continuous-integration.yml

# 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: cache-${{ matrix.os }}-${{ 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 single-process tests with Pytest
        working-directory: ./pytest
        run: >- 
          python -m pytest -n auto --cov psydac
          --cov-config $GITHUB_WORKSPACE/pyproject.toml
          --cov-report=""
          --pyargs psydac -m "not parallel and not petsc"

      - name: Generate coverage report for Codacy
        working-directory: ./pytest
        run: |
          coverage xml

      - name: Upload coverage report to Codacy
        uses: codacy/codacy-coverage-reporter-action@v1.3.0
        with:
          project-token: ${{ secrets.CODACY_PROJECT_TOKEN }}
          coverage-reports: ./pytest/coverage.xml

      - name: Print detailed coverage results
        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