Enable use of pandoc --file-scope for input files originating from multiple Rmds

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: rmarkdown
 Type: Package
 Title: Dynamic Documents for R
-Version: 2.2.1
+Version: 2.2.2
 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")),

NEWS.md

@@ -1,6 +1,8 @@
 rmarkdown 2.3
 ================================================================================
 
+- Added `file_scope` option to `render()`, a function used to split markdown inputs to pandoc into multiple files. This is for the purpose of invoking pandoc with the `--file-scope` option, which in turn enables graceful handling of duplicate footnote numbers across chapters (#1837).
+
 - Added the customizable `lang` atrribute to `ioslides_presentation` output (thanks, @jooyoungseo, #1841).
 
 

R/render.R

@@ -190,6 +190,14 @@ NULL
 #' uses knitr's \code{root.dir} knit option. If \code{NULL} then the behavior
 #' will follow the knitr default, which is to use the parent directory of the
 #' document.
+#' @param file_scope An optional function that will split markdown
+#' inputs to pandoc into multiple files. This is for the purpose of invoking
+#' pandoc with the \code{--file-scope} option, which allows footnotes in
+#' different files with the same identifiers to work as expected. This is
+#' useful when the caller has concatenated a set of Rmd files together (as
+#' \pkg{bookdown} does), and those files may have conflicting footnote numbers.
+#' The function should return a named list of files w/ \code{name} and
+#' \code{content} for each file.
 #' @param runtime The runtime target for rendering. The \code{static} option
 #' produces output intended for static files; \code{shiny} produces output
 #' suitable for use in a Shiny document (see \code{\link{run}}). The default,
@@ -242,6 +250,7 @@ render <- function(input,
                    output_yaml = NULL,
                    intermediates_dir = NULL,
                    knit_root_dir = NULL,
+                   file_scope = NULL,
                    runtime =  c("auto", "static", "shiny", "shiny_prerendered"),
                    clean = TRUE,
                    params = NULL,
@@ -286,6 +295,7 @@ render <- function(input,
                        output_options = output_options,
                        intermediates_dir = intermediates_dir,
                        knit_root_dir = knit_root_dir,
+                       file_scope = file_scope,
                        runtime = runtime,
                        clean = clean,
                        params = params,
@@ -847,12 +857,34 @@ render <- function(input,
       utf8_input <- path.expand(utf8_input)
       output     <- path.expand(output)
 
+      # determine args and input files (if we have an file_scope then we
+      # we need to split the files use it here)
+      pandoc_args <- output_format$pandoc$args
+      input_files <- utf8_input
+      if (!is.null(file_scope)) {
+
+        # add the --file-scope option
+        pandoc_args <- c(pandoc_args, "--file-scope")
+
+        # determine new input files
+        inputs <- file_scope(utf8_input)
+        input_files <- unlist(lapply(inputs, function(input) {
+          file <- file_with_meta_ext(input$name, "split", "md")
+          file <- file.path(dirname(utf8_input), file)
+          write_utf8(input$content, file)
+          file
+        }))
+
+        # cleanup the split files after render
+        on.exit(unlink(input_files), add = TRUE)
+      }
+
       # if we don't detect any invalid shell characters in the
       # target path, then just call pandoc directly
       if (!grepl(.shell_chars_regex, output) && !grepl(.shell_chars_regex, utf8_input)) {
         return(pandoc_convert(
-          utf8_input, pandoc_to, output_format$pandoc$from, output,
-          citeproc, output_format$pandoc$args, !quiet
+          input_files, pandoc_to, output_format$pandoc$from, output,
+          citeproc, pandoc_args, !quiet
         ))
       }
 
@@ -874,8 +906,8 @@ render <- function(input,
 
       # call pandoc to render file
       status <- pandoc_convert(
-        utf8_input, pandoc_to, output_format$pandoc$from, pandoc_output_tmp,
-        citeproc, output_format$pandoc$args, !quiet
+        input_files, pandoc_to, output_format$pandoc$from, pandoc_output_tmp,
+        citeproc, pandoc_args, !quiet
       )
 
       # construct output path (when passed only a file name to '--output',