Codacy code coverage reporting #2569
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| # This workflow will install Python dependencies and run tests with a variety of Python versions | |
| # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions | |
| name: Run tests | |
| on: | |
| push: | |
| branches: [ devel ] | |
| pull_request: | |
| branches: [ devel ] | |
| jobs: | |
| test: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ ubuntu-latest ] | |
| python-version: [ 3.9, '3.10', '3.11', '3.12' ] | |
| isMerge: | |
| - ${{ github.event_name == 'push' && github.ref == 'refs/heads/devel' }} | |
| exclude: | |
| - { isMerge: false, python-version: '3.10' } | |
| - { isMerge: false, python-version: '3.11' } | |
| include: | |
| - os: macos-latest | |
| python-version: '3.10' | |
| - os: macos-latest | |
| python-version: '3.11' | |
| name: ${{ matrix.os }} / Python ${{ matrix.python-version }} | |
| env: | |
| PSYDAC_MESH_DIR: ${{ github.workspace }}/mesh | |
| OMP_NUM_THREADS: 2 | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| cache: 'pip' | |
| cache-dependency-path: | | |
| pyproject.toml | |
| requirements.txt | |
| requirements_extra.txt | |
| - name: Install non-Python dependencies on Ubuntu | |
| if: matrix.os == 'ubuntu-latest' | |
| uses: awalsh128/cache-apt-pkgs-action@latest | |
| with: | |
| packages: gfortran openmpi-bin libopenmpi-dev libhdf5-openmpi-dev | |
| version: 1.0 | |
| execute_install_scripts: true | |
| # When loading cached apt packages, the default MPI compiler isn't set. | |
| # Workaround is to 'reinstall' openmpi-bin, which doesn't actually perform | |
| # installation (since openmpi-bin already exists), but instead reruns | |
| # `update-alternatives` which fixes the symlinks to mpicc/mpif90. | |
| - name: Set default MPI and HDF5 C compilers on Ubuntu | |
| if: matrix.os == 'ubuntu-latest' | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install --reinstall openmpi-bin libhdf5-openmpi-dev | |
| - name: Install non-Python dependencies on macOS | |
| if: matrix.os == 'macos-latest' | |
| run: | | |
| brew install open-mpi | |
| brew install hdf5-mpi | |
| brew install libomp | |
| GFORTRAN_HOME=$(which gfortran || true) | |
| echo "GFORTRAN_HOME : $GFORTRAN_HOME" | |
| if [[ ! -f "$GFORTRAN_HOME" ]]; then | |
| gfort=$(find ${PATH//:/\/ } -name 'gfortran-*' -exec basename {} \; | sort | tail -n 1 || true) | |
| echo "Found $gfort" | |
| gfort_path=$(which ${gfort}) | |
| folder=$(dirname ${gfort_path}) | |
| ln -s ${gfort_path} ${folder}/gfortran | |
| fi | |
| echo "MPI_OPTS=--oversubscribe" >> $GITHUB_ENV | |
| - name: Print information on MPI and HDF5 libraries | |
| run: | | |
| ompi_info | |
| h5pcc -showconfig -echo || true | |
| - name: Upgrade pip | |
| run: | | |
| python -m pip install --upgrade pip | |
| - name: Determine directory of parallel HDF5 library | |
| run: | | |
| if [[ "${{ matrix.os }}" == "ubuntu-latest" ]]; then | |
| HDF5_DIR=$(dpkg -L libhdf5-openmpi-dev | grep libhdf5.so | xargs dirname) | |
| elif [[ "${{ matrix.os }}" == "macos-latest" ]]; then | |
| HDF5_DIR=$(brew list hdf5-mpi | grep "libhdf5.dylib" | xargs dirname | xargs dirname) | |
| fi | |
| echo $HDF5_DIR | |
| echo "HDF5_DIR=$HDF5_DIR" >> $GITHUB_ENV | |
| - name: Cache PETSc | |
| uses: actions/cache@v4 | |
| id: cache-petsc | |
| env: | |
| cache-name: cache-PETSc | |
| with: | |
| path: "./petsc" | |
| key: petsc-${{ matrix.os }}-${{ matrix.python-version }} | |
| - if: steps.cache-petsc.outputs.cache-hit != 'true' | |
| name: Download a specific release of PETSc | |
| run: | | |
