Ruff format mk2

.circleci/config.yml

@@ -12,11 +12,11 @@ install-python-components: &install-python-components
     pip3 install git+https://github.com/FEniCS/ffcx.git
 
 ruff-isort-python-code: &ruff-isort-python-code
-  name: ruff and isort checks on Python code
+  name: ruff checks on Python code
   command: |
     cd python/
     ruff check .
-    isort --check .
+    ruff format --check .
 
 configure-cpp: &configure-cpp
   name: Configure (C++)

.github/workflows/ccpp.yml

@@ -60,16 +60,16 @@ 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: ruff and isort C++ .py file checks
+      - name: ruff C++ .py file checks
         run: |
           cd cpp/
           ruff check .
-          python3 -m isort --check .
-      - name: ruff and isort Python interface checks
+          ruff format --check .
+      - name: ruff Python interface checks
         run: |
           cd python/
           ruff check .
-          python3 -m isort --check .
+          ruff format --check .
       - name: mypy checks
         run: |
           cd python/

cpp/cmake/scripts/generate-cmakefiles.py

@@ -7,8 +7,7 @@
 import os
 import warnings
 
-cmakelists_noufl_str = \
-    """# This file was generated by running
+cmakelists_noufl_str = """# This file was generated by running
 #
 # python cmake/scripts/generate-cmakefiles.py from dolfinx/cpp
 #
@@ -51,8 +50,7 @@
 """
 
 
-cmakelists_nocomplex_str = \
-    """# This file was generated by running
+cmakelists_nocomplex_str = """# This file was generated by running
 #
 # python cmake/scripts/generate-cmakefiles from dolfinx/cpp
 #
@@ -117,8 +115,7 @@
 endif()
 """
 
-cmakelists_str = \
-    """# This file was generated by running
+cmakelists_str = """# This file was generated by running
 #
 # python cmake/scripts/generate-cmakefiles from dolfinx/cpp
 #
@@ -205,7 +202,6 @@ def generate_cmake_files(subdirectory, generated_files):
     executable_prefix = executable_prefixes[subdirectory]
     main_file_name = main_file_names[subdirectory]
     for root, dirs, files in os.walk(cwd + "/" + subdirectory):
-
         cpp_files = set()
         ufl_files = set()
         ufl_c_files = set()
@@ -224,9 +220,7 @@ def generate_cmake_files(subdirectory, generated_files):
             continue
 
         if "main.cpp" in os.listdir(program_dir):
-            name_forms = dict(
-                project_name=executable_prefix + program_name, src_files="NOT_SET"
-            )
+            name_forms = dict(project_name=executable_prefix + program_name, src_files="NOT_SET")
             for f in os.listdir(program_dir):
                 filename, extension = os.path.splitext(f)
                 if extension == ".cpp":
@@ -242,8 +236,7 @@ def generate_cmake_files(subdirectory, generated_files):
             continue
 
         if len(ufl_files) > 1:
-            raise RuntimeError(
-                "CMake generation supports exactly one UFL file")
+            raise RuntimeError("CMake generation supports exactly one UFL file")
 
         # Name of demo and cpp source files
         # print("**, ", main_file_name, cpp_files)
@@ -260,9 +253,7 @@ def generate_cmake_files(subdirectory, generated_files):
         if program_name not in executable_names:
             executable_names.add(program_name)
         else:
-            warnings.warn(
-                "Duplicate executable names found when generating CMakeLists.txt files."
-            )
+            warnings.warn("Duplicate executable names found when generating CMakeLists.txt files.")
 
         # Write file
         filename = os.path.join(program_dir, "CMakeLists.txt")

cpp/demo/biharmonic/biharmonic.py

@@ -5,9 +5,23 @@
 # the variational problem in UFL terms in a separate form file
 # :download:`biharmonic.py`.  We begin by defining the finite element::
 from basix.ufl import element
-from ufl import (CellDiameter, Coefficient, Constant, FacetNormal,
-                 FunctionSpace, Mesh, TestFunction, TrialFunction, avg, div,
-                 dS, dx, grad, inner, jump)
+from ufl import (
+    CellDiameter,
+    Coefficient,
+    Constant,
+    FacetNormal,
+    FunctionSpace,
+    Mesh,
+    TestFunction,
+    TrialFunction,
+    avg,
+    div,
+    dS,
+    dx,
+    grad,
+    inner,
+    jump,
+)
 
 e = element("Lagrange", "triangle", 2)
 
