GromacsWrapper/.github/workflows/ci.yaml at main · Becksteinlab/GromacsWrapper · GitHub

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name: CI

on:
  # run every month on day 14 and 28 at 4:44 UTC
  schedule:
    - cron: "44 4 14,28 * *"
  push:
    branches:
      - "main"
  pull_request:
    branches:
      - "main"

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:
        os: [ubuntu-latest]
        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
        gromacs-version: ["2023.1"]
        # 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.
        include:
          - os: ubuntu-latest
            python-version: "3.11"
            gromacs-version: "4.6.5"
          - os: ubuntu-latest
            python-version: "3.11"
            gromacs-version: "2018.6"
          - os: ubuntu-latest
            python-version: "3.11"
            gromacs-version: "2019.1"
          - os: ubuntu-latest
            python-version: "3.11"
            gromacs-version: "2020.6"
          - os: ubuntu-latest
            python-version: "3.11"
            gromacs-version: "2021.1"
          - os: ubuntu-latest
            python-version: "3.11"
            gromacs-version: "2022.4"
          - os: ubuntu-latest
            python-version: "3.11"
            gromacs-version: "2023.4"
          - os: ubuntu-latest
            python-version: "3.11"
            gromacs-version: "2024.2"
          # explicitly include a few macOS runners; finding a version that works
          # on the GH runners is tricky (eg some are compiled for rdtscp CPU instructions
          # that are not available); 2018.6 (bioconda) worked for a while, but then stopped
          # being resolved. 2024.2 (conda-forge) runs at the moment
          - os: macOS-latest
            python-version: "3.11"
            gromacs-version: "2024.2"
          - os: macOS-latest
            python-version: "3.12"
            gromacs-version: "2024.2"


    env:
      MPLBACKEND: agg


    steps:
    - name: git checkout
      uses: actions/checkout@v4
      with:
        fetch-tags: true

    - name: micromamba package and testing environment installation (Python ${{ matrix.python-version }}, GROMACS ${{ matrix.gromacs-version }})
      uses: mamba-org/setup-micromamba@v2
      with:
        environment-file: ci/conda-envs/test_env.yaml
        condarc: |
           channels:
              - conda-forge
              - bioconda
           channel_priority: flexible
        cache-downloads: true
        cache-environment: true
        create-args: >-
           python=${{ matrix.python-version }}.*=*_cp*
           gromacs==${{ matrix.gromacs-version }}

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

    - name: micromamba environment information
      run: |
         micromamba info
         micromamba list
         cat /proc/cpuinfo || (/usr/sbin/system_profiler SPHardwareDataType; /usr/sbin/sysctl -a | grep machdep.cpu)
         micromamba list | grep python | grep ${{ matrix.python-version }}

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

    - name: Run tests
      run: >-
        pytest -v
        --disable-pytest-warnings
        --durations=20
        --low-performance
        --cov-config=pyproject.toml
        --cov="./gromacs"
        --cov-report=xml
        --cov-report=term
        --color=yes
        ./tests

    - name: Coverage report
      run: |
        coverage report --show-missing

    - name: Codecov
      uses: codecov/codecov-action@v5
      with:
        token: ${{ secrets.CODECOV_TOKEN }}
        name: codecov-${{ matrix.os }}-py${{ matrix.python-version }}
        files: ./coverage.xml
        fail_ci_if_error: false