From 090394d5ed03c1beab8ac66e9cfea7197128cacf Mon Sep 17 00:00:00 2001 From: Candace Savonen Date: Wed, 26 Jun 2024 16:02:27 -0400 Subject: [PATCH 01/17] reorg --- NAMESPACE | 14 +- R/coursera_and_leanpub.R | 4 +- R/data.R | 26 +++ R/example_data.R | 89 -------- R/{bookdown_to_leanpub.R => iframe_leanpub.R} | 17 +- R/leanpub_checks.R | 206 ------------------ R/remove_yaml.R | 51 ----- R/set_up.R | 39 ++-- R/simple_references.R | 80 ------- R/utils.R | 32 --- man/bad_quiz_path.Rd | 2 +- man/bookdown_file.Rd | 17 -- man/{bookdown_path.Rd => course_path.Rd} | 10 +- ...n_to_book_txt.Rd => course_to_book_txt.Rd} | 10 +- man/coursera.Rd | 4 +- man/example_repo_cleanup.Rd | 29 --- man/example_repo_setup.Rd | 24 -- man/get_bookdown_spec.Rd | 2 +- man/get_chapters.Rd | 6 +- man/good_quiz_path.Rd | 19 -- man/leanpub_check.Rd | 19 -- man/make_embed_markdown.Rd | 2 +- man/remove_yaml_header.Rd | 22 -- man/set_up_leanpub.Rd | 2 +- man/simple_references.Rd | 23 -- ...leanpub.Rd => website_to_embed_leanpub.Rd} | 19 +- 26 files changed, 77 insertions(+), 691 deletions(-) delete mode 100644 R/example_data.R rename R/{bookdown_to_leanpub.R => iframe_leanpub.R} (95%) delete mode 100644 R/leanpub_checks.R delete mode 100644 R/remove_yaml.R delete mode 100644 R/simple_references.R delete mode 100644 man/bookdown_file.Rd rename man/{bookdown_path.Rd => course_path.Rd} (67%) rename man/{bookdown_to_book_txt.Rd => course_to_book_txt.Rd} (76%) delete mode 100644 man/example_repo_cleanup.Rd delete mode 100644 man/example_repo_setup.Rd delete mode 100644 man/good_quiz_path.Rd delete mode 100644 man/leanpub_check.Rd delete mode 100644 man/remove_yaml_header.Rd delete mode 100644 man/simple_references.Rd rename man/{bookdown_to_embed_leanpub.Rd => website_to_embed_leanpub.Rd} (82%) diff --git a/NAMESPACE b/NAMESPACE index 6d54d6f..e63a04a 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -5,11 +5,7 @@ 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) @@ -19,9 +15,9 @@ 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) @@ -33,12 +29,10 @@ export(get_image_link_from_slide) export(get_object_id_notes) export(get_slide_id) export(get_slide_page) -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(parse_q_tag) export(parse_quiz) @@ -46,16 +40,14 @@ export(parse_quiz_df) export(pptx_notes) export(pptx_slide_note_df) export(pptx_slide_text_df) -export(remove_yaml_header) 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) diff --git a/R/coursera_and_leanpub.R b/R/coursera_and_leanpub.R index df478e8..32afae0 100644 --- a/R/coursera_and_leanpub.R +++ b/R/coursera_and_leanpub.R @@ -197,9 +197,9 @@ 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. #' #' @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" diff --git a/R/data.R b/R/data.R index 09b36e8..29e2342 100644 --- a/R/data.R +++ b/R/data.R @@ -73,3 +73,29 @@ encrypt_creds_user_path <- function() { full.names = TRUE ) } + +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 + ) +} diff --git a/R/example_data.R b/R/example_data.R deleted file mode 100644 index 1af693f..0000000 --- a/R/example_data.R +++ /dev/null @@ -1,89 +0,0 @@ -# C. Savonen 2021 - -#' Path to good example quiz -#' -#' @export -#' @return The file path to an example good quiz included in the package that will pass the quiz checks. -#' @examples -#' -#' quiz_path <- good_quiz_path() -#' -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 - ) -} - -#' Set up example repo files -#' -#' @param dest_dir The destination directory you would like the example repo files to be placed. By default is current directory. -#' @return Sets up example files that can be used to test 'ottrpal' functions. -#' -#' @export -#' -#' @importFrom fs dir_copy -#' @examples \dontrun{ -#' -#' # Run this to get the files we need -#' example_files <- ottrpal::example_repo_setup() -#' } -example_repo_setup <- function(dest_dir = tempdir()) { - bookdown_path <- list.files( - pattern = "_bookdown.yml$", - system.file("extdata/", package = "ottrpal"), - full.names = TRUE - ) - - # Copy over whole directory - fs::dir_copy(dirname(bookdown_path), dest_dir, overwrite = TRUE) - - copied_files <- list.files(dirname(bookdown_path), full.names = TRUE) - - return(copied_files) -} - -#' Clean up example repo files -#' -#' @param files_to_remove List of example files to delete. -#' @param verbose TRUE/FALSE would you like progress messages? -#' @return Will delete example files copied from [ottrpal::example_repo_setup()] function -#' @export -#' -#' @examples \dontrun{ -#' -#' # Run this to get the files we need -#' example_files <- ottrpal::example_repo_setup() -#' -#' # Run this to delete them -#' example_repo_cleanup(files_to_remove = basename(example_files)) -#' } -example_repo_cleanup <- function(files_to_remove, verbose = FALSE) { - message("Cleaning up and removing example repo files") - - lapply(files_to_remove, function(file2remove, verbose = verbose) { - if (file.exists(file2remove)) { - message(paste0("Removing: ", file2remove)) - file.remove(file2remove) - } - }) -} diff --git a/R/bookdown_to_leanpub.R b/R/iframe_leanpub.R similarity index 95% rename from R/bookdown_to_leanpub.R rename to R/iframe_leanpub.R index 4ae7a95..a5215fb 100644 --- a/R/bookdown_to_leanpub.R +++ b/R/iframe_leanpub.R @@ -1,12 +1,11 @@ -#' 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` file or #' @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 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 #' @param default_img A google slide link to the default image to