@@ -41,18 +55,20 @@
 # Normal component, mesh size and right-hand side
 n = FacetNormal(mesh)
 h = CellDiameter(mesh)
-h_avg = (h('+') + h('-')) / 2
+h_avg = (h("+") + h("-")) / 2
 alpha = Constant(mesh)
 
 # Finally, we define the bilinear and linear forms according to the
 # variational formulation of the equations. Integrals over
 # internal facets are indicated by ``*dS``. ::
 
 # Bilinear form
-a = inner(div(grad(u)), div(grad(v))) * dx \
-    - inner(avg(div(grad(u))), jump(grad(v), n)) * dS \
-    - inner(jump(grad(u), n), avg(div(grad(v)))) * dS \
+a = (
+    inner(div(grad(u)), div(grad(v))) * dx
+    - inner(avg(div(grad(u))), jump(grad(v), n)) * dS
+    - inner(jump(grad(u), n), avg(div(grad(v)))) * dS
     + alpha / h_avg * inner(jump(grad(u), n), jump(grad(v), n)) * dS
+)
 
 # Linear form
 L = inner(f, v) * dx

cpp/demo/hyperelasticity/hyperelasticity.py

@@ -9,18 +9,31 @@
 # dimensions, so first we need the appropriate finite element space and
 # trial and test functions on this space::
 from basix.ufl import element
-from ufl import (Coefficient, FunctionSpace, Identity, Mesh, TestFunction,
-                 TrialFunction, derivative, det, diff, dx, grad, ln, tr,
-                 variable)
+from ufl import (
+    Coefficient,
+    FunctionSpace,
+    Identity,
+    Mesh,
+    TestFunction,
+    TrialFunction,
+    derivative,
+    det,
+    diff,
+    dx,
+    grad,
+    ln,
+    tr,
+    variable,
+)
 
 # Function spaces
 e = element("Lagrange", "tetrahedron", 1, shape=(3,))
 mesh = Mesh(e)
 V = FunctionSpace(mesh, e)
 
 # Trial and test functions
-du = TrialFunction(V)     # Incremental displacement
-v = TestFunction(V)      # Test function
+du = TrialFunction(V)  # Incremental displacement
+v = TestFunction(V)  # Test function
 
 # Note that ``element`` with `shape=(3,)` creates a finite element space
 # of vector fields.
@@ -29,17 +42,17 @@
 # traction ``T`` and the displacement solution itself ``u``::
 
 # Functions
-u = Coefficient(V)        # Displacement from previous iteration
+u = Coefficient(V)  # Displacement from previous iteration
 # B = Coefficient(element)        # Body force per unit volume
 # T = Coefficient(element)        # Traction force on the boundary
 
 # Now, we can define the kinematic quantities involved in the model::
 
 # Kinematics
 d = len(u)
-I = Identity(d)         # Identity tensor  # noqa: E741
-F = variable(I + grad(u))         # Deformation gradient
-C = F.T * F               # Right Cauchy-Green tensor
+I = Identity(d)  # Identity tensor  # noqa: E741
+F = variable(I + grad(u))  # Deformation gradient
+C = F.T * F  # Right Cauchy-Green tensor
 
 # Invariants of deformation tensors
 Ic = tr(C)
@@ -60,7 +73,7 @@
 # ``derivative``::
 
 # Stored strain energy density (compressible neo-Hookean model)
-psi = (mu / 2) * (Ic - 3) - mu * ln(J) + (lmbda / 2) * (ln(J))**2
+psi = (mu / 2) * (Ic - 3) - mu * ln(J) + (lmbda / 2) * (ln(J)) ** 2
 
 # Total potential energy
 Pi = psi * dx  # - inner(B, u) * dx - inner(T, u) * ds

cpp/demo/poisson/poisson.py

@@ -5,8 +5,18 @@
 # the variational problem in UFL terms in a separate form file
 # :download:`poisson.py`.  We begin by defining the finite element::
 from basix.ufl import element
-from ufl import (Coefficient, Constant, FunctionSpace, Mesh, TestFunction,
-                 TrialFunction, ds, dx, grad, inner)
+from ufl import (
+    Coefficient,
+    Constant,
+    FunctionSpace,
+    Mesh,
+    TestFunction,
+    TrialFunction,
+    ds,
+    dx,
+    grad,
+    inner,
+)
 
