Merge pull request #144 from jhudsl/cansavvy/reorg

Reorganize the files and functions here

.github/workflows/R-CMD-check.yaml

@@ -39,7 +39,6 @@ jobs:
           GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
       - name: Check testthat
-        if: runner.os != 'Windows'
         id: check_check
         run: |
             error_num=$(Rscript --vanilla '.github/workflows/check_testthat.R')

.github/workflows/check_testthat.R

@@ -8,21 +8,38 @@ library(magrittr)
 # Find .git root directory
 root_dir <- rprojroot::find_root(rprojroot::has_dir(".git"))
 
+# Read in the testthat results
 out_file <- list.files(pattern = "testthat.Rout$|Rout.fail$", file.path(root_dir, "check"),
  recursive = TRUE, full.names = TRUE)
 
-check_content <- readLines(out_file)
-test_result <- grep("\\[ FAIL", check_content, value = TRUE)[1]
-test_result <- unlist(strsplit(test_result, "\\||\\[|\\]"))
+# Extract testhat results
+testthat_check_content <- readLines(out_file)
+testthat_result <- grep("\\[ FAIL", testthat_check_content, value = TRUE)[1]
+testthat_result <- unlist(strsplit(testthat_result, "\\||\\[|\\]"))
+
+# Read in standard check results
+check_content <- readLines(file.path(root_dir, "check", "ottrpal.Rcheck", "00check.log"))
+
+# Extract standard check results
+check_result <- grep("Status\\:", check_content, value = TRUE)
+check_result <- unlist(strsplit(check_result, ","))
+check_result <- stringr::str_remove(check_result, "Status:| ")
 
 # Format the data into a dataframe
-test_result_df <- data.frame(result = trimws(test_result)) %>%
+testthat_result_df <- data.frame(result = trimws(testthat_result)) %>%
   dplyr::filter(result != "") %>%
   tidyr::separate(result, sep = " ", into = c("test_name", "num")) %>%
   dplyr::mutate(num = as.numeric(num))
 
-fail_num <- test_result_df %>%
-  dplyr::filter(test_name %in% c("FAIL", "WARN")) %>%
+# Do the same for the check results
+check_result_df <- data.frame(result = trimws(check_result)) %>%
+  tidyr::separate(result, sep = " ", into = c("num", "test_name")) %>%
+  dplyr::mutate(num = as.numeric(num)) %>%
+  dplyr::select("test_name", "num")
+
+# We only want warnings or errors or fails
+fail_num <- dplyr::bind_rows(check_result_df, testthat_result_df) %>%
+  dplyr::filter(test_name %in% c("FAIL", "WARN", "WARNINGs", "ERROR")) %>%
   dplyr::summarize(total = sum(num))
 
 fail_num <- as.character(fail_num$total)

DESCRIPTION

@@ -23,7 +23,6 @@ Imports:
     curl,
     dplyr,
     fs,
-    glue,
     httr,
     jsonlite,
     knitr (>= 1.33),

NAMESPACE

@@ -4,12 +4,6 @@ export("%>%")
 export(auth_from_secret)
 export(authorize)
 export(bad_quiz_path)
-export(bookdown_destination)
-export(bookdown_file)
-export(bookdown_path)
-export(bookdown_rmd_files)
-export(bookdown_to_book_txt)
-export(bookdown_to_embed_leanpub)
 export(check_all_questions)
 export(check_question)
 export(check_quiz)
@@ -18,44 +12,40 @@ export(check_quiz_question_attributes)
 export(check_quizzes)
 export(convert_coursera_quizzes)
 export(convert_quiz)
-export(convert_utube_link)
+export(course_path)
+export(course_to_book_txt)
 export(download_ottr_template)
-export(example_repo_cleanup)
-export(example_repo_setup)
 export(extract_meta)
 export(extract_object_id)
 export(extract_quiz)
-export(get_bookdown_spec)
 export(get_chapters)
 export(get_gs_pptx)
 export(get_image_from_slide)
 export(get_image_link_from_slide)
 export(get_object_id_notes)
 export(get_slide_id)
 export(get_slide_page)
+export(get_yaml_spec)
 export(good_quiz_path)
 export(gs_id_from_slide)
 export(gs_png_download)
 export(gs_png_url)
 export(include_slide)
-export(leanpub_check)
 export(make_embed_markdown)
+export(output_destination)
 export(parse_q_tag)
 export(parse_quiz)
 export(parse_quiz_df)
 export(pptx_notes)
 export(pptx_slide_note_df)
 export(pptx_slide_text_df)
-export(remove_yaml_header)
+export(qrmd_files)
 export(render_without_toc)
-export(replace_html)
-export(replace_single_html)
 export(set_knitr_image_path)
 export(set_up_leanpub)
-export(simple_references)
 export(unzip_pptx)
+export(website_to_embed_leanpub)
 export(xml_notes)
-importFrom(fs,dir_copy)
 importFrom(httr,GET)
 importFrom(httr,accept_json)
 importFrom(httr,config)

R/coursera_and_leanpub.R

@@ -197,9 +197,10 @@ convert_coursera_quizzes <- function(input_quiz_dir = "quizzes",
   )
 }
 
