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CWL: Fix --no-container & prepull #5188

Merged
merged 3 commits into from
Jan 17, 2025
Merged

CWL: Fix --no-container & prepull #5188

merged 3 commits into from
Jan 17, 2025

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mr-c
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@mr-c mr-c commented Dec 17, 2024

I hit this bug while testing #5187 on a system that had podman but not docker.

Changelog Entry

To be copied to the draft changelog by merger:

    • CWL container prepull: no reason to if extensions are enabled, they are now supported by cwl-utils 0.36+
    • CWL container prepull: skip if --no-containers is specified

Reviewer Checklist

  • Make sure it is coming from issues/XXXX-fix-the-thing in the Toil repo, or from an external repo.
    • If it is coming from an external repo, make sure to pull it in for CI with:
      contrib/admin/test-pr otheruser theirbranchname issues/XXXX-fix-the-thing
      
    • If there is no associated issue, create one.
  • Read through the code changes. Make sure that it doesn't have:
    • Addition of trailing whitespace.
    • New variable or member names in camelCase that want to be in snake_case.
    • New functions without type hints.
    • New functions or classes without informative docstrings.
    • Changes to semantics not reflected in the relevant docstrings.
    • New or changed command line options for Toil workflows that are not reflected in docs/running/{cliOptions,cwl,wdl}.rst
    • New features without tests.
  • Comment on the lines of code where problems exist with a review comment. You can shift-click the line numbers in the diff to select multiple lines.
  • Finish the review with an overall description of your opinion.

Merger Checklist

  • Make sure the PR passed tests, including the Gitlab tests, for the most recent commit in its branch.
  • Make sure the PR has been reviewed. If not, review it. If it has been reviewed and any requested changes seem to have been addressed, proceed.
  • Merge with the Github "Squash and merge" feature.
    • If there are multiple authors' commits, add Co-authored-by to give credit to all contributing authors.
  • Copy its recommended changelog entry to the Draft Changelog.
  • Append the issue number in parentheses to the changelog entry.

@mr-c mr-c force-pushed the cwl_no_container branch from 75aedfa to e886b66 Compare January 13, 2025 10:38
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@adamnovak adamnovak left a comment

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This looks fine to me!

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@adamnovak adamnovak left a comment

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I was wrong, though.

src/toil/test/cwl/cwlTest.py Outdated Show resolved Hide resolved
@adamnovak adamnovak merged commit 55d4048 into master Jan 17, 2025
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@adamnovak adamnovak deleted the cwl_no_container branch January 17, 2025 17:17
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2 participants