Pre release #17
Workflow file for this run
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| name: Integration tests | |
| on: | |
| pull_request: | |
| push: | |
| branches: [main, test] | |
| merge_group: | |
| jobs: | |
| end-to-end: | |
| name: End to end tests | |
| runs-on: ubuntu-24.04 | |
| steps: | |
| - uses: actions/checkout@v4.2.2 | |
| - uses: astral-sh/setup-uv@v6 | |
| with: | |
| python-version: "3.11" | |
| version: "0.8.15" | |
| - name: Install dependencies | |
| run: uv sync --locked --group test | |
| - name: Create basedir | |
| run: | | |
| mkdir -p testrun | |
| gunzip -k tests/data/alignments.fasta.gz | |
| - name: Import alignments | |
| run: uv run sc2ts import-alignments -i testrun/dataset.zarr tests/data/alignments.fasta | |
| - name: Import metadata | |
| run: uv run sc2ts import-metadata testrun/dataset.zarr tests/data/metadata.tsv | |
| - name: Info dataset | |
| run: uv run sc2ts info-dataset testrun/dataset.zarr | |
| - name: Run inference | |
| run: | | |
| # doing ~10 days here as this is taking a while | |
| uv run sc2ts infer tests/data/testrun-conf.toml --stop 2020-02-03 | |
| - name: Validate | |
| run: uv run sc2ts validate -v --date-field=date testrun/dataset.zarr testrun/results/test/test_2020-02-02.ts | |
| - name: MatchDB | |
| run: uv run sc2ts info-matches testrun/test.matches.db | |
| bare-api: | |
| name: Bare API tests | |
| runs-on: ubuntu-24.04 | |
| steps: | |
| - uses: actions/checkout@v4.2.2 | |
| - uses: astral-sh/setup-uv@v6 | |
| with: | |
| python-version: "3.11" | |
| version: "0.8.15" | |
| - name: Run tests | |
| run: | | |
| # Minimal deps only; avoid picking up conftest and fixtures | |
| uv run pytest -v -c /dev/null -p no:sc2ts_fixtures tests/test_api.py |