{bio}[foss/2023a] pyGenomeTracks v3.9, cooler v0.10.2, HiCMatrix v17.2 + use PyPI source tarball and `gfbf/2023a` toolchain for pyBigWig #20881

WilleBell · 2024-06-21T13:54:25Z

(created using eb --new-pr)

Add pyGenomeTracks, cooler, HiCMatrix
Fix pyBigWig-0.3.22 to pass pip_check and drop to gfbf toolchain
Remove preinstallopts for TOBIAS-0.16.1-foss-2023a.eb (not needed with pyBigWig fix)

… for TOBIAS are not needed with this fix

easybuild/easyconfigs/p/pyGenomeTracks/pyGenomeTracks-3.9-foss-2023a.eb

…-2023a.eb Co-authored-by: Bob Dröge <b.e.droge@rug.nl>

bedroge · 2024-06-25T08:17:58Z

Test report by @bedroge
SUCCESS
Build succeeded for 5 out of 5 (5 easyconfigs in total)
interactive1 - Linux Rocky Linux 8.9, x86_64, AMD EPYC-Milan Processor (zen2), Python 3.6.8
See https://gist.github.com/bedroge/146cd4c0d379f7d0eaa98ae242567498 for a full test report.

bedroge · 2024-06-25T08:44:04Z

Test report by @bedroge
SUCCESS
Build succeeded for 5 out of 5 (5 easyconfigs in total)
bob-Latitude-5300 - Linux Ubuntu 22.04, x86_64, Intel(R) Core(TM) i7-8665U CPU @ 1.90GHz, Python 3.10.12
See https://gist.github.com/bedroge/4e8c184aa729d4727fb4afb5eb33f841 for a full test report.

pavelToman · 2024-06-25T09:32:00Z

Hello,
I made pyBigWig for foss/2023a and I see you fix it there. The options = {'modulename': name} is still there so how is it fixed? I do not know why but pip for foss/2023a do the wrong check - import pybigwig instead of import pyBigWig, but the right one is import pyBigWig

WilleBell · 2024-06-25T11:19:31Z

Hello, I made pyBigWig for foss/2023a and I see you fix it there. The options = {'modulename': name} is still there so how is it fixed? I do not know why but pip for foss/2023a do the wrong check - import pybigwig instead of import pyBigWig, but the right one is import pyBigWig

The fix does not involve the import pyBigWig but it involves the metadata of pyBigWig. The build from the GitHub seems to fail to create it but the PYPI source creates the pyBigWig-0.3.22.dist-info directory which fixes the "version" issue and avoids pip_check to fail when pyBigWig is a dependency (as in TOBIAS-0.16.1-foss-2023a.eb). At least this is what I could understand about what is going on, I might have gotten something wrong.

easybuild/easyconfigs/t/TOBIAS/TOBIAS-0.16.1-foss-2023a.eb

bedroge · 2024-06-25T13:53:47Z

@boegelbot please test @ jsc-zen3

boegelbot · 2024-06-25T14:00:11Z

@bedroge: 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=20881 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_20881 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 4460

Test results coming soon (I hope)...

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boegel · 2024-06-25T14:04:28Z

Hello, I made pyBigWig for foss/2023a and I see you fix it there. The options = {'modulename': name} is still there so how is it fixed? I do not know why but pip for foss/2023a do the wrong check - import pybigwig instead of import pyBigWig, but the right one is import pyBigWig

The fix does not involve the import pyBigWig but it involves the metadata of pyBigWig. The build from the GitHub seems to fail to create it but the PYPI source creates the pyBigWig-0.3.22.dist-info directory which fixes the "version" issue and avoids pip_check to fail when pyBigWig is a dependency (as in TOBIAS-0.16.1-foss-2023a.eb). At least this is what I could understand about what is going on, I might have gotten something wrong.

@WilleBell Makes total sense, thanks for clarifying.

