Merge branch 'main' into schnellerhase/vtx-timeseries

Author: schnellerhase

.github/workflows/build-wheels.yml

@@ -201,7 +201,7 @@ jobs:
             cmake -G Ninja -S dolfinx/cpp -B dolfinx-build-dir/ \
               -DPython3_EXECUTABLE=$(which python) \
               -DCMAKE_PREFIX_PATH=/usr/lib64/mpich \
-              -DCMAKE_BUILD_TYPE=RelWithDebug \
+              -DCMAKE_BUILD_TYPE=RelWithDebInfo \
               -DDOLFINX_ENABLE_SUPERLU_DIST=ON \
               -DDOLFINX_ENABLE_SCOTCH=ON \
               -DDOLFINX_ENABLE_PARMETIS=OFF &&
@@ -240,7 +240,7 @@ jobs:
               -DDOLFINX_ENABLE_SCOTCH=ON \
               -DDOLFINX_ENABLE_PARMETIS=OFF \
               -DDOLFINX_ENABLE_SUPERLU_DIST=ON \
-              -DCMAKE_BUILD_TYPE=RelWithDebug &&
+              -DCMAKE_BUILD_TYPE=RelWithDebInfo &&
             cmake --build $GITHUB_WORKSPACE/dolfinx-build-dir/ &&
             sudo cmake --install dolfinx-build-dir/
           # As of 6/26 DOLFINx uses std::jthread which is only officially
@@ -271,7 +271,7 @@ jobs:
             wheel pack {dest_dir}/unpacked/* -d {dest_dir} &&
             pipx run abi3audit --verbose --strict --report {wheel}
           CIBW_TEST_REQUIRES: pytest-xdist
-          CIBW_TEST_EXTRAS: test
+          CIBW_TEST_GROUPS: test
           CIBW_TEST_COMMAND_LINUX: >
             . /etc/profile &&
             module load mpi/mpich-$(arch) &&
@@ -313,7 +313,7 @@ jobs:
           sudo git clean -fdx && cd ../ &&
           docker run -v $(pwd)/dolfinx:/dolfinx -v $(pwd)/simple:/shared \
             --env PIP_INDEX_URL=file:///shared --env PIP_EXTRA_INDEX_URL=https://pypi.org/simple python:3.13 \
-            /bin/bash -l -c "pip install mpich fenics-dolfinx[test] && mpiexec -n 2 python -m pytest -m 'not adios2 and not petsc4py' /dolfinx/python/test/unit"
+            /bin/bash -l -c "pip install --group /dolfinx/python/pyproject.toml:test mpich fenics-dolfinx && mpiexec -n 2 python -m pytest -m 'not adios2 and not petsc4py' /dolfinx/python/test/unit"
 
       - name: Test in clean python image with pypi Intel MPI (x86_64 only)
         if: runner.os == 'Linux' && runner.arch == 'X64'
@@ -322,15 +322,15 @@ jobs:
           sudo git clean -fdx && cd ../ &&
           docker run -v $(pwd)/dolfinx:/dolfinx -v $(pwd)/simple:/shared \
             --env PIP_INDEX_URL=file:///shared --env PIP_EXTRA_INDEX_URL=https://pypi.org/simple python:3.14 \
-            /bin/bash -l -c "pip install impi-rt fenics-dolfinx[test] && mpiexec -n 2 python -m pytest -m 'not adios2 and not petsc4py' /dolfinx/python/test/unit"
+            /bin/bash -l -c "pip install --group /dolfinx/python/pyproject.toml:test impi-rt fenics-dolfinx && mpiexec -n 2 python -m pytest -m 'not adios2 and not petsc4py' /dolfinx/python/test/unit"
 
