Merge changes on rstudio/rmarkdown@master.

Merge remote-tracking branch 'rstudio_origin/master' into css-slash-fix

# By Yihui Xie (12) and others
# Via GitHub
* rstudio_origin/master: (22 commits)
  fix rstudio#1905: a chunk with the class "fold-hide" should only hide itself (rstudio#1906)
  bump version after merging rstudio#1899
  lua filter -> Lua filter
  Add an argument `lua_filters` to pandoc_options() to store them in the output format object (rstudio#1899)
  recursve into the parent dir at the end
  also suppor dir input in proj_root()
  list.files() with full.names = TRUE (so the files could be read with corret paths), and pass down the `file`/`pattern` arguments in the recursion
  use our own proj_root() instead of introducing a dependency
  rename package_root() to proj_root()
  generalize the package_root() function to work with more types of projects
  Discover site generators in index.Rmd files in parent directories (rstudio#1898)
  only install pkgdown for website build (rstudio#1900)
  Generalize number sections (rstudio#1879)
  enable figure cropping in pdf_document() only when both pdfcrop and ghostscript are found (yihui/knitr#954), and do not limit this feature to non-Windows platforms
  add the citation entry for the R Markdown Cookbook
  add lua filter vignette to pkgdown website (rstudio#1894)
  close rstudio#1889: evaluate the output argument before changing working directory in pandoc_convert() (rstudio#1890)
  tweak news
  require Pandoc >= 1.14
  xfun 0.16 is on CRAN now
  ...

# Conflicts:
#	NEWS.md

.travis.yml

@@ -29,6 +29,8 @@ jobs:
     - r: release
       name: R release / RStudio Pandoc
       env: NETLIFY_SITE_ID=5d77c13c-e2ee-4a31-87ca-2fe657196160
+      before_cache:
+        - Rscript -e 'xfun::pkg_load2("pkgdown")'
       after_success:
         - "[[ ${TRAVIS_BRANCH}  = master  ]] || exit 0"
         - "[[ -z ${NETLIFY_AUTH_TOKEN} ]] && exit 0"

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: rmarkdown
 Type: Package
 Title: Dynamic Documents for R
-Version: 2.3.2
+Version: 2.3.9
 Authors@R: c(
   person("JJ", "Allaire", role = "aut", email = "[email protected]"),
   person("Yihui", "Xie", role = c("aut", "cre"), email = "[email protected]", comment = c(ORCID = "0000-0003-0645-5666")),
@@ -16,7 +16,9 @@ Authors@R: c(
   #
   # Contributors, ordered alphabetically by first name
   person("Andrew", "Dunning", role = "ctb", comment = c(ORCID = "0000-0003-0464-5036")),
-  person("Atsushi", "Yasumoto", role = "ctb", comment = c(ORCID = "0000-0002-8335-495X")),
+  person("Atsushi", "Yasumoto", role = c("ctb", "cph"),
+         comment = c(ORCID = "0000-0002-8335-495X",
+                     cph = "Number sections Lua filter")),
   person("Barret", "Schloerke", role = "ctb"),
   person("Christophe", "Dervieux", role = "ctb"),
   person("Frederik", "Aust", role = "ctb", email = "[email protected]", comment = c(ORCID = "0000-0003-4900-788X")),
@@ -70,9 +72,9 @@ Authors@R: c(
   person("Aidan", "Lister", role = c("ctb", "cph"), 
          comment = "jQuery StickyTabs"),
   person("Benct Philip", "Jonsson", role = c("ctb", "cph"), 
-         comment = "pagebreak lua filter"),
+         comment = "pagebreak Lua filter"),
   person("Albert", "Krewinkel", role = c("ctb", "cph"), 
-         comment = "pagebreak lua filter")
+         comment = "pagebreak Lua filter")
   )
 Maintainer: Yihui Xie <[email protected]>
 Description: Convert R Markdown documents into a variety of formats.
@@ -85,7 +87,6 @@ Imports:
     yaml (>= 2.1.19),
     htmltools (>= 0.3.5),
     evaluate (>= 0.13),
-    base64enc,
     jsonlite,
     mime,
     tinytex (>= 0.11),
@@ -100,12 +101,11 @@ Suggests:
     dygraphs,
     tibble,
     fs,
-    pkgdown,
     rsconnect
-SystemRequirements: pandoc (>= 1.12.3) - http://pandoc.org
+SystemRequirements: pandoc (>= 1.14) - http://pandoc.org
 URL: https://github.com/rstudio/rmarkdown
 BugReports: https://github.com/rstudio/rmarkdown/issues
 License: GPL-3
-RoxygenNote: 7.1.0
+RoxygenNote: 7.1.1
 Encoding: UTF-8
 VignetteBuilder: knitr

