Pydantic v2.11 model_fields-on-instance deprecation (models.py:117)

[tavateva]

Split out from #61 as a pre-existing warning that predates PR #96 and is out-of-scope for the coverage work.

Symptom

Observed in the test_coverage CI run (e.g. https://github.com/ChengLabResearch/ouroboros/actions/runs/28622389980):

test/helpers/test_models.py::test_model_with_json
  .../python/ouroboros/helpers/models.py:117: PydanticDeprecatedSince211: Accessing the 'model_fields' attribute on the instance is deprecated. Instead, you should access this attribute from the model class. Deprecated in Pydantic V2.11 to be removed in V3.0.
    for field in self.model_fields.keys():

Cause

copy_values_from_other (models.py:117) accesses self.model_fields.keys() on a BaseModel instance. Pydantic V2.11 deprecated instance-level model_fields; V3.0 will remove it entirely.

def copy_values_from_other(self: BaseModel, other: BaseModel):
    for field in self.model_fields.keys():          # <-- deprecated
        setattr(self, field, getattr(other, field))

Fix

Access model_fields off the class instead:

def copy_values_from_other(self: BaseModel, other: BaseModel):
    for field in type(self).model_fields.keys():
        setattr(self, field, getattr(other, field))

Or explicitly self.__class__.model_fields. Either satisfies Pydantic V3.0 while keeping subclass polymorphism.

Acceptance

• models.py:117 uses class-level model_fields access.
• test_coverage workflow run for the branch shows the PydanticDeprecatedSince211 warning gone.
• Ripgrep confirms no other instance-level model_fields / model_fields_set / model_computed_fields access remains in python/ouroboros/.

Verification

cd python
poetry run pytest test/helpers/test_models.py -W error::pydantic.PydanticDeprecatedSince211

Should exit 0 after the fix (currently errors on the deprecation).

Out of scope

• SharedNPArray.__del__ AttributeError warning — tracked separately in SharedNPArray.__del__ AttributeError on partially-constructed instance (mem.py:76) #97 (or whatever number gets assigned).