Build_gh-pages.yml

# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples and adapted
on:
  push:
    branches: [main]

name: Build_gh-pages.yml #shown when action is run

jobs:
  pkgdown:
    runs-on: ubuntu-latest
    env:
      GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} #to push results to gh-pages branch!
    steps: #Series of steps that is executed sequencially: https://github.com/r-lib/actions/
      - uses: actions/checkout@v4 # goes to gh-pages branch to work there

      - name: Install libglpk40
        run: sudo apt-get install -y libglpk40

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

      - uses: r-lib/actions/setup-r@v2 #installs R
        with:
          use-public-rspm: true

      - name: Install fgsea & pkgdown
        run: |
          Rscript -e 'install.packages("remotes")'
          Rscript -e 'remotes::install_github("ctlab/fgsea")'  # see: https://github.com/ctlab/fgsea/issues/165
          Rscript -e 'install.packages("pkgdown")'

      - name: Install MetaProViz from GitHub by remotes
        run: Rscript -e 'remotes::install_github("saezlab/MetaProViz")' #we install from GitHub as if we are a random user

      - name: Build pkgdown site
        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
        shell: Rscript {0}

      - name: Deploy to GitHub pages 🚀
        if: github.event_name != 'pull_request'
        uses: JamesIves/github-pages-deploy-action@v4.5.0
        with:
          clean: false
          branch: gh-pages
          folder: docs