NAMESPACE

@@ -62,6 +62,7 @@ export(pandoc_exec)
 export(pandoc_highlight_args)
 export(pandoc_include_args)
 export(pandoc_latex_engine_args)
+export(pandoc_lua_filter_args)
 export(pandoc_metadata_arg)
 export(pandoc_options)
 export(pandoc_path_arg)

NEWS.md

@@ -1,14 +1,26 @@
 rmarkdown 2.4
 ================================================================================
 
-- Fix path separators for "css" parameters in YAML frontmatter for HTML files under Windows. Previously, these were converted to backslashes even if they appeared in the "css" argument as forward slashes. Now hrefs for css links are generated with forward slashes under Windows.
+- Lua filters handling has been improved internally with some user-facing changes (#1899):
+    - New exported function `pandoc_lua_filter_args()` to return the Pandoc command-line argument to add a Lua filter.
+    - New argument `lua_filters` in `pandoc_options()` to pass the Lua filter paths to use with a format. This allow output format authors to add filters for a custom format using the `pandoc` argument of `output_format()` and to get filters from a format using `fmt$pandoc$lua_filters`.
+    - The Lua filters of an output format are now passed to Pandoc in `render()`. By default, they are passed to Pandoc before any other format-defined or user-defined Pandoc arguments (usually via the `pandoc_args` option of an output format). This ensures that filters of an output format are executed first. To change the default, you need to deal with it in a custom format (i.e., modify the elements in `fmt$pandoc$lua_filters`, such as reordering them).
+
+- Fix path separators for "css" parameters in YAML frontmatter for HTML files under Windows. Previously, these were converted to backslashes even if they appeared in the "css" (thanks, @jonathan-g, #1862)
 
 - Since **rmarkdown** 1.16, Pandoc's fenced `Div`'s are converted to LaTeX environments when the output format is LaTeX, e.g., `::: {.center data-latex=""}` is converted to `\begin{center}`. The attribute `data-latex` of the `Div` was mandatory, even if it is empty. In **rmarkdown** 2.2, we silently drop this requirement, which means `::: {.center}` is converted to `\begin{center}`. This turns out to be a bad idea, because users have no control over which Div's to be converted to LaTeX environments. Previously, they could opt-in by the `data-latex` attribute, but with **rmarkdown** 2.3, all Div's are converted to LaTeX environments unconditionally. What's more, this change led to bugs like https://stackoverflow.com/q/62340425/559676 and https://github.com/rstudio/bookdown/issues/883. Therefore the `data-latex` attribute became mandatory again in this version. If the LaTeX environment does not need arguments, you may use `data-latex=""`.
 
 - The two Lua fitlers `pagebreak.lua` and `latex-div.lua` (introduced in **rmarkdown** 1.16) are also applied to the output format `beamer_presentation` now (thanks, @XiangyunHuang, #1815).
 
 - When customizing formats with the `output_format` function, `pre_knit`, `opts_hooks`, and `knit_hooks` can now refer to `rmarkdown::metadata`. Previously, `rmarkdown::metadata` returned `list()` in these functions (thanks, @atusy, #1855).
 
