Use ruff instead of flake8

.github/workflows/ci.yml

@@ -94,11 +94,10 @@ jobs:
           echo "[[tool.mypy.overrides]]" >> pyproject.toml
           echo 'module = "dolfinx.*"' >> pyproject.toml
           echo "ignore_missing_imports = true" >> pyproject.toml
-          sed -i 's@exclude = \[".eggs", "build", "dist"\]@exclude = [".eggs", "build", "dist", "rbnicsx/backends", "tests/unit/backends"]@g' 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 flake8 on python files
+      - name: Run ruff on python files
         run: |
-          python3 -m flake8 .
+          python3 -m ruff .
       - name: Run isort on python files
         run: |
           python3 -m isort --check --diff .
@@ -151,10 +150,10 @@ jobs:
           python3 -m pytest --ipynb-action=create-notebooks --np=2 tutorials || (($?==$NO_TESTS_COLLECTED))
           python3 -m pytest --ipynb-action=create-notebooks --tag-collapse --np=2 tutorials || (($?==$NO_TESTS_COLLECTED))
         shell: bash
-      - name: Run flake8 on tutorial files
+      - name: Run ruff on tutorial files
         if: startsWith(matrix.backend, 'none') != true
         run: |
-          python3 -m nbqa flake8 .
+          python3 -m nbqa ruff .
       - name: Run isort on tutorial files
         if: startsWith(matrix.backend, 'none') != true
         run: |

pyproject.toml

@@ -61,14 +61,9 @@ docs = [
     "sphinx"
 ]
 lint = [
-    "flake8",
-    "flake8-annotations",
-    "flake8-docstrings",
-    "flake8-import-restrictions",
-    "flake8-isort",
-    "Flake8-pyproject",
-    "flake8-quotes",
+    "isort",
     "mypy",
+    "ruff",
     "yamllint"
 ]
 tests = [
@@ -85,25 +80,6 @@ tutorials = [
     "viskex @ git+https://github.com/viskex/viskex.git"
 ]
 
-[tool.flake8]
-max-line-length = 120
-show-source = true
-docstring-convention = "numpy"
-inline-quotes = "double"
-imr241_exclude = ["__future__", "rbnicsx", "rbnicsx.*"]
-imr245_include = "*"
-imr245_exclude = ["__future__", "rbnicsx", "rbnicsx.*"]
-ignore = ["ANN101", "W503"]
-exclude = [".eggs", "build", "dist"]
-per-file-ignores = [
-    "rbnicsx/__init__.py: I001, I004",
-    "rbnicsx/**/__init__.py: F401",
-    "tutorials/0*.py: D100, F401, I004",
-    "tutorials/1*.py: D100, F401, I004",
-    "tutorials/**/0*.py: D100, F401, I004",
-    "tutorials/**/1*.py: D100, F401, I004"
-]
-
 [tool.isort]
 line_length = 120
 multi_line_output = 4
@@ -164,6 +140,26 @@ ignore_missing_imports = true
 module = "ufl"
 ignore_missing_imports = true
 
+[tool.ruff]
+line-length = 120
+select = ["ANN", "D", "E", "F", "ICN", "N", "Q", "RUF", "W"]
+ignore = ["ANN101"]
+
+[tool.ruff.per-file-ignores]
+"rbnicsx/**/__init__.py" = ["F401"]
+"rbnicsx/**/*.py" = ["N802", "N803", "N806"]
+"tests/unit/**/*.py" = ["N802", "N803", "N806"]
+"tutorials/0*.py" = ["D100", "F401", "N803", "N806"]
+"tutorials/1*.py" = ["D100", "F401", "N803", "N806"]
+"tutorials/**/0*.py" = ["D100", "F401", "N803", "N806"]
+"tutorials/**/1*.py" = ["D100", "F401", "N803", "N806"]
+
+[tool.ruff.pycodestyle]
+max-doc-length = 120
+
+[tool.ruff.pydocstyle]
+convention = "numpy"
+
 [tool.scikit-build]
 cmake.source-dir = "rbnicsx/_cpp"
 wheel.packages = ["rbnicsx"]

rbnicsx/_backends/functions_list.py

@@ -179,12 +179,10 @@ def __len__(self: Self) -> int:
 
     @typing.overload
     def __getitem__(self: Self, key: int) -> Function:  # pragma: no cover
-        """Stub of __getitem__ for type checking. See the concrete implementation below."""
         ...
 
