Improve preferred-citation handling (#38)

* Improve preferred-citation * Create preferred-citation only if a CITATION file is detected #37 * Update docs with pkgdev * Fix Roxygen warning Co-authored-by: dieghernan <dieghernan@users.noreply.github.com>
ropensci · Aug 29, 2022 · 732c2d0 · 732c2d0
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diff --git a/CITATION.cff b/CITATION.cff
@@ -1,5 +1,5 @@
 # -----------------------------------------------------------
-# CITATION file created with {cffr} R package, v0.2.2
+# CITATION file created with {cffr} R package, v0.2.3.9000
 # See also: https://docs.ropensci.org/cffr/
 # -----------------------------------------------------------
 
@@ -8,7 +8,7 @@ message: 'To cite package "cffr" in publications use:'
 type: software
 license: GPL-3.0-or-later
 title: 'cffr: Generate Citation File Format (''cff'') Metadata for R Packages'
-version: 0.2.3
+version: 0.2.3.9000
 doi: 10.21105/joss.03900
 abstract: The Citation File Format version 1.2.0 <doi:10.5281/zenodo.5171937> is a
   human and machine readable file format which provides citation metadata for software.
@@ -78,7 +78,7 @@ references:
     given-names: Gábor
     email: csardi.gabor@gmail.com
   year: '2022'
-  url: https://CRAN.R-project.org/package=crayon
+  url: https://github.com/r-lib/crayon#readme
   version: '>= 1.4.1'
 - type: software
   title: desc
@@ -94,7 +94,6 @@ references:
     given-names: Jim
     email: james.f.hester@gmail.com
   year: '2022'
-  url: https://CRAN.R-project.org/package=desc
   version: '>= 1.3.0'
 - type: software
   title: jsonlite
@@ -106,7 +105,6 @@ references:
     email: jeroen@berkeley.edu
     orcid: https://orcid.org/0000-0002-4035-0289
   year: '2022'
-  url: https://CRAN.R-project.org/package=jsonlite
   version: '>= 1.7.2'
 - type: software
   title: jsonvalidate
@@ -123,7 +121,6 @@ references:
   - family-names: Poberezkin
     given-names: Evgeny
   year: '2022'
-  url: https://CRAN.R-project.org/package=jsonvalidate
   version: '>= 1.1.0'
 - type: software
   title: yaml
@@ -156,7 +153,7 @@ references:
   - family-names: Kamvar
     given-names: Zhian N.
   year: '2022'
-  url: https://CRAN.R-project.org/package=yaml
+  url: https://github.com/vubiostat/r-yaml/
   version: '>= 2.2.1'
 - type: software
   title: knitr
@@ -168,7 +165,7 @@ references:
     email: xie@yihui.name
     orcid: https://orcid.org/0000-0003-0645-5666
   year: '2022'
-  url: https://CRAN.R-project.org/package=knitr
+  url: https://yihui.org/knitr/
 - type: software
   title: lifecycle
   abstract: 'lifecycle: Manage the Life Cycle of your Package Functions'
@@ -182,7 +179,6 @@ references:
     email: hadley@rstudio.com
     orcid: https://orcid.org/0000-0003-4757-117X
   year: '2022'
-  url: https://CRAN.R-project.org/package=lifecycle
 - type: software
   title: rmarkdown
   abstract: 'rmarkdown: Dynamic Documents for R'
@@ -221,7 +217,6 @@ references:
     email: rich@rstudio.com
     orcid: https://orcid.org/0000-0003-3925-190X
   year: '2022'
-  url: https://CRAN.R-project.org/package=rmarkdown
 - type: software
   title: testthat
   abstract: 'testthat: Unit Testing for R'
@@ -231,7 +226,6 @@ references:
     given-names: Hadley
     email: hadley@rstudio.com
   year: '2022'
-  url: https://CRAN.R-project.org/package=testthat
   version: '>= 3.0.0'
 - type: software
   title: usethis
@@ -251,4 +245,3 @@ references:
     email: malcolmbarrett@gmail.com
     orcid: https://orcid.org/0000-0003-0299-5825
   year: '2022'
-  url: https://CRAN.R-project.org/package=usethis
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: cffr
 Title: Generate Citation File Format ('cff') Metadata for R Packages
-Version: 0.2.3
+Version: 0.2.3.9000
 Authors@R: c(
     person("Diego", "Hernangómez", , "diego.hernangomezherrero@gmail.com", role = c("aut", "cre", "cph"),
            comment = c(ORCID = "0000-0001-8457-4658")),

