support pydantic 3.13

[atravitz]

related to OpenFreeEnergy/gufe#808

LLM / AI generated code disclosure

LLMs or other AI-powered tools (beyond simple IDE use cases) were used in this contribution: no

Checklist

• All new code is appropriately documented (user-facing code must have complete docstrings).
• Added a news entry, or the changes are not user-facing.
• Ran pre-commit: you can run pre-commit locally or comment on this PR with pre-commit.ci autofix.
• Filled in the AI generated code disclosure.

Manual Tests: these are slow so don't need to be run every commit, only before merging and when relevant changes are made (generally at reviewer-discretion).

• GPU integration tests
• example notebook testing
• packaging tests: run this for any large feature PRs or PRs that add test data.

Developers certificate of origin

• I certify that this contribution is covered by the MIT License here and the Developer Certificate of Origin at https://developercertificate.org/.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 90.76%. Comparing base (5e6fb2e) to head (2c29142).
⚠️ Report is 1 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #2058      +/-   ##
==========================================
- Coverage   95.10%   90.76%   -4.34%     
==========================================
  Files         212      212              
  Lines       20703    20702       -1     
==========================================
- Hits        19689    18791     -898     
- Misses       1014     1911     +897     

Flag	Coverage Δ
fast-tests	90.76% <ø> (?)
slow-tests	?

Flags with carried forward coverage won't be shown. Click here to find out more.

☔ View full report in Codecov by Harness.
📢 Have feedback on the report? Share it here.

🚀 New features to boost your workflow:

• ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

[atravitz]

note, I still need to resolve:

pydantic/_internal/_generate_schema.py:2274: UnsupportedFieldAttributeWarning: The 'validate_default' attribute with value True was provided to the `Field()` function, which has no effect in the context it was used. 'validate_default' is field-specific metadata, and can only be attached to a model field using `Annotated` metadata or by assignment. This may have happened because an `Annotated` type alias using the `type` statement was used, or if the `Field()` function was attached to a single member of a union type.

[github-actions]

No API break detected ✅

View workflow run

Griffe output

$ griffe check "openfe" -s src --no-inspection --no-color --verbose -a origin/main

$ griffe check "openfecli" -s src --no-inspection --no-color --verbose -a origin/main