     @typing.overload
     def __getitem__(self: Self, key: slice) -> Self:  # pragma: no cover
-        """Stub of __getitem__ for type checking. See the concrete implementation below."""
         ...
 
     def __getitem__(self: Self, key: typing.Union[int, slice]) -> typing.Union[Function, Self]:

rbnicsx/_backends/online_tensors.py

@@ -350,7 +350,7 @@ def __iter__(self) -> typing.Iterator[  # type: ignore[no-any-unimported]
                 typing.Tuple[int, int, petsc4py.PETSc.Mat]]:
             """Iterate over blocks."""
             with contextlib.ExitStack() as wrapper_stack:
-                for (I, row_indices_) in enumerate(self._row_indices):
+                for (I, row_indices_) in enumerate(self._row_indices):  # noqa: E741
                     for (J, col_indices_) in enumerate(self._col_indices):
                         wrapper = MatSubMatrixContextManager(self._A, row_indices_, col_indices_)
                         yield (I, J, wrapper_stack.enter_context(wrapper))

rbnicsx/_backends/tensors_array.py

@@ -218,12 +218,10 @@ def contraction(  # type: ignore[no-any-unimported]
     def __getitem__(  # type: ignore[no-any-unimported]
         self: Self, key: typing.Union[int, typing.Tuple[int, ...]]
     ) -> typing.Union[petsc4py.PETSc.Mat, petsc4py.PETSc.Vec]:  # pragma: no cover
-        """Stub of __getitem__ for type checking. See the concrete implementation below."""
         ...
 
     @typing.overload
     def __getitem__(self: Self, key: typing.Union[slice, typing.Tuple[slice, slice]]) -> Self:  # pragma: no cover
-        """Stub of __getitem__ for type checking. See the concrete implementation below."""
         ...
 
     def __getitem__(  # type: ignore[no-any-unimported]

rbnicsx/_backends/tensors_list.py

@@ -224,12 +224,10 @@ def __len__(self: Self) -> int:
     @typing.overload
     def __getitem__(self: Self, key: int) -> typing.Union[  # type: ignore[no-any-unimported]
             petsc4py.PETSc.Mat, petsc4py.PETSc.Vec]:  # pragma: no cover
-        """Stub of __getitem__ for type checking. See the concrete implementation below."""
         ...
 
     @typing.overload
     def __getitem__(self: Self, key: slice) -> Self:  # pragma: no cover
-        """Stub of __getitem__ for type checking. See the concrete implementation below."""
         ...
 
     def __getitem__(self: Self, key: typing.Union[int, slice]) -> typing.Union[  # type: ignore[no-any-unimported]

rbnicsx/backends/projection.py

@@ -73,7 +73,7 @@ def project_vector(  # type: ignore[no-any-unimported] # noqa: F811
 
 
 @plum.dispatch
-def project_vector(*args, **kwargs):  # type: ignore[no-untyped-def] # noqa: F811
+def project_vector(*args, **kwargs):  # type: ignore[no-untyped-def] # noqa: ANN002, ANN003, ANN201, F811
     """Project a linear form onto the reduced basis."""
     raise NotImplementedError("The abstract case has not been implemented")  # pragma: no cover
 
@@ -127,7 +127,7 @@ def project_vector_block(  # type: ignore[no-any-unimported] # noqa: F811
 
 
 @plum.dispatch
-def project_vector_block(*args, **kwargs):  # type: ignore[no-untyped-def] # noqa: F811
+def project_vector_block(*args, **kwargs):  # type: ignore[no-untyped-def] # noqa: ANN002, ANN003, ANN201, F811
     """Project a list of linear forms onto the reduced basis."""
     raise NotImplementedError("The abstract case has not been implemented")  # pragma: no cover
 
@@ -191,7 +191,7 @@ def project_matrix(  # type: ignore[no-any-unimported] # noqa: F811
 
 
 @plum.dispatch
-def project_matrix(*args, **kwargs):  # type: ignore[no-untyped-def] # noqa: F811
+def project_matrix(*args, **kwargs):  # type: ignore[no-untyped-def] # noqa: ANN002, ANN003, ANN201, F811
     """Project a bilinear form onto the reduced basis."""
     raise NotImplementedError("The abstract case has not been implemented")  # pragma: no cover
 
