Merge remote-tracking branch 'rstudio/master'

* rstudio/master: (61 commits) make metadata available before running pre_knit (rstudio#1855) fix rstudio#1815: apply the lua filters pagebreak.lua and latex-div.lua to beamer_presentation require the data-latex attribute on fenced Div's again: rstudio#1779 (comment) start the next version CRAN release v2.3 fold any code blocks with the class `foldable` for html_document output (rstudio#1835) fix rstudio#1828: add aria-hidden = "true" to empty <a> tags in highlighted code blocks generated by Pandoc to improve screen reader accessibility (rstudio#1833) add a news item for rstudio#1832 roxygenize no need to turn on --file-scope or actually write the split content into files if the split content is of length < 2 eliminate renumber_footnotes option only test two pandoc versions (devel and RStudio version) and upgrade default to 2.7.3 (rstudio#1846) close rstudio#1838: test more R versions on Travis (rstudio#1845) renumber_footnotes output format option add the <div class="kable-table"> only when the output format is HTML, otherwise the div will be converted to a LaTeX environment, leading to the bug https://stackoverflow.com/q/62340425/559676 change name of file_scope argument to references_scope re-roxygenize Add `publish_site()` function for "one-button" publishing of R Markdown websites. Enable use of pandoc --file-scope for input files originating from multiple Rmds (rstudio#1837) Added missing lang attribute to ioslides_presentation template (rstudio#1841) ...
jonathan-g · Jul 7, 2020 · af66857 · af66857
2 parents 15580e5 + ff1b279
commit af66857
Show file tree

Hide file tree

Showing 68 changed files with 886 additions and 327 deletions.
diff --git a/.travis.yml b/.travis.yml
@@ -2,25 +2,38 @@ dist: bionic
 language: r
 cache:
   packages: yes
-pandoc_version: 2.3.1
+  directories:
+  - "$PANDOC"
+pandoc_version: 2.7.3
 cran: https://cran.rstudio.com
 
 env:
   global:
     - _R_CHECK_TESTS_NLINES_=0
-  matrix:
-    - PANDOC_VERSION=default NETLIFY_SITE_ID=5d77c13c-e2ee-4a31-87ca-2fe657196160
-    - PANDOC_VERSION=latest PATH=$HOME/bin:$PATH
 
 before_install:
-  - "[[ ${PANDOC_VERSION} = latest ]] && ./tools/install-pandoc.sh || true"
   - pandoc --version
-  - tlmgr install units
 
-after_success:
-  - "[[ ${TRAVIS_BRANCH}  = master  ]] || exit 0"
-  - "[[ ${PANDOC_VERSION} = default ]] || exit 0"
-  - "[[ -z ${NETLIFY_AUTH_TOKEN} ]] && exit 0"
-  - nvm install stable
-  - npm install netlify-cli -g
-  - Rscript -e 'pkgdown::build_site(".", document = FALSE, preview = FALSE)' && netlify deploy --prod --dir docs
+jobs:
+  include:
+    - r: 3.3
+    - r: 3.4
+    - r: 3.5
+    - r: 3.6
+    - r: release
+      name: R release / Pandoc devel
+      env: PATH=$HOME/bin:$PATH
+      before_install:
+        - ./tools/install-pandoc.sh || true
+        - pandoc --version
+    - r: release
+      name: R release / RStudio Pandoc
+      env: NETLIFY_SITE_ID=5d77c13c-e2ee-4a31-87ca-2fe657196160
+      after_success:
+        - "[[ ${TRAVIS_BRANCH}  = master  ]] || exit 0"
+        - "[[ -z ${NETLIFY_AUTH_TOKEN} ]] && exit 0"
+        - nvm install stable
+        - npm install netlify-cli -g
+        - Rscript -e 'pkgdown::build_site(".", document = FALSE, preview = FALSE)' && netlify deploy --prod --dir docs
+    - r: devel
+
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: rmarkdown
 Type: Package
 Title: Dynamic Documents for R
-Version: 2.0.5
+Version: 2.3.2
 Authors@R: c(
   person("JJ", "Allaire", role = "aut", email = "jj@rstudio.com"),
   person("Yihui", "Xie", role = c("aut", "cre"), email = "xie@yihui.name", comment = c(ORCID = "0000-0003-0645-5666")),
@@ -30,7 +30,7 @@ Authors@R: c(
   person("Sergio", "Oller", role = "ctb"),
   #
   # Copyright holders
-  person(family = "RStudio, Inc.", role = "cph"),
+  person(family = "RStudio, PBC", role = "cph"),
   person(family = "jQuery Foundation", role = "cph",
          comment = "jQuery library"),
   person(family = "jQuery contributors", role = c("ctb", "cph"),
@@ -101,11 +101,11 @@ Suggests:
     tibble,
     fs,
     pkgdown,
-    callr (>= 2.0.0)
+    rsconnect
 SystemRequirements: pandoc (>= 1.12.3) - http://pandoc.org
 URL: https://github.com/rstudio/rmarkdown
 BugReports: https://github.com/rstudio/rmarkdown/issues
 License: GPL-3
-RoxygenNote: 7.0.2
+RoxygenNote: 7.1.0
 Encoding: UTF-8
 VignetteBuilder: knitr
diff --git a/NAMESPACE b/NAMESPACE
@@ -15,6 +15,7 @@ export(default_output_format)
 export(default_site_generator)
 export(draft)
 export(find_external_resources)
+export(find_pandoc)
 export(from_rmarkdown)
 export(github_document)
 export(html_dependency_bootstrap)
@@ -61,6 +62,7 @@ export(pandoc_exec)
 export(pandoc_highlight_args)
 export(pandoc_include_args)
 export(pandoc_latex_engine_args)
+export(pandoc_metadata_arg)
 export(pandoc_options)
 export(pandoc_path_arg)
 export(pandoc_self_contained_html)
@@ -71,6 +73,7 @@ export(pandoc_version)
 export(parse_html_notebook)
 export(pdf_document)
 export(powerpoint_presentation)
+export(publish_site)
 export(relative_to)
 export(render)
 export(render_delayed)

