[feat]: integrate {journals} package bib files as default bibliographies

DESCRIPTION

@@ -28,6 +28,7 @@ Imports:
     fs,
     glue,
     gt,
+    journals,
     purrr,
     stats,
     stringi,
@@ -49,7 +50,8 @@ Suggests:
     testthat (>= 3.0.0),
     withr
 Remotes:
-    nmfs-ost/stockplotr
+    nmfs-ost/stockplotr,
+    nmfs-ost/journals
 Config/Needs/website: quarto
 Config/roxygen2/version: 8.1.0
 Config/testthat/edition: 3

R/create_template.R

@@ -89,10 +89,11 @@
 #'
 #' Default: NULL
 #'
-#' @param bib_file File path to bibliography file (`.bib`) used for citing references in
-#' the report
+#' @param bib_file File path to additional bibliography file (`.bib`) used for citing references in
+#' the report. By default, all bibliogrphy files from the journals package and 
+#' references for all NMFS stock assessment reports are provided.
 #'
-#' Default: "asar_references.bib"
+#' Default: NULL
 #'
 #' @param new_template TRUE/FALSE; Create a new template? If true,
 #' will pull the last saved stock assessment report skeleton.
@@ -249,7 +250,7 @@ create_template <- function(
   tables_dir = getwd(),
   figures_dir = getwd(),
   spp_image = NULL,
-  bib_file = "asar_references.bib",
+  bib_file = NULL,
   new_template = TRUE,
   rerender_skeleton = FALSE,
   custom_sections = NULL,
@@ -501,16 +502,18 @@ create_template <- function(
     }
 
     # Add bib file
-    if (bib_file == "asar_references.bib") {
-      bib_loc <- system.file("resources", "asar_references.bib", package = "asar")
-      bib_name <- bib_file
+    if (is.null(bib_file)) {
+      if (!rerender_skeleton) {
+        bib_dir <- file.path(subdir, "bibliography_files")
+        dir.create(bib_dir, recursive = FALSE)
+        journals::download_bibs(bib_dir)
+        bib_file <- list.files(bib_dir, pattern = ".bib", full.names = TRUE)
+        bib_name <- list.files(bib_dir, pattern = ".bib", full.names = FALSE)
+      } else {
+        bib_name <- NULL
+      }
     } else {
-      # check if enter file exists
-      # if (!file.exists(bib_file)) stop(".bib file not found.")
-      cli::cli_alert_warning("Bibliography file {bib_file} not in the report directory.")
-      cli::cli_alert_info("The file will not be read in on render if not in the same path as the skeleton file.")
-
-      bib_loc <- bib_file # dirname(bib_file)
+      file.copy(bib_file, subdir, overwrite = TRUE) |> suppressWarnings()
       bib_name <- stringr::str_extract(bib_file, "[^/]+$") # utils::tail(stringr::str_split(bib_file, "/")[[1]], n = 1)
     }
 
@@ -576,7 +579,7 @@ create_template <- function(
     } else {
       #### Copy template files to report folder ----
       # Check if there are already files in the folder
-      if (length(list.files(subdir)) < 2) {
+      if (length(list.files(subdir)) < 3) {
         # copy quarto files
         file.copy(file.path(current_folder, files_to_copy), new_folder, overwrite = FALSE)
         # copy before-body tex
@@ -587,8 +590,6 @@ create_template <- function(
         create_inheader_tex(species = species, year = year, subdir = supdir)
         # Copy species image from package
         file.copy(spp_image, supdir, overwrite = FALSE) |> suppressWarnings()
-        # Copy bib file
-        file.copy(bib_loc, subdir, overwrite = TRUE) |> suppressWarnings()
         # Copy us doc logo
         file.copy(system.file("resources", "us_doc_logo.png", package = "asar"), supdir, overwrite = FALSE) |> suppressWarnings()
         # Copy glossary
@@ -645,8 +646,6 @@ create_template <- function(
           create_inheader_tex(species = species, year = year, subdir = supdir)
           # Copy species image from package
           file.copy(spp_image, supdir, overwrite = FALSE) |> suppressWarnings()
-          # Copy bib file
-          file.copy(bib_loc, subdir, overwrite = TRUE) |> suppressWarnings()
           # Copy us doc logo
           file.copy(system.file("resources", "us_doc_logo.png", package = "asar"), supdir, overwrite = FALSE) |> suppressWarnings()
           # Copy glossary

R/create_yaml.R

@@ -16,8 +16,6 @@
 #' @param author_list A list of strings containing pre-formatted author names
 #' and affiliations that would be found in the format in a yaml of a quarto
 #' file when using base R function `cat()`.
-#' @param bib_name Name of a bib file being added into the yaml. For example,
-#' "asar.bib".
 #'
 #' @return Create a string indicating the important formatting pieces for a
 #' quarto file for a stock assessment report.
@@ -64,7 +62,7 @@ create_yaml <- function(
   spp_image = NULL,
   year = NULL,
   bib_name = NULL,
-  bib_file = "asar_references.bib",
+  bib_file = NULL,
   author_list = NULL,
   title = "[TITLE]",
   rerender_skeleton = FALSE,
@@ -189,20 +187,11 @@ create_yaml <- function(
     } # close if params to be included in template
 
     # add bib file name
-    if (bib_name != "asar_references.bib") {
-      # check if input bib file contains a path
-      if (file.exists(bib_file)) {
-        cli::cli_alert("Copying bibliography file to report folder...")
-        file.copy(bib_file, file_dir)
-        # bib_file_only <- stringr::str_extract(bib_file, "[^/]+$")
-        bib_format <- paste("-  ", bib_name, sep = "")
-      } else if (!file.exists(file.path(file_dir, bib_file))) {
-        cli::cli_alert_warning("Bibliography file {bib_file} is not in the report directory. The file will not be read in on render if it is not in the same path as the skeleton file.",
-          wrap = TRUE
-        )
-        bib_format <- paste("-  ", bib_name, sep = "")
-      }
+    if (!is.null(bib_name)) {
+      new_bib_name <- bib_name[grepl(bib_name), new_bibs]
+      bib_format <- paste("-  ", bib_name, sep = "")
     }
+
     yaml <- paste(yaml, collapse = " \n")
   } else { # not rerendering skeleton
     # Creating YAML
@@ -326,7 +315,7 @@ create_yaml <- function(
     bib <- glue::glue(
       "bibliography: ", "\n"
     )
-    bib_all <- paste0("  ", "- ", bib_file, "\n", collapse = "")
+    bib_all <- paste0("  ", "- ", paste0("bibliography_files/", bib_name), "\n", collapse = "")
     bib <- glue::glue("{bib} \n {bib_all}")
     yaml <- paste(yaml, bib, sep = "")
     # add citation style
@@ -335,7 +324,6 @@ create_yaml <- function(
       "csl: support_files/cjfas.csl\n"
     )
     # }
-    # add in else statement once a national .bib file is made
 
     # Close yaml
     yaml <- glue::glue("{yaml}---\n")