sc2ts/.github/workflows/integration.yml at 50fdf477bd488eb5fa0b6914b8c9c59ad5af9264 · tskit-dev/sc2ts · GitHub

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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: Install package only
        run: uv pip install -e .
      - 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