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Add AdjacencyList python wrapper #32426

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Add AdjacencyList python wrapper

Add AdjacencyList python wrapper #32426

Workflow file for this run

.github/workflows/ccpp.yml at ae8e606
name: DOLFINx CI
on:
push:
branches:
- "**"
tags:
- "v*"
pull_request:
branches:
- main
merge_group:
branches:
- main
workflow_dispatch:
inputs:
ffcx_ref:
description: "FFCx branch or tag"
default: "main"
type: string
basix_ref:
description: "Basix branch or tag"
default: "main"
type: string
ufl_ref:
description: "UFL branch or tag"
default: "main"
type: string
jobs:
lint:
runs-on: ubuntu-latest
name: Lint
steps:
- uses: actions/checkout@v4
- name: Set up Python
uses: actions/setup-python@v5
with:
python-version: '3.12'
- name: Install linting tools
run: pip install clang-format cmake-format[YAML] mypy ruff
- name: ruff .py files in C++ code
run: |
cd cpp/
ruff check .
ruff format --check .
- name: ruff Python interface checks
run: |
cd python/
ruff check .
ruff format --check .
- name: mypy checks
run: |
cd python/
mypy dolfinx
mypy demo
mypy test
- name: clang-format C++ checks (non-blocking)
continue-on-error: true
run: |
cd cpp
clang-format --version
find . -type f \( -name "*.cpp" -o -name "*.h" \) | xargs clang-format --dry-run --Werror
- name: clang-format Python binding checks (non-blocking)
continue-on-error: true
run: |
cd python/dolfinx/wrappers
clang-format --version
find . -type f \( -name "*.cpp" -o -name "*.h" \) | xargs clang-format --dry-run --Werror
- name: cmake-format (non-blocking)
continue-on-error: true
run: |
find . -type f \( -name "*.cmake" -o -name "*.cmake.in" -o -name "CMakeLists.txt" \) | xargs cmake-format --check
build:
runs-on: ubuntu-latest
needs: lint
env:
OMPI_ALLOW_RUN_AS_ROOT: 1
OMPI_ALLOW_RUN_AS_ROOT_CONFIRM: 1
PRTE_MCA_rmaps_default_mapping_policy: :oversubscribe # Newer OpenMPI
OMPI_MCA_rmaps_base_oversubscribe: true # Older OpenMPI
name: Build and test
steps:
- uses: actions/checkout@v4
- name: Install dependencies
run: |
sudo apt-get update
sudo apt-get install catch2 cmake g++ libboost-dev libhdf5-mpi-dev libparmetis-dev libpugixml-dev libspdlog-dev mpi-default-dev ninja-build pkg-config
- name: Set up Python
uses: actions/setup-python@v5
with:
python-version: "3.12"
- name: Install Python build dependencies
run: |
pip install --upgrade -r python/build-requirements.txt
- name: Install FEniCS Python components (default branches/tags)
if: github.event_name != 'workflow_dispatch'
run: |
pip install git+https://github.com/FEniCS/ufl.git
pip install git+https://github.com/FEniCS/basix.git
pip install git+https://github.com/FEniCS/ffcx.git
- name: Install FEniCS Python components
if: github.event_name == 'workflow_dispatch'
run: |
pip install git+https://github.com/FEniCS/ufl.git@${{ github.event.inputs.ufl_ref }}
pip install git+https://github.com/FEniCS/basix.git@${{ github.event.inputs.basix_ref }}
pip install git+https://github.com/FEniCS/ffcx.git@${{ github.event.inputs.ffcx_ref }}
- name: Configure and install C++
run: |
cmake -G Ninja -DDOLFINX_ENABLE_PETSC=false -DCMAKE_BUILD_TYPE=Developer -B build -S cpp/
cmake --build build
sudo cmake --install build
- name: Build C++ unit tests
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)
run: |
cd build/test
ctest -V --output-on-failure -R unittests
- name: Run C++ unit tests (MPI)
run: |
cd build/test
mpirun -n 3 ctest -V --output-on-failure -R unittests
- name: Build Python interface
