pythonpackage.yml

name: PythonKorAPClient CI unit test

on: [push, pull_request]

jobs:
  build:

    runs-on: ${{ matrix.os }}
    strategy:
      max-parallel: 6
      fail-fast: false
      matrix:
        python-version: ['3.11', '3.13']
        r-version: [release]
        os: [macos-15, ubuntu-latest]
    steps:
    - uses: actions/checkout@v4
    - name: Set up Python ${{ matrix.python-version }}
      uses: actions/setup-python@v5
      with:
        python-version: ${{ matrix.python-version }}
        cache: 'pip' # caching pip dependencies
    - name: Set up R ${{ matrix.r-version }}
      uses: r-lib/actions/setup-r@v2
      with:
        r-version: ${{ matrix.r-version }}
        use-public-rspm: true
    - name: Set env commands (Linux)
      if: runner.os == 'Linux'
      run: |
          echo "VENV_ACTIVATE=source pyenv_base/bin/activate" >> $GITHUB_ENV
          echo "LD_LIBRARY_PATH=$(dirname $(find / -name libR.so  2> /dev/null)):${LD_LIBRARY_PATH}" >> $GITHUB_ENV
          echo "R_LIBRARY=export LD_LIBRARY_PATH=$(python -m rpy2.situation LD_LIBRARY_PATH):${LD_LIBRARY_PATH}" >> $GITHUB_ENV
    - name: Set env commands (MacOS)
      if: "startsWith(matrix.os, 'macos')"
      run: |
          echo "VENV_ACTIVATE=source pyenv_base/bin/activate" >> $GITHUB_ENV
          echo "R_LIBRARY=$(find /Library -name libR.dylib 2> /dev/null | head -1)" >> $GITHUB_ENV
          echo "LD_LIBRARY_PATH=$(dirname $(find /Library -name libR.dylib 2> /dev/null | head -1)):${LD_LIBRARY_PATH}" >> $GITHUB_ENV
    - name: Set virtualenv activation command (Windows)
      if: startsWith(matrix.os, 'windows')
      shell: bash
      run: |
          echo "VENV_ACTIVATE=pyenv_base\Scripts\activate" >> $GITHUB_ENV
          echo "R_LIBRARY=''" >> $GITHUB_ENV
    - name: Patch GHA issue with macos - Missing C library
      if: startsWith(matrix.os, 'macos')
      shell: bash
      run: |
        LIB_ARCHIVES=(\
          libdeflate-1.23-darwin.20-arm64.tar.xz \
          zstd-1.5.5-darwin.20-arm64.tar.xz \
        )
        for name in "${LIB_ARCHIVES[@]}"
        do
            curl -LO https://mac.r-project.org/bin/darwin20/arm64/"${name}"
            sudo tar xJf "${name}" -C /
        done
    - name: Install dependencies
      run: |
        python -m pip install --upgrade pip
        python -m pip install setuptools build
    - name: Set up package maintainers R on Linux
      run: |
        sudo apt-get update -y
        sudo apt-get install -y libglpk-dev libsodium-dev libxml2-dev libcurl4-openssl-dev
        sudo mkdir -p /usr/local/lib/R/site-library
        sudo chown $(whoami) /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('pak')"
        Rscript -e "pak::pak('RKorAPClient')"
    - name: Cache R packages on Linux
      uses: actions/cache@v3
      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@v3
      with:
        path: ${{ env.R_LIBS_USER }}
        key: ${{ runner.os }}-r-${{ matrix.config.r-version }}-${{ hashFiles('DESCRIPTION') }}
      if: runner.os != 'Linux'
    - name: Install package
      if: runner.os != 'Windows'
      run: |
        pip install rpy2
        pip install .
    - name: Install package on Windows
      if: runner.os == 'Windows'
      run: |
        pip install rpy2
        pip install .
      env:
        R_HOME: "c:/R"
        R_USER: "c:/R"
        PATH: "c:/R/bin;c:/R/bin/x64;${{ env.PATH }}"
    - name: Test with pytest on POSIX
      if: runner.os != 'Windows'
      run: |
        export LD_LIBRARY_PATH=$(dirname $R_LIBRARY):${LD_LIBRARY_PATH}
        echo $LD_LIBRARY_PATH
        python -m ensurepip --upgrade
        python -m pip install pytest
        pytest KorAPClient/tests  --junitxml=junit/test-results-${{ 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/v4
      with:
        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
        BRANCH: gh-pages # The branch the action should deploy to.
        FOLDER: build/doc # The folder the action should deploy.
        TARGET_FOLDER: doc
    - name: Upload check results
      if: failure()
      uses: actions/upload-artifact@v4
      with:
        name: pytest-results-${{ matrix.python-version }}
        path: junit/test-results-${{ matrix.python-version }}.xml