ci.yml

name: CI

on:
  push:
    branches:
      - main
  pull_request:
    branches_ignore: []
    
jobs:
  cancel-previous:
    runs-on: ubuntu-latest
    if: github.ref != 'refs/heads/main'
    steps:
      - uses: khan/pull-request-workflow-cancel@1.0.0
        with:
          workflows: "main.yml"
        env:
          GITHUB_TOKEN: '${{ secrets.GITHUB_TOKEN }}'
          
  testing-R:
    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-version:
          - "3.12"
    steps:
      - name: Checkout repository
        uses: actions/checkout@v4

      - name: Set up Miniforge
        uses: conda-incubator/setup-miniconda@v3
        with:
          activate-environment: stemcnv-check-general-R
          channels: conda-forge,bioconda
          environment-file: stemcnv_check/envs/general-R.yaml
          miniforge-version: latest
          auto-activate-base: false
      - name: Run tests
        shell: bash -l {0}
        run: Rscript -e "testthat::test_local()"
#         env:
#           DIFF_MAIN: ${{ github.event_name == 'pull_request' }}
#           DIFF_LAST_COMMIT: ${{ github.ref == 'refs/heads/main' }}

  testing-py:
    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-version:
          - "3.12"
    steps:
      - name: Checkout repository
        uses: actions/checkout@v4

      - name: Set up Python ${{ matrix.python-version }}
        uses: actions/setup-python@v5
        with:
          python-version: ${{ matrix.python-version }}
          cache: 'pip'
      
      - name: Install dependencies
        run: pip install .[test]
      
      - run: pytest