test-snake.yml

name: Snakemake CI

on:
  push:
    branches: [ main ]
  pull_request:
    branches: [ main ]

jobs:
  build:
    runs-on: ubuntu-latest
    strategy:
      fail-fast: true
      matrix:
        python-version: ["3.11.2"]
        poetry-version: ["1.8.3"]

    steps:
      - name: Checkout Code
        uses: actions/checkout@v4
        with:
          fetch-depth: 0
      
      # Run Super-Linter only on Snakefile and .smk files
      - name: Lint Snakefiles Only
        uses: github/super-linter/slim@v5
        env:
          VALIDATE_SNAKEMAKE_SNAKEFMT: true
          FILTER_REGEX_INCLUDE: '(^Snakefile$|.*\.smk$)' # Only include Snakefile and .smk files
          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
          DISABLE_ERRORS: true

      - name: Set up Python ${{ matrix.python-version }}
        uses: actions/setup-python@v4
        with:
          python-version: ${{ matrix.python-version }}
          cache: "pip"

      - uses: mamba-org/setup-micromamba@v1
        with:
          micromamba-version: '1.5.6-0' 
          environment-file: environment.yml
          init-shell: >-
            bash
          cache-environment: true
          post-cleanup: 'all'

      - name: Install dependencies
        run: |
          pip install -e .
          pip install pytest
          pip install snakefmt==0.10.2
      - name: Snakemake Linting
        run: |
          snakefmt workflow/

      - name: Snakemake Testing
        run: |
          pytest workflow/.tests