Convert dev-only extras to PEP 735 dependency groups

Move build/docs/lint/mypy/test/ci from optional-dependencies to
dependency-groups, keeping demo/optional/petsc4py as real extras since
they are user-facing runtime features or (test) installed against
built wheels. Update CI workflows and Dockerfiles to use `pip install
--group` instead of `.[...]`, and replace the scikit_build_core.build
requires trick with the new `build` group.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

Author: jhale

.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 clang-format
       - 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: |
@@ -151,7 +150,7 @@ 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"
@@ -208,8 +207,7 @@ 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 +263,7 @@ 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 +317,7 @@ 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 +333,7 @@ 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/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/windows.yml

@@ -150,13 +150,12 @@ jobs:
       - name: Install DOLFINx Python build dependencies
         working-directory: dolfinx-src/python
         run: |
-          pip install scikit-build-core
-          python -m pip install (python -m scikit_build_core.build requires | Out-String | ConvertFrom-Json)
+          pip install --group pyproject.toml:build
 
       - name: Install DOLFINx (Python)
         working-directory: dolfinx-src/python
         run: |
-          pip -v install --check-build-dependencies --no-build-isolation .[test] --config-settings=cmake.build-type="Release" --config-settings=cmake.args=-DBasix_DIR="D:/a/dolfinx/basix-install/lib/cmake/basix" --config-settings=cmake.args=-Dufcx_DIR="D:/a/dolfinx/ufcx-install/share/ufcx/cmake" --config-settings=cmake.args=-DDOLFINX_DIR="D:/a/dolfinx/dolfinx-install/lib/cmake/dolfinx" --config-settings=cmake.args=-DCMAKE_TOOLCHAIN_FILE="$env:VCPKG_INSTALLATION_ROOT/scripts/buildsystems/vcpkg.cmake" --config-settings=cmake.args=-DVCPKG_OVERLAY_PORTS="../cpp/.vcpkg-overlay"
+          pip -v install --group pyproject.toml:test --check-build-dependencies --no-build-isolation . --config-settings=cmake.build-type="Release" --config-settings=cmake.args=-DBasix_DIR="D:/a/dolfinx/basix-install/lib/cmake/basix" --config-settings=cmake.args=-Dufcx_DIR="D:/a/dolfinx/ufcx-install/share/ufcx/cmake" --config-settings=cmake.args=-DDOLFINX_DIR="D:/a/dolfinx/dolfinx-install/lib/cmake/dolfinx" --config-settings=cmake.args=-DCMAKE_TOOLCHAIN_FILE="$env:VCPKG_INSTALLATION_ROOT/scripts/buildsystems/vcpkg.cmake" --config-settings=cmake.args=-DVCPKG_OVERLAY_PORTS="../cpp/.vcpkg-overlay"
 
       - name: Run tests, skip test_mixed_topology_partitioning (Python, serial)
         working-directory: dolfinx-src/python/test

AGENTS.md

@@ -262,6 +262,13 @@ disclosure process.
   for parallel-aware tests where relevant.
 - Run the relevant formatter/linter and the affected test suite before
   calling a change done — don't rely on CI to catch formatting.
+- Dependency groups (`build`, `docs`, `lint`, `mypy`, `test`, `ci` in
+  `python/pyproject.toml`) use PEP 735 syntax and require `pip >= 25.1`
+  (or another PEP 735-compliant build frontend) for the `--group` flag.
+  `demo`, `optional`, and `petsc4py` remain real
+  `[project.optional-dependencies]` extras since they are user-facing
+  runtime features, or (in the case of `test`) are installed against
+  built wheels where dependency groups are unavailable.
 
 ## Verifying changes locally
 

README.md

@@ -45,8 +45,7 @@ To install the Python interface, first install the C++ core, and then in
 the `python/` directory run:
 
 ```shell
-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
 pip install --check-build-dependencies --no-build-isolation .
 ```
 

docker/Dockerfile.end-user

@@ -67,12 +67,11 @@ ONBUILD COPY dolfinx/docker/ffcx_options.json /root/.config/ffcx/ffcx_options.js
 # CMake build type for DOLFINx C++ build. See CMake documentation.
 ONBUILD ARG DOLFINX_CMAKE_BUILD_TYPE="Release"
 
-# Using pip install `.[test]` with --no-dependencies and --no-build-isolation
-# does not install necessary packages, hence install build and optional
-# dependencies manually here.
+# --no-build-isolation means build dependencies (the `build` dependency
+# group in pyproject.toml) are not installed automatically; also install
+# the packages needed for testing and optional features here.
 ONBUILD RUN cd dolfinx/python && \
-            pip install --no-cache-dir scikit-build-core && \
-            python -m scikit_build_core.build requires | python -c "import sys, json; print(' '.join(json.load(sys.stdin)))" | xargs pip install --no-cache-dir && \
+            pip install --no-cache-dir --group pyproject.toml:build && \
             pip install --no-cache-dir pyamg pytest scipy matplotlib numba # test + optional set
 
 # The dolfinx-onbuild container expects to have folders basix/ ufl/

python/README.md

@@ -6,8 +6,7 @@ Below is guidance for building the DOLFINx Python interface.
 
 2. Ensure the Python interface build requirements are installed:
 
-       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
 
 3. Build DOLFINx Python interface:
 
@@ -21,9 +20,9 @@ Note that Developer mode is significantly stricter than CMake's default Debug mo
 
 # Type checking with mypy
 
-1. Install DOLFINx Python with the `[mypy]` optional dependencies set, e.g.:
+1. Install DOLFINx Python with the `mypy` dependency group, e.g.:
 
-       pip install .[mypy]
+       pip install --group mypy .
 
 2. Check with mypy, e.g.:
 

python/doc/README.md

@@ -2,9 +2,9 @@
 
 To build the documentation:
 
-1. Install DOLFINx Python interface using the ``docs`` optional dependency set, e.g.
+1. Install DOLFINx Python interface using the ``docs`` dependency group, e.g.
 
-       python -m pip install .[docs]
+       python -m pip install --group docs .
 
    It must be possible to import the module ``dolfinx`` to build the documentation.
 

python/doc/source/installation.rst

@@ -120,7 +120,7 @@ Python
 After installation of the C++ interface, from the ``python/`` directory
 the Python interface can be installed using::
 
-    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
     pip install --check-build-dependencies --no-build-isolation .