Implementing musculoskeletal model driven by FES #94
Workflow file for this run
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| 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 config --show | |
| mamba info | |
| mamba list | |
| - name: Install bioptim on Windows | |
| run: | | |
| pwd | |
| cd external | |
| ./bioptim_install_windows.sh 4 ${{ env.PREFIX_WINDOWS }} | |
| cd .. | |
| # if: matrix.os == 'windows-latest' && matrix.shard == 1 | |
| - name: Install extra dependencies | |
| run: mamba install pytest-cov black pytest pytest-cov codecov packaging -cconda-forge | |
| - name: Run tests with code coverage | |
| run: pytest -v --color=yes --cov-report term-missing --cov=cocofest --cov-report=xml:coverage.xml tests/shard${{ 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 config --show | |
| mamba info | |
| - name: Install bioptim on Windows | |
| run: | | |
| pwd | |
| cd external | |
| ./bioptim_install_windows.sh 4 ${{ env.PREFIX_WINDOWS }} | |
| cd .. | |
| - name: Install extra dependencies | |
| run: pip install coverage | |
| #mamba install coverage -cconda-forge | |
| - name: Download all workflow run artifacts | |
| id: download | |
| uses: actions/download-artifact@v3 | |
| - name: Rename coverage files | |
| run: | | |
| for shard in {1,2}; do | |
| mv coverage${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 }} |