Add commas and gha check

.github/workflows/render-leanpub.yml

@@ -0,0 +1,38 @@
+
+# Adapted for this jhudsl repository by Candace Savonen Aug 2021
+
+name: Render and publish Leanpub
+
+# Triggers the workflow on pull requests for the master branch OR can be manually triggered
+on:
+  workflow_dispatch:
+  pull_request:
+    branches: [ master ]
+
+jobs:
+  publish:
+    runs-on: ubuntu-latest
+    # I have it check out the image that is built from: https://github.com/jhudsl/DaSL_Course_Template_Bookdown/blob/main/docker/Dockerfile
+    container:
+      image: jhudsl/course_template
+
+    steps:
+      # Checks-out the _Leanpub repository to run the checks
+      - name: Checkout code from Leanpub test repo
+        uses: actions/checkout@v2
+        with:
+          repository: jhudsl/DaSL_Course_Template_Leanpub
+          token: ${{ secrets.GH_PAT }}
+
+      # Copy over the latest leanbuild and use that for the run
+      - name: Get latest leanbuild
+        run: |
+          sudo apt-get install  -y --no-install-recommends subversion
+
+          # Copy over the latest leanbuild build
+          svn export https://github.com/${GITHUB_REPOSITORY}.git/branches/${GITHUB_HEAD_REF} leanbuild/
+
+      # Run leanpub rendering
+      - name: Run leanbuild::bookdown_to_leanpub
+        run: |
+          Rscript -e "devtools::load_all('leanbuild'); leanbuild::bookdown_to_leanpub(footer_text = 'check if footer works')"

.github/workflows/update-leanpub.yml

@@ -0,0 +1,63 @@
+
+# Adapted for this jhudsl repository by Candace Savonen Aug 2021
+
+name: Render and publish Leanpub
+
+# Triggers the workflow AFTER changes to leanbuild have been merged
+on:
+  workflow_dispatch:
+  push:
+    branches: [ master ]
+
+jobs:
+  publish:
+    runs-on: ubuntu-latest
+    # I have it check out the image that is built from: https://github.com/jhudsl/DaSL_Course_Template_Bookdown/blob/main/docker/Dockerfile
+    container:
+      image: jhudsl/course_template
+
+    steps:
+      # Checks-out the _Leanpub repository to run the checks
+      - name: Checkout code from Leanpub test repo
+        uses: actions/checkout@v2
+        with:
+          repository: jhudsl/DaSL_Course_Template_Leanpub
+          token: ${{ secrets.GH_PAT }}
+
+      # Copy over the latest leanbuild and use that for the run
+      - name: Get latest leanbuild
+        run: |
+          sudo apt-get install  -y --no-install-recommends subversion
+
+          # Copy over the latest leanbuild build
+          svn export https://github.com/${GITHUB_REPOSITORY}.git/branches/${GITHUB_HEAD_REF} leanbuild/
+
+      # Run leanpub rendering
+      - name: Run leanbuild::bookdown_to_leanpub
+        run: |
+          Rscript -e "devtools::load_all('leanbuild'); leanbuild::bookdown_to_leanpub(footer_text = 'check if footer works')"
+
+
+      - name: Create PR with newly rendered docs files
+        uses: peter-evans/create-pull-request@v3
+        id: cpr
+        with:
+          token: ${{ secrets.GH_PAT }}
+          commit-message: Show latest leanbuild changes
+          signoff: false
+          branch: auto_copy_rendered_files
+          delete-branch: true
+          title: 'GHA: Automated transfer of leanbuild-needed files from Bookdown repository'
+          body: |
+            ### Description:
+             This PR has changes to this repository's files using the latest leanbuild package changes!
+             If they don't look right, file an issue on the leanbuild package: https://github.com/jhudsl/leanbuild/issuesand do not merge. 
+          labels: |
+            automated
+          reviewers: $GITHUB_ACTOR
+
+      # Write out PR info
+      - name: Check outputs
+        run: |
+          echo "Pull Request Number - ${{ steps.cpr.outputs.pull-request-number }}"
+          echo "Pull Request URL - ${{ steps.cpr.outputs.pull-request-url }}"

