utilitr-template: Templates for the utilitR Project

# #' The GitBook output format
# #'
# #' This output format function ported a style provided by GitBook
# #' (\url{https://www.gitbook.com}) for R Markdown.
# #' @inheritParams html_chapters
# #' @param fig_caption,number_sections,self_contained,anchor_sections,lib_dir,pandoc_args ...
# #'   Arguments to be passed to \code{rmarkdown::\link{html_document}()}
# #'   (\code{...} not including \code{toc}, and \code{theme}).
# #' @param template Pandoc template to use for rendering. Pass \code{"default"}
# #'   to use the bookdown default template; pass a path to use a custom template.
# #'   The default template should be sufficient for most use cases. In case you
# #'   want to develop a custom template, we highly recommend to start from the
# #'   default template:
# #'   \url{https://github.com/rstudio/bookdown/blob/master/inst/templates/gitbook.html}.
# #'
# #' @param config A list of configuration options for the gitbook style, such as
# #'   the font/theme settings.
# #' @param table_css \code{TRUE} to load gitbook's default CSS for tables. Choose
# #' \code{FALSE} to unload and use customized CSS (for exmaple, bootstrap) via
# #' the \code{css} option. Default is \code{TRUE}.
# #' @export
#
# #' @import xfun
# gitbook2 = function(
#   fig_caption = TRUE, number_sections = TRUE, self_contained = FALSE,
#   anchor_sections = TRUE, lib_dir = 'libs', pandoc_args = NULL, ..., template = 'default',
#   split_by = c('chapter', 'chapter+number', 'section', 'section+number', 'rmd', 'none'),
#   split_bib = TRUE, config = list(), table_css = TRUE
# ) {
#
#   html_document2 = function(..., extra_dependencies = list()) {
#     rmarkdown::html_document(
#       ..., extra_dependencies = c(bookdown:::gitbook_dependency(table_css), extra_dependencies)
#     )
#   }
#   gb_config = config
#   if (identical(template, 'default')) {
#     template = bookdown_file:::bookdown_file('templates', 'gitbook.html')
#   }
#   config = html_document2(
#     toc = TRUE, number_sections = number_sections, fig_caption = fig_caption,
#     self_contained = self_contained, anchor_sections = anchor_sections,
#     lib_dir = lib_dir, theme = NULL,
#     template = template, pandoc_args = bookdown:::pandoc_args2(pandoc_args), ...
#   )
#   split_by = match.arg(split_by)
#   post = config$post_processor  # in case a post processor have been defined
#   config$post_processor = function(metadata, input, output, clean, verbose) {
#     if (is.function(post)) output = post(metadata, input, output, clean, verbose)
#     on.exit(bookdown:::write_search_data(), add = TRUE)
#
#     # a hack to remove Pandoc's margin for code blocks since gitbook has already
#     # defined margin on <pre> (there would be too much bottom margin)
#     x = xfun::read_utf8(output)
#     x = x[x != 'div.sourceCode { margin: 1em 0; }']
#     xfun::write_utf8(x, output)
#
#     bookdown:::move_files_html(output, lib_dir)
#     output2 = bookdown:::split_chapters(
#       output, bookdown:::gitbook_page, number_sections, split_by, split_bib, gb_config, split_by
#     )
#     if (file.exists(output) && !xfun::same_path(output, output2)) file.remove(output)
#     bookdown:::move_files_html(output2, lib_dir)
#     output2
#   }
#   config = bookdown:::common_format_config(config, 'html')
#   config
# }

# gitbook_search = local({
#   data = NULL
#   list(
#     get = function() data,
#     collect = function(...) data <<- c(data, ...),
#     empty = function() data <<- NULL
#   )
# })
#
# write_search_data = function() {
#   x = gitbook_search$get()
#   if (length(x) == 0) return()
#   gitbook_search$empty()
#   x = matrix(bookdown:::strip_search_text(x), nrow = 3)
#   x = apply(x, 2, xfun::json_vector, to_array = TRUE)
#   x = paste0('[\n', paste0(x, collapse = ',\n'), '\n]')
#   x = gsub('[^[:print:]]', '', x)
#   xfun::write_utf8(x, bookdown:::output_path('search_index.json'))
# }
#
# gitbook_dependency = function(table_css) {
#   assets = bookdown:::bookdown_file('resources', 'gitbook')
#   owd = setwd(assets); on.exit(setwd(owd), add = TRUE)
#   app = if (file.exists('js/app.min.js')) 'app.min.js' else 'app.js'
#   list(bookdown:::jquery_dependency(), htmltools::htmlDependency(
#     'gitbook', '2.6.7', src = assets,
#     stylesheet = file.path('css', c(
#       'style.css', if (table_css) 'plugin-table.css', 'plugin-bookdown.css',
#       'plugin-highlight.css', 'plugin-search.css', 'plugin-fontsettings.css',
#       'plugin-clipboard.css'
#     )),
#     script = file.path('js', c(
#       app, 'lunr.js', 'clipboard.min.js', 'plugin-search.js', 'plugin-sharing.js',
#       'plugin-fontsettings.js', 'plugin-bookdown.js', 'jquery.highlight.js',
#       'plugin-clipboard.js'
#     ))
#   ))
# }
#
# gitbook_page = function(
#   head, toc, chapter, link_prev, link_next, rmd_cur, html_cur, foot,
#   config, split_by
# ) {
#   toc = gitbook_toc(toc, rmd_cur, config[['toc']])
#
#   has_prev = length(link_prev) > 0
#   has_next = length(link_next) > 0
#   a_prev = if (has_prev) sprintf(
#     '<a href="%s" class="navigation navigation-prev %s" aria-label="Previous page"><i class="fa fa-angle-left"></i></a>',
#     link_prev, if (has_next) '' else 'navigation-unique'
#   ) else ''
#   a_next = if (has_next) sprintf(
#     '<a href="%s" class="navigation navigation-next %s" aria-label="Next page"><i class="fa fa-angle-right"></i></a>',
#     link_next, if (has_prev) '' else 'navigation-unique'
#   ) else ''
#   foot = sub('<!--bookdown:link_prev-->', a_prev, foot)
#   foot = sub('<!--bookdown:link_next-->', a_next, foot)
#
#   l_prev = if (has_prev) sprintf('<link rel="prev" href="%s"/>', link_prev) else ''
#   l_next = if (has_next) sprintf('<link rel="next" href="%s"/>', link_next) else ''
#   head = sub('<!--bookdown:link_prev-->', l_prev, head)
#   head = sub('<!--bookdown:link_next-->', l_next, head)
#   head = sub('#bookdown:version#', packageVersion('bookdown'), head)
#
#   # gitbook JS scripts only work after the DOM has been loaded, so move them
#   # from head to foot
#   i = grep('^\\s*<script src=".+/gitbook([^/]+)?/js/[.a-z-]+[.]js"></script>\\s*$', head)
#   # it is probably a self-contained page, so look for script node.
#   # from pandoc2, they are not always base64 encoded scripts, so start and end of scripts
#   # node must be found and moved.
#   if (length(i) == 0) {
#     s_start = grep(
#       '^\\s*<script( src="data:application/(x-)?javascript;base64,[^"]+")?>', head
#     )
#     s_end = grep("</script>\\s*$", head)
#     # find all lines to move
#     i = unlist(mapply(seq.int, s_start, s_end, SIMPLIFY = FALSE))
#   }
#   s = head[i]; head[i] = ''
#   j = grep('<!--bookdown:config-->', foot)[1]
#   foot[j] = paste(c(s, foot[j]), collapse = '\n')
#
#   titles = paste(grep('^<(h[12])(>| ).+</\\1>.*$', chapter, value = TRUE), collapse = ' ')
#   # when not rendering via render_book()  (but e.g. rmarkdown::render()), do not
#   # collect search data because the output will be a single page: Ctrl + F!
#   if (is.null(opts$get('book_filename'))) {
#     config$search = FALSE
#   } else {
#     gitbook_search$collect(html_cur, titles, paste(chapter, collapse = ' '))
#   }
#
#   # you can set the edit setting in either _bookdown.yml or _output.yml
#   for (type in c('edit', 'history', 'view')) {
#     if (is.list(setting <- source_link_setting(config[[type]], type = type)))
#       config[[type]] = setting
#     if (length(rmd_cur) && is.list(config[[type]]))
#       config[[type]][["link"]] = sprintf(config[[type]]$link, rmd_cur)
#   }
#
#   config$download = download_filenames(config)
#
#   foot = sub('<!--bookdown:config-->', gitbook_config(config), foot)
#
#   c(head, toc, chapter, foot)
# }
#
# gitbook_toc = function(x, cur, config) {
#   i1 = bookdown:::find_token(x, '<!--bookdown:toc2:start-->')
#   i2 = bookdown:::find_token(x, '<!--bookdown:toc2:end-->')
#   x[i1] = ''; x[i2] = ''
#   if (i2 - i1 < 2) return(x)
#   toc = x[(i1 + 1):(i2 - 1)]
#
#   # numbered sections
#   r = '^<li><a href="([^#]*)(#[^"]+)"><span class="toc-section-number">([.A-Z0-9]+)</span>(.+)(</a>.