Lighter switch to ruff (#2998)

* Basic configuration from other branch.

* Ignore X | Y, our supported Python to old

* Cannot use isort package from ruff.

* Use traditional isort + ruff --fix .

* Unsafe fixes.

* Add back in isort.

* Add ruff.toml

* Fix.

* Ignore RUF012

* Fix circleci

* Remove deprecated numpy random call.

* Add back isort.

* Move Python minimum to 3.9 (discuss).

* More fixes.

* ruff fix.

* Fix isort configuration and re-isort.

* Fixes.

* Python 3.10

* Not necessary.

* Add back in some removals.

* isort.

* Rocky and Intel OneAPI on Python 3.9

* Seed random number generator.

* Remove | stuff.

* Fix circleci.

.circleci/config.yml

@@ -11,13 +11,12 @@ install-python-components: &install-python-components
     pip3 install git+https://github.com/FEniCS/ufl.git
     pip3 install git+https://github.com/FEniCS/ffcx.git
 
-flake8-python-code: &flake8-python-code
-  name: Flake8 checks on Python code
+ruff-isort-python-code: &ruff-isort-python-code
+  name: ruff and isort checks on Python code
   command: |
     cd python/
-    python3 -m flake8 dolfinx
-    python3 -m flake8 demo
-    python3 -m flake8 test
+    ruff check .
+    isort --check .
 
 configure-cpp: &configure-cpp
   name: Configure (C++)
@@ -101,7 +100,7 @@ jobs:
     steps:
       - checkout
       - run: *install-python-components
-      - run: *flake8-python-code
+      - run: *ruff-isort-python-code
       - run: *configure-cpp
       - run: *build-install-cpp
 
@@ -131,7 +130,7 @@ jobs:
     steps:
       - checkout
       - run: *install-python-components
-      - run: *flake8-python-code
+      - run: *ruff-isort-python-code
       - run: *configure-cpp
       - run: *build-install-cpp
 

.github/workflows/ccpp.yml

@@ -60,24 +60,15 @@ jobs:
           python3 -m pip install git+https://github.com/FEniCS/basix.git@${{ github.event.inputs.basix_ref }}
           python3 -m pip install git+https://github.com/FEniCS/ffcx.git@${{ github.event.inputs.ffcx_ref }}
 
-      - name: Flake8 checks
-        run: |
-          cd cpp/
-          python3 -m flake8 cmake
-          python3 -m flake8 demo
-          python3 -m flake8 test
-          cd ..
-          cd python/
-          python3 -m flake8 dolfinx
-          python3 -m flake8 demo
-          python3 -m flake8 test
-      - name: isort checks (non-blocking)
-        continue-on-error: true
+      - name: ruff and isort C++ .py file checks
         run: |
           cd cpp/
+          ruff check .
           python3 -m isort --check .
-          cd ..
+      - name: ruff and isort Python interface checks
+        run: |
           cd python/
+          ruff check .
           python3 -m isort --check .
       - name: mypy checks
         run: |

cpp/ruff.toml

@@ -0,0 +1 @@
+extend = "../python/pyproject.toml"

python/demo/demo_biharmonic.py

@@ -120,8 +120,7 @@
 from dolfinx import fem, io, mesh, plot
 from dolfinx.fem.petsc import LinearProblem
 from dolfinx.mesh import CellType, GhostMode
-from ufl import (CellDiameter, FacetNormal, avg, div, dS, dx, grad, inner,
-                 jump, pi, sin)
+from ufl import CellDiameter, FacetNormal, avg, div, dS, dx, grad, inner, jump, pi, sin
 
 # -
 

python/demo/demo_cahn-hilliard.py

@@ -202,7 +202,8 @@
 u.x.array[:] = 0.0
 
 # Interpolate initial condition
-u.sub(0).interpolate(lambda x: 0.63 + 0.02 * (0.5 - np.random.rand(x.shape[1])))
+rng = np.random.default_rng(42)
+u.sub(0).interpolate(lambda x: 0.63 + 0.02 * (0.5 - rng.random(x.shape[1])))
 u.x.scatter_forward()
 # -
 