It's a bit nasty that the sources from GitHub and PyPI are not equivalent, but when we have the choice it's better to use the source tarball from PyPI, since that may be "enriched", as this case shows...

boegelbot · 2024-06-25T14:06:09Z

Test report by @boegelbot
FAILED
Build succeeded for 3 out of 5 (5 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/443b169869bdba347cdbb4f3d61d4568 for a full test report.

boegel · 2024-06-25T14:08:19Z

Hmm, I'm confused now...

tobias 0.16.1 requires pybigwig, which is not installed

boegel · 2024-06-25T14:08:24Z

@boegelbot please test @ generoso

boegelbot · 2024-06-25T14:10:05Z

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

PR test command 'EB_PR=20881 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_20881 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 13815

Test results coming soon (I hope)...

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bedroge · 2024-06-25T14:11:51Z

Hmm, I'm confused now...

tobias 0.16.1 requires pybigwig, which is not installed

That's probably the same thing that I ran into locally as well, it's still building the foss version as well all the time (see slack). I could only work around it by adding --minimal-toolchains.

boegelbot · 2024-06-25T14:21:20Z

Test report by @boegelbot
FAILED
Build succeeded for 3 out of 5 (5 easyconfigs in total)
cns2 - 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/b5a0fcb3887ec66e51cbeef1cb739da4 for a full test report.

bedroge · 2024-06-25T14:27:02Z

@boegelbot please test @ generoso
EB_ARGS="--minimal-toolchains"

boegelbot · 2024-06-25T14:30:09Z

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

PR test command 'EB_PR=20881 EB_ARGS="--minimal-toolchains" EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_20881 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 13816

Test results coming soon (I hope)...

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boegelbot · 2024-06-25T14:42:52Z

Test report by @boegelbot
SUCCESS
Build succeeded for 5 out of 5 (5 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/3fc583e45c3a6563d40df1c0fd936bed for a full test report.

boegel · 2024-06-25T17:17:12Z

Hmm, I'm confused now...
tobias 0.16.1 requires pybigwig, which is not installed
That's probably the same thing that I ran into locally as well, it's still building the foss version as well all the time (see slack). I could only work around it by adding --minimal-toolchains.

It's not building the pyBigWig using foss/2023a, but it is picking up that existing module when resolving dependencies (for TOBIAS for example).
Since that's the "crippled" one (which pip check fails on), there's trouble.

I'll remove that pyBigWig/0.3.22-foss-2023a module in both test systems (generoso + jsc-zen3)...

boegel · 2024-06-25T17:17:34Z

@boegelbot please test @ jsc-zen3

boegelbot · 2024-06-25T17:20:07Z

@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=20881 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_20881 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 4461

Test results coming soon (I hope)...

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boegelbot · 2024-06-25T17:26:04Z

Test report by @boegelbot
FAILED
Build succeeded for 4 out of 6 (5 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/034a70f3a51c815fa8feff83e6bef117 for a full test report.

boegel · 2024-06-25T17:29:33Z

Test report by @boegel
FAILED
Build succeeded for 3 out of 5 (5 easyconfigs in total)
node3104.skitty.os - Linux RHEL 8.8, x86_64, Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz, Python 3.6.8
See https://gist.github.com/boegel/607eb7d33677e88333b3b360b8cc75e2 for a full test report.

boegel · 2024-06-25T18:01:04Z

Ah, no, indeed, if pyBigWig/0.3.22-foss-2023a is not available yet, it will get installed through this PR.
That's definitely a bug in EasyBuild...

boegel · 2024-06-25T18:02:25Z

@boegelbot please test @ jsc-zen3
EB_ARGS="cooler-0.10.2-foss-2023a.eb HiCMatrix-17.2-foss-2023a.eb pyBigWig-0.3.22-gfbf-2023a.eb pyGenomeTracks-3.9-foss-2023a.eb TOBIAS-0.16.1-foss-2023a.eb"

boegelbot · 2024-06-25T18:10:10Z

@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=20881 EB_ARGS="cooler-0.10.2-foss-2023a.eb HiCMatrix-17.2-foss-2023a.eb pyBigWig-0.3.22-gfbf-2023a.eb pyGenomeTracks-3.9-foss-2023a.eb TOBIAS-0.16.1-foss-2023a.eb" EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_20881 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 4462

Test results coming soon (I hope)...

