unittests.yml

name: fieldbioinformatics_unit_tests

on: [push, pull_request]

jobs:
  build:
    runs-on: ubuntu-latest
    strategy:
      fail-fast: false
    steps:
      - uses: actions/checkout@v3
      - uses: mamba-org/setup-micromamba@v1
        name: Setup dependencies
        with:
          environment-file: environment.yml
          init-shell: >-
            bash
          cache-environment: true
          post-cleanup: "all"

      - name: Pip install artic
        run: |
          python3 -m pip install -e .
        shell: micromamba-shell {0}

      - name: Run unit tests
        run: |
          pytest -s tests/*_unit_test.py
        shell: micromamba-shell {0}

      - name: Run clair3 test
        run: |
          ./test-runner.sh clair3
        shell: micromamba-shell {0}

      - name: Run minion_validator tests
        run: |
          pytest -s tests/minion_validator.py
        shell: micromamba-shell {0}