Fix kBET test for 1.1.6 #282
Workflow file for this run
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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', '3.12'] | |
| 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: ['3.10', '3.12'] | |
| 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 |