Solving issue #35

DESCRIPTION

@@ -1,27 +1,33 @@
 Package: rbbt
 Title: R Interface to the Better BiBTex Zotero Connector
-Version: 0.0.0.9000
+Version: 0.0.1
+Date: 2023-08-02
 Authors@R: c(person("Dewey", "Dunnington", 
                     email = "dewey@fishandwhistle.net", role = c("aut", "cre")),
              person("Brenton M.", "Wiernik", 
-                    email = "brenton@wiernik.org", role = c("aut"))
+                    email = "brenton@wiernik.org", role = c("aut")),
+             person("Wencheng", "Lau-Medrano", 
+                    email = "brenton@wiernik.org", role = c("ctb"))        
              )
 Description: Connects R to the Better Bibtex for Zotero connector 
   <https://retorque.re/zotero-better-bibtex/>.
-Depends: R (>= 3.4.0)
+Depends: R (>= 4.1.0)
 License: GPL-3
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.1.1
+RoxygenNote: 7.2.3
 Imports: 
     httr,
     rstudioapi,
     clipr,
     knitr,
+    xfun,
     readr,
     stringr,
     rmarkdown,
-    fs
+    fs,
+    tools,
+    utils
 Roxygen: list(markdown = TRUE)
 URL: https://github.com/paleolimbot/rbbt
 BugReports: https://github.com/paleolimbot/rbbt/issues

NAMESPACE

@@ -22,3 +22,30 @@ export(bbt_return)
 export(bbt_update_bib)
 export(bbt_write_bib)
 export(has_bbt)
+importFrom(clipr,clipr_available)
+importFrom(clipr,read_clip)
+importFrom(clipr,write_clip)
+importFrom(fs,is_absolute_path)
+importFrom(httr,GET)
+importFrom(httr,POST)
+importFrom(httr,build_url)
+importFrom(httr,content)
+importFrom(httr,parse_url)
+importFrom(knitr,current_input)
+importFrom(knitr,purl)
+importFrom(readr,default_locale)
+importFrom(readr,read_file)
+importFrom(readr,write_file)
+importFrom(rmarkdown,yaml_front_matter)
+importFrom(rstudioapi,getActiveDocumentContext)
+importFrom(rstudioapi,insertText)
+importFrom(rstudioapi,isAvailable)
+importFrom(stringr,regex)
+importFrom(stringr,str_extract)
+importFrom(stringr,str_match_all)
+importFrom(stringr,str_subset)
+importFrom(tools,file_ext)
+importFrom(utils,URLencode)
+importFrom(utils,citation)
+importFrom(utils,toBibtex)
+importFrom(xfun,split_lines)

R/addin.R

@@ -1,7 +1,7 @@
 
 bbt_cite_addin <- function() {
   # get the likely citation type from the current document context
-  context <- rstudioapi::getActiveDocumentContext()
+  context <- getActiveDocumentContext()
   bbt_cite_cayw(
     format = bbt_guess_format(bbt_rstudio_editor_filepath()),
     .action = bbt_insert
@@ -17,7 +17,7 @@ bbt_bib_addin <- function() {
 
 bbt_update_bib_addin <- function() {
   context <- bbt_rstudio_editor_filepath()
-  if (!(tools::file_ext(context) %in% c("qmd", "Qmd", "rmd", "Rmd"))) {
+  if (!(file_ext(context) %in% c("qmd", "Qmd", "rmd", "Rmd"))) {
     stop("Currently selected editor is not a .qmd, .rmd or .Rmd file", call. = FALSE)
   }
 
@@ -26,7 +26,7 @@ bbt_update_bib_addin <- function() {
 }
 
 bbt_rstudio_editor_filepath <- function() {
-  context <- rstudioapi::getActiveDocumentContext()
+  context <- getActiveDocumentContext()
   if (is.character(context$path)) {
     context$path
   } else {

R/api.R

@@ -38,7 +38,7 @@ assert_bbt <- function() {
 #'
 bbt_call <- function(.endpoint, ...) {
   url <- bbt_url(.endpoint = .endpoint, ...)
-  httr::content(httr::GET(url), as = "text", encoding = "UTF-8")
+  content(GET(url), as = "text", encoding = "UTF-8")
 }
 
