pages.yml

# Simple workflow for deploying static content to GitHub Pages
name: Deploy documentation to GitHub Pages

on:
  # Allows you to run this workflow manually from the Actions tab
  workflow_dispatch:
  # Runs on pushes targeting the main branch
  push:
    branches: [ main, develop ]

jobs:
  build-docs:
    runs-on: ubuntu-latest

    steps:
    - name: Checkout
      uses: actions/checkout@v3
      with:
        fetch-depth: 0 # otherwise, you will fail to push refs to dest repo
        ref: main
    
    - name: Set up Python 3.
      uses: actions/setup-python@v4
      with:
        python-version: 3.9

    - name: Install Python dependencies
      run: |
        pip install sphinx
        pip install sphinx-rtd-theme

    - name: Set up JDK 17
      uses: actions/setup-java@v3
      with:
        java-version: '17'
        distribution: 'adopt'

    - name: Generate examples and build documentation
      run: |
        ## Init the target folder. 
        # We will put all site documentation there.
        mkdir -p gh-pages
        touch gh-pages/.nojekyll
        
        function build_docs {
          # The function will checkout a branch and build the Javadoc & documentation 
          # into provided documentation directory.
          BRANCH=${1}
          DOCDIR=${2}
        
          git checkout ${BRANCH}
          git fetch
          git pull
          ## Init the target folder.
          # We will put all site documentation there.
          mkdir -p gh-pages/${DOCDIR}
        
          ## Javadoc
          # Build the aggregated Javadoc.
          ./mvnw --quiet clean
          ./mvnw --quiet -Ddoclint=none -Dinherited=false javadoc:aggregate
          
          # Copy aggregated Javadoc into `apidocs` folder.
          APIDOCS=$(pwd)/gh-pages/${DOCDIR}/apidocs
          printf "Copying Javadocs from %s to %s\n" $(pwd)/target/site/apidocs ${APIDOCS}
          cp -r target/site/apidocs ${APIDOCS}
          
          ## Generate examples
          # Find the CLI jar and run the `examples` command.
          ./mvnw --quiet -Prelease -DskipTests package
          jar=$(find phenopacket-tools-cli/target \
            -regextype posix-extended \
            -regex ".*[0-9]+\.[0-9]+\.[0-9]+(-RC[1-9][0-9]*)?(-SNAPSHOT)?\.jar$")
          if [ -f "${jar}" ]; then
            printf "Generating Phenopacket examples using ${jar}\n"
            java -jar ${jar} examples -v --output-directory ./gh-pages/${DOCDIR}/examples
          else
            printf "Could not find phenopacket-tools JAR file\n"
            tree -L 3 .
            exit 1
          fi
          
          ## Build the docs
          # Generate the HTML pages and move the generated content into the target folder.
          printf "Building the %s documentation\n" ${DOCDIR}
          cd docs/
          # Replace the `release_tag` placeholder to the right value in place. 
          # This must be done *prior* generating docs in several files
          sed -i "s/release_tag/${DOCDIR}/g" examples.rst
          make clean html
          cd ..
          mv docs/_build/html/* gh-pages/${DOCDIR}
        }
        
        # We store the docs for `master` in `stable` dir
        build_docs main stable
        # We store the docs for `develop` in `latest` dir
        build_docs develop latest


    - name: Deploy documentation.
      if: ${{ github.event_name == 'push' }}
      uses: JamesIves/github-pages-deploy-action@v4.4.1
      with:
        branch: gh-pages
        force: true
        folder: gh-pages