{bio}[foss/2023a] Single-cell-python-bundle v2024.02 by pavelToman · Pull Request #20116 · easybuilders/easybuild-easyconfigs

pavelToman · 2024-03-14T14:03:56Z

(created using eb --new-pr)
resolves vscentrum/vsc-software-stack#214

Requires:

TODO:

homepage
description
scvi-tools.eb (requires {tools}[gfbf/2023a] jax v0.4.25 w/ CUDA 12.1.1 #20119)
scArches.eb - required scvi-tools
scib-metrics.eb - required scvi-tools

Exts to add:

...uild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb

pavelToman · 2024-04-24T14:23:02Z

@boegelbot please test @ generoso

boegelbot · 2024-04-24T14:25:09Z

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

PR test command 'EB_PR=20116 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_20116 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 13358

Test results coming soon (I hope)...

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boegelbot · 2024-04-24T14:29:52Z

Test report by @boegelbot
FAILED
Build succeeded for 2 out of 3 (3 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/dcf932b3e169d70e35d85f6d7d7d5ff3 for a full test report.

edit: missing Arrow module is probably caused by failed test report in #20414

boegel · 2024-05-02T17:55:49Z

@boegelbot please test @ generoso

boegelbot · 2024-05-02T17:56:05Z

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

PR test command 'EB_PR=20116 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_20116 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 13387

Test results coming soon (I hope)...

Details

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boegelbot · 2024-05-02T18:03:24Z

Test report by @boegelbot
FAILED
Build succeeded for 2 out of 3 (3 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/8e543ead43a29076b1f872cd24df4999 for a full test report.

...uild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb

boegel · 2024-05-06T09:01:05Z

@boegelbot please test @ generoso

boegelbot · 2024-05-06T09:05:14Z

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

PR test command 'EB_PR=20116 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_20116 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 13409

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 · 2024-05-06T09:16:14Z

Test report by @boegelbot
FAILED
Build succeeded for 2 out of 3 (3 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/d9a00039fd124d758716ac462e0a20af for a full test report.

pavelToman · 2024-05-06T16:49:04Z

Fix for the fsspec error: #20477

...uild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb

pavelToman · 2024-05-09T13:18:26Z

@boegelbot please test @ generoso

boegelbot · 2024-05-09T13:20:04Z

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

PR test command 'EB_PR=20116 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_20116 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 13435

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 · 2024-05-09T13:36:12Z

Test report by @boegelbot
SUCCESS
Build succeeded for 3 out of 3 (3 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/5fd5414096ff22a13f9e4c40d2d73e17 for a full test report.

…-cell-python-bundle202402

pavelToman · 2024-06-26T08:18:33Z

@boegelbot please test @ generoso

boegelbot · 2024-06-26T08:20:05Z

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

PR test command 'EB_PR=20116 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_20116 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 13819

Test results coming soon (I hope)...

Details

- notification for comment with ID 2191099266 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 · 2024-06-26T08:31:20Z

Test report by @boegelbot
FAILED
Build succeeded for 3 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/e2858603ac4657eff2857d357def8dd7 for a full test report.

pavelToman · 2024-06-26T12:23:54Z

@boegelbot please test @ generoso

boegelbot · 2024-06-26T12:25:09Z

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

PR test command 'EB_PR=20116 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_20116 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 13820

Test results coming soon (I hope)...

Details

- notification for comment with ID 2191557835 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 · 2024-06-26T13:44:04Z

Test report by @boegelbot
FAILED
Build succeeded for 4 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/377161a87e9bfdc11f25e09571b3431e for a full test report.

pavelToman · 2024-06-26T14:06:23Z

Test report by @boegelbot FAILED Build succeeded for 4 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/377161a87e9bfdc11f25e09571b3431e for a full test report.

Seems GDAL/3.7.1-foss-2023a is missing on generoso?

EDIT: GDAL fixed

pavelToman · 2024-06-26T14:06:33Z

@boegelbot please test @ jsc-zen3

boegelbot · 2024-06-26T14:10:14Z

@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=20116 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_20116 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 4467

Test results coming soon (I hope)...

Details

- notification for comment with ID 2191804015 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 · 2024-06-26T15:11:44Z

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/12ebca74f4f0b9104fc74da2366c5886 for a full test report.

pavelToman · 2024-06-27T10:06:57Z

@boegelbot please test @ generoso

boegelbot · 2024-06-27T10:10:08Z

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

PR test command 'EB_PR=20116 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_20116 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 13831

Test results coming soon (I hope)...

Details

- notification for comment with ID 2194294717 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 · 2024-06-27T11:51:17Z

Test report by @boegelbot
SUCCESS
Build succeeded for 5 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/c8a1724b7945eb4efb9f9321dd253127 for a full test report.

boegel · 2024-07-04T12:36:47Z

Test report by @boegel
SUCCESS
Build succeeded for 5 out of 5 (5 easyconfigs in total)
node3158.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/4cba265b4d6d703bae34ed679496de75 for a full test report.

boegel

lgtm

boegel · 2024-07-05T20:03:33Z

Going in, thanks @pavelToman!

adding easyconfigs: Single-cell-python-bundle-2024.02-foss-2023a.eb

6bb1bcb

pavelToman marked this pull request as draft March 14, 2024 14:04

pavelToman mentioned this pull request Mar 14, 2024

Single-cell python bundle request vscentrum/vsc-software-stack#214

Closed

32 tasks

pavelToman added 3 commits March 15, 2024 10:23

update1 bundle

248a561

update bundle + add adjustText pycodestyle

6a42985

tascCODA added, cassiopeia remove

06537c9

boegel added the new label Mar 26, 2024

boegel added this to the 4.x milestone Mar 26, 2024

boegel requested changes Apr 5, 2024

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...uild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb Outdated Show resolved Hide resolved

pavelToman added 2 commits April 8, 2024 11:03

cassiopeia added, homepage, description

f988b1d

add another dependencies

4ea7063

boegel requested changes May 2, 2024

View reviewed changes

...uild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb Outdated Show resolved Hide resolved

poetry as a builddep

90be71a

delete comments to let tests pass

9b4d482

boegel mentioned this pull request May 7, 2024

update version of fsspec extension in easyconfig for Squidpy 1.4.1 to be compatible with s3fs provided via PyTorch-bundle #20477

Merged

boegel reviewed May 7, 2024

View reviewed changes

...uild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb Outdated Show resolved Hide resolved

update comment for tascCODA deletion in setup.py

97b22a8

pavelToman and others added 6 commits June 5, 2024 14:44

add pyomo, the dep of pertpy

6a51ca7

fix jax

b427446

move pycodestyle and adjustText to separate PR

be9f9a0

Merge branch 'easybuilders:develop' into 20240314150352_new_pr_Single…

d06cae5

…-cell-python-bundle202402

try update

835da85

move jax dependent ecs to separate PR

40383aa

pavelToman mentioned this pull request Jun 13, 2024

{bio}[foss/2023a] scArches v0.6.1, scib-metrics v0.5.1, scvi-tools v1.1.2, ... #20814

Merged

Update graph-tool-2.59-foss-2023a.eb boost-python version

8082288

update graph-tools deps + fix preinstallopts of tascCODA

347c72d

update adjustText version

16954b2

boegel approved these changes Jul 5, 2024

View reviewed changes

boegel merged commit 2234e91 into easybuilders:develop Jul 5, 2024

boegel modified the milestones: 4.x, release after 4.9.2 Jul 5, 2024

boegel mentioned this pull request Jul 6, 2024

{2023.06}[foss/2023a] Single-cell-python-bundle 2024.02 EESSI/software-layer#637

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