be used for all chapters @@ -32,15 +31,14 @@ #' #' @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, - bookdown_index = file.path(base_url, "index.html"), base_url = NULL, clean_up = FALSE, default_img = NULL, @@ -148,7 +146,7 @@ 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` file or #' @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 @@ -158,7 +156,7 @@ 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", @@ -166,7 +164,7 @@ bookdown_to_book_txt <- function(path = ".", # 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$" @@ -293,7 +291,6 @@ make_embed_markdown <- function(url, #' 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 #' diff --git a/R/leanpub_checks.R b/R/leanpub_checks.R deleted file mode 100644 index 6f32e1a..0000000 --- a/R/leanpub_checks.R +++ /dev/null @@ -1,206 +0,0 @@ -#' Check Leanpub Course or Book -#' -#' @param path path to the Leanpub book/course -#' @param verbose print diagnostic messages -#' -#' @return A list of output files and diagnostics -#' @export -#' -leanpub_check <- function(path = ".", - verbose = TRUE) { - if (verbose) { - message("Checking the Book.txt files") - } - check_book_txt(path = path) - extra_book_result <- check_extra_md_files(path = path) - - if (verbose) { - message("Checking if HTML is present") - } - html_result <- full_html_check(path = path) - attribute_result <- full_attribute_check(path = path) - - files <- get_md_files(path) - - L <- list( - extra_book_result = extra_book_result, - html_result = html_result, - attribute_result = attribute_result - ) - return(L) -} - -check_book_txt <- function(path = ".") { - file <- file.path(path, "Book.txt") - # if Book.txt not there, fail - stopifnot(file.exists(file)) - x <- readLines(file, warn = FALSE) - files <- file.path(path, x) - fe <- file.exists(files) - if (!all(fe)) { - msg <- paste(x[fe], collapse = ", ") - msg <- paste0("Book.txt has files specified, but missing: ", msg) - stop(msg) - } - return(NULL) -} -get_md_files <- function(path) { - files <- list.files(pattern = ".md$", ignore.case = TRUE, path = path) - files -} - -check_extra_md_files <- function(path = ".") { - files <- get_md_files(path) - bn <- basename(files) - file <- file.path(path, "Book.txt") - # if Book.txt not there, fail - stopifnot(file.exists(file)) - x <- readLines(file, warn = FALSE) - sd <- setdiff(files, x) - if (length(sd) > 0) { - sd <- paste(sd, collapse = ", ") - warning( - "Markdown files exist in path but are not in Book.txt, may be left out ", - sd - ) - return(FALSE) - } - return(FALSE) -} - -full_html_check <- function(path = ".") { - files <- get_md_files(path) - out <- lapply(files, check_html) - names(out) <- basename(files) - html_result <- any(sapply(out, function(x) x$result)) - if (any(html_result)) { - tag_list <- mapply(function(x, name) { - if (!x$result) { - return(NULL) - } - paste0("file ", name, ": ", paste(x$tags_found, collapse = ", ")) - }, SIMPLIFY = FALSE) - tag_list <- c(unlist(tag_list)) - tag_list <- paste(tag_list, collapse = "\n\n") - message(tag_list) - warning(tag_list) - return(FALSE) - } - return(TRUE) -} - -check_html <- function(x) { - if (length(x) == 1 && file.exists(x)) { - x <- readLines(x, warn = FALSE) - } - # taken from dput(names(shiny::tags)) - tags_to_check <- c( - "a", "abbr", "address", "animate", "animateMotion", "animateTransform", - "area", "article", "aside", "audio", "b", "base", "bdi", "bdo", - "blockquote", "body", "br", "button", "canvas", "caption", "circle", - "cite", "clipPath", "code", "col", "colgroup", "color-profile", - "command", "data", "datalist", "dd", "defs", "del", "desc", "details", - "dfn", "dialog", "discard", "div", "dl", "dt", "ellipse", "em", - "embed", "eventsource", "feBlend", "feColorMatrix", "feComponentTransfer", - "feComposite", "feConvolveMatrix", "feDiffuseLighting", "feDisplacementMap", - "feDistantLight", "feDropShadow", "feFlood", "feFuncA", "feFuncB", - "feFuncG", "feFuncR", "feGaussianBlur", "feImage", "feMerge", - "feMergeNode", "feMorphology", "feOffset", "fePointLight", "feSpecularLighting", - "feSpotLight", "feTile", "feTurbulence", "fieldset", "figcaption", - "figure", "filter", "footer", "foreignObject", "form", "g", "h1", - "h2", "h3", "h4", "h5", "h6", "hatch", "hatchpath", "head", "header", - "hgroup", "hr", "html", "i", "iframe", "image", "img", "input", - "ins", "kbd", "keygen", "label", "legend", "li", "line", "linearGradient", - "link", "main", "map", "mark", "marker", "mask", "menu", "meta", - "metadata", "meter", "mpath", "nav", "noscript", "object", "ol", - "optgroup", "option", "output", "p", "param", "path", "pattern", - "picture", "polygon", "polyline", "pre", "progress", "q", "radialGradient", - "rb", "rect", "rp", "rt", "rtc", "ruby", "s", "samp", "script", - "section", "select", "set", "slot", "small", "solidcolor", "source", - "span", "stop", "strong", "style", "sub", "summary", "sup", "svg", - "switch", "symbol", "table", "tbody", "td", "template", "text", - "textarea", "textPath", "tfoot", "th", "thead", "time", "title", - "tr", "track", "tspan", "u", "ul", "use", "var", "video", "view", - "wbr" - ) - agrepl <- function(...) { - any(grepl(...)) - } - start_strings <- paste("<\\s*", tags_to_check, ".*>") - start_res <- sapply(start_strings, function(pattern) { - agrepl(x = x, pattern = pattern) - }) - end_strings <- paste("<\\s*/", tags_to_check, ".