-#' Create TOC-less Bookdown for use in Coursera
+#' Create TOC-less course website for use in Coursera or Leanpub
 #'
-#' Create a version of Leanpub that does not have a TOC and has quizzes in the Coursera yaml format. Requires Bookdown output files including "assets", "resources", and "libs".
+#' Create a version of the course that does not have a TOC and has quizzes in the Coursera yaml format.
+#' This is only needed to be used on Bookdown courses. Quarto has a simple command for this. 
 #'
 #' @param output_dir A folder (existing or not) that the TOC-less Bookdown for Coursera files should be saved. By default is file.path("docs", "coursera")
 #' @param output_yaml A output.yml file to be provided to bookdown. By default is "_output.yml"
@@ -220,8 +221,8 @@ render_without_toc <- function(output_dir = file.path("docs", "no_toc"),
                                input_quiz_dir = "quizzes",
                                output_quiz_dir = "coursera_quizzes",
                                verbose = TRUE) {
-  # Find root directory by finding `_bookdown.yml` file
-  root_dir <- bookdown_path()
+  # Find root directory by finding `.git` folder
+  root_dir <- course_path()
 
   # Output files:
   output_dir <- file.path(root_dir, output_dir)

R/data.R

@@ -47,6 +47,38 @@ download_ottr_template <- function(dir = "inst/extdata", type = "rmd") {
   return(output_dir)
 }
 
+
+#' Path to good example quiz
+#'
+#' @export
+#' @return The file path to an example good quiz included in the package that should pass the quiz checks.
+#'
+good_quiz_path <- function() {
+  list.files(
+    pattern = "quiz_good.md$",
+    recursive = TRUE,
+    system.file("extdata", package = "ottrpal"),
+    full.names = TRUE
+  )
+}
+
+#' Path to bad example quiz
+#'
+#' @export
+#' @return The file path to an example bad quiz included in the package that will fail the quiz checks.
+#'
+#' @examples
+#'
+#' quiz_path <- bad_quiz_path()
+bad_quiz_path <- function() {
+  list.files(
+    pattern = "quiz_bad.md$",
+    recursive = TRUE,
+    system.file("extdata", package = "ottrpal"),
+    full.names = TRUE
+  )
+}
+
 #' Get file path to an key encryption RDS
 key_encrypt_creds_path <- function() {
   list.files(

R/bookdown_to_leanpub.R → R/iframe_leanpub.R

@@ -1,6 +1,6 @@
-#' Convert Bookdown to Leanpub
+#' Convert Website Course to Leanpub
 #'
-#' @param path path to the bookdown book, must have a `_bookdown.yml` file
+#' @param path path to the bookdown or quarto course repository, must have a `_bookdown.yml` or `_quarto.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.
@@ -17,13 +17,11 @@
 #' @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 [ottrpal::bookdown_to_book_txt()] be run
+#' @param make_book_txt Should [ottrpal::course_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 clean_up TRUE/FALSE the old output directory should be deleted and
-#' everything created fresh.
 #' @param footer_text Optionally can add a bit of text that will be added to the
 #' end of each file before the references section.
 #'
@@ -32,19 +30,18 @@
 #'
 #' @examples \dontrun{
 #'
-#' ottrpal::bookdown_to_embed_leanpub(
+#' ottrpal::website_to_embed_leanpub(
 #'   base_url = "https://jhudatascience.org/OTTR_Template/",
 #'   make_book_txt = TRUE,
 #'   quiz_dir = NULL
 #' )
 #' }
-bookdown_to_embed_leanpub <- function(path = ".",
+website_to_embed_leanpub <- function(path = ".",
                                       chapt_img_key = NULL,
+                                      render = NULL,
                                       html_page = file.path(base_url, "index.html"),
                                       base_url = NULL,
-                                      clean_up = FALSE,
                                       default_img = NULL,
-                                      render = TRUE,
                                       output_dir = "manuscript",
                                       make_book_txt = FALSE,
                                       quiz_dir = "quizzes",
@@ -55,8 +52,6 @@ bookdown_to_embed_leanpub <- function(path = ".",
   # Run the set up
   set_up_leanpub(
     path = path,
-    embed = TRUE,
-    clean_up = clean_up,
     render = render,
     output_dir = output_dir,
     make_book_txt = make_book_txt,
@@ -110,10 +105,10 @@ bookdown_to_embed_leanpub <- function(path = ".",
   ####################### Book.txt creation ####################################
   out <- NULL
   if (make_book_txt) {
-    if (verbose) message("Running bookdown_to_book_txt")
+    if (verbose) message("Running course_to_book_txt")
     md_files <- basename(unlist(md_output_files))
 
-    bookdown_to_book_txt(
+    course_to_book_txt(
       md_files = md_files,
       output_dir = output_dir,
       quiz_dir = quiz_dir,
@@ -149,7 +144,7 @@ bookdown_to_embed_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
+#' @param path path to the bookdown or quarto course repository, must have a `_bookdown.yml` or `_quarto.yml` file
 #' @param md_files vector of file path of the md's to be included
 #' @param output_dir output directory to put files.  It should likely be
 #' relative to path
@@ -159,20 +154,20 @@ bookdown_to_embed_leanpub <- function(path = ".",
 #' @return A list of quiz and chapter files in order in a file called Book.txt -- How Leanpub wants it.
 #' @export
 #'
-bookdown_to_book_txt <- function(path = ".",
+course_to_book_txt <- function(path = ".",
                                  md_files = NULL,
                                  output_dir = "manuscript",
                                  quiz_dir = "quizzes",
                                  verbose = TRUE) {
   # If md_files are not specified, then try to get them
   if (is.null(md_files)) {
     # Establish path
-    path <- bookdown_path(path)
+    path <- course_path(path)
 
     rmd_regex <- "[.][R|r]md$"
 
     # Extract the names of the Rmd files (the chapters)
-    md_files <- bookdown_rmd_files(path = path)
+    md_files <- qrmd_files(path = path)
   }
 
   if (!is.null(quiz_dir)) {