run: |
pip install --check-build-dependencies --no-build-isolation --config-settings=cmake.build-type="Debug" 'python/[test]'
python -c "from mpi4py import MPI; import dolfinx; assert not dolfinx.has_petsc4py"
- name: Run demos (Python, serial)
run: |
pip install pytest-xdist
python -m pytest -n auto -m serial --durations=10 python/demo/test.py
- name: Run demos (Python, MPI (np=3))
run: python -m pytest -m mpi --num-proc=3 python/demo/test.py
- name: Run unit tests
run: python -m pytest -n auto -m "not petsc4py and not adios2" python/test/unit
- name: Run unit tests (MPI, np=3)
run: mpirun -np 3 python -m pytest -m "not petsc4py and not adios2" python/test/unit
build-with-petsc:
runs-on: ubuntu-latest
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 }}
env:
PETSC_ARCH: ${{ matrix.petsc_arch }}
OMPI_ALLOW_RUN_AS_ROOT: 1
OMPI_ALLOW_RUN_AS_ROOT_CONFIRM: 1
PRTE_MCA_rmaps_default_mapping_policy: :oversubscribe
name: Build and test (${{ matrix.petsc_arch }}, ${{ matrix.docker_image }})
steps:
- uses: actions/checkout@v4
- name: Install FEniCS Python components (default branches/tags)
if: github.event_name != 'workflow_dispatch'
run: |
pip install git+https://github.com/FEniCS/ufl.git
pip install git+https://github.com/FEniCS/basix.git
pip install git+https://github.com/FEniCS/ffcx.git
- name: Install FEniCS Python components
if: github.event_name == 'workflow_dispatch'
run: |
pip install git+https://github.com/FEniCS/ufl.git@${{ github.event.inputs.ufl_ref }}
pip install git+https://github.com/FEniCS/basix.git@${{ github.event.inputs.basix_ref }}
pip install git+https://github.com/FEniCS/ffcx.git@${{ github.event.inputs.ffcx_ref }}
- name: Configure, build and install C++ library
run: |
cmake -G Ninja -DCMAKE_BUILD_TYPE=Developer -DDOLFINX_ENABLE_ADIOS2=true -DDOLFINX_ENABLE_KAHIP=true -DDOLFINX_ENABLE_PARMETIS=false -DDOLFINX_ENABLE_PETSC=true -DDOLFINX_ENABLE_SCOTCH=true -DDOLFINX_ENABLE_SLEPC=true -B build -S cpp/
cmake --build build
cmake --install build
- name: Build C++ unit tests
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)
run: |
cd build/test
ctest -V --output-on-failure -R unittests
- name: Run C++ unit tests (MPI)
run: |
cd build/test
mpirun -n 3 ctest -V --output-on-failure -R unittests
- name: Build and run C++ regression tests (serial and MPI (np=2))
run: |
cmake -G Ninja -DCMAKE_BUILD_TYPE=Developer -B build/demo/ -S cpp/demo/
cmake --build build/demo --parallel 3
cd build/demo
ctest -V -R demo -R serial
ctest -V -R demo -R mpi_2
- name: Install Python build dependencies
run: pip install -r python/build-requirements.txt
- name: Build Python interface
run: |
pip install --check-build-dependencies --no-build-isolation --config-settings=cmake.build-type="Debug" 'python/[test]'
python -c "from mpi4py import MPI; import dolfinx; assert dolfinx.has_adios2; assert dolfinx.has_kahip; assert not dolfinx.has_parmetis; assert dolfinx.has_petsc; assert dolfinx.has_petsc4py; assert dolfinx.has_ptscotch; assert dolfinx.has_slepc; assert dolfinx.has_complex_ufcx_kernels"
- 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 demos (Python, serial)
run: |
pip install pytest-xdist
python -m pytest -n auto -m serial --durations=10 python/demo/test.py
- name: Run demos (Python, MPI (np=3))
run: python -m pytest -m mpi --num-proc=3 python/demo/test.py
- name: Run Python unit tests (serial)
run: python -m pytest -m "petsc4py or adios2" -n=auto --durations=50 python/test/unit/
- name: Run Python unit tests (MPI, np=3)
