tut-build-publish.yml

name: Render and publish the tutorials

on:
  workflow_dispatch:
#  pull_request:
#  push:
#    branches: ['release']

jobs:
  render-tutorials:
    runs-on: ubuntu-latest
    env:
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

    name: ${{ matrix.config.r }}

    strategy:
      fail-fast: false
      matrix:
        config:
        - { r: '4.3.3' }

    steps:
      - name: Checkout repository
        uses: actions/checkout@v4
        with: 
          fetch-depth: 0  # ensure that more than the last commit is checked out so that we can get time stamps
      # Restore the timestamps - I am going to try to use these to work out what is new and what is not    
      - name: Restore Timestamps
        uses: chetan/git-restore-mtime-action@v1

      # Install system dependencies
      - name: Install system dependencies
        run: |
          sudo apt-get update
          sudo apt-get install -y libcurl4-openssl-dev libssl-dev libxml2-dev make
          
      # install graphviz
      - name: Install Graphviz
        run: sudo apt-get install graphviz
        
      # install R
      - uses: r-lib/actions/setup-r@v2
        with:
          r-version: ${{ matrix.config.R }}

      - name: Repos
        run: |
          cat("\noptions(repos=c(stan='https://mc-stan.org/r-packages/',CRAN ='https://cloud.r-project.org'))\n", file = "~/.Rprofile", append = TRUE)
        shell: Rscript {0}
        
      ## Install R packages
      - name: install R packages
        uses: r-lib/actions/setup-r-dependencies@v2
        with:
          cache-version: 2
          packages: |
            any::rmarkdown
            any::magick
            any::pdftools
            any::quarto
            any::tidyverse
            any::mvabund
            any::pander
            any::GGally
            any::plotrix
            any::PBSmapping
            any::gmodels
            any::mvtnorm
            any::coda
            any::gganimate
            any::gridExtra
            any::ggfortify
            any::DHARMa
            any::glmmTMB
            any::performance
            any::see
            stan-dev/cmdstanr
            any::brms
            any::knitr
            any::simstudy
            any::sf
            any::stars
            any::gstat
            any::patchwork
            any::remotes
            any::inlabru
            any::Hmisc
            any::igraph
            any::ggraph
            any::easystats
            any::gridGraphics
            any::HDInterval
            any::bayestestR
            any::emmeans
            github::jmgirard/standist

      - name: Install other R packages
        run: |
          Rscript -e "install.packages('INLA',repos=c(getOption('repos'),INLA='https://inla.r-inla-download.org/R/stable'), dep=TRUE)"
          Rscript -e "install.packages('RandomFields', repos = c('https://spatstat.r-universe.dev', 'https://cloud.r-project.org'))"
          Rscript -e "install.packages('RandomFieldsUtils', repos = c('https://spatstat.r-universe.dev', 'https://cloud.r-project.org'))"
          Rscript -e "install.packages('tidybayes')"

          Rscript -e "remotes::install_github('jmgirard/standist')"

      - name: Install CmdStan
        shell: Rscript {0}
        run: |
          cmdstanr::check_cmdstan_toolchain(fix = TRUE)
          cmdstanr::install_cmdstan(cores = parallel::detectCores())
          #install.packages("cmdstanr", repos = c("https://mc-stan.org/r-packages/", getOption("repos")))
          #cmdstanr::check_cmdstan_toolchain(fix = TRUE)
          #cmdstanr::install_cmdstan(cores = 2)
          #version <- "2.35.0"
          #url <- sprintf("https://github.com/stan-dev/cmdstan/releases/download/v%s/cmdstan-%s.tar.gz", version, version)
          #cmdstanr::install_cmdstan(cores = 2, release_url = url)        
          #cmdstanr::check_cmdstan_toolchain(fix = TRUE)
          #cmdstanr::install_cmdstan(cores = 2)
          #cmdstan <- file.path(Sys.getenv("RUNNER_TEMP"), "cmdstan")
          #file.rename(cmdstanr::cmdstan_path(), cmdstan)
          #lines <- paste0("\nCMDSTAN=", cmdstan, "\n")
          #cat(lines, file = "~/.Renviron", append = TRUE)
          cmdstanr:::get_cmdstan_flags("STANCFLAGS")
          cmdstanr::cmdstanr_example()
          