       - name: Test in clean virtual environment with pypi OpenMPI (macOS)
         if: runner.os == 'macOS'
         run: |
           cd dolfinx && git clean -fdx && cd ../
           python -m venv venv-test
           source venv-test/bin/activate
-          PIP_EXTRA_INDEX_URL="file://${GITHUB_WORKSPACE}/simple" pip install openmpi fenics-dolfinx[test]
+          PIP_EXTRA_INDEX_URL="file://${GITHUB_WORKSPACE}/simple" pip install --group dolfinx/python/pyproject.toml:test openmpi fenics-dolfinx
           which mpiexec
           mpiexec -n 2 python -m pytest -m "not adios2 and not petsc4py" dolfinx/python/test/unit
 

.github/workflows/ccpp.yml

@@ -15,6 +15,13 @@ on:
       - main
   workflow_dispatch:
 
+# Cancel superseded runs: a new commit on a pull request makes the
+# previous run's result irrelevant. Pushes to 'main' and 'release' are
+# left to finish, since they populate caches and publish artefacts.
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: ${{ github.event_name == 'pull_request' }}
+
 jobs:
 
   lint:
@@ -33,7 +40,7 @@ jobs:
         run: cat .github/workflows/fenicsx-refs.env >> $GITHUB_ENV
 
       - name: Install linting tools
-        run: pip install clang-format gersemi mypy ruff
+        run: pip install --group python/pyproject.toml:lint
       - name: ruff .py files in C++ code
         run: |
           cd cpp/
@@ -56,13 +63,6 @@ jobs:
           find . -type f \( -name "*.cpp" -o -name "*.h" \) | xargs clang-format --dry-run --Werror
       - name: gersemi
         run: gersemi --check .
-      - name: mypy checks (no installed)
-        run: |
-          cd python/
-          MYPY_FLAGS="--ignore-missing-imports --disable-error-code no-any-unimported --disable-error-code unused-ignore --disable-error-code attr-defined --disable-error-code name-defined --disable-error-code no-any-return"
-          mypy $MYPY_FLAGS dolfinx
-          mypy $MYPY_FLAGS demo
-          mypy $MYPY_FLAGS test
 
 
   ccpp-build:
@@ -96,8 +96,7 @@ jobs:
       - name: Install Python build dependencies
         working-directory: python
         run: |
-          pip install scikit-build-core setuptools
-          python -m scikit_build_core.build requires | python -c "import sys, json; print(' '.join(json.load(sys.stdin)))" | xargs pip install
+          pip install --group pyproject.toml:build setuptools
 
       - name: Install UFL
         run: |
@@ -151,28 +150,19 @@ jobs:
 
       - name: Build Python interface
         run: >
-          pip install  'python/[test,mypy]'
+          pip install --group python/pyproject.toml:test 'python/[demo]'
           --check-build-dependencies
           --no-build-isolation
           --config-settings=cmake.build-type="Developer"
 
       - name: Check Python configuration
         run: python -c "from mpi4py import MPI; import dolfinx; assert not dolfinx.has_petsc; assert not dolfinx.has_petsc4py; assert dolfinx.has_superlu_dist"
 
-      - name: Install gmsh and pyvista (and dependencies)
+      - name: Install system dependencies for gmsh and pyvista
         run: |
           sudo apt-get install libglu1-mesa libgl1 libxrender1 libxcursor1 libxft2 libxinerama1
           sudo apt-get install libegl1
-          pip install gmsh pyvista
 
-      - name: mypy checks (no petsc4py)
-        run: |
-          DISABLE_FLAGS="--disable-error-code import-not-found --disable-error-code no-any-unimported"
-          mypy --config-file python/pyproject.toml -p dolfinx --exclude 'petsc\.py|io/utils\.py' $DISABLE_FLAGS
-          cd python/
-          DISABLE_FLAGS="$DISABLE_FLAGS --disable-error-code attr-defined --disable-error-code name-defined --disable-error-code unused-ignore"
-          mypy demo $DISABLE_FLAGS
-          mypy test $DISABLE_FLAGS
 
