pipeline.yml

name: github pages

on:
  push:
    branches:
    #  - main  # Set a branch to deploy
      - develop # Note has logic around deployment
  #schedule:
  #  - cron: 0 13 * * 1 # At 13:00 on Monday

jobs:
  deploy:
    runs-on: ubuntu-22.04
    concurrency:
     group: ${{ github.workflow }}-${{ github.ref }}
    steps:
      - uses: actions/checkout@v4.1.1
        with:
          submodules: true  # Fetch Hugo themes (true OR recursive)
          fetch-depth: 0    # Fetch all history for .GitInfo and .Lastmod

      - name: Install curl
        run: sudo apt update && sudo apt-get install -y libcurl4-openssl-dev

      - name: Setup R
        uses: r-lib/actions/setup-r@v2
        with:
          r-version: '4.2.0'

      - name: Setup renv
        uses: r-lib/actions/setup-renv@v2
        with:
          cache-version: 2

      # - name: Run scripts
      #   run: |
      #     Rscript scripts/add_badges.R
      #     Rscript scripts/add_contributions.R
      #   env:
      #     GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

      - name: Run visualisations
        if: ${{ github.ref == 'refs/heads/main' }}
        run: |
          Rscript scripts/add_hexwall_network.R
        env:
          GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

      - name: Setup Hugo
        uses: peaceiris/actions-hugo@v2
        with:
          hugo-version: '0.85.0'
          extended: true

# IF main
      - name: Build
        if: ${{ github.ref == 'refs/heads/main' }}
        run: hugo --minify

      - name: Deploy
        uses: peaceiris/actions-gh-pages@v3
        if: ${{ github.ref == 'refs/heads/main' }}
        with:
          github_token: ${{ secrets.GITHUB_TOKEN }}
          publish_dir: ./public

# IF develop
      - name: Build
        if: ${{ github.ref == 'refs/heads/develop' }}
        run: hugo -e staging

      - name: Check
        if: ${{ github.ref == 'refs/heads/develop' }}
        run: ls -la /home/runner/work \ ls -la /home/runner/work/pharmaverse
      #- name: Copy public to staging
      #  if: ${{ github.ref == 'refs/heads/develop' }}
      #  run: cp -R public home/runner/work/pharmaverse/pharmaverse/

      #- name: Deploy to Posit Connect
      #  if: ${{ github.ref == 'refs/heads/develop' }}
      #  env:
      #    CONNECT_SERVER: ${{ secrets.POSIT_CONNECT_SERVER }}
      #    CONNECT_API_KEY: ${{ secrets.POSIT_CONNECT_API_KEY }}
      #    DEPLOYMENT_NAME: "pharmaverse-staging"
      #  run: |
      #    Rscript -e '
      #      print(list.files("public"));
      #      print(Sys.getenv("$CONNECT_SERVER"));
      #      rsconnect::addServer(url = Sys.getenv("CONNECT_SERVER"), name = Sys.getenv("DEPLOYMENT_NAME"));
      #      rsconnect::connectApiUser(apiKey = Sys.getenv("CONNECT_API_KEY"), server = Sys.getenv("DEPLOYMENT_NAME"));
      #      rsconnect::deployApp(
      #        appDir = "./public",
      #        appName = Sys.getenv("DEPLOYMENT_NAME"),
      #        server = Sys.getenv("DEPLOYMENT_NAME")
      #      );
      #    '