Use low-level tsinfer components directly #335
Workflow file for this run
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| 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 |