nipype / pydra

Pydra Dataflow Engine
https://nipype.github.io/pydra/
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Update Slurm container image in GitHub Actions workflow #688

Closed adi611 closed 1 year ago

adi611 commented 1 year ago

Types of changes

Summary

Update the Slurm container image in testslurm.yml workflow to giovtorres/docker-centos7-slurm:latest which uses Slurm version 21.08.0. GitHub: link; Docker Hub: link.

Checklist

codecov[bot] commented 1 year ago

Codecov Report

Patch coverage has no change and project coverage change: -0.48% :warning:

Comparison is base (f796a9c) 83.23% compared to head (93782de) 82.75%.

:exclamation: Current head 93782de differs from pull request most recent head 3f85037. Consider uploading reports for the commit 3f85037 to get more accurate results

Additional details and impacted files ```diff @@ Coverage Diff @@ ## master #688 +/- ## ========================================== - Coverage 83.23% 82.75% -0.48% ========================================== Files 22 22 Lines 4848 4848 Branches 1392 0 -1392 ========================================== - Hits 4035 4012 -23 - Misses 809 836 +27 + Partials 4 0 -4 ``` | [Flag](https://app.codecov.io/gh/nipype/pydra/pull/688/flags?src=pr&el=flags&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=nipype) | Coverage Δ | | |---|---|---| | [unittests](https://app.codecov.io/gh/nipype/pydra/pull/688/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=nipype) | `82.75% <ø> (-0.48%)` | :arrow_down: | Flags with carried forward coverage won't be shown. [Click here](https://docs.codecov.io/docs/carryforward-flags?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=nipype#carryforward-flags-in-the-pull-request-comment) to find out more. [see 5 files with indirect coverage changes](https://app.codecov.io/gh/nipype/pydra/pull/688/indirect-changes?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=nipype)

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djarecka commented 1 year ago

@adi611 - can you check what version of pyld is installed within the container?

And perhaps you can check if you can run

from pyld import jsonld
jsonld.get_document_loader()
djarecka commented 1 year ago

it looks like jsonld.get_document_loader() returns a dummy loader and there are issues with setting jsonld.requests_document_loader due to older version of OpenSSL. You can try to update OpenSSL in the container, but it would be also fine to disable these four tests in this pytest run (the tests are not related to the slurm worker anyway)

djarecka commented 1 year ago

could you please resolve the conflict

adi611 commented 1 year ago

could you please resolve the conflict

Yes I'm working on it.

adi611 commented 1 year ago

For the Slurm GA workflow, the Run pytest part in running perfectly after excluding the 5 tests, but the Upload to codecov part throws an error: ImportError: urllib3 v2.0 only supports OpenSSL 1.1.1+, currently the 'ssl' module is compiled with 'OpenSSL 1.0.2k-fips 26 Jan 2017'.

adi611 commented 1 year ago

@djarecka - could you please re-run the Slurm workflow?

adi611 commented 1 year ago

The Slurm workflow seems to be working fine now, please let me know if further changes are required.