Merged changes in jg-tree-fix.

Merge branch 'jg-tree-fix' into jg-devel # By Yihui Xie (9) and others # Via Jonathan Gilligan (3) and Yihui Xie (1) * jg-tree-fix: import bslib (rstudio#2154) CRAN release v2.11 https://rmarkdown.rstudio.com/authoring_bibliographies_and_citations.html -> https://pandoc.org/MANUAL.html#citations Add a specific dirname for sass caching roxygenize and bump version export convert_ipynb() per suggestion of @acircleda use sass::output_template() instead of storing a copy in rmarkdown fix yihui/xaringan#331: respect relative paths in parent directories in the `css` argument of `html_document()` Bump version Prerender shiny rmd in separate environment (rstudio#2203) Mark result of citeproc conversion as UTF-8 (rstudio#2202) Fixed conflicts with rstudio main version. Update documentation for html_document. Add self (JG) as a contributor in DESCRIPTION. Resolve conflicts with new updates to RStudio main branch. pin the jquery version to 3: rstudio#2197 (comment) # Conflicts: # DESCRIPTION # NEWS.md
jonathan-g · Sep 17, 2021 · bf4c982 · bf4c982
2 parents af48995 + 8ee68eb
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: rmarkdown
 Type: Package
 Title: Dynamic Documents for R
-Version: 2.10.1
+Version: 2.11.1.9000
 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")),
@@ -25,7 +25,7 @@ Authors@R: c(
   person("Devon", "Ryan", role = "ctb", email = "[email protected]", comment = c(ORCID = "0000-0002-8549-0971")),
   person("Frederik", "Aust", role = "ctb", email = "[email protected]", comment = c(ORCID = "0000-0003-4900-788X")),
   person("Jeff", "Allen", role = "ctb", email = "[email protected]"),
-  person("Jonathan", "Gilligan", role = "ctb", email="[email protected]", comment=c(ORCID="0000-0003-1375-6686")),
+  person("Jonathan", "Gilligan", role = "ctb", email = "[email protected]", comment = c(ORCID = "0000-0003-1375-6686")),
   person("JooYoung", "Seo", role="ctb", comment = c(ORCID = "0000-0002-4064-6012")),
   person("Malcolm", "Barrett", role = "ctb"),
   person("Rob", "Hyndman", role = "ctb", email = "[email protected]"),
@@ -90,6 +90,7 @@ Imports:
     tinytex (>= 0.31),
     xfun (>= 0.21),
     jquerylib,
+    bslib (>= 0.2.5.1),
     methods,
     stringr (>= 1.2.0)
 Suggests:
@@ -103,12 +104,11 @@ Suggests:
     fs,
     rsconnect,
     withr (>= 2.4.2),
-    bslib (>= 0.2.5.1),
     sass (>= 0.4.0)
 SystemRequirements: pandoc (>= 1.14) - http://pandoc.org
 URL: https://github.com/rstudio/rmarkdown, https://pkgs.rstudio.com/rmarkdown/
 BugReports: https://github.com/rstudio/rmarkdown/issues
 License: GPL-3
-RoxygenNote: 7.1.1
+RoxygenNote: 7.1.2
 Encoding: UTF-8
 VignetteBuilder: knitr
diff --git a/NAMESPACE b/NAMESPACE
@@ -11,6 +11,7 @@ export(all_output_formats)
 export(beamer_presentation)
 export(clean_site)
 export(context_document)
+export(convert_ipynb)
 export(default_output_format)
 export(default_site_generator)
 export(draft)

diff --git a/NEWS.md b/NEWS.md
@@ -1,4 +1,4 @@
-rmarkdown 2.11
+rmarkdown 2.12
 ================================================================================
 
 - `html_document` output allows `lib_dir` to point to a parent of the output 
@@ -8,6 +8,18 @@ rmarkdown 2.11
   where there is a shared master library with css, javascript, etc. and separate 
   child directories with RMarkdown files. #146 and #1859.
 
+rmarkdown 2.11
+================================================================================
+
+- Relative paths in parent directories in the `css` argument of `html_document()` were incorrectly normalized to absolute paths by #2095 in v2.8. Now relative paths in parent directories will no longer be converted to absolute paths (thanks, @daijiang, yihui/xaringan#331).
+
+- It is possible to specify the version of jQuery via a global option now, e.g., `options(rmarkdown.jquery.version = 2)` (note that the default major version is `3`). This is mainly for advanced users and developers to test different versions of jQuery.
+
+- `pandoc_citeproc_convert()` now handles correctly bib file containing specific UTF-8 characters on non default UTF-8 systems like Windows (thanks, @mitchelloharawild, #2195).
+
+- Shiny prerendered documents are now pre-rendered in a child environment to avoid allowing the results of static code chunks to exist in the Shiny app environment (@gadenbuie, #2203).
+
+- The previously unexported function `convert_ipynb()` is exported now (thanks, @acircleda).
 
