Update codecov with token (#407) #248
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| name: Test | |
| on: | |
| push: | |
| branches: [main] | |
| pull_request: | |
| branches: [main] | |
| jobs: | |
| lint: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: '3.10' | |
| - uses: actions/cache@v3 | |
| with: | |
| path: ~/.cache/pre-commit | |
| key: precommit-${{ env.pythonLocation }}-${{ hashFiles('**/.pre-commit-config.yaml') }} | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pre-commit | |
| - name: Run pre-commit | |
| run: | | |
| pre-commit run --color=always --show-diff-on-failure --all-files | |
| metrics: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| python: ['3.9', '3.11'] | |
| os: [ubuntu-latest, macos-latest] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python ${{ matrix.python }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python }} | |
| - name: Install build dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install build twine | |
| - name: Build a binary wheel and a source tarball | |
| run: | | |
| python -m build --sdist --wheel --outdir dist/ | |
| twine check dist/* | |
| - name: Install package with test dependencies | |
| run: | | |
| pip install dist/*.whl | |
| pip install '.[test,louvain]' | |
| - name: Test with pytest | |
| if: ${{ matrix.os != 'macos-latest'}} | |
| run: | | |
| pytest --cov=scib --cov-report=xml -vv --ignore=tests/integration/ --ignore=tests/metrics/rpy2 -vv | |
| mv coverage.xml "$(echo 'coverage_metrics_${{ matrix.os }}_${{ matrix.python }}.xml' | sed 's/[^a-z0-9\.\/]/_/g')" | |
| - name: Upload coverage to GitHub Actions | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: metrics | |
| path: coverage_*.xml | |
| rpy2: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| r: ['4.2'] | |
| python: ['3.10'] | |
| os: [ubuntu-latest] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python ${{ matrix.python }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python }} | |
| - name: Set up R | |
| uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: ${{ matrix.r }} | |
| - name: Install dependencies | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install '.[test,rpy2]' | |
| Rscript -e "install.packages('remotes')" | |
| Rscript -e "remotes::install_github('theislab/kBET')" | |
| - name: Test with pytest | |
| run: | | |
| pytest --cov=scib --cov-report=xml -vv --tb=native -k rpy2 | |
| mv coverage.xml "$(echo 'coverage_rpy2_${{ matrix.os }}_${{ matrix.python }}.xml' | sed 's/[^a-z0-9\.\/]/_/g')" | |
| - name: Upload coverage to GitHub Actions | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: rpy2 | |
| path: coverage_*.xml | |
| integration: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| python: ['3.9', '3.11'] | |
| os: [ubuntu-latest] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python ${{ matrix.python }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python }} | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install '.[test,scanorama,scvi,harmony]' | |
| - name: Test with pytest | |
| run: | | |
| pytest --cov=scib --cov-report=xml -vv --tb=native -k integration | |
| mv coverage.xml "$(echo 'coverage_integration_${{ matrix.os }}_${{ matrix.python }}.xml' | sed 's/[^a-z0-9\.\/]/_/g')" | |
| - name: Upload coverage to GitHub Actions | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: integration | |
| path: coverage_*.xml | |
| upload-codecov: | |
| needs: [metrics, rpy2] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| - name: Download coverage from GitHub Actions | |
| uses: actions/download-artifact@v3 | |
| - name: Upload coverage | |
| uses: codecov/codecov-action@v4 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| flags: unittests | |
| fail_ci_if_error: ${{ github.repository == 'theislab/scib' }} | |
| verbose: true | |
| - name: Delete coverage artifacts | |
| uses: geekyeggo/delete-artifact@v4 |