 e = element("Lagrange", "triangle", 1)
 

cpp/demo/poisson_matrix_free/poisson.py

@@ -1,8 +1,18 @@
 # UFL input for the Matrix-free Poisson Demo
 # ==================================
 from basix.ufl import element
-from ufl import (Coefficient, Constant, FunctionSpace, Mesh, TestFunction,
-                 TrialFunction, action, dx, grad, inner)
+from ufl import (
+    Coefficient,
+    Constant,
+    FunctionSpace,
+    Mesh,
+    TestFunction,
+    TrialFunction,
+    action,
+    dx,
+    grad,
+    inner,
+)
 
 coord_element = element("Lagrange", "triangle", 1, shape=(2,))
 mesh = Mesh(coord_element)

cpp/doc/source/conf.py

@@ -17,25 +17,26 @@
 
 # -- Project information -----------------------------------------------------
 
-project = 'DOLFINx'
-copyright = '2022, FEniCS Project'
-author = 'FEniCS Project'
+project = "DOLFINx"
+copyright = "2022, FEniCS Project"
+author = "FEniCS Project"
 
 # The full version, including alpha/beta/rc tags
-release = '0.3.1'
+release = "0.3.1"
 
 
 # -- General configuration ---------------------------------------------------
 
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
-extensions = ['sphinx.ext.mathjax',
-              'breathe',
-              ]
+extensions = [
+    "sphinx.ext.mathjax",
+    "breathe",
+]
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
@@ -61,10 +62,10 @@
 
 breathe_projects = {"DOLFINx": "../xml/"}
 breathe_default_project = "DOLFINx"
-breathe_implementation_filename_extensions = ['.c', '.cc', '.cpp']
+breathe_implementation_filename_extensions = [".c", ".cc", ".cpp"]
 
 # Tell sphinx what the primary language being documented is.
-primary_domain = 'cpp'
+primary_domain = "cpp"
 
 # Tell sphinx what the pygments highlight language should be.
-highlight_language = 'cpp'
+highlight_language = "cpp"

cpp/test/poisson.py

@@ -1,6 +1,15 @@
 from basix.ufl import element
-from ufl import (Coefficient, Constant, FunctionSpace, Mesh, TestFunction,
-                 TrialFunction, dx, grad, inner)
+from ufl import (
+    Coefficient,
+    Constant,
+    FunctionSpace,
+    Mesh,
+    TestFunction,
+    TrialFunction,
+    dx,
+    grad,
+    inner,
+)
 
 e = element("Lagrange", "tetrahedron", 2)
 coord_element = element("Lagrange", "tetrahedron", 1, shape=(3,))

docker/Dockerfile.test-env

@@ -154,7 +154,7 @@ RUN if [ "$MPI" = "mpich" ]; then \
 #   documentation or run tests.
 RUN pip3 install --no-cache-dir --upgrade setuptools pip && \
     pip3 install --no-cache-dir cffi mpi4py numba numpy==${NUMPY_VERSION} scikit-build-core[pyproject] && \
-    pip3 install --no-cache-dir breathe clang-format cmakelang flake8 isort jupytext matplotlib mypy myst-parser nanobind==${NANOBIND_VERSION} pytest pytest-xdist ruff scipy sphinx sphinx_rtd_theme types-setuptools
+    pip3 install --no-cache-dir breathe clang-format cmakelang jupytext matplotlib mypy myst-parser nanobind==${NANOBIND_VERSION} pytest pytest-xdist ruff scipy sphinx sphinx_rtd_theme types-setuptools
 
 # Install KaHIP
 RUN wget -nc --quiet https://github.com/kahip/kahip/archive/v${KAHIP_VERSION}.tar.gz && \

python/demo/conftest.py

@@ -2,10 +2,13 @@
 
 
 def pytest_addoption(parser):
-    parser.addoption("--mpiexec", action="store", default="mpirun",
-                     help="Name of program to run MPI, e.g. mpiexec")
-    parser.addoption("--num-proc", action="store", default=1,
-                     help="Number of MPI processes to use")
+    parser.addoption(
+        "--mpiexec",
+        action="store",
+        default="mpirun",
+        help="Name of program to run MPI, e.g. mpiexec",
+    )
+    parser.addoption("--num-proc", action="store", default=1, help="Number of MPI processes to use")
 
 
 @pytest.fixture