chore: Spring clean for CRAN (#41)

Linting and tidying

.Rbuildignore

@@ -14,3 +14,4 @@
 ^man-roxygen
 ^pkgdown$
 ^codecov\.yml$
+^.lintr$

.lintr

@@ -0,0 +1,9 @@
+linters: linters_with_defaults(
+  assignment_linter = NULL,
+  indentation_linter = NULL,
+  commented_code_linter = NULL,
+  object_length_linter = NULL,
+  line_length_linter(100),
+  cyclocomp_linter(complexity_limit = 15),
+  undesirable_operator_linter = undesirable_operator_linter(
+    op = list("<-" = "Please use '=' for assignment")))

DESCRIPTION

@@ -1,41 +1,23 @@
 Package: namer
 Title: Names Your 'R Markdown' Chunks
-Version: 0.1.8
-Authors@R: 
-    c(person(given = "Colin",
-             family = "Gillespie",
-             role = c("aut", "cre"),
-             email = "[email protected]"),
-    person(given = "Steph",
-             family = "Locke",
-             role = c("aut"),
-             email = "[email protected]"),
-      person(given = "Maëlle",
-             family = "Salmon",
-             role = "aut",
-             email = "[email protected]",
-             comment = c(ORCID = "0000-0002-2815-0399")),
-      person(given = "Ellis",
-             family = "Valentiner",
-             role = "ctb"),
-      person(given = "Charlie",
-             family = "Hadley",
-             role = "ctb",
-             comment = c(ORCID = "0000-0002-3039-6849")),
-      person(given = "Jumping Rivers",
-             role = "fnd",
-             comment = "https://jumpingrivers.com"),
-      person(given = "Han",
-             family = "Oostdijk",
-             role = "ctb",
-             comment = c(ORCID = "0000-0001-6710-4566")),
-      person(given = "Patrick",
-             family = "Schratz",
-             role = "ctb",
-             email = "[email protected]",
-             comment = c(ORCID = "0000-0003-0748-6624")))
-Description: It names the 'R Markdown' chunks of files based on
-    the filename.
+Version: 0.1.9
+Authors@R: c(
+    person("Colin", "Gillespie", , "[email protected]", role = c("aut", "cre")),
+    person("Steph", "Locke", , "[email protected]", role = "aut"),
+    person("Maëlle", "Salmon", , "[email protected]", role = "aut",
+           comment = c(ORCID = "0000-0002-2815-0399")),
+    person("Ellis", "Valentiner", role = "ctb"),
+    person("Charlie", "Hadley", role = "ctb",
+           comment = c(ORCID = "0000-0002-3039-6849")),
+    person("Jumping Rivers", role = "fnd",
+           comment = "https://jumpingrivers.com"),
+    person("Han", "Oostdijk", role = "ctb",
+           comment = c(ORCID = "0000-0001-6710-4566")),
+    person("Patrick", "Schratz", , "[email protected]", role = "ctb",
+           comment = c(ORCID = "0000-0003-0748-6624"))
+  )
+Description: It names the 'R Markdown' chunks of files based on the
+    filename.
 License: MIT + file LICENSE
 URL: https://github.com/jumpingrivers/namer,
     https://jumpingrivers.github.io/namer/

LICENSE

@@ -1,2 +1,2 @@
-YEAR: 2022
+YEAR: 2025
 COPYRIGHT HOLDER: namer authors

LICENSE.md

@@ -1,6 +1,6 @@
 # MIT License
 
-Copyright (c) 2022 namer authors
+Copyright (c) 2025 namer authors
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

NEWS.md

@@ -1,10 +1,20 @@
+# namer 0.1.9 _2025-01-23_
+
+  * Allow to choose prefix for chunk names #2 (@statnmap, #30)
+  * New addins: (@statnmap, #30)
+    - Name current Rmd file
+    - Name file chosen in a directory
+    - Name chunks from a folder
+
 # namer 0.1.8
 