run: mpirun -np 3 python -m pytest -m "petsc4py or adios2" python/test/unit/
build-and-publish-docs:
runs-on: ubuntu-latest
container: "ghcr.io/fenics/test-env:current-openmpi"
env:
PETSC_ARCH: linux-gnu-real64-32
OMPI_ALLOW_RUN_AS_ROOT: 1
OMPI_ALLOW_RUN_AS_ROOT_CONFIRM: 1
PRTE_MCA_rmaps_default_mapping_policy: :oversubscribe
name: Build and publish docs
steps:
- uses: actions/checkout@v4
- name: Install FEniCS Python components (default branches/tags)
if: github.event_name != 'workflow_dispatch'
run: |
pip install git+https://github.com/FEniCS/ufl.git
pip install git+https://github.com/FEniCS/basix.git
pip install git+https://github.com/FEniCS/ffcx.git
- name: Install FEniCS Python components
if: github.event_name == 'workflow_dispatch'
run: |
pip install git+https://github.com/FEniCS/ufl.git@${{ github.event.inputs.ufl_ref }}
pip install git+https://github.com/FEniCS/basix.git@${{ github.event.inputs.basix_ref }}
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/
cmake --build build
cmake --install build
- name: Build Python interface
run: |
pip install -r python/build-requirements.txt
pip install --check-build-dependencies --no-build-isolation --config-settings=cmake.build-type="Debug" 'python/[docs]'
- name: Build C++ interface documentation
run: |
export DOLFINX_VERSION=`cmake -L build | grep DOXYGEN_DOLFINX_VERSION | cut -f2 -d "="`
echo $DOLFINX_VERSION
cd cpp/doc
doxygen Doxyfile
make html
- name: Upload C++ Doxygen documentation artifact
uses: actions/upload-artifact@v4
with:
name: docs-cpp-doxygen
path: cpp/doc/html
retention-days: 2
- name: Upload C++ Sphinx documentation artifact
uses: actions/upload-artifact@v4
with:
name: docs-cpp-sphinx
path: cpp/doc/build/html
retention-days: 2
- name: Build Python interface documentation
run: |
cd python/doc
python -m sphinx -W -b html source/ build/html/
- name: Upload Python documentation artifact
uses: actions/upload-artifact@v4
with:
name: docs-python
path: python/doc/build/html
retention-days: 2
- name: Checkout FEniCS/docs
if: ${{ github.repository == 'FEniCS/dolfinx' && ( github.ref == 'refs/heads/main' || startsWith(github.ref, 'refs/tags/v') ) }}
uses: actions/checkout@v4
with:
repository: "FEniCS/docs"
path: "docs"
ssh-key: "${{ secrets.SSH_GITHUB_DOCS_PRIVATE_KEY }}"
- name: Set version name
if: ${{ github.repository == 'FEniCS/dolfinx' && ( github.ref == 'refs/heads/main' || startsWith(github.ref, 'refs/tags/v') ) }}
run: |
echo "VERSION_NAME=${GITHUB_REF#refs/*/}" >> $GITHUB_ENV
- name: Copy documentation into repository
if: ${{ github.repository == 'FEniCS/dolfinx' && ( github.ref == 'refs/heads/main' || startsWith(github.ref, 'refs/tags/v') ) }}
run: |
cd docs
git rm -r --ignore-unmatch dolfinx/${{ env.VERSION_NAME }}/cpp
git rm -r --ignore-unmatch dolfinx/${{ env.VERSION_NAME }}/python
mkdir -p dolfinx/${{ env.VERSION_NAME }}/cpp
mkdir -p dolfinx/${{ env.VERSION_NAME }}/cpp/doxygen
mkdir -p dolfinx/${{ env.VERSION_NAME }}/python
cp -r ../cpp/doc/build/html/* dolfinx/${{ env.VERSION_NAME }}/cpp/
cp -r ../cpp/doc/html/* dolfinx/${{ env.VERSION_NAME }}/cpp/doxygen
cp -r ../python/doc/build/html/* dolfinx/${{ env.VERSION_NAME }}/python
- name: Commit and push documentation to FEniCS/docs
if: ${{ github.repository == 'FEniCS/dolfinx' && ( github.ref == 'refs/heads/main' || startsWith(github.ref, 'refs/tags/v') ) }}
run: |
cd docs
git config --global user.email "[email protected]"
git config --global user.name "FEniCS GitHub Actions"
git add --all
git commit --allow-empty -m "C++/Python FEniCS/dolfinx@${{ github.sha }}"
git push