Merged with Rstudio main branch.

Merge remote-tracking branch 'rstudio/main' into jg-devel # By Yihui Xie (10) and others # Via GitHub * rstudio/main: Fix Pandoc nightly install in GHA (rstudio#2559) feat(beamer): support latex_dependencies (rstudio#2558) start the next version CRAN release 2.27 export S3 method rsconnect::deploySite() has combined the arguments account and server in the doc Update forum url (rstudio#2555) Fix regression w/ image path processing from absolute to relative (rstudio#2554) Update posit forum URL provide an option to set the `*_files/` directory suffix (rstudio#2550) start the next version CRAN release v2.26 use _PACKAGE as recommended by roxygen2 use \describe{} instead of \itemize{} (r-devel will warn against it) [GHA] Remove duplicate entry in matrix new r-lib/actions@v2 has newer setup-pandoc [GHA] New setup pandoc action (rstudio#2543) Correctly avoid writing to the input file when there are no preserved HTML chunks (rstudio#2535) Create FUNDING.yml Fix small grammatical error (rstudio#2533) # Conflicts: # DESCRIPTION # R/publish_site.R
jonathan-g · Aug 7, 2024 · 73ec42f · 73ec42f
2 parents ca6f80b + a9497ff
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diff --git a/.github/FUNDING.yml b/.github/FUNDING.yml
@@ -0,0 +1,3 @@
+github: [yihui]
+patreon:
+custom:
diff --git a/.github/ISSUE_TEMPLATE/bug-report.md b/.github/ISSUE_TEMPLATE/bug-report.md
@@ -7,7 +7,7 @@ assignees: ''
 ---
 
 <!--
-Welcome to the rmarkdown GitHub repo!
+Welcome to the rmarkdown GitHub repo !
 
 We are always happy to hear feedback from our users. 
 
@@ -31,4 +31,5 @@ When filing a _bug report_, please check the boxes below to confirm that you hav
 
 - [ ] upgraded all your packages to their latest versions (including your versions of R, the RStudio IDE, and relevant R packages)?
 
-- [ ] installed and tested your bug with the development version of the rmarkdown package using `remotes::install_github("rstudio/rmarkdown")`?
+- [ ] installed and tested your bug with the development version of the rmarkdown package using `remotes::install_github("rstudio/rmarkdown")` ?
+
diff --git a/.github/ISSUE_TEMPLATE/config.yml b/.github/ISSUE_TEMPLATE/config.yml
@@ -3,8 +3,8 @@ contact_links:
   - name: Issue guide
     url: https://yihui.org/issue/
     about: First time here or need a refresh? Please consult the issue guide before posting.
-  - name: Ask a question on RStudio Community
-    url: https://community.rstudio.com/c/r-markdown/10
+  - name: Ask a question on Posit Forum
+    url: https://forum.posit.co/
     about: Please ask and answer questions here.
   - name: Ask a question on Stack Overflow
     url: https://stackoverflow.com/questions/tagged/r+r-markdown

diff --git a/.github/ISSUE_TEMPLATE/feature-request.md b/.github/ISSUE_TEMPLATE/feature-request.md
@@ -8,7 +8,7 @@ assignees: ''
 
 <!--
 
-Welcome to the rmarkdown GitHub repo 👋
+Welcome to the rmarkdown GitHub repo !
 
 Thanks for taking the time to file a feature request! Please start by searching for an existing feature request to avoid creating duplicate requests. If you find an existing feature request, please give it a thumbs-up reaction, as we'll use these reactions to help prioritize the implementation of these features in the future.
 

