fix #405 and fix #852: execute R scripts specified in before_chapter_…

…script and after_chapter_scripts separately, instead of writing them into the Rmd files as code chunks

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: bookdown
 Type: Package
 Title: Authoring Books and Technical Documents with R Markdown
-Version: 0.17.1
+Version: 0.17.2
 Authors@R: c(
     person("Yihui", "Xie", role = c("aut", "cre"), email = "xie@yihui.name", comment = c(ORCID = "0000-0003-0645-5666")),
     person("JJ", "Allaire", role = "ctb"),

NEWS.md

@@ -4,6 +4,8 @@
 
 - Cross-referencing works correctly now with `gitbook` when using `split_by: section` or `split_by: section+number` (thanks, @ThierryO, @cderv, #787)
 
+- When using the Knit-and-Merge approach to compile a book (`new_session: true` in `_bookdown.yml`) and the fields `before_chapter_script` and/or `after_chapter_script` are configured in `_bookdown.yml`, the original Rmd files are no longer touched (thanks, @clauswilke #405 and @bob-carpenter https://stackoverflow.com/q/50554196/559676), and the scripts specified in `before/after_chapter_script` are no longer inserted into the Rmd files (they are read and evaluated separately), so the line numbers will be correct in case of **knitr** errors (thanks, @arencambre, #852).
+
 # CHANGES IN bookdown VERSION 0.17
 
 ## NEW FEATURES

R/render.R

@@ -169,26 +169,12 @@ render_new_session = function(files, main, config, output_format, clean, envir,
   # if input is index.Rmd or not preview mode, compile all Rmd's
   rerun = !opts$get('preview') || identical(opts$get('input_rmd'), 'index.Rmd')
   if (!rerun) rerun = files %in% opts$get('input_rmd')
-  add1 = insert_chapter_script(config, 'before')
-  add2 = insert_chapter_script(config, 'after')
+  add1 = merge_chapter_script(config, 'before')
+  add2 = merge_chapter_script(config, 'after')
+  on.exit(unlink(c(add1, add2)), add = TRUE)
   # compile chapters in separate R sessions
-  for (f in files[rerun]) {
-    if (length(add1) + length(add2) == 0) {
-      Rscript_render(f, render_args, render_meta)
-      next
-    }
-    # first backup the original Rmd to a tempfile
-    f2 = tempfile('bookdown', '.', fileext = '.bak')
-    file.copy(f, f2, overwrite = TRUE)
-    # write add1/add2 to the original Rmd, compile it, and restore it
-    tryCatch({
-      txt = c(add1, read_utf8(f), add2)
-      write_utf8(txt, f)
-      Rscript_render(f, render_args, render_meta)
-    }, finally = {
-      if (file.copy(f2, f, overwrite = TRUE)) file.remove(f2)
-    })
-  }
+  for (f in files[rerun]) Rscript_render(f, render_args, render_meta, add1, add2)
+
   if (!all(dirname(files_md) == '.'))
     file.copy(files_md[!rerun], basename(files_md[!rerun]), overwrite = TRUE)
 

R/utils.R

@@ -163,12 +163,25 @@ insert_code_chunk = function(x, before, after) {
 }
 
 insert_chapter_script = function(config, where = 'before') {
-  script = config[[sprintf('%s_chapter_script', where)]]
+  script = get_chapter_script(config, where)
   if (is.character(script)) {
-    c('```{r include=FALSE, cache=FALSE}', unlist(lapply(script, read_utf8)), '```')
+    c('```{r include=FALSE, cache=FALSE}', script, '```')
   }
 }
 
+get_chapter_script = function(config, where) {
+  script = config[[sprintf('%s_chapter_script', where)]]
+  unlist(lapply(script, read_utf8))
+}
+
+merge_chapter_script = function(config, where) {
+  if (!is.character(script <- get_chapter_script(config, where)) || length(script) == 0)
+    return('')
+  f = tempfile(fileext = '.R')
+  write_utf8(script, f)
+  f
+}
+
 check_special_chars = function(filename) {
   reg = rmarkdown:::.shell_chars_regex
   for (i in grep(reg, filename)) warning(
@@ -186,6 +199,11 @@ Rscript_render = function(file, ...) {
   if (Rscript(args) != 0) stop('Failed to compile ', file)
 }
 
+source_utf8 = function(file) {
+  if (file == '') return()
+  eval(xfun::parse_only(read_utf8(file)), envir = globalenv())
+}
+
 clean_meta = function(meta_file, files) {
   meta = readRDS(meta_file)
   for (i in setdiff(names(meta), files)) meta[[i]] = NULL

inst/scripts/render_one.R

@@ -1,12 +1,17 @@
 # compile an Rmd file without running Pandoc; arguments are passed from Rscript;
 # the three arguments are 1) the Rmd filename; 2) the render arguments; 3) the
-# filename to save the returned value of render()
+# filename to save the returned value of render(); 4) before_chapter_script; 5)
+# after_chapter_script
 library(methods)
 local({
   args = commandArgs(TRUE)
+
+  bookdown:::source_utf8(args[4])
   out = do.call(
     rmarkdown::render, c(args[1], readRDS(args[2]), list(run_pandoc = FALSE, encoding = 'UTF-8'))
   )
+  bookdown:::source_utf8(args[5])
+
   out_expected = xfun::with_ext(args[1], '.md')
   if (out != out_expected) {
     file.rename(out, out_expected)