publish.yml

on:
  workflow_dispatch:
  schedule:
    - cron: '0 20 * * *'
  push:
    branches: main

name: Quarto Publish

jobs:
  build-deploy:
    runs-on: ubuntu-latest
    env:
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
    container: rocker/geospatial:latest
    permissions:
      contents: write
    steps:

      - run: git config --system --add safe.directory '*'

      - uses: actions/checkout@v4
        with:
           fetch-depth: 0
           set-safe-directory: '*'

      - name: Install packages
        shell: Rscript {0}
        run: source('install.R')

      #- uses: quarto-dev/quarto-actions/setup@v2
      #  #with:
      #  version: 1.4.146

      - name: Render
        run: |
          quarto render

      - name: Update data
        run: |
          git config user.name github-actions
          git config user.email github-actions@github.com
          git add data/saved_parameter_chain.csv
          git add data/site_carbon_data.csv
          git add data/PF_analysis_0.Rdata
          git add data/PF_analysis_1.Rdata
          git commit -a -m "update data" || echo "nothing to commit"
          git push https://${GITHUB_PAT}:${GITHUB_PAT}@github.com/${GITHUB_REPOSITORY}

      - name: Publish
        run: |
          git config user.name github-actions
          git config user.email github-actions@github.com
          git checkout gh-pages
          cp -r _book/* .
          git add .
          git commit -a -m "update pages" || echo "nothing to commit"
          git push https://${GITHUB_PAT}:${GITHUB_PAT}@github.com/${GITHUB_REPOSITORY}