Merge branch 'main' into dokken/document_refinement

.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/ISSUE_TEMPLATE/feature_request.yml

@@ -18,7 +18,7 @@ body:
   - type: textarea
     id: code-block
     attributes:
-      label: Suggestion user interface
+      label: Suggested user interface
       description: Please create a minimal (Python) code that shows how you would like the feature to work.
       render: python3
-      placeholder: No 3x``` encapsulation of code required
+      placeholder: No 3x``` encapsulation of code required

.github/workflows/ccpp.yml

@@ -28,48 +28,21 @@ on:
         type: string
 
 jobs:
-  build:
-    if: "!(contains(github.event.head_commit.message, '[ci skip]') || contains(github.event.head_commit.message, '[skip ci]'))"
+  lint:
     runs-on: ubuntu-latest
     container: ghcr.io/fenics/test-env:current-openmpi
-
-    env:
-      PETSC_ARCH: ${{ matrix.petsc_arch }}
-      OMPI_ALLOW_RUN_AS_ROOT: 1
-      OMPI_ALLOW_RUN_AS_ROOT_CONFIRM: 1
-
-    strategy:
-      matrix:
-        petsc_arch: [linux-gnu-real32-32, linux-gnu-real64-32, linux-gnu-complex64-32, linux-gnu-complex128-32, linux-gnu-real64-64, linux-gnu-complex128-64]
-
-    name: Build and test (${{ matrix.petsc_arch }})
-
     steps:
       - uses: actions/checkout@v4
-
-      - name: Install FEniCS Python components (default branches/tags)
-        if: github.event_name != 'workflow_dispatch'
-        run: |
-          python3 -m pip install git+https://github.com/FEniCS/ufl.git
-          python3 -m pip install git+https://github.com/FEniCS/basix.git
-          python3 -m pip install git+https://github.com/FEniCS/ffcx.git
-      - name: Install FEniCS Python components
-        if: github.event_name == 'workflow_dispatch'
-        run: |
-          python3 -m pip install git+https://github.com/FEniCS/ufl.git@${{ github.event.inputs.ufl_ref }}
-          python3 -m pip install git+https://github.com/FEniCS/basix.git@${{ 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 .py files in C++ code
         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/
@@ -93,6 +66,68 @@ jobs:
         run: |
           find . -type f \( -name "*.cmake" -o -name "*.cmake.in" -o -name "CMakeLists.txt" \) | xargs cmake-format --check
 
+  build:
+    if: "!(contains(github.event.head_commit.message, '[ci skip]') || contains(github.event.head_commit.message, '[skip ci]'))"
+    runs-on: ubuntu-latest
+    container: ghcr.io/fenics/test-env:current-openmpi
+    env:
+      SCOTCH_DIR: /usr/local/petsc/linux-gnu-real64-32
+
+    steps:
+      - name: Install FEniCS Python components (default branches/tags)
+        if: github.event_name != 'workflow_dispatch'
+        run: |
+          python3 -m pip install git+https://github.com/FEniCS/ufl.git
+          python3 -m pip install git+https://github.com/FEniCS/basix.git
+          python3 -m pip install git+https://github.com/FEniCS/ffcx.git
+      - name: Install FEniCS Python components
+        if: github.event_name == 'workflow_dispatch'
+        run: |
+          python3 -m pip install git+https://github.com/FEniCS/ufl.git@${{ github.event.inputs.ufl_ref }}
+          python3 -m pip install git+https://github.com/FEniCS/basix.git@${{ github.event.inputs.basix_ref }}
+          python3 -m pip install git+https://github.com/FEniCS/ffcx.git@${{ github.event.inputs.ffcx_ref }}
+
+      - uses: actions/checkout@v4
+      - name: Configure C++
+        run: cmake -G Ninja -DDOLFINX_ENABLE_PETSC=false -DCMAKE_BUILD_TYPE=Developer -B build -S cpp/
+      - name: Build and install C++ library
+        run: |
+          cmake --build build
+          cmake --install build
+      - name: Build Python interface
+        run: python3 -m pip -v install --check-build-dependencies --no-build-isolation --config-settings=cmake.build-type="Debug" python/
+      - name: Test Python import
+        run: python3 -c "import dolfinx; print(dolfinx.__version__)"
+
+  build-with-petsc:
+    if: "!(contains(github.event.head_commit.message, '[ci skip]') || contains(github.event.head_commit.message, '[skip ci]'))"
+    runs-on: ubuntu-latest
+    container: ghcr.io/fenics/test-env:current-openmpi
+    env:
+      PETSC_ARCH: ${{ matrix.petsc_arch }}
+      OMPI_ALLOW_RUN_AS_ROOT: 1
+      OMPI_ALLOW_RUN_AS_ROOT_CONFIRM: 1
+    strategy:
+      matrix:
+        petsc_arch: [linux-gnu-real32-32, linux-gnu-real64-32, linux-gnu-complex64-32, linux-gnu-complex128-32, linux-gnu-real64-64, linux-gnu-complex128-64]
+
+    name: Build and test (${{ matrix.petsc_arch }})
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install FEniCS Python components (default branches/tags)
+        if: github.event_name != 'workflow_dispatch'
+        run: |
+          python3 -m pip install git+https://github.com/FEniCS/ufl.git
+          python3 -m pip install git+https://github.com/FEniCS/basix.git
+          python3 -m pip install git+https://github.com/FEniCS/ffcx.git
+      - name: Install FEniCS Python components
+        if: github.event_name == 'workflow_dispatch'
+        run: |
+          python3 -m pip install git+https://github.com/FEniCS/ufl.git@${{ github.event.inputs.ufl_ref }}
+          python3 -m pip install git+https://github.com/FEniCS/basix.git@${{ github.event.inputs.basix_ref }}
+          python3 -m pip install git+https://github.com/FEniCS/ffcx.git@${{ github.event.inputs.ffcx_ref }}
+
       - name: Configure C++
         run: cmake -G Ninja -DCMAKE_BUILD_TYPE=Developer -B build -S cpp/
 