diff --git a/NEWS.md b/NEWS.md
@@ -1,6 +1,69 @@
+rmarkdown 2.4
+================================================================================
+
+- 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).
+
+rmarkdown 2.3
+================================================================================
+
+- Addressed an accessibility issue in highlighted code blocks of HTML output for screen reader users: screen readers no longer read out an unnecessary code line id values (thanks, @jooyoungseo and @atusy, #1833).
+
+- Added `file_scope` option to output format definition. This enables handling of duplicate numeric footnote identifiers (e.g. across bookdown chapters) via the pandoc `--file-scope` option (#1837).
+
+- Added the customizable `lang` attribute to `ioslides_presentation` output (thanks, @jooyoungseo, #1841).
+
+- Added `publish_site()` function for "one-button" publishing of R Markdown websites.
+
+- When the `df_print` option is `kable` and the output format is not HTML, `<div class="kable-table">` is no longer added to the `kable()` output, because recent versions of Pandoc will convert the `div` to a LaTeX environment when the output format is LaTeX (thanks, Laurens, https://stackoverflow.com/q/62340425/559676).
+
+- `html_vignette()` only warns against differences in the vignette title and the vignette index entry for R >= 3.6.0 (thanks, @krlmlr, #1832).
+
+- `html_document()` can apply `code_folding` on any chunk engines if the `foldable` class is added to a source code block via the chunk options (`class.source` or `attr.source`). You may apply this feature to all the source code blocks, for example, by setting `knitr::opts_chunk$set(class.source = "foldable")` at the beginning of your document (thanks, @atusy, #1835).
+
+
+rmarkdown 2.2
+================================================================================
+
+- Exported the internal function `find_pandoc()`, and also added two arguments, `dir` and `version`, so that users can provide a custom directory under which this function may find Pandoc, as well as an expected version of Pandoc to be found (thanks, @connorp, #1785).
+
+- `pandoc_metadata_arg()` is a new Pandoc helper function to generate `--metadata` argument for Pandoc command line (thanks, @cderv, #1789).
+
+- The output format `html_vignette()` now warns against differences in the vignette title specified in the `title` field in the YAML metadata and the one specified inside `\VignetteIndexEntry{}`. Normally they are expected to be identical (#1789).
+
+- Fixed a bug with encoding when rendering `html_notebook` containing HTML widgets (thanks, @cderv, #1799).
+
+- TOC title can now be specified for `html_document` via the top-level option `toc-title` in the YAML frontmatter (thanks, @atusy, #1771).
+
+- Floating TOC can now distinguish upper/lower-cases (thanks, @atusy, #1783).
+
+- When `code_folding='show'` for the output format `html_document`, code blocks can be individually hidden initially by specifying the chunk option `class.source='fold-hide'` (thanks, @atusy, #1798).
+
+- For LaTeX/PDF output formats `pdf_document`, `beamer_presentation`, and `context_document`, the argument `citation_package = 'none'` was deprecated, and `citation_package = 'default'` should be used instead if citations are to be processed by `pandoc-citeproc` (thanks, @njbart, rstudio/bookdown#754).
+
+- `output_format()` can now inherit `keep_md` and `clean_supporting` from `base_format` when `NULL` is passed to these arguments. Previously, you must explicitly specify `keep_md` and/or `clean_supporting` as `TRUE` or `FALSE` in `output_format()` since they could not inherit the corresponding options of `base_format`. This behavior was not consisent with other arguments of `output_format()` (thanks, @atusy, #1823).
+
+- The `smart` argument of most output formats has been removed, because Pandoc's `smart` extension is enabled by default, and setting `smart: false` for an output format did not really have any effect (which could be considered a bug, but we want to get rid of this option since it existed only for a historical reason for Pandoc 1.x, and Pandoc 2.x has been released for more than two years). If you want to disable the `smart` extension, you can use the option `md_extensions: -smart` of the output format (thanks, @atusy, #1774).
+
+- `pdf_document()` should not specify the `geometry` variable when the `documentclass` variable is passed to Pandoc (thanks, @jpcirrus, #1782).
+
+- `render()` now respects the YAML metadata in the R script when rendering the script with Pandoc 2.8 or later (thanks, @nsoranzo #1740, @cderv #1741).
+
+- For `pandoc_convert()`, when the argument `to = 'pdf'`, it will be changed to `'latex'` internally (thanks, @JohannesFriedrich, #1802).
+
+- `render(run_pandoc = FALSE)` no longer cleans up the Markdown file (typically knitted from Rmd) (thanks, @BrianDiggs, #1812).
+
+
 rmarkdown 2.1
 ================================================================================
 
