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MatthiasZepper merged 5 commits into from
Nov 18, 2025
Merged

Enable CI tests for pipelines/download #3898

MatthiasZepper merged 5 commits into from
Nov 18, 2025

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@rrahn
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@rrahn rrahn commented Nov 13, 2025 •
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This PR reactivates some of the download tests that stopped running after restructuring the tests. It also includes fixes for undetected errors. Note the last commit adds a new error message type. I haven't validated if this is due to singularity changing the error message in the past or if something else went wrong. So you maybe take a deeper look at this.

PR checklist

  • This comment contains a description of changes (with reason)
  • CHANGELOG.md is updated
  • If you've fixed a bug or added code that should be tested, add tests!
  • Documentation in docs is updated

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codecov bot commented Nov 13, 2025 •
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Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 78.60%. Comparing base (eae5c97) to head (01acabf).
⚠️ Report is 45 commits behind head on dev.

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@rrahn rrahn force-pushed the fix/pipelines-download-tests branch from 602241d to 8be4478 Compare November 13, 2025 14:01
@rrahn rrahn force-pushed the fix/pipelines-download-tests branch from 8be4478 to bae5110 Compare November 14, 2025 14:08
MatthiasZepper
MatthiasZepper approved these changes Nov 17, 2025
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Thanks a lot for this very observant bug fix!

No objections, just thinking we should also directly bump the Singularity version in the process. That may also explain the different error messages...

.github/workflows/pytest.yml
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@MatthiasZepper MatthiasZepper Nov 17, 2025 •
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Excellent catch! It totally escaped me, that we are running Singularity tests in that action as well.

In the pipeline template, we have upgraded the download test nf_core/pipeline-template/.github/workflows/download_pipeline.yml to Apptainer 1.34 instead of Singularity 3.8.3, which is about 3 years more recent. I think, this would be a good opportunity to piggy-back this change to the #tools test as well.

@mirpedrol @mashehu, @JulianFlesch any opinions against which Apptainer version we should test the pipelines and thus also tools?

@MatthiasZepper MatthiasZepper added this to the 3.5.0 milestone Nov 17, 2025
@rrahn @MatthiasZepper
Swich to Apptainer in pytest
01acabf 
Co-authored-by: Matthias Zepper <[email protected]>
@mashehu mashehu modified the milestones: 3.5.0, 3.6.0 Nov 18, 2025
@MatthiasZepper MatthiasZepper merged commit b4f5d50 into nf-core:dev Nov 18, 2025
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