.github/workflows/conda.yml

@@ -15,7 +15,7 @@ jobs:
     name: Conda install and test
     strategy:
       matrix:
-        os: [ubuntu-22.04, macos-12, macos-13]
+        os: [ubuntu-22.04, macos-13, macos-14]
       fail-fast: false
     runs-on: ${{ matrix.os }}
     timeout-minutes: 30
@@ -30,15 +30,6 @@ jobs:
         run: |
           conda update conda
 
-      - name: Install DOLFINx (py3-9)
-        run: |
-          conda create -n env3-9 -c conda-forge python=3.9 fenics-dolfinx mpich
-          conda env export -n env3-9
-      - name: Test (py3-9)
-        run: |
-          conda run -n env3-9 python -c "from mpi4py import MPI; import dolfinx; dolfinx.mesh.create_rectangle(comm=MPI.COMM_WORLD, points=((0, 0), (2, 1)), n=(32, 16))"
-          conda run -n env3-9 mpirun -np 2 python -c "from mpi4py import MPI; import dolfinx; dolfinx.mesh.create_rectangle(comm=MPI.COMM_WORLD, points=((0, 0), (2, 1)), n=(32, 16))"
-
       - name: Install DOLFINx (py3-10)
         run: |
           conda create -n env3-10 -c conda-forge python=3.10 fenics-dolfinx mpich
@@ -48,11 +39,29 @@ jobs:
           conda run -n env3-10 python -c "from mpi4py import MPI; import dolfinx; dolfinx.mesh.create_rectangle(comm=MPI.COMM_WORLD, points=((0, 0), (2, 1)), n=(32, 16))"
           conda run -n env3-10 mpirun -np 2 python -c "from mpi4py import MPI; import dolfinx; dolfinx.mesh.create_rectangle(comm=MPI.COMM_WORLD, points=((0, 0), (2, 1)), n=(32, 16))"
 
-      - name: Install DOLFINx (py3-10, petsc-complex)
+      - name: Install DOLFINx (py3-11)
+        run: |
+          conda create -n env3-11 -c conda-forge python=3.11 fenics-dolfinx mpich
+          conda env export -n env3-11
+      - name: Test (py3-11)
+        run: |
+          conda run -n env3-11 python -c "from mpi4py import MPI; import dolfinx; dolfinx.mesh.create_rectangle(comm=MPI.COMM_WORLD, points=((0, 0), (2, 1)), n=(32, 16))"
+          conda run -n env3-11 mpirun -np 2 python -c "from mpi4py import MPI; import dolfinx; dolfinx.mesh.create_rectangle(comm=MPI.COMM_WORLD, points=((0, 0), (2, 1)), n=(32, 16))"
+
+      - name: Install DOLFINx (py3-12)
+        run: |
+          conda create -n env3-12 -c conda-forge python=3.12 fenics-dolfinx mpich
+          conda env export -n env3-12
+      - name: Test (py3-12)
+        run: |
+          conda run -n env3-12 python -c "from mpi4py import MPI; import dolfinx; dolfinx.mesh.create_rectangle(comm=MPI.COMM_WORLD, points=((0, 0), (2, 1)), n=(32, 16))"
+          conda run -n env3-12 mpirun -np 2 python -c "from mpi4py import MPI; import dolfinx; dolfinx.mesh.create_rectangle(comm=MPI.COMM_WORLD, points=((0, 0), (2, 1)), n=(32, 16))"
+
+      - name: Install DOLFINx (py3-12, petsc-complex)
         run: |
-          conda create -n env3-10-complex -c conda-forge python=3.10 fenics-dolfinx petsc=*=complex* mpich
-          conda env export -n env3-10-complex
-      - name: Test (py3-10-complex)
+          conda create -n env3-12-complex -c conda-forge python=3.12 fenics-dolfinx petsc=*=complex* mpich
+          conda env export -n env3-12-complex
+      - name: Test (py3-12-complex)
         run: |
-          conda run -n env3-10-complex python -c "from mpi4py import MPI; import dolfinx; dolfinx.mesh.create_rectangle(comm=MPI.COMM_WORLD, points=((0, 0), (2, 1)), n=(32, 16))"
-          conda run -n env3-10-complex mpirun -np 2 python -c "from mpi4py import MPI; import dolfinx; dolfinx.mesh.create_rectangle(comm=MPI.COMM_WORLD, points=((0, 0), (2, 1)), n=(32, 16))"
+          conda run -n env3-12-complex python -c "from mpi4py import MPI; import dolfinx; dolfinx.mesh.create_rectangle(comm=MPI.COMM_WORLD, points=((0, 0), (2, 1)), n=(32, 16))"
+          conda run -n env3-12-complex mpirun -np 2 python -c "from mpi4py import MPI; import dolfinx; dolfinx.mesh.create_rectangle(comm=MPI.COMM_WORLD, points=((0, 0), (2, 1)), n=(32, 16))"