+- Added the `number_sections` argument to following formats: `github_document`, `ioslides_presentation`, `md_document`, `odt_document`, `powerpoint_presentation`, `rtf_document`, `slidy_presentation`, `word_document`. These are powered by a Lua filter and requires Pandoc > 2.0. It will silently have no effect has before with previous pandoc version (thanks @atusy 1893).  Pandoc >= 2.10.1 adds `--number-sections` for docx format, and thus `word_document` prefers the native feature to the Lua filter (thanks, @jooyoungseo, #1869).
+
+- For the output format `pdf_document`, the option `fig_crop` will not be enabled unless both the programs `pdfcrop` and `ghostscript` are found (thanks, @dalupus, yihui/knitr#954).
+
+- Fixed a bug that a chunk with a class `fold-hide` hides the rest of the chunks even the output format setting `html_document(code_folding = "show")` (thanks, @atusy, #1906).
+
+
 rmarkdown 2.3
 ================================================================================
 
@@ -146,13 +158,13 @@ rmarkdown 1.16
 
 - Added `self_contained` argument to `html_vignette` to keep intermediate directory if `self_contained = FALSE` (thanks, @cderv, #1641).
 
-- It is now possible to add pagebreak in HTML, Word, LaTeX, and ODT documents using the `\newpage` or `\pagebreak` command in an Rmd file. This is possible thanks to the [Pandoc's pagebreak lua filter](https://github.com/pandoc/lua-filters/tree/master/pagebreak). See `vignette("lua-filters", package = "rmarkdown")` (thanks, @cderv, #1626).
+- It is now possible to add pagebreak in HTML, Word, LaTeX, and ODT documents using the `\newpage` or `\pagebreak` command in an Rmd file. This is possible thanks to the [Pandoc's pagebreak Lua filter](https://github.com/pandoc/lua-filters/tree/master/pagebreak). See `vignette("lua-filters", package = "rmarkdown")` (thanks, @cderv, #1626).
 
 - The Pandoc extension `ascii_identifiers` is no longer enabled by default. If you still need it, you may use the argument `md_extensions = "+ascii_identifiers"` in the output format function. However, please note that this will trigger an error in a future version of Pandoc.
 
 - Output formats can be configured by arbitrary YAML files, which used to be restricted to `_output.yml` or `_output.yaml`. They can be specified via the `output_yaml` argument of `render()` or the `output_yaml` top-level parameter of YAML front matter, and the first existing one will be used. If `output_yaml` is specified both for `render()` and YAML front matter, then `render()` has the priority. If none are found, then `_output.yml` or `_output.yaml` will be used if they exist (thanks, @atusy, #1634).
 
-- Added a Pandoc lua filter to convert fenced Divs to LaTeX environments when the output format is `latex` or `beamer`. Basically a fenced Div `::: {.NAME data-latex="[OPTIONS]"}` is converted to `\begin{NAME}[OPTIONS] \end{NAME}` in LaTeX. The attribute `data-latex` must be provided, even if it is an empty string (meaning that the LaTeX environment does not have any optional arguments). For example, `::: {.verbatim data-latex=""}` generates a `verbatim` environment, and `::: {.minipage data-latex="{.5\textwidth}"}` generates `\begin{minipage}{.5\textwidth}`. This lua filter was originally written by @RLesur at https://github.com/yihui/bookdown-crc/issues/1. It will allow users to create custom blocks that work for both HTML and LaTeX output (e.g., info boxes or warning boxes).
+- Added a Pandoc Lua filter to convert fenced Divs to LaTeX environments when the output format is `latex` or `beamer`. Basically a fenced Div `::: {.NAME data-latex="[OPTIONS]"}` is converted to `\begin{NAME}[OPTIONS] \end{NAME}` in LaTeX. The attribute `data-latex` must be provided, even if it is an empty string (meaning that the LaTeX environment does not have any optional arguments). For example, `::: {.verbatim data-latex=""}` generates a `verbatim` environment, and `::: {.minipage data-latex="{.5\textwidth}"}` generates `\begin{minipage}{.5\textwidth}`. This Lua filter was originally written by @RLesur at https://github.com/yihui/bookdown-crc/issues/1. It will allow users to create custom blocks that work for both HTML and LaTeX output (e.g., info boxes or warning boxes).
 