python/demo/demo_elasticity.py

@@ -31,13 +31,10 @@
 import dolfinx
 import ufl
 from dolfinx import la
-from dolfinx.fem import (Expression, Function, FunctionSpace, dirichletbc,
-                         form, functionspace, locate_dofs_topological)
-from dolfinx.fem.petsc import (apply_lifting, assemble_matrix, assemble_vector,
-                               set_bc)
+from dolfinx.fem import Expression, Function, FunctionSpace, dirichletbc, form, functionspace, locate_dofs_topological
+from dolfinx.fem.petsc import apply_lifting, assemble_matrix, assemble_vector, set_bc
 from dolfinx.io import XDMFFile
-from dolfinx.mesh import (CellType, GhostMode, create_box,
-                          locate_entities_boundary)
+from dolfinx.mesh import CellType, GhostMode, create_box, locate_entities_boundary
 from ufl import dx, grad, inner
 
 dtype = PETSc.ScalarType  # type: ignore

python/demo/demo_lagrange_variants.py

@@ -17,7 +17,6 @@
 #
 # We begin this demo by importing the required modules.
 
-import typing
 
 from mpi4py import MPI
 
@@ -166,8 +165,8 @@ def saw_tooth(x):
     uh = fem.Function(V)
     uh.interpolate(lambda x: saw_tooth(x[0]))
     if MPI.COMM_WORLD.size == 1:  # Skip this plotting in parallel
-        pts: typing.List[typing.List[float]] = []
-        cells: typing.List[int] = []
+        pts: list[list[float]] = []
+        cells: list[int] = []
         for cell in range(10):
             for i in range(51):
                 pts.append([cell / 10 + i / 50 / 10, 0, 0])

python/demo/demo_mixed-poisson.py

@@ -101,8 +101,7 @@
 from basix.ufl import element, mixed_element
 from dolfinx import fem, io, mesh
 from dolfinx.fem.petsc import LinearProblem
-from ufl import (Measure, SpatialCoordinate, TestFunctions, TrialFunctions,
-                 div, exp, inner)
+from ufl import Measure, SpatialCoordinate, TestFunctions, TrialFunctions, div, exp, inner
 
 msh = mesh.create_unit_square(MPI.COMM_WORLD, 32, 32, mesh.CellType.quadrilateral)
 

python/demo/demo_navier-stokes.py

@@ -171,8 +171,8 @@
 
 from dolfinx import default_real_type, fem, io, mesh
 from dolfinx.fem.petsc import assemble_matrix_block, assemble_vector_block
-from ufl import (CellDiameter, FacetNormal, TestFunction, TrialFunction, avg,
-                 conditional, div, dot, dS, ds, dx, grad, gt, inner, outer)
+from ufl import (CellDiameter, FacetNormal, TestFunction, TrialFunction, avg, conditional, div, dot, dS, ds, dx, grad,
+                 gt, inner, outer)
 
 if np.issubdtype(PETSc.ScalarType, np.complexfloating):  # type: ignore
     print("Demo should only be executed with DOLFINx real mode")

python/demo/demo_pml/demo_pml.py

@@ -17,7 +17,7 @@
 # +
 import sys
 from functools import partial
-from typing import Tuple, Union
+from typing import Union
 
 from mpi4py import MPI
 
@@ -358,7 +358,7 @@ def pml_coordinates(x: ufl.indexed.Indexed, alpha: float, k0: complex, l_dom: fl
 
 def create_eps_mu(pml: ufl.tensors.ListTensor,
                   eps_bkg: Union[float, ufl.tensors.ListTensor],
-                  mu_bkg: Union[float, ufl.tensors.ListTensor]) -> Tuple[ufl.tensors.ComponentTensor,
+                  mu_bkg: Union[float, ufl.tensors.ListTensor]) -> tuple[ufl.tensors.ComponentTensor,
                                                                          ufl.tensors.ComponentTensor]:
     J = ufl.grad(pml)
 

python/demo/demo_pml/efficiencies_pml_demo.py

@@ -64,7 +64,6 @@
 # & q_{\mathrm{abs}} = q_{\mathrm{ext}} - q_{\mathrm{sca}}
 # $$
 
-from typing import Tuple
 
 import numpy as np
 from scipy.special import h2vp, hankel2, jv, jvp
@@ -107,7 +106,7 @@ def compute_a(nu: int, m: complex, alpha: float) -> float:
 
 def calculate_analytical_efficiencies(eps: complex, n_bkg: float,
                                       wl0: float, radius_wire: float,
-                                      num_n: int = 50) -> Tuple[float, float, float]:
+                                      num_n: int = 50) -> tuple[float, float, float]:
     m = np.sqrt(np.conj(eps)) / n_bkg
     alpha = 2 * np.pi * radius_wire / wl0 * n_bkg
     c = 2 / alpha

python/demo/demo_pml/mesh_wire_pml.py

@@ -30,7 +30,6 @@
 
 import sys
 from functools import reduce
-from typing import List
 
 import numpy.typing
 
@@ -117,7 +116,7 @@ def generate_mesh_wire(radius_wire: float, radius_scatt: float, l_dom: float, l_
     gmsh.model.addPhysicalGroup(dim, y_group, tag=pml_tag + 2)
 