*>") - end_res <- sapply(start_strings, function(pattern) { - agrepl(x = x, pattern = pattern) - }) - res <- start_res | end_res - tag_df <- tibble::tibble( - tag = tags_to_check, - start_present = start_res, - end_present = end_res, - present = res - ) - L <- list( - result = any(res), - tag_data = tag_df - ) - if (any(res)) { - L$tags_found <- tag_df$tag[tag_df$present] - } - L -} - -is_html_present <- function(x) { - out <- check_html(x) - out$result -} - - - -make_sure_attributes_above <- function(x) { - if (length(x) == 1 && file.exists(x)) { - x <- readLines(x, warn = FALSE) - } - index <- lag_attribute <- lag_trimmed <- trimmed <- link <- link_index <- NULL - rm(list = c( - "link_index", "link", "trimmed", "lag_trimmed", - "lag_attribute", "index" - )) - df <- tibble::tibble( - x = x, - index = 1:length(x), - trimmed = trimws(x) - ) %>% - dplyr::mutate( - link = grepl(trimmed, pattern = "^!\\s*\\[.*\\]\\s*\\("), - attributes = grepl(pattern = "^\\{", trimmed), - lag_trimmed = dplyr::lag(trimmed, n = 1), - lag_attribute = grepl(pattern = "^\\{", lag_trimmed) - ) - if (!any(df$link)) { - return(TRUE) - } - bad <- df %>% - dplyr::filter(link & !lag_attribute) - if (nrow(bad) > 0) { - bad_lines <- df %>% - dplyr::filter(index %in% c(bad$index, bad$index - 1)) %>% - dplyr::select(x, index) %>% - as.data.frame() - warning("Links without attributes in the last") - print(bad_lines) - return(FALSE) - } - return(TRUE) -} - -# See if any filenames are duplicated in resources/ and resources/images/ -# just PNGs -# list.files() -# if image specified, see if image actually exists *somewhere* - -full_attribute_check <- function(path = ".") { - files <- get_md_files(path) - out <- lapply(files, make_sure_attributes_above) -} diff --git a/R/remove_yaml.R b/R/remove_yaml.R deleted file mode 100644 index e98dde9..0000000 --- a/R/remove_yaml.R +++ /dev/null @@ -1,51 +0,0 @@ -partition_yaml_front_matter <- function(input_lines) { - # taken from rmarkdown package - validate_front_matter <- function(delimiters) { - if (length(delimiters) >= 2 && (delimiters[2] - delimiters[1] > - 1) && grepl("^---\\s*$", input_lines[delimiters[1]])) { - if (delimiters[1] == 1) { - TRUE - } else { - all(grepl( - "^\\s*()?\\s*$", - input_lines[1:delimiters[1] - 1] - )) - } - } else { - FALSE - } - } - delimiters <- grep("^(---|\\.\\.\\.)\\s*$", input_lines) - if (validate_front_matter(delimiters)) { - front_matter <- input_lines[(delimiters[1]):(delimiters[2])] - input_body <- c() - if (delimiters[1] > 1) { - input_body <- c(input_body, input_lines[1:delimiters[1] - - 1]) - } - if (delimiters[2] < length(input_lines)) { - input_body <- c(input_body, input_lines[-(1:delimiters[2])]) - } - list(front_matter = front_matter, body = input_body) - } else { - list(front_matter = NULL, body = input_lines) - } -} - -#' Remove YAML header -#' -#' @param file file name of the markdown file -#' -#' @return A character vector of the text without the YAML header -#' @export -#' -#' @examples -#' file <- system.file("extdata/00_template.Rmd", package = "ottrpal") -#' out <- remove_yaml_header(file) -#' head(out) -remove_yaml_header <- function(file) { - file <- readLines(file, warn = FALSE) - out <- partition_yaml_front_matter(file) - out <- out$body - return(out) -} diff --git a/R/set_up.R b/R/set_up.R index d0fe7bf..78d5d32 100644 --- a/R/set_up.R +++ b/R/set_up.R @@ -1,13 +1,14 @@ #' 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 +#' @param path Where to look for the _bookdown.yml file. 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) + + root_dir <- course_path(path = file.path(path)) + file_path <- file.path(root_dir, "_bookdown.yml") # Read in yaml suppressWarnings({ @@ -17,35 +18,21 @@ get_bookdown_spec <- function(path = ".") { return(yaml_contents) } -#' Find main Bookdown directory +#' Find main course git 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 = ".") { +course_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)) + path <- rprojroot::find_root(rprojroot::has_file(".git"), 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 @@ -62,7 +49,7 @@ bookdown_rmd_files <- function(path = ".") { "No bookdown specification of the files, using ", "list.files(pattern ='.Rmd')" ) - root_dir <- bookdown_path(path = file.path(path)) + root_dir <- course_path(path = file.path(path)) files <- list.files( pattern = "[.]Rmd", ignore.case = TRUE, path = root_dir, full.names = FALSE @@ -80,7 +67,7 @@ bookdown_rmd_files <- function(path = ".") { #' bookdown_destination <- function(path = ".") { # Find _bookdown.yml - root_dir <- bookdown_path(path = file.path(path)) + root_dir <- course_path(path = file.path(path)) # Get specs from _bookdown.yml spec <- get_bookdown_spec(path = file.path(path)) @@ -108,7 +95,7 @@ copy_resources <- function(path = ".", images_dir = "resources", output_dir = "manuscript") { # Get file path to bookdown.yml - path <- bookdown_path(path) + path <- course_path(path) # Assume image directory is `resources/images` res_image_dir <- file.path(path, images_dir) @@ -133,7 +120,7 @@ copy_docs <- function(path = ".", output_dir = "manuscript") { } copy_bib <- function(path = ".", output_dir = "manuscript") { - path <- bookdown_path(path) + path <- course_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) @@ -178,7 +165,7 @@ copy_quizzes <- function(quiz_dir = "quizzes", output_dir = "manuscript") { #' 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. -#' @param embed is this being run by bookdown_to_embed_leanpub? TRUE/FALSE +#' @param embed is this being run by website_to_embed_leanpub? TRUE/FALSE #' @return A list of output files and diagnostics #' @export #' @@ -209,7 +196,7 @@ set_up_leanpub <- function(path = ".", rmd_regex <- "[.][R|r]md$" # Get the path to the _bookdown.yml - path <- bookdown_path(path) + path <- course_path(path) if (verbose) { message(paste0("Looking for bookdown file in ", path)) diff --git a/R/simple_references.R b/R/simple_references.R deleted file mode 100644 index c4e3efa..0000000 --- a/R/simple_references.R +++ /dev/null @@ -1,80 +0,0 @@ -#' Run Simple References -#' -#' @param x A filename of a markdown or Rmarkdown file, or the full output -#' from `readLines` on that file -#' @param bib_files bibliography files to use for pandoc -#' @param add_reference_header Should the `## References` header be added at the -#' end of the output? -#' -#' @return A character vector of the file, with references subbed in -#' @export -simple_references <- function(x, bib_files, add_reference_header = FALSE) { - if (length(x) == 1 && file.exists(x)) { - x <- readLines(x, warn = FALSE) - } - # indices = grepl("\\[\\s*[@]", x) - indices <- grepl("@", x) - # [@bookdown2016 #bookdown2016] - all_refs <- x[indices] - # out = x - bad_string <- "ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ" - result <- lapply(all_refs, function(out) { - stopifnot(!any(grepl(bad_string, out))) - out <- c(out, "", bad_string) - tfile <- tempfile(fileext = ".md") - writeLines(out, tfile, sep = "\n") - pandoc_args <- c( - paste0("--bibliography=", path.expand(normalizePath(bib_files))), - "--wrap=none" - ) - o2 <- tempfile(fileext = ".md") - rmarkdown::pandoc_convert( - input = tfile, - to = "markdown_strict", - output = o2, - citeproc = TRUE, - options = pandoc_args - ) - o2_text <- readLines(o2) - }) - all_references <- lapply(result, function(o2_text) { - references <- grep(bad_string, o2_text) - stopifnot(length(references) == 1) - if (references == length(o2_text)) { - return(NULL) - } - references <- o2_text[(references + 1):length(o2_text)] - references <- references[!references %in% ""] - references - }) - # dangerous - final_refs <- unique(unlist(unique(all_references))) - if (length(final_refs) > 0 && all(nchar(final_refs) > 0)) { - final_refs <- paste0(final_refs, "\n\n") - } - - all_output <- lapply(result, function(o2_text) { - references <- grep(bad_string, o2_text) - stopifnot(length(references) == 1) - stopifnot(o2_text[references - 1] == "") - out <- o2_text[-((references - 1):length(o2_text))] - }) - all_output <- mapply(function(x, y, z) { - if (is.null(z)) { - out <- x - } else { - out <- y - } - paste(out, collapse = "\n") - }, all_refs, all_output, all_references, SIMPLIFY = TRUE) - all_output <- c(unlist(all_output)) - out_x <- x - out_x[indices] <- all_output - - out_x <- c( - out_x, "", - if (add_reference_header && length(final_refs) > 0) "## References", - final_refs - ) - out_x -} diff --git a/R/utils.R b/R/utils.R index 701902d..c590607 100644 --- a/R/utils.R +++ b/R/utils.R @@ -9,38 +9,6 @@ utils::globalVariables(c( )) -# get script path and number of paragraphs -paragraph_from_script <- function(x) { - if (file.exists(x)) { - para <- readLines(x, warn = FALSE) - para <- trimws(para) - para <- para[!para %in% c("", " ")] - return(para) - } else { - return(NA) - } -} - -n_para <- function(x) { - x <- paragraph_from_script(x) - if (length(x) == 0) { - return(0) - } - ifelse(all(is.na(x)), NA, length(x)) -} - -length0 <- function(x) { - length(x) == 0 -} - -length0_to_NA <- function(x) { - if (length0(x)) { - x <- NA - } - x -} - - #' Google Slides Helper Functions #' #' @param file markdown file for manuscript diff --git a/man/bad_quiz_path.Rd b/man/bad_quiz_path.Rd index 1dd4bd3..2655347 100644 --- a/man/bad_quiz_path.Rd +++ b/man/bad_quiz_path.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/example_data.R +% Please edit documentation in R/data.R \name{bad_quiz_path} \alias{bad_quiz_path} \title{Path to bad example quiz} diff --git a/man/bookdown_file.Rd b/man/bookdown_file.Rd deleted file mode 100644 index 78d133f..0000000 --- a/man/bookdown_file.Rd +++ /dev/null @@ -1,17 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/set_up.R -\name{bookdown_file} -\alias{bookdown_file} -\title{Find file path to _bookdown.yml} -\usage{ -bookdown_file(path = ".") -} -\arguments{ -\item{path}{Where to look for the _bookdown.yml file. Passes to the bookdown_file() function. By default looks in current directory} -} -\value{ -The file path to _bookdown.yml -} -\description{ -Find file path to _bookdown.yml -} diff --git a/man/bookdown_path.Rd b/man/course_path.Rd similarity index 67% rename from man/bookdown_path.Rd rename to man/course_path.Rd index 27a0817..b26792d 100644 --- a/man/bookdown_path.Rd +++ b/man/course_path.Rd @@ -1,10 +1,10 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/set_up.R -\name{bookdown_path} -\alias{bookdown_path} -\title{Find main Bookdown directory} +\name{course_path} +\alias{course_path} +\title{Find main course git directory} \usage{ -bookdown_path(path = ".") +course_path(path = ".") } \arguments{ \item{path}{Where to look for the file. By default looks in current directory.