Fix the mypy errors at source instead of exempting two modules

The previous commit exempted 'dolfinx.la' and 'dolfinx.fem.petsc' from
disallow_any_unimported and warn_unused_ignores. That is a blunt
instrument: it turns off two checks for every line of two modules to
silence three specific errors. Remove it and address them where they
occur, which is what AGENTS.md asks for -- PETSc-related type checking
disabled on a per-line basis.

  - 'la.to_scipy' declares a scipy return type, and scipy is untyped, so
    the declaration itself trips disallow_any_unimported. Ignore that one
    signature.
  - The two '# type: ignore[attr-defined]' comments on the cffi lib
    attributes in 'fem/petsc.py' are never used, because the attributes
    are Any while cffi is untyped. Delete them.

scipy and cffi move into the existing third-party ignore_missing_imports
list, beside ufl, ffcx, gmsh and the rest, rather than sitting in a block
of their own.

Verified in a container reproducing the CI leg: 'Success' for all three
targets, 30, 27 and 84 source files.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>

Author: garth-wells

python/dolfinx/fem/petsc.py

@@ -2059,12 +2059,12 @@ def set_vals(A: int,
                                     """
         )
 
-        MatSetValuesLocal = _lib_cffi.MatSetValuesLocal  # type: ignore[attr-defined]
+        MatSetValuesLocal = _lib_cffi.MatSetValuesLocal
         """See PETSc `MatSetValuesLocal
         <https://petsc.org/release/manualpages/Mat/MatSetValuesLocal>`_
         documentation."""
 
-        MatSetValuesBlockedLocal = _lib_cffi.MatSetValuesBlockedLocal  # type: ignore[attr-defined]
+        MatSetValuesBlockedLocal = _lib_cffi.MatSetValuesBlockedLocal
         """See PETSc `MatSetValuesBlockedLocal
         <https://petsc.org/release/manualpages/Mat/MatSetValuesBlockedLocal>`_
         documentation."""

python/dolfinx/la/__init__.py

@@ -276,7 +276,9 @@ def to_dense(self) -> npt.NDArray[Scalar]:
         """
         return self._cpp_object.to_dense()  # type: ignore[return-value]
 
-    def to_scipy(self, ghosted: bool = False) -> _sparse.csr_matrix | _sparse.bsr_matrix:
+    def to_scipy(  # type: ignore[no-any-unimported]
+        self, ghosted: bool = False
+    ) -> _sparse.csr_matrix | _sparse.bsr_matrix:
         """Convert to a SciPy CSR/BSR matrix. Data is shared.
 
         Note:

python/pyproject.toml

@@ -111,24 +111,6 @@ warn_unused_ignores = true
 show_error_codes = true
 ignore_missing_imports = false
 
-# scipy and cffi ship no type information, and no stub packages are
-# installed in the environments CI checks in: the Spack legs run mypy
-# against the environment's interpreter, which has no pip, so stubs cannot
-# be added to it. Treat the two as untyped rather than reporting every use
-# of them.
-[[tool.mypy.overrides]]
-module = ["scipy.*", "cffi", "cffi.*", "_cffi_backend"]
-ignore_missing_imports = true
-
-# Consequences of the above, kept as narrow as the module list allows:
-# 'dolfinx.la' returns a scipy sparse matrix, whose type is therefore Any,
-# and the '# type: ignore[attr-defined]' comments on the cffi lib
-# attributes in 'dolfinx.fem.petsc' read as unused while cffi is untyped.
-[[tool.mypy.overrides]]
-module = ["dolfinx.la", "dolfinx.fem.petsc"]
-disallow_any_unimported = false
-warn_unused_ignores = false
-
 # Test bodies are unannotated pytest functions exercising loose numpy/dtype
 # patterns; check_untyped_defs and no_implicit_optional are not enforced
 # there.
@@ -195,6 +177,10 @@ module = [
       "pyvista",
       "pyvistaqt",
       "networkx",
+      "scipy.*",
+      "cffi",
+      "cffi.*",
+      "_cffi_backend",
 ]
 ignore_missing_imports = true