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Don't drop stdout in subprocess call for LSF #5078

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merged 1 commit into from
Sep 3, 2024

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stxue1
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@stxue1 stxue1 commented Aug 29, 2024

Closes #4605

Changelog Entry

To be copied to the draft changelog by merger:

  • Fix bjobs stdout getting lost in LSF

Reviewer Checklist

  • Make sure it is coming from issues/XXXX-fix-the-thing in the Toil repo, or from an external repo.
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      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.
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    • 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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LGTM.

@DailyDreaming DailyDreaming merged commit 8a8fed4 into master Sep 3, 2024
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@DailyDreaming DailyDreaming deleted the issues/4605-lsf-stdout branch September 3, 2024 17:21
@DailyDreaming DailyDreaming restored the issues/4605-lsf-stdout branch September 3, 2024 17:21
@DailyDreaming DailyDreaming deleted the issues/4605-lsf-stdout branch September 3, 2024 17:21
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Successfully merging this pull request may close these issues.

Fails to parse subprocess.run stdout when running on LSF
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