Skip to content

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

Merged
boegel merged 1 commit intoeasybuilders:developfrom
pavelToman:20240506125356_new_pr_Squidpy141
May 7, 2024
Merged

update version of fsspec extension in easyconfig for Squidpy 1.4.1 to be compatible with s3fs provided via PyTorch-bundle#20477
boegel merged 1 commit intoeasybuilders:developfrom
pavelToman:20240506125356_new_pr_Squidpy141

Conversation

@pavelToman
Copy link
Copy Markdown
Collaborator

@pavelToman pavelToman commented May 6, 2024

(created using eb --new-pr)

edit (by @boegel): fix for pip check failure in #20116 where both PyTorch-Lightning (via CellRank) and Squidpy are dependencies:

s3fs 2024.2.0 has requirement fsspec==2024.2.0, but you have fsspec 2023.6.0

Although we don't like to make in-place updates of extensions in merged easyconfigs, I consider it OK in this case because the Squidpy easyconfig was merged in #20109 after the release of the latest EasyBuild version (v4.9.1), so this change is limited to the develop branch (and for a relatively "obscure" software project, not one commonly used as a dependency).

@pavelToman pavelToman changed the title update fsspec version to be compatible with s3fs Squidpy - update fsspec version to be compatible with s3fs May 6, 2024
@pavelToman
Copy link
Copy Markdown
Collaborator Author

@pavelToman
Copy link
Copy Markdown
Collaborator Author

@boegelbot please test @ generoso

@boegelbot
Copy link
Copy Markdown
Collaborator

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

PR test command 'EB_PR=20477 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_20477 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

  • exit code: 0
  • output:
Submitted batch job 13410

Test results coming soon (I hope)...

Details

- notification for comment with ID 2095780933 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
Copy link
Copy Markdown
Collaborator

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 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/fbd1bfa5287b7eea41cc371967ac3776 for a full test report.

@pavelToman
Copy link
Copy Markdown
Collaborator Author

@boegelbot please test @ jsc-zen3

@boegelbot
Copy link
Copy Markdown
Collaborator

@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=20477 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_20477 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

  • exit code: 0
  • output:
Submitted batch job 4070

Test results coming soon (I hope)...

Details

- notification for comment with ID 2095870099 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
Copy link
Copy Markdown
Collaborator

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.3, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.18
See https://gist.github.com/boegelbot/fc19f3506a6b2ccae56bb63e4905b0d7 for a full test report.

@boegel boegel changed the title Squidpy - update fsspec version to be compatible with s3fs update version of fsspec extension in easyconfig for Squidpy 1.4.1 to be compatible with s3fs provided via PyTorch-bundle May 7, 2024
@boegel boegel added this to the release after 4.9.1 milestone May 7, 2024
Copy link
Copy Markdown
Member

@boegel boegel left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

lgtm

@boegel
Copy link
Copy Markdown
Member

boegel commented May 7, 2024

Test report by @boegel
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
node3101.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/140c4f9f649ee0686404e1298f4e8fee for a full test report.

@boegel
Copy link
Copy Markdown
Member

boegel commented May 7, 2024

Going in, thanks @pavelToman!

@boegel boegel merged commit dd0a3c8 into easybuilders:develop May 7, 2024
@boegel boegel changed the title update version of fsspec extension in easyconfig for Squidpy 1.4.1 to be compatible with s3fs provided via PyTorch-bundle update version of fsspec extension in easyconfig for Squidpy 1.4.1 to be compatible with s3fs provided via PyTorch-bundle May 7, 2024
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Projects

None yet

Development

Successfully merging this pull request may close these issues.

3 participants