@@ -260,7 +260,7 @@ def project_matrix_block(  # type: ignore[no-any-unimported] # noqa: F811
 
 
 @plum.dispatch
-def project_matrix_block(*args, **kwargs):  # type: ignore[no-untyped-def] # noqa: F811
+def project_matrix_block(*args, **kwargs):  # type: ignore[no-untyped-def] # noqa: ANN002, ANN003, ANN201, F811
     """Project a matrix of bilinear forms onto the reduced basis."""
     raise NotImplementedError("The abstract case has not been implemented")  # pragma: no cover
 

rbnicsx/backends/proper_orthogonal_decomposition.py

@@ -100,7 +100,9 @@ def proper_orthogonal_decomposition(  # type: ignore[no-any-unimported] # noqa:
 
 
 @plum.dispatch
-def proper_orthogonal_decomposition(*args, **kwargs):  # type: ignore[no-untyped-def] # noqa: F811
+def proper_orthogonal_decomposition(  # type: ignore[no-untyped-def] # noqa: ANN201, F811
+    *args, **kwargs  # noqa: ANN002, ANN003
+):
     """Compute the proper orthogonal decomposition of a set of snapshots or tensors."""
     raise NotImplementedError("The abstract case has not been implemented")  # pragma: no cover
 

rbnicsx/online/projection.py

@@ -71,7 +71,7 @@ def project_vector(  # type: ignore[no-any-unimported] # noqa: F811
 
 
 @plum.dispatch
-def project_vector(*args, **kwargs):  # type: ignore[no-untyped-def] # noqa: F811
+def project_vector(*args, **kwargs):  # type: ignore[no-untyped-def] # noqa: ANN002, ANN003, ANN201, F811
     """Project a linear form onto the reduced basis."""
     raise NotImplementedError("The abstract case has not been implemented")  # pragma: no cover
 
@@ -123,7 +123,7 @@ def project_vector_block(  # type: ignore[no-any-unimported] # noqa: F811
 
 
 @plum.dispatch
-def project_vector_block(*args, **kwargs):  # type: ignore[no-untyped-def] # noqa: F811
+def project_vector_block(*args, **kwargs):  # type: ignore[no-untyped-def] # noqa: ANN002, ANN003, ANN201, F811
     """Project a list of linear forms onto the reduced basis."""
     raise NotImplementedError("The abstract case has not been implemented")  # pragma: no cover
 
@@ -183,7 +183,7 @@ def project_matrix(  # type: ignore[no-any-unimported] # noqa: F811
 
 
 @plum.dispatch
-def project_matrix(*args, **kwargs):  # type: ignore[no-untyped-def] # noqa: F811
+def project_matrix(*args, **kwargs):  # type: ignore[no-untyped-def] # noqa: ANN002, ANN003, ANN201, F811
     """Project a bilinear form onto the reduced basis."""
     raise NotImplementedError("The abstract case has not been implemented")  # pragma: no cover
 
@@ -255,7 +255,7 @@ def project_matrix_block(  # type: ignore[no-any-unimported] # noqa: F811
 
 
 @plum.dispatch
-def project_matrix_block(*args, **kwargs):  # type: ignore[no-untyped-def] # noqa: F811
+def project_matrix_block(*args, **kwargs):  # type: ignore[no-untyped-def] # noqa: ANN002, ANN003, ANN201, F811
     """Project a matrix of bilinear forms onto the reduced basis."""
     raise NotImplementedError("The abstract case has not been implemented")  # pragma: no cover
 

rbnicsx/online/proper_orthogonal_decomposition.py

@@ -26,7 +26,7 @@
 
 
 @plum.overload
-def proper_orthogonal_decomposition(  # type: ignore[no-any-unimported] # noqa: F811
+def proper_orthogonal_decomposition(  # type: ignore[no-any-unimported]
     functions_list: FunctionsList, inner_product: petsc4py.PETSc.Mat, N: int = -1,
     tol: petsc4py.PETSc.RealType = real_zero, normalize: bool = True
 ) -> typing.Tuple[
@@ -99,7 +99,9 @@ def proper_orthogonal_decomposition(  # type: ignore[no-any-unimported] # noqa:
 
