Build and deploy the book automatically on GHA (#339)

cderv · web-flow · commit c2f249e9e7cb · 2021-05-26T13:37:21.000+02:00
diff --git a/.Rprofile b/.Rprofile
@@ -1,3 +1,4 @@
+# source("renv/activate.R")
 if (file.exists('~/.Rprofile')) sys.source('~/.Rprofile', envir = environment())
 
 options(
diff --git a/.github/.gitignore b/.github/.gitignore
@@ -0,0 +1 @@
+*.html
diff --git a/.github/workflows/build-book.yaml b/.github/workflows/build-book.yaml
@@ -0,0 +1,103 @@
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches:
+      - master
+
+name: build-book
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    env:
+      RSPM: https://packagemanager.rstudio.com/cran/__linux__/focal/latest
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v2
+
+      - name: Setup R
+        id: install-r
+        uses: r-lib/actions/setup-r@v1
+
+      - name: Setup pandoc
+        uses: r-lib/actions/setup-pandoc@v1
+        with:
+          pandoc-version: '2.13'
+
+      - name: Install TinyTeX
+        uses: r-lib/actions/setup-tinytex@v1
+        env:
+          # install full prebuilt version
+          TINYTEX_INSTALLER: TinyTeX
+
+      - name: Install pak and query dependencies
+        run: |
+          install.packages("pak", repos = "https://r-lib.github.io/p/pak/dev/")
+          saveRDS(pak::local_dev_deps_tree(), ".github/r-depends.rds")
+        shell: Rscript {0}
+
+      - name: Cache R packages
+        uses: actions/cache@v2
+        with:
+          path: |
+            ${{ env.R_LIBS_USER }}/*
+            !${{ env.R_LIBS_USER }}/pak
+          key: ${{ runner.os }}-${{ steps.install-r.outputs.installed-r-version }}-1-${{ hashFiles('.github/r-depends.rds') }}
+          restore-keys: ${{ runner.os }}-${{ steps.install-r.outputs.installed-r-version }}-1-
+
+      - name: Install system dependencies
+        if: runner.os == 'Linux'
+        run: |
+          pak::local_system_requirements(execute = TRUE)
+        shell: Rscript {0}
+
+      - name: Install missing system dependencies
+        if: runner.os == 'Linux'
+        run: sudo apt-get install -y libgtk2.0-dev asymptote
+
+      - name: Install dependencies
+        run: |
+          pak::local_install_dev_deps(upgrade = TRUE)
+        shell: Rscript {0}
+
+      - name: Install phantomjs
+        run: |
+          webshot::install_phantomjs()
+        shell: Rscript {0}
+
+      - name: Build Gitbook
+        if: github.event_name == 'pull_request'
+        run: make gitbook
+
+      - name: Build and Deploy all book
+        # if: github.event_name == 'push'
+        env:
+          CONNECT_API_KEY: ${{ secrets.RSC_BOOKDOWN_ORG_TOKEN }}
+          CONTENT_ID: 7b3dedfa-fd98-45dd-bec4-75d915fb27dd
+        run: make all
+
+      - uses: actions/github-script@v3
+        env:
+          URL: https://bookdown.org/yihui/rmarkdown-cookbook/
+        with:
+          github-token: ${{secrets.GITHUB_TOKEN}}
+          script: |
+            github.repos.createCommitStatus({
+              owner: context.repo.owner,
+              repo: context.repo.repo,
+              sha: context.sha,
+              state: "success",
+              target_url: "${{ env.URL}}",
+              description: "Book deployed!",
+              context: "bookdown.org"
+            })
+
+      - name: Upload book folder for debug
+        if: failure()
+        uses: actions/upload-artifact@main
+        with:
+          name: book-dir
+          path: _book
diff --git a/.travis.yml b/.travis.yml
diff --git a/15-languages.Rmd b/15-languages.Rmd
@@ -72,7 +72,7 @@ Next we show an example of an alternative Python engine^[In practice, you should
 knitr::knit_engines$set(py = function(options) {
   code <- paste(options$code, collapse = '\n')
   out  <- system2(
-    'python', c('-c', shQuote(code)), stdout = TRUE
+    'python3', c('-c', shQuote(code)), stdout = TRUE
   )
   knitr::engine_output(options, code, out)
 })
diff --git a/18-references.Rmd b/18-references.Rmd
@@ -7,7 +7,7 @@
 # References {-}
 '`
 
