Run the tests workflow (pyomeca/bioptim)

name: Run the tests
 
on: [pull_request]
 
concurrency:
  group: ${{ github.workflow }}-${{ github.ref }}
  cancel-in-progress: true
 
jobs:
  build:
    timeout-minutes: 30
    strategy:
      fail-fast: false
      matrix:
        os: [ubuntu-latest]
        shard: [1, 2, 3, 4, 5, 6]
    name: Tests on ${{ matrix.os }}-shard ${{ matrix.shard }}
    runs-on: ${{ matrix.os }}
    defaults:
      run:
        shell: bash -l {0}
 
    steps:
      - name: Checkout code
        uses: actions/checkout@v3
 
      - name: Checkout submodules
        if: matrix.shard == 1
        run: git submodule update --init --recursive
        
      - name: Setup environment
        uses: conda-incubator/setup-miniconda@v3
        with:
          miniforge-version: latest
          activate-environment: bioptim
          environment-file: environment.yml
 
      - name: Print conda info
        run: |
          conda info
          conda list
 
      - name: Install extra dependencies
        run: | 
          conda install "numpy>=2.4,<3" pip pytest-cov black pytest pytest-cov codecov packaging pytest-mpl -cconda-forge
          sudo apt install -y librhash-dev
 
      - name: Install ACADOS on Linux
        run: |
          pwd
          cd external
          ./acados_install_linux.sh 4 $CONDA_PREFIX
          cd ..
        if: matrix.shard == 1
 
      - name: Test installed version of bioptim
        run: |
          pip install .
          cd
          python -c "import bioptim"
        if: matrix.shard == 1
 
      - name: Run tests with code coverage
        run: pytest -v --color=yes --cov-report term-missing --cov=bioptim tests/shard${{ matrix.shard }} --mpl-baseline-path=bioptim/tests/plot_reference_images
        if: matrix.os == 'ubuntu-latest'
 
      - name: Archive coverage report
        id: archive
        uses: actions/upload-artifact@v4
        with:
          name: coverage-${{ matrix.shard }}
          path: .coverage
          if-no-files-found: error
          include-hidden-files: true
 
  merge-coverage:
    timeout-minutes: 30
    needs: build
    runs-on: latchkey-small
    defaults:
      run:
        shell: bash -l {0}
 
    steps:
      - name: Checkout code
        uses: actions/checkout@v3
 
      - name: Install extra dependencies
        run: |
          sudo apt install -y python3-pip
          pip3 install coverage
 
      - name: Download all workflow run artifacts
        id: download
        uses: actions/download-artifact@v4
        with:
          pattern: coverage-*
 
      - name: Rename coverage files
        run: |
          for shard in {1,2,3,4,5,6}; do
            mv coverage-${shard}/.coverage .coverage${shard}
          done
 
      - name: Merge coverage reports
        run: coverage combine .coverage1 .coverage2 .coverage3 .coverage4 .coverage5 .coverage6
 
      - name: Generate XML report
        run: |
          coverage xml
          coverage report -m
 
      - uses: codecov/codecov-action@v5
        with:
          files: ./coverage.xml
          flags: unittests
          fail_ci_if_error: true
          verbose: true