+- Added the returned output from `shiny::runApp()` within `rmarkdown::run()` (thanks, @schloerke, #1760).
+
+- YAML header is now correctly parsed in `html_notebook`'s intermediate `.knit.md` file so that features like adding bibliography works again (thanks, @everdark, @cderv, #1747).
+
 - `ioslides_presentation` template no longer generates an empty `<h2>` tag when `subtitle` is not specified in YAML (thanks, @jooyoungseo #1735, @cgrudz #1663).
 
 - No longer center the `#header` element in the `html_vignette()` output (thanks, @EmilHvitfeldt, #1742).
@@ -11,6 +74,8 @@ rmarkdown 2.1
 
 - Removed the jQuery dependency in `html_document_base()` (#1723). To avoid bugs like #1723, Pandoc 2.8 users have to upgrade to Pandoc 2.9+.
 
+- For `pdf_document`, horizontal rules generated by Pandoc (before v2.8) stopped working in recent versions of TeX Live, and the same fix as the one to https://github.com/jgm/pandoc/issues/5801 (i.e., hard-code `\linethickness` to `0.5pt`) was applied in **rmarkdown** (thanks, @cderv, https://stackoverflow.com/a/58646915/559676).
+
 
 rmarkdown 2.0
 ================================================================================

diff --git a/R/beamer_presentation.R b/R/beamer_presentation.R
@@ -66,7 +66,7 @@ beamer_presentation <- function(toc = FALSE,
                                 keep_tex = FALSE,
                                 keep_md = FALSE,
                                 latex_engine = "pdflatex",
-                                citation_package = c("none", "natbib", "biblatex"),
+                                citation_package = c("default", "natbib", "biblatex"),
                                 self_contained = TRUE,
                                 includes = NULL,
                                 md_extensions = NULL,
@@ -115,8 +115,7 @@ beamer_presentation <- function(toc = FALSE,
   args <- c(args, pandoc_latex_engine_args(latex_engine))
 
   # citation package
-  citation_package <- match.arg(citation_package)
-  if (citation_package != "none") args <- c(args, paste0("--", citation_package))
+  args <- c(args, citation_package_arg(citation_package))
 