| git clone --depth 1 --branch v3.21.4 https://gitlab.com/petsc/petsc.git | |
| - if: steps.cache-petsc.outputs.cache-hit != 'true' | |
| name: Install PETSc with complex support | |
| working-directory: ./petsc | |
| run: | | |
| export PETSC_DIR=$(pwd) | |
| export PETSC_ARCH=petsc-cmplx | |
| ./configure --with-scalar-type=complex --with-fortran-bindings=0 --have-numpy=1 | |
| make all | |
| echo "PETSC_DIR=$PETSC_DIR" > petsc.env | |
| echo "PETSC_ARCH=$PETSC_ARCH" >> petsc.env | |
| # This step is not really necessary and could be combined with PETSc install | |
| # step; however it's good to verify if the cached PETSc installation really works! | |
| - name: Test PETSc installation | |
| working-directory: ./petsc | |
| run: | | |
| source petsc.env | |
| make check | |
| echo "PETSC_DIR=$PETSC_DIR" >> $GITHUB_ENV | |
| echo "PETSC_ARCH=$PETSC_ARCH" >> $GITHUB_ENV | |
| - name: Install petsc4py | |
| working-directory: ./petsc | |
| run: | | |
| python -m pip install wheel Cython numpy | |
| python -m pip install src/binding/petsc4py | |
| - name: Install Python dependencies | |
| run: | | |
| export CC="mpicc" | |
| export HDF5_MPI="ON" | |
| python -m pip install -r requirements.txt | |
| python -m pip install -r requirements_extra.txt --no-build-isolation | |
| python -m pip list | |
| - name: Check parallel h5py installation | |
| run: | | |
| python -c " | |
| from mpi4py import MPI | |
| import h5py | |
| # This particular instantiation of h5py.File will fail if parallel h5py isn't installed | |
| f = h5py.File('parallel_test.hdf5', 'w', driver='mpio', comm=MPI.COMM_WORLD) | |
| print(f)" | |
| - name: Install project | |
| run: | | |
| python -m pip install .[test] | |
| python -m pip freeze | |
| - name: Test Pyccel optimization flags | |
| run: | | |
| pytest --pyargs psydac -m pyccel --capture=no | |
| - name: Initialize test directory | |
| run: | | |
| mkdir pytest | |
| cp mpi_tester.py pytest | |
| - name: Run coverage tests on macOS | |
| if: matrix.os == 'macos-latest' | |
| working-directory: ./pytest | |
| run: >- | |
| python -m pytest -n auto | |
| --cov psydac | |
| --cov-config $GITHUB_WORKSPACE/pyproject.toml | |
| --cov-report xml | |
| --pyargs psydac -m "not parallel and not petsc" | |
| - name: Run single-process tests with Pytest on Ubuntu | |
| if: matrix.os == 'ubuntu-latest' | |
| working-directory: ./pytest | |
| run: | | |
| python -m pytest -n auto --pyargs psydac -m "not parallel and not petsc" | |
| - name: Upload coverage report to Codacy | |
| if: matrix.os == 'macos-latest' | |
| uses: codacy/[email protected] | |
| with: | |
| project-token: ${{ secrets.CODACY_PROJECT_TOKEN }} | |
| coverage-reports: ./pytest/coverage.xml | |
| - name: Print detailed coverage results on macOS | |
| if: matrix.os == 'macos-latest' | |
| working-directory: ./pytest | |
| run: | | |
| coverage report --ignore-errors --show-missing --sort=cover | |
| - name: Run MPI tests with Pytest | |
| working-directory: ./pytest | |
| run: | | |
| python mpi_tester.py --mpirun="mpiexec -n 4 ${MPI_OPTS}" --pyargs psydac -m "parallel and not petsc" | |
| - name: Run single-process PETSc tests with Pytest | |
| working-directory: ./pytest | |
| run: | | |
| python -m pytest -n auto --pyargs psydac -m "not parallel and petsc" | |
| - name: Run MPI PETSc tests with Pytest | |
| working-directory: ./pytest | |
| run: | | |
| python mpi_tester.py --mpirun="mpiexec -n 4 ${MPI_OPTS}" --pyargs psydac -m "parallel and petsc" | |
| - name: Remove test directory | |
| if: always() | |
| run: | | |
| rm -rf pytest |