     # Marker interior surface in bkg group
-    boundaries: List[numpy.typing.NDArray[numpy.int32]] = []
+    boundaries: list[numpy.typing.NDArray[numpy.int32]] = []
     for tag in bkg_group:
         boundary_pairs = gmsh.model.get_boundary([(dim, tag)], oriented=False)
         boundaries.append(numpy.asarray([pair[1] for pair in boundary_pairs], dtype=numpy.int32))

python/demo/demo_pyvista.py

@@ -29,8 +29,7 @@
 
 import dolfinx.plot as plot
 from dolfinx.fem import Function, functionspace
-from dolfinx.mesh import (CellType, compute_midpoints, create_unit_cube,
-                          create_unit_square, meshtags)
+from dolfinx.mesh import CellType, compute_midpoints, create_unit_cube, create_unit_square, meshtags
 
 try:
     import pyvista

python/demo/demo_scattering_boundary_conditions/analytical_efficiencies_wire.py

@@ -64,7 +64,6 @@
 # & q_{\mathrm{abs}} = q_{\mathrm{ext}} - q_{\mathrm{sca}}
 # $$
 
-from typing import Tuple
 
 import numpy as np
 from scipy.special import h2vp, hankel2, jv, jvp
@@ -106,7 +105,7 @@ def compute_a(nu: int, m: complex, alpha: float) -> float:
 
 
 def calculate_analytical_efficiencies(eps: complex, n_bkg: float, wl0: float, radius_wire: float,
-                                      num_n: int = 50) -> Tuple[float, float, float]:
+                                      num_n: int = 50) -> tuple[float, float, float]:
     m = np.sqrt(np.conj(eps)) / n_bkg
     alpha = 2 * np.pi * radius_wire / wl0 * n_bkg
     c = 2 / alpha

python/demo/demo_scattering_boundary_conditions/demo_scattering_boundary_conditions.py

@@ -31,7 +31,6 @@
 
 # +
 import sys
-from typing import Tuple
 
 from mpi4py import MPI
 
@@ -115,7 +114,7 @@ def __init__(self, theta: float, n_bkg: float, k0: complex):
         self.k0 = k0  # vacuum wavevector
         self.n_bkg = n_bkg  # background refractive index
 
-    def eval(self, x: np.typing.NDArray[np.float64]) -> Tuple[np.typing.NDArray[np.complex128],
+    def eval(self, x: np.typing.NDArray[np.float64]) -> tuple[np.typing.NDArray[np.complex128],
                                                               np.typing.NDArray[np.complex128]]:
         kx = self.n_bkg * self.k0 * np.cos(self.theta)
         ky = self.n_bkg * self.k0 * np.sin(self.theta)

python/demo/demo_static-condensation.py

@@ -33,16 +33,13 @@
 import ufl
 from basix.ufl import element
 from dolfinx import geometry
-from dolfinx.fem import (Form, Function, IntegralType, dirichletbc, form,
-                         form_cpp_class, functionspace,
+from dolfinx.fem import (Form, Function, IntegralType, dirichletbc, form, form_cpp_class, functionspace,
                          locate_dofs_topological)
-from dolfinx.fem.petsc import (apply_lifting, assemble_matrix, assemble_vector,
-                               set_bc)
+from dolfinx.fem.petsc import apply_lifting, assemble_matrix, assemble_vector, set_bc
 from dolfinx.io import XDMFFile
 from dolfinx.jit import ffcx_jit
 from dolfinx.mesh import locate_entities_boundary, meshtags
-from ffcx.codegeneration.utils import \
-    numba_ufcx_kernel_signature as ufcx_signature
+from ffcx.codegeneration.utils import numba_ufcx_kernel_signature as ufcx_signature
 
 if PETSc.RealType == np.float32:  # type: ignore
     print("float32 not yet supported for this demo.")

