ci.yml

name: CI

on:
  push:
    branches:
    - main
  pull_request:
    branches:
    - main
  # Run daily at 0:01 UTC
  schedule:
  - cron:  '1 0 * * *'
  workflow_dispatch:


jobs:
  test:
    runs-on: ${{ matrix.os }}
    strategy:
      matrix:
        os: [ubuntu-latest]
        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']

    steps:
    - name: Checkout code
      uses: actions/checkout@v4

    - name: Set up Python ${{ matrix.python-version }}
      uses: actions/setup-python@v5
      with:
        python-version: ${{ matrix.python-version }}

    - name: Install external dependencies
      run: |
        sudo apt-get update -y
        sudo apt-get install -y graphviz libgraphviz-dev

    - name: Install Python dependencies
      # c.f. https://github.com/astral-sh/uv/issues/4333 for why snakemake lower bound
      run: |
        python -m pip install uv
        uv pip install --system --upgrade pip wheel
        uv pip install --system '.[develop,local,reana]' 'snakemake>6.8.0'

    - name: List installed dependencies
      run: python -m pip list

    - name: Run unit tests
      run: |
        pytest tests/