document-and-deploy.yaml

# Run CI for R using https://eddelbuettel.github.io/r-ci/

name: document-and-deploy

on:
  push:
  pull_request:
  release:
  
env:
  _R_CHECK_FORCE_SUGGESTS_: "false"
  R_DEFAULT_REPOS: 'https://cloud.r-project.org/'

jobs:
  document-and-deploy:
    runs-on: ubuntu-latest

    steps:
      - name: Checkout
        uses: actions/checkout@v4
        
      - name: Set up R version
        uses: r-lib/actions/setup-r@v2
        with:
          r-version: '4.3.1'  # Compatible version for ShinyApps.io

      - uses: r-lib/actions/setup-pandoc@v2

      - name: Setup
        uses: eddelbuettel/github-actions/r-ci-setup@master

      - name: Bootstrap
        run: ./run.sh bootstrap

      #- name: Dependencies
      #  run: ./run.sh install_deps

      - name: All Dependencies
        run: ./run.sh install_all

      - name: Create documentation
        run: |
          R -e "
            options(repos = c(CRAN = 'https://cloud.r-project.org/'));
            install.packages(c('rcmdcheck', 'roxygen2', 'devtools'));
            file.remove('NAMESPACE');
            descr <- readLines('DESCRIPTION');
            descr <- stringr::str_replace(descr, '^Date.*$', paste('Date:', Sys.Date()));
            writeLines(descr, 'DESCRIPTION');
            roxygen2::roxygenise();
            try(devtools::build_manual())
          "
        
      - name: commit
        run: |
          git config --local user.email "actions@github.com"
          git config --local user.name "GitHub Actions"
          git add -f man/\* NAMESPACE
          git commit -m 'Documentation' || echo "No changes to commit"
          git push origin || echo "No changes to commit"
    
      - name: Deploy latest from dev
        if: github.ref == 'refs/heads/dev'
        env:
          GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
        run: |
          R -e "
            options(repos = c(CRAN = 'https://cloud.r-project.org/'));
            install.packages(c('rsconnect', 'remotes'));
            bspm::disable();
            remotes::install_github('ESHackathon/CiteSource', force = TRUE);
            rsconnect::setAccountInfo(name=${{secrets.SHINY_LUKAS_ACCOUNT}}, token=${{secrets.SHINY_LUKAS_TOKEN}}, secret=${{secrets.SHINY_LUKAS_SECRET}}); 
            rsconnect::deployApp(appName = 'CiteSource_latest', appDir = './inst/shiny-app/CiteSource', forceUpdate = TRUE)"   

      - name: Deploy stable version from main
        if: github.ref == 'refs/heads/main' || github.ref == 'refs/heads/master'
        run: |
          R -e "
             options(repos = c(CRAN = 'https://cloud.r-project.org/'));
            rsconnect::deployApp(appName = 'CiteSource', appDir = './inst/shiny-app/CiteSource', forceUpdate = TRUE)"   

      - name: Create pkgdown
        run: |
          R -e "
            install.packages('pkgdown');   
            pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)"
      
      - name: Deploy to GitHub pages 🚀
        if: github.ref == 'refs/heads/main' || github.ref == 'refs/heads/master'
        uses: JamesIves/github-pages-deploy-action@v4
        with:
          clean: true
          branch: gh-pages
          folder: docs