ci.yaml

name: CI

on:
  # run once every Sunday at 5:55 UTC
  schedule:
    - cron: "55 5 * * 1"
  push:
    branches:
      - "develop"
      - "master"
  pull_request:
    branches:
      - "develop"

concurrency:
  group: "${{ github.ref }}-${{ github.head_ref }}"
  cancel-in-progress: true

defaults:
  run:
    shell: bash -l {0}

jobs:
  test:
    runs-on: ${{ matrix.os }}
    strategy:
      fail-fast: false
      matrix:
        # only test all GROMACS version on the latest
        # Python to keep the testing matrix manageable and only use 1
        # macos runners (latest GROMACS, latest Python)
      
        os: [ubuntu-latest]
        python-version: ["3.12"]
        gromacs-version: ["4.6.5", "2018.6", "2020.6", "2021.1", "2022.4", "2023.1", "2024.3"]
        include:
          - os: ubuntu-latest
            python-version: "3.10"
            gromacs-version: "2024.3"
          - os: ubuntu-latest
            python-version: "3.11"
            gromacs-version: "2024.3"	    
          - os: macos-latest
            python-version: "3.12"
            gromacs-version: "2024.3"

    env:
      MPLBACKEND: agg
        

    steps:
    - uses: actions/checkout@v4

    - name: mamba environment and package installation
      uses: mamba-org/setup-micromamba@v2
      with:
        environment-file: devtools/conda-envs/test_env.yaml
        condarc: |
           channels:
              - conda-forge
              - bioconda
           channel_priority: flexible
        cache-downloads: true
        cache-environment: true
        create-args: >-
           python=${{ matrix.python-version }}
          
    - name: Python version information
      run: |
         python -c "import sys; print(sys.version)"                

    - name: micromamba environment information
      run: |
         micromamba info
         micromamba list

    - name: Install pybol (fixture staging tool)
      run: |
         python -m pip install pybol

    - name: Install GROMACS (${{ matrix.gromacs-version }})
      # include mdanalysis here AGAIN to work around micromamba removing mdanalysis 
      # while downgrading libxml2 (see issue #252)
      run: |
         micromamba install 'gromacs==${{ matrix.gromacs-version }}' pocl mdanalysis

    - name: Install package (with no dependencies)
      run: |
        python -m pip install . --no-deps

    - name: Run tests
      run: |
        pytest -v --durations=20 --cov=mdpow --cov-report=xml --color=yes ./mdpow/tests

    - name: Codecov
      uses: codecov/codecov-action@v4
      with:
        token: ${{ secrets.CODECOV_TOKEN }}
        name: codecov-${{ matrix.os }}-py${{ matrix.python-version }}
        file: ./coverage.xml
        fail_ci_if_error: true