Round trip tests #56
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: CI | |
| on: | |
| pull_request: | |
| push: | |
| branches: | |
| - main | |
| jobs: | |
| # pre-commit: | |
| # name: Lint | |
| # runs-on: ubuntu-latest | |
| # steps: | |
| # - uses: actions/checkout@v4 | |
| # - uses: actions/setup-python@v5 | |
| # with: | |
| # python-version: '3.11' | |
| # - uses: pre-commit/[email protected] | |
| test: | |
| name: Test | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.11' | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install '.[dev,analysis]' | |
| - name: Run tests | |
| run: | | |
| pytest --cov=sc2ts | |
| # - name: Upload coverage to Coveralls | |
| # uses: coverallsapp/[email protected] | |
| # with: | |
| # github-token: ${{ secrets.GITHUB_TOKEN }} | |
| # # The first coveralls upload will succeed and others seem to fail now. | |
| # # This is a quick workaround for doing a proper "parallel" setup: | |
| # # https://github.com/coverallsapp/github-action | |
| # fail-on-error: false | |
| end_to_end: | |
| name: End to end tests | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.11' | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install '.[dev,analysis]' | |
| - name: Export alignments and metadata | |
| run: | | |
| mkdir -p test_data | |
| python -m sc2ts export-alignments tests/data/viridian-subset.ts.tsz > test_data/alignments.fasta | |
| python -m sc2ts export-metadata tests/data/viridian-subset.ts.tsz > test_data/metadata.tsv | |
| - name: Import alignments | |
| run: | | |
| python3 -m sc2ts import-alignments test_data/alignments.db test_data/alignments.fasta | |
| python3 -m sc2ts info-alignments test_data/alignments.db | |
| - name: Import metadata | |
| run: | | |
| python3 -m sc2ts import-metadata test_data/metadata.tsv test_data/metadata.db | |
| python3 -m sc2ts info-metadata test_data/metadata.db | |
| - name: Run inference | |
| run: | | |
| mkdir -p test_inference | |
| python3 -m sc2ts daily-extend -v test_data/alignments.db test_data/metadata.db \ | |
| test_inference --stop-date=2020-02-14 | |
| - name: Validate | |
| run: | | |
| python3 -m sc2ts validate -v test_data/alignments.db test_inference/2020-02-14.ts | |
| - name: MatchDB | |
| run: | | |
| python3 -m sc2ts info-matches test_inference/match.db | |
| packaging: | |
| name: Packaging | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.11' | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install build twine validate-pyproject[all] | |
| - name: Check and install package | |
| run: | | |
| validate-pyproject pyproject.toml | |
| python -m build | |
| python -m twine check --strict dist/* | |
| python -m pip install dist/*.whl |