run_tests_win.yml

name: Run the tests

on: [pull_request]

env:
  PREFIX_WINDOWS: C:\Miniconda3\envs\cocofest

jobs:
  build:
    strategy:
      fail-fast: false
      matrix:
        os: [windows-latest]
        shard: [1, 2]
    name: Tests on ${{ matrix.os }}-shard ${{ matrix.shard }}
    runs-on: ${{ matrix.os }}
    defaults:
      run:
        shell: bash -l {0}

    steps:
      - name: Set prefix windows
        run: |
          echo "PREFIX=${{ env.PREFIX_WINDOWS }}" >> $GITHUB_ENV
        if: matrix.os == 'windows-latest'

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

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

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

      - name: Install bioptim on Windows
        run: |
          pwd
          cd external
          ./bioptim_install_windows.sh 4 ${{ env.PREFIX_WINDOWS }}
          cd ..

      - name: Install extra dependencies
        run: mamba install pytest-cov black pytest pytest-cov codecov packaging -cconda-forge

      - name: Run tests with code coverage
        run: pytest -v --color=yes --cov-report term-missing --cov=cocofest --cov-report=xml:coverage.xml tests/shard${{ matrix.shard }}

      - 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: windows-latest
    defaults:
      run:
        shell: bash -l {0}

    steps:
      - name: Set prefix windows
        run: |
          echo "PREFIX=${{ env.PREFIX_WINDOWS }}" >> $GITHUB_ENV

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

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

      - name: Print mamba info
        run: |
          mamba info

      - name: Install bioptim on Windows
        run: |
          pwd
          cd external
          ./bioptim_install_windows.sh 4 ${{ env.PREFIX_WINDOWS }}
          cd ..

      - name: Install extra dependencies
        run: pip 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}; 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

      - 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
          token: ${{ secrets.CODECOV_TOKEN }}