From 3ac4471fe4c0474e04dd6adf74170cb534a4917f Mon Sep 17 00:00:00 2001
From: Candace Savonen <cansav09@gmail.com>
Date: Fri, 4 Feb 2022 10:58:33 -0500
Subject: [PATCH 01/11] Add embed option

---
 R/bookdown_to_leanpub.R | 460 ++++++++++++++++++----------------------
 R/set_up.R              | 282 ++++++++++++++++++++++++
 2 files changed, 492 insertions(+), 250 deletions(-)
 create mode 100644 R/set_up.R

diff --git a/R/bookdown_to_leanpub.R b/R/bookdown_to_leanpub.R
index 7a657a3..9a6dee1 100644
--- a/R/bookdown_to_leanpub.R
+++ b/R/bookdown_to_leanpub.R
@@ -1,170 +1,4 @@
 
-#' 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 = ".") {
-
-  # Get the file path to _bookdown.yaml
-  file_path <- bookdown_file(path = path)
-
-  # Read in yaml
-  suppressWarnings({
-    yaml_contents <- yaml::yaml.load_file(file_path)
-  })
-
-  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 = ".") {
-
-  # See what unzip is being used
-  operating_system <- Sys.info()[1]
-
-  path <- rprojroot::find_root(rprojroot::has_file("_bookdown.yml"), path = file.path(path))
-
-  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 = file.path(path))
-  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(file.path(path))
-
-  files <- spec$rmd_files
-  if (is.null(files) || all(is.na(files)) || length(files) == 0) {
-    warning(
-      "No bookdown specification of the files, using ",
-      "list.files(pattern ='.Rmd')"
-    )
-    root_dir <- bookdown_path(path = file.path(path))
-    files <- list.files(
-      pattern = "[.]Rmd", ignore.case = TRUE,
-      path = root_dir, full.names = FALSE
-    )
-  }
-  return(files)
-}
-
-#' Declare file path to docs/ folder
-#'
-#' @param path  Where to look for the _bookdown.yml file. Passes toget_bookdown_spec() function. By default looks in current directory
-#'
-#' @return The file paths to Rmds listed in the _bookdown.yml file.
-#' @export
-#'
-bookdown_destination <- function(path = ".") {
-
-  # Find _bookdown.yml
-  root_dir <- bookdown_path(path = file.path(path))
-
-  # Get specs from _bookdown.yml
-  spec <- get_bookdown_spec(path = file.path(path))
-
-  # Find output directory declared in the bookdown.yml
-  output_dir <- spec$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 = "/")
-
-  return(full_output_dir)
-}
-
-copy_resources <- function(path = ".",
-                           images_dir = "resources",
-                           output_dir = "manuscript") {
-
-  # Get file path to bookdown.yml
-  path <- bookdown_path(path)
-
-  # Assume image directory is `resources/images`
-  res_image_dir <- file.path(path, images_dir)
-
-  # Create the directory if it doesn't exist
-  dir.create(res_image_dir, showWarnings = FALSE, recursive = TRUE)
-
-  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 (dir.exists(res_image_dir)) {
-    R.utils::copyDirectory(res_image_dir, manuscript_image_dir, recursive = TRUE, overwrite = TRUE)
-  }
-}
-
-copy_docs <- function(path = ".", output_dir = "manuscript") {
-  path <- bookdown_destination(path)
-  R.utils::copyDirectory(path, file.path(output_dir), recursive = TRUE, overwrite = TRUE)
-}
-
-copy_bib <- function(path = ".", output_dir = "manuscript") {
-  path <- bookdown_path(path)
-  files <- list.files(path = path, full.names = TRUE, pattern = ".bib$")
-  if (length(files) > 0) {
-    file.copy(files, file.path(output_dir), overwrite = TRUE)
-  }
-}
-
-copy_quizzes <- function(quiz_dir = "quizzes", output_dir = "manuscript") {
-  quiz_dir <- file.path(quiz_dir)
-
-  if (!dir.exists(quiz_dir)) {
-    stop(paste(
-      "The quiz directory specified by quiz_dir:", quiz_dir, "does not exist.",
-      "If you don't have quizzes, set quiz_dir = NULL"
-    ))
-  }
-  quizzes <- list.files(path = file.path(quiz_dir), full.names = TRUE, pattern = "\\.md$")
-  if (length(quizzes) > 0) {
-    fs::file_copy(quizzes, file.path(output_dir, basename(quizzes)),
-      overwrite = TRUE
-    )
-  }
-}
-
-
-
 #' Convert Bookdown to Leanpub
 #'
 #' @param path path to the bookdown book, must have a `_bookdown.yml` file
@@ -195,69 +29,7 @@ bookdown_to_leanpub <- function(path = ".",
                                 remove_resources_start = FALSE,
                                 verbose = TRUE,
                                 footer_text = NULL) {
-
-  # Declare regex for finding rmd files
-  rmd_regex <- "[.][R|r]md$"
-
-  # Get the path to the _bookdown.yml
-  path <- bookdown_path(path)
-
-  if (verbose) {
-    message(paste0("Looking for bookdown file in ", path))
-  }
-  rmd_files <- bookdown_rmd_files(path = path)
-
-  if (verbose) {
-    message(paste0(c("Processing these files: ", rmd_files), collapse = "\n"))
-  }
-
-  if (render) {
-    if (verbose) {
-      message("Rendering the Book")
-    }
-    # Get the index file path
-    index_file <- grep("index", rmd_files, ignore.case = TRUE, value = TRUE)
-
-    index_file <- normalizePath(index_file)
-
-    if (length(index_file) == 0 || is.na(index_file)) {
-      index_file <- rmd_files[1]
-    }
-    message(paste("index_file is", index_file))
-
-    if (rmarkdown::pandoc_version() >= "2.11") {
-      output_format <- bookdown::gitbook(pandoc_args = "--citeproc")
-      output_format$pandoc$args <- c(output_format$pandoc$args, "--citeproc")
-    } else {
-      warning("Pandoc version is not greater than 2.11 so citations will not be able to be rendered properly")
-      output_format <- NULL
-    }
-    bookdown::render_book(
-      input = index_file,
-      output_format = output_format,
-      clean_envir = FALSE
-    )
-  }
-
-  # may be irrelevant since copy_docs does everything
-  if (verbose) {
-    message("Copying Resources")
-  }
-  copy_resources(path, output_dir = output_dir)
-
-  if (verbose) {
-    message("Copying Docs folder")
-  }
-
-  copy_docs(path, output_dir = output_dir)
-  if (verbose) {
-    message("Copying docs files")
-  }
-
-  copy_bib(path, output_dir = output_dir)
-  if (verbose) {
-    message("Copying bib files")
-  }
+  set_up_leanpub(...)
 
   bib_files <- list.files(pattern = "[.]bib$")
   if (length(bib_files) > 0) {
@@ -291,23 +63,121 @@ bookdown_to_leanpub <- function(path = ".",
       )
     }
   }
-  if (!is.null(quiz_dir)) {
-    #### Run quiz checks
-    if (run_quiz_checks) {
-      message("Checking quizzes")
-      quiz_checks <- check_quizzes(quiz_dir,
-        verbose = verbose
-      )
+  ####################### Book.txt creation ####################################
+  out <- NULL
+  if (make_book_txt) {
+    if (verbose > 1) {
+      message("Running bookdown_to_book_txt")
     }
-    copy_quizzes(
+    bookdown_to_book_txt(
+      path = path,
+      output_dir = output_dir,
       quiz_dir = quiz_dir,
-      output_dir = output_dir
+      verbose = verbose
     )
-    if (verbose) {
-      message("Copying quiz files")
+    out <- book_txt_file <- file.path(output_dir, "Book.txt")
+  } else {
+    # If false, look for Book.txt file to copy to output folder.
+    book_txt_file <- file.path(path, "Book.txt")
+
+    if (file.exists(book_txt_file)) {
+      # Copy over an existing book.txt file if it exists
+      file.copy(from = book_txt_file, to = file.path(output_dir, "Book.txt"))
+
+      out <- book_txt_file <- file.path(output_dir, "Book.txt")
+    } else {
+      # If none exists and make_book_txt is false: stop.
+      stop(paste0(
+        "Book.txt file does not exist in the main directory: ", path, "and make_book_txt is set to FALSE.",
+        "There is no Book.txt file. Leanpub needs one. Either make one and place it in the directory path or ",
+        "use make_book_txt = TRUE and one will be generated for you."
+      ))
     }
   }
+  ############################# Wrapping up ####################################
+  message(paste(
+    "Leanpub ready files are saved to",
+    output_dir,
+    "Go to https://leanpub.com/ to publish them using the GitHub writing mode."
+  ))
+}
 