 * Update maintainer
 
 # namer 0.1.7
 
-* `name_dir_chunks()` now also names chunks in Quarto-Files. Note that Quarto chunks are labelled in the RMarkdown style (` ```{r mylabel} `), *not* in the Quarto style (see below):
+* `name_dir_chunks()` now also names chunks in Quarto-Files. 
+  Note that Quarto chunks are labelled in the RMarkdown style (` ```{r mylabel} `), 
+  *not* in the Quarto style (see below):
 
 ````
 ```{r}
@@ -17,7 +27,9 @@
 
 # namer 0.1.5
 
-* `name_chunks()` and `name_dir_chunks()` are now able to unname all chunks before naming them. This ensures a consistent naming for all chunks instead of just labelling unnamed chunks (@pat-s, #23).
+* `name_chunks()` and `name_dir_chunks()` are now able to unname all chunks before naming them. 
+  This ensures a consistent naming for all chunks instead of 
+  just labelling unnamed chunks (@pat-s, #23).
 
 * new function `unname_dir_chunks()` that works in the same way as `name_dir_chunks()` (@pat-s, #23)
 

R/name_chunks.R

@@ -1,6 +1,7 @@
 #' @title Name chunks in a single file
 #'
-#' @description Name unnamed chunks in a single file using the filename with extension stripped as basis.
+#' @description Name unnamed chunks in a single file using the
+#' filename with extension stripped as basis.
 #'
 #' @details When using namer, please check the edits
 #'  before pushing them to your code base. Such automatic
@@ -24,15 +25,15 @@
 #' file.edit(temp_file_path)
 #' }
 #' file.remove(temp_file_path)
-name_chunks <- function(path, unname = FALSE, prefix){
+name_chunks <- function(path, unname = FALSE, prefix) {
   # read the whole file
   lines <- readLines(path)
 
   # get chunk info
   chunk_headers_info <- get_chunk_info(lines)
 
   # early exit if no chunk
-  if(is.null(chunk_headers_info)){
+  if (is.null(chunk_headers_info)) {
     return(invisible(TRUE))
   }
 
@@ -48,9 +49,8 @@ name_chunks <- function(path, unname = FALSE, prefix){
   # count unnamed chunks
   no_unnamed <- length(unique(unnamed$index))
 
-
   # act only if needed!
-  if(no_unnamed > 0){
+  if (no_unnamed > 0) {
     if (missing(prefix)) {
       # create new chunk names
       filename <- fs::path_ext_remove(path)
@@ -68,7 +68,7 @@ name_chunks <- function(path, unname = FALSE, prefix){
     existing_names <- unique(chunk_headers_info$name)
     existing_names <- existing_names[!is.na(existing_names)]
 
-    if(any(new_chunk_names %in% existing_names)){
+    if (any(new_chunk_names %in% existing_names)) {
       new_chunk_names[new_chunk_names %in% existing_names] <-
         glue::glue("{new_chunk_names[new_chunk_names %in% existing_names]}-bis")
     }
@@ -87,15 +87,15 @@ name_chunks <- function(path, unname = FALSE, prefix){
 
     # re-get chunk names
     new_chunk_headers_info <- get_chunk_info(lines)
-    if(length(unique(new_chunk_headers_info$name)) != nrow(new_chunk_headers_info)){
+    if (length(unique(new_chunk_headers_info$name)) != nrow(new_chunk_headers_info)) {
       stop("Despite our efforts we'd be creating duplicate names.
 Had you run our script on your R Markdown before?
 Maybe namer::unname_chunks before running name_chunks.")
     }
 
     # save file
     writeLines(lines, path)
-}
+  }
   return(invisible(TRUE))
 }
 
@@ -128,7 +128,7 @@ Maybe namer::unname_chunks before running name_chunks.")
 #' file.edit(file.path(temp_dir,
 #'                    "examples", "example1.Rmd"))
 #' }
-name_dir_chunks <- function(dir, unname = FALSE){
+name_dir_chunks = function(dir, unname = FALSE) {
 
   if (isTRUE(unname)) {
     cli::cat_rule("Unnaming all chunks")
@@ -137,13 +137,13 @@ name_dir_chunks <- function(dir, unname = FALSE){
 
   cli::cat_rule("Naming all chunks")
 
