main.yml

name: Tests

on:
  push:
    branches:
      - main
      - dev
  pull_request:
    branches-ignore: []
  schedule:
    - cron: '0 0 1 * *'

jobs:
  build-linux:
    runs-on: ubuntu-latest
    strategy:
      max-parallel: 5
      matrix:
        python: [3.8, 3.9, '3.10']
      fail-fast: false


    steps:

    - name: install graphviz
      run: |
        sudo apt-get install -y graphviz

    - name: checkout git repo
      uses: actions/checkout@v2

    - name: Set up Python 3.X
      uses: actions/setup-python@v2
      with:
        python-version: ${{ matrix.python }}

    - name: Add conda to system path
      run: |
        # $CONDA is an environment variable pointing to the root of the miniconda directory
        echo $CONDA/bin >> $GITHUB_PATH

    - name: conda
      run: |
        conda install -c conda-forge -c bioconda --quiet -y python=${{ matrix.python }}

    - name: Install dependencies
      run: |
        pip install coveralls pytest-cov pytest pytest-xdist

    - name: install package itself
      run: |
         pip install .

    - name: testing
      run: |
        pytest -v --cov-report term-missing --cov=sequana_pipelines.multicov

    - name: coveralls
      run: |
        echo $COVERALLS_REPO_TOKEN
        coveralls --service=github
      env:
          GITHUB_TOKEN: ${{ github.token }}