} @@ -13,5 +13,5 @@ bookdown_path(path = ".") Returns the directory where the _bookdown.yml is contained. } \description{ -Find main Bookdown directory +Find main course git directory } diff --git a/man/bookdown_to_book_txt.Rd b/man/course_to_book_txt.Rd similarity index 76% rename from man/bookdown_to_book_txt.Rd rename to man/course_to_book_txt.Rd index a0b46cd..2b963f0 100644 --- a/man/bookdown_to_book_txt.Rd +++ b/man/course_to_book_txt.Rd @@ -1,10 +1,10 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/bookdown_to_leanpub.R -\name{bookdown_to_book_txt} -\alias{bookdown_to_book_txt} +% Please edit documentation in R/iframe_leanpub.R +\name{course_to_book_txt} +\alias{course_to_book_txt} \title{Create Book.txt file from files existing in quiz directory} \usage{ -bookdown_to_book_txt( +course_to_book_txt( path = ".", md_files = NULL, output_dir = "manuscript", @@ -13,7 +13,7 @@ bookdown_to_book_txt( ) } \arguments{ -\item{path}{path to the bookdown book, must have a `_bookdown.yml` file} +\item{path}{path to the bookdown or quarto course repository, must have a `_bookdown.yml` file or} \item{md_files}{vector of file path of the md's to be included} diff --git a/man/coursera.Rd b/man/coursera.Rd index 4b45007..ff7e610 100644 --- a/man/coursera.Rd +++ b/man/coursera.Rd @@ -2,7 +2,7 @@ % Please edit documentation in R/coursera_and_leanpub.R \name{render_without_toc} \alias{render_without_toc} -\title{Create TOC-less Bookdown for use in Coursera} +\title{Create TOC-less course website for use in Coursera or Leanpub} \usage{ render_without_toc( output_dir = file.path("docs", "no_toc"), @@ -30,5 +30,5 @@ render_without_toc( A folder of coursera ready quiz files and html chapter files saved to output directories specified. } \description{ -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. } diff --git a/man/example_repo_cleanup.Rd b/man/example_repo_cleanup.Rd deleted file mode 100644 index b896198..0000000 --- a/man/example_repo_cleanup.Rd +++ /dev/null @@ -1,29 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/example_data.R -\name{example_repo_cleanup} -\alias{example_repo_cleanup} -\title{Clean up example repo files} -\usage{ -example_repo_cleanup(files_to_remove, verbose = FALSE) -} -\arguments{ -\item{files_to_remove}{List of example files to delete.} - -\item{verbose}{TRUE/FALSE would you like progress messages?} -} -\value{ -Will delete example files copied from [ottrpal::example_repo_setup()] function -} -\description{ -Clean up example repo files -} -\examples{ -\dontrun{ - -# Run this to get the files we need -example_files <- ottrpal::example_repo_setup() - -# Run this to delete them -example_repo_cleanup(files_to_remove = basename(example_files)) -} -} diff --git a/man/example_repo_setup.Rd b/man/example_repo_setup.Rd deleted file mode 100644 index aa64399..0000000 --- a/man/example_repo_setup.Rd +++ /dev/null @@ -1,24 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/example_data.R -\name{example_repo_setup} -\alias{example_repo_setup} -\title{Set up example repo files} -\usage{ -example_repo_setup(dest_dir = tempdir()) -} -\arguments{ -\item{dest_dir}{The destination directory you would like the example repo files to be placed. By default is current directory.} -} -\value{ -Sets up example files that can be used to test 'ottrpal' functions. -} -\description{ -Set up example repo files -} -\examples{ -\dontrun{ - -# Run this to get the files we need -example_files <- ottrpal::example_repo_setup() -} -} diff --git a/man/get_bookdown_spec.Rd b/man/get_bookdown_spec.Rd index 1bfd9b3..162ce0b 100644 --- a/man/get_bookdown_spec.Rd +++ b/man/get_bookdown_spec.Rd @@ -7,7 +7,7 @@ get_bookdown_spec(path = ".") } \arguments{ -\item{path}{Where to look for the _bookdown.yml file. Passes to the bookdown_file() function. By default looks in current directory} +\item{path}{Where to look for the _bookdown.yml file. By default looks in current directory} } \value{ The yaml contents using yaml::yaml.load_file() diff --git a/man/get_chapters.Rd b/man/get_chapters.Rd index 348fa23..010e0bb 100644 --- a/man/get_chapters.Rd +++ b/man/get_chapters.Rd @@ -1,14 +1,12 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/bookdown_to_leanpub.R +% Please edit documentation in R/iframe_leanpub.R \name{get_chapters} \alias{get_chapters} \title{Make Leanpub file that has embed webpage of a chapter} \usage{ -get_chapters(html_page = file.path("docs", "index.html")) +get_chapters(html_page = file.path("docs", "index.html"), base_url = ".") } \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} } diff --git a/man/good_quiz_path.Rd b/man/good_quiz_path.Rd deleted file mode 100644 index 3e93973..0000000 --- a/man/good_quiz_path.Rd +++ /dev/null @@ -1,19 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/example_data.R -\name{good_quiz_path} -\alias{good_quiz_path} -\title{Path to good example quiz} -\usage{ -good_quiz_path() -} -\value{ -The file path to an example good quiz included in the package that will pass the quiz checks. -} -\description{ -Path to good example quiz -} -\examples{ - -quiz_path <- good_quiz_path() - -} diff --git a/man/leanpub_check.Rd b/man/leanpub_check.Rd deleted file mode 100644 index ff27850..0000000 --- a/man/leanpub_check.Rd +++ /dev/null @@ -1,19 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/leanpub_checks.R -\name{leanpub_check} -\alias{leanpub_check} -\title{Check Leanpub Course or Book} -\usage{ -leanpub_check(path = ".", verbose = TRUE) -} -\arguments{ -\item{path}{path to the Leanpub book/course} - -\item{verbose}{print diagnostic messages} -} -\value{ -A list of output files and diagnostics -} -\description{ -Check Leanpub Course or Book -} diff --git a/man/make_embed_markdown.Rd b/man/make_embed_markdown.Rd index ea34f1d..59c2fdd 100644 --- a/man/make_embed_markdown.Rd +++ b/man/make_embed_markdown.