Switch to rstudio/bookdown

But don't deploy yet
JeldorPKU · Feb 16, 2016 · acc8f77 · acc8f77
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Showing 69 changed files with 30 additions and 10,650 deletions.
diff --git a/.gitignore b/.gitignore
@@ -1,16 +1,6 @@
 .Rproj.user
 .Rhistory
-_site
-cache
-temp.Rmd
-/*.html
 *_cache
 *_files
-figures
-.Rapp.history
-_main.Rmd
-book_assets
-.bundle
-vendor
-*.md
-_main.rds
+_main.*
+book
diff --git a/.travis.yml b/.travis.yml
@@ -1,29 +1,23 @@
 language: R
 cache:
   packages: true
-  directores:
-  - vendor/bundle
+  directories:
+  - *_cache
+  - *_files
 
 addons:
   apt:
     packages:
       - libxml2-dev
 
-# Install ruby gems
-before_script:
-  - rvm use 2.2.0
-  - bundle install --jobs=3 --retry=3 --deployment
+script: _build.sh
 
-script: bundle exec jekyll build
-
-after_success:
-  - cp -r figures/ _site/figures
-
-deploy:
-  provider: s3
-  access_key_id: AKIAJ6PXDYWD72R6HBYA
-  secret_access_key:
-     secure: "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"
-  bucket: r4ds.had.co.nz
-  local-dir: _site
-  skip_cleanup: true
+## Disable deployment until bookdown output is polished
+# deploy:
+#   skip_cleanup: true
+#   provider: s3
+#   access_key_id: AKIAJ6PXDYWD72R6HBYA
+#   secret_access_key:
+#      secure: "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"
+#   bucket: r4ds.had.co.nz
+#   local-dir: www
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -37,6 +37,5 @@ Remotes:
   hadley/purrr,
   hadley/stringr,
   hadley/ggplot2,
-  hadley/bookdown,
   hadley/nycflights13,
-  yihui/knitr
+  rstudio/bookdown
diff --git a/Gemfile b/Gemfile
diff --git a/Gemfile.lock b/Gemfile.lock
diff --git a/_bookdown.yml b/_bookdown.yml
@@ -1,6 +1,7 @@
 new_session: yes
 
 rmd_files: [
+  "index.rmd",
   "understand.Rmd",
   "visualize.Rmd",
   "transform.Rmd",
@@ -24,3 +25,5 @@ rmd_files: [
   "rmarkdown.Rmd",
   "shiny.Rmd",
 ]
+
+output_dir: "book"
diff --git a/_build.sh b/_build.sh
@@ -0,0 +1,2 @@
+#!/usr/bin/env Rscript
+bookdown::render_book("index.rmd")
diff --git a/_config.yml b/_config.yml
diff --git a/_includes/.DS_Store b/_includes/.DS_Store
diff --git a/_includes/package-nav.html b/_includes/package-nav.html
diff --git a/_layouts/default.html b/_layouts/default.html
diff --git a/_layouts/post.html b/_layouts/post.html
diff --git a/_plugins/knit.r b/_plugins/knit.r
diff --git a/_plugins/rmarkdown.rb b/_plugins/rmarkdown.rb
diff --git a/functions.Rmd b/functions.Rmd
@@ -8,8 +8,7 @@ title: Expressing yourself in code
 ```{r, include = FALSE}
 source("common.R")
 knitr::opts_chunk$set(
-  cache = TRUE,
-  fig.path = "figures/functions/"
+  cache = TRUE
 )
 library(dplyr)
 diamonds <- ggplot2::diamonds

diff --git a/index.rmd b/index.rmd
@@ -6,18 +6,14 @@ knit: "bookdown::render_book"
 output:
   bookdown::html_chapters:
     lib_dir: "book_assets"
+    toc_depth: 1
+    html_names: "chapter"
 ---
 
-# R for Data Science
+# Welcome
 
 This is the book site for __"R for data science"__. This book will teach you how to do data science with R: You'll learn how to get your data into R, get it into the most useful structure, transform it, visualise it and model it. In this book, you will find a practicum of skills for data science. Just as a chemist learns how to clean test tubes and stock a lab, you'll learn how to clean data and draw plots---and many other things besides. These are the skills that allow data science to happen, and here you will find the best practices for doing each of these things with R. You'll learn how to use the grammar of graphics, literate programming, and reproducible research to save time. You'll also learn how to manage cognitive resources to facilitate discoveries when wrangling, visualizing, and exploring data. (__R for Data Science__ was formally called __Data Science with R__ in __Hands-On Programming with R__)
 
 To be published by O'Reilly in July 2016. 
 
 <img src="cover.png" width="250" height="328" alt="Cover image" />
-
-## Table of contents {#toc}
-
-<ul class="toc">
-  {% include package-nav.html %}
-</ul>
diff --git a/r4ds.Rproj b/r4ds.Rproj
@@ -15,6 +15,5 @@ LaTeX: XeLaTeX
 AutoAppendNewline: Yes
 StripTrailingWhitespace: Yes
 
-BuildType: Package
-PackageUseDevtools: Yes
-PackageInstallArgs: --no-multiarch --with-keep.source
+BuildType: Custom
+CustomScriptPath: _build.sh
diff --git a/relational-data.Rmd b/relational-data.Rmd
@@ -11,7 +11,7 @@ library(nycflights13)
 library(ggplot2)
 source("common.R")
 options(dplyr.print_min = 6, dplyr.print_max = 6)
-knitr::opts_chunk$set(fig.path = "figures/", cache = TRUE)
+knitr::opts_chunk$set(cache = TRUE)
 ```
 
 It's rare that a data analysis involves only a single table of data. Typically you have many tables of data, and you must combine them to answer the questions that you're interested in. Collectively, multiple tables of data are called __relational data__ because it is the relations, not just the individual datasets, that are particularly important.

diff --git a/toc.rds b/toc.rds
diff --git a/toc.yaml b/toc.yaml
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		#!/usr/bin/env Rscript
		bookdown::render_book("index.rmd")