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,8 @@
+# cffr (development version)
+
+-   `preferred-citation` is only produced when a CITATION (**R**) file has been
+    provided with the package (#37).
+
 # cffr 0.2.3
 
 -   Fix HTML5 issue as per CRAN request

diff --git a/R/cff_create.R b/R/cff_create.R
@@ -104,9 +104,9 @@ cff_create <- function(x,
                        cff_version = "1.2.0",
                        gh_keywords = TRUE,
                        dependencies = TRUE) {
+  # On missing use package root
   if (missing(x)) x <- getwd()
 
-
   if (!is.cff(x) && !is.character(x)) {
     stop("x should be a cff or a character",
       call. = FALSE
@@ -126,32 +126,31 @@ cff_create <- function(x,
     cffobj <- x
     cffobj["cff-version"] <- cff_version
   } else {
-    # Need to parse with desc_path
-
-    if (x %in% instpack) {
-
-      # Installed package, have to parse
-      desc_path <- file.path(find.package(x), "DESCRIPTION")
-
-      # Parse citation from installation
-      citobj <- lapply(citation(x), cff_parse_citation)
-      if (length(citobj) == 0) citobj <- NULL
-      citobj <- drop_null(citobj)
-    } else if (x == getwd()) {
+    # Detect a package
+    if (x %in% instpack) x <- file.path(find.package(x), "DESCRIPTION")
+    # If is on the root create DESCRIPTION path
+    if (x == getwd()) x <- file.path(x, "DESCRIPTION")
 
-      # In development package
-      # nocov start
-      desc_path <- file.path(x, "DESCRIPTION")
-      cit_path <- file.path(x, "inst/CITATION")
+    if (isTRUE(grep("DESCRIPTION", x) == 1)) {
+      # Call for a DESCRIPTION file
+      desc_path <- x
+      # Look if a CITATION file on inst/ folder
+      # for in-development packages
+      cit_path <- gsub("DESCRIPTION$", "inst/CITATION", x)
+      # If it doesn't exists look on the root
+      # this is for call to installed packages with system.file()
+      if (!file.exists(cit_path)) {
+        cit_path <- gsub(
+          "DESCRIPTION$",
+          "CITATION", x
+        )
+      }
       if (file.exists(cit_path)) {
         citobj <- parse_r_citation(desc_path, cit_path)
         citobj <- lapply(citobj, cff_parse_citation)
         if (length(citobj) == 0) citobj <- NULL
         citobj <- drop_null(citobj)
       }
-      # nocov end
-    } else if (isTRUE(grep("DESCRIPTION", x) == 1)) {
-      desc_path <- x
     } else {
       stop("object x: '", x, "' not valid. If it is a package ",
         "you may need to install it.",
@@ -197,8 +196,10 @@ cff_create <- function(x,
   cffobjend <- cffobjend[cff_schema_keys()]
 
   # Enhance authors info
-  cffobjend$`preferred-citation`$authors <- enhance_pref_authors(cffobjend)
 
+  if (!is.null(cffobjend$`preferred-citation`)) {
+    cffobjend$`preferred-citation`$authors <- enhance_pref_authors(cffobjend)
+  }
   cffobjend <- as.cff(cffobjend)
   cffobjend
 }
@@ -208,6 +209,12 @@ cff_create <- function(x,
 #' @noRd
 merge_desc_cit <- function(cffobj, citobj) {
 
