run_tests_linux.yml

name: Run the tests

on: [pull_request]

env:
  PREFIX_LINUX: /usr/share/miniconda3/envs/bioptim

jobs:
  build:
    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: Set prefix Linux
        run: echo "PREFIX=${{ env.PREFIX_LINUX }}" >> $GITHUB_ENV

      - name: Checkout code
        uses: actions/checkout@v3

      - name: Setup environment
        uses: conda-incubator/setup-miniconda@v2
        with:
          miniforge-version: latest
          use-mamba: true
          activate-environment: bioptim
          environment-file: environment.yml

      - name: Print mamba info
        run: |
          conda info
          conda list

      - name: Install extra dependencies
        run: | 
          conda install pytest-cov black pytest pytest-cov codecov packaging -cconda-forge
          sudo apt install -y librhash-dev

      - name: Install ACADOS on Linux
        run: |
          pwd
          cd external
          ./acados_install_linux.sh 4 ${{ env.PREFIX_LINUX }}
          cd ..
        if: matrix.shard == 1

      - name: Install pytorch on Linux
        run: |
          git submodule update --init --recursive
          cd external/l4casadi
          pip install torch>=2.0
          pip install setuptools>=68.1 scikit-build>=0.17 cmake>=3.27 ninja>=1.11
          pip install . --no-build-isolation
          cd ../..
        if: matrix.shard == 3

      - name: Test installed version of bioptim
        run: |
          python setup.py 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 --cov-report=xml:coverage.xml tests/shard${{ matrix.shard }}
        if: matrix.os == 'ubuntu-latest'

      - name: Archive coverage report
        id: archive
        uses: actions/upload-artifact@v3
        with:
          name: coverage${{ matrix.shard }}
          path: |
            coverage.xml
            .coverage


  merge-coverage:
    needs: build
    runs-on: ubuntu-latest
    defaults:
      run:
        shell: bash -l {0}

    steps:
      - name: Set prefix Linux
        run:
            echo "PREFIX=${{ env.PREFIX_LINUX }}" >> $GITHUB_ENV


      - name: Checkout code
        uses: actions/checkout@v3

      - name: Setup environment
        uses: conda-incubator/setup-miniconda@v2
        with:
          miniforge-version: latest
          use-mamba: true
          activate-environment: bioptim
          environment-file: environment.yml

      - name: Print mamba info
        run: |
          conda info
#          mamba list

      - name: Install extra dependencies
        run: |
          sudo apt-get install -y python3-pip
          pip3 install coverage

      - name: Download all workflow run artifacts
        id: download
        uses: actions/download-artifact@v3

      - name: Rename coverage files
        run: |
          for shard in {1,2,3,4,5,6}; do
            mv coverage${shard}/coverage.xml coverage${shard}.xml
            mv coverage${shard}/.coverage* .coverage${shard}
          done

      - name: Show current dir content
        run: pwd; ls -a -l

      - name: Merge coverage reports
        run: coverage combine .coverage1 .coverage2 .coverage3 .coverage4

      - name: Show current dir content with new .coverage file
        run: pwd; ls -a

      - name: Generate XML report
        run: |
          coverage xml
          coverage report -m

      - name: Upload coverage to Codecov
        uses: codecov/codecov-action@v2
        with:
          #token: ${{ secrets.CODECOV_TOKEN }}
          file: ./coverage.xml
          #files: ./coverage1.xml, ./coverage2.xml, ./coverage3.xml, ./coverage4.xml
          flags: unittests
          fail_ci_if_error: true
          verbose: true