      - name: install tinytex
        uses: r-lib/actions/setup-tinytex@v2
      - run: |
          tlmgr --version
          tlmgr update --self

      - name: Install additional LaTeX packages
        run: |
          tlmgr install titlesec
          tlmgr list --only-installed

      - name: Install Google Fonts
        run: |
          ## The following wget can no longer be performed as google returns a html rather than a zip
          #wget -O Architects_Daughter.zip https://fonts.google.com/download?family=Architects%20Daughter
          # unzip -d architects_daughter/ Architects_Daughter.zip
          # mv architects_daughter /usr/share/fonts/
          unzip -d architects_daughter/ resources/Architects_Daughter.zip
          mv architects_daughter /usr/share/fonts/

          
          #wget -O inconsolata.zip https://fonts.google.com/download?family=Inconsolata
          unzip -d inconsolata/ resources/Inconsolata.zip
          mv inconsolata /usr/share/fonts/

          #wget -O noto_sans.zip https://fonts.google.com/download?family=Noto%20Sans
          unzip -d noto_sans/ resources/Noto_Sans.zip
          mv noto_sans /usr/share/fonts/

          fc-cache -fv
          fc-list
          ##fc-list -v | grep -i archi
          ##fc-list -v | grep -i inconsolata
          ##fc-list -v | grep -i noto

      # install quarto
      - name: Install quarto
        uses: quarto-dev/quarto-actions/setup@v2
      - name: Change ImageMagick policy to allow pdf->png conversion.
        run: |
          sudo sed -i 's/^.*policy.*coder.*none.*PDF.*//' /etc/ImageMagick-6/policy.xml
          
      # configure git
      - name: Configure git
        run: |
          git config --global user.name "pcinereus"
          git config --global user.email "i.obesulus@gmail.com"
          git config --global init.defaultBranch main

      # Checkout the gh-pages branch into the tut folder    
      # - name: Retrieve previous compiled pages
      #   uses: actions/checkout@v4
      #   with:
      #     path: tut  # Specify the target folder for checkout
      #     ref: gh-pages  
          
      - name: Touch those files that have changed since the last commit
        run: |
          git diff --name-only HEAD HEAD~1 | xargs touch
        
      # - name: Check that the docs folder is there and populated
      #   run: | 
      #     ls -la
      #     ls -la docs
      #     ls -la tut


      # Download artifacts
      #- name: download artifacts
      #  uses: actions/download-artifact@v4
      #  with: 
      #    name: artifact
      #    github-token: ${{ secrets.GH_PAT }} # token with actions:read permissions on target repo
      #    path: data
      #    run-id: 8493870822
      #- name: Display structure of downloaded files
      #  run: ls -R data
  
      # render tutorials
      - name: Make tutorials
        run: |
          echo "library(quarto); quarto_render(\"tut/index.qmd\")" | R --no-save --no-restore;
          #make -i tut
          make -i pres
        #run: |
        #  echo "library(quarto); quarto_render(\"tut/index.qmd\")" | R --no-save --no-restore;
        #  echo "library(quarto); quarto_render(\"tut/10_git.qmd\")" | R --no-save --no-restore;

      # upload artifacts  
      #- name: upload artifacts
      #  uses: actions/upload-artifact@v4
      #  with: 
      #    name: artifact
      #    path: data/reef_data_synthetic_*.csv
      #    if-no-files-found: ignore
      #    overwrite: true
        
      # Deploy site to gh-pages branch
      - name: Deploy
        uses: JamesIves/github-pages-deploy-action@4.1.4
        with:
          branch: gh-pages
          folder: .