.github/workflows/macos.yml

@@ -9,27 +9,27 @@ on:
 jobs:
   mac-os-build:
     name: macOS Homebrew install and test
-    runs-on: macos-13
+    runs-on: macos-14
     env:
       PETSC_ARCH: arch-darwin-c-opt
       PETSC_DIR: ${{ github.workspace }}/petsc
 
     steps:
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
-          python-version: "3.11"
+          python-version: "3.12"
 
       - name: Install Homebrew dependencies
         run: |
-          # brew install adios2 boost cmake hdf5-mpi ninja open-mpi pkg-config pugixml python # FEniCS
-          brew install boost cmake hdf5-mpi make ninja open-mpi pkg-config pugixml # FEniCS
+          brew install adios2 boost cmake hdf5-mpi make ninja open-mpi pkg-config pugixml # FEniCS
           brew install bison flex # PETSc
 
       - name: Install Python dependencies
         run: |
           python -m pip install --upgrade pip setuptools wheel
-          python -m pip install cython numpy mpi4py
+          python -m pip install cffi cppimport cython numba numpy pytest pytest-xdist scipy
+          python -m pip install --no-build-isolation mpi4py
 
       - name: Install minimal PETSc and petsc4py
         run: |
@@ -43,10 +43,13 @@ jobs:
             --with-scalar-type=real \
             --with-shared-libraries \
             --with-scalar-type=real \
-            --download-ptscotch
+            --download-metis \
+            --download-parmetis \
+            --download-ptscotch \
+            --download-superlu_dist
           make all
           cd src/binding/petsc4py
-          PETSC_DIR=$GITHUB_WORKSPACE/petsc PETSC_ARCH=arch-darwin-c-opt arch -x86_64 python -m pip install --no-cache-dir -v .
+          arch -arm64 python -m pip install --no-build-isolation --no-cache-dir -v .
 
       - name: Install FEniCSx dependencies
         run: |
@@ -59,20 +62,43 @@ jobs:
           path: dolfinx
 
       - name: Build and install DOLFINx C++ library
+        working-directory: dolfinx
         run: |
-          cmake -G Ninja -B build -S dolfinx/cpp/
+          cmake -G Ninja -B build -S cpp/
           cmake --build build
-          cmake --install build
+          sudo cmake --install build
+
+      - name: Build C++ unit tests
+        working-directory: dolfinx
+        run: |
+          cmake -G Ninja -DCMAKE_BUILD_TYPE=Developer -B build/test/ -S cpp/test/
+          cmake --build build/test --parallel 3
+
+      - name: Run C++ unit tests (serial)
+        working-directory: dolfinx
+        run: |
+          cd build/test
+          ctest -V --output-on-failure -R unittests
+      - name: Run C++ unit tests (MPI)
+        working-directory: dolfinx
+        run: |
+          cd build/test
+          mpiexec -np 3 ctest -V --output-on-failure -R unittests
 
       - name: Build and install DOLFINx Python interface
-        env:
-          PYTHONPATH: ${{ github.workspace }}/petsc/${{ env.PETSC_ARCH }}/lib:${{ env.PYTHONPATH }}
+        working-directory: dolfinx
         run: |
-          python -m pip install -r dolfinx/python/build-requirements.txt
-          python -m pip install --check-build-dependencies --no-build-isolation dolfinx/python/
+          python -m pip install -r python/build-requirements.txt
+          python -m pip install --check-build-dependencies --no-build-isolation python/
+
       - name: Basic test
-        env:
-          PYTHONPATH: ${{ github.workspace }}/petsc/${{ env.PETSC_ARCH }}/lib:${{ env.PYTHONPATH }}
         run: |
           python -c "import dolfinx; from mpi4py import MPI; dolfinx.mesh.create_rectangle(comm=MPI.COMM_WORLD, points=((0, 0), (2, 1)), n=(32, 16))"
           mpirun -np 2 python -c "import dolfinx; from mpi4py import MPI; dolfinx.mesh.create_rectangle(comm=MPI.COMM_WORLD, points=((0, 0), (2, 1)), n=(32, 16))"
+
+      - name: Run Python unit tests (serial)
+        working-directory: dolfinx
+        run: python3 -m pytest -n=auto --durations=50 python/test/unit/
+      - name: Run Python unit tests (MPI, np=3)
+        working-directory: dolfinx
+        run: mpirun -np 3 python3 -m pytest python/test/unit/