 #' @rdname bbt_call
@@ -50,8 +50,8 @@ bbt_cayw <- function(..., .action = bbt_print) {
 #' @rdname bbt_call
 #' @export
 bbt_call_json_rpc <- function(.method, ...) {
-  httr::content(
-    httr::POST(
+  content(
+    POST(
       bbt_url("json-rpc"),
       body = list(
         jsonrpc = "2.0",
@@ -71,15 +71,15 @@ bbt_url <- function(.endpoint, ...) {
   if(is.null(names(args))) {
     url <- paste0(
       .endpoint, "?", paste0(
-        vapply(args, utils::URLencode, reserved=TRUE, FUN.VALUE = character(1)),
+        vapply(args, URLencode, reserved=TRUE, FUN.VALUE = character(1)),
         collapse = "&"
       )
     )
   } else {
     stopifnot(all(names(args) != ""))
-    url <- httr::parse_url(.endpoint)
+    url <- parse_url(.endpoint)
     url$query <- as.list(args)
-    url <- httr::build_url(url)
+    url <- build_url(url)
   }
 
   url

R/bbt-libraries.R

@@ -14,7 +14,7 @@
 #' if (has_bbt()) bbt_libraries()
 #'
 bbt_libraries <- function() {
-  groups <- rbbt::bbt_call_json_rpc("user.groups")
+  groups <- bbt_call_json_rpc("user.groups")
   data.frame(
     id = vapply(groups$result, function(x) x$id, integer(1)),
     name = vapply(groups$result, function(x) x$name, character(1)),

R/bbt.R

@@ -83,6 +83,35 @@ bbt_bib <- function(keys, translator = getOption("rbbt.default.translator", "bib
     return(.action(""))
   }
 
+  index <- grep(pattern = "^rpkg_", x = keys, ignore.case = TRUE)
+
+  if(length(index) > 0){
+    rPkgs <- keys[index]
+
+    rPkgs <- gsub(pattern = "^rpkg_", replacement = "", x = rPkgs, ignore.case = TRUE)
+    rPkgs <- rPkgs |>
+
+      lapply(citation) |>
+
+      lapply(\(x) x[[1]]) |>
+
+      lapply(toBibtex) |>
+
+      lapply(as.character)
+
+    rPkgs <- mapply(x = rPkgs, y = keys[index],
+                    FUN = \(x, y) c(gsub(pattern = "\\{[[:graph:]]*,$",
+                                         replacement = sprintf("\\{%s,", y),
+                                         x = x[1]), x[-1]),
+                    SIMPLIFY = FALSE) |>
+
+      sapply(paste, collapse = "\n") |>
+
+      paste(collapse = "\n\n")
+
+    keys <- keys[-index]
+  }
+
   assert_bbt()
   translator <- match.arg(translator, choices = c("json", "biblatex", "bibtex", "cslyaml"))
   result <- bbt_call_json_rpc(
@@ -95,6 +124,12 @@ bbt_bib <- function(keys, translator = getOption("rbbt.default.translator", "bib
   if (!is.null(result$error)) {
     stop(result$error$message, call. = FALSE)
   } else {
+
+    if(length(index) > 0){
+      result$result[[3]] <- paste0(c(result$result[[3]], rPkgs, ""),
+                                   collapse = "\n")
+    }
+
     .action(result$result[[3]])
   }
 }
@@ -110,8 +145,8 @@ bbt_bib <- function(keys, translator = getOption("rbbt.default.translator", "bib
 #'
 bbt_insert <- function(text) {
   text <- paste(text, collapse = "\n")
-  if(rstudioapi::isAvailable()) {
-    rstudioapi::insertText(text = text)
+  if(isAvailable()) {
+    insertText(text = text)
   } else {
     cat(text)
   }
@@ -138,6 +173,6 @@ bbt_return <- function(text) {
 bbt_copy <- function(text) {
   text <- paste(text, collapse = "\n")
   message("Text copied to clipboard")
-  clipr::write_clip(text)
+  write_clip(text)
   invisible(text)
 }

R/detect-citations.R

@@ -1,4 +1,3 @@
-
 #' Detect pandoc-style citations
 #'
 #' By default, this omits any references within code chunks, inline R code,
@@ -7,8 +6,8 @@
 #' [nocite front matter field](https://rmarkdown.rstudio.com/authoring_bibliographies_and_citations.html#Unused_References_(nocite)).
 #'
 #' @param path A character vector, file or URL whose contents may contain citation keys.
-#'   Multiple files can be passed in as a vector (e.g., from [list.files()]).
-#' @param locale See [readr::default_locale()]. Use if encoding might
+#'   Multiple files can be passed in as a vector (e.g., from \link{list.files}).
+#' @param locale See \link[readr]{default_locale}. Use if encoding might
 #'   be a problem.
 #'
 #' @return A character vector of unique citation keys.
@@ -17,15 +16,15 @@
 #' @examples
 #' bbt_detect_citations("\n@citation1 and [@citation2] but not \\@citation3")
 #'
-bbt_detect_citations <- function(path = bbt_guess_citation_context(), locale = readr::default_locale()) {
-  text <- vapply(path, readr::read_file, locale = locale, FUN.VALUE = character(1))
+bbt_detect_citations <- function(path = bbt_guess_citation_context(), locale = default_locale()) {
+  text <- vapply(path, read_file, locale = locale, FUN.VALUE = character(1))
   bbt_detect_citations_chr(text)
 }
 