       - name: Run demos (Python, serial)
         run: |
@@ -191,22 +181,16 @@ jobs:
     needs: [lint]
     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]
-        docker_image: ["ghcr.io/fenics/test-env:current-openmpi"]
-        include:
-          - docker_image: "ghcr.io/fenics/test-env:current-mpich"
-            petsc_arch: linux-gnu-real64-32
-          - docker_image: "ghcr.io/fenics/test-env:current-mpich"
-            petsc_arch: linux-gnu-complex128-32
-    container: ${{ matrix.docker_image }}
+        petsc_arch: [linux-gnu-real64-32, linux-gnu-complex128-32, linux-gnu-real64-64]
+    container: "ghcr.io/fenics/test-env:current"
     env:
       PETSC_ARCH: ${{ matrix.petsc_arch }}
       OMPI_ALLOW_RUN_AS_ROOT: 1
       OMPI_ALLOW_RUN_AS_ROOT_CONFIRM: 1
       PRTE_MCA_rmaps_default_mapping_policy: :oversubscribe
       PYTEST_ADDOPTS: "-W error"
 
-    name: Build and test (${{ matrix.petsc_arch }}, ${{ matrix.docker_image }})
+    name: Build and test (${{ matrix.petsc_arch }})
     steps:
       - uses: actions/checkout@v7
 
@@ -216,8 +200,7 @@ jobs:
       - name: Install Python build dependencies
         working-directory: python
         run: |
-          pip install scikit-build-core
-          python -m scikit_build_core.build requires | python -c "import sys, json; print(' '.join(json.load(sys.stdin)))" | xargs pip install
+          pip install --group pyproject.toml:build
 
       - name: Install UFL
         run: |
@@ -273,7 +256,7 @@ jobs:
 
       - name: Build Python interface
         run: >
-          pip install 'python/[test,mypy]'
+          pip install --group python/pyproject.toml:test 'python/'
           --check-build-dependencies
           --no-build-isolation
           --config-settings=cmake.build-type="Developer"
@@ -294,13 +277,6 @@ jobs:
           apt-get install libegl1 libxrender1
           pip install pyvista
 
-      - name: mypy checks (with petsc4py)
-        run: |
-          mypy --config-file python/pyproject.toml -p dolfinx --exclude superlu_dist.py
-          cd python/
-          mypy demo
-          mypy test
-
       - name: Run demos (Python, serial)
         run: |
           pip install pytest-xdist
@@ -316,7 +292,7 @@ jobs:
   build-and-publish-docs:
     runs-on: ubuntu-26.04
     needs: [lint]
-    container: "ghcr.io/fenics/test-env:current-openmpi"
+    container: "ghcr.io/fenics/test-env:current"
     env:
       PETSC_ARCH: linux-gnu-real64-32
       OMPI_ALLOW_RUN_AS_ROOT: 1
@@ -333,8 +309,7 @@ jobs:
       - name: Install Python build dependencies
         working-directory: python
         run: |
-          pip install scikit-build-core setuptools
-          python -m scikit_build_core.build requires | python -c "import sys, json; print(' '.join(json.load(sys.stdin)))" | xargs pip install
+          pip install --group pyproject.toml:build setuptools
 
       - name: Install FEniCS Python components
         run: |
@@ -350,7 +325,7 @@ jobs:
 
       - name: Build Python interface
         run: >
-          pip install 'python/[docs]'
+          pip install --group python/pyproject.toml:docs 'python/'
           --check-build-dependencies
           --no-build-isolation
 

.github/workflows/ci-spack.yml

@@ -14,6 +14,13 @@ on:
       - main
   workflow_dispatch:
 
+# Cancel superseded runs: a new commit on a pull request makes the
+# previous run's result irrelevant. Pushes to 'main' and 'release' are
+# left to finish, since they populate caches and publish artefacts.
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: ${{ github.event_name == 'pull_request' }}
+
 env:
   GITHUB_USER: ${{ github.actor }}
   GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
@@ -34,6 +41,10 @@ jobs:
     runs-on: ubuntu-26.04
     container: ghcr.io/almalinux/almalinux:10
     strategy:
+      # One compiler failing must not cancel the other: the legs share a
+      # build cache, so a cancelled leg loses its diagnostics and its
+      # pushed binaries.
+      fail-fast: false
       matrix:
         compiler: ["gcc", "oneapi"]
 