+#' Convert Bookdown to Embed version of Leanpub
+#'
+#' @param path path to the bookdown book, must have a `_bookdown.yml` file
+#' @param chapt_img_key File path to a TSV whose contents are the chapter urls (`url`),
+#' the chapter titles (`chapt_title`), the file path to the image to be used for the chapter (`img_path`).
+#' Column names `url`, `chapt_title`, and `img_path` must be used.
+#' If no chapter title column supplied, the basename of the url will be used,
+#' If no image column supplied, default image used.
+#' @param default_img A google slide link to the default image to be used for all chapters
+#' @param output_dir output directory to put files.  It should likely be
+#' relative to path
+#' @param render if `TRUE`, then [bookdown::render_book()] will be run on each Rmd.
+#' @param verbose print diagnostic messages
+#' @param remove_resources_start remove the word `resources/` at the front
+#' of any image path.
+#' @param run_quiz_checks TRUE/FALSE run quiz checks
+#' @param make_book_txt Should [ottr::bookdown_to_book_txt()] be run
+#' to create a `Book.txt` in the output directory?
+#' @param quiz_dir directory that contains the quiz .md files that should be
+#' checked and incorporated into the Book.txt file. If you don't have quizzes,
+#' set this to NULL
+#' @param footer_text Optionally can add a bit of text that will be added to the
+#' end of each file before the references section.
+#'
+#' @return A list of output files and diagnostics
+#' @export
+#'
+bookdown_to_embed_leanpub <- function(path = ".",
+                                      chapt_img_key = NULL,
+                                      bookdown_index = file.path("docs", "index.html"),
+                                      base_url = NULL,
+                                      default_img = NULL,
+                                      render = TRUE,
+                                      output_dir = "manuscript",
+                                      make_book_txt = FALSE,
+                                      quiz_dir = "quizzes",
+                                      run_quiz_checks = FALSE,
+                                      remove_resources_start = FALSE,
+                                      verbose = TRUE,
+                                      footer_text = NULL) {
+  set_up_leanpub(...)
+
+  
+  if (!is.null(chapt_img_key)) {
+    message(paste("Reading in a chapt_img_key TSV file:", chapt_img_key))
+    readr::read_tsv(chapt_img_key)
+  } else {
+    message("Creating a chapt_img_key TSV file")
+    chapt_df <- get_chapters(bookdown_index = bookdown_index, 
+                             base_url = base_url)
+  }
+  
+  
+  # If there's no img_path supplied, then use a default image for each. 
+  if (!("img_path" %in% colnames(chapt_df))) {
+    if (is.null(default_img)) {
+      default_img <- "https://docs.google.com/presentation/d/1jEUxUY1qXDZ3DUtvTU6NCc6ASG5nx4Gwczv5aAglYX4/edit#slide=id.p"
+    }
+    # Set up location to store default image
+    img_dir <- file.path(output_dir, "embed_chapt_images")
+
+    if (!dir.exists(img_dir)) {
+      dir.create(img_dir, recursive = TRUE)
+    }
+    
+    # Download default image
+    chapt_df$img_path <- leanbuild::gs_png_download(url = default_img, output_dir = file.path(img_dir, "embed_chapt_images"), overwrite = TRUE)
+  }
+  
+  output_files <- chapt_df %>% 
+    # Make the data.frame be in the same order
+    dplyr::select(dplyr::any_of(url, chapt_title, img_path)) %>% 
+    # Run it make_embed_markdown on each row
+    purrr::pmap( ~ make_embed_markdown(url = ..1, chapt_title = ..2, img_path = ..3))
+
+  ####################### Book.txt creation ####################################
   out <- NULL
   if (make_book_txt) {
     if (verbose > 1) {
@@ -338,6 +208,8 @@ bookdown_to_leanpub <- function(path = ".",
       ))
     }
   }
+
+  ############################# Wrapping up ####################################
   message(paste(
     "Leanpub ready files are saved to",
     output_dir,
@@ -345,7 +217,6 @@ bookdown_to_leanpub <- function(path = ".",
   ))
 }
 
-
 #' Create Book.txt file from files existing in quiz directory
 #'
 #' @param path path to the bookdown book, must have a `_bookdown.yml` file
@@ -370,17 +241,17 @@ bookdown_to_book_txt <- function(path = ".",
   rmd_files <- bookdown_rmd_files(path = path)
 
   if (!is.null(quiz_dir)) {
-  # Find the quiz files in the quiz directory
-  quiz_files <- list.files(pattern = "\\.md$", quiz_dir)
+    # Find the quiz files in the quiz directory
+    quiz_files <- list.files(pattern = "\\.md$", quiz_dir)
 
-  # Put files in one vector
-  all_files <- c(rmd_files, quiz_files)
+    # Put files in one vector
+    all_files <- c(rmd_files, quiz_files)
 