 #' @rdname bbt_detect_citations
 #' @export
 bbt_guess_citation_context <- function() {
-  knitr_doc <- knitr::current_input()
+  knitr_doc <- current_input()
   if (!is.null(knitr_doc)) {
     knitr_doc
   } else {
@@ -49,10 +48,12 @@ bbt_detect_citations_chr <- function(text) {
   text <- gsub("\\(http.+?\\)", "", text)
   text <- gsub("<http.+?>", "", text)
 
-  refs <- stringr::str_match_all(
-    text,
-    stringr::regex("[^a-zA-Z0-9\\\\]@([a-zA-Z0-9_\\.\\-:]+[a-zA-Z0-9])", multiline = TRUE, dotall = TRUE)
+  refs <- str_match_all(string = text, pattern = regex("[^a-zA-Z0-9\\\\]@([a-zA-Z0-9_\\.\\-:]+[a-zA-Z0-9])",
+                   multiline = TRUE, dotall = TRUE)
   )[[1]][, 2, drop = TRUE]
 
+  index <- !grepl(pattern = "(^fig-)|(^tbl-)", x = refs, ignore.case = TRUE)
+  refs <- refs[index]
+
   unique(refs)
 }

R/rbbt.R

@@ -0,0 +1,13 @@
+# rbbt
+#' @importFrom clipr clipr_available read_clip write_clip
+#' @importFrom httr content POST parse_url build_url GET
+#' @importFrom rstudioapi getActiveDocumentContext isAvailable insertText
+#' @importFrom knitr current_input purl
+#' @importFrom xfun split_lines
+#' @importFrom readr default_locale read_file write_file
+#' @importFrom stringr str_match_all regex str_subset str_extract
+#' @importFrom rmarkdown yaml_front_matter
+#' @importFrom fs is_absolute_path
+#' @importFrom tools file_ext
+#' @importFrom utils URLencode toBibtex citation
+NULL

R/update.R

@@ -6,7 +6,7 @@
 #'
 #' @param path_rmd The path to the RMarkdown file.
 #' @param path_bib The path to the bibliography file.
-#' @param encoding Passed to [rmarkdown::yaml_front_matter()]
+#' @param encoding Passed to \link[rmarkdown]{yaml_front_matter}
 #' @param quiet Use `TRUE` to suppress message on successful write.
 #' @inheritParams bbt_write_bib
 #'
@@ -39,7 +39,7 @@ bbt_update_bib <- function(path_rmd,
 #' @rdname bbt_update_bib
 #' @export
 bbt_guess_bib_file <- function(path_rmd, encoding = "UTF-8") {
-  front_matter <- rmarkdown::yaml_front_matter(path_rmd, encoding = encoding)
+  front_matter <- yaml_front_matter(path_rmd, encoding = encoding)
   if (length(front_matter$bibliography) != 1) {
     stop(
       sprintf("Can't guess bibliography file from '%s' front matter", path_rmd),
@@ -48,7 +48,7 @@ bbt_guess_bib_file <- function(path_rmd, encoding = "UTF-8") {
   }
 
   bib_file <- front_matter$bibliography
-  if (!fs::is_absolute_path(bib_file)) {
+  if (!is_absolute_path(bib_file)) {
     file.path(dirname(path_rmd), bib_file)
   } else {
     bib_file

R/write-bib.R

@@ -41,7 +41,7 @@ bbt_write_bib <- function(path,
   force(keys)
 
   assert_bbt()
-  readr::write_file(
+  write_file(
     bbt_bib(
       setdiff(keys, ignore),
       translator,

README.Rmd

@@ -41,24 +41,28 @@ You will also need [Zotero](https://www.zotero.org/) installed and running, and
 
 This package is most useful for the RStudio addins that insert citations and references into the editor. The "Insert Zotero Citation" will pop up a zotero search where you can search for a reference to add to your writing (Markdown, RMarkdown, or LaTeX). The "Insert Zotero Bibliography" addin inserts the bibliographical information corresponding to the selected item in the Zotero window. Finally, "Update bibliography for current document" runs `bbt_update_bib()` to update the bibliography based on the .Rmd file currently in the editor window. You can bind either of these to keyboard shortcuts in RStudio. The addins may behave differently depending on which file you have open (e.g., if you have a .bib file open, it will use the biblatex translator)...if you need more fine-grained control, try one of the console functions (like `bbt_bib()`!).
 
