build-deploy-rmd.yaml

on:
  push:
    branches:
      - master
  pull_request:
    branches:
      - master
  schedule:
    - cron: '0 9 * * 3'
  workflow_dispatch:

name: build-deploy-rmd

# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
# permissions:
#   contents: read
#   pages: write
#   id-token: write

# Allow only one concurrent deployment, skipping runs queued between the run in-progress and latest queued.
# However, do NOT cancel in-progress runs as we want to allow these production deployments to complete.
# concurrency:
#   group: "pages"
#   cancel-in-progress: false

jobs:
  build-rmd:
    runs-on: ${{ matrix.config.os }}

    name: ${{ matrix.config.os }} (${{ matrix.config.r }})

    strategy:
      fail-fast: false
      matrix:
        config:
          - {os: macOS-latest, r: 'release'}

    env:
      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
      RSPM: ${{ matrix.config.rspm }}
      CRAN: ${{ matrix.config.cran }}
      GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

    steps:
      - name: Check out repo
        uses: actions/checkout@v2
        with:
          submodules: true

      - name: Set up R
        uses: r-lib/actions/setup-r@v2
        with:
          r-version: ${{ matrix.config.r }}

      - name: Set up pandoc
        uses: r-lib/actions/setup-pandoc@v2

        ## rcrossref requires an email address associated with a query
      - name: Set up crossref email
        run: |
          echo crossref_email=\"${{ secrets.CROSSREF_EMAIL }}\" >> ~/.Renviron
          
      - name: Install dependencies
        run: |
          install.packages(c('remotes', 'dplyr', 'ggplot2', 'rmarkdown',
                             'knitr', 'tibble', 'tidyr',
                             'lubridate', 'gh', 'jsonlite', 'purrr',
                             'DT', 'plotly', 'citecorp', 'readr', 
                             'viridis', 'wordcloud', 'stringr', 'gt', 
                             'rworldmap', 'openalexR'), Ncpu = 2L)
          remotes::install_github('ropensci/rcrossref')
        shell: Rscript {0}

      - name: Session info
        run: |
          install.packages('sessioninfo', Ncpus = 2L)
          options(width = 100)
          pkgs <- installed.packages()[, "Package"]
          sessioninfo::session_info(pkgs, include_base = TRUE)
        shell: Rscript {0}
        
      - name: Render site
        run: |
          rmarkdown::render(input = "joss-submission-analytics.Rmd", clean = FALSE)
        shell: Rscript {0}

      - name: Prepare files to deploy
        run: |
          mkdir _site
          touch _site/.nojekyll
          cp -r joss-submission-analytics_files joss-submission-analytics.html _site/
          cp -r joss_submission_analytics.rds _site/
          cp -r joss_submission_citations_byjournal.tsv _site/
          cp -r joss_submission_citations.tsv _site/
          
      - name: Deploy 🚀
        uses: JamesIves/github-pages-deploy-action@releases/v4
        with:
          ACCESS_TOKEN: ${{ secrets.GITHUB_TOKEN }}
          BRANCH: gh-pages
          FOLDER: _site

      - name: Upload check results
        if: failure()
        uses: actions/upload-artifact@v4
        with:
          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
          path: check

      - name: upload artifact
        uses: actions/upload-artifact@v4
        with:
          name: submissionanalytics
          path: joss_submission_analytics.rds
    
        ## From 2024-06-30, need to use GitHub Actions for deployment
      # - name: Setup Pages
      #   uses: actions/configure-pages@v5
      #   
      # - name: Build with Jekyll
      #   uses: actions/jekyll-build-pages@v1
      #   with:
      #     source: ./_site
      #     destination: ./_site_jkl
      #     
      # - name: Upload artifact
      #   uses: actions/upload-pages-artifact@v3
      #   with:
      #     path: ./_site_jkl

  # Deployment job
  # deploy:
  #   environment:
  #     name: github-pages
  #     url: ${{ steps.deployment.outputs.page_url }}
  #   runs-on: ubuntu-latest
  #   needs: build-rmd
  #   
  #   steps:
  #     - name: Deploy to GitHub Pages
  #       id: deployment
  #       uses: actions/deploy-pages@v4