@@ -47,7 +58,9 @@ jobs:
         uses: spack/setup-spack@16b756799ede8b28951287f89bcd3fdb32ec1ca3 # v3.0.0
         with:
           spack_ref: v1.2.2
-          packages_ref: v2026.06.0
+          # spack-packages 'develop' at 2026-08-17. Bumping re-solves the
+          # graph and can invalidate cached binaries; warm the cache first.
+          packages_ref: 1ccf95574922e2a7f7ef0351bd67758ad4634b7a
 
       - name: Checkout DOLFINx
         uses: actions/checkout@v7
@@ -62,13 +75,9 @@ jobs:
           spack -e py add mpi petsc+mpi+shared+mumps+superlu-dist slepc parmetis pkgconfig \
             hdf5+mpi boost pugixml spdlog
           spack -e py add python py-nanobind py-numpy py-mpi4py py-petsc4py py-slepc4py \
-            py-scikit-build-core+pyproject py-setuptools py-cffi
+            py-scikit-build-core@1+pyproject py-setuptools py-cffi
           spack -e py add py-pip cmake catch2 py-pytest py-pytest-xdist ninja
-          # NOTE: freetype@2.13.3 works around a raster overflow bug in
-          # freetype@2.14.2 (2026-07). Re-check and drop once a fixed
-          # freetype (2.14.3+) lands in the spack-packages recipe.
-          spack -e py add openblas
-          spack -e py add py-gmsh ^gmsh~fltk~med~mmg+external ^opencascade~draw py-pyvista ^mesa~llvm ^freetype@2.13.3 \
+          spack -e py add py-gmsh ^gmsh~fltk~med~mmg+external ^opencascade~draw py-pyvista ^mesa~llvm \
             py-networkx py-matplotlib py-pyamg py-numba  ^llvm~clang~lldb~lld~offload~libomptarget~polly targets=x86 \
             py-scipy
           # gmsh's compiled library dlopens libGLU.so.1 and several X11
@@ -87,7 +96,7 @@ jobs:
         run: spack -e py add intel-oneapi-compilers
 
       - name: Install Spack packages
-        run: spack -e py install -j 4 --use-buildcache auto
+        run: spack -e py install -j $(nproc) --use-buildcache auto
 
       - name: Push packages to Spack cache and update index
         env:
@@ -146,12 +155,6 @@ jobs:
       - name: Build Python interface (editable install)
         run: |
           spack env activate py
-          # The Spack recipe pinned by packages_ref above only goes up to
-          # py-scikit-build-core@0.12.2, whose editable install support
-          # predates the fix this project's build-system requirement now
-          # depends on (see python/pyproject.toml) -- fetch a newer one
-          # from PyPI for this step.
-          pip install --upgrade "scikit-build-core>=1.0.0"
           pip install --check-build-dependencies --no-build-isolation --config-settings=cmake.build-type=Developer --config-settings=build-dir="build" -e 'dolfinx-src/python/'
         shell: spack-bash {0}
 
@@ -164,7 +167,10 @@ jobs:
         run: |
           spack env activate py
           python -m pytest -n auto -m serial --durations=10 dolfinx-src/python/demo/test.py
-          python -m pytest -m mpi --num-proc=2 dolfinx-src/python/demo/test.py
+          # demo_navier-stokes.py deadlocks at np=2 in its MUMPS direct solve
+          # (singular-system ICNTLs); it passes in the serial run above.
+          # Deselected by name, not node id, whose path index follows glob order.
+          python -m pytest -m mpi --num-proc=2 -k "not navier-stokes" dolfinx-src/python/demo/test.py
         shell: spack-bash {0}
 
       - name: Run Python unit tests (serial and MPI)