-  # Make a vector specifying the file type: quiz or not
-  file_type <- c(
-    rep("non-quiz", length(rmd_files)),
-    rep("quiz", length(quiz_files))
-  )
+    # Make a vector specifying the file type: quiz or not
+    file_type <- c(
+      rep("non-quiz", length(rmd_files)),
+      rep("quiz", length(quiz_files))
+    )
   } else {
     all_files <- rmd_files
     file_type <- rep("non-quiz", length(rmd_files))
@@ -417,3 +288,92 @@ bookdown_to_book_txt <- function(path = ".",
   # need to fix about quiz
   writeLines(all_files, con = book_txt)
 }
+
+
+#' Make Leanpub file that has embed webpage of a chapter
+#'
+#' @param url The url to the chapter that is to be embed
+#' @param chapt_name Title of chapter to be used as file name and printed on iframe
+#' @param img File path to image to use for poster
+#' @return A
+#'
+#' @export
+make_embed_markdown <- function(url,
+                                chapt_title,
+                                img_path,
+                                output_dir = "manuscript",
+                                verbose = TRUE) {
+  # Arguments:
+  #   url: The url to the chapter
+  #   chapt_name: The title of the chapter to be used as a header
+  #   img: file path to the image to be used in the preview
+  #
+  # Returns: A markdown document ready for Leanpub and the image copied to the manuscript folder
+
+  chapt_file_name <- gsub(" ", "-", chapt_title)
+
+  # Declare output file
+  output_file <- file.path(output_dir, paste0(chapt_file_name, ".md"))
+
+  file_contents <- c(
+    paste("#", chapt_title),
+    " ",
+    paste0("{type: iframe, title:", chapt_title, " width: 400, height: 400, poster:", img_path, "}"),
+    paste0("![](", url, ")")
+  )
+
+  write(file_contents, file = output_file)
+
+  manuscript_dir <- file.path(output_dir, dirname(img_path))
+
+  if (!dir.exists(manuscript_dir)) {
+    dir.create(manuscript_dir, recursive = TRUE)
+  }
+
+  file.copy(from = img_path, to = file.path(output_dir, img_path), overwrite = TRUE)
+
+  if (verbose) {
+    message(paste0("Output saved to: ", output_file))
+  }
+
+  return(output_file)
+}
+
+#' Make Leanpub file that has embed webpage of a chapter
+#'
+#' @param bookdown_index The file path of the rendered bookdown index.html file
+#' @param base_url The base url of where the chapters are published -- the url to provide to the iframe in Leanpub
+#' e.g. https://jhudatascience.org/OTTR_Template/coursera
+#' 
+#' @return A data.frame of the chapter urls and their titles that are to be ported to Leanpub. 
+#' This can be passed to 
+#'
+#' @export
+#'
+get_chapters <- function(bookdown_index = file.path("docs", "index.html"),
+                         base_url = NULL) {
+
+  # Read in html
+  index_html <- suppressWarnings(try(xml2::read_html(paste(bookdown_index, collapse = "\n"))))
+
+  # Extract chapter nodes
+  nodes <- rvest::html_nodes(index_html, xpath = paste0("//", 'li[@class="chapter"]'))
+
+  if (length(nodes) > 0) {
+    # Format into a data.frame
+    chapt_data <- rvest::html_attrs(nodes) %>%
+      dplyr::bind_rows() %>%
+      dplyr::rename_with(~ gsub("-", "_", .x, fixed = TRUE)) %>%
+      dplyr::mutate(
+        chapt_name = stringr::word(rvest::html_text(nodes), sep = "\n", 1),
+        url = paste0(base_url, data_path)
+      ) %>%
+      dplyr::select(url, chapt_title = chapt_name) %>%
+      as.data.frame() %>%
+      dplyr::distinct(url, .keep_all = TRUE)
+  } else {
+    stop(paste("Chapter retrieval from:", bookdown_index, "Failed."))
+  }
+
+  return(chapt_data)
+}
diff --git a/R/set_up.R b/R/set_up.R
new file mode 100644
index 0000000..66307cf
--- /dev/null
+++ b/R/set_up.R
@@ -0,0 +1,282 @@
+#' 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 = ".") {
+
+  # Get the file path to _bookdown.yaml
+  file_path <- bookdown_file(path = path)
+
+  # Read in yaml
+  suppressWarnings({
+    yaml_contents <- yaml::yaml.load_file(file_path)
+  })
+
+  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 = ".") {
+
+  # See what unzip is being used
+  operating_system <- Sys.info()[1]
+
+  path <- rprojroot::find_root(rprojroot::has_file("_bookdown.yml"), path = file.path(path))
+
+  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 = file.path(path))
+  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(file.path(path))
+
+  files <- spec$rmd_files
+  if (is.null(files) || all(is.na(files)) || length(files) == 0) {
+    warning(
+      "No bookdown specification of the files, using ",
+      "list.files(pattern ='.Rmd')"
+    )
+    root_dir <- bookdown_path(path = file.path(path))
+    files <- list.files(
+      pattern = "[.]Rmd", ignore.case = TRUE,
+      path = root_dir, full.names = FALSE
+    )
+  }
+  return(files)
+}
+
+#' Declare file path to docs/ folder
+#'
+#' @param path  Where to look for the _bookdown.yml file. Passes toget_bookdown_spec() function. By default looks in current directory
+#'
+#' @return The file paths to Rmds listed in the _bookdown.yml file.
+#' @export
+#'
+bookdown_destination <- function(path = ".") {
+
+  # Find _bookdown.yml
+  root_dir <- bookdown_path(path = file.path(path))
+
+  # Get specs from _bookdown.yml
+  spec <- get_bookdown_spec(path = file.path(path))
+
+  # Find output directory declared in the bookdown.yml
+  output_dir <- spec$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 = "/")
+
+  return(full_output_dir)
+}
+
+copy_resources <- function(path = ".",
+                           images_dir = "resources",
+                           output_dir = "manuscript") {
+
+  # Get file path to bookdown.yml
+  path <- bookdown_path(path)
+
+  # Assume image directory is `resources/images`
+  res_image_dir <- file.path(path, images_dir)
+
+  # Create the directory if it doesn't exist
+  dir.create(res_image_dir, showWarnings = FALSE, recursive = TRUE)
+
+  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 (dir.exists(res_image_dir)) {
+    R.utils::copyDirectory(res_image_dir, manuscript_image_dir, recursive = TRUE, overwrite = TRUE)
+  }
+}
+
+copy_docs <- function(path = ".", output_dir = "manuscript") {
+  path <- bookdown_destination(path)
+  R.utils::copyDirectory(path, file.path(output_dir), recursive = TRUE, overwrite = TRUE)
+}
+
+copy_bib <- function(path = ".", output_dir = "manuscript") {
+  path <- bookdown_path(path)
+  files <- list.files(path = path, full.names = TRUE, pattern = ".bib$")
+  if (length(files) > 0) {
+    file.copy(files, file.path(output_dir), overwrite = TRUE)
+  }
+}
+
+copy_quizzes <- function(quiz_dir = "quizzes", output_dir = "manuscript") {
+  quiz_dir <- file.path(quiz_dir)
+
+  if (!dir.exists(quiz_dir)) {
+    stop(paste(
+      "The quiz directory specified by quiz_dir:", quiz_dir, "does not exist.",
+      "If you don't have quizzes, set quiz_dir = NULL"
+    ))
+  }
+  quizzes <- list.files(path = file.path(quiz_dir), full.names = TRUE, pattern = "\\.md$")
+  if (length(quizzes) > 0) {
+    fs::file_copy(quizzes, file.path(output_dir, basename(quizzes)),
+      overwrite = TRUE
+    )
+  }
+}
+
+#' Set up Manuscript folder for Leanpub publishing
+#'
+#' @param path path to the bookdown book, must have a `_bookdown.yml` file
+#' @param output_dir output directory to put files.  It should likely be
+#' relative to path
+#' @param render if `TRUE`, then [bookdown::render_book()] will be run on each Rmd.
+#' @param verbose print diagnostic messages
+#' @param remove_resources_start remove the word `resources/` at the front
+#' of any image path.
+#' @param run_quiz_checks TRUE/FALSE run quiz checks
+#' @param make_book_txt Should [ottr::bookdown_to_book_txt()] be run
+#' to create a `Book.txt` in the output directory?
+#' @param quiz_dir directory that contains the quiz .md files that should be
+#' checked and incorporated into the Book.txt file. If you don't have quizzes,
+#' set this to NULL
+#' @param footer_text Optionally can add a bit of text that will be added to the
+#' end of each file before the references section.
+#'
+#' @return A list of output files and diagnostics
+#' @export
+#'
+set_up_leanpub <- function(path = ".",
+                           clean_up = FALSE
+                           render = TRUE,
+                           output_dir = "manuscript",
+                           make_book_txt = FALSE,
+                           quiz_dir = "quizzes",
+                           run_quiz_checks = FALSE,
+                           remove_resources_start = FALSE,
+                           verbose = TRUE,
+                           footer_text = NULL) {
+
+  if (clean_up && dir.exists(output_dir)) {
+    message(paste("Clearing out old version of output files:", output_dir))
+    file.remove(output_dir, recursive = TRUE)
+    dir.create(output_dir, showWarnings = FALSE)
+  }
+  
+  # Declare regex for finding rmd files
+  rmd_regex <- "[.][R|r]md$"
+
+  # Get the path to the _bookdown.yml
+  path <- bookdown_path(path)
+
+  if (verbose) {
+    message(paste0("Looking for bookdown file in ", path))
+  }
+  rmd_files <- bookdown_rmd_files(path = path)
+
+  if (verbose) {
+    message(paste0(c("Processing these files: ", rmd_files), collapse = "\n"))
+  }
+
+  if (render) {
+    if (verbose) {
+      message("Rendering the Book")
+    }
+    # Get the index file path
+    index_file <- grep("index", rmd_files, ignore.case = TRUE, value = TRUE)
+
+    index_file <- normalizePath(index_file)
+
+    if (length(index_file) == 0 || is.na(index_file)) {
+      index_file <- rmd_files[1]
+    }
+    message(paste("index_file is", index_file))
+
+    if (rmarkdown::pandoc_version() >= "2.11") {
+      output_format <- bookdown::gitbook(pandoc_args = "--citeproc")
+      output_format$pandoc$args <- c(output_format$pandoc$args, "--citeproc")
+    } else {
+      warning("Pandoc version is not greater than 2.11 so citations will not be able to be rendered properly")
+      output_format <- NULL
+    }
+    bookdown::render_book(
+      input = index_file,
+      output_format = output_format,
+      clean_envir = FALSE
+    )
+  }
+
+  # may be irrelevant since copy_docs does everything
+  if (verbose) {
+    message("Copying Resources")
+  }
+  copy_resources(path, output_dir = output_dir)
+
+  if (verbose) {
+    message("Copying Docs folder")
+  }
+
+  copy_docs(path, output_dir = output_dir)
+  if (verbose) {
+    message("Copying docs files")
+  }
+
+  copy_bib(path, output_dir = output_dir)
+  if (verbose) {
+    message("Copying bib files")
+  }
+
+  if (!is.null(quiz_dir)) {
+    #### Run quiz checks
+    if (run_quiz_checks) {
+      message("Checking quizzes")
+      quiz_checks <- check_quizzes(quiz_dir,
+        verbose = verbose
+      )
+    }
+    copy_quizzes(
+      quiz_dir = quiz_dir,
+      output_dir = output_dir
+    )
+    if (verbose) {
+      message("Copying quiz files")
+    }
+  }
+}