- notification for comment with ID 2189636390 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 · 2024-06-25T18:16:02Z

Test report by @boegelbot
FAILED
Build succeeded for 4 out of 6 (5 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/c442ef6ae6e0826c297fe6b6a177f58b for a full test report.

boegel · 2024-06-25T18:34:33Z

@boegelbot please test @ jsc-zen3
EB_ARGS="--minimal-toolchains"

boegelbot · 2024-06-25T18:40:08Z

@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=20881 EB_ARGS="--minimal-toolchains" EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_20881 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 4464

Test results coming soon (I hope)...

- notification for comment with ID 2189700464 processed

Message to humans: this is just bookkeeping information for me,
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boegelbot · 2024-06-25T18:46:09Z

Test report by @boegelbot
SUCCESS
Build succeeded for 5 out of 5 (5 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/a492487ae68145edd79d5df9f656b6b3 for a full test report.

boegel · 2024-06-25T19:41:51Z

Test report by @boegel
SUCCESS
Build succeeded for 5 out of 5 (5 easyconfigs in total)
node3104.skitty.os - Linux RHEL 8.8, x86_64, Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz, Python 3.6.8
See https://gist.github.com/boegel/2f7b42296e56840d16dc336b83b64c5c for a full test report.

boegel

lgtm

boegel · 2024-06-25T20:59:07Z

Going in, thanks @WilleBell!

Add pyGenomeTracks and fix pyBigWig to pass pip_check, preinstallopts…

301e2bd

… for TOBIAS are not needed with this fix

WilleBell changed the title ~~Add pyGenomeTracks and fix pyBigWig to pass pip_check, preinstallopts for TOBIAS are not needed with this fix~~ Add pyGenomeTracks and fix pyBigWig Jun 21, 2024

Using pypi source fixes version issue (no patch needed)

b13fe34

bedroge reviewed Jun 25, 2024

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bedroge added enhancement update labels Jun 25, 2024

WilleBell and others added 2 commits June 25, 2024 09:47

Update easybuild/easyconfigs/p/pyGenomeTracks/pyGenomeTracks-3.9-foss…

bffc4f3

…-2023a.eb Co-authored-by: Bob Dröge <b.e.droge@rug.nl>

Update easybuild/easyconfigs/p/pyGenomeTracks/pyGenomeTracks-3.9-foss…

086e33c

…-2023a.eb Co-authored-by: Bob Dröge <b.e.droge@rug.nl>

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boegel changed the title ~~Add pyGenomeTracks and fix pyBigWig~~ {bio}[foss/2023a] pyGenomeTracks v3.9, cooler v0.10.2, HiCMatrix v17.2 + use PyPI source tarball and gfbf/2023a toolchain for pyBigWig Jun 25, 2024

boegel added bug fix and removed enhancement labels Jun 25, 2024

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boegel merged commit 1c08d80 into easybuilders:develop Jun 25, 2024
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{bio}[foss/2023a] pyGenomeTracks v3.9, cooler v0.10.2, HiCMatrix v17.2 + use PyPI source tarball and `gfbf/2023a` toolchain for pyBigWig #20881

{bio}[foss/2023a] pyGenomeTracks v3.9, cooler v0.10.2, HiCMatrix v17.2 + use PyPI source tarball and `gfbf/2023a` toolchain for pyBigWig #20881

WilleBell commented Jun 21, 2024 •

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{bio}[foss/2023a] pyGenomeTracks v3.9, cooler v0.10.2, HiCMatrix v17.2 + use PyPI source tarball and gfbf/2023a toolchain for pyBigWig #20881

{bio}[foss/2023a] pyGenomeTracks v3.9, cooler v0.10.2, HiCMatrix v17.2 + use PyPI source tarball and gfbf/2023a toolchain for pyBigWig #20881

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{bio}[foss/2023a] pyGenomeTracks v3.9, cooler v0.10.2, HiCMatrix v17.2 + use PyPI source tarball and `gfbf/2023a` toolchain for pyBigWig #20881

{bio}[foss/2023a] pyGenomeTracks v3.9, cooler v0.10.2, HiCMatrix v17.2 + use PyPI source tarball and `gfbf/2023a` toolchain for pyBigWig #20881

WilleBell commented Jun 21, 2024 •

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