Update Python dependencies

[galaxybot]

by running make update-dependencies.

[nsoranzo]

@davelopez Any idea about this error?

RuntimeError: Cannot update undefined schema for $ref=#/components/schemas/galaxy__schema__notifications__PersonalNotificationCategory-Input__1

Traceback in https://github.com/galaxyproject/galaxy/actions/runs/11983603557/job/33413355009?pr=19190 (and others).

[davelopez]

Hmmm I've never seen that one before, likely something changed in the new Pydantic version that our custom OpenAPI schema generation, FastAPI schema generation, or a combination of them broke it :thinking:

https://github.com/galaxyproject/galaxy/blob/1d99e6ddff433c4f006de1483fb09bf8738f7b2f/lib/galaxy/webapps/openapi/utils.py#L69

I'll try to investigate... :mag_right:

[nsoranzo]

Hmmm I've never seen that one before, likely something changed in the new Pydantic version that our custom OpenAPI schema generation, FastAPI schema generation, or a combination of them broke it 🤔

https://github.com/galaxyproject/galaxy/blob/1d99e6ddff433c4f006de1483fb09bf8738f7b2f/lib/galaxy/webapps/openapi/utils.py#L69

I'll try to investigate... 🔎

Thanks! :pray:

[davelopez]

It looks like this is the issue https://github.com/pydantic/pydantic/issues/10960

The PersonalNotificationCategory enum is used as a key of PersonalNotificationPreferences here:

https://github.com/galaxyproject/galaxy/blob/7a689110515a627ec1f0902f4c4c603022a920dc/lib/galaxy/schema/notifications.py#L463

We can pin pydantic for now or wait a bit if the fix is coming soon.

[nsoranzo]

Thanks for looking into this @davelopez ! Let's see if the pydantic issue gets fixed fast, otherwise we can pin it. In the meantime I still have 280 UP031 errors to fix for the Python linting :laughing: