Merge pull request #45 from Pakillo/citekeys-regex

Fix problem with dashes in citation keys #44

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: grateful
 Title: Facilitate Citation of R Packages
-Version: 0.2.7
+Version: 0.2.8
 Authors@R: c(
     person("Francisco", "Rodriguez-Sanchez", 
             email = "[email protected]", 

NEWS.md

@@ -1,3 +1,6 @@
+# grateful 0.2.8
+
+* Fix problem with citation keys containing non-alphanumeric characters (-) (issue #44, thanks @jkylearmstrong).
 
 # grateful 0.2.7
 

R/cite_packages.R

@@ -226,7 +226,7 @@ cite_packages <- function(output = c("file", "paragraph", "table", "citekeys"),
 
 
   if (output == "citekeys") {
-    return(unlist(pkgs.df$citekeys))
+    return(unname(unlist(pkgs.df$citekeys)))
   }
 
 }

R/get_citations.R

@@ -5,7 +5,7 @@
 #'
 #' @return A file on the specified `out.dir` containing the package references
 #' in BibTeX format. If assigned a name, `get_citations` will also return a list
-#'  with citation keys for each citation (without @@).
+#'  with citation keys for each package (without @@).
 #'
 #' @export
 #'
@@ -42,9 +42,10 @@ get_citations <- function(pkgs = NULL,
 
   pkgs.notidy <- pkgs[pkgs != "tidyverse"]
   cites.bib <- lapply(pkgs.notidy, get_citation_and_citekey)
+  names(cites.bib) <- pkgs.notidy
 
   if ("tidyverse" %in% pkgs) {
-    cites.bib[[length(cites.bib) + 1]] <- add_citekey("tidyverse", tidyverse.citation)
+    cites.bib$tidyverse <- add_citekey("tidyverse", tidyverse.citation)
   }
 
   if (include.RStudio == TRUE) {
@@ -55,7 +56,7 @@ get_citations <- function(pkgs = NULL,
       rstudio_cit <- tryCatch(rstudioapi::versionInfo()$citation,
                               error = function(e) NULL)
       if (!is.null(rstudio_cit)) {
-        cites.bib[[length(cites.bib) + 1]] <- add_citekey("rstudio", rstudio_cit)
+        cites.bib$rstudio <- add_citekey("rstudio", rstudio_cit)
       }
     }
   }
@@ -65,8 +66,13 @@ get_citations <- function(pkgs = NULL,
              con = file.path(out.dir, paste0(bib.file, ".bib")),
              useBytes = TRUE)
 
-  # get the citekeys and format them appropriately before returning them
-  citekeys <- unname(grep("\\{[[:alnum:]]+,$", unlist(cites.bib), value = TRUE))
-  citekeys <- gsub(".*\\{([[:alnum:]]+),$", "\\1", citekeys)
-  invisible(citekeys)
+  # get the citekeys for each package
+  get_pkg_citekeys <- function(pkg) {
+    citekeys <- unname(grep("\\{[[:alnum:]_-]+,$", pkg, value = TRUE))
+    citekeys <- gsub(".*\\{([[:alnum:]_-]+),$", "\\1", citekeys)
+    return(citekeys)
+  }
+  pkg_citekeys <- lapply(cites.bib, get_pkg_citekeys)
+
+  invisible(pkg_citekeys)
 }

R/get_csl.R

@@ -41,7 +41,7 @@ get_csl <- function(name = NULL, out.dir = NULL) {
   }
 
   if (is.null(out)) {
-    file.remove(destfile)
+    if (file.exists(destfile)) file.remove(destfile)
     stop("The citation style '", name, "' could not be downloaded. Please check the style name and your internet connection.")
   } else {
     destfile

R/get_pkgs_info.R

@@ -39,12 +39,11 @@ get_pkgs_info <- function(pkgs = "All",
                             bib.file = bib.file,
                             include.RStudio = include.RStudio)
 
+  if (isTRUE(include.RStudio)) {
+    citekeys <- citekeys[names(citekeys) != "rstudio"]
+  }
 
-  # Group all citations from same package
-  pkgs.df$citekeys <- lapply(pkgs.df$pkg, function(pkg) {
-    pkgname_clean <- gsub("[^[:alnum:]]", "", pkg)
-    citekeys[grep(paste0("^", pkgname_clean, "(\\d{4}[a-z]?)?$"), citekeys, perl = TRUE)]
-  })
+  pkgs.df$citekeys <- citekeys
 
   pkgs.df
 

tests/testthat/test-cite_packages.R

@@ -9,21 +9,24 @@ test_that("providing wrong arguments return error", {
 test_that("cite_packages returns correct citekeys", {
 
   expect_identical(cite_packages(output = "citekeys",
-                                 pkgs = c("remotes", "renv"),
+                                 pkgs = c("remotes", "renv", "knitr"),
                                  out.dir = tempdir()),
-                   c("remotes", "renv"))
+                   c("knitr2024", "knitr2015", "knitr2014", "remotes", "renv"))
 })
 
 
 test_that("cite_packages returns correct table", {
 
   tabla <- cite_packages(output = "table",
-                         pkgs = c("remotes", "renv"),
+                         pkgs = c("remotes", "renv", "knitr"),
                          out.dir = tempdir())
-  expect_true(nrow(tabla) == 2)
+  expect_true(nrow(tabla) == 3)
   expect_identical(names(tabla), c("Package", "Version", "Citation"))
-  expect_identical(tabla$Package, c("remotes", "renv"))
-  expect_identical(tabla$Citation, list("@remotes", "@renv"))
+  expect_identical(tabla$Package, c("knitr", "remotes", "renv"))
+  expect_identical(tabla$Citation,
+                   list(knitr = "@knitr2014; @knitr2015; @knitr2024",
+                        remotes = "@remotes",
+                        renv = "@renv"))
 
 })
 

tests/testthat/test-get_citations.R

@@ -10,7 +10,7 @@ test_that("get_citations returns error if wrong arguments provided", {
 
 test_that("get_citations works", {
   citkeys <- get_citations("grateful", out.dir = tempdir())
-  expect_identical(citkeys, "grateful")
+  expect_identical(citkeys, list(grateful = "grateful"))
 })
 
 # test_that("get_citations adds Rstudio citation if asked", {

tests/testthat/test-get_pkgs_info.R

@@ -1,6 +1,10 @@
 test_that("get_pkgs_info works", {
-  info <- get_pkgs_info(pkgs = c("renv", "remotes", "dplyr", "ggplot2"),
+  info <- get_pkgs_info(pkgs = c("renv", "remotes", "dplyr", "ggplot2", "knitr"),
                         out.dir = tempdir())
-  expect_identical(info$pkg, c("remotes", "renv", "tidyverse"))
-  expect_identical(info$citekeys, list("remotes", "renv", "tidyverse"))
+  expect_identical(info$pkg, c("knitr", "remotes", "renv", "tidyverse"))
+  expect_identical(info$citekeys,
+                   list(knitr = c("knitr2024", "knitr2015", "knitr2014"),
+                        remotes = "remotes",
+                        renv = "renv",
+                        tidyverse = "tidyverse"))
 })