 - Added `keep_html` argument to `github_document` so to save a preview HTML file in a working directory (thanks, @atusy, #1650).
 

R/base64.R

@@ -1,15 +1,3 @@
-base64_encode_file <- function(in_file, encoder) {
-
-  file_size <- file.info(in_file)$size
-
-  if (file_size <= 0) {
-    warning(in_file, 'is empty!')
-    return(in_file)
-  }
-  paste0('data:', mime::guess_type(in_file), ';base64,',
-         encoder(readBin(in_file, 'raw', n = file_size)))
-}
-
 # processes an HTML resource, given a regular expression that locates
 # instances of that resource
 process_html_res <- function(html, reg, processor) {
@@ -29,21 +17,14 @@ process_images <- function(html, processor) {
     processor)
 }
 
-base64_encode_images <- function(html, encoder) {
+base64_encode_images <- function(html) {
   base64_encode_img <- function(img_src, src) {
     in_file <- utils::URLdecode(src)
     if (length(in_file) && file.exists(in_file)) {
-      img_src <- sub(src, base64_encode_file(in_file, encoder), img_src,
-                     fixed = TRUE)
+      img_src <- sub(src, xfun::base64_uri(in_file), img_src, fixed = TRUE)
     }
     img_src
   }
   html <- process_images(html, base64_encode_img)
   process_html_res(html, "<[^>]*style=\"[^\"]*url\\(([^\\)]+)\\)", base64_encode_img)
 }
-
-base64_image_encode <- function(data) {
-  base64_encode_images(data, base64enc::base64encode)
-}
-
-

R/beamer_presentation.R

@@ -126,8 +126,6 @@ beamer_presentation <- function(toc = FALSE,
   # make sure the graphics package is always loaded
   if (identical(template, "default")) args <- c(args, "--variable", "graphics=yes")
 
-  args <- c(args, pandoc_lua_filters(c("pagebreak.lua", "latex-div.lua")))
-
   # custom args
   args <- c(args, pandoc_args)
 
@@ -151,11 +149,14 @@ beamer_presentation <- function(toc = FALSE,
   # return format
   output_format(
     knitr = knitr_options_pdf(fig_width, fig_height, fig_crop, dev),
-    pandoc = pandoc_options(to = "beamer",
-                            from = from_rmarkdown(fig_caption, md_extensions),
-                            args = args,
-                            latex_engine = latex_engine,
-                            keep_tex = keep_tex),
+    pandoc = pandoc_options(
+      to = "beamer",
+      from = from_rmarkdown(fig_caption, md_extensions),
+      args = args,
+      latex_engine = latex_engine,
+      keep_tex = keep_tex,
+      lua_filters = pkg_file_lua(c("pagebreak.lua", "latex-div.lua"))
+    ),
     pre_processor = pre_processor,
     intermediates_generator = intermediates_generator,
     clean_supporting = !keep_tex,

R/context_document.R

@@ -90,9 +90,6 @@ context_document <- function(toc = FALSE,
   # content includes
   args <- c(args, includes_to_pandoc_args(includes))
 
-  # lua filters (added if pandoc > 2)
-  args <- c(args, pandoc_lua_filters("pagebreak.lua"))
-
   # args args
   args <- c(args, pandoc_args)
 