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/iframe_leanpub.R \name{make_embed_markdown} \alias{make_embed_markdown} \title{Make Leanpub file that has embed webpage of a chapter} diff --git a/man/remove_yaml_header.Rd b/man/remove_yaml_header.Rd deleted file mode 100644 index b2fcae5..0000000 --- a/man/remove_yaml_header.Rd +++ /dev/null @@ -1,22 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/remove_yaml.R -\name{remove_yaml_header} -\alias{remove_yaml_header} -\title{Remove YAML header} -\usage{ -remove_yaml_header(file) -} -\arguments{ -\item{file}{file name of the markdown file} -} -\value{ -A character vector of the text without the YAML header -} -\description{ -Remove YAML header -} -\examples{ -file <- system.file("extdata/00_template.Rmd", package = "ottrpal") -out <- remove_yaml_header(file) -head(out) -} diff --git a/man/set_up_leanpub.Rd b/man/set_up_leanpub.Rd index e65eec2..e506ba0 100644 --- a/man/set_up_leanpub.Rd +++ b/man/set_up_leanpub.Rd @@ -46,7 +46,7 @@ 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{embed}{is this being run by bookdown_to_embed_leanpub? TRUE/FALSE} +\item{embed}{is this being run by website_to_embed_leanpub? TRUE/FALSE} } \value{ A list of output files and diagnostics diff --git a/man/simple_references.Rd b/man/simple_references.Rd deleted file mode 100644 index 8ecedc9..0000000 --- a/man/simple_references.Rd +++ /dev/null @@ -1,23 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/simple_references.R -\name{simple_references} -\alias{simple_references} -\title{Run Simple References} -\usage{ -simple_references(x, bib_files, add_reference_header = FALSE) -} -\arguments{ -\item{x}{A filename of a markdown or Rmarkdown file, or the full output -from `readLines` on that file} - -\item{bib_files}{bibliography files to use for pandoc} - -\item{add_reference_header}{Should the `## References` header be added at the -end of the output?} -} -\value{ -A character vector of the file, with references subbed in -} -\description{ -Run Simple References -} diff --git a/man/bookdown_to_embed_leanpub.Rd b/man/website_to_embed_leanpub.Rd similarity index 82% rename from man/bookdown_to_embed_leanpub.Rd rename to man/website_to_embed_leanpub.Rd index b741b9d..9960b2a 100644 --- a/man/bookdown_to_embed_leanpub.Rd +++ b/man/website_to_embed_leanpub.Rd @@ -1,13 +1,12 @@ % 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 Leanpub} +% Please edit documentation in R/iframe_leanpub.R +\name{website_to_embed_leanpub} +\alias{website_to_embed_leanpub} +\title{Convert Website Course to Leanpub} \usage{ -bookdown_to_embed_leanpub( +website_to_embed_leanpub( path = ".", chapt_img_key = NULL, - bookdown_index = file.path(base_url, "index.html"), base_url = NULL, clean_up = FALSE, default_img = NULL, @@ -22,7 +21,7 @@ bookdown_to_embed_leanpub( ) } \arguments{ -\item{path}{path to the bookdown book, must have a `_bookdown.yml` file} +\item{path}{path to the bookdown or quarto course repository, must have a `_bookdown.yml` file or} \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`). @@ -30,8 +29,6 @@ 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{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} @@ -66,12 +63,12 @@ end of each file before the references section.} A directory of output files in a folder 'manuscript' for publishing on Leanpub. } \description{ -Convert Bookdown to Leanpub +Convert Website Course to Leanpub } \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 From 8244b8f228bcad2357dc629be667dabe8543ea09 Mon Sep 17 00:00:00 2001 From: Candace Savonen Date: Mon, 1 Jul 2024 09:21:36 -0400 Subject: [PATCH 02/17] Update check_testthat.R --- .github/workflows/R-CMD-check.yaml | 1 - .github/workflows/check_testthat.R | 29 +++++++++++++++++++++++------ 2 files changed, 23 insertions(+), 7 deletions(-) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index b542e23..091012f 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.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') diff --git a/.github/workflows/check_testthat.R b/.github/workflows/check_testthat.R index 7f33880..831d1d2 100644 --- a/.github/workflows/check_testthat.R +++ b/.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$total) From 6484c235039efa4abf5303a07627262a7c584650 Mon Sep 17 00:00:00 2001 From: Candace Savonen Date: Mon, 1 Jul 2024 09:25:39 -0400 Subject: [PATCH 03/17] Export good_quiz_path() --- R/data.R | 50 ++++++++++++++++++++++++++++---------------------- 1 file changed, 28 insertions(+), 22 deletions(-) diff --git a/R/data.R b/R/data.R index b3bc611..c0d1c2f 100644 --- a/R/data.R +++ b/R/data.R @@ -47,55 +47,61 @@ download_ottr_template <- function(dir = "inst/extdata", type = "rmd") { return(output_dir) } -#' Get file path to an key encryption RDS -key_encrypt_creds_path <- function() { + +#' Path to good example quiz +#' +#' @export +#' @return The file path to an example good quiz included in the package that should pass the quiz checks. +#' +good_quiz_path <- function() { list.files( - pattern = "encrypt_pass.rds", + pattern = "quiz_good.md$", recursive = TRUE, system.file("extdata", package = "ottrpal"), full.names = TRUE ) } -#' Get file path to an encrypted credentials RDS -encrypt_creds_path <- function() { + +#' 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 = "encrypt.rds", + pattern = "quiz_bad.md$", recursive = TRUE, system.file("extdata", package = "ottrpal"), full.names = TRUE ) } -#' Get file path to an default credentials RDS -encrypt_creds_user_path <- function() { +#' Get file path to an key encryption RDS +key_encrypt_creds_path <- function() { list.files( - pattern = "encrypted_default_user_creds.rds", + pattern = "encrypt_pass.rds", recursive = TRUE, system.file("extdata", package = "ottrpal"), full.names = TRUE ) } - -good_quiz_path <- function() { +#' Get file path to an encrypted credentials RDS +encrypt_creds_path <- function() { list.files( - pattern = "quiz_good.md$", + pattern = "encrypt.rds", 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() { +#' Get file path to an default credentials RDS +encrypt_creds_user_path <- function() { list.files( - pattern = "quiz_bad.md$", + pattern = "encrypted_default_user_creds.rds", recursive = TRUE, system.file("extdata", package = "ottrpal"), full.names = TRUE From 190cc635676726851fdfecf3afd0f4128392dc8d Mon Sep 17 00:00:00 2001 From: Candace Savonen Date: Mon, 1 Jul 2024 09:28:16 -0400 Subject: [PATCH 04/17] Fixing some notes --- R/coursera_and_leanpub.R | 4 ++-- R/iframe_leanpub.R | 6 +++--- R/set_up.R | 2 +- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/R/coursera_and_leanpub.R b/R/coursera_and_leanpub.R index 32afae0..faa2cec 100644 --- a/R/coursera_and_leanpub.R +++ b/R/coursera_and_leanpub.R @@ -199,7 +199,7 @@ convert_coursera_quizzes <- function(input_quiz_dir = "quizzes", #' Create TOC-less course website for use in Coursera or Leanpub #' -#' Create a version of the course that does not have a TOC and has quizzes in the Coursera yaml format. +#' Create a version of the course that does not have a TOC and has quizzes in the Coursera yaml format. #' #' @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" @@ -221,7 +221,7 @@ render_without_toc <- function(output_dir = file.path("docs", "no_toc"), output_quiz_dir = "coursera_quizzes", verbose = TRUE) { # Find root directory by finding `_bookdown.yml` file - root_dir <- bookdown_path() + root_dir <- course_path() # Output files: output_dir <- file.path(root_dir, output_dir) diff --git a/R/iframe_leanpub.R b/R/iframe_leanpub.R index 5e3c179..0040c62 100644 --- a/R/iframe_leanpub.R +++ b/R/iframe_leanpub.R @@ -17,7 +17,7 @@ #' @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, @@ -110,10 +110,10 @@ website_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, diff --git a/R/set_up.R b/R/set_up.R index 78d5d32..755cdf6 100644 --- a/R/set_up.R +++ b/R/set_up.R @@ -158,7 +158,7 @@ copy_quizzes <- function(quiz_dir = "quizzes", output_dir = "manuscript") { #' @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, From 451511a8241d0ba033085929a1f74288e8cecaab Mon Sep 17 00:00:00 2001 From: Candace Savonen Date: Mon, 1 Jul 2024 09:31:27 -0400 Subject: [PATCH 05/17] I don't think we need replace_html.R --- R/replace_html.R | 514 ----------------------------------------------- 1 file changed, 514 deletions(-) delete mode 100644 R/replace_html.R diff --git a/R/replace_html.R b/R/replace_html.R deleted file mode 100644 index 26026bc..0000000 --- a/R/replace_html.R +++ /dev/null @@ -1,514 +0,0 @@ -#' Convert youtube link -#' -#' @param utube_link a link to a youtube video that may or may not be "www.youtube.com/embed" or "www.youtube.com/watch?v=" -#' format. -#' -#' @return Returns a youtube link in the "watch" format so it will render properly in Leanpub or Coursera-friendly files -#' @export -#' -convert_utube_link <- function(utube_link) { - # If it has a youtube embed link, switch to the watch format link - if (grepl("www.youtube.com/embed", utube_link)) { - utube_link <- paste0( - "https://www.youtube.com/watch?v=", - strsplit(utube_link, - split = "www.youtube.com/embed/" - )[[1]][2] - ) - } - return(utube_link) -} - - -get_html_element <- function(x, element = "img") { - x <- paste(x, collapse = "\n") - doc <- xml2::read_html(x) - nodes <- rvest::html_nodes(doc, xpath = paste0("//", element)) - nodes -} - - -get_figure_div <- function(x) { - div <- get_html_element(x, element = 'div[@class="figure"]') - types <- div %>% - rvest::html_elements(xpath = ".//img|.//iframe") %>% - rvest::html_name() - img <- div %>% - rvest::html_elements(xpath = ".//img|.//iframe") %>% - rvest::html_attrs() - # missing something - not a img or iframe - stopifnot(length(img) == length(div)) - div_aligns <- div %>% - rvest::html_attr(name = "style") - div_aligns <- trimws(sub("text-align: ", "", div_aligns)) - # markua - div_aligns[div_aligns == "center"] <- "middle" - div_aligns[is.na(div_aligns)] <- "middle" - captions <- div %>% - rvest::html_elements(xpath = './p[@class="caption"]') %>% - rvest::html_text() - img <- mapply(function(x, y) { - c(x, caption = y) - }, img, captions, SIMPLIFY = FALSE) - img <- mapply(function(x, y) { - c(x, element_type = y) - }, img, types, SIMPLIFY = FALSE) - img <- mapply(function(x, y) { - y[y %in% ""] <- NA_character_ - if (!all(is.na(y))) { - x <- c(x, align = y) - } - x - }, img, div_aligns, SIMPLIFY = FALSE) - - return(img) -} - - - -get_html_attr <- function(x, element = "img", name = "src") { - x <- get_html_element(x, element = element) - rvest::html_attr(x, name) -} - -get_iframe_attr <- function(x, name = "src") { - x <- get_html_attr(x, element = "iframe", name = name) -} - -get_img_attr <- function(x, name = "src") { - x <- get_html_attr(x, element = "img", name = name) -} - -get_iframe_src <- get_iframe_attr -get_img_src <- get_img_attr - -get_iframe_alt <- function(x) { - get_iframe_attr(x, name = "alt") -} - -get_img_alt <- function(x) { - get_img_attr(x, name = "alt") -} - - - - -find_figure_div <- function(x) { - regex <- paste0('
") - end <- which(grepl(regex, x = x) & !grepl("^ - - - + + + + - Page not found (404) • ottrpal - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + - - - - -
-
- + +
+ +
+ - - -
+

