[nanobind] merge pyproject change from main (#2840)

* Improve comment (#2839)

* Use `pyproject.toml` for install of Python part (#2707)

* Try using pyproject

* fixup pip command

* Find python

* debug

* Try by adding path explicitly

* Try no build isolation on mac.

* Try this on macos.

* Update CI

* Typo

* Fix.

* Should be dependency of scikit-build-core.

* Attempt fix for ubuntu.

* Fix?

* Add pyproject variant

* Typo.

* Explicit python intepreter.

* Try forcing x86-64 arch.

* Try this ordering.

* Upgrade pip etc.

* And on mac.

* This works locally on my macOS system.

pip install --no-build-isolation is required.

* Works locally, not totally happy with the RPATH stuff.

* Tidy.

* Fix circleci

* Tidy.

* Update minimum pybind11.

* Don't think these belong here.

* Change email.

* Tweaks to Dockerfiles and workflows.

* Update macos workflow

* Typo

* Fix.

* Get cmake to set rpath automatically.

* Don't understand why but doesn't run on circleci, try this.

* Typo

* Tweak.

* Update macos.yml

* Try removing.

* Exclude .cpp files as suggested.

* Add --check-build-dependencies

* Not necessary, think this is well known now.

* Fix typo no install.

* Update build-requirements.txt

* Update pyproject.toml

---------

Co-authored-by: Jack S. Hale <mail@jackhale.co.uk>
Co-authored-by: Garth N. Wells <gnw20@cam.ac.uk>

* Update config

* Small updates

---------

Co-authored-by: Chris Richardson <chris@bpi.cam.ac.uk>
Co-authored-by: Jack S. Hale <mail@jackhale.co.uk>

.circleci/config.yml

@@ -52,11 +52,12 @@ regression-tests-cpp-mpi: &regression-tests-cpp-mpi
     ctest --verbose -R demo -R mpi_3
 
 build-python-interface: &build-python-interface
-  name: Build Python/pybind11 interface
+  name: Build Python/nanobind interface
   command: |
     export CMAKE_BUILD_PARALLEL_LEVEL=2
     cd python
-    pip3 -v install --global-option build --global-option --debug . --user
+    pip3 install -r build-requirements.txt
+    pip3 -v install --config-setting cmake.build-type=Debug --no-build-isolation --user .
 
 demos-python: &demos-python
   name: Run demos (Python, serial)
@@ -81,14 +82,14 @@ unit-tests-python: &unit-tests-python
   name: Run unit tests (Python, serial)
   command: |
     mkdir -p ~/junit
-    cd python/test/unit
-    python3 -m pytest -n=4 --durations=50 --junitxml=~/junit/test-results.xml .
+    cd python/test
+    python3 -m pytest -n=4 --durations=50 --junitxml=~/junit/test-results.xml unit/
 
 unit-tests-python-mpi: &unit-tests-python-mpi
   name: Run unit tests (Python, MPI)
   command: |
-    cd python/test/unit
-    mpirun -np 3 python3 -m pytest .
+    cd python/test
+    mpirun -np 3 python3 -m pytest unit/
 
 jobs:
   build-real:

.github/workflows/ccpp.yml

@@ -65,8 +65,6 @@ 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: Install matplotlib
-        run: pip3 install matplotlib
       - name: Flake8 checks
         run: |
           cd python/
@@ -80,7 +78,7 @@ jobs:
           python3 -m isort --check .
       - name: mypy checks
         run: |
-          python3 -m pip install types-setuptools mypy --upgrade
+          python3 -m pip install mypy types-setuptools --upgrade # TO REMOVE
           cd python/
           mypy dolfinx
           mypy demo
@@ -112,7 +110,7 @@ jobs:
 
       - name: Build C++ interface documentation
         run: |
-          python3 -m pip install breathe
+          python3 -m pip install breathe # TO REMOVE
           export DOLFINX_VERSION=`cmake -L build | grep DOXYGEN_DOLFINX_VERSION | cut -f2 -d "="`
           echo $DOLFINX_VERSION
           cd cpp/doc
@@ -142,10 +140,11 @@ jobs:
       - name: Build Python interface
         run: |
           python3 -m pip install git+https://github.com/wjakob/nanobind.git
-          CMAKE_BUILD_TYPE=Debug python3 -m pip -v install python/
+          python3 -m pip install -r python/build-requirements.txt # TO REMOVE
+          python3 -m pip -v install python/
       - name: Build Python interface documentation
         run: |
-          python3 -m pip install sphinx==5.0.2
+          python3 -m pip install sphinx==5.0.2 # TO REMOVE
           cd python/doc
           make html
 