From 58c894225c8f44084caaee7007be3d1b1f63f58c Mon Sep 17 00:00:00 2001
From: Candace Savonen <cansav09@gmail.com>
Date: Fri, 4 Feb 2022 11:07:42 -0500
Subject: [PATCH 02/11] Somewhat working

---
 R/bookdown_to_leanpub.R | 10 ++++------
 R/set_up.R              |  2 +-
 2 files changed, 5 insertions(+), 7 deletions(-)

diff --git a/R/bookdown_to_leanpub.R b/R/bookdown_to_leanpub.R
index 9a6dee1..69ee7fd 100644
--- a/R/bookdown_to_leanpub.R
+++ b/R/bookdown_to_leanpub.R
@@ -144,7 +144,6 @@ bookdown_to_embed_leanpub <- function(path = ".",
                                       footer_text = NULL) {
   set_up_leanpub(...)
 
-  
   if (!is.null(chapt_img_key)) {
     message(paste("Reading in a chapt_img_key TSV file:", chapt_img_key))
     readr::read_tsv(chapt_img_key)
@@ -154,7 +153,6 @@ bookdown_to_embed_leanpub <- function(path = ".",
                              base_url = base_url)
   }
   
-  
   # If there's no img_path supplied, then use a default image for each. 
   if (!("img_path" %in% colnames(chapt_df))) {
     if (is.null(default_img)) {
@@ -168,12 +166,12 @@ bookdown_to_embed_leanpub <- function(path = ".",
     }
     
     # Download default image
-    chapt_df$img_path <- leanbuild::gs_png_download(url = default_img, output_dir = file.path(img_dir, "embed_chapt_images"), overwrite = TRUE)
+    chapt_df$img_path <- leanbuild::gs_png_download(url = default_img, output_dir = img_dir, overwrite = TRUE)
   }
   
-  output_files <- chapt_df %>% 
+  md_output_files <- chapt_df %>% 
     # Make the data.frame be in the same order
-    dplyr::select(dplyr::any_of(url, chapt_title, img_path)) %>% 
+    dplyr::select(dplyr::any_of("url"), dplyr::any_of("chapt_title"), dplyr::any_of("img_path")) %>% 
     # Run it make_embed_markdown on each row
     purrr::pmap( ~ make_embed_markdown(url = ..1, chapt_title = ..2, img_path = ..3))
 
@@ -184,7 +182,7 @@ bookdown_to_embed_leanpub <- function(path = ".",
       message("Running bookdown_to_book_txt")
     }
     bookdown_to_book_txt(
-      path = path,
+      path = output_dir,
       output_dir = output_dir,
       quiz_dir = quiz_dir,
       verbose = verbose
diff --git a/R/set_up.R b/R/set_up.R
index 66307cf..6e285dc 100644
--- a/R/set_up.R
+++ b/R/set_up.R
@@ -184,7 +184,7 @@ copy_quizzes <- function(quiz_dir = "quizzes", output_dir = "manuscript") {
 #' @export
 #'
 set_up_leanpub <- function(path = ".",
-                           clean_up = FALSE
+                           clean_up = FALSE,
                            render = TRUE,
                            output_dir = "manuscript",
                            make_book_txt = FALSE,

From d2b13cee78e6456138d8d585d4490b06c3883c7b Mon Sep 17 00:00:00 2001
From: Candace Savonen <cansav09@gmail.com>
Date: Fri, 4 Feb 2022 11:25:27 -0500
Subject: [PATCH 03/11] Update docs

---
 DESCRIPTION                      |  2 +-
 NAMESPACE                        |  4 ++
 R/bookdown_to_leanpub.R          | 17 ++++++-
 man/bookdown_destination.Rd      |  2 +-
 man/bookdown_file.Rd             |  2 +-
 man/bookdown_path.Rd             |  2 +-
 man/bookdown_rmd_files.Rd        |  2 +-
 man/bookdown_to_embed_leanpub.Rd | 76 ++++++++++++++++++++++++++++++++
 man/get_bookdown_spec.Rd         |  2 +-
 man/get_chapters.Rd              | 21 +++++++++
 man/make_embed_markdown.Rd       | 27 ++++++++++++
 man/set_up_leanpub.Rd            | 50 +++++++++++++++++++++
 12 files changed, 200 insertions(+), 7 deletions(-)
 create mode 100644 man/bookdown_to_embed_leanpub.Rd
 create mode 100644 man/get_chapters.Rd
 create mode 100644 man/make_embed_markdown.Rd
 create mode 100644 man/set_up_leanpub.Rd

