Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

[24.1] Tighten axt sniffer #18204

Merged
merged 7 commits into from
May 29, 2024
Merged

Conversation

martenson
Copy link
Member

e.g. it would incorrectly sniff chain as axt since the comment line starts with "##matrix=axtChain"

How to test the changes?

(Select all options that apply)

  • I've included appropriate automated tests.
  • This is a refactoring of components with existing test coverage.
  • Instructions for manual testing are as follows:
    1. [add testing steps and prerequisites here if you didn't write automated tests covering all your changes]

License

  • I agree to license these and all my past contributions to the core galaxy codebase under the MIT license.

e.g. it would incorrectly sniff chain as axt since the comment line starts with "##matrix=axtChain"
@martenson martenson added this to the 24.1 milestone May 22, 2024
@jdavcs jdavcs changed the title [24.1] tighten axt sniffer [24.1] Tighten axt sniffer May 23, 2024
Copy link
Contributor

@bernt-matthias bernt-matthias left a comment

Choose a reason for hiding this comment

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

Would it be an option to add a test case for the case that was a false positive before?

lib/galaxy/datatypes/sequence.py Outdated Show resolved Hide resolved
lib/galaxy/datatypes/sequence.py Outdated Show resolved Hide resolved
lib/galaxy/datatypes/sequence.py Show resolved Hide resolved
@martenson
Copy link
Member Author

@bernt-matthias thanks for the suggestion! I added the test in 9ed4eda

@nsoranzo
Copy link
Member

The failed integration test is relevant.

martenson added 3 commits May 24, 2024 10:14
properly ignore comments
do not read the dataset unbounded, I think we have enough info from the headers and the first data line
@mvdbeek mvdbeek merged commit f0d4f52 into galaxyproject:release_24.1 May 29, 2024
46 of 49 checks passed
@martenson martenson deleted the tight-axt branch June 8, 2024 03:59
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Projects
None yet
Development

Successfully merging this pull request may close these issues.

4 participants