Add argument to **unname_all_chunks** specifying which chunks to unname

DESCRIPTION

@@ -10,17 +10,22 @@ Authors@R:
              family = "Salmon",
              role = "aut",
              email = "maelle.salmon@yahoo.se",
-             comment = c(ORCID = "0000-0002-2815-0399")),
+             comment = structure("0000-0002-2815-0399", .Names = "ORCID")),
       person(given = "Ellis",
              family = "Valentiner",
              role = "ctb"),
       person(given = "Martin",
              family = "Hadley",
              role = "ctb",
-             comment = c(ORCID = "0000-0002-3039-6849")),
+             comment = structure("0000-0002-3039-6849", .Names = "ORCID")),
       person(given = "Locke Data",
              role = "fnd",
-             comment = "https://itsalocke.com"))
+             comment = "https://itsalocke.com"),
+      person(given = "Han",
+             family = "Oostdijk",
+             role = "ctb",
+             comment = structure("0000-0001-6710-4566", .Names = "ORCID"))
+      )
 Description: It names the 'R Markdown' chunks of files based on the filename.
 License: GPL-3
 Encoding: UTF-8

NEWS.md

@@ -1,4 +1,5 @@
 # namer (development version)
+* unname_all_chunks now accepts argument `chunk_name_prefix` with the prefix of the chunknames to be unnamed (@HanOostdijk, #22)
 
 # namer 0.1.4
 

R/unname_all_chunks.R

@@ -1,23 +1,36 @@
 #' @title Unname chunks in a single file
 #'
-#' @description Unname all chunks except the setup chunk, in a single file
+#' @description Unname in a single file all chunks,
+#' or alternatively only unname the chunknames with a given prefix.
+#' In both cases, the chunk name "setup" is preserved, that chunk is never unnamed.
 #'
 #' @inherit name_chunks details
 #'
 #' @param path Path to file
+#' @param chunk_name_prefix Character string with prefix of chunknames that will be removed. Default: NULL (indicating all chunknames will be removed except the one named `setup`)
 #'
 #' @export
 #'
 #' @examples
-#' temp_file_path <- file.path(tempdir(), "test.Rmd")
+#' # remove all chunklabels except the one named 'setup'
+#' temp_file_path <- file.path(tempdir(), "test1.Rmd")
 #' file.copy(system.file("examples", "example4.Rmd", package = "namer"),
 #'           temp_file_path,
 #'           overwrite = TRUE)
 #' unname_all_chunks(temp_file_path)
 #' if(interactive()){
 #' file.edit(temp_file_path)
 #' }
-unname_all_chunks <- function(path){
+#' # remove all chunk labels starting with 'example4'
+#' temp_file_path <- file.path(tempdir(), "test2.Rmd")
+#' file.copy(system.file("examples", "example4.Rmd", package = "namer"),
+#'           temp_file_path,
+#'           overwrite = TRUE)
+#' unname_all_chunks(temp_file_path,chunk_name_prefix='example4')
+#' if(interactive()){
+#' file.edit(temp_file_path)
+#' }
+unname_all_chunks <- function(path,chunk_name_prefix=NULL){
   # read the whole file
   lines <- readLines(path)
 
@@ -29,8 +42,17 @@ unname_all_chunks <- function(path){
     return(invisible("TRUE"))
   }
 
-  # preserve the setup label, delete the others
-  chunk_headers_info$name[chunk_headers_info$name != "setup"] <- ""
+  if ( is.null(chunk_name_prefix)){
+    # preserve the setup label, delete the others
+    chunk_headers_info$name[chunk_headers_info$name != "setup"] <- ""
+  } else {
+    # preserve labels not starting with chunk_name_prefix
+    del_labels <- strtrim(chunk_headers_info$name,nchar(chunk_name_prefix)) %in%
+      chunk_name_prefix
+    setup_label <- !(chunk_headers_info$name %in% 'setup')
+    del_labels <- del_labels & setup_label
+    chunk_headers_info$name[del_labels] <- ""
+  }
 
   newlines <- re_write_headers(chunk_headers_info)
 

README.md

@@ -32,6 +32,8 @@ file.edit("test/example1.Rmd")
 
 There's also `name_chunks` for use on a single R Markdown file; and `unname_all_chunks` to unname all chunks of a single R Markdown file which can be useful when cleaning your chunk labels.
 
+By default `unname_all_chunks` unnames all chunks with exception of the 'setup' chunk. By using the argument `chunk_name_prefix` one can indicate the prefix of the labels that will be unnamed. Useful when one refers to a label by using chunk option `ref.label` so that it is inconvenient when that labeel is unnamed. By setting `chunk_name_prefix` equal to 'the filename with extension stripped' followed with a '-' (dash) only the labels generated by `name_chunks` will be unnamed.
+
 If you're working with RStudio, installing the package will have installed an addin for labelling chunks of *any R Markdown document you select*.
 