diff --git a/DESCRIPTION b/DESCRIPTION
index 4a1b192..796ecda 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -50,4 +50,4 @@ Type: Package
 VignetteBuilder: knitr
 URL: https://github.com/jhudsl/ottr
 BugReports: https://github.comjhudsl/ottr/issues
-RoxygenNote: 7.1.1
+RoxygenNote: 7.1.2
diff --git a/NAMESPACE b/NAMESPACE
index bb12a5c..b352783 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -7,6 +7,7 @@ export(bookdown_file)
 export(bookdown_path)
 export(bookdown_rmd_files)
 export(bookdown_to_book_txt)
+export(bookdown_to_embed_leanpub)
 export(bookdown_to_leanpub)
 export(check_all_questions)
 export(check_question)
@@ -24,6 +25,7 @@ export(example_repo_setup)
 export(extract_meta)
 export(extract_quiz)
 export(get_bookdown_spec)
+export(get_chapters)
 export(get_image_from_slide)
 export(get_image_link_from_slide)
 export(get_slide_id)
@@ -34,6 +36,7 @@ export(gs_png_download)
 export(gs_png_url)
 export(include_slide)
 export(leanpub_check)
+export(make_embed_markdown)
 export(parse_q_tag)
 export(parse_quiz)
 export(parse_quiz_df)
@@ -42,6 +45,7 @@ export(render_coursera)
 export(replace_html)
 export(replace_single_html)
 export(set_knitr_image_path)
+export(set_up_leanpub)
 export(simple_references)
 importFrom(fs,dir_copy)
 importFrom(magrittr,"%>%")
diff --git a/R/bookdown_to_leanpub.R b/R/bookdown_to_leanpub.R
index 69ee7fd..3192aac 100644
--- a/R/bookdown_to_leanpub.R
+++ b/R/bookdown_to_leanpub.R
@@ -110,6 +110,9 @@ bookdown_to_leanpub <- function(path = ".",
 #' Column names `url`, `chapt_title`, and `img_path` must be used.
 #' If no chapter title column supplied, the basename of the url will be used,
 #' If no image column supplied, default image used.
+#' @param bookdown_index The file path of the rendered bookdown index.html file
+#' @param s The base url of where the chapters are published -- the url to provide to the iframe in Leanpub
+#' e.g. https://jhudatascience.org/OTTR_Template/coursera
 #' @param default_img A google slide link to the default image to be used for all chapters
 #' @param output_dir output directory to put files.  It should likely be
 #' relative to path
@@ -128,7 +131,16 @@ bookdown_to_leanpub <- function(path = ".",
 #'
 #' @return A list of output files and diagnostics
 #' @export
-#'
+#' 
+#' @examples
+#' \dontrun{
+#' 
+#' ottr::bookdown_to_embed_leanpub(base_url = ")
+#' 
+#' ottr::bookdown_to_embed_leanpub(chapt_img_key = "chapt)
+#' 
+#' 
+#' }
 bookdown_to_embed_leanpub <- function(path = ".",
                                       chapt_img_key = NULL,
                                       bookdown_index = file.path("docs", "index.html"),
@@ -149,6 +161,9 @@ bookdown_to_embed_leanpub <- function(path = ".",
     readr::read_tsv(chapt_img_key)
   } else {
     message("Creating a chapt_img_key TSV file")
+    if (is.null(base_url)) {
+      stop("No base_url is supplied and no chapt_img_key file was supplied. Need one or the other.")
+    }
     chapt_df <- get_chapters(bookdown_index = bookdown_index, 
                              base_url = base_url)
   }
diff --git a/man/bookdown_destination.Rd b/man/bookdown_destination.Rd
index bc86e03..c677cf0 100644
--- a/man/bookdown_destination.Rd
+++ b/man/bookdown_destination.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/bookdown_to_leanpub.R
+% Please edit documentation in R/set_up.R
 \name{bookdown_destination}
 \alias{bookdown_destination}
 \title{Declare file path to docs/ folder}
diff --git a/man/bookdown_file.Rd b/man/bookdown_file.Rd
index 2cfedfa..78d133f 100644
--- a/man/bookdown_file.Rd
+++ b/man/bookdown_file.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/bookdown_to_leanpub.R
+% Please edit documentation in R/set_up.R
 \name{bookdown_file}
 \alias{bookdown_file}
 \title{Find file path to _bookdown.yml}
diff --git a/man/bookdown_path.Rd b/man/bookdown_path.Rd
index aa28e6d..27a0817 100644
--- a/man/bookdown_path.Rd
+++ b/man/bookdown_path.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/bookdown_to_leanpub.R
+% Please edit documentation in R/set_up.R
 \name{bookdown_path}
 \alias{bookdown_path}
 \title{Find main Bookdown directory}
diff --git a/man/bookdown_rmd_files.Rd b/man/bookdown_rmd_files.Rd
index b637f82..e085722 100644
--- a/man/bookdown_rmd_files.Rd
+++ b/man/bookdown_rmd_files.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/bookdown_to_leanpub.R
+% Please edit documentation in R/set_up.R
 \name{bookdown_rmd_files}
 \alias{bookdown_rmd_files}
 \title{Get file paths all Rmds in the bookdown directory}
diff --git a/man/bookdown_to_embed_leanpub.Rd b/man/bookdown_to_embed_leanpub.Rd
new file mode 100644
index 0000000..179f7bc
--- /dev/null
+++ b/man/bookdown_to_embed_leanpub.Rd
@@ -0,0 +1,76 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/bookdown_to_leanpub.R
+\name{bookdown_to_embed_leanpub}
+\alias{bookdown_to_embed_leanpub}
+\title{Convert Bookdown to Embed version of Leanpub}
+\usage{
+bookdown_to_embed_leanpub(
+  path = ".",
+  chapt_img_key = NULL,
+  bookdown_index = file.path("docs", "index.html"),
+  base_url = NULL,
+  default_img = NULL,
+  render = TRUE,
+  output_dir = "manuscript",
+  make_book_txt = FALSE,
+  quiz_dir = "quizzes",
+  run_quiz_checks = FALSE,
+  remove_resources_start = FALSE,
+  verbose = TRUE,
+  footer_text = NULL
+)
+}
+\arguments{
+\item{path}{path to the bookdown book, must have a `_bookdown.yml` file}
+
+\item{chapt_img_key}{File path to a TSV whose contents are the chapter urls (`url`),
+the chapter titles (`chapt_title`), the file path to the image to be used for the chapter (`img_path`).
+Column names `url`, `chapt_title`, and `img_path` must be used.
+If no chapter title column supplied, the basename of the url will be used,
+If no image column supplied, default image used.}
+
+\item{bookdown_index}{The file path of the rendered bookdown index.html file}
+
+\item{default_img}{A google slide link to the default image to be used for all chapters}
+
+\item{render}{if `TRUE`, then [bookdown::render_book()] will be run on each Rmd.}
+
+\item{output_dir}{output directory to put files.  It should likely be
+relative to path}
+
+\item{make_book_txt}{Should [ottr::bookdown_to_book_txt()] be run
+to create a `Book.txt` in the output directory?}
+
+\item{quiz_dir}{directory that contains the quiz .md files that should be
+checked and incorporated into the Book.txt file. If you don't have quizzes,
+set this to NULL}
+
+\item{run_quiz_checks}{TRUE/FALSE run quiz checks}
+
+\item{remove_resources_start}{remove the word `resources/` at the front
+of any image path.}
+
+\item{verbose}{print diagnostic messages}
+
+\item{footer_text}{Optionally can add a bit of text that will be added to the
+end of each file before the references section.}
+
+\item{s}{The base url of where the chapters are published -- the url to provide to the iframe in Leanpub
+e.g. https://jhudatascience.org/OTTR_Template/coursera}
+}
+\value{
+A list of output files and diagnostics
+}
+\description{
+Convert Bookdown to Embed version of Leanpub
+}
+\examples{
+\dontrun{
+
+ottr::bookdown_to_embed_leanpub(base_url = ")
+
+ottr::bookdown_to_embed_leanpub(chapt_img_key = "chapt)
+
+
+}
+}
diff --git a/man/get_bookdown_spec.Rd b/man/get_bookdown_spec.Rd
index b483ade..1bfd9b3 100644
--- a/man/get_bookdown_spec.Rd
+++ b/man/get_bookdown_spec.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/bookdown_to_leanpub.R
+% Please edit documentation in R/set_up.R
 \name{get_bookdown_spec}
 \alias{get_bookdown_spec}
 \title{Load in Bookdown specifications from _bookdown.yml}
diff --git a/man/get_chapters.Rd b/man/get_chapters.Rd
new file mode 100644
index 0000000..9e57d5c
--- /dev/null
+++ b/man/get_chapters.Rd
@@ -0,0 +1,21 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/bookdown_to_leanpub.R
+\name{get_chapters}
+\alias{get_chapters}
+\title{Make Leanpub file that has embed webpage of a chapter}
+\usage{
+get_chapters(bookdown_index = file.path("docs", "index.html"), base_url = NULL)
+}
+\arguments{
+\item{bookdown_index}{The file path of the rendered bookdown index.html file}
+
+\item{base_url}{The base url of where the chapters are published -- the url to provide to the iframe in Leanpub
+e.g. https://jhudatascience.org/OTTR_Template/coursera}
+}
+\value{
+A data.frame of the chapter urls and their titles that are to be ported to Leanpub. 
+This can be passed to
+}
+\description{
+Make Leanpub file that has embed webpage of a chapter
+}
diff --git a/man/make_embed_markdown.Rd b/man/make_embed_markdown.Rd
new file mode 100644
index 0000000..eff5f2b
--- /dev/null
+++ b/man/make_embed_markdown.Rd
@@ -0,0 +1,27 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/bookdown_to_leanpub.R
+\name{make_embed_markdown}
+\alias{make_embed_markdown}
+\title{Make Leanpub file that has embed webpage of a chapter}
+\usage{
+make_embed_markdown(
+  url,
+  chapt_title,
+  img_path,
+  output_dir = "manuscript",
+  verbose = TRUE
+)
+}
+\arguments{
+\item{url}{The url to the chapter that is to be embed}
+
+\item{chapt_name}{Title of chapter to be used as file name and printed on iframe}
+
+\item{img}{File path to image to use for poster}
+}
+\value{
+A
+}
+\description{
+Make Leanpub file that has embed webpage of a chapter
+}
diff --git a/man/set_up_leanpub.Rd b/man/set_up_leanpub.Rd
new file mode 100644
index 0000000..9d78606
--- /dev/null
+++ b/man/set_up_leanpub.Rd
@@ -0,0 +1,50 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/set_up.R
+\name{set_up_leanpub}
+\alias{set_up_leanpub}
+\title{Set up Manuscript folder for Leanpub publishing}
+\usage{
+set_up_leanpub(
+  path = ".",
+  clean_up = FALSE,
+  render = TRUE,
+  output_dir = "manuscript",
+  make_book_txt = FALSE,
+  quiz_dir = "quizzes",
+  run_quiz_checks = FALSE,
+  remove_resources_start = FALSE,
+  verbose = TRUE,
+  footer_text = NULL
+)
+}
+\arguments{
+\item{path}{path to the bookdown book, must have a `_bookdown.yml` file}
+
+\item{render}{if `TRUE`, then [bookdown::render_book()] will be run on each Rmd.}
+
+\item{output_dir}{output directory to put files.  It should likely be
+relative to path}
+
+\item{make_book_txt}{Should [ottr::bookdown_to_book_txt()] be run
+to create a `Book.txt` in the output directory?}
+
+\item{quiz_dir}{directory that contains the quiz .md files that should be
+checked and incorporated into the Book.txt file. If you don't have quizzes,
+set this to NULL}
+
+\item{run_quiz_checks}{TRUE/FALSE run quiz checks}
+
+\item{remove_resources_start}{remove the word `resources/` at the front
+of any image path.}
+
+\item{verbose}{print diagnostic messages}
+
+\item{footer_text}{Optionally can add a bit of text that will be added to the
+end of each file before the references section.}
+}
+\value{
+A list of output files and diagnostics
+}
+\description{
+Set up Manuscript folder for Leanpub publishing
+}

