# ==================================================================== #
# TITLE:                                                               #
# AMR: An R Package for Working with Antimicrobial Resistance Data     #
#                                                                      #
# SOURCE CODE:                                                         #
# https://github.com/msberends/AMR                                     #
#                                                                      #
# PLEASE CITE THIS SOFTWARE AS:                                        #
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C    #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance  #
# Data. Journal of Statistical Software, 104(3), 1-31.                 #
# https://doi.org/10.18637/jss.v104.i03                                #
#                                                                      #
# Developed at the University of Groningen and the University Medical  #
# Center Groningen in The Netherlands, in collaboration with many      #
# colleagues from around the world, see our website.                   # 
#                                                                      #
# This R package is free software; you can freely use and distribute   #
# it for both personal and commercial purposes under the terms of the  #
# GNU General Public License version 2.0 (GNU GPL-2), as published by  #
# the Free Software Foundation.                                        #
# We created this package for both routine data analysis and academic  #
# research and it was publicly released in the hope that it will be    #
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
#                                                                      #
# Visit our website for the full manual and a complete tutorial about  #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/   #
# ==================================================================== #

# Create a website from the R documentation using pkgdown
# Git commit and push to the 'gh-pages' branch

on:
  push:
    # only on main
    branches: 'main'

name: Update website

jobs:
  update-website:
    runs-on: ubuntu-latest
    continue-on-error: true
    steps:

      - uses: actions/checkout@v3
        with:
          # this is to keep timestamps, the default fetch-depth: 1 gets the timestamps of the moment of cloning
          fetch-depth: 0

      - name: Preserve timestamps
        run: |
          sudo apt install git-restore-mtime
          git restore-mtime

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

      - name: Set up R
        uses: r-lib/actions/setup-r@v2
        with:
          r-version: "release"
          # use RStudio Package Manager (RSPM) to quickly install packages
          use-public-rspm: true

      - name: Set up R dependencies
        uses: r-lib/actions/setup-r-dependencies@v2
        with:
          # add extra packages for website articles:
          extra-packages: |
            any::pkgdown
            any::tidymodels
            any::data.table

      # Send updates to repo using GH Actions bot
      - name: Create website in separate branch
        run: |
          git config user.name "github-actions"
          git config user.email "41898282+github-actions[bot]@users.noreply.github.com"
          Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE, clean = TRUE, install = TRUE, branch = "gh-pages")'