 **When using `namer`, please check the edits before pushing them to your code base. Such automatic chunk labelling is best paired with [version control](http://happygitwithr.com/).**

inst/examples/example4.Rmd

@@ -37,3 +37,7 @@ plot(pressure)
 
 
 Note that the `echo = FALSE` parameter was added to the code chunk to prevent printing of the R code that generated the plot.
+
+```{r sessioninfo}
+sessionInfo()
+```

tests/testthat/test-unname_all_chunks.R

@@ -1,6 +1,6 @@
 context("test-unname_all_chunks")
 
-test_that("unname_all_chunks works", {
+test_that("unname_all_chunks works in case is.null(chunk_name_prefix) == TRUE", {
   # check arg of tempdir
   R_version <- paste(R.version$major,
                      R.version$minor,
@@ -17,6 +17,38 @@ test_that("unname_all_chunks works", {
   lines <- readLines(temp_file_path)
   chunk_info <- get_chunk_info(lines)
 
+  testthat::expect_identical(chunk_info$name[1],'setup')
+  testthat::expect_true(all(is.na(chunk_info$name[-1])))
+
+  rendering <- rmarkdown::render(temp_file_path)
+  testthat::expect_is(rendering, "character")
+
+  file.remove(temp_file_path)
+
+  basename <- fs::path_ext_remove(temp_file_path)
+
+  file.remove(paste0(basename, ".html"))
+})
+
+test_that("unname_all_chunks works in case is.null(chunk_name_prefix) == FALSE", {
+  # check arg of tempdir
+  R_version <- paste(R.version$major,
+    R.version$minor,
+    sep = ".")
+
+  skip_if_not(R_version >= "3.5.0")
+
+  temp_file_path <- file.path(tempdir(check = TRUE), "example4.Rmd")
+
+  file.copy(system.file("examples", "example4.Rmd", package = "namer"),
+    temp_file_path)
+  unname_all_chunks(temp_file_path,chunk_name_prefix='example4')
+
+  lines <- readLines(temp_file_path)
+  chunk_info <- get_chunk_info(lines)
+
+  testthat::expect_identical(chunk_info$name[1],'setup')
+  testthat::expect_identical(chunk_info$name[6],'sessioninfo')
   testthat::expect_true(all(is.na(chunk_info$name[2:5])))
 
   rendering <- rmarkdown::render(temp_file_path)
@@ -28,3 +60,36 @@ test_that("unname_all_chunks works", {
 
   file.remove(paste0(basename, ".html"))
 })
+
+test_that("unname_all_chunks works in case chunk_name_prefix == 'setup' ", {
+  # check arg of tempdir
+  R_version <- paste(R.version$major,
+    R.version$minor,
+    sep = ".")
+
+  skip_if_not(R_version >= "3.5.0")
+
+  temp_file_path <- file.path(tempdir(check = TRUE), "example4.Rmd")
+
+  file.copy(system.file("examples", "example4.Rmd", package = "namer"),
+    temp_file_path)
+  unname_all_chunks(temp_file_path,chunk_name_prefix='setup')
+
+  lines <- readLines(temp_file_path)
+  chunk_info <- get_chunk_info(lines)
+
+  testthat::expect_identical(chunk_info$name[1],'setup')
+  testthat::expect_identical(chunk_info$name[3],'example4-1')
+  testthat::expect_identical(chunk_info$name[4],'example4-1-bis')
+  testthat::expect_identical(chunk_info$name[6],'sessioninfo')
+  testthat::expect_true(all(is.na(chunk_info$name[c(2,5)])))
+
+  rendering <- rmarkdown::render(temp_file_path)
+  testthat::expect_is(rendering, "character")
+
+  file.remove(temp_file_path)
+
+  basename <- fs::path_ext_remove(temp_file_path)
+
+  file.remove(paste0(basename, ".html"))
+})

vignettes/namer.Rmd

@@ -41,6 +41,21 @@ if(interactive()){
 fs::dir_delete(temp_dir)
 ```
 
-There's also `name_chunks` for use on a single R Markdown file; and `unname_all_chunks` to unname all chunks of a single R Markdown file which can be useful when cleaning your chunk labels.
+There's also `name_chunks` for use on a single R Markdown file; and `unname_all_chunks` to unname all chunks of a single R Markdown file which can be useful when cleaning your chunk labels. 
+
+By default `unname_all_chunks` unnames all chunks with exception of the 'setup' chunk. By using the argument `chunk_name_prefix` one can indicate the prefix of the labels that will be unnamed. Useful when one refers to a label by using chunk option `ref.label` so that it is inconvenient when that label is unnamed. By setting `chunk_name_prefix` equal to 'the filename with extension stripped' followed with a '-' (dash) only the labels generated by `name_chunks` will be unnamed. In the following example the chunks labeled 'setup' and 'sessioninfo' will not be unnamed.
+
+```r
+temp_file_path <- file.path(tempdir(check = TRUE), "example4.Rmd")
+
+file.copy(system.file("examples", "example4.Rmd", package = "namer"),
+          temp_file_path)
+unname_all_chunks(temp_file_path,chunk_name_prefix='example4-')
+if(interactive()){
+  file.edit(temp_file_path)
+}
+
+file.remove(temp_file_path)
+```
 
 **When using `namer`, please check the edits before pushing them to your code base. Such automatic chunk labelling is best paired with [version control](http://happygitwithr.com/).**