From 8c089d1682e84329cbae0483c543593bc3824f4c Mon Sep 17 00:00:00 2001
From: Candace Savonen <cansav09@gmail.com>
Date: Fri, 4 Feb 2022 11:54:34 -0500
Subject: [PATCH 04/11] Update some vignette things

---
 R/bookdown_to_leanpub.R                 | 28 ++++++++++++++++---------
 inst/extdata/{ => quizzes}/quiz_bad.md  |  0
 inst/extdata/{ => quizzes}/quiz_good.md |  0
 man/bookdown_to_embed_leanpub.Rd        |  8 +++----
 man/bookdown_to_leanpub.Rd              |  3 ++-
 5 files changed, 24 insertions(+), 15 deletions(-)
 rename inst/extdata/{ => quizzes}/quiz_bad.md (100%)
 rename inst/extdata/{ => quizzes}/quiz_good.md (100%)

diff --git a/R/bookdown_to_leanpub.R b/R/bookdown_to_leanpub.R
index 3192aac..d310532 100644
--- a/R/bookdown_to_leanpub.R
+++ b/R/bookdown_to_leanpub.R
@@ -28,9 +28,18 @@ bookdown_to_leanpub <- function(path = ".",
                                 run_quiz_checks = FALSE,
                                 remove_resources_start = FALSE,
                                 verbose = TRUE,
-                                footer_text = NULL) {
-  set_up_leanpub(...)
+                                footer_text = NULL,
+                                ...) {
+  set_up_leanpub()
 
+  # Establish path
+  path <- bookdown_path(path)
+  
+  rmd_regex <- "[.][R|r]md$"
+  
+  # Extract the names of the Rmd files (the chapters)
+  rmd_files <- bookdown_rmd_files(path = path)
+  
   bib_files <- list.files(pattern = "[.]bib$")
   if (length(bib_files) > 0) {
     pandoc_args <- paste0("--bibliography=", path.expand(normalizePath(bib_files)))
@@ -132,13 +141,11 @@ bookdown_to_leanpub <- function(path = ".",
 #' @return A list of output files and diagnostics
 #' @export
 #' 
-#' @examples
-#' \dontrun{
-#' 
-#' ottr::bookdown_to_embed_leanpub(base_url = ")
+#' @examples \dontrun{
 #' 
-#' ottr::bookdown_to_embed_leanpub(chapt_img_key = "chapt)
+#' ottr::bookdown_to_embed_leanpub(base_url = "")
 #' 
+#' ottr::bookdown_to_embed_leanpub(chapt_img_key = "chapter_urls.tsv")
 #' 
 #' }
 bookdown_to_embed_leanpub <- function(path = ".",
@@ -153,8 +160,9 @@ bookdown_to_embed_leanpub <- function(path = ".",
                                       run_quiz_checks = FALSE,
                                       remove_resources_start = FALSE,
                                       verbose = TRUE,
-                                      footer_text = NULL) {
-  set_up_leanpub(...)
+                                      footer_text = NULL, 
+                                      ...) {
+  set_up_leanpub()
 
   if (!is.null(chapt_img_key)) {
     message(paste("Reading in a chapt_img_key TSV file:", chapt_img_key))
@@ -181,7 +189,7 @@ bookdown_to_embed_leanpub <- function(path = ".",
     }
     
     # Download default image
-    chapt_df$img_path <- leanbuild::gs_png_download(url = default_img, output_dir = img_dir, overwrite = TRUE)
+    chapt_df$img_path <- gs_png_download(url = default_img, output_dir = img_dir, overwrite = TRUE)
   }
   
   md_output_files <- chapt_df %>% 
diff --git a/inst/extdata/quiz_bad.md b/inst/extdata/quizzes/quiz_bad.md
similarity index 100%
rename from inst/extdata/quiz_bad.md
rename to inst/extdata/quizzes/quiz_bad.md
diff --git a/inst/extdata/quiz_good.md b/inst/extdata/quizzes/quiz_good.md
similarity index 100%
rename from inst/extdata/quiz_good.md
rename to inst/extdata/quizzes/quiz_good.md
diff --git a/man/bookdown_to_embed_leanpub.Rd b/man/bookdown_to_embed_leanpub.Rd
index 179f7bc..3923782 100644
--- a/man/bookdown_to_embed_leanpub.Rd
+++ b/man/bookdown_to_embed_leanpub.Rd
@@ -17,7 +17,8 @@ bookdown_to_embed_leanpub(
   run_quiz_checks = FALSE,
   remove_resources_start = FALSE,
   verbose = TRUE,
-  footer_text = NULL
+  footer_text = NULL,
+  ...
 )
 }
 \arguments{
@@ -67,10 +68,9 @@ Convert Bookdown to Embed version of Leanpub
 \examples{
 \dontrun{
 
-ottr::bookdown_to_embed_leanpub(base_url = ")
-
-ottr::bookdown_to_embed_leanpub(chapt_img_key = "chapt)
+ottr::bookdown_to_embed_leanpub(base_url = "")
 
+ottr::bookdown_to_embed_leanpub(chapt_img_key = "chapter_urls.tsv")
 
 }
 }
diff --git a/man/bookdown_to_leanpub.Rd b/man/bookdown_to_leanpub.Rd
index 552cf8c..de1c59e 100644
--- a/man/bookdown_to_leanpub.Rd
+++ b/man/bookdown_to_leanpub.Rd
@@ -13,7 +13,8 @@ bookdown_to_leanpub(
   run_quiz_checks = FALSE,
   remove_resources_start = FALSE,
   verbose = TRUE,
-  footer_text = NULL
+  footer_text = NULL,
+  ...
 )
 }
 \arguments{