DESCRIPTION

@@ -30,7 +30,8 @@ Imports:
     curl,
     rprojroot,
     magrittr,
-    yaml
+    yaml, 
+    here
 Suggests:
     didactr,
     knitr,

R/bookdown_to_leanpub.R

@@ -1,22 +1,66 @@
 
+#' Load in Bookdown specifications from _bookdown.yml
+#'
+#' @param path  Where to look for the _bookdown.yml file. Passes to the bookdown_file() function. By default looks in current directory
+#'
+#' @return The yaml contents using yaml::yaml.load_file()
+#' @export
+
 get_bookdown_spec <- function(path = ".") {
-  file <- bookdown_file(path = path)
+
+  # Get the file path to _bookdown.yaml
+  file_path <- bookdown_file(path = path)
+
+  # Read in yaml
   suppressWarnings({
-    out <- yaml::yaml.load_file(file)
+    yaml_contents <- yaml::yaml.load_file(file_path)
   })
-  out
+
+  return(yaml_contents)
 }
+
+#' Find main Bookdown directory
+#'
+#' @param path  Where to look for the file. By default looks in current directory.
+#'
+#' @return Returns the directory where the _bookdown.yml is contained.
+#' @export
+
 bookdown_path <- function(path = ".") {
+
   rprojroot::find_root(rprojroot::has_file("_bookdown.yml"), path = path)
+
+  path <- dirname(here::here("_bookdown.yml"))
+
+  return(path)
 }
 
+#' Find file path to _bookdown.yml
+#'
+#' @param path  Where to look for the _bookdown.yml file. Passes to the bookdown_file() function. By default looks in current directory
+#'
+#' @return The file path to _bookdown.yml
+#' @export
+#' 
 bookdown_file <- function(path = ".") {
+
   root_dir <- bookdown_path(path = path)
-  file.path(root_dir, "_bookdown.yml")
+  file_path <- file.path(root_dir, "_bookdown.yml")
+
+  return(file_path)
 }
 
+#' Get file paths all Rmds in the bookdown directory
+#'
+#' @param path  Where to look for the _bookdown.yml file. Passes toget_bookdown_spec() function. By default looks in current directory
+#'
+#' @return The file paths to Rmds listed in the _bookdown.yml file. 
+#' @export
+#' 
 bookdown_rmd_files <- function(path = ".") {
+
   spec <- get_bookdown_spec(path)
+
   files <- spec$rmd_files
   if (is.null(files) || all(is.na(files)) || length(files) == 0) {
     warning(
@@ -32,33 +76,74 @@ bookdown_rmd_files <- function(path = ".") {
   return(files)
 }
 
+#' Declare file path to docs/ folder
+#'
+#' @param path  Where to look for the _bookdown.yml file. Passes toget_bookdown_spec() function. By default looks in current directory
+#'
+#' @return The file paths to Rmds listed in the _bookdown.yml file. 
+#' @export
+#'
 bookdown_destination <- function(path = ".") {
+
+  # Find _bookdown.yml
   root_dir <- bookdown_path(path = path)
+
+  # Get specs from _bookdown.yml
   spec <- get_bookdown_spec(path = path)
+
+  # Find output directory declared in the bookdown.yml
   output_dir <- spec$output_dir
+
+  # If none specified, assume its called docs/
   if (is.null(output_dir)) {
     output_dir <- "docs"
   }
+  # Get the full file path
   full_output_dir <- file.path(root_dir, output_dir)
+
+  # If the output dir doesn't exist, make it
   dir.create(full_output_dir, showWarnings = FALSE, recursive = TRUE)
+
+  # Declare full paths
   full_output_dir <- normalizePath(full_output_dir, winslash = "/")
-  full_output_dir
+
+  return(full_output_dir)
 }
 
