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 🤔

galaxy/lib/galaxy/webapps/openapi/utils.py

Line 69 in 1d99e6d

field_mapping, definitions = get_definitions(

I'll try to investigate... 🔎

[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 🤔

galaxy/lib/galaxy/webapps/openapi/utils.py

Line 69 in 1d99e6d

field_mapping, definitions = get_definitions(

I'll try to investigate... 🔎

Thanks! 🙏

[davelopez]

It looks like this is the issue pydantic/pydantic#10960

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

galaxy/lib/galaxy/schema/notifications.py

Line 463 in 7a68911

PersonalNotificationPreferences = Dict[PersonalNotificationCategory, NotificationCategorySettings]

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 😆

[davelopez]

The pydantic issue should be fixed in https://github.com/pydantic/pydantic/releases/tag/v2.10.3

[nsoranzo]

The pydantic issue should be fixed in https://github.com/pydantic/pydantic/releases/tag/v2.10.3

Yes, I noticed yesterday and already re-run the update process. The previous issue is indeed solved, although we need to update the OpenAPI schemas and fix some type annotation issues due to the new pydantic.

Something else is now breaking the ToolShed tests though (and I am not yet finished fixing the new UP031 errors), so it may be worth to split out the pydantic update and related fixes in a separate PR.

[nsoranzo]

Test failures unrelated (at last!)