re written chapter 25 + renders with quarto

.Rbuildignore

@@ -0,0 +1,23 @@
+^\.netlify$
+^\.github$
+^\.quarto$
+^\.vscode$
+^cpp$
+^emoji$
+^99-rename-rmd-to-qmd\.sh$
+^advancedrsolutions\.Rproj$
+^images$
+.*\.bib$
+.*\.cls$
+.*\.csl$
+.*\.csv$
+.*\.md$
+.*\.qmd$
+.*\.rds$
+.*\.r$
+.*\.R$
+.*tex$
+^_.*
+.*_cache$
+.*_files$
+^docs$

.gitattributes

@@ -1,2 +1,2 @@
-*.Rmd linguist-language=R
+*.qmd linguist-language=R
 *.R linguist-language=R

.github/workflows/bookdown.yaml

@@ -1,61 +1,53 @@
 on:
   push:
-    branches:
-      - main
+    branches: main
 
-name: bookdown
+name: Render and Publish
 
 jobs:
-  build:
-    runs-on: macOS-latest
-    env:
-      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+  build-deploy:
+    runs-on: ubuntu-latest
     steps:
-      - name: Checkout repo
-        uses: actions/checkout@v2
-
+      - name: Check out repository
+        uses: actions/checkout@v3
+      
       - name: Setup R
-        uses: r-lib/actions/setup-r@v1
+        uses: r-lib/actions/setup-r@v2
 
-      - name: Install pandoc and pandoc citeproc
-        run: |
-          brew install pandoc
+      - name: Setup pandoc
+        uses: r-lib/actions/setup-pandoc@v2
 
-      - name: Cache Renv packages
-        uses: actions/cache@v2
-        with:
-          path: $HOME/.local/share/renv
-          key: r-${{ hashFiles('renv.lock') }}
-          restore-keys: r-
+      - name: Get R version
+        id: get-r-version
+        run: echo "version=$(Rscript -e 'cat(as.character(getRversion()))')" >> $GITHUB_OUTPUT
+        shell: bash  
 
-      - name: Cache bookdown results
-        uses: actions/cache@v2
+      - name: Cache R packages
+        uses: actions/cache@v3
         with:
-          path: _bookdown_files
-          key: bookdown-${{ hashFiles('**/*Rmd') }}
-          restore-keys: bookdown-
+          path: ${{ env.R_LIBS_USER }}
+          key: ${{ runner.os }}-${{ steps.get-r-version.outputs.version }}-3-
 
-      - name: Install packages
+      - name: Install dependencies
         run: |
-          R -e 'install.packages("renv")'
-          R -e 'renv::restore()'
-          R -e 'install.packages("remotes")'
-          R -e 'remotes::install_github("hadley/emo")'
-          R -e 'remotes::install_github("rstudio/bslib")'
-          R -e 'remotes::install_deps(dependencies = TRUE)'
-
-      - name: Build site
-        run: Rscript -e 'bookdown::render_book("index.Rmd", quiet = TRUE)'
-
-      - name: Install npm
-        uses: actions/setup-node@v1
-
-      - name: Deploy to Netlify
-        if: github.ref == 'refs/heads/main'
-        # NETLIFY_AUTH_TOKEN and NETLIFY_SITE_ID added in the repo's secrets
-        env:
+          install.packages("pak", repos = "https://r-lib.github.io/p/pak/dev/")
+          pak::local_install_dev_deps()
+        shell: Rscript {0}
+
+      - name: Set up Quarto
+        uses: quarto-dev/quarto-actions/setup@v2
+        with:
+          tinytex: false
+
+      # - name: Publish to GitHub Pages (and render)
+      #   uses: quarto-dev/quarto-actions/publish@v2
+      #   with:
+      #     target: gh-pages
+      #   env:
+      #     GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # this secret is always available for github actions
+
+      - name: Publish to Netlify (and render)
+        uses: quarto-dev/quarto-actions/publish@v2
+        with:
+          target: netlify
           NETLIFY_AUTH_TOKEN: ${{ secrets.NETLIFY_AUTH_TOKEN }}
-          NETLIFY_SITE_ID: ${{ secrets.NETLIFY_SITE_ID }}
-        run: |
-          npm install netlify-cli -g
-          netlify deploy --prod --dir=_book

.gitignore

@@ -13,6 +13,11 @@ libs
 *.md
 *_files
 *_cache
-.Rbuildignore
 .idea
 _main.docx
+
+/.quarto/
+_freeze
+_cache$
+pdf.tex
+/.vscode/

book_cover.Rmd → 00_01_Book_Cover.qmd

@@ -153,5 +153,3 @@ ggraph(mygraph, layout = 'circlepack') +
 # geom_node_label( aes(label = part_label), color = "white", size = 5, fill = alpha(c("white"), 0), label.size = 0) +
 # geom_node_label( aes(label = chapter_label, color = as.factor(depth)), size = 5, fill = alpha(c("white"), 0), label.size = 0)
 ```
-
-

01_Preface.Rmd → 00_02_Preface.qmd

@@ -1,3 +1,7 @@
+---
+bibliography: references.bib
+---
+
 # Preface {-}
 
 Welcome to *Advanced R Solutions*!
@@ -72,7 +76,7 @@ contribs_all <- contribs_all %>% unique()
 
 # Get info for all contributors
 needed_json <- map(
-  contribs_all$login, 
+  contribs_all$login,
   ~ gh::gh("/users/:username", username = .x)
 )
 info_all <- tibble(
@@ -88,15 +92,15 @@ write_csv(info_all, "contributors.csv")
 library(dplyr)
 contributors <- read.csv("contributors.csv", encoding = "UTF-8")
 
-contributors <- contributors %>% 
-  filter(!login %in% c("hadley", "henningsway", "Tazinho", "toebR")) %>% 
+contributors <- contributors %>%
+  filter(!login %in% c("hadley", "henningsway", "Tazinho", "toebR")) %>%
   mutate(
     login = paste0("\\@", login),
     desc = ifelse(is.na(name), login, paste0(name, " (", login, ")"))
-  ) %>% 
+  ) %>%
   arrange(login)
 
-cat(glue::glue_collapse(contributors$desc, sep = ", ", last = ", and ")) 
+cat(glue::glue_collapse(contributors$desc, sep = ", ", last = ", and "))
 cat(".\n")
 ```
 
@@ -140,3 +144,7 @@ See you around!
 Malte Grosser [`@malte_grosser`](https://twitter.com/malte_grosser)
 
 Henning Bumann [`@henningsway`](https://twitter.com/henningsway)
+
+Mauricio Vargas Sepulveda `m.sepulveda@mail.utoronto.ca`
+
+## References