Merge branch 'main' into garth/mesh-optimise-2

Author: garth-wells

.github/workflows/build-wheels.yml

@@ -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

@@ -40,7 +40,7 @@ jobs:
         run: cat .github/workflows/fenicsx-refs.env >> $GITHUB_ENV
 
       - name: Install linting tools
-        run: pip install clang-format gersemi ruff
+        run: pip install --group python/pyproject.toml:lint
       - name: ruff .py files in C++ code
         run: |
           cd cpp/
@@ -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: |
@@ -151,19 +150,18 @@ jobs:
 
       - name: Build Python interface
         run: >
-          pip install  'python/[test]'
+          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: Run demos (Python, serial)
@@ -208,8 +206,7 @@ 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: |
@@ -265,7 +262,7 @@ jobs:
 
       - name: Build Python interface
         run: >
-          pip install 'python/[test]'
+          pip install --group python/pyproject.toml:test 'python/'
           --check-build-dependencies
           --no-build-isolation
           --config-settings=cmake.build-type="Developer"
@@ -319,8 +316,7 @@ 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: |
@@ -336,7 +332,7 @@ 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

@@ -41,6 +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"]
 
@@ -54,8 +58,9 @@ jobs:
         uses: spack/setup-spack@16b756799ede8b28951287f89bcd3fdb32ec1ca3 # v3.0.0
         with:
           spack_ref: v1.2.2
-          packages_ref: d342cee94fb90fb020776c8bd8500b54a19c63cf
-          # 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
@@ -72,11 +77,8 @@ jobs:
           spack -e py add python py-nanobind py-numpy py-mpi4py py-petsc4py py-slepc4py \
             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
@@ -95,7 +97,7 @@ 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:
@@ -166,7 +168,10 @@ 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)

.github/workflows/ci.yml

@@ -80,8 +80,9 @@ jobs:
         uses: spack/setup-spack@16b756799ede8b28951287f89bcd3fdb32ec1ca3 # v3.0.0
         with:
           spack_ref: v1.2.2
-          packages_ref: d342cee94fb90fb020776c8bd8500b54a19c63cf
-          # 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
 
       # Pinned, like spack itself and its packages repo above: an unpinned
       # 'main' changes what CI builds with no commit here, which makes a
@@ -163,7 +164,7 @@ jobs:
           spack -e ci add py-fenics-dolfinx@main${{ matrix.petsc && '+petsc4py+slepc4py' || '~petsc4py~slepc4py' }} commit=${{ github.sha }} build_type=Developer
           spack -e ci add py-gmsh ^gmsh~med~fltk+external ^opencascade~draw py-pyamg py-matplotlib \
             py-networkx \
-            py-numba  ^llvm~clang~lldb~lld~offload~libomptarget~polly targets=x86 \
+            py-numba ^llvm~clang~lldb~lld~offload~libomptarget~polly targets=x86 \
             py-pytest py-pytest-xdist py-scipy \
             "py-pyvista ^[virtuals=gl] osmesa"
           spack -e ci add catch2 ninja
@@ -236,7 +237,10 @@ jobs:
           # dolfinx, petsc4py and the rest.
           apt-get install -y --no-install-recommends python3-venv
           python3 -m venv /tmp/mypy-venv
-          /tmp/mypy-venv/bin/pip install --quiet mypy
+          # types-cffi, types-setuptools and scipy-stubs mirror the `typing`
+          # extra in python/pyproject.toml; installed by name rather than via
+          # '.[typing]' to avoid triggering a full DOLFINx build in this venv.
+          /tmp/mypy-venv/bin/pip install --quiet mypy types-cffi types-setuptools scipy-stubs
           # Distinguishes a broken install from mypy reporting errors.
           /tmp/mypy-venv/bin/mypy --version
           ENV_PYTHON=$(command -v python)
@@ -282,4 +286,4 @@ jobs:
           || github.event.pull_request.head.repo.full_name == github.repository) }}
         run: |
           spack -e ci buildcache push --base-image ubuntu:26.04 --allow-missing --update-index local-buildcache \
-            py-gmsh py-matplotlib py-networkx py-numba py-pytest py-pytest-xdist py-scipy py-pyvista
+            catch2 py-gmsh py-matplotlib py-networkx py-numba py-pyamg py-pytest py-pytest-xdist py-scipy py-pyvista

.github/workflows/macos.yml

@@ -134,9 +134,8 @@ jobs:
         working-directory: python
         run: |
           pip install pyamg
-          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 --check-build-dependencies --no-build-isolation --config-settings=cmake.build-type="Developer" './[test]'
+          pip install --group pyproject.toml:build
+          pip install --group pyproject.toml:test --check-build-dependencies --no-build-isolation --config-settings=cmake.build-type="Developer" '.'
 
       - name: Basic test
         run: |

.github/workflows/spack-config/gh-actions-env-test.yml

@@ -38,7 +38,7 @@ spack:
 
   mirrors:
     local-buildcache:
-      url: oci://ghcr.io/fenics/dolfinx-spack-buildcache
+      url: oci://ghcr.io/fenics/spack-buildcache
       binary: true
       signed: false
       access_pair:

.github/workflows/spack-config/gh-actions-env.yml

@@ -5,14 +5,18 @@ spack:
       root: /opt/spack
       padded_length: 128
 
+  concretizer:
+      unify: true
+      reuse: false
+
   packages:
     all:
       require:
       - target=x86_64_v3
 
   mirrors:
     local-buildcache:
-      url: oci://ghcr.io/fenics/spack-rh-buildcache
+      url: oci://ghcr.io/fenics/spack-buildcache
       binary: true
       signed: false
       access_pair: