ci.yaml

name: CI

on:
  # run every Sunday at 4:44 UTC
  schedule:
    - cron: "44 4 * * 0"
  push:
    branches:
      - "main"
  pull_request:
    branches:
      - "main"

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

jobs:
  test:
    runs-on: ${{ matrix.os }}
    strategy:
      fail-fast: false
      matrix:
        os: [ubuntu-latest, macOS-latest]
        python-version: ["2.7", "3.6", "3.7", "3.8", "3.9", "3.10", "3.11"]
        gromacs-version: ["2021.1"]
        # Test other GROMACS versions selectively on a recent Python.
        # On macOS only test one GROMACS version and two Python versions
        # to keep the testing matrix manageable.
        exclude:
          - os: macOS-latest
            python-version: "3.6"
          - os: macOS-latest
            python-version: "3.7"
          - os: macOS-latest
            python-version: "3.8"
          - os: macOS-latest
            python-version: "3.9"
          - os: macOS-latest
            python-version: "3.10"
        include:
          - os: ubuntu-latest
            python-version: "2.7"
            gromacs-version: "4.6.5"    
          - os: ubuntu-latest
            python-version: "3.10"
            gromacs-version: "4.6.5"
          - os: ubuntu-latest
            python-version: "3.10"
            gromacs-version: "2018.6"
          - os: ubuntu-latest
            python-version: "3.10"
            gromacs-version: "2019.1"
          - os: ubuntu-latest
            python-version: "3.10"
            gromacs-version: "2020.6"
          - os: ubuntu-latest
            python-version: "3.10"
            gromacs-version: "2022.4"

    env:
      MPLBACKEND: agg
        

    steps:
    - uses: actions/checkout@v3

    - name: setup miniconda (Python ${{ matrix.python-version }})
      uses: conda-incubator/setup-miniconda@v2
      with:
        python-version: ${{ matrix.python-version }}
        auto-update-conda: true
        mamba-version: "*"
        channels: conda-forge,bioconda,defaults
        channel-priority: true
        show-channel-urls: true
          
    - name: Conda info
      shell: bash -l {0}
      run: |
         conda info
         conda list
         conda config --show-sources
         conda config --show

    - name: Python version ${{ matrix.python-version }}
      shell: bash -l {0}
      run: |
         python -c "import sys; print(sys.version)"                

    - name: Install package dependencies
      shell: bash -l {0}
      run: |
         mamba install six numpy scipy matplotlib-base pandas numkit

    - name: Install pytest and plugins
      shell: bash -l {0}
      run: |
         mamba install pytest pytest-pep8 pytest-cov codecov

    - name: Install GROMACS (${{ matrix.gromacs-version }})
      shell: bash -l {0}
      run: |
         mamba install 'gromacs==${{ matrix.gromacs-version }}' pocl

    - name: Install package
      shell: bash -l {0}
      run: |
        python -m pip install --no-deps .

    - name: Run tests
      shell: bash -l {0}
      run: |
        pytest -v --disable-pytest-warnings --durations=20 --low-performance --cov=gromacs --cov-report=xml --color=yes ./tests

    - name: Codecov
      uses: codecov/codecov-action@v3
      with:
        name: codecov-${{ matrix.os }}-py${{ matrix.python-version }}
        file: ./coverage.xml
        fail_ci_if_error: false