-## knitr + rmarkdown integration
+## RStudio shortcuts
 
-To make this work seamlessly with [knitr](https://yihui.org/knitr/) and [rmarkdown](https://rmarkdown.rstudio.com/), use the "Update bibliography for current document" addin to write your bibliography file based on the citations in the currently selected document. You can use `bbt_update_bib("some_file.Rmd")` to detect citations and write your bibliography file from the console.
+In RStudio, it is possible to assign a keyboard shortcut for **rbbt** addins. Just go to *Tools --> Modify Keyboard Shortcuts* and a small window will open with all the available commands to assign a keyboard shortcut. Then, using the **Scope** column, find the *Addin* type and configure the shortcuts for **rbbt** commands. For example: to set a shortcut for `bbt_update_bib()`, go to the row assigned for **"Update bibliography for current document from Zotero "**, click on the **Shortcut** column and press the desired key combination. It is recommended to define shortcuts for **"Update bibliography for current document from Zotero "** and **"Insert Zotero citation "** as they will be the most used.
 
-## Programmatically fetch bibliography info
+It should be noted that RStudio comes configured with some keyboard shortcuts, so it should be avoided that the newly defined shortcuts overlap (if this happens, a warning icon will be displayed in the shortcut assignment window).
 
-Fetch bibliography text using a list of Better BibTex citation keys:
+Also, for the commands to work correctly, they must be executed having the Rmd or Qmd file in the active tab in RStudio. That is to say, both addins mentioned above will detect the citations and the bibliography file from the active tab (from the main .Rmd or .Qmd file) from where the shortcut is executed, so you must make sure to have that document active when executing the commands, otherwise you will receive the following error message: **"Currently selected editor is not a .qmd, .rmd or .Rmd file "**.
 
-```{r, comment=""}
-# uses the citation keys you've defined with Better BibTeX
-rbbt::bbt_bib("dunnington_etal18", translator = "biblatex", .action = bbt_print)
-```
+In RStudio, it is possible to assign a keyboard shortcut for rbbt addins. Just go to Tools --> Modify Keyboard Shortcuts and a small window will open with all the available commands to assign a keyboard shortcut. Then, using the **Scope** column, find the **Addin** type and configure the shortcuts for **rbbt** commands. For example: to set a shortcut for `bbt_update_bib()`, go to the row assigned for **"Update bibliography for current document from Zotero "**, click on the **Shortcut** column and press the desired key combination. It is recommended to define shortcuts for **"Update bibliography for current document from Zotero "** and **"Insert Zotero citation "** as they will be the most used.
 
-Fetch bibliography text from selected items in Zotero:
+## knitr + rmarkdown integration
 
-```{r, comment=""}
-# uses whatever is currently selected in the zotero window
-rbbt::bbt_bib_selected(translator = "biblatex", .action = bbt_print)
-```
+To make this work seamlessly with [knitr](https://yihui.org/knitr/) and [rmarkdown](https://rmarkdown.rstudio.com/), use the "Update bibliography for current document" addin to write your bibliography file based on the citations in the currently selected document. You can use `bbt_update_bib("some_file.Rmd")` to detect citations and write your bibliography file from the console.
+
+# Versions
+
+## 0.0.1
+* Add functionality for citing R packages. Now, if the user wants to cite a R package, could indicate it in the Rmd/Qmd file with the syntax `@rpkg_NameOfPackage` (e.g. `@rpkg_rbbt`). `bbt_detect_citations` and `bbt_update_bib` are now prepared for identify this syntax and adding to the bibliography using `citation` and `toBibtex` tools.
+* R native pipe is used in some functions so now it is necessary to run **rbbt** in **R >= 4.1.0**.
+* Subtle corrections and improvements in code and documentation.
+
+## 0.0.0.9002
 
-<!-- lazy way to test the bbt_update_bib() addon: @dunnington_etal18 -->
+* Changes in `bbt_detect_citations` in order to avoid including citations that starts whether with *fig-* or *tbl-* (associtaed with Quarto syntaxis).
+* Minor improvements in definiton of external functions and dependencies.