   # generate a self-contained LaTeX document (including preamble)
   if (self_contained) args <- c(args, "--self-contained")
@@ -127,6 +126,8 @@ 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)
 

diff --git a/R/context_document.R b/R/context_document.R
@@ -85,8 +85,7 @@ context_document <- function(toc = FALSE,
     args <- c(args, "--template", pandoc_path_arg(template))
 
   # citation package
-  citation_package <- match.arg(citation_package)
-  if (citation_package != "none") args <- c(args, paste0("--", citation_package))
+  args <- c(args, citation_package_arg(citation_package))
 
   # content includes
   args <- c(args, includes_to_pandoc_args(includes))

diff --git a/R/html_dependencies.R b/R/html_dependencies.R
@@ -71,6 +71,18 @@ html_dependency_tocify <- function() {
     stylesheet = "jquery.tocify.css")
 }
 
+# Create an HTML dependency for Pandoc code block accessibility
+html_dependency_accessible_code_block <- function() {
+  ver <- pandoc_version()
+  if (ver < '2.7.3' || ver > '2.9.2.1') return()
+  htmlDependency(
+    name = "accessible-code-block",
+    version = "0.0.1",
+    src = pkg_file("rmd/h/accessibility"),
+    script = "empty-anchor.js"
+  )
+}
+
 # Create an HTML dependency for FontAwesome
 #' @rdname html-dependencies
 #' @export

diff --git a/R/html_document.R b/R/html_document.R
@@ -39,9 +39,6 @@
 #'  chunks by default.
 #'@param code_download Embed the Rmd source code within the document and provide
 #'  a link that can be used by readers to download the code.
-#'@param smart Produce typographically correct output, converting straight
-#'  quotes to curly quotes, \code{---} to em-dashes, \code{--} to en-dashes, and
-#'  \code{...} to ellipses.
 #'@param self_contained Produce a standalone HTML file with no external
 #'  dependencies, using data: URIs to incorporate the contents of linked
 #'  scripts, stylesheets, images, and videos. Note that even for self contained
@@ -191,7 +188,6 @@ html_document <- function(toc = FALSE,
                           df_print = "default",
                           code_folding = c("none", "show", "hide"),
                           code_download = FALSE,
-                          smart = TRUE,
                           self_contained = TRUE,
                           theme = "default",
                           highlight = "default",
@@ -216,8 +212,6 @@ html_document <- function(toc = FALSE,
   # table of contents
   args <- c(args, pandoc_toc_args(toc, toc_depth))
 
-  md_extensions <- smart_extension(smart, md_extensions)
-
   # toc_float
   if (toc && !identical(toc_float, FALSE)) {
 
@@ -285,9 +279,15 @@ html_document <- function(toc = FALSE,
   args <- c(args, pandoc_html_highlight_args(template, highlight))
 
   # add highlight.js html_dependency if required
-  if (identical(template, "default") && is_highlightjs(highlight)) {
-    extra_dependencies <- append(extra_dependencies, list(html_dependency_highlightjs(highlight)))
-  }
+  extra_dependencies <- append(
+    extra_dependencies,
+    if (identical(template, "default") && is_highlightjs(highlight)) {
+      list(html_dependency_highlightjs(highlight))
+    } else if (!is.null(highlight)) {
+      # for screen-reader accessibility improvement
+      list(html_dependency_accessible_code_block())
+    }
+  )
 
   # numbered sections
   if (number_sections)
@@ -439,7 +439,7 @@ html_document <- function(toc = FALSE,
     post_knit = post_knit,
     pre_processor = pre_processor,
     on_exit = on_exit,
-    base_format = html_document_base(smart = smart, theme = theme,
+    base_format = html_document_base(theme = theme,
                                      self_contained = self_contained,
                                      lib_dir = lib_dir, mathjax = mathjax,
                                      template = template,

diff --git a/R/html_document_base.R b/R/html_document_base.R
@@ -7,15 +7,16 @@
 #'
 #' @param dependency_resolver A dependency resolver
 #' @param copy_resources Copy resources
-#' @param extra_dependencies Extra dependencies
+#' @param extra_dependencies Extra dependencies as a list of the
+#'   \code{html_dependency} class objects typically generated by
+#'   \code{htmltools::\link{htmlDependency}()}.
 #' @param bootstrap_compatible Bootstrap compatible
 #' @param ... Ignored
 #'
 #' @return HTML base output format.
 #'
 #' @export
-html_document_base <- function(smart = TRUE,
-                               theme = NULL,
+html_document_base <- function(theme = NULL,
                                self_contained = TRUE,
                                lib_dir = NULL,
                                mathjax = "default",
@@ -33,10 +34,6 @@ html_document_base <- function(smart = TRUE,
 
   args <- c()
 
