Merge pull request #387 from jeromekelleher/refactor-match-tsinfer #354
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] | |
| unit: | |
| name: Unit tests | |
| 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: | | |
| python -m pytest --cov=sc2ts tests/ | |
| # - 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: Create basedir and copy data | |
| run: | | |
| mkdir -p testrun | |
| cp -R tests/data testrun/data | |
| gunzip testrun/data/alignments.fasta.gz | |
| - name: Import alignments | |
| run: | | |
| sc2ts import-alignments testrun/alignments.db testrun/data/alignments.fasta | |
| sc2ts info-alignments testrun/alignments.db | |
| - name: Import metadata | |
| run: | | |
| sc2ts import-metadata testrun/data/metadata.tsv testrun/metadata.db | |
| sc2ts info-metadata testrun/metadata.db | |
| - name: Run inference | |
| run: | | |
| # doing 10 days here as this is taking a while | |
| last_ts=testrun/initial.ts | |
| sc2ts initialise -v $last_ts testrun/match.db | |
| for date in `sc2ts list-dates testrun/metadata.db | head -n 10`; do | |
| out_ts=testrun/$date.ts | |
| sc2ts extend $last_ts $date \ | |
| testrun/alignments.db testrun/metadata.db \ | |
| testrun/match.db $out_ts -v --min-group-size=2 | |
| last_ts=$out_ts | |
| done | |
| - name: Validate | |
| run: | | |
| sc2ts validate -v testrun/alignments.db testrun/2020-02-02.ts | |
| - name: Info | |
| run: | | |
| sc2ts info-ts testrun/2020-02-02.ts | |
| - name: MatchDB | |
| run: | | |
| sc2ts info-matches testrun/match.db | |
| packaging: | |
| name: Packaging 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 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 |