code_coverage.yml

name: Test code

on: [pull_request, push]

jobs:
  test:
    runs-on: ${{ matrix.os }}
    strategy:
      matrix:
        os: [ubuntu-latest] # , macos-latest, windows-latest

    env:
      OS: ${{ matrix.os }}
      PYTHON: "3.10"

    name: Test FastqWiper
    steps:
      - uses: actions/checkout@v4
        name: Clone repository

      - name: Install Miniconda (Mambaforge)
        uses: conda-incubator/setup-miniconda@v3
        with:
          auto-update-conda: true
          auto-activate-base: true
          show-channel-urls: true
          channels: conda-forge,bioconda,defaults
          python-version: ${{ env.PYTHON }}
          environment-file: .devcontainer/environment.yml

      - name: Run tests and collect coverage
        shell: bash -el {0}
        run: pytest --pyargs ./tests --cov-config=.coveragerc --cov=./fastqwiper --cov-report=xml

      - name: Upload coverage reports to Codecov
        uses: codecov/codecov-action@v3
        with:
          token: ${{ secrets.CODECOV_TOKEN }}
          env_vars: OS,PYTHON
          files: ./coverage.xml # optional
          flags: pytest # optional
          name: codecov-umbrella # optional
          fail_ci_if_error: true # optional (default = false)
          verbose: true # optional (default = false)