 rmarkdown 2.10
 ================================================================================

diff --git a/R/beamer_presentation.R b/R/beamer_presentation.R
@@ -14,7 +14,7 @@
 #'
 #' R Markdown documents also support citations. You can find more information on
 #' the markdown syntax for citations in the
-#' \href{https://rmarkdown.rstudio.com/authoring_bibliographies_and_citations.html}{Bibliographies
+#' \href{https://pandoc.org/MANUAL.html#citations}{Bibliographies
 #' and Citations} article in the online documentation.
 #' @inheritParams pdf_document
 #' @inheritParams html_document

diff --git a/R/context_document.R b/R/context_document.R
@@ -14,7 +14,7 @@
 #'
 #' R Markdown documents also support citations. You can find more information on
 #' the markdown syntax for citations in the
-#' \href{https://rmarkdown.rstudio.com/authoring_bibliographies_and_citations.html}{Bibliographies
+#' \href{https://pandoc.org/MANUAL.html#citations}{Bibliographies
 #' and Citations} article in the online documentation.
 #' @inheritParams pdf_document
 #' @param context_path Path of the ConTeXt executable. If not provided, ConTeXt has

diff --git a/R/html_dependencies.R b/R/html_dependencies.R
@@ -16,7 +16,7 @@ NULL
 #' @rdname html-dependencies
 #' @export
 html_dependency_jquery <- function()  {
-  jquerylib::jquery_core()
+  jquerylib::jquery_core(major_version = getOption('rmarkdown.jquery.version', 3))
 }
 
 # Create an HTML dependency for jQuery UI

diff --git a/R/html_document.R b/R/html_document.R
@@ -12,7 +12,7 @@
 #'
 #' R Markdown documents also support citations. You can find more information on
 #' the markdown syntax for citations in the
-#' \href{https://rmarkdown.rstudio.com/authoring_bibliographies_and_citations.html}{Bibliographies
+#' \href{https://pandoc.org/MANUAL.html#citations}{Bibliographies
 #' and Citations} article in the online documentation.
 #'
 #'@inheritParams output_format

diff --git a/R/html_document_base.R b/R/html_document_base.R
@@ -102,15 +102,15 @@ html_document_base <- function(theme = NULL,
         f <- sass::sass(
           sass::sass_file(f),
           # write output file to `lib_dir/sass-{sass:::sass_hash()}{[basename(f)}`
-          output = sass_output_template(
+          output = sass::output_template(
             basename = xfun::sans_ext(basename(f)),
-            tmpdir = lib_dir
+            dirname = "sass",
+            path = lib_dir
           ),
           options = sass::sass_options(output_style = "compressed")
         )
+        f <- normalized_relative_to(output_dir, f)
       }
-      # do not normalize web path
-      if (!xfun::is_web_path(f)) f <- normalized_relative_to(output_dir, f)
       args <- c(args, "--css", pandoc_path_arg(f, backslash = FALSE))
     }
 
@@ -257,26 +257,3 @@ extract_preserve_chunks <- function(input_file, extract = extractPreserveChunks)
   if (!identical(preserve$value, input_str)) write_utf8(preserve$value, input_file)
   preserve$chunks
 }
-
-
-# inspired by sass::output_template but writes to a custom temp dir instead of only tempdir()
-# TODO: use the one from sass package when sass 0.3.2 in on CRAN (rstudio/sass#77)
-sass_output_template <- function(basename = "rmarkdown", dirname = "sass",
-                                 fileext = NULL, tmpdir = tempdir()) {
-  function(options = list(), suffix = NULL) {
-    fileext <- fileext %||% if (isTRUE(options$output_style %in%
-                                       c(2, 3)))
-      ".min.css"
-    else ".css"
-    out_dir <- if (is.null(suffix)) {
-      tempfile(tmpdir = tmpdir, pattern = dirname)
-    }
-    else {
-      file.path(tmpdir, paste0(dirname, suffix))
-    }
-    if (!dir.exists(out_dir)) {
-      dir.create(out_dir, recursive = TRUE)
-    }
-    file.path(out_dir, paste0(basename, fileext))
-  }
-}
diff --git a/R/jupyter.R b/R/jupyter.R
@@ -19,7 +19,7 @@
 #' @param input Path to the input \file{.ipynb} file.
 #' @param output The output file path.
 #' @return The output file path (invisibly).
-#' @keywords internal
+#' @export
 #' @examples
 #' # this is not a real ipynb file, but illustrates what convert_ipynb() does
 #' nb_data <- list(

diff --git a/R/odt_document.R b/R/odt_document.R
@@ -11,7 +11,7 @@
 #'
 #' R Markdown documents also support citations. You can find more information on
 #' the markdown syntax for citations in the
-#' \href{https://rmarkdown.rstudio.com/authoring_bibliographies_and_citations.html}{Bibliographies
+#' \href{https://pandoc.org/MANUAL.html#citations}{Bibliographies
 #' and Citations} article in the online documentation.
 #' @inheritParams pdf_document
 #' @inheritParams html_document

diff --git a/R/pandoc.R b/R/pandoc.R
@@ -157,6 +157,8 @@ pandoc_citeproc_convert <- function(file, type = c("list", "json", "yaml")) {
     stop("Error ", status, " occurred building shared library.")
   }
 