From f0d4dd43c9b77a3a16d33847ec3e0bb98ea4415c Mon Sep 17 00:00:00 2001
From: Candace Savonen <cansav09@gmail.com>
Date: Fri, 4 Feb 2022 12:09:32 -0500
Subject: [PATCH 05/11] Update documentation

---
 DESCRIPTION                      |  3 ++-
 R/bookdown_to_leanpub.R          | 17 ++++++++++-------
 R/set_up.R                       |  2 ++
 man/bookdown_to_embed_leanpub.Rd |  6 +++---
 man/make_embed_markdown.Rd       | 11 ++++++++---
 man/set_up_leanpub.Rd            |  3 +++
 6 files changed, 28 insertions(+), 14 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 796ecda..36e1207 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -37,7 +37,8 @@ Imports: googledrive,
     yaml,
     stringr,
     knitr (>= 1.33),
-    qpdf
+    qpdf,
+    purrr
 Suggests:
     remotes,
     testthat
diff --git a/R/bookdown_to_leanpub.R b/R/bookdown_to_leanpub.R
index d310532..960470b 100644
--- a/R/bookdown_to_leanpub.R
+++ b/R/bookdown_to_leanpub.R
@@ -120,7 +120,7 @@ bookdown_to_leanpub <- function(path = ".",
 #' If no chapter title column supplied, the basename of the url will be used,
 #' If no image column supplied, default image used.
 #' @param bookdown_index The file path of the rendered bookdown index.html file
-#' @param s The base url of where the chapters are published -- the url to provide to the iframe in Leanpub
+#' @param base_url The base url of where the chapters are published -- the url to provide to the iframe in Leanpub
 #' e.g. https://jhudatascience.org/OTTR_Template/coursera
 #' @param default_img A google slide link to the default image to be used for all chapters
 #' @param output_dir output directory to put files.  It should likely be
@@ -314,9 +314,12 @@ bookdown_to_book_txt <- function(path = ".",
 #' Make Leanpub file that has embed webpage of a chapter
 #'
 #' @param url The url to the chapter that is to be embed
-#' @param chapt_name Title of chapter to be used as file name and printed on iframe
-#' @param img File path to image to use for poster
-#' @return A
+#' @param chapt_title Title of chapter to be used as file name and printed on iframe
+#' @param img_path File path to image to use for poster
+#' @param output_dir output directory to put files.  It should likely be
+#' relative to path
+#' @param verbose print diagnostic messages
+#' @return A markdown file with an iframe of the provided chapter
 #'
 #' @export
 make_embed_markdown <- function(url,
@@ -326,7 +329,7 @@ make_embed_markdown <- function(url,
                                 verbose = TRUE) {
   # Arguments:
   #   url: The url to the chapter
-  #   chapt_name: The title of the chapter to be used as a header
+  #   chapt_title: The title of the chapter to be used as a header
   #   img: file path to the image to be used in the preview
   #
   # Returns: A markdown document ready for Leanpub and the image copied to the manuscript folder
@@ -386,10 +389,10 @@ get_chapters <- function(bookdown_index = file.path("docs", "index.html"),
       dplyr::bind_rows() %>%
       dplyr::rename_with(~ gsub("-", "_", .x, fixed = TRUE)) %>%
       dplyr::mutate(
-        chapt_name = stringr::word(rvest::html_text(nodes), sep = "\n", 1),
+        chapt_title = stringr::word(rvest::html_text(nodes), sep = "\n", 1),
         url = paste0(base_url, data_path)
       ) %>%
-      dplyr::select(url, chapt_title = chapt_name) %>%
+      dplyr::select(url, chapt_title) %>%
       as.data.frame() %>%
       dplyr::distinct(url, .keep_all = TRUE)
   } else {
diff --git a/R/set_up.R b/R/set_up.R
index 6e285dc..d288e1a 100644
--- a/R/set_up.R
+++ b/R/set_up.R
@@ -167,6 +167,8 @@ copy_quizzes <- function(quiz_dir = "quizzes", output_dir = "manuscript") {
 #' @param path path to the bookdown book, must have a `_bookdown.yml` file
 #' @param output_dir output directory to put files.  It should likely be
 #' relative to path
+#' @param clean_up TRUE/FALSE the old output directory should be deleted and 
+#' everything created fresh.
 #' @param render if `TRUE`, then [bookdown::render_book()] will be run on each Rmd.
 #' @param verbose print diagnostic messages
 #' @param remove_resources_start remove the word `resources/` at the front
diff --git a/man/bookdown_to_embed_leanpub.Rd b/man/bookdown_to_embed_leanpub.Rd
index 3923782..ae6b284 100644
--- a/man/bookdown_to_embed_leanpub.Rd
+++ b/man/bookdown_to_embed_leanpub.Rd
@@ -32,6 +32,9 @@ If no image column supplied, default image used.}
 
 \item{bookdown_index}{The file path of the rendered bookdown index.html file}
 
+\item{base_url}{The base url of where the chapters are published -- the url to provide to the iframe in Leanpub
+e.g. https://jhudatascience.org/OTTR_Template/coursera}
+
 \item{default_img}{A google slide link to the default image to be used for all chapters}
 
 \item{render}{if `TRUE`, then [bookdown::render_book()] will be run on each Rmd.}
@@ -55,9 +58,6 @@ of any image path.}
 
 \item{footer_text}{Optionally can add a bit of text that will be added to the
 end of each file before the references section.}
-
-\item{s}{The base url of where the chapters are published -- the url to provide to the iframe in Leanpub
-e.g. https://jhudatascience.org/OTTR_Template/coursera}
 }
 \value{
 A list of output files and diagnostics
diff --git a/man/make_embed_markdown.Rd b/man/make_embed_markdown.Rd
index eff5f2b..b9e6cdb 100644
--- a/man/make_embed_markdown.Rd
+++ b/man/make_embed_markdown.Rd
@@ -15,12 +15,17 @@ make_embed_markdown(
 \arguments{
 \item{url}{The url to the chapter that is to be embed}
 
-\item{chapt_name}{Title of chapter to be used as file name and printed on iframe}
+\item{chapt_title}{Title of chapter to be used as file name and printed on iframe}
 
-\item{img}{File path to image to use for poster}
+\item{img_path}{File path to image to use for poster}
+
+\item{output_dir}{output directory to put files.  It should likely be
+relative to path}
+
+\item{verbose}{print diagnostic messages}
 }
 \value{
-A
+A markdown file with an iframe of the provided chapter
 }
 \description{
 Make Leanpub file that has embed webpage of a chapter
diff --git a/man/set_up_leanpub.Rd b/man/set_up_leanpub.Rd
index 9d78606..d64d819 100644
--- a/man/set_up_leanpub.Rd
+++ b/man/set_up_leanpub.Rd
@@ -20,6 +20,9 @@ set_up_leanpub(
 \arguments{
 \item{path}{path to the bookdown book, must have a `_bookdown.yml` file}
 
+\item{clean_up}{TRUE/FALSE the old output directory should be deleted and 
+everything created fresh.}
+
 \item{render}{if `TRUE`, then [bookdown::render_book()] will be run on each Rmd.}
 
 \item{output_dir}{output directory to put files.  It should likely be

From 47887c12e31e2ac34f63f169df0a5b4ee05bf515 Mon Sep 17 00:00:00 2001
From: Candace Savonen <cansav09@gmail.com>
Date: Fri, 4 Feb 2022 12:12:46 -0500
Subject: [PATCH 06/11] Update docs and make some stops warnings instead