+#' Copying directory contents
+#'
+#' @param from  Where the files to copy are located. 
+#' @param to  Where the files to copy are to be copied should go to.  
+#'
+#' @return The file paths to Rmds listed in the _bookdown.yml file. 
+#' @export
+#'
 copy_directory_contents <- function(from, to) {
-  x <- list.files(
+
+  file_list <- list.files(
     path = from, full.names = TRUE, all.files = TRUE,
     recursive = TRUE
   )
-  file.copy(x, to, recursive = TRUE, overwrite = TRUE)
+  file.copy(file_list, to, recursive = TRUE, overwrite = TRUE)
 }
 
-copy_resources <- function(path = ".", output_dir = "manuscript") {
+copy_resources <- function(path = ".",
+                           images_dir = "resources/images",
+                           output_dir = "manuscript") {
+
+  # Get file path to bookdown.yml
   path <- bookdown_path(path)
-  res_image_dir <- file.path(path, "resources/images")
+
+  # Assume image directory is `resources/images`
+  res_image_dir <- file.path(path, images_dir )
+
+  # Creat the directory if it doesn't exist
   dir.create(res_image_dir, showWarnings = FALSE, recursive = TRUE)
-  manuscript_image_dir <- file.path(output_dir, "resources/images")
+
+  manuscript_image_dir <- file.path(output_dir, images_dir )
+
   dir.create(manuscript_image_dir, showWarnings = FALSE, recursive = TRUE)
+
   manuscript_image_dir <- normalizePath(manuscript_image_dir)
   if (file.exists(res_image_dir)) {
     copy_directory_contents(res_image_dir, manuscript_image_dir)
@@ -101,27 +186,46 @@ copy_bib <- function(path = ".", output_dir = "manuscript") {
 bookdown_to_leanpub <- function(path = ".",
                                 render = TRUE,
                                 output_dir = "manuscript",
-                                make_book_txt = TRUE,
+                                make_book_txt = FALSE,
                                 remove_resources_start = FALSE,
                                 verbose = TRUE, 
                                 footer_text = NULL) {
+
+  # Declare regex for finding rmd files
   rmd_regex <- "[.][R|r]md$"
 
+  # Get the path to the _bookdown.yml
   path <- bookdown_path(path)
-
+
+  if (verbose) {
+    message(paste0("Looking for bookdown file in ", path))
+  }
   rmd_files <- bookdown_rmd_files(path = path)
+
+  if (verbose) {
+    message(paste0(c("Processing these files: ", rmd_files), collapse = "\n"))
+  }
+
   if (render) {
     if (verbose) {
       message("Rendering the Book")
     }
-    input <- rmd_files[grepl("index", rmd_files, ignore.case = TRUE)][1]
-    if (length(input) == 0 || is.na(input)) {
-      input <- rmd_files[1]
+    # Get the index file path
+    index_file <- grep("index", rmd_files, ignore.case = TRUE, value = TRUE)
+
+    index_file <- normalizePath(index_file)
+
+    if (length(index_file) == 0 || is.na(index_file)) {
+      index_file <- rmd_files[1]
     }
+    message(paste("index_file is", index_file))
+
     output_format <- bookdown::gitbook(pandoc_args = "--citeproc")
     # output_format$pandoc$to = output_format$pandoc$from
     output_format$pandoc$args <- c(output_format$pandoc$args, "--citeproc")
-    bookdown::render_book(input = input, output_format = output_format)
+    bookdown::render_book(input = index_file, 
+                          output_format = output_format, 
+                          clean_envir = FALSE)
   }
 
   # may be irrelevant since copy_docs does everything

R/replace_html.R

@@ -220,9 +220,9 @@ build_image <- function(src, ..., caption = NULL, embed = NULL,
     'alt: "{alt}",',
     'height: "{height}",',
     'width: "{width}",',
-    'align: "{align}"',
-    'type: "{type}"',
-    'poster: "{poster}"',
+    'align: "{align}",',
+    'type: "{type}",',
+    'poster: "{poster}",',
     'embed: "{embed}"'
   )
   if (is.null(fullbleed) ||