Merged RStudio rmarkdown 2.20 release.

Merge remote-tracking branch 'rstudio/main' into jg-devel

# By Yihui Xie (3) and others
# Via Yihui Xie
* rstudio/main:
  start the next version
  CRAN release v2.20
  make sure `ioslides_presentation` is properly self-contained when requested (rstudio#2428)
  More tests needs fixing
  Newer Pandoc (currently devel) fixes GFM toc previously written in HTML instead of Markdown
  make sure to avoid creating invalid paths when copying resources (rstudio#2429)
  Fix rstudio#1508: do not resolve input files that are symlinks (rstudio#2438)

# Conflicts:
#	DESCRIPTION

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: rmarkdown
 Title: Dynamic Documents for R
-Version: 2.19.2.9000
+Version: 2.20.1.9000
 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")),
@@ -69,7 +69,7 @@ Imports:
     tinytex (>= 0.31),
     tools,
     utils,
-    xfun (>= 0.30),
+    xfun (>= 0.36),
     yaml (>= 2.1.19)
 Suggests:
     digest,

NEWS.md

@@ -1,4 +1,4 @@
-rmarkdown 2.20
+rmarkdown 2.21
 ================================================================================
 
 - `html_document` output allows `lib_dir` to point to a parent of the output 
@@ -8,8 +8,18 @@ rmarkdown 2.20
   where there is a shared master library with css, javascript, etc. and separate 
   child directories with RMarkdown files. #146 and #1859.
 
+
+rmarkdown 2.20
+================================================================================
+
 - The defunct `tufte_handout()` has been removed from **rmarkdown**. Please use `tufte::tufte_handout()` instead.
 
+- If an input path to `rmarkdown::render()` is a symbolic link, it is no longer resolved to its real path (thanks, @SamDM @jmw86069, #1508).
+
+- Make sure to avoid creating invalid paths when copying resources (thanks, @mnazarov, #2429).
+
+- Make sure `logo` is properly embedded in `ioslides_presentation()` when `self_contained = TRUE` (thanks, @mnazarov, #2428).
+
 
 rmarkdown 2.19
 ================================================================================

R/html_resource_copy.R

@@ -25,6 +25,14 @@ copy_html_resources <- function(html_str, lib_dir, output_dir) {
   copy_resources(html_str, lib_dir, output_dir, resource_locator)
 }
 
+make_abs_path_safe <- function(path) {
+  if (xfun::is_windows()) {
+    sub("^.:(/|\\\\)*", "", path)  # windows
+  } else {
+    sub("^[/]*", "", path)  # *nix
+  }
+}
+
 copy_resources <- function(input_str, lib_dir, output_dir, resource_locator) {
   # ensure the lib directory exists
   dir.create(lib_dir, recursive = TRUE, showWarnings = FALSE)
@@ -49,7 +57,7 @@ copy_resources <- function(input_str, lib_dir, output_dir, resource_locator) {
         target_dir <- if (dirname(in_file) == ".")
           lib_dir
         else
-          file.path(lib_dir, dirname(in_file))
+          file.path(lib_dir, make_abs_path_safe(dirname(in_file)))
         dir.create(target_dir, recursive = TRUE, showWarnings = FALSE)
         target_res_file <- file.path(target_dir, basename(in_file))
 
@@ -61,7 +69,7 @@ copy_resources <- function(input_str, lib_dir, output_dir, resource_locator) {
         if (identical(lib_dir, output_dir))
           res_src <- in_file
         else
-          res_src <- file.path(relative_lib, src)
+          res_src <- file.path(relative_lib, make_abs_path_safe(src))
       } else {
         # inside the library, fix up the URL
         res_src <- file.path(relative_lib, res_src)

R/includes.R

@@ -47,6 +47,8 @@ includes_to_pandoc_args <- function(includes,
 
 # simple wrapper over normalizePath that preserves NULLs and applies pandoc-
 # friendly defaults
-normalize_path <- function(path, winslash = "/", must_work = NA) {
-  if (!is.null(path)) normalizePath(path, winslash = winslash, mustWork = must_work)
+normalize_path <- function(path, ..., must_work = NA) {
+  if (!is.null(path)) xfun::normalize_path(
+    path, ..., must_work = must_work, resolve_symlink = FALSE
+  )
 }

R/ioslides_presentation.R

@@ -332,6 +332,8 @@ ioslides_presentation <- function(number_sections = FALSE,
   if (!length(grep('--wrap', pandoc_args)))
     pandoc_args <- c('--wrap', 'none', pandoc_args)
 
+  logo_placeholder <- "data:,LOGO"
+
   # pre-processor for arguments that may depend on the name of the
   # the input file (e.g. ones that need to copy supporting files)
   pre_processor <- function(metadata, input_file, runtime, knit_meta, files_dir,
@@ -360,7 +362,8 @@ ioslides_presentation <- function(number_sections = FALSE,
         file.copy(from = logo, to = logo_path)
         logo_path <- normalized_relative_to(output_dir, logo_path)
       } else {
-        logo_path <- pandoc_path_arg(logo_path)
+        # placeholder, will be replaced by base64-encoded logo in post_processor
+        logo_path <- logo_placeholder
       }
       args <- c(args, "--variable", paste("logo=", logo_path, sep = ""))
     }
@@ -450,14 +453,18 @@ ioslides_presentation <- function(number_sections = FALSE,
     # read the slides
     slides_lines <- read_utf8(output_tmpfile)
 
