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Update pyproject.toml with defusedxml in web #1337

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@kkaris kkaris commented Dec 22, 2024

This PR adds defusedxml as a dependency in web to avoid ModuleNotFoundError on startup.

Closes #1336.

@kkaris kkaris requested a review from cthoyt December 22, 2024 03:39
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bgyori commented Dec 22, 2024

Thanks so much for looking into this so promptly! One thing I am confused about is that we do seem to have curies[fastapi] listed here https://github.com/biopragmatics/bioregistry/blob/main/pyproject.toml#L136 and in turn defusedxml is listed in the fastapi dependencies at https://github.com/biopragmatics/curies/blob/main/pyproject.toml#L82. What could explain this?

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bgyori commented Dec 22, 2024

I think the more appropriate solution would be to limit to curies[fastapi]<0.10 for now, this is because the issue is not explicitly limited to just defusexml (see biopragmatics/curies#147).

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kkaris commented Jan 2, 2025

The latest image, c4cc41f73811 from Dec 28, seems to work fine. Closing this PR.

@kkaris kkaris closed this Jan 2, 2025
@cthoyt cthoyt deleted the fix-dependency branch January 13, 2025 09:29
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Latest docker image, e1513f80a4f3, fails to start due to ModuleNotFoundError
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