-  # smart quotes, etc.
-  if (smart && !pandoc2.0())
-    args <- c(args, "--smart")
-
   # no email obfuscation
   args <- c(args, "--email-obfuscation", "none")
 

diff --git a/R/html_fragment.R b/R/html_fragment.R
@@ -23,7 +23,6 @@ html_fragment <- function(number_sections = FALSE,
                           fig_caption = TRUE,
                           dev = 'png',
                           df_print = "default",
-                          smart = TRUE,
                           mathjax = TRUE,
                           includes = NULL,
                           keep_md = FALSE,
@@ -37,7 +36,7 @@ html_fragment <- function(number_sections = FALSE,
   html_document(
     number_sections = number_sections, fig_width = fig_width,
     fig_height = fig_height, fig_retina = fig_retina, fig_caption = fig_caption,
-    dev = dev, df_print = df_print, smart = smart, keep_md = keep_md,
+    dev = dev, df_print = df_print, keep_md = keep_md,
     md_extensions = md_extensions, pandoc_args = pandoc_args, includes = includes,
     mathjax = NULL, section_divs = section_divs, highlight = NULL, theme = NULL, ...,
     template = pkg_file("rmd/fragment/default.html")

diff --git a/R/html_notebook.R b/R/html_notebook.R
@@ -25,7 +25,6 @@ html_notebook <- function(toc = FALSE,
                           fig_retina = 2,
                           fig_caption = TRUE,
                           code_folding = "show",
-                          smart = TRUE,
                           theme = "default",
                           highlight = "textmate",
                           mathjax = "default",
@@ -200,7 +199,6 @@ html_notebook <- function(toc = FALSE,
                                fig_retina = fig_retina,
                                fig_caption = fig_caption,
                                code_folding = code_folding,
-                               smart = smart,
                                theme = theme,
                                highlight = highlight,
                                mathjax = mathjax,

diff --git a/R/html_paged.R b/R/html_paged.R
@@ -205,7 +205,25 @@ paged_table_html <- function(x, options = NULL) {
 #' Create a table in HTML with support for paging rows and columns
 #'
 #' @param x a data frame to be rendered as a paged table.
-#' @param options options for printing the paged table
+#' @param options options for printing the paged table. See details for specifics.
+#'
+#' @details
+#' Below are the recognized table pagination options.
+#'
+#' \tabular{rll}{
+#' Option \tab Description \tab Default \cr
+#' \code{max.print} \tab The number of rows to print. \tab 1000 \cr
+#' \code{sql.max.print} \tab The number of rows to print from a SQL data table. \tab 1000 \cr
+#' \code{rows.print} \tab The number of rows to display. \tab 10 \cr
+#' \code{cols.print} \tab The number of columns to display. \tab 10 \cr
+#' \code{cols.min.print} \tab The minimum number of columns to display. \tab - \cr
+#' \code{pages.print} \tab The number of pages to display under page navigation. \tab - \cr
+#' \code{paged.print} \tab When set to FALSE turns off paged tables. \tab TRUE \cr
+#' \code{rownames.print} \tab When set to FALSE turns off row names. \tab TRUE
+#' }
+#'
+#' \bold{Note:} There is a hard cap of 10,000 rows to ensure that pandoc will not
+#' fail when rendering the document.
 #'
 #' @export
 paged_table <- function(x, options = NULL) {

diff --git a/R/html_resources.R b/R/html_resources.R
@@ -345,7 +345,7 @@ discover_rmd_resources <- function(rmd_file, discover_single_resource) {
   )
 
   # clean up output file and its supporting files directory
-  temp_files <- c(temp_files, html_file, knitr_files_dir(md_file))
+  temp_files <- c(temp_files, html_file, knitr_files_dir(md_file), knitr_files_dir(html_file))
 
   # run the HTML resource discovery mechanism on the rendered output
   discover_html_resources(html_file, discover_single_resource)