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -30,10 +30,11 @@ jobs:
       matrix:
         config:
           # testing R release with last shipped pandoc version in RStudio IDE and new pandoc
-          - {os: windows-latest, pandoc: '3.1.6.2',  r: 'release'}
-          - {os: macOS-latest,   pandoc: '3.1.6.2',  r: 'release'}
+          - {os: windows-latest, pandoc: 'latest',  r: 'release'}
+          - {os: macOS-latest,   pandoc: 'latest',  r: 'release'}
           - {os: ubuntu-latest,  pandoc: 'devel',    r: 'release'}
           # testing older pandoc versions
+          - {os: ubuntu-latest,  pandoc: '3.1.11',   r: 'release'}
           - {os: ubuntu-latest,  pandoc: '2.19.2',   r: 'release'}
           - {os: ubuntu-latest,  pandoc: '2.18',     r: 'release'}
           - {os: ubuntu-latest,  pandoc: '2.17.1.1', r: 'release'}
@@ -43,15 +44,18 @@ jobs:
           - {os: ubuntu-latest,  pandoc: '2.7.3',    r: 'release'}
           - {os: ubuntu-latest,  pandoc: '2.5',      r: 'release'}
           # testing other R versions
-          - {os: ubuntu-latest,  pandoc: '2.11.4',   r: 'devel', http-user-agent: 'release'}
-          - {os: ubuntu-latest,  pandoc: '2.11.4',   r: 'oldrel-1'}
-          - {os: ubuntu-latest,  pandoc: '2.11.4',   r: 'oldrel-2'}
-          - {os: ubuntu-latest,  pandoc: '2.11.4',   r: 'oldrel-3'}
+          - {os: ubuntu-latest,  pandoc: 'latest',   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,  pandoc: 'latest',   r: 'oldrel-1'}
+          - {os: ubuntu-latest,  pandoc: 'latest',   r: 'oldrel-2'}
+          - {os: ubuntu-latest,  pandoc: 'latest',   r: 'oldrel-3'}
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
 
+    permissions:
+      actions: read
+
     steps:
       - uses: actions/checkout@v3
 

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Type: Package
 Package: rmarkdown
 Title: Dynamic Documents for R
-Version: 2.25.2.9000
+Version: 2.27.1.9000
 Authors@R: c(
     person("JJ", "Allaire", , "[email protected]", role = "aut"),
     person("Yihui", "Xie", , "[email protected]", role = c("aut", "cre"), comment = c(ORCID = "0000-0003-0645-5666")),
@@ -84,9 +84,11 @@ Suggests:
     tibble,
     vctrs,
     cleanrmd,
-    withr (>= 2.4.2)
+    withr (>= 2.4.2),
+    xml2
 VignetteBuilder: knitr
 Config/Needs/website: rstudio/quillt, pkgdown
+Config/testthat/edition: 3
 Encoding: UTF-8
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 SystemRequirements: pandoc (>= 1.14) - http://pandoc.org
diff --git a/NAMESPACE b/NAMESPACE
@@ -8,6 +8,7 @@ S3method(prepare_evaluate_output,default)
 S3method(prepare_evaluate_output,htmlwidget)
 S3method(prepare_evaluate_output,knit_asis)
 S3method(prepare_evaluate_output,list)
+S3method(print,paged_df)
 export(all_output_formats)
 export(available_templates)
 export(beamer_presentation)

diff --git a/NEWS.md b/NEWS.md
@@ -1,4 +1,4 @@
-rmarkdown 2.26
+rmarkdown 2.28
 ================================================================================
 
 - `html_document` output allows `lib_dir` to point to a parent of the output 
@@ -9,6 +9,19 @@ rmarkdown 2.26
   child directories with RMarkdown files. #146 and #1859.
   (thanks, @jonathan-g, #2199)
 
+- `beamer_presentation` support handling latex dependencies via the new `extra_dependencies` argument and declarations within chunks (e.g., `knitr::asis_output("", meta = list(rmarkdown::latex_dependency("longtable")))`) (thanks, @cderv, @atusy, #2478).
+
+rmarkdown 2.27
+================================================================================
+
+- Provide a global option `rmarkdown.files.suffix` to configure the suffix of the directory for auxiliary files (thanks, @certara-tzweers, #2550). By default, this suffix is `_files`, which can cause HTML output files to be deleted automatically on Microsoft OneDrive or Google Drive. If that is the case for you, you may set a different suffix in your `.Rprofile`, e.g., `options(rmarkdown.files.suffix = "_rmdfiles")`.
+
+- Fix a regression in 2.26 regarding image paths post-processing in `html_document_base()`. Now absolute paths to image in the output directory (`output_dir`) are correctly made relative to the output directory again.
+
+
+rmarkdown 2.26
+================================================================================
+
 - **rmarkdown** now requires **knitr** >= 1.43.
 
 - Get rid of the superfluous warning in `find_pandoc()` (thanks, @jszhao, #2527).
@@ -17,6 +30,8 @@ rmarkdown 2.26
 
 - For the output format option `fig_crop: auto`, it will now use the same logic as in **knitr** to decide if cropping is possible (yihui/knitr#2246).
 
+- Avoid corrupting input files by accident (thanks, @J-Moravec, #2534).
+
 
 rmarkdown 2.25
 ================================================================================

diff --git a/R/base64.R b/R/base64.R
@@ -1,6 +1,7 @@
 # processes an HTML resource, given a regular expression that locates
 # instances of that resource
 process_html_res <- function(html, reg, processor) {
+  html <- one_string(html)
   m <- gregexpr(reg, html, perl = TRUE, ignore.case = TRUE)
   regmatches(html, m) <- lapply(regmatches(html, m), function(img_src) {
     src <- sub(reg, '\\1', img_src, ignore.case = TRUE)
@@ -10,7 +11,7 @@ process_html_res <- function(html, reg, processor) {
       character(1)
     )
   })
-  html
+  strsplit(html, "\n", fixed = TRUE)[[1]]
 }
 
 process_images <- function(html, processor) {

diff --git a/R/beamer_presentation.R b/R/beamer_presentation.R
@@ -71,7 +71,8 @@ beamer_presentation <- function(toc = FALSE,
                                 self_contained = TRUE,
                                 includes = NULL,
                                 md_extensions = NULL,
-                                pandoc_args = NULL) {
+                                pandoc_args = NULL,
+                                extra_dependencies = NULL) {
 
   # base pandoc options for all beamer output
   args <- c()
@@ -144,6 +145,12 @@ beamer_presentation <- function(toc = FALSE,
     # https://github.com/rstudio/rmarkdown/issues/2294
     args <- append_in_header(process_header_includes(metadata))
 
+    if (length(extra_dependencies) || has_latex_dependencies(knit_meta)) {
+      extra_dependencies <- latex_dependencies(extra_dependencies)
+      all_dependencies <- append(extra_dependencies, flatten_latex_dependencies(knit_meta))
+      args <- c(args, append_in_header(latex_dependencies_as_string(all_dependencies)))
+    }
+
     # no-op other than caching dir location
     args
   }

diff --git a/R/html_document_base.R b/R/html_document_base.R
@@ -263,7 +263,12 @@ html_document_base <- function(theme = NULL,
 }
 
 extract_preserve_chunks <- function(input_file, extract = extractPreserveChunks) {
-  input_str <- read_utf8(input_file)
+  # Don't try to modify the input file if it's not .md, otherwise the original
+  # input could be corrupted (#2534). In theory, preserved chunks should only
+  # exist in the intermediate .md file from knit(). If the .md file is not
+  # intermediate but original, this processing should be harmless.
+  if (!xfun::file_ext(input_file) %in% c('md', 'markdown')) return()
+  input_str <- one_string(read_utf8(input_file))
   preserve <- extract(input_str)
   if (!identical(preserve$value, input_str)) write_utf8(preserve$value, input_file)
   preserve$chunks

diff --git a/R/html_paged.R b/R/html_paged.R
@@ -238,6 +238,7 @@ paged_table <- function(x, options = NULL) {
   x
 }
 