.github/workflows/macos.yml

@@ -28,32 +28,31 @@ jobs:
 
       - name: Install Python dependencies
         run: |
-          pip install pip --upgrade
-          pip install numpy setuptools wheel
-          pip install cython
-          pip install mpi4py
+          python -m pip install --upgrade pip setuptools wheel
+          python -m pip install cython numpy mpi4py
 
-      - name: Install minimal PETSc and petsc4y
+      - name: Install minimal PETSc and petsc4py
         run: |
           export PATH="$(brew --prefix bison)/bin:$PATH"
           git clone -b release https://gitlab.com/petsc/petsc.git petsc
           cd petsc
-          ./configure \
+          python ./configure \
             --with-64-bit-indices=no \
             --with-debugging=no \
             --with-fortran-bindings=no \
             --with-scalar-type=real \
             --with-shared-libraries \
             --with-scalar-type=real \
-            -–with-petsc4py=yes \
             --download-ptscotch
           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 .
 
       - name: Install FEniCSx dependencies
         run: |
-          pip install git+https://github.com/FEniCS/basix.git
-          pip install git+https://github.com/FEniCS/ufl.git
-          pip install git+https://github.com/FEniCS/ffcx.git
+          python -m pip install git+https://github.com/FEniCS/basix.git
+          python -m pip install git+https://github.com/FEniCS/ufl.git
+          python -m pip install git+https://github.com/FEniCS/ffcx.git
 
       - uses: actions/checkout@v4
         with:
@@ -69,9 +68,9 @@ jobs:
         env:
           PYTHONPATH: ${{ github.workspace }}/petsc/${{ env.PETSC_ARCH }}/lib:${{ env.PYTHONPATH }}
         run: |
-          echo "Path: ${PYTHONPATH}"
           pip install git+https://github.com/wjakob/nanobind.git
-          pip install dolfinx/python/
+          python -m pip install -r dolfinx/python/build-requirements.txt
+          python -m pip install --check-build-dependencies --no-build-isolation dolfinx/python/
       - name: Basic test
         env:
           PYTHONPATH: ${{ github.workspace }}/petsc/${{ env.PETSC_ARCH }}/lib:${{ env.PYTHONPATH }}

.github/workflows/oneapi.yml

@@ -88,24 +88,26 @@ jobs:
         run: |
           . /opt/intel/oneapi/setvars.sh
           pip install git+https://github.com/wjakob/nanobind.git
-          pip install python/
+          pip -v install -r python/build-requirements.txt # TO REMOVE
+          pip -v install --check-build-dependencies --no-build-isolation python/
       - name: Set default DOLFINx JIT options
         run: |
           mkdir -p ~/.config/dolfinx
           echo '{ "cffi_extra_compile_args": ["-g0", "-O0" ] }' > ~/.config/dolfinx/dolfinx_jit_options.json
       - name: Run DOLFINx demos (Python, serial)
         run: |
           . /opt/intel/oneapi/setvars.sh
-          pip install matplotlib
-          pytest -n=2 -m serial --durations=10 python/demo/test.py
+          pip install matplotlib # TO REMOVE
+          pytest -v -n=2 -m serial --durations=10 python/demo/test.py
       - name: Run DOLFINx demos (Python, MPI (np=2))
         run: |
           . /opt/intel/oneapi/setvars.sh
           pytest -m mpi --num-proc=2 python/demo/test.py
       - name: Run DOLFINx Python unit tests (serial)
         run: |
           . /opt/intel/oneapi/setvars.sh
-          pytest -n=auto --durations=50 python/test/unit/
+          cd python/test
+          pytest -n=auto --durations=50 unit/
       - name: Run DOLFINx Python unit tests (MPI, np=2)
         run: |
           . /opt/intel/oneapi/setvars.sh