---
 R/aaa_utils.R | 2 +-
 R/quiz.R      | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/R/aaa_utils.R b/R/aaa_utils.R
index a2730e1..5031b48 100644
--- a/R/aaa_utils.R
+++ b/R/aaa_utils.R
@@ -1,7 +1,7 @@
 
 utils::globalVariables(c(
   "num", "quiz_dir", "type_url", "file_name", "trimmed", "quiz",
-  "quiz_path", "type", "q_num", "verbose"
+  "quiz_path", "type", "q_num", "verbose", "chapt_title", "data_path"
 ))
 
 # get script path and number of paragraphs
diff --git a/R/quiz.R b/R/quiz.R
index c1d770b..598784e 100644
--- a/R/quiz.R
+++ b/R/quiz.R
@@ -245,10 +245,10 @@ extract_quiz <- function(quiz_lines) {
   end <- grep("^\\s*\\{\\s*/\\s*quiz", quiz_lines)
 
   if (length(start) == 0) {
-    stop("Quiz should start with a { } tag and end with {\\quiz}.")
+    warning("Quiz should start with a { } tag and end with {\\quiz}.")
   }
   if (length(end) == 0) {
-    stop("Could not find end tag of quiz; should end with: {\\quiz}.")
+    warning("Could not find end tag of quiz; should end with: {\\quiz}.")
   }
   # Extract main quiz tag
   quiz_tag <- quiz_lines[start]

From 0f655805959a4ab0c2af27c288da81405cde3d19 Mon Sep 17 00:00:00 2001
From: Candace Savonen <cansav09@gmail.com>
Date: Fri, 4 Feb 2022 12:23:17 -0500
Subject: [PATCH 07/11] Edits

---
 .Rbuildignore                 | 8 ++++++++
 R/bookdown_to_leanpub.R       | 6 ++----
 vignettes/getting-started.Rmd | 4 ++--
 3 files changed, 12 insertions(+), 6 deletions(-)

diff --git a/.Rbuildignore b/.Rbuildignore
index ab9ac70..d2a75c4 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -20,3 +20,11 @@ vignettes/.httr-oauth$
 ^run_test\.R$
 ^\.github$
 ^pkgdown$
+^vignettes/01-intro.Rmd$
+^vignettes/02-example-chapter.Rmd$
+^vignettes/_bookdown.yml$
+^vignettes/index.Rmd$
+^vignettes/quizzes$
+^vignettes/references.bib$
+^vignettes/toc_close.css$
+^package_bundles/$
diff --git a/R/bookdown_to_leanpub.R b/R/bookdown_to_leanpub.R
index 960470b..6b3130a 100644
--- a/R/bookdown_to_leanpub.R
+++ b/R/bookdown_to_leanpub.R
@@ -28,8 +28,7 @@ bookdown_to_leanpub <- function(path = ".",
                                 run_quiz_checks = FALSE,
                                 remove_resources_start = FALSE,
                                 verbose = TRUE,
-                                footer_text = NULL,
-                                ...) {
+                                footer_text = NULL) {
   set_up_leanpub()
 
   # Establish path
@@ -160,8 +159,7 @@ bookdown_to_embed_leanpub <- function(path = ".",
                                       run_quiz_checks = FALSE,
                                       remove_resources_start = FALSE,
                                       verbose = TRUE,
-                                      footer_text = NULL, 
-                                      ...) {
+                                      footer_text = NULL) {
   set_up_leanpub()
 
   if (!is.null(chapt_img_key)) {
diff --git a/vignettes/getting-started.Rmd b/vignettes/getting-started.Rmd
index 39b674e..1c3e4be 100644
--- a/vignettes/getting-started.Rmd
+++ b/vignettes/getting-started.Rmd
@@ -223,8 +223,8 @@ If there is text you would like added to the end of each chapter (like a link to
 survey_link <- "Please provide any feedback you have in [this survey](www.some_link.org)"
 
 # Supply the footer text in the main function
-ottr::bookdown_to_leanpub(make_book_txt = TRUE, 
-                               footer_text = survey_link)
+ottr::bookdown_to_leanpub(make_book_txt = TRUE,
+                          footer_text = survey_link)
 ```
 
 ### Wrapping up 

From 2873ab4d06cb76de47f254959e8698f3fd522f10 Mon Sep 17 00:00:00 2001
From: Candace Savonen <cansav09@gmail.com>
Date: Fri, 4 Feb 2022 12:29:13 -0500
Subject: [PATCH 08/11] Update documentation

---
 man/bookdown_to_embed_leanpub.Rd | 3 +--
 man/bookdown_to_leanpub.Rd       | 3 +--
 2 files changed, 2 insertions(+), 4 deletions(-)

diff --git a/man/bookdown_to_embed_leanpub.Rd b/man/bookdown_to_embed_leanpub.Rd
index ae6b284..d355c26 100644
--- a/man/bookdown_to_embed_leanpub.Rd
+++ b/man/bookdown_to_embed_leanpub.Rd
@@ -17,8 +17,7 @@ bookdown_to_embed_leanpub(
   run_quiz_checks = FALSE,
   remove_resources_start = FALSE,
   verbose = TRUE,
-  footer_text = NULL,
-  ...
+  footer_text = NULL
 )
 }
 \arguments{
diff --git a/man/bookdown_to_leanpub.Rd b/man/bookdown_to_leanpub.Rd
index de1c59e..552cf8c 100644
--- a/man/bookdown_to_leanpub.Rd
+++ b/man/bookdown_to_leanpub.Rd
@@ -13,8 +13,7 @@ bookdown_to_leanpub(
   run_quiz_checks = FALSE,
   remove_resources_start = FALSE,
   verbose = TRUE,
-  footer_text = NULL,
-  ...
+  footer_text = NULL
 )
 }
 \arguments{

From 3e3085d69a363a60f106ba1d7f6e14db40d6f8b1 Mon Sep 17 00:00:00 2001
From: Candace Savonen <cansav09@gmail.com>
Date: Fri, 4 Feb 2022 12:36:19 -0500
Subject: [PATCH 09/11] Move some dependencies to suggestions

---
 DESCRIPTION | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 36e1207..489e2ce 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -22,8 +22,6 @@ Imports: googledrive,
     httr,
     fs,
     jsonlite,
-    utils,
-    tibble,
     rmarkdown (>= 2.10),
     xml2,
     rvest,
@@ -41,7 +39,9 @@ Imports: googledrive,
     purrr
 Suggests:
     remotes,
-    testthat
+    testthat,
+    tibble,
+    utils
 Encoding: UTF-8
 LazyData: true
 Remotes: jhudsl/text2speech,

From c084aad6f337623d28615675217fbda447485a10 Mon Sep 17 00:00:00 2001
From: Candace Savonen <cansav09@gmail.com>
Date: Fri, 4 Feb 2022 12:44:28 -0500
Subject: [PATCH 10/11] Make another stop -> warning

---
 R/quiz.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/quiz.R b/R/quiz.R
index 598784e..8563b6d 100644
--- a/R/quiz.R
+++ b/R/quiz.R
@@ -452,7 +452,7 @@ check_question <- function(question_df, quiz_name = NA, verbose = TRUE) {
 
   # Get prompt if its there
   if (!any(grepl("^\\? ", question_df$original))) {
-    stop("Could not find prompt for question. Question prompts start line with '?'")
+    warning("Could not find prompt for question. Question prompts start line with '?'")
   }
   prompt <- question_df$original[question_df$type == "prompt"]
 

From 5dcee8a82e65a3f94f3269a3cb244e826b9e30aa Mon Sep 17 00:00:00 2001
From: Candace Savonen <cansav09@gmail.com>
Date: Fri, 4 Feb 2022 12:47:45 -0500
Subject: [PATCH 11/11] Don't fail on warning

---
 .github/workflows/R-CMD-check.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index fb7b370..d894284 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.github/workflows/R-CMD-check.yaml
@@ -75,7 +75,7 @@ jobs:
           _R_CHECK_CRAN_INCOMING_REMOTE_: false
         run: |
           options(crayon.enabled = TRUE)
-          rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
+          rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), check_dir = "check")
         shell: Rscript {0}
 
       - name: Upload check results