-  rmds <- fs::dir_ls(dir, regexp = "*.[RrQq]md")
+  rmds = fs::dir_ls(dir, regexp = "*.[RrQq]md")
   purrr::walk(rmds, chatty_name_chunks)
 
   return(invisible(TRUE))
 }
 
-chatty_name_chunks <- function(path){
+chatty_name_chunks = function(path) {
   message(glue::glue("Scanning {path}..."))
   name_chunks(path)
 }

R/name_chunks_addin.R

@@ -1,9 +1,9 @@
-name_chunks_file_addin <- function(){
+name_chunks_file_addin = function() {
   name_chunks(path = rstudioapi::selectFile(filter = "R Markdown Files (*.Rmd)"))
 }
 
-name_chunks_addin <- function(){
-  prefix <- rstudioapi::showPrompt(title = "Chunk names prefix",
+name_chunks_addin = function() {
+  prefix = rstudioapi::showPrompt(title = "Chunk names prefix",
                                    message = "Leave empty to use filename (Default)", default = "")
   if (prefix == "") {
     name_chunks(path = rstudioapi::getActiveDocumentContext()$path)
@@ -12,6 +12,6 @@ name_chunks_addin <- function(){
   }
 }
 
-name_chunks_directory_addin <- function(){
+name_chunks_directory_addin = function() {
   namer::name_dir_chunks(rstudioapi::selectDirectory())
 }

R/unname_chunks.R

@@ -40,18 +40,18 @@ unname_chunks <- function(path, chunk_name_prefix = NULL) {
   chunk_headers_info <- get_chunk_info(lines)
 
   # early exit if no chunk
-  if(is.null(chunk_headers_info)){
+  if (is.null(chunk_headers_info)) {
     return(invisible("TRUE"))
   }
 
-  if ( is.null(chunk_name_prefix)){
+  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$name,nchar(chunk_name_prefix)) %in%
+    del_labels <- strtrim(chunk_headers_info$name, nchar(chunk_name_prefix)) %in%
       chunk_name_prefix
-    setup_label <- !(chunk_headers_info$name %in% 'setup')
+    setup_label <- !(chunk_headers_info$name %in% "setup")
     del_labels <- del_labels & setup_label
     chunk_headers_info$name[del_labels] <- ""
   }
@@ -94,13 +94,13 @@ unname_chunks <- function(path, chunk_name_prefix = NULL) {
 #' file.edit(file.path(temp_dir,
 #'                    "examples", "example1.Rmd"))
 #' }
-unname_dir_chunks <- function(dir){
+unname_dir_chunks <- function(dir) {
   rmds <- fs::dir_ls(dir, regexp = "*.[Rr]md")
   purrr::walk(rmds, chatty_unname_chunks)
   return(invisible(TRUE))
 }
 
-chatty_unname_chunks <- function(path){
+chatty_unname_chunks <- function(path) {
   message(glue::glue("Scanning {path}..."))
   unname_chunks(path)
 }
@@ -111,5 +111,5 @@ chatty_unname_chunks <- function(path){
 #' @export
 unname_all_chunks <- function(path, chunk_name_prefix = NULL) {
   warning("please use unname_chunks() instead of unname_all_chunks()", call. = FALSE)
-  unname_chunks(path,chunk_name_prefix = NULL)
+  unname_chunks(path, chunk_name_prefix = NULL)
 }

R/utils.R

@@ -1,12 +1,12 @@
 # not elegant, given a part of a header,
 # transform it into the row of a tibble
-transform_params <- function(params){
-  params_string <- try(eval(parse(text = paste('alist(', quote_label(params), ')'))),
+transform_params <- function(params) {
+  params_string <- try(eval(parse(text = paste("alist(", quote_label(params), ")"))),
                silent = TRUE)
 