 
 @plum.dispatch
-def proper_orthogonal_decomposition(*args, **kwargs):  # type: ignore[no-untyped-def] # noqa: F811
+def proper_orthogonal_decomposition(  # type: ignore[no-untyped-def] # noqa: ANN201, F811
+    *args, **kwargs  # noqa: ANN002, ANN003
+):
     """Compute the proper orthogonal decomposition of a set of online snapshots or tensors."""
     raise NotImplementedError("The abstract case has not been implemented")  # pragma: no cover
 

rbnicsx/online/tensors_array.py

@@ -66,7 +66,7 @@ def flattened_shape(self) -> typing.Tuple[typing.Union[int, typing.List[int]], .
         if isinstance(self._content_shape, tuple):
             return self.shape + self.content_shape  # type: ignore[operator]
         else:
-            return self.shape + (self.content_shape, )  # type: ignore[operator]
+            return self.shape + (self.content_shape, )  # type: ignore[operator] # noqa: RUF005
 
     @property
     def content_shape(self) -> typing.Union[

rbnicsx/test/order_of_magnitude.py

@@ -14,7 +14,6 @@
 
 @typing.overload
 def order_of_magnitude(numbers: typing.Union[float, np.float32, np.float64]) -> np.int32:  # pragma: no cover
-    """Stub of order_of_magnitude for type checking. See the concrete implementation below."""
     ...
 
 
@@ -24,7 +23,6 @@ def order_of_magnitude(  # type: ignore[no-any-unimported]
         np.typing.NDArray[typing.Union[np.float32, np.float64, petsc4py.PETSc.RealType]],
         typing.List[typing.Union[np.float32, np.float64, petsc4py.PETSc.RealType]]]
 ) -> np.typing.NDArray[np.int32]:  # pragma: no cover
-    """Stub of order_of_magnitude for type checking. See the concrete implementation below."""
     ...
 
 

tests/unit/online/test_online_tensors.py

@@ -288,7 +288,7 @@ def test_online_vector_block_sub_vector_wrapper_context_manager() -> None:
     for i in range(5):
         online_vec.setValue(i, i + 1)
     with rbnicsx.online.BlockVecSubVectorWrapper(online_vec, N) as online_vec_wrapper:
-        for (I, online_subvec) in enumerate(online_vec_wrapper):
+        for (I, online_subvec) in enumerate(online_vec_wrapper):  # noqa: E741
             assert isinstance(online_subvec, petsc4py.PETSc.Vec)
             assert online_subvec.size == N[I]
             for i in range(N[I]):
@@ -306,7 +306,7 @@ def test_online_vector_block_sub_vector_copier_context_manager() -> None:
     for i in range(5):
         online_vec.setValue(i, i + 1)
     with rbnicsx.online.BlockVecSubVectorCopier(online_vec, N) as online_vec_copier:
-        for (I, online_subvec) in enumerate(online_vec_copier):
+        for (I, online_subvec) in enumerate(online_vec_copier):  # noqa: E741
             assert isinstance(online_subvec, petsc4py.PETSc.Vec)
             assert online_subvec.size == N[I]
             for i in range(N[I]):
@@ -372,7 +372,7 @@ def test_online_matrix_block_sub_matrix_wrapper_context_manager() -> None:
             online_mat.setValue(i, j, i * 9 + j + 1)
     online_mat.assemble()
     with rbnicsx.online.BlockMatSubMatrixWrapper(online_mat, M, N) as online_mat_wrapper:
-        for (I, J, online_submat) in online_mat_wrapper:
+        for (I, J, online_submat) in online_mat_wrapper:  # noqa: E741
             assert isinstance(I, int)
             assert isinstance(J, int)
             assert isinstance(online_submat, petsc4py.PETSc.Mat)
@@ -400,7 +400,7 @@ def test_online_matrix_block_sub_matrix_copier_context_manager() -> None:
             online_mat.setValue(i, j, i * 9 + j + 1)
     online_mat.assemble()
     with rbnicsx.online.BlockMatSubMatrixCopier(online_mat, M, N) as online_mat_copier:
-        for (I, J, online_submat) in online_mat_copier:
+        for (I, J, online_submat) in online_mat_copier:  # noqa: E741
             assert isinstance(I, int)
             assert isinstance(J, int)
             assert isinstance(online_submat, petsc4py.PETSc.Mat)