Run mypy on conftest.py files separately to avoid duplicate module error

.github/workflows/ci.yml

@@ -81,16 +81,19 @@ jobs:
             python3 -m pip install --check-build-dependencies --no-build-isolation --config-settings=build-dir="build" --config-settings=cmake.build-type="Debug" --verbose .[docs,lint,tests,tutorials]
           fi
         shell: bash
+      - name: Clean build files
+        run: |
+          git clean -xdf
       - name: Update mypy configuration
         if: startsWith(matrix.backend, 'none') == true
         run: |
+          sed -i 's@\[tool\.mypy\]@[tool.mypy]\nexclude = "(^rbnicsx/backends|^tests/unit/backends)"@g' pyproject.toml
           echo "[[tool.mypy.overrides]]" >> pyproject.toml
           echo 'module = "dolfinx"' >> pyproject.toml
           echo "ignore_missing_imports = true" >> pyproject.toml
           echo "[[tool.mypy.overrides]]" >> pyproject.toml
           echo 'module = "dolfinx.*"' >> pyproject.toml
           echo "ignore_missing_imports = true" >> pyproject.toml
-          sed -i 's@exclude = "(^\\\\.eggs|^build|^dist|conftest\\\\.py\$)"@exclude = "(^\\\\.eggs|^build|^dist|conftest\\\\.py\$|^rbnicsx/backends|^tests/unit/backends)"@g' pyproject.toml
       - name: Run ruff on python files
         run: |
           python3 -m ruff .
@@ -99,7 +102,9 @@ jobs:
           python3 -m isort --check --diff .
       - name: Run mypy on python files
         run: |
-          python3 -m mypy .
+          python3 -m mypy --exclude=conftest.py .
+          python3 -m mypy tests/unit/conftest.py
+          python3 -m mypy tutorials/conftest.py
       - name: Run yamllint on workflows
         run: |
           python3 -m yamllint -d "{extends: default, rules: {document-start: {present: false}, line-length: disable, truthy: {check-keys: false}}}" .

pyproject.toml

@@ -91,7 +91,6 @@ known_first_party = ["rbnicsx"]
 check_untyped_defs = true
 disallow_any_unimported = true
 disallow_untyped_defs = true
-exclude = "(^\\.eggs|^build|^dist|conftest\\.py$)"
 implicit_reexport = true
 no_implicit_optional = true
 pretty = true
@@ -128,6 +127,14 @@ ignore_missing_imports = true
 module = "plum"
 ignore_missing_imports = true
 
+[[tool.mypy.overrides]]
+module = "scipy"
+ignore_missing_imports = true
+
+[[tool.mypy.overrides]]
+module = "scipy.*"
+ignore_missing_imports = true
+
 [[tool.mypy.overrides]]
 module = "slepc4py"
 ignore_missing_imports = true

rbnicsx/_backends/projection.py

@@ -122,8 +122,8 @@ def project_matrix_block(  # type: ignore[no-any-unimported]
     assert all(len(row) == len(a[0]) for row in a[1:]), "Matrix of forms has incorrect rows"
     assert len(B[1]) == len(a[0])
 
-    M = [len(B_i) for B_i in B[0]]
-    N = [len(B_j) for B_j in B[1]]
+    M = [len(B_i) for B_i in B[0]]  # type: ignore[arg-type]
+    N = [len(B_j) for B_j in B[1]]  # type: ignore[arg-type]
     assert A.size == (sum(M), sum(N))
     with BlockMatSubMatrixWrapper(A, M, N) as A_wrapper:
         for (i, j, A_ij) in A_wrapper:

tests/unit/conftest.py

@@ -25,10 +25,11 @@
 def to_dense_matrix() -> typing.Callable[  # type: ignore[no-any-unimported]
         [petsc4py.PETSc.Mat], np.typing.NDArray[petsc4py.PETSc.ScalarType]]:
     """Fixture that returns a function to convert the local part of a sparse PETSc Mat into a dense numpy ndarray."""
-    def _(mat: petsc4py.PETSc.Mat) -> np.typing.NDArray[petsc4py.PETSc.ScalarType]:
+    def _(mat: petsc4py.PETSc.Mat) -> np.typing.NDArray[petsc4py.PETSc.ScalarType]:  # type: ignore[no-any-unimported]
         """Convert the local part of a sparse PETSc Mat into a dense numpy ndarray."""
         ai, aj, av = mat.getValuesCSR()
-        return scipy.sparse.csr_matrix((av, aj, ai), shape=(mat.getLocalSize()[0], mat.getSize()[1])).toarray()
+        return scipy.sparse.csr_matrix(  # type: ignore[no-any-return]
+            (av, aj, ai), shape=(mat.getLocalSize()[0], mat.getSize()[1])).toarray()
     return _
 
 
@@ -37,7 +38,7 @@ def pytest_addoption(parser: pytest.Parser) -> None:
     parser.addoption("--skip-backends", action="store_true", help="Skip tests which require backends to be installed")
 
 
-def pytest_ignore_collect(
+def pytest_ignore_collect(  # type: ignore[no-any-unimported]
     collection_path: pathlib.Path, path: _pytest.compat.LEGACY_PATH, config: pytest.Config
 ) -> bool:
     """Honor the --skip-backends option to skip tests which require backends to be installed."""