+    # read the output file
+    output_lines <- read_utf8(output_file)
+
     # base64 encode if needed
     if (self_contained) {
       slides_lines <- base64_encode_images(slides_lines)
+      if (!is.null(logo)) {
+        logo_base64 <- if (grepl("^data:", logo)) logo else xfun::base64_uri(logo)
+        output_lines <- gsub(logo_placeholder, logo_base64, output_lines, fixed = TRUE)
+      }
     }
 
-    # read the output file
-    output_lines <- read_utf8(output_file)
-
     # substitute slides for the sentinel line
     sentinel_line <- grep("^RENDERED_SLIDES$", output_lines)
     if (length(sentinel_line) == 1) {

tests/testthat/_snaps/pandoc-3/github_document/github-toc-numbered.md

@@ -0,0 +1,11 @@
+
+- [1 Section](#1-section)
+- [2 Header](#2-header)
+
+# 1 Section
+
+Sentence.
+
+# 2 Header
+
+Sentence

tests/testthat/_snaps/pandoc-3/github_document/github-toc.md

@@ -0,0 +1,11 @@
+
+- [10 Section](#10-section)
+- [Header](#header)
+
+# 10 Section
+
+Sentence.
+
+# Header
+
+Sentence

tests/testthat/_snaps/pandoc-3/lua-filters.md

@@ -0,0 +1,44 @@
+# number_sections Lua filter works
+
+    # 1 A
+
+    ## 1.1 B
+
+    # 2 C
+
+    ## 2.1 D
+
+    See [A](#a)
+
+---
+
+    # 1 A
+
+    ## 1.1 B
+
+    # 2 C
+
+    ## 2.1 D
+
+    See [A](#1-a)
+
+---
+
+    Test
+    ================
+
+    - [1 A](#1-a)
+      - [1.1 B](#11-b)
+    - [2 C](#2-c)
+      - [2.1 D](#21-d)
+
+    # 1 A
+
+    ## 1.1 B
+
+    # 2 C
+
+    ## 2.1 D
+
+    See [A](#1-a)
+

tests/testthat/test-github_document.R

@@ -7,7 +7,9 @@ test_that("toc has correct identifier", {
   tmp_file <- local_rmd_file(
     c("# 10 Section","","Sentence.","", "# Header","","Sentence ")
   )
-  pandoc_version <- if (pandoc_available("2.18.0.1")) {
+  pandoc_version <- if (pandoc_available("3")) {
+    "pandoc-3"
+  } else if (pandoc_available("2.18.0.1")) {
     "after-pandoc-2.18"
   } else if (pandoc_available("2.18")) {
     "pandoc-2.18"
@@ -24,7 +26,9 @@ test_that("toc has correct identifier also when sections are numbered ", {
   tmp_file <- local_rmd_file(
     c("# Section","","Sentence.","", "# Header","","Sentence ")
   )
-  pandoc_version <- if (pandoc_available("2.18.0.1")) {
+  pandoc_version <- if (pandoc_available("3")) {
+    "pandoc-3"
+  } else if (pandoc_available("2.18.0.1")) {
     "after-pandoc-2.18"
   } else if (pandoc_available("2.18")) {
     "pandoc-2.18"

tests/testthat/test-ioslides.R

@@ -179,3 +179,31 @@ test_ioslides_presentation_css <- function() {
 
 
 test_that("ioslides presentation is styled", test_ioslides_presentation_css())
+
+test_ioslides_presentation_logo <- function() {
+
+  outputdir <- tempfile()
+  dir.create(outputdir)
+  on.exit(unlink(outputdir), add = TRUE)
+
+  # Generate mock md file with logo
+  void <- file.copy("resources/empty.png", file.path(outputdir, "logo.png"))
+  mdtext <- c("# Slide One\n")
+  mock <- mock_markdown(mdtext = mdtext, outputdir = outputdir, self_contained = TRUE, logo = "logo.png")
+  html <- mock$html_file
+
+  slide_lines <- c(
+    !any(grepl("logo\\.png", html))
+    , any(grep("favIcon: 'data:image/png;base64,[^']*'", html))
+    , any(grepl("background: url\\(data:image/png;base64,[^\\)]*)", html))
+  )
+  expect_true(all(slide_lines), info = "slide lines - self contained logo")
+
+  # if logo is passed as base64 string, do not re-encode
+  logobase64 <- xfun::base64_uri("resources/empty.png")
+  mock2 <- mock_markdown(mdtext = mdtext, outputdir = outputdir, self_contained = TRUE, logo = logobase64)
+  html2 <- mock2$html_file
+  expect_equal(html, html2)
+}
+
+test_that("ioslides presentation embeds logo", test_ioslides_presentation_logo())

tests/testthat/test-lua-filters.R

@@ -34,7 +34,9 @@ test_that("number_sections Lua filter works", {
   headers <- c("# A", "## B", "# C", "## D")
   rmd <- c(paste0(headers, "\n\n"), "See [A]")
   # Variant for snapshot: pandoc 2.11.2 default to atx headers
-  pandoc_versions <- if (pandoc_available("2.18.0.1")) {
+  pandoc_versions <- if (pandoc_available("3")) {
+    "pandoc-3"
+  } else if (pandoc_available("2.18.0.1")) {
     "after-pandoc-2.18"
   } else if (pandoc_available("2.18")) {
     "pandoc-2.18"