CI.yaml

name: CI

on:
  # GitHub has started calling new repo's first branch "main" https://github.com/github/renaming
  # Existing codes likely still have "master" as the primary branch
  # Both are tracked here to keep legacy and new codes working
  push:
    branches:
      - "master"
      - "main"
  pull_request:
    branches:
      - "master"
      - "main"
  schedule:
    # Nightly tests run on master by default:
    #   Scheduled workflows run on the latest commit on the default or base branch.
    #   (from https://help.github.com/en/actions/reference/events-that-trigger-workflows#scheduled-events-schedule)
    - cron: "0 0 * * *"
  workflow_dispatch:
    inputs:
      CACHE_NUMBER:
        type: number
        default: 0
      RUN_TESTS:
        type: boolean
        default: true
        
jobs:
  test:
    name: Test on ${{ matrix.os }}, Python ${{ matrix.python-version }}
    runs-on: ${{ matrix.os }}
    strategy:
      matrix:
        # os: [macOS-latest, ubuntu-latest]
        os: [ubuntu-latest]
        python-version: [3.9]
        include:
          - os: ubuntu-latest
            label: linux-64
            # prefix: /usr/share/miniconda3/envs/openmm7.6
            environment-file: devtools/conda-envs/fep_env.yaml
            miniforge-variant: Mambaforge
            miniforge-version: 4.9.2-4
          #- os: macos-latest
          #  label: osx-64
          #  # prefix: /Users/runner/miniconda3/envs/openmm7.6
          #  environment-file: devtools/conda-envs/openmm7.6.yaml
          #  miniforge-variant: Mambaforge-pypy3

    steps:
    - uses: actions/checkout@v3

    - name: Additional info about the build
      shell: bash
      run: |
        uname -a
        df -h
        ulimit -a

    - name: Set cache date
      run: echo "DATE=$(date +'%Y%m%d')" >> $GITHUB_ENV
      
    - name: Make Cache (no worflow_dispatch)
      if: ${{ github.event_name != 'workflow_dispatch' }}
      uses: actions/cache@v3
      with:
        path: ~/conda_pkgs_dir # ${{ matrix.prefix }}
        # Increase the last number (0) to reset cache manually
        key: ${{ matrix.label }}-conda-${{ hashFiles('devtools/conda-envs/fep_env.yaml') }}-${{ env.DATE }}-0
      id: cache1
      
    - name: Make Cache (worflow_dispatch)
      if: ${{ github.event_name == 'workflow_dispatch' }}
      uses: actions/cache@v2
      with:
        path: ~/conda_pkgs_dir # ${{ matrix.prefix }}
        key: ${{ matrix.label }}-conda-${{ hashFiles('devtools/conda-envs/fep_env.yaml') }}-${{ env.DATE }}-${{ inputs.CACHE_NUMBER }}
      id: cache2


    # More info on options: https://github.com/conda-incubator/setup-miniconda
    - uses: conda-incubator/setup-miniconda@v2
      with:
        python-version: ${{ matrix.python-version }}
        condarc-file: ${{ matrix.condarc-file }}
        environment-file: ${{ matrix.environment-file }}
        miniforge-variant: ${{ matrix.miniforge-variant }}
        miniforge-version: ${{ matrix.miniforge-version }}
        use-mamba: true
        # mamba-version: "*"
        # environment-file: devtools/conda-envs/fep_env.yaml
        channels: conda-forge,defaults
        # channel-priority: true
        activate-environment: fep
        #auto-update-conda: false
        auto-activate-base: false
        #show-channel-urls: true
        use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly!
  
    - name: Update environment
      run: conda env update -n fep -f devtools/conda-envs/fep_env.yaml        

    - name: Install package

      # conda setup requires this special shell
      shell: bash -l {0}
      run: |
        python -m pip install . --no-deps
        conda info
        conda list
        conda config --show-sources
        conda config --show
        printenv | sort


    - name: Run tests

      # conda setup requires this special shell
      shell: bash -l {0}

      run: |
        conda activate fep
        pytest -v --cov=transformato --cov-report=xml --color=yes transformato/tests/

    - name: CodeCov
      uses: codecov/codecov-action@v1
      with:
        file: ./coverage.xml
        flags: unittests
        name: codecov-${{ matrix.os }}-py${{ matrix.python-version }}