-```{r include=FALSE, tidy=FALSE}
+```{r include=FALSE, tidy=FALSE, warning = FALSE}
 # list cited packages
 pkgs <- c(
   .packages(),
@@ -90,12 +90,10 @@ pkgs <- c(
   # JavaScript: 'DataTables'
 )
 
-# install packages if missing
-lapply(pkgs, function(pkg) {
-    if (system.file(package = pkg) != '') return()
-    install.packages(pkg, repos = "https://cloud.r-project.org/") 
-    }
-)
+# Warn to add new deps in DESCRIPTION
+pkg2 <- setdiff(pkgs, knitr:::.base.pkgs)
+in_desc <-  pkg2 %in% desc::desc_get_deps()$package
+if (any(!in_desc)) warning("To add to DESCRIPTION: ", paste0(pkg2[!in_desc], collapse = ", "))
 
 # automatically create a bib database for R packages
 knitr::write_bib(pkgs, file = 'packages.bib', lib.loc = c(.libPaths(), '~/R-tmp'))
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,84 @@
-Package: placeholder
 Type: Book
-Title: Does not matter.
-Version: 0.0.1
-Imports: bookdown, DiagrammeR, blogdown, webshot, fs, here, sass
-Remotes: yihui/xfun, yihui/knitr, rstudio/bookdown
+Package: rmarkdowncookbook
+Title: R Markdown Cookbook
+Version: 1.0.1
+Imports: 
+    animation,
+    blastula,
+    blogdown,
+    bookdown,
+    broom,
+    Cairo,
+    cairoDevice,
+    condformat,
+    dagitty,
+    desc,
+    diagram,
+    DiagrammeR,
+    distill,
+    downloadthis,
+    DT,
+    equatiomatic,
+    ezknitr,
+    flair,
+    flexdashboard,
+    flextable,
+    formatR,
+    formattable,
+    gganimate,
+    ggdag,
+    ggplot2,
+    gifski,
+    googledrive,
+    govdown,
+    gt,
+    gtsummary,
+    here,
+    huxtable,
+    jsonlite,
+    kableExtra,
+    knitcitations,
+    knitr,
+    learnr,
+    magick,
+    nomnoml,
+    officedown,
+    officer,
+    pagedown,
+    pander,
+    pdftools,
+    pixiedust,
+    pkgdown,
+    printr,
+    r2d3,
+    reactable,
+    reticulate,
+    revealjs,
+    rgl,
+    rhandsontable,
+    rmarkdown,
+    rmdformats,
+    roxygen2,
+    rsconnect,
+    rticles,
+    sass,
+    spelling,
+    stargazer,
+    styler,
+    svglite,
+    tables,
+    tangram,
+    tikzDevice,
+    tinytex,
+    tufte,
+    usethis,
+    webshot,
+    workflowr,
+    xaringan,
+    xfun,
+    xtable,
+    yaml,
+    ztable
+Suggests:
+    rsconnect
+Encoding: UTF-8
diff --git a/Makefile b/Makefile
@@ -13,3 +13,6 @@ gitbook:
 
 pdf2:
 	BOOKDOWN_FULL_PDF=false Rscript --quiet _render.R "bookdown::pdf_book"
+
+clean:
+	Rscript -e 'bookdown::clean_book(TRUE)'
diff --git a/SETUP.md b/SETUP.md
@@ -10,15 +10,45 @@ When contribution to the book, it is a good practice to build it locally to ensu
 
 ### R Packages
 
-To render the book, you must first install the `bookdown` R package. 
+For this book, dependencies are required to execute R chunks and to generate references of others packages mentioned. Dependencies are tracked using a DESCRIPTION files. 
 