python/demo/demo_stokes.py

@@ -93,8 +93,7 @@
 import ufl
 from basix.ufl import element, mixed_element
 from dolfinx import fem, la
-from dolfinx.fem import (Constant, Function, dirichletbc,
-                         extract_function_spaces, form, functionspace,
+from dolfinx.fem import (Constant, Function, dirichletbc, extract_function_spaces, form, functionspace,
                          locate_dofs_topological)
 from dolfinx.fem.petsc import assemble_matrix_block, assemble_vector_block
 from dolfinx.io import XDMFFile

python/demo/demo_tnt-elements.py

@@ -23,18 +23,17 @@
 from mpi4py import MPI
 
 # +
-import matplotlib
+import matplotlib as mpl
 import matplotlib.pylab as plt
 import numpy as np
 
 import basix
 import basix.ufl
 from dolfinx import fem, mesh
 from dolfinx.fem.petsc import LinearProblem
-from ufl import (SpatialCoordinate, TestFunction, TrialFunction, cos, div, dx,
-                 grad, inner, sin)
+from ufl import SpatialCoordinate, TestFunction, TrialFunction, cos, div, dx, grad, inner, sin
 
-matplotlib.use('agg')
+mpl.use('agg')
 # -
 
 # ## Defining a degree 1 TNT element

python/demo/demo_waveguide/demo_half_loaded_waveguide.py

@@ -50,8 +50,7 @@
 from basix.ufl import element, mixed_element
 from dolfinx import default_scalar_type, fem, io, plot
 from dolfinx.fem.petsc import assemble_matrix
-from dolfinx.mesh import (CellType, create_rectangle, exterior_facet_indices,
-                          locate_entities)
+from dolfinx.mesh import CellType, create_rectangle, exterior_facet_indices, locate_entities
 
 try:
     import pyvista

python/dolfinx/__init__.py

@@ -20,11 +20,9 @@
 
 from dolfinx import common
 from dolfinx import cpp as _cpp
-from dolfinx import (fem, geometry, graph, io, jit, la, log, mesh, nls, plot,
-                     utils)
+from dolfinx import fem, geometry, graph, io, jit, la, log, mesh, nls, plot, utils
 # Initialise logging
-from dolfinx.common import (TimingType, git_commit_hash, has_debug, has_kahip,
-                            has_parmetis, list_timings, timing)
+from dolfinx.common import TimingType, git_commit_hash, has_debug, has_kahip, has_parmetis, list_timings, timing
 from dolfinx.cpp import __version__
 
 _cpp.common.init_logging(sys.argv)

python/dolfinx/common.py

@@ -9,8 +9,7 @@
 import typing
 
 from dolfinx import cpp as _cpp
-from dolfinx.cpp.common import (IndexMap, git_commit_hash, has_adios2,  # noqa
-                                has_debug, has_kahip, has_parmetis)
+from dolfinx.cpp.common import IndexMap, git_commit_hash, has_adios2, has_debug, has_kahip, has_parmetis  # noqa
 
 __all__ = ["IndexMap", "Timer", "timed"]
 

python/dolfinx/fem/__init__.py

@@ -5,21 +5,16 @@
 # SPDX-License-Identifier:    LGPL-3.0-or-later
 """Tools for assembling and manipulating finite element forms."""
 
-from dolfinx.cpp.fem import (IntegralType,
-                             create_nonmatching_meshes_interpolation_data)
+from dolfinx.cpp.fem import IntegralType, create_nonmatching_meshes_interpolation_data
 from dolfinx.cpp.fem import create_sparsity_pattern as _create_sparsity_pattern
 from dolfinx.cpp.fem import transpose_dofmap
-from dolfinx.fem.assemble import (apply_lifting, assemble_matrix,
-                                  assemble_scalar, assemble_vector,
-                                  create_matrix, create_vector, set_bc)
-from dolfinx.fem.bcs import (DirichletBC, bcs_by_block, dirichletbc,
-                             locate_dofs_geometrical, locate_dofs_topological)
+from dolfinx.fem.assemble import (apply_lifting, assemble_matrix, assemble_scalar, assemble_vector, create_matrix,
+                                  create_vector, set_bc)
+from dolfinx.fem.bcs import DirichletBC, bcs_by_block, dirichletbc, locate_dofs_geometrical, locate_dofs_topological
 from dolfinx.fem.dofmap import DofMap
 from dolfinx.fem.element import CoordinateElement, coordinate_element
-from dolfinx.fem.forms import (Form, extract_function_spaces, form,
-                               form_cpp_class)
-from dolfinx.fem.function import (Constant, ElementMetaData, Expression,
-                                  Function, FunctionSpace, functionspace)
+from dolfinx.fem.forms import Form, extract_function_spaces, form, form_cpp_class
+from dolfinx.fem.function import Constant, ElementMetaData, Expression, Function, FunctionSpace, functionspace
 
 
 def create_sparsity_pattern(a: Form):