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Add WDL conformance tests to CI #4530

Merged
merged 22 commits into from
Jul 21, 2023
Merged

Add WDL conformance tests to CI #4530

merged 22 commits into from
Jul 21, 2023

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stxue1
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@stxue1 stxue1 commented Jul 12, 2023

This resolves #4508. I also updated MiniWDL from 1.9.1 to 1.10.0 as the latest version fixes an issue with expression placeholders that lets two more conformance tests to run. I also marked them as slow as on my machine, each took about 2 minutes to run.

Changelog Entry

To be copied to the draft changelog by merger:

  • Added WDL conformance tests for toil-wdl-runner to CI

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 passes tests.
  • Make sure the PR has been reviewed since its last modification. If not, review it.
  • 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.

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@DailyDreaming DailyDreaming left a comment

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One comment, otherwise looks great! Thanks for adding these.

@@ -1,3 +1,4 @@
import hashlib
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Added by accident?

@adamnovak
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Looks like CI is failing in the spot autoscaling tests; probably the spot price is too high for them or something.

I am going to merge this anyway since it has nothing to do with them.

@adamnovak adamnovak merged commit 070f54e into master Jul 21, 2023
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Add WDL conformance test suite to Toil CI
3 participants