*)$'
#   i = grep(r, toc)
#   toc[i] = gsub(
#     r,
#     '<li class="chapter" data-level="\\3" data-path="\\1"><a href="\\1\\2"><i class="fa fa-check"></i><b>\\3</b>\\4\\5',
#     toc[i]
#   )
#   toc[i] = sub(' data-path="">', paste0(' data-path="', xfun::with_ext(cur, '.html'), '">'), toc[i])
#
#   # unnumbered sections
#   r = '^<li><a href="([^#]*)(#[^"]+)">([^<]+</a>.*)$'
#   i = grep(r, toc)
#   toc[i] = gsub(
#     r,
#     '<li class="chapter" data-level="" data-path="\\1"><a href="\\1\\2"><i class="fa fa-check"></i>\\3',
#     toc[i]
#   )
#
#   # remove the hash from the first TOC item if it has following items that share
#   # the same base pathname, e.g. [index.html#foo, index.html#bar] ->
#   # [index.html, index.html#bar]
#   r = '^(<li class="chapter" data-level="[.A-Z0-9]*" data-path="[^"]+"><a href=")([^#]+)(#[^"]+)(">.+)$'
#   i = grep(r, toc)
#   i = i[!duplicated(gsub(r, '\\2', toc[i]))]
#   toc[i] = gsub(r, '\\1\\2\\4', toc[i])
#
#   # collapse sections under chapters
#   if (isTRUE(config[['collapse']])) {
#     r = '^<li .+ data-level="([^.]+)?" .+>.+</a><ul>$'
#     i = grep(r, toc)
#     toc[i] = gsub('<ul>$', '<ul style="display:none;">', toc[i])
#   }
#
#   if (toc[1] == '<ul>') {
#     toc[1] = '<ul class="summary">'
#     if (!is.null(extra <- config[['before']])) {
#       toc[1] = paste(c(toc[1], extra, '<li class="divider"></li>'), collapse = '\n')
#     }
#   }
#   n = length(toc)
#   if (toc[n] == '</ul>') {
#     if (!is.null(extra <- config[['after']])) {
#       toc[n] = paste(c('<li class="divider"></li>', extra, toc[n]), collapse = '\n')
#     }
#   }
#   x[(i1 + 1):(i2 - 1)] = toc
#   x
# }
#
# gitbook_config = function(config = list()) {
#   default = list(
#     sharing = list(
#       github = FALSE, facebook = TRUE, twitter = TRUE,
#       linkedin = FALSE, weibo = FALSE, instapaper = FALSE, vk = FALSE,
#       all = c('facebook', 'twitter', 'linkedin', 'weibo', 'instapaper')
#     ),
#     fontsettings = list(theme = 'white', family = 'sans', size = 2),
#     edit = list(link = NULL, text = NULL),
#     history = list(link = NULL, text = NULL),
#     view = list(link = NULL, text = NULL),
#     download = NULL,
#     # toolbar = list(position = 'static'),
#     toc = list(collapse = 'subsection')
#   )
#   config = utils::modifyList(default, config, keep.null = TRUE)
#   # remove these TOC config items since we don't need them in JavaScript
#   config$toc$before = NULL; config$toc$after = NULL
#   config = sprintf('gitbook.start(%s);', xfun::tojson(config))
#   paste(
#     '<script>', 'gitbook.require(["gitbook"], function(gitbook) {', config, '});',
#     '</script>', sep = '\n'
#   )
# }
#
# # infer pdf/epub/mobi filenames from the book filename
# download_filenames = function(config) {
#   if (length(exts <- bookdown:::load_config()[['download']]) == 0) exts = config$download
#   if (identical(exts, FALSE)) return()
#   if (is.list(exts)) return(exts)  # I assume you are doing it correctly
#   if ((n <- length(grep('[.]', exts))) > 0) {
#     if (length(exts) != n) stop(
#       'You must provide either pure file extensions or full filenames'
#     )
#     return(exts)
#   }
#   # no downloads if not rendering with render_book() but render()
#   if (is.null(book_name <- opts$get('book_filename'))) return()
#   if (isTRUE(exts) || length(exts) == 0) {
#     exts = c('pdf', 'epub', 'mobi')
#     downloads = xfun::with_ext(book_name, exts)
#     xfun::in_dir(bookdown:::output_path('.'), {
#       downloads = downloads[file.exists(downloads)]
#     })
#   } else {
#     downloads = xfun::with_ext(book_name, exts)
#     i = match('rmd', exts)
#     if (!is.na(i)) {
#       r = '^(https://github.com/[^/]+/[^/]+)/edit/'
#       if (is.character(link <- config$edit$link) && grepl(r, link)) {
#         downloads[i] = gsub(r, '\\1/raw/', link)
#       } else {
#         warning('The edit link was not specified, and the download link for RMD will not work')
#         downloads = downloads[-i]
#       }
#     }
#   }
#   if (length(downloads)) I(downloads)
# }