apptainer.yml

name: Apptainer Run

on:
  push:
    branches:
      - main
      - dev
  workflow_dispatch:
  pull_request:
    branches-ignore: []
  schedule:
    - cron: '0 0 28 * *'

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


    steps:

    - name: precleanup
      run: |
        sudo rm -rf /usr/share/dotnet
        sudo rm -rf "$AGENT_TOOLSDIRECTORY"
    - name: install graphviz
      run: |
        sudo apt update
        sudo apt-get install -y graphviz software-properties-common
        sudo add-apt-repository -y ppa:apptainer/ppa
        sudo apt update
        sudo apt install -y apptainer

    - name: checkout git repo
      uses: actions/checkout@v3

    - name: Set up Python 3.X
      uses: actions/setup-python@v3
      with:
        python-version: ${{ matrix.python }}

    - name: Install dependencies
      run: |
        pip install .[testing]

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

    - name: testing
      run: |
        sequana_revcomp --input-directory test/data/  --use-apptainer && cd revcomp && sh revcomp.sh