Fix all mypy static typing errors

[Copilot]

hatch run types:check reported 24 errors across 6 files. This resolves all of them.

pyproject.toml

• Add [[tool.mypy.overrides]] to ignore missing linkml_runtime.* stubs (no py.typed marker upstream)

src/pydantic2linkml/tools.py

• Cast strip_function_schema to match Callable[[CoreSchema], CoreSchema] dict value type (contravariance mismatch with AnyFunctionSchema parameter)
• Add @overload signatures to bucketize() so return type correctly reflects whether value_func is provided:

@overload
def bucketize(items: Iterable[T], key_func: Callable[[T], K]) -> defaultdict[K, list[T]]: ...

@overload
def bucketize(items: Iterable[T], key_func: Callable[[T], K], value_func: Callable[[T], V]) -> defaultdict[K, list[V]]: ...

src/pydantic2linkml/gen_linkml.py

• Replace union-typed to_sorted_lst helper with explicitly typed model_lst: list[type[BaseModel]] and enum_lst: list[type[Enum]] — fixes 3 downstream errors (dict-key, arg-type, union-attr)
• type: ignore[attr-defined] for _typing_extra.all_literal_values (renamed to literal_values in Pydantic 2.10)
• type: ignore[typeddict-item] for schema["schema"] access guarded by mode != "plain" (mypy can't narrow union of TypedDicts via string comparison)

Tests

• type: ignore[assignment] on intentional incompatible override in test_tools.py
• Replace walrus operator := in @pytest.mark.parametrize tuples with explicit literals (mypy doesn't track assignment expressions in decorator args)

Original prompt

---

This section details on the original issue you should resolve

<issue_title>Fix static typing errors</issue_title>
<issue_description>Currently, running static type checking via hatch run types:check 2>&1 produces the following output.

`hatch run types:check 2>&1` output

src/pydantic2linkml/tools.py:15: error: Skipping analyzing "linkml_runtime.linkml_model": module is installed, but missing library stubs or py.typed marker  [import-untyped]
src/pydantic2linkml/tools.py:16: error: Skipping analyzing "linkml_runtime.utils.formatutils": module is installed, but missing library stubs or py.typed marker  [import-untyped]
src/pydantic2linkml/tools.py:156: error: Dict entry 0 has incompatible type "str": "Callable[[AfterValidatorFunctionSchema | BeforeValidatorFunctionSchema | WrapValidatorFunctionSchema | PlainValidatorFunctionSchema], Mapping[str, Any]]"; expected "str": "Callable[[Mapping[str, Any]], Mapping[str, Any]]"  [dict-item]
src/pydantic2linkml/tools.py:157: error: Dict entry 1 has incompatible type "str": "Callable[[AfterValidatorFunctionSchema | BeforeValidatorFunctionSchema | WrapValidatorFunctionSchema | PlainValidatorFunctionSchema], Mapping[str, Any]]"; expected "str": "Callable[[Mapping[str, Any]], Mapping[str, Any]]"  [dict-item]
src/pydantic2linkml/tools.py:158: error: Dict entry 2 has incompatible type "str": "Callable[[AfterValidatorFunctionSchema | BeforeValidatorFunctionSchema | WrapValidatorFunctionSchema | PlainValidatorFunctionSchema], Mapping[str, Any]]"; expected "str": "Callable[[Mapping[str, Any]], Mapping[str, Any]]"  [dict-item]
src/pydantic2linkml/tools.py:159: error: Dict entry 3 has incompatible type "str": "Callable[[AfterValidatorFunctionSchema | BeforeValidatorFunctionSchema | WrapValidatorFunctionSchema | PlainValidatorFunctionSchema], Mapping[str, Any]]"; expected "str": "Callable[[Mapping[str, Any]], Mapping[str, Any]]"  [dict-item]
src/pydantic2linkml/tools.py:308: error: Argument 1 to "append" of "list" has incompatible type "T | V"; expected "T"  [arg-type]
src/pydantic2linkml/tools.py:309: error: Incompatible return value type (got "defaultdict[K, list[T]]", expected "defaultdict[K, list[V]]")  [return-value]
src/pydantic2linkml/gen_linkml.py:14: error: Skipping analyzing "linkml_runtime.linkml_model": module is installed, but missing library stubs or py.typed marker  [import-untyped]
src/pydantic2linkml/gen_linkml.py:21: error: Skipping analyzing "linkml_runtime.linkml_model.meta": module is installed, but missing library stubs or py.typed marker  [import-untyped]
src/pydantic2linkml/gen_linkml.py:22: error: Skipping analyzing "linkml_runtime.utils.schema_builder": module is installed, but missing library stubs or py.typed marker  [import-untyped]
src/pydantic2linkml/gen_linkml.py:62: error: Module has no attribute "all_literal_values"  [attr-defined]
src/pydantic2linkml/gen_linkml.py:121: error: Key expression in dictionary comprehension has incompatible type "type[Enum] | type[BaseModel]"; expected type "type[BaseModel]"  [misc]
src/pydantic2linkml/gen_linkml.py:121: error: Argument 1 to "get_locally_defined_fields" has incompatible type "type[Enum] | type[BaseModel]"; expected "type[BaseModel]"  [arg-type]
src/pydantic2linkml/gen_linkml.py:158: error: Item "ModelMetaclass" of "type[Enum] | type[BaseModel]" has no attribute "__iter__" (not iterable)  [union-attr]
src/pydantic2linkml/gen_linkml.py:965: error: TypedDict "PlainValidatorFunctionSchema" has no key "schema"  [typeddict-item]
src/pydantic2linkml/cli/__init__.py:6: error: Skipping analyzing "linkml_runtime.dumpers": module is installed, but missing library stubs or py.typed marker  [import-untyped]
src/pydantic2linkml/cli/__init__.py:6: note: See https://mypy.readthedocs.io/en/stable/running_mypy.html#missing-imports
tests/test_tools.py:10: error: Skipping analyzing "linkml_runtime.linkml_model": module is installed, but missing library stubs or py.typed marker  [import-untyped]
tests/test_tools.py:83: note: By default the bodies of untyped functions are not checked, consider using --check-untyped-defs  [annotation-unchecked]
tests/test_tools.py:84: note: By default the bodies of untyped functions are not checked, consider using --check-untyped-defs  [annotation-unchecked]
tests/test_tools.py:85: note: By default the bodies of untyped functions are not checked, consider using --check-untyped-defs  [annotation-unchecked]
tests/test_tools.py:137: note: By default the bodies of untyped functions are not checked, consider using --check-untyped-defs  [annotation-unchecked]
tests/test_tools.py:138: note: By default the bodies of untyped functions are not checked, consider using --check-untyped-defs  [annotation-unchecked]
tests/test_tools.py:155: note: By default the bodies of untyped functions are not checked, consider using --check-untyped-defs  [annotation-unchecked]
tests/test_tools.py:156: note: By default the bodies of untyped functions are not check...

</details>



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- Fixes dandi/pydantic2linkml#26

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