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{tools}[foss/2021a] cwltool v3.1.20221018083734 w/ Python 3.9.5 #16503

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merged 5 commits into from
Nov 4, 2022
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{tools}[foss/2021a] cwltool v3.1.20221018083734 w/ Python 3.9.5 #16503

merged 5 commits into from
Nov 4, 2022

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SIB-software
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(created using eb --new-pr)

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boegel commented Oct 28, 2022

@boegelbot please test @ generoso

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

PR test command 'EB_PR=16503 EB_ARGS= EB_CONTAINER= /opt/software/slurm/bin/sbatch --job-name test_PR_16503 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

  • exit code: 0
  • output:
Submitted batch job 9402

Test results coming soon (I hope)...

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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).

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Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
cns1 - 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/8e018d3284544623a99d4da7df0c3959 for a full test report.

@boegel boegel added the new label Oct 28, 2022
@boegel boegel added this to the 4.x milestone Oct 28, 2022
boegel
boegel reviewed Oct 28, 2022
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easybuild/easyconfigs/c/cwltool/cwltool-3.1.20221018083734-GCCcore-10.3.0.eb Outdated
}),
('cwlformat', '2022.2.18', {
'modulename': 'cwlformat',
'source_tmpl': 'cwlformat-%(version)s-py3-none-any.whl',
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Any reason why you're not using the .tar.gz here, but using the prebuilt wheel instead?

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The build failed with the tarball: an issue with a missing README file.

No issue with the whl file

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That's a bug in the source package in PyPI, maybe report this upstream?

Since this is Python-only, using a wheel file or source tarball doesn't matter much, so fine as is

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@smoretti smoretti Nov 4, 2022 •
edited by boegel
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Reported upstream
edit: see rabix/cwl-format#19

@easybuilders easybuilders deleted a comment from boegelbot Nov 4, 2022
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boegel commented Nov 4, 2022

@boegelbot please test @ generoso

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

PR test command 'EB_PR=16503 EB_ARGS= EB_CONTAINER= /opt/software/slurm/bin/sbatch --job-name test_PR_16503 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

  • exit code: 0
  • output:
Submitted batch job 9442

Test results coming soon (I hope)...

- notification for comment with ID 1303980716 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
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Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
cns1 - 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/09ad64bf7274aa5f26e0d023d8aeae2b for a full test report.

@boegel boegel changed the title {tools}[GCCcore/10.3.0] cwltool v3.1.20221018083734 w/ Python 3.9.5 {tools}[foss/2021a] cwltool v3.1.20221018083734 w/ Python 3.9.5 Nov 4, 2022
@boegel boegel modified the milestones: 4.x, next release (4.6.3?) Nov 4, 2022
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boegel commented Nov 4, 2022

Test report by @boegel
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
node3121.skitty.os - Linux RHEL 8.4, x86_64, Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz (skylake_avx512), Python 3.6.8
See https://gist.github.com/ca8a3272815df038d14829be1ff4578a for a full test report.

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boegel commented Nov 4, 2022

Going in, thanks @SIB-software!

@boegel boegel merged commit e9852e0 into easybuilders:develop Nov 4, 2022
@smoretti smoretti deleted the 20221028135409_new_pr_cwltool3120221018083734 branch November 5, 2022 09:25
@boegel boegel added the BioHack2022 Related to EU BioHackathon 2022 label Nov 7, 2022
mr-c
mr-c reviewed Nov 9, 2022
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easybuild/easyconfigs/c/cwltool/cwltool-3.1.20221018083734-foss-2021a.eb
('mistune', '0.8.4', {
'checksums': ['59a3429db53c50b5c6bcc8a07f8848cb00d7dc8bdb431a4ab41920d201d4756e'],
}),
('schema-salad', '8.3.20221016151607', {
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Thanks for this!

Please consider either using the pre-built binary wheels for schema-salad, or compile your own using mypyc

Examples from other packaging systems

https://github.com/conda-forge/schema-salad-feedstock/blob/b4719fc95e2e4f8ebf85e2c266af0983312ddc3a/recipe/meta.yaml#L17
https://github.com/common-workflow-language/schema_salad/blob/b86efc78a4dc4c1f4055ab24615504e177e7e053/schema_salad.Dockerfile#L9

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@mr-c Can you elaborate on the benefit of using mypyc instead of a regular pip install for schema-salad?

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mypyc can be used to compile Python projects with type hints into fast binary modules. For example, the Python code formatter black is distributed in a binary wheel this way (despite being a pure Python codebase)

https://pypi.org/project/black/#files

https://mypyc.readthedocs.io/en/latest/introduction.html

@mr-c mr-c mentioned this pull request Nov 9, 2022
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