Fix biology quartile (#72) #467
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| name: Testing | |
| on: | |
| push: | |
| branches: | |
| - "main" | |
| pull_request: | |
| branches: | |
| - "*" | |
| jobs: | |
| check_skip: | |
| name: Check CI Skip | |
| runs-on: ubuntu-latest | |
| outputs: | |
| skip: ${{ steps.result_step.outputs.ci-skip }} | |
| steps: | |
| - uses: actions/checkout@v2 | |
| with: | |
| fetch-depth: 0 | |
| - id: result_step | |
| uses: mstachniuk/ci-skip@master | |
| with: | |
| commit-filter: '[skip ci];[ci skip];[skip github]' | |
| commit-filter-separator: ';' | |
| Linting: | |
| name: Running pre-commit | |
| needs: check_skip | |
| if: ${{ needs.check_skip.outputs.skip == 'false' }} | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: actions/setup-python@v4 | |
| - name: Set PY variable | |
| run: echo "PY=$(python -VV | sha256sum | cut -d' ' -f1)" >> $GITHUB_ENV | |
| - uses: actions/cache@v2 | |
| with: | |
| path: ~/.cache/pre-commit | |
| key: pre-commit|${{ env.PY }}|${{ hashFiles('.pre-commit-config.yaml') }} | |
| - name: Install pre-commit | |
| run: | | |
| pip install pre-commit | |
| pre-commit install | |
| - name: Run pre-commit | |
| run: SKIP=no-commit-to-branch pre-commit run --all-files | |
| Testing: | |
| needs: check_skip | |
| if: ${{ needs.check_skip.outputs.skip == 'false' }} | |
| runs-on: "ubuntu-latest" | |
| name: 'Testing on ubuntu' | |
| defaults: | |
| run: | |
| shell: bash | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - uses: actions/setup-java@v1 | |
| with: | |
| java-version: 1.8 | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: '3.7' | |
| - name: Install eds-scikit | |
| shell: bash {0} | |
| run: ./build_tools/github/install.sh | |
| - name: Run tests | |
| shell: bash {0} | |
| run: ./build_tools/github/test.sh | |
| - name: Upload coverage data | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: coverage-data-${{ matrix.python-version }} | |
| path: .coverage.* | |
| if-no-files-found: ignore | |
| if: success() | |
| - name: Check dependencies licenses | |
| run: | | |
| liccheck | |
| Coverage: | |
| needs: Testing | |
| uses: aphp/foldedtensor/.github/workflows/coverage.yml@main | |
| with: | |
| base-branch: main | |
| coverage-data-pattern: coverage-data-* | |
| coverage-report: coverage.txt | |
| coverage-badge: coverage.svg | |
| coverage-branch: coverage | |
| Documentation: | |
| needs: check_skip | |
| if: ${{ needs.check_skip.outputs.skip == 'false' }} | |
| name: Building documentation | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.7" | |
| - name: Cap pip version | |
| run: pip install -U "pip<23" | |
| - name: Install dependencies | |
| run: pip install .[doc] | |
| - name: Build documentation | |
| run: | | |
| mkdocs build --clean |