+  # If no citobj then return null
+
+  if (is.null(citobj)) {
+    return(cffobj)
+  }
+
   # Add doi from citation if missing
   if (is.null(cffobj$doi)) {
     cffobj$doi <- clean_str(citobj[[1]]$doi)
@@ -226,14 +233,6 @@ merge_desc_cit <- function(cffobj, citobj) {
     oldids
   )
 
-  # Add auto preferred if not present
-  if (is.null(cffobjend[["preferred-citation"]])) {
-    pref_auto <- parse_preferred_auto(cffobjend)
-    cffobjend <- c(cffobjend,
-      "preferred-citation" = list(pref_auto)
-    )
-  }
-
   # Reorder
   cffobjfinal <- c(
     cffobjend[!names(cffobjend) %in% c("identifiers", "references")],

diff --git a/R/cff_to_bibtex.R b/R/cff_to_bibtex.R
@@ -1,4 +1,4 @@
-#' Create a BibTeX entry from a CITATION file or a `cff` object
+#' Create a BibTeX entry from a CITATION.cff file or a `cff` object
 #'
 #' Creates a `bibentry` object ([bibentry()]) from a `cff` object
 #'
@@ -33,6 +33,9 @@
 #' obj
 #'
 #' toBibtex(obj)
+#'
+#' # Same info as
+#' toBibtex(citation("rmarkdown")[1])
 #' }
 cff_to_bibtex <- function(x) {
   if (is.null(x)) {

diff --git a/R/parse_citation.R b/R/parse_citation.R
@@ -49,38 +49,46 @@ parse_package_meta <- function(desc_path) {
   meta
 }
 
-
-#' Used for creating an auto preferred-citation from an
-#' cff object if not present
-#' It mocks citation(auto = meta) of base R
-#' @noRd
-parse_preferred_auto <- function(cffobjend) {
-  valid <- cff_schema_definitions_refs()
-
-  pref <- cffobjend[names(cffobjend) %in%
-    valid]
-
-  pref$type <- "manual"
-
-  # Handle year
-
-  date_rel <- pref[["date-released"]]
-
-  if (is.null(date_rel)) {
-    year <- format(Sys.Date(), "%Y")
-  } else {
-    year <- format(as.Date(pref[["date-released"]]), "%Y")
-  }
-
-  pref$year <- year
-
-  # Order and output
-  ordernames <- unique(c("type", "title", "authors", names(pref)))
-  pref <- pref[unique(c(ordernames, "identifiers"))]
-  pref <- as.cff(pref)
-
-  pref
-}
+# DEPRECATED
+# Used for creating an auto preferred-citation from an
+# cff object if not present
+# It mocks citation(auto = meta) of base R
+# parse_preferred_auto <- function(cffobjend) {
+#   valid <- cff_schema_definitions_refs()
+#
+#   pref <- cffobjend[names(cffobjend) %in%
+#     valid]
+#
+#   pref$type <- "manual"
+#
+#   # Handle year
+#
+#   date_rel <- pref[["date-released"]]
+#
+#   if (is.null(date_rel)) {
+#     year <- format(Sys.Date(), "%Y")
+#   } else {
+#     year <- format(as.Date(pref[["date-released"]]), "%Y")
+#   }
+#
+#   pref$year <- year
+#   pref$notes <- NULL
+#   if (!is.null(pref$version)) {
+#     pref$notes <- paste("R package version", pref$version)
+#   }
+#   # If it has a repository (CRAN) use that as url
+#   if (!is.null(pref$repository)) pref$url <- pref$repository
+#
+#   # Order and output
+#   ordernames <- c(
+#     "type", "title", "authors", "year",
+#     "notes", "url"
+#   )
+#   pref <- pref[ordernames]
+#   pref <- as.cff(pref)
+#
+#   pref
+# }
 ## Building blocks ----
 
 #' BB for doi