeasybuilders:developfrom
boegel:20230920172051_new_pr_PyPy7312
Sep 27, 2023
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add missing required PyPy dependency for Clair3, also copy preprocess and shared subdirectories, and enhance sanity check for provided libclair3 Python package#18847
verdurin merged 1 commit intoeasybuilders:developfrom
boegel:20230920172051_new_pr_PyPy7312

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@boegel boegel commented Sep 20, 2023

(created using eb --new-pr)

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add missing required PyPy dependency for Clair3, also copy preprocess…
7b08244 
… and shared subdirectories, and enhance sanity check for provided libclair3 Python package
@boegel boegel added this to the next release (4.8.2?) milestone Sep 20, 2023
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boegel commented Sep 20, 2023

@boegelbot please test @ generoso

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boegelbot commented Sep 20, 2023

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

PR test command 'EB_PR=18847 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_18847 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

  • exit code: 0
  • output:
Submitted batch job 11763

Test results coming soon (I hope)...

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it is of no use to you (unless you think I have a bug, which I don't).

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boegelbot commented Sep 20, 2023

Test report by @boegelbot
SUCCESS
Build succeeded for 2 out of 2 (2 easyconfigs in total)
cns3 - Linux Rocky Linux 8.5, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/boegelbot/f296fe3175c6ebb99e30dd985b971429 for a full test report.

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boegel commented Sep 20, 2023

@boegelbot please test @ jsc-zen2

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boegelbot commented Sep 20, 2023

@boegel: Request for testing this PR well received on jsczen2l1.int.jsc-zen2.easybuild-test.cluster

PR test command 'EB_PR=18847 EB_ARGS= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --mem-per-cpu=4000M --job-name test_PR_18847 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen2.sh' executed!

  • exit code: 0
  • output:
Submitted batch job 3411

Test results coming soon (I hope)...

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Message to humans: this is just bookkeeping information for me,
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boegelbot commented Sep 20, 2023

Test report by @boegelbot
SUCCESS
Build succeeded for 2 out of 2 (2 easyconfigs in total)
jsczen2c1.int.jsc-zen2.easybuild-test.cluster - Linux Rocky Linux 8.5, x86_64, AMD EPYC 7742 64-Core Processor (zen2), Python 3.6.8
See https://gist.github.com/boegelbot/582763c39e64a8dd2d466c7dbeb3dff0 for a full test report.

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boegel commented Sep 20, 2023

Test report by @boegel
SUCCESS
Build succeeded for 2 out of 2 (2 easyconfigs in total)
node3141.skitty.os - Linux RHEL 8.6, x86_64, Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz (skylake_avx512), Python 3.6.8
See https://gist.github.com/boegel/eb3d382732dcd47b4010d71007520747 for a full test report.

boegel
boegel commented Sep 20, 2023
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Comment thread easybuild/easyconfigs/c/Clair3/Clair3-1.0.4-foss-2022a.eb
('zstd', '1.5.2'),
('HTSlib', '1.15.1'),
('libdeflate', '1.10'),
('PyPy', '7.3.12', '-3.10', SYSTEM),
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I spent quite a bit of time in trying to get PyPy to build from source rather than using pre-built binaries, but I didn't manage to get it fully working yet (and I gave up for now), see #18848

@boegel boegel mentioned this pull request Sep 20, 2023
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verdurin commented Sep 27, 2023

Test report by @verdurin
SUCCESS
Build succeeded for 4 out of 4 (2 easyconfigs in total)
easybuild-c7.novalocal - Linux CentOS Linux 7.9.2009, x86_64, Intel Xeon Processor (Skylake, IBRS), Python 3.6.8
See https://gist.github.com/verdurin/8bbdc18c7da5397000ae2e7da2cc4ffa for a full test report.

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verdurin approved these changes Sep 27, 2023
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Looks fine.

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verdurin commented Sep 27, 2023

Going in, thanks @boegel!

@verdurin verdurin merged commit 1e2cf95 into easybuilders:develop Sep 27, 2023
@boegel boegel deleted the 20230920172051_new_pr_PyPy7312 branch September 28, 2023 10:01
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