Skip to content

CWL: pass mutable=True to readGlobalFile as appropriate - #5648

Merged
adamnovak merged 3 commits into
masterfrom
cwl_readGlobalFile_mutable
Oct 15, 2026
Merged

adamnovak merged 3 commits into
masterfrom
cwl_readGlobalFile_mutable

Conversation

@mr-c

@mr-c mr-c commented Oct 14, 2026

Copy link
Copy Markdown
Contributor

In response to #4647 (comment)

  • CWL: pass mutable=True to readGlobalFile as appropriate
  • formatting
  • Makefile: skip exporting these variables as it slows down Make unnecessarily
  • docs autoapi: skip most of the tests

Changelog Entry

To be copied to the draft changelog by merger:

  • PR submitter writes their recommendation for a changelog entry here

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_readGlobalFile_mutable branch from b451f36 to 20f2d32 Compare October 14, 2026 09:22
mr-c added 2 commits October 14, 2026 12:36
56% speedup in `make docs`: from 3 minutes, 2 seconds to 1 minute,
18 seconds.
@mr-c
mr-c force-pushed the cwl_readGlobalFile_mutable branch from 20f2d32 to 31615f5 Compare October 14, 2026 10:36

@adamnovak adamnovak left a comment

Copy link
Copy Markdown
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

There's a lot of re-formatting but this looks like it might work.

It might be nice to have a test, but we also might not be able to do that without actually fixing #4647.

@adamnovak
adamnovak merged commit 28af54a into master Oct 15, 2026
3 checks passed
@adamnovak
adamnovak deleted the cwl_readGlobalFile_mutable branch October 15, 2026 19:31
@adamnovak

Copy link
Copy Markdown
Member

I'm not really sure how the Makefile change with not exporting the variables speeds anything up though.

@mr-c

mr-c commented Oct 15, 2026

Copy link
Copy Markdown
Contributor Author

I'm not really sure how the Makefile change with not exporting the variables speeds anything up though.

Before it was calling the python version script repeatedly for every shell evaluation, due to the exports

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

None yet

Projects

None yet

Development

Successfully merging this pull request may close these issues.

2 participants