.github/workflows/redhat.yml

@@ -24,6 +24,10 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
+      - name: Upgrade pip and setuptools
+        run: |
+          python3 -m pip install --upgrade pip setuptools wheel
+
       - name: Install FEniCS Python components
         run: |
           python3 -m pip install git+https://github.com/FEniCS/ufl.git
@@ -61,7 +65,8 @@ jobs:
       - name: Build Python interface
         run: |
           python3 -m pip install git+https://github.com/wjakob/nanobind.git
-          python3 -m pip install --global-option build --global-option --debug python/
+          python3 -m pip -v install -r python/build-requirements.txt # TO REMOVE
+          python3 -m pip -v install --check-build-dependencies --no-build-isolation --config-settings=cmake.build-type=Debug python/
 
       - name: Set default DOLFINx JIT options
         run: |

cpp/dolfinx/fem/utils.h

@@ -1195,8 +1195,8 @@ pack_coefficients(const Expression<T, U>& e,
   return {std::move(c), cstride};
 }
 
-/// @brief Pack constants of u of generic type U ready for assembly
-/// @warning This function is subject to change
+/// @brief Pack constants of u into a sigle array ready for assembly.
+/// @warning This function is subject to change.
 template <typename U>
 std::vector<typename U::scalar_type> pack_constants(const U& u)
 {

docker/Dockerfile.end-user

@@ -90,7 +90,7 @@ ONBUILD RUN cd dolfinx && \
     PETSC_ARCH=linux-gnu-real64-32 cmake -G Ninja -DCMAKE_INSTALL_PREFIX=/usr/local/dolfinx-real -DCMAKE_BUILD_TYPE=${DOLFINX_CMAKE_BUILD_TYPE} -DCMAKE_CXX_FLAGS=${DOLFINX_CMAKE_CXX_FLAGS} ../cpp && \
     ninja install && \
     cd ../python && \
-    CXXFLAGS=${DOLFINX_CMAKE_CXX_FLAGS} PETSC_ARCH=linux-gnu-real64-32 pip3 install -v --target /usr/local/dolfinx-real/lib/python${PYTHON_VERSION}/dist-packages --no-dependencies --no-cache-dir . && \
+    CXXFLAGS=${DOLFINX_CMAKE_CXX_FLAGS} PETSC_ARCH=linux-gnu-real64-32 pip3 install -v --no-build-isolation --target /usr/local/dolfinx-real/lib/python${PYTHON_VERSION}/dist-packages --no-dependencies --no-cache-dir . && \
     git clean -fdx && \
     cd ../ && \
     mkdir -p build-complex && \
@@ -99,7 +99,7 @@ ONBUILD RUN cd dolfinx && \
     ninja install && \
     . /usr/local/dolfinx-complex/lib/dolfinx/dolfinx.conf && \
     cd ../python && \
-    CXXFLAGS=${DOLFINX_CMAKE_CXX_FLAGS} PETSC_ARCH=linux-gnu-complex128-32 pip3 install -v --target /usr/local/dolfinx-complex/lib/python${PYTHON_VERSION}/dist-packages --no-dependencies --no-cache-dir .
+    CXXFLAGS=${DOLFINX_CMAKE_CXX_FLAGS} PETSC_ARCH=linux-gnu-complex128-32 pip3 install -v --no-build-isolation --target /usr/local/dolfinx-complex/lib/python${PYTHON_VERSION}/dist-packages --no-dependencies --no-cache-dir .
 
 # Real by default.
 ONBUILD ENV PKG_CONFIG_PATH=/usr/local/dolfinx-real/lib/pkgconfig:$PKG_CONFIG_PATH \

docker/Dockerfile.oneapi

@@ -58,7 +58,7 @@ ENV CC=icx \
 
 # Install Python packages (via pip)
 RUN . /opt/intel/oneapi/setvars.sh && \
-    pip install --no-cache-dir cppimport mpi4py nanobind==${NANOBIND_VERSION} pytest pytest-xdist
+    pip install --no-cache-dir cppimport matplotlib mpi4py nanobind==${NANOBIND_VERSION} pytest pytest-xdist scikit-build-core[pyproject]
 