+#' @export
 print.paged_df <- function(x, ...) {
   knitr::asis_output(
     paged_table_html(x, options = attr(x, "options")),

diff --git a/R/ioslides_presentation.R b/R/ioslides_presentation.R
@@ -87,7 +87,7 @@
 #' @section Display Modes:
 #'   The following single character keyboard shortcuts enable alternate display
 #'   modes:
-#'   \itemize{
+#'   \describe{
 #'     \item{`'f'`      }{enable fullscreen mode}
 #'     \item{`'w'`      }{toggle widescreen mode}
 #'     \item{`'o'`      }{enable overview mode}

diff --git a/R/publish_site.R b/R/publish_site.R
@@ -7,12 +7,12 @@
 #' @param site_name Name for the site (names must be unique within an account). Defaults
 #'   to the `name` provided by the site generator (or to the name of the site_dir if
 #'   there is no `name` specified).
+#' @param method Publishing method (currently only "rsconnect" is available)
 #' @param server Server name. Required only if you use the same account name on
 #'   multiple servers.
 #' @param account Account to deploy application to. This parameter is only required for
 #'   the initial deployment of an application when there are multiple accounts configured
 #'   on the system.
-#' @param method Publishing method (currently only "rsconnect" is available)
 #' @param render `TRUE` to render the site locally before publishing.
 #' @param launch_browser If `TRUE`, the system's default web browser will be launched
 #'   automatically after the site is deployed. Defaults to `TRUE` in interactive sessions

diff --git a/R/render.R b/R/render.R
@@ -801,7 +801,7 @@ render <- function(input,
         stop2("Functions that produce HTML output found in document targeting ",
              pandoc_to, " output.\nPlease change the output type ",
              "of this document to HTML.\n",
-             "If your aiming to have some HTML widgets shown in non-HTML format as a screenshot,\n",
+             "If you're aiming to have some HTML widgets shown in non-HTML format as a screenshot,\n",
              "please install webshot or webshot2 R package for knitr to do the screenshot, and configure it by looking at its documentation.\n",
              "Alternatively, you can allow HTML output in non-HTML formats\n",
              "by adding this option to the YAML front-matter of\nyour rmarkdown file:\n\n",

diff --git a/R/rmarkdown-package.R b/R/rmarkdown-package.R
@@ -25,5 +25,4 @@
 #'   \link{word_document}, \link{beamer_presentation}
 #' @name rmarkdown-package
 #' @aliases rmarkdown
-#' @docType package
-NULL
+"_PACKAGE"
diff --git a/R/util.R b/R/util.R
@@ -184,7 +184,8 @@ file_with_meta_ext <- function(file, meta_ext, ext = xfun::file_ext(file)) {
 }
 
 knitr_files_dir <- function(file) {
-  paste(xfun::sans_ext(file), "_files", sep = "")
+  suffix <- getOption("rmarkdown.files.suffix", "_files")
+  paste(xfun::sans_ext(file), suffix, sep = "")
 }
 
 knitr_root_cache_dir <- function(file) {

diff --git a/README.md b/README.md
@@ -69,7 +69,7 @@ You can also click "Knit to HTML" again to render the full document with all cod
 
 There are two main places to get help:
 
-1. The [RStudio community](https://community.rstudio.com/c/r-markdown/10) is a friendly place to ask any questions about rmarkdown and the R Markdown family of packages.
+1. The [Posit community](https://forum.posit.co/c/quarto-r-markdown/10) is a friendly place to ask any questions about rmarkdown and the R Markdown family of packages.
 
 1. [Stack Overflow](https://stackoverflow.com/questions/tagged/r-markdown) is a great source of answers to common rmarkdown questions. It is also a great place to get help, once you have created a reproducible example that illustrates your problem.
 

diff --git a/man/beamer_presentation.Rd b/man/beamer_presentation.Rd
diff --git a/man/ioslides_presentation.Rd b/man/ioslides_presentation.Rd
diff --git a/man/publish_site.Rd b/man/publish_site.Rd
diff --git a/man/rmarkdown-package.Rd b/man/rmarkdown-package.Rd
-Original file line number
+Diff line change
@@ Expand Up / @@ -8,7 +8,7 @@ assignees: '' @@
     <!--
-    Welcome to the rmarkdown GitHub repo 👋
+    Welcome to the rmarkdown GitHub repo !
     Thanks for taking the time to file a feature request! Please start by searching for an existing feature request to avoid creating duplicate requests. If you find an existing feature request, please give it a thumbs-up reaction, as we'll use these reactions to help prioritize the implementation of these features in the future.
@@ Expand Down @@