Page not found (404)

@@ -130,31 +85,31 @@

Page not found (404)

+
-
-
-

Developed by John Muschelli, Candace Savonen.

+
+

+

Developed by Candace Savonen, John Muschelli.

-

Site built with pkgdown 1.6.1.

+

+

Site built with pkgdown 2.0.9.

-
+
+ + - - diff --git a/docs/LICENSE.html b/docs/LICENSE.html index 500ddc9..0a6986f 100644 --- a/docs/LICENSE.html +++ b/docs/LICENSE.html @@ -1,66 +1,12 @@ - - - - - - - -GNU General Public License • ottrpal - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -GNU General Public License • ottrpal - - - - + + -
-
- -
- -
+

GNU General Public License

@@ -127,11 +58,10 @@

GNU General Public License

-

Version 3, 29 June 2007
Copyright © 2007 Free Software Foundation, Inc. <http://fsf.org/>

+

Version 3, 29 June 2007
Copyright © 2007 Free Software Foundation, Inc. <http://fsf.org/>

Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed.

-
-

-Preamble

+
+

Preamble

The GNU General Public License is a free, copyleft license for software and other kinds of works.

The licenses for most software and other practical works are designed to take away your freedom to share and change the works. By contrast, the GNU General Public License is intended to guarantee your freedom to share and change all versions of a program–to make sure it remains free software for all its users. We, the Free Software Foundation, use the GNU General Public License for most of our software; it applies also to any other work released this way by its authors. You can apply it to your programs, too.

When we speak of free software, we are referring to freedom, not price. Our General Public Licenses are designed to make sure that you have the freedom to distribute copies of free software (and charge for them if you wish), that you receive source code or can get it if you want it, that you can change the software or use pieces of it in new free programs, and that you know you can do these things.

@@ -143,12 +73,10 @@

Finally, every program is threatened constantly by software patents. States should not allow patents to restrict development and use of software on general-purpose computers, but in those that do, we wish to avoid the special danger that patents applied to a free program could make it effectively proprietary. To prevent this, the GPL assures that patents cannot be used to render the program non-free.

The precise terms and conditions for copying, distribution and modification follow.

-
-

-TERMS AND CONDITIONS

-
-

-0. Definitions

+
+

TERMS AND CONDITIONS

+
+

0. Definitions

“This License” refers to version 3 of the GNU General Public License.

“Copyright” also means copyright-like laws that apply to other kinds of works, such as semiconductor masks.

“The Program” refers to any copyrightable work licensed under this License. Each licensee is addressed as “you”. “Licensees” and “recipients” may be individuals or organizations.

@@ -158,9 +86,8 @@

To “convey” a work means any kind of propagation that enables other parties to make or receive copies. Mere interaction with a user through a computer network, with no transfer of a copy, is not conveying.

An interactive user interface displays “Appropriate Legal Notices” to the extent that it includes a convenient and prominently visible feature that (1) displays an appropriate copyright notice, and (2) tells the user that there is no warranty for the work (except to the extent that warranties are provided), that licensees may convey the work under this License, and how to view a copy of this License. If the interface presents a list of user commands or options, such as a menu, a prominent item in the list meets this criterion.

-
-

-1. Source Code

+
+

1. Source Code

The “source code” for a work means the preferred form of the work for making modifications to it. “Object code” means any non-source form of a work.

A “Standard Interface” means an interface that either is an official standard defined by a recognized standards body, or, in the case of interfaces specified for a particular programming language, one that is widely used among developers working in that language.

The “System Libraries” of an executable work include anything, other than the work as a whole, that (a) is included in the normal form of packaging a Major Component, but which is not part of that Major Component, and (b) serves only to enable use of the work with that Major Component, or to implement a Standard Interface for which an implementation is available to the public in source code form. A “Major Component”, in this context, means a major essential component (kernel, window system, and so on) of the specific operating system (if any) on which the executable work runs, or a compiler used to produce the work, or an object code interpreter used to run it.

@@ -168,31 +95,26 @@

The Corresponding Source need not include anything that users can regenerate automatically from other parts of the Corresponding Source.

The Corresponding Source for a work in source code form is that same work.

-
-

-2. Basic Permissions

+
+

2. Basic Permissions

All rights granted under this License are granted for the term of copyright on the Program, and are irrevocable provided the stated conditions are met. This License explicitly affirms your unlimited permission to run the unmodified Program. The output from running a covered work is covered by this License only if the output, given its content, constitutes a covered work. This License acknowledges your rights of fair use or other equivalent, as provided by copyright law.

You may make, run and propagate covered works that you do not convey, without conditions so long as your license otherwise remains in force. You may convey covered works to others for the sole purpose of having them make modifications exclusively for you, or provide you with facilities for running those works, provided that you comply with the terms of this License in conveying all material for which you do not control copyright. Those thus making or running the covered works for you must do so exclusively on your behalf, under your direction and control, on terms that prohibit them from making any copies of your copyrighted material outside their relationship with you.

Conveying under any other circumstances is permitted solely under the conditions stated below. Sublicensing is not allowed; section 10 makes it unnecessary.

-