 # Install KaHIP
 RUN . /opt/intel/oneapi/setvars.sh && \

docker/Dockerfile.redhat

@@ -63,7 +63,7 @@ RUN curl -L -O https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-${HDF5_SERIES
 
 # First set of dependencies for building and running Python DOLFINx
 # Second set of dependencies for running DOLFINx tests
-RUN python3 -m pip install --no-cache-dir cffi numba mpi4py nanobind wheel && \
+RUN python3 -m pip install --no-cache-dir cffi numba mpi4py nanobind scikit-build-core[pyproject] wheel && \
     python3 -m pip install --no-cache-dir cppimport pytest pytest-xdist scipy matplotlib
 
 # Build PETSc

docker/Dockerfile.test-env

@@ -153,8 +153,8 @@ RUN if [ "$MPI" = "mpich" ]; then \
 # - Second set of packages are recommended and/or required to build
 #   documentation or run tests.
 RUN pip3 install --no-cache-dir --upgrade setuptools pip && \
-    pip3 install --no-cache-dir cffi mpi4py numba numpy==${NUMPY_VERSION} scipy && \
-    pip3 install --no-cache-dir clang-format cppimport cmakelang flake8 isort jupytext matplotlib mypy myst-parser nanobind==${PYBIND11_VERSION} pytest pytest-xdist sphinx sphinx_rtd_theme
+    pip3 install  -no-cache-dir cffi mpi4py numba numpy==${NUMPY_VERSION} scikit-build-core[pyproject] && \
+    pip3 install --no-cache-dir breath clang-format cppimport cmakelang flake8 isort jupytext matplotlib mypy myst-parser nanobind==${NANOBIND_VERSION} pytest pytest-xdist scipy sphinx==5.0.2 sphinx_rtd_theme types-setuptools
 
 # Install KaHIP
 RUN wget -nc --quiet https://github.com/kahip/kahip/archive/v${KAHIP_VERSION}.tar.gz && \

python/.flake8

@@ -0,0 +1,3 @@
+[flake8]
+max-line-length = 120
+ignore = W503

python/CMakeLists.txt

@@ -1,4 +1,4 @@
-cmake_minimum_required(VERSION 3.16)
+cmake_minimum_required(VERSION 3.18)
 
 project(dolfinx_nanobind)
 
@@ -8,22 +8,11 @@ set(CMAKE_CXX_STANDARD_REQUIRED ON)
 set(CMAKE_CXX_EXTENSIONS OFF)
 # set(CMAKE_BUILD_TYPE Debug)
 
-# Development component which includes both Development.Module and
-# Development.Embed is not required for building a Python module.  Correct
-# COMPONENT specification Development.Module added only in CMake 3.18 and above.
-if(${CMAKE_VERSION} VERSION_GREATER_EQUAL "3.18.0")
-  find_package(
-    Python3
-    COMPONENTS Interpreter Development.Module
-    REQUIRED
-  )
-else()
-  find_package(
-    Python3
-    COMPONENTS Interpreter Development
-    REQUIRED
-  )
-endif()
+find_package(
+  Python3
+  COMPONENTS Interpreter Development.Module
+  REQUIRED
+)
 
 execute_process(
   COMMAND
@@ -38,11 +27,12 @@ find_package(nanobind CONFIG REQUIRED)
 
 execute_process(
   COMMAND
-  ${Python3_EXECUTABLE} -c "import basix, os, sys; sys.stdout.write(os.path.dirname(basix.__file__))"
+  ${Python3_EXECUTABLE} -c "import os, sys, basix; sys.stdout.write(os.path.dirname(basix.__file__))"
   OUTPUT_VARIABLE BASIX_PY_DIR
   RESULT_VARIABLE BASIX_PY_COMMAND_RESULT
-  ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE
+  ERROR_VARIABLE BASIX_ERROR_OUT OUTPUT_STRIP_TRAILING_WHITESPACE
 )
+
 find_package(Basix REQUIRED CONFIG HINTS ${BASIX_PY_DIR})
 
 find_package(DOLFINX REQUIRED CONFIG)
@@ -109,3 +99,7 @@ if(NOT MPI4PY_COMMAND_RESULT)
 else()
   message(FATAL_ERROR "mpi4py could not be found.")
 endif()
+
+set_target_properties(cpp PROPERTIES INSTALL_RPATH_USE_LINK_PATH TRUE)
+
+install(TARGETS cpp DESTINATION dolfinx)

python/README.rst

@@ -1,24 +1,21 @@
 DOLFINx Python interface
 ========================
 
-Building the DOLFINx Python interface uses nanobind.
+This document explains how to install the DOLFINx Python interface. Note that
+this interface must be built without PEP517 build isolation by passing
+`--no-build-isolation` flag to `pip install`. This is because the Python
+interface explicitly depends on the system built petsc4py and mpi4py.
 
