.github/workflows/pythonpackage.yml

name: PythonKorAPClient CI unit test

on: [push, pull_request]

jobs:
  build:

    runs-on: ${{ matrix.os }}
    strategy:
      max-parallel: 4
      matrix:
        python-version: [3.7, 3.8]
        r-version: [3.6, 4.0]
        os: [windows-latest, macOS-latest, ubuntu-20.04]
        exclude:
          - os: macOS-latest
            python-version: 3.7
          - os: macOS-latest
            r-version: 4.0
          - os: windows-latest
            python-version: 3.7
          - os: windows-latest
            r-version: 3.6
          - os: ubuntu-20.04
            r-version: 4.0
    steps:
    - uses: actions/checkout@v2
    - name: Set up Python ${{ matrix.python-version }}
      uses: actions/setup-python@v2
      with:
        python-version: ${{ matrix.python-version }}
    - name: Cache pip
      uses: actions/cache@v2
      with:
        # This path is specific to Ubuntu
        path: ~/.cache/pip
        # Look to see if there is a cache hit for the corresponding requirements file
        key: ${{ runner.os }}-pip-${{ hashFiles('requirements.txt') }}
        restore-keys: |
          ${{ runner.os }}-pip-
          ${{ runner.os }}-
    - name: Set up R ${{ matrix.r-version }}
      uses: r-lib/actions/setup-r@master
      with:
        r-version: ${{ matrix.r-version }}
      if: runner.os != 'Linux'
    - name: Set up package maintainers R on Linux
      run: |
        sudo apt-get update -y
        sudo apt-get install -y r-base r-base-dev r-cran-tidyverse r-cran-r.utils r-cran-pixmap r-cran-webshot r-cran-ade4 r-cran-segmented r-cran-purrr r-cran-dygraphs r-cran-cvst r-cran-quantmod r-cran-graphlayouts r-cran-rappdirs r-cran-ggdendro r-cran-seqinr r-cran-heatmaply r-cran-igraph r-cran-plotly libcurl4-gnutls-dev libssl-dev libxml2-dev libsodium-dev python3-pip python3-rpy2 python3-pandas
        sudo chown $USER /usr/local/lib/R/site-library
        export R_LIBS_USER=/usr/local/lib/R/site-library
      if: runner.os == 'Linux'
    - name: Install R dependencies
      run: Rscript -e "install.packages('RKorAPClient')"
    - name: Cache R packages on Linux
      uses: actions/cache@v1
      with:
        path: /usr/local/lib/R/site-library
        key: ${{ runner.os }}-r-${{ matrix.config.r-version }}-${{ hashFiles('DESCRIPTION') }}
      if: runner.os == 'Linux'
    - name: Cache R packages
      uses: actions/cache@v1
      with:
        path: ${{ env.R_LIBS_USER }}
        key: ${{ runner.os }}-r-${{ matrix.config.r-version }}-${{ hashFiles('DESCRIPTION') }}
      if: runner.os != 'Linux'
    - name: Install dependencies
      run: |
        python -m pip install --upgrade pip
        pip install wheel
    - name: Install package
      run: |
        pip install .
    - name: Test with pytest on POSIX
      if: runner.os != 'Windows'
      run: |
        export LD_LIBRARY_PATH=$(python -m rpy2.situation LD_LIBRARY_PATH):${LD_LIBRARY_PATH}
        pip install pytest
        pytest KorAPClient/tests  --junitxml=junit/test-results-${{ matrix.python-version }}.xml
    - name: Test with pytest on Windows
      if: runner.os == 'Windows'
      run: |
        pip install pytest
        pytest KorAPClient/tests  --junitxml=junit/test-results-${{ matrix.python-version }}.xml
      env:
        R_HOME: "c:/R"
        R_USER: "c:/R"
        PATH: "c:/R/bin/x64;${{ env.PATH }}"
    - name: Build documentation un Linux
      if: runner.os == 'Linux'
      run: |
        pip install pdoc3
        pdoc KorAPClient --force --html -o build/doc
    - name: Deploy documentation on Linux
      if: runner.os == 'Linux'
      uses: JamesIves/github-pages-deploy-action@releases/v3
      with:
        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
        BRANCH: gh-pages # The branch the action should deploy to.
        FOLDER: build/doc # The folder the action should deploy.
        TARGET_FOLDER: doc
    - name: Upload check results
      if: failure()
      uses: actions/upload-artifact@master
      with:
        name: pytest-results-${{ matrix.python-version }}
        path: junit/test-results-${{ matrix.python-version }}.xml