-  if(inherits(params_string, "try-error")){
+  if (inherits(params_string, "try-error")) {
     params <- sub(" ", ", ", params)
-    params_string <- eval(parse(text = paste('alist(', quote_label(params), ')')))
+    params_string <- eval(parse(text = paste("alist(", quote_label(params), ")")))
   }
 
   label <- parse_label(params_string[[1]])
@@ -16,23 +16,22 @@ transform_params <- function(params){
                  options = sub(params_string[[1]], "", params))
 }
 
-
-parse_label <- function(label){
+parse_label <- function(label) {
   language_name <- sub(" ", "\\/", label)
   language_name <- unlist(strsplit(language_name, "\\/"))
 
-  if(length(language_name) == 1){
+  if (length(language_name) == 1) {
     tibble::tibble(language = trimws(language_name[1]),
                    name = NA)
-  }else{
+  } else {
     tibble::tibble(language = trimws(language_name[1]),
                    name = trimws(language_name[2]))
   }
 }
 
 # from a chunk header
 # to a tibble with language, name, option, option values
-parse_chunk_header <- function(chunk_header){
+parse_chunk_header <- function(chunk_header) {
   # remove boundaries
   chunk_header <- gsub("```\\{", "", chunk_header)
   chunk_header <- gsub("\\}", "", chunk_header)
@@ -43,7 +42,7 @@ parse_chunk_header <- function(chunk_header){
 }
 
 digest_chunk_header <- function(chunk_header_index,
-                                lines){
+                                lines) {
   # parse the chunk header
   chunk_info <- parse_chunk_header(
     lines[chunk_header_index])
@@ -57,7 +56,7 @@ digest_chunk_header <- function(chunk_header_index,
 
 # helper to go from tibble with chunk info
 # to header to write in R Markdown
-re_write_headers <- function(info_df){
+re_write_headers <- function(info_df) {
   info_df %>%
     dplyr::group_by(.data$index) %>%
     dplyr::summarise(line = glue::glue("```{(language[1]) (name[1])(options)}",
@@ -69,12 +68,12 @@ re_write_headers <- function(info_df){
 }
 
 # helper to create a data.frame of chunk info
-get_chunk_info <- function(lines){
+get_chunk_info = function(lines) {
   # find which lines are chunk starts
-  chunk_header_indices <- which(grepl("^```\\{[a-zA-Z0-9]", lines))
+  chunk_header_indices = which(grepl("^```\\{[a-zA-Z0-9]", lines))
 
   # null if no chunks
-  if(length(chunk_header_indices) == 0){
+  if (length(chunk_header_indices) == 0L) {
     return(NULL)
   }
   # parse these chunk headers
@@ -87,7 +86,7 @@ get_chunk_info <- function(lines){
 # https://github.com/yihui/knitr/blob/2b3e617a700f6d236e22873cfff6cbc3568df568/R/parser.R#L148
 # quote the chunk label if necessary
 quote_label = function(x) {
-  x = gsub('^\\s*,?', '', x)
+  x = gsub("^\\s*,?", "", x)
   if (grepl('^\\s*[^\'"](,|\\s*$)', x)) {
     # <<a,b=1>>= ---> <<'a',b=1>>=
     x = gsub('^\\s*([^\'"])(,|\\s*$)', "'\\1'\\2", x)
@@ -99,8 +98,7 @@ quote_label = function(x) {
 }
 
 # from knitr:::escape_latex()
-clean_latex_special_characters <- function (x, newlines = FALSE, spaces = FALSE)
-{
+clean_latex_special_characters <- function(x, newlines = FALSE, spaces = FALSE) {
   x <- gsub("\\\\", "-", x)
   x <- gsub("([#$%&_{}])", "-", x)
   x <- gsub("\\\\textbackslash", "-", x)

README.Rmd

@@ -50,3 +50,7 @@ remotes::install_github("jumpingrivers/namer")
 ## Code of Conduct
 
 Please note that the namer project is released with a [Contributor Code of Conduct](https://jumpingrivers.github.io/namer/CODE_OF_CONDUCT.html). By contributing to this project, you agree to abide by its terms.
+
+---
+
+Maintained by [Jumping Rivers](https://www.jumpingrivers.com)