-1. Install nanobind from source, e.g.::
+1. Build and install the DOLFINx C++ library in the usual way.
 
-     python3 -m pip install git+https://github.com/wjakob/nanobind.git
+2. Ensure the build time requirements are installed::
 
-   The FEniCS Docker images are configured with nanobind.
-
-2. Build and install the DOLFINx C++ library in the usual way.
+     pip install -v -r build-requirements.txt
 
 3. Build DOLFINx Python interface::
 
-     pip3 -v install . --user
-
-To install in a local build directory::
-
-  python3 setup.py build
+     pip -v install --check-build-dependencies --no-build-isolation .
 
-and set the ``PYTHONPATH``. To build in debug mode::
+   To build in debug and editable mode for development::
 
-  python3 setup.py build --debug
+     pip -v install --check-build-dependencies --config-settings=build-dir="build" --config-settings=cmake.build-type="Debug" --no-build-isolation -e .

python/build-requirements.txt

@@ -0,0 +1,4 @@
+nanobind>=1.7.0
+scikit-build-core[pyproject]
+petsc4py
+mpi4py

python/demo/conftest.py

@@ -3,7 +3,7 @@
 
 def pytest_addoption(parser):
     parser.addoption("--mpiexec", action="store", default="mpirun",
-                     help="Name of program to run MPI, e.g. mpiexex")
+                     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")
 

python/pyproject.toml

@@ -0,0 +1,48 @@
+# The DOLFINx Python interface must be built without build isolation (PEP517)
+# due to its runtime and build time dependency on system built petsc4py and
+# mpi4py.
+# pip install -r build-requirements.txt
+[build-system]
+requires = ["scikit-build-core[pyproject]", "nanobind>=1.6.0", "petsc4py", "mpi4py"]
+build-backend = "scikit_build_core.build"
+
+[project]
+name = "fenics-dolfinx"
+version = "0.8.0.dev0"
+description = "DOLFINx Python interface"
+readme = "../README.md"
+requires-python = ">=3.8.0"
+license = {file = "../COPYING"}
+authors = [{email="fenics-steering-council@googlegroups.com"}, {name="FEniCS Steering Council"}]
+packages = ["dolfinx"]
+dependencies = ["numpy>=1.21", "cffi", "petsc4py", "mpi4py",
+	        "fenics-ffcx>=0.8.0.dev0,<0.9.0",
+    		"fenics-ufl>=2023.3.0.dev0,<2023.4.0"]
+
+[project.optional-dependencies]
+docs = ["markdown", "pylit3", "pyyaml", "sphinx==5.0.2", "sphinx_rtd_theme"]
+lint = ["flake8", "pydocstyle"]
+optional = ["numba"]
+test = ["pytest", "sympy", "scipy", "matplotlib", "fenics-dolfinx[optional]"]
+ci = ["mypy", "pytest-xdist", "types-setuptools", "fenics-dolfinx[build]",
+      "fenics-dolfinx[docs]", "fenics-dolfinx[lint]", "fenics-dolfinx[optional]",
+      "fenics-dolfinx[test]"]
+
+[tool.scikit-build]
+wheel.packages = ["dolfinx"]
+sdist.exclude = ["*.cpp"]
+
+[tool.pytest]
+junit_family = "xunit2"
+
+[tool.mypy]
+# Suggested at https://blog.wolt.com/engineering/2021/09/30/professional-grade-mypy-configuration/
+# Goal would be to make all of the below True long-term
+disallow_untyped_defs = false
+disallow_any_unimported = false
+no_implicit_optional = false
+check_untyped_defs = false
+warn_return_any = false
+warn_unused_ignores = false
+show_error_codes = true
+ignore_missing_imports = true