-Additional dependencies are installed automatically the first time you buid the book. Packages that are used within the book are listed in the [index.Rmd](https://github.com/yihui/rmarkdown-cookbook/blob/master/index.Rmd) file, and packages referenced in the book (and used to generate their own references) are listed in the [18-references.Rmd](https://github.com/yihui/rmarkdown-cookbook/blob/master/18-references.Rmd) file. 
+To render the book, you can install the required packages using **renv**, **remotes** or **pak**
+
+#### Using **renv**
+
+This project contains a lockfile that you can use to reinstall packages in a project library, separated from your other global packages installation. 
+
+```r
+install.packages('renv')
+renv::activate()
+renv::restore()
+```
+
+#### Using **remotes**
+
+```r
+install.packages("remotes")
+remotes::install_deps(".")
+```
+
+#### Using **pak**
+
+**pak** benefits from a caching mechanism of installed packages and offers fast installation.
+
+```r
+install.packages("pak", repos = "https://r-lib.github.io/p/pak/dev/")
+pak::local_install_dev_deps(upgrade = TRUE)
+```
+
+This methods is used in CI. 
 
 ### LaTeX Packages
 
-The TinyTex LaTeX distribution is required to build the book. This is installed on the first render of [01-installation.Rmd](https://github.com/yihui/rmarkdown-cookbook/blob/master/18-references.Rmd) if not already installed (which can be done with `tinytex::install_tinytex()`).
+The TinyTeX LaTeX distribution is required to build the book. This can be done using `tinytex::install_tinytex()`. 
+
+This command will be run on the first render of [01-installation.Rmd](https://github.com/yihui/rmarkdown-cookbook/blob/master/01-installation.Rmd) TinyTeX is not already installed.
 
-Additionally, the `pgf`, `preview`, and `xcolor` packages are required to build [11-chunk-options.Rmd](https://github.com/yihui/rmarkdown-cookbook/blob/master/11-chunk-options.Rmd) and will be installed as needed when running that chapter. 
+Other required LaTeX packages should be installed automatically during the build of the book. Know required packages are the `pgf`, `preview`, and `xcolor` packages used in [11-chunk-options.Rmd](https://github.com/yihui/rmarkdown-cookbook/blob/master/11-chunk-options.Rmd) and they will be installed as needed when running that chapter. 
 
 ### Other System Dependencies
 
diff --git a/_render.R b/_render.R
@@ -1,6 +1,5 @@
 quiet = "--quiet" %in% commandArgs(FALSE)
 formats = commandArgs(TRUE)
-travis = !is.na(Sys.getenv('CI', NA))
 
 # provide default formats if necessary
 if (length(formats) == 0) formats = c('bookdown::pdf_book', 'bookdown::gitbook')
@@ -12,15 +11,7 @@ for (fmt in formats) {
 }
 unlink('rmarkdown-cookbook.log')
 
-r = '<body onload="window.location = \'https://bookdown.org/yihui\'+location.pathname">'
-if (travis) for (f in list.files('_book', '[.]html$', full.names = TRUE)) {
-  x = readLines(f)
-  if (length(i <- grep('^\\s*<body>\\s*$', x)) == 0) next
-  # patch HTML files in gh-pages if built on Travis, to redirect to bookdown.org
-  x[i[1]] = r
-  writeLines(x, f)
-}
-
+# creates redirects
 redirect = function(from, to) {
   to = paste0('https://bookdown.org/yihui/rmarkdown-cookbook/', to)
   writeLines(sprintf(
@@ -31,6 +22,23 @@ redirect = function(from, to) {
 redirect('r-markdown-components.html', 'rmarkdown-process.html')
 redirect('acknowledgements.html', 'acknowledgments.html')
 