@@ -129,11 +126,13 @@ context_document <- function(toc = FALSE,
   # return format
   output_format(
     knitr = knitr_options_pdf(fig_width, fig_height, fig_crop, dev),
-    pandoc = pandoc_options(to = paste(c("context", output_extensions), collapse = ""),
-                            from = from_rmarkdown(fig_caption, md_extensions),
-                            args = args,
-                            keep_tex = FALSE,
-                            ext = ext),
+    pandoc = pandoc_options(
+      to = paste(c("context", output_extensions), collapse = ""),
+      from = from_rmarkdown(fig_caption, md_extensions),
+      args = args,
+      keep_tex = FALSE,
+      ext = ext,
+      lua_filters = pkg_file_lua("pagebreak.lua")),
     clean_supporting = !isTRUE(keep_tex),
     keep_md = keep_md,
     df_print = df_print,

R/github_document.R

@@ -18,6 +18,7 @@
 #' @export
 github_document <- function(toc = FALSE,
                             toc_depth = 3,
+                            number_sections = FALSE,
                             fig_width = 7,
                             fig_height = 5,
                             dev = 'png',
@@ -30,20 +31,23 @@ github_document <- function(toc = FALSE,
                             keep_html = FALSE) {
 
   # add special markdown rendering template to ensure we include the title fields
+  # and add an optional feature to number sections
   pandoc_args <- c(
-    pandoc_args, "--template", pkg_file_arg(
-      "rmarkdown/templates/github_document/resources/default.md")
+    pandoc_args, "--template",
+    pkg_file_arg("rmarkdown/templates/github_document/resources/default.md")
   )
 
+
   pandoc2 <- pandoc2.0()
   # use md_document as base
   variant <- if (pandoc2) "gfm" else "markdown_github"
   if (!hard_line_breaks) variant <- paste0(variant, "-hard_line_breaks")
 
   format <- md_document(
     variant = variant, toc = toc, toc_depth = toc_depth,
-    fig_width = fig_width, fig_height = fig_height, dev = dev,
-    df_print = df_print, includes = includes, md_extensions = md_extensions,
+    number_sections = number_sections, fig_width = fig_width,
+    fig_height = fig_height, dev = dev, df_print = df_print,
+    includes = includes, md_extensions = md_extensions,
     pandoc_args = pandoc_args
   )
 

R/html_document.R

@@ -312,7 +312,7 @@ html_document <- function(toc = FALSE,
       source_file <<- basename(input)
       source_code <<- paste0(
         '<div id="rmd-source-code">',
-        base64enc::base64encode(input),
+        xfun::base64_encode(input),
         '</div>')
     }
   }

R/html_document_base.R

@@ -106,9 +106,6 @@ html_document_base <- function(theme = NULL,
 
     preserved_chunks <<- extract_preserve_chunks(input_file)
 
-    # a lua filters added if pandoc2.0
-    args <- c(args, pandoc_lua_filters(c("pagebreak.lua", "latex-div.lua")))
-
     args
   }
 
@@ -170,7 +167,9 @@ html_document_base <- function(theme = NULL,
 
   output_format(
     knitr = NULL,
-    pandoc = pandoc_options(to = "html", from = NULL, args = args),
+    pandoc = pandoc_options(
+      to = "html", from = NULL, args = args,
+      lua_filters = pkg_file_lua(c("pagebreak.lua", "latex-div.lua"))),
     keep_md = FALSE,
     clean_supporting = FALSE,
     pre_knit = pre_knit,

R/html_notebook.R

@@ -257,7 +257,7 @@ parse_html_notebook <- function(path) {
     if (!identical(c(matches), -1L)) {
       start <- c(attr(matches, "capture.start"))
       end   <- start + c(attr(matches, "capture.length")) - 1
-      decoded <- rawToChar(base64enc::base64decode(substring(line, start, end)))
+      decoded <- rawToChar(xfun::base64_decode(substring(line, start, end)))
       rmd_contents <- strsplit(decoded, "\\r?\\n", perl = TRUE)[[1]]
       next
     }

R/html_notebook_output.R

@@ -39,7 +39,7 @@ html_notebook_render_base64_data <- function(path = NULL,
   # read (if necessary) and encode data
   if (is.null(bytes))
     bytes <- read_file(path, binary = TRUE)
-  encoded <- base64enc::base64encode(bytes)
+  encoded <- xfun::base64_encode(bytes)
 
