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[24.2] Handle isatools dependency #19582

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merged 3 commits into from
Feb 11, 2025

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jdavcs
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@jdavcs jdavcs commented Feb 10, 2025

As discussed in committers channel, there's a dependency conflict preventing publishing the galaxy-data package to pypi. The isa-rwval dependency is currently installed from a github fork due to the incompatibility of the original package with numpy 2.0 (see ISA-tools/isa-rwval#17 for context). However, such dependencies cannot be uploaded to PyPI.

The proposed solution is to remove the isatools dependency from the data package and wrap the import in datatypes in a try block.

Another option would be to publish the fork on PyPI.

(Thanks to @nsoranzo for proposed approach)

TODO:

  • package unit test error

License

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

@jdavcs jdavcs added kind/bug dependencies Pull requests that update a dependency file labels Feb 10, 2025
@jdavcs jdavcs added this to the 24.2 milestone Feb 10, 2025
@github-actions github-actions bot changed the title [24.2] Handle isatools dependency Handle isatools dependency Feb 10, 2025
@nsoranzo
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I'd do it as in https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/datatypes/molecules.py i.e. set the modules to None if the import failed, and check for not None before using them.

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jdavcs commented Feb 11, 2025

Test failures unrelated.

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I suppose you wanted to target release_24.2?

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Pushed a commit, hope it's OK.

@nsoranzo nsoranzo changed the base branch from dev to release_24.2 February 11, 2025 12:07
@github-actions github-actions bot changed the title Handle isatools dependency [24.2] Handle isatools dependency Feb 11, 2025
@jdavcs jdavcs merged commit c15a897 into galaxyproject:release_24.2 Feb 11, 2025
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