-if (length(formats) > 1 && Sys.getenv('USER') == 'yihui') {
-  bookdown::publish_book(account = 'yihui', server = 'bookdown.org')
+
+if (length(formats) > 1) {
+  if (!is.na(Sys.getenv('CI', NA))) {
+    xfun::pkg_load2("rsconnect")
+    # On CI connect to server, using API KEY and deploy using appId
+    rsconnect::addConnectServer('https://bookdown.org', 'bookdown.org')
+    rsconnect::connectApiUser(
+      account = 'GHA', server = 'bookdown.org',
+      apiKey = Sys.getenv('CONNECT_API_KEY')
+    )
+    rsconnect::deploySite(
+      appId = Sys.getenv('CONTENT_ID'),
+      server = 'bookdown.org',
+      render = 'none', logLevel = 'verbose',
+      forceUpdate = TRUE)
+  } else if (Sys.getenv('USER') == 'yihui') {
+    # for local deployment when rsconnect/ is available
+    bookdown::publish_book('rmarkdown-cookbook', server = 'bookdown.org', render = 'none')
+  }
 }
diff --git a/index.Rmd b/index.Rmd
@@ -23,7 +23,7 @@ cover-image: images/cover.png
 ```{r setup, include=FALSE}
 set.seed(0728)
 
-knitr::opts_chunk$set(tidy = TRUE)
+knitr::opts_chunk$set(tidy = TRUE, webshot = "webshot")
 
 if (knitr::is_html_output()) {
   # ignore percentage widths for HTML output, unless they are used for multiple
@@ -35,22 +35,6 @@ if (knitr::is_html_output()) {
   })
 }
 
-# packages only available on Github
-remote_pkgs = c(character())  # e.g., c(equatiomatic = 'datalorax')
-
-lapply(c(
-  'remotes', 'webshot', 'DiagrammeR', 'stargazer', 'gt', 'flextable', 'formatR',
-  'equatiomatic', 'gifski', 'magick', 'pdftools', 'tikzDevice', 'xaringan',
-  'kableExtra', 'blogdown', 'jsonlite', 'nomnoml'
-  ), function(pkg) {
-    if (system.file(package = pkg) != '') return()
-    repo = remote_pkgs[pkg]
-    if (is.na(repo)) install.packages(pkg) else {
-      remotes::install_github(paste(repo, pkg, sep = '/'))
-    }
-  }
-)
-
 # screenshot HTML widgets
 if (is.null(webshot:::find_phantom())) webshot::install_phantomjs()
 
diff --git a/renv.lock b/renv.lock
diff --git a/renv/.gitignore b/renv/.gitignore
diff --git a/renv/activate.R b/renv/activate.R
diff --git a/renv/settings.dcf b/renv/settings.dcf

Original file line number	Diff line number	Diff line change
`@@ -1,3 +1,4 @@`
	`1`	`+# source("renv/activate.R")`
`1`	`2`	`if (file.exists('~/.Rprofile')) sys.source('~/.Rprofile', envir = environment())`
`2`	`3`
`3`	`4`	`options(`
Original file line number	Diff line number	Diff line change
`@@ -72,7 +72,7 @@ Next we show an example of an alternative Python engine^[In practice, you should`
`72`	`72`	`knitr::knit_engines$set(py = function(options) {`
`73`	`73`	`code <- paste(options$code, collapse = '\n')`
`74`	`74`	`out <- system2(`
`75`		`- 'python', c('-c', shQuote(code)), stdout = TRUE`
	`75`	`+ 'python3', c('-c', shQuote(code)), stdout = TRUE`
`76`	`76`	`)`
`77`	`77`	`knitr::engine_output(options, code, out)`
`78`	`78`	`})`