+  Encoding(result) <- "UTF-8"
+
   # convert the output if requested
   if (type == "list") {
     jsonlite::fromJSON(result, simplifyVector = FALSE)

diff --git a/R/pdf_document.R b/R/pdf_document.R
@@ -14,7 +14,7 @@
 #'
 #' R Markdown documents also support citations. You can find more information on
 #' the markdown syntax for citations in the
-#' \href{https://rmarkdown.rstudio.com/authoring_bibliographies_and_citations.html}{Bibliographies
+#' \href{https://pandoc.org/MANUAL.html#citations}{Bibliographies
 #' and Citations} article in the online documentation.
 #'
 #' Many aspects of the LaTeX template used to create PDF documents can be

diff --git a/R/rtf_document.R b/R/rtf_document.R
@@ -11,7 +11,7 @@
 #'
 #' R Markdown documents also support citations. You can find more information on
 #' the markdown syntax for citations in the
-#' \href{https://rmarkdown.rstudio.com/authoring_bibliographies_and_citations.html}{Bibliographies
+#' \href{https://pandoc.org/MANUAL.html#citations}{Bibliographies
 #' and Citations} article in the online documentation.
 #' @inheritParams pdf_document
 #' @inheritParams html_document

diff --git a/R/shiny_prerendered.R b/R/shiny_prerendered.R
@@ -117,9 +117,12 @@ shiny_prerendered_html <- function(input_rmd, render_args) {
 
   # prerender if necessary
   if (prerender) {
+    args <- merge_lists(list(input = input_rmd), render_args)
+    # force prerender to execute in separate environment to ensure that
+    # running w/ prerender step is equivalent to running the prerendered app
+    args$envir <- new.env(parent = args$envir %||% globalenv())
 
     # execute the render
-    args <- merge_lists(list(input = input_rmd), render_args)
     rendered_html <- do.call(render, args)
   }
 

diff --git a/R/word_document.R b/R/word_document.R
@@ -11,7 +11,7 @@
 #'
 #' R Markdown documents also support citations. You can find more information on
 #' the markdown syntax for citations in the
-#' \href{https://rmarkdown.rstudio.com/authoring_bibliographies_and_citations.html}{Bibliographies
+#' \href{https://pandoc.org/MANUAL.html#citations}{Bibliographies
 #' and Citations} article in the online documentation.
 #' @inheritParams pdf_document
 #' @inheritParams html_document

diff --git a/man/beamer_presentation.Rd b/man/beamer_presentation.Rd
diff --git a/man/context_document.Rd b/man/context_document.Rd
diff --git a/man/convert_ipynb.Rd b/man/convert_ipynb.Rd
diff --git a/man/html_document.Rd b/man/html_document.Rd
diff --git a/man/md_document.Rd b/man/md_document.Rd
diff --git a/man/odt_document.Rd b/man/odt_document.Rd
diff --git a/man/pdf_document.Rd b/man/pdf_document.Rd
diff --git a/man/rtf_document.Rd b/man/rtf_document.Rd
diff --git a/man/word_document.Rd b/man/word_document.Rd
diff --git a/tests/testthat/_snaps/pandoc.md b/tests/testthat/_snaps/pandoc.md
@@ -0,0 +1,49 @@
+# Converting bib file is working
+
+    list(list(author = list(list(family = "Conceição", given = "Sérgio")), 
+        "container-title" = "Portuguese History", id = "conc2021", 
+        issue = "1", issued = list("date-parts" = list(list(2021L))), 
+        title = "História da habitação", type = "article-journal"))
+
+---
+
+     [1] "["                                               
+     [2] "  {"                                             
+     [3] "    \"author\": ["                               
+     [4] "      {"                                         
+     [5] "        \"family\": \"Conceição\","              
+     [6] "        \"given\": \"Sérgio\""                   
+     [7] "      }"                                         
+     [8] "    ],"                                          
+     [9] "    \"container-title\": \"Portuguese History\","
+    [10] "    \"id\": \"conc2021\","                       
+    [11] "    \"issue\": \"1\","                           
+    [12] "    \"issued\": {"                               
+    [13] "      \"date-parts\": ["                         
+    [14] "        ["                                       
+    [15] "          2021"                                  
+    [16] "        ]"                                       
+    [17] "      ]"                                         
+    [18] "    },"                                          
+    [19] "    \"title\": \"História da habitação\","       
+    [20] "    \"type\": \"article-journal\""               
+    [21] "  }"                                             
+    [22] "]"                                               
+
+---
+
+     [1] "---"                                  
+     [2] "nocite: \"[@*]\""                     
+     [3] "references:"                          
+     [4] "- author:"                            
+     [5] "  - family: Conceição"                
+     [6] "    given: Sérgio"                    
+     [7] "  container-title: Portuguese History"
+     [8] "  id: conc2021"                       
+     [9] "  issue: 1"                           
+    [10] "  issued: 2021"                       
+    [11] "  title: História da habitação"       
+    [12] "  type: article-journal"              
+    [13] "---"                                  
+    [14] ""                                     
+