deploy-toolkit.yml

# # Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
# # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
---
name: Deploy Toolkit

on:
  push:
    branches: [main, master]
  pull_request:
    branches: [main, master]
  release:
    types: [published]
  workflow_dispatch:
  
jobs:
  deploy_toolkit:
    runs-on: ubuntu-latest
    # Only restrict concurrency for non-PR jobs
    concurrency:
      group: deploy-staging-${{ github.event_name != 'pull_request' || github.run_id }}
    env:
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
    
    permissions:
      contents: write
      pages: write
    
    steps:
      - name: Checkout repository
        uses: actions/checkout@v3

      - name: Set up R and Pandoc
        uses: r-lib/actions/setup-pandoc@v2
        with:
          pandoc-version: 'latest'

      - name: Set up R
        uses: r-lib/actions/setup-r@v2
        with:
          use-public-rspm: true

      - name: Install system dependencies
        run: |
          sudo apt-get install -y libudunits2-dev libgdal-dev
          sudo apt-get install libmagick++-dev

      - name: Install R packages
        run: |
          R -e 'install.packages(c("bookdown", "rmarkdown", "plotly", "shiny", "tidycensus", "tidyverse", "viridis", "ggmap", "ggplot2", "maps", "dplyr", "knitr", "latticeExtra", "pals", "classInt", "sf", "udunits2", "tmap", "lubridate", "gifski", "magick", "cowplot"))'
          R -e 'if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager"); BiocManager::install("Biobase")'
  
      - name: Build site for staging branch
        run: R -e 'bookdown::render_book(".", "bookdown::gitbook")'

      - name: Debug Repository State
        run: |
          git status
          ls -la

      - name: Deploy to GitHub pages 🚀
        if: github.event_name != 'pull_request'
        uses: JamesIves/github-pages-deploy-action@v4.4.1
        with:
          clean: false
          branch: gh-pages
          folder: ./docs