only consider R code chunks as code

Author: lorenzwalthert

R/transform-code.R

@@ -29,48 +29,65 @@ transform_code <- function(path, fun, verbose = FALSE, ...) {
 #' @param transformer_fun A styler transformer function
 #' @importFrom purrr flatten_chr
 transform_rmd <- function(lines, transformer_fun) {
-  chunks <- identify_chunks(lines)
+  chunks <- separate_chunks(lines)
   chunks$r_chunks <- map(chunks$r_chunks, transformer_fun)
 
   map2(chunks$text_chunks, c(chunks$r_chunks, list(character(0))), c) %>%
     flatten_chr()
 }
 
 
-#' Identify chunks within Rmd contents
-#'
-#' Identifies the code and text chunks within an Rmd file, and returns these
-#' as a nested list.
+#' Separate chunks within Rmd contents
 #'
+#' Identifies and separates the code and text chunks (the latter includes non-R
+#' code) within an Rmd file, and returns these separately.
 #' @param lines a character vector of lines from an Rmd file
-#'
 #' @importFrom purrr map2
 #' @importFrom rlang seq2
-identify_chunks <- function(lines) {
+separate_chunks <- function(lines) {
+  r_raw_chunks <- identify_r_raw_chunks(lines)
+  r_chunks <- map2(
+    r_raw_chunks$starts, r_raw_chunks$ends, ~lines[seq2(.x + 1, .y - 1)]
+  )
+
+  text_chunks <- map2(
+    c(1, r_raw_chunks$ends), c(r_raw_chunks$starts, length(lines)),
+    ~lines[seq2(.x, .y)]
+  )
+  lst(r_chunks, text_chunks)
+}
+
+#' Identifies raw R code chunks
+#'
+#' Raw in the sense that these chunks don't contain pure R code, but they
+#' contain a header and footer of markdown. Only code chunks that have an engine
+#' whose name matches `engine-pattern` are considered as R code.
+#' @inheritParams separate_chunks
+#' @param engine_pattern A regular expression that must match the engine name.
+identify_r_raw_chunks <- function(lines, engine_pattern = "[rR]") {
   pattern <- get_knitr_pattern(lines)
   if (is.null(pattern$chunk.begin) || is.null(pattern$chunk.end)) {
     stop("Unrecognized chunk pattern!", call. = FALSE)
   }
-
   starts <- grep(pattern$chunk.begin, lines, perl = TRUE)
   ends <- grep(pattern$chunk.end, lines, perl = TRUE)
 
   if (length(starts) != length(ends)) {
     stop("Malformed file!", call. = FALSE)
   }
 
-  r_chunks <- map2(starts, ends, ~lines[seq2(.x + 1, .y - 1)])
-
-  text_chunks <- map2(c(1, ends), c(starts, length(lines)), ~lines[seq2(.x, .y)])
-
-  lst(r_chunks, text_chunks)
+  is_r_code <- grepl(
+    paste0("^[\t >]*```+\\s*\\{(", engine_pattern, ".*)\\}\\s*$"),
+    lines[starts], perl = TRUE
+  )
+  list(starts = starts[is_r_code], ends = ends[is_r_code])
 }
 
 #' Get chunk pattern
 #'
 #' Determine a regex pattern for identifying R code chunks.
 #'
-#' @inheritParams identify_chunks
+#' @inheritParams separate_chunks
 get_knitr_pattern <- function(lines) {
   knitr::all_patterns[["md"]]
 }