{bio}[foss/2023a] scArches v0.6.1, scib-metrics v0.5.1, scvi-tools v1.1.2, ... by pavelToman · Pull Request #20814 · easybuilders/easybuild-easyconfigs

pavelToman · 2024-06-13T10:08:48Z

(created using eb --new-pr)
for #20116

…foss-2023a.eb, scvi-tools-1.1.2-foss-2023a.eb, Optax-0.2.2-foss-2023a.eb, ml-collections-0.1.1-foss-2023a.eb, jax-0.4.25-foss-2023a.eb and patches: jax-0.4.25_fix-pybind11-systemlib.patch, jax-0.4.25_fix_env_test_no_log_spam.patch

pavelToman · 2024-06-13T10:09:05Z

@boegelbot please test @ generoso

boegelbot · 2024-06-13T10:10:09Z

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

PR test command 'EB_PR=20814 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_20814 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 13726

Test results coming soon (I hope)...

Details

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j551n-ncloud · 2024-06-13T10:40:39Z

(created using eb --new-pr)

PR for #20116

Hi my name is Johannes Nguyen i have one question im new to Easybuild and i create an recipe for BamUtil and i want to merge it how are the steps for that. A replay would be helpful bc im new to this @ johannes.nguyen@dkfz-heidelberg.de :D

boegelbot · 2024-06-13T13:12:42Z

Test report by @boegelbot
FAILED
Build succeeded for 5 out of 6 (6 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/21f7e6c06a2d0aa50497d8230508feec for a full test report.

smoors · 2024-06-13T17:41:36Z

(created using eb --new-pr)
PR for #20116

Hi my name is Johannes Nguyen i have one question im new to Easybuild and i create an recipe for BamUtil and i want to merge it how are the steps for that. A replay would be helpful bc im new to this @ johannes.nguyen@dkfz-heidelberg.de :D

see here for documentation on how to contribute an easyconfig file:
https://docs.easybuild.io/contributing/#contributing_easyconfigs

smoors · 2024-06-13T17:52:03Z

    import pyproject_metadata
ModuleNotFoundError: No module named 'pyproject_metadata'

missing python package

pavelToman · 2024-06-14T09:40:26Z

(created using eb --new-pr)
PR for #20116

Hi my name is Johannes Nguyen i have one question im new to Easybuild and i create an recipe for BamUtil and i want to merge it how are the steps for that. A replay would be helpful bc im new to this @ johannes.nguyen@dkfz-heidelberg.de :D

I do it like that:
First you need to setup your GitHub account with EB then the eb --check-github should work.
Then you can do eb --new-pr your_easyconfig.eb and it will push it as a PR to easybuild.
Next time please ask on Easybuild Slack in #general: https://easybuild.slack.com/

pavelToman · 2024-06-14T09:56:05Z

@boegelbot please test @ generoso

boegelbot · 2024-06-14T10:00:11Z

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

PR test command 'EB_PR=20814 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_20814 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 13737

Test results coming soon (I hope)...

Details

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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).

pavelToman · 2024-06-14T11:01:51Z

jax created from: #20119

boegelbot · 2024-06-14T13:01:41Z

Test report by @boegelbot
FAILED
Build succeeded for 5 out of 6 (6 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/4611aa5d703e2e179fb933cfa9c0d8d3 for a full test report.

easybuild/easyconfigs/s/scArches/scArches-0.6.1-foss-2023a.eb

pavelToman · 2024-06-18T13:40:48Z

@boegelbot please test @ generoso

boegelbot · 2024-06-18T13:45:09Z

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

PR test command 'EB_PR=20814 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_20814 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 13766

Test results coming soon (I hope)...

Details

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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).

boegelbot · 2024-06-18T16:51:53Z

Test report by @boegelbot
SUCCESS
Build succeeded for 6 out of 6 (6 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/05e547d800bcceb5a4d5db5a8807981e for a full test report.

pavelToman · 2024-06-19T09:51:51Z

@boegelbot please test @ jsc-zen3

boegelbot · 2024-06-19T10:00:15Z

@pavelToman: 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=20814 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_20814 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 4419

Test results coming soon (I hope)...

Details

- notification for comment with ID 2178254248 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 · 2024-06-19T11:09:09Z

Test report by @boegelbot
FAILED
Build succeeded for 5 out of 6 (6 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/b673b9d2ac36d4458d277fd9001addd1 for a full test report.

boegel · 2024-06-19T11:22:20Z

@pavelToman

  hint: A `urllib.error.HTTPError` indicates that the issue is related to the
        network or the availability of NodeJS release files. It may mean the node
        version that this tool is trying to fetch is no longer available, for
        example if there is no compatible NodeJS binary for the operating system.
  link: https://sphinx-theme-builder.rtfd.io/errors/#nodeenv-creation-failed
  error: subprocess-exited-with-error

Can we convince this thing to use nodejs we provide as dependency instead?

boegel · 2024-06-19T11:24:04Z

@pavelToman This looks helpful: https://sphinx-theme-builder.readthedocs.io/en/latest/build-process/#controlling-nodejs

pavelToman · 2024-06-19T12:49:27Z

It seems I add either the deps that are for building docs - so I remove them, hope they are not necessary. scArches can be installed on donphan without them.

pavelToman · 2024-06-19T12:49:33Z

@boegelbot please test @ jsc-zen3

boegelbot · 2024-06-19T12:50:07Z

@pavelToman: 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=20814 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_20814 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 4420

Test results coming soon (I hope)...

Details

- notification for comment with ID 2178637714 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 · 2024-06-19T13:57:55Z

Test report by @boegelbot
SUCCESS
Build succeeded for 6 out of 6 (6 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/02775418985166f41bd2f2592a0c0b52 for a full test report.

boegel · 2024-06-25T21:07:13Z

@boegelbot please test @ generoso

boegel

lgtm

boegelbot · 2024-06-25T21:10:05Z

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

PR test command 'EB_PR=20814 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_20814 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 13818

Test results coming soon (I hope)...

Details

- notification for comment with ID 2189971574 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 · 2024-06-26T00:12:46Z

Test report by @boegelbot
SUCCESS
Build succeeded for 6 out of 6 (6 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/a9a123ae4efd742dde63897f15ec09c7 for a full test report.

boegel · 2024-06-26T00:14:45Z

Test report by @boegel
SUCCESS
Build succeeded for 6 out of 6 (6 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/78561687ce1509898e6f33b0a91040a0 for a full test report.

boegel · 2024-06-26T06:48:46Z

Going in, thanks @pavelToman!

pavelToman mentioned this pull request Jun 13, 2024

{bio}[foss/2023a] Single-cell-python-bundle v2024.02 #20116

Merged

38 tasks

add builddep for pyproject_metadata

6fd6449

boegel requested changes Jun 18, 2024

View reviewed changes

easybuild/easyconfigs/s/scArches/scArches-0.6.1-foss-2023a.eb Outdated Show resolved Hide resolved

add pyproject-metadata to exts

deb66d0

update scArches deps

db19c29

boegel added the update label Jun 25, 2024

boegel added this to the 4.x milestone Jun 25, 2024

boegel approved these changes Jun 25, 2024

View reviewed changes

boegel merged commit 6904f4c into easybuilders:develop Jun 26, 2024

boegel modified the milestones: 4.x, release after 4.9.2 Jun 27, 2024

This was referenced Jun 16, 2025

WIP: {bio}[foss/2022a] scvi-tools v0.20.3 w/ Python 3.10.4 #17758

Closed

WIP: {data}[foss/2022a] panpipes v0.1.3 w/ Python 3.10.4 #17757

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