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

Vendorise packaging.versions.LegacyVersion #16058

Merged

Conversation

nsoranzo
Copy link
Member

@nsoranzo nsoranzo commented May 7, 2023

from packaging 21.3 .
This allows us to unpin packaging . Fix #15898 .

Additionally:

  • Use packaging.version.Version() instead of packaging.version.parse() for parsing versions of Galaxy, Pulsar, conda and conda-build, i.e. assume these are always PEP-440 compliant.
  • Use galaxy.tool_util.version.parse_version() (equivalent to packaging.version.parse() from packaging 21.3) for parsing (possibly non-PEP440-compliant) versions of Galaxy tools and conda packages (there is e.g. a samtools-1.2.rglab package in the bioconda channel).

This is the first step to fix the Galaxy tool sorting issue partially addressed by #13570 .

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.

Copy link
Member

@mvdbeek mvdbeek left a comment

Choose a reason for hiding this comment

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

Thank you so much @nsoranzo!

@mvdbeek mvdbeek merged commit 0dfc1dd into galaxyproject:dev May 8, 2023
@nsoranzo nsoranzo deleted the vendorise_packaging.versions.LegacyVersion branch May 8, 2023 10:07
nsoranzo added a commit to nsoranzo/galaxy that referenced this pull request Jun 27, 2023
Follow-up on galaxyproject#16058
where the pin was removed from ``pyproject.toml`` .
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.

Using packaging version <22 starts to conflict with other dependencies
2 participants