   # generate html attributes
   sprintf(format, to_html_attributes(attributes), encoded)

R/ioslides_presentation.R

@@ -223,7 +223,8 @@
 #'   To create a PDF version of a presentation you can use Print to PDF
 #'   from Google Chrome.
 #' @export
-ioslides_presentation <- function(logo = NULL,
+ioslides_presentation <- function(number_sections = FALSE,
+                                  logo = NULL,
                                   slide_level = 2,
                                   incremental = FALSE,
                                   fig_width = 7.5,
@@ -343,6 +344,10 @@ ioslides_presentation <- function(logo = NULL,
     # add any custom pandoc args
     args <- c(args, pandoc_args)
 
+    # number sections
+    if (number_sections)
+      args <- c(args, pandoc_lua_filter_args(pkg_file_lua("number-sections.lua")))
+
     lua_writer <- file.path(dirname(input_file), "ioslides_presentation.lua")
     # The input directory may not be writable (on e.g. Shiny Server), so write
     # to the output directory in this case. We don't always do this since
@@ -412,7 +417,7 @@ ioslides_presentation <- function(logo = NULL,
 
     # base64 encode if needed
     if (self_contained) {
-      slides_lines <- base64_image_encode(slides_lines)
+      slides_lines <- base64_encode_images(slides_lines)
     }
 
     # read the output file

R/md_document.R

@@ -37,6 +37,7 @@ md_document <- function(variant = "markdown_strict",
                         preserve_yaml = FALSE,
                         toc = FALSE,
                         toc_depth = 3,
+                        number_sections = FALSE,
                         fig_width = 7,
                         fig_height = 5,
                         fig_retina = NULL,
@@ -75,10 +76,12 @@ md_document <- function(variant = "markdown_strict",
   # return format
   output_format(
     knitr = knitr_options_html(fig_width, fig_height, fig_retina, FALSE, dev),
-    pandoc = pandoc_options(to = variant,
-                            from = from_rmarkdown(extensions = md_extensions),
-                            args = args,
-                            ext = ext),
+    pandoc = pandoc_options(
+      to = variant,
+      from = from_rmarkdown(extensions = md_extensions),
+      args = args,
+      ext = ext,
+      lua_filters = if (number_sections) pkg_file_lua("number-sections.lua")),
     clean_supporting = FALSE,
     df_print = df_print,
     post_processor = post_processor

R/odt_document.R

@@ -31,7 +31,8 @@
 #' render("input.Rmd", odt_document(highlight = "zenburn"))
 #' }
 #' @export
-odt_document <- function(fig_width = 5,
+odt_document <- function(number_sections = FALSE,
+                         fig_width = 5,
                          fig_height = 4,
                          fig_caption = TRUE,
                          template = "default",
@@ -62,9 +63,6 @@ odt_document <- function(fig_width = 5,
   # reference odt
   args <- c(args, reference_doc_args("odt", reference_odt))
 
-  # lua filters (added if pandoc > 2)
-  args <- c(args, pandoc_lua_filters("pagebreak.lua"))
-
   # pandoc args
   args <- c(args, pandoc_args)
 
@@ -81,9 +79,12 @@ odt_document <- function(fig_width = 5,
   # return output format
   output_format(
     knitr = knitr,
-    pandoc = pandoc_options(to = "odt",
-                            from = from_rmarkdown(fig_caption, md_extensions),
-                            args = args),
+    pandoc = pandoc_options(
+      to = "odt",
+      from = from_rmarkdown(fig_caption, md_extensions),
+      args = args,
+      lua_filters = pkg_file_lua(c(
+        "pagebreak.lua", if (number_sections) "number-sections.lua"))),
     keep_md = keep_md,
     pre_processor = pre_processor,
     intermediates_generator = intermediates_generator