scorpio.yml

name: scorpio
on: [push, pull_request]
defaults:
  run:
    shell: bash -l {0}

jobs:
  run_pangolin_test:
    name: Scorpio test on ${{ matrix.os }}
    runs-on: ${{ matrix.os }}
    strategy:
      matrix:
        os: ["ubuntu-latest", "macos-latest"]
    steps:
      - uses: actions/checkout@v2
      - uses: conda-incubator/setup-miniconda@v2
        with:
          environment-file: environment.yml
          activate-environment: scorpio
          channels: conda-forge,bioconda,defaults
      - name: Install scorpio
        run: pip install -e .
      - name: Install pytest
        run: pip install pytest
      - name: Check scorpio version
        run: scorpio --version
      - name: Run scorpio unittests
        run: pytest 2>&1 | tee scorpio_pytests.log
      - name: Run scorpio in pangolin mode with test data
        run: scorpio classify -i scorpio/tests/data/type_constellations/test.fa --pangolin --output-counts --long 2>&1 | tee scorpio_pangolin.log
# add more tests here