Merge pull request #75 from ropensci/crandoi

Recognize CRAN DOI

CITATION.cff

@@ -10,6 +10,9 @@ license: GPL-3.0-or-later
 title: 'cffr: Generate Citation File Format (''cff'') Metadata for R Packages'
 version: 1.0.1.9000
 doi: 10.21105/joss.03900
+identifiers:
+- type: doi
+  value: 10.32614/CRAN.package.cffr
 abstract: The Citation File Format version 1.2.0 <https://doi.org/10.5281/zenodo.5171937>
   is a human and machine readable file format which provides citation metadata for
   software. This package provides core utilities to generate and validate this metadata.
@@ -108,6 +111,7 @@ references:
     given-names: Gábor
     email: csardi.gabor@gmail.com
   year: '2024'
+  doi: 10.32614/CRAN.package.cli
   version: '>= 2.0.0'
 - type: software
   title: desc
@@ -125,6 +129,7 @@ references:
     given-names: Jim
     email: james.f.hester@gmail.com
   year: '2024'
+  doi: 10.32614/CRAN.package.desc
   version: '>= 1.3.0'
 - type: software
   title: jsonlite
@@ -141,6 +146,7 @@ references:
   identifiers:
   - type: url
     value: https://arxiv.org/abs/1403.2805
+  doi: 10.32614/CRAN.package.jsonlite
   version: '>= 1.7.2'
 - type: software
   title: jsonvalidate
@@ -159,6 +165,7 @@ references:
   - family-names: Poberezkin
     given-names: Evgeny
   year: '2024'
+  doi: 10.32614/CRAN.package.jsonvalidate
   version: '>= 1.1.0'
 - type: software
   title: yaml
@@ -193,6 +200,7 @@ references:
   - family-names: Kamvar
     given-names: Zhian N.
   year: '2024'
+  doi: 10.32614/CRAN.package.yaml
   version: '>= 2.2.1'
 - type: software
   title: bibtex
@@ -210,6 +218,7 @@ references:
     email: diego.hernangomezherrero@gmail.com
     orcid: https://orcid.org/0000-0001-8457-4658
   year: '2024'
+  doi: 10.32614/CRAN.package.bibtex
   version: '>= 0.5.0'
 - type: software
   title: knitr
@@ -223,6 +232,7 @@ references:
     email: xie@yihui.name
     orcid: https://orcid.org/0000-0003-0645-5666
   year: '2024'
+  doi: 10.32614/CRAN.package.knitr
 - type: software
   title: lifecycle
   abstract: 'lifecycle: Manage the Life Cycle of your Package Functions'
@@ -238,6 +248,7 @@ references:
     email: hadley@posit.co
     orcid: https://orcid.org/0000-0003-4757-117X
   year: '2024'
+  doi: 10.32614/CRAN.package.lifecycle
 - type: software
   title: rmarkdown
   abstract: 'rmarkdown: Dynamic Documents for R'
@@ -281,6 +292,7 @@ references:
     email: rich@posit.co
     orcid: https://orcid.org/0000-0003-3925-190X
   year: '2024'
+  doi: 10.32614/CRAN.package.rmarkdown
 - type: software
   title: testthat
   abstract: 'testthat: Unit Testing for R'
@@ -292,6 +304,7 @@ references:
     given-names: Hadley
     email: hadley@posit.co
   year: '2024'
+  doi: 10.32614/CRAN.package.testthat
   version: '>= 3.0.0'
 - type: software
   title: usethis
@@ -317,4 +330,5 @@ references:
     email: andy.teucher@posit.co
     orcid: https://orcid.org/0000-0002-7840-692X
   year: '2024'
+  doi: 10.32614/CRAN.package.usethis
 

NEWS.md

@@ -1,5 +1,14 @@
 # cffr (development version)
 
+-   Now **cffr** adds automatically dois to packages on **CRAN** (e.g.
+    <https://doi.org/10.32614/CRAN.package.cffr>):
+    -   If the package has a `CITATION` file providing a doi, the `CITATION` doi
+        would be used as the main `CITATION.cff` `doi` and the **CRAN** doi
+        would be added as an `identifier`.
+    -   Otherwise, **CRAN** doi would be used as `doi`.
+    -   When extracting dependencies (e.g `cff_create(dependencies = TRUE)` and
+        the package dependency is on **CRAN**, the **CRAN** doi would be used
+        for the dependency in the `references` key.
 -   Extract `commit` from `RemoteSha`.
 
 # cffr 1.0.1

R/cff_read.R

@@ -179,7 +179,8 @@ cff_read_description <- function(path, cff_version = "1.2.0",
     contact = get_desc_contacts(pkg),
     keywords = get_desc_keywords(pkg),
     license = unlist(get_desc_license(pkg)),
-    commit = get_desc_sha(pkg)
+    commit = get_desc_sha(pkg),
+    doi = get_desc_doi(pkg)
   )
 
   if (gh_keywords) {

R/utils-cff_read.R

@@ -366,3 +366,13 @@ get_desc_sha <- function(pkg) {
 
   sha
 }
+
+get_desc_doi <- function(pkg) {
+  pkg <- pkg$get("Package")
+  if (is.null(search_on_repos(pkg))) {
+    return(NULL)
+  }
+
+  doi <- paste0("10.32614/CRAN.package.", pkg)
+  clean_str(doi)
+}

R/utils-create.R

@@ -6,6 +6,15 @@ merge_desc_cit <- function(cffobj, citobj) {
   if (is.null(citobj)) {
     return(cffobj)
   }
+  # Play with cran DOI
+  cran_doi <- NULL
+  has_cran_doi <- FALSE
+  if (all(!is.null(cffobj$doi), grepl("CRAN", cffobj$doi))) {
+    has_cran_doi <- TRUE
+    cran_doi <- cffobj$doi
+    # First the citation object
+    cffobj$doi <- NULL
+  }
 
   # Add doi from citation if missing
   if (is.null(cffobj$doi)) {
@@ -21,8 +30,16 @@ merge_desc_cit <- function(cffobj, citobj) {
 
 
   # Merge identifiers
-  oldids <- cffobjend$identifiers
-  cffobjend$identifiers <- c(citobj[[1]]$identifiers, oldids)
+  merged_ids <- c(citobj[[1]]$identifiers, cffobjend$identifiers)
+
+
+  if (has_cran_doi) {
+    cranid <- as_cff(list(
+      list(type = "doi", value = clean_str(cran_doi))
+    ))
+    merged_ids <- c(cranid, merged_ids)
+  }
+  cffobjend$identifiers <- merged_ids
 
   # Reorder
   cffobjfinal <- c(
@@ -136,6 +153,10 @@ get_dependencies <- function(desc_path,
       # Avoid cluttering the output
       mod$abstract <- mod$title
       mod$title <- n$package
+      # If on CRAN add CRAN DOI
+      if (!is.null(n$package)) {
+        mod$doi <- paste0("10.32614/CRAN.package.", n$package)
+      }
     }
 
     mod$type <- "software"

R/utils-schema.R

@@ -83,19 +83,19 @@ cff_schema_keys <- function(sorted = FALSE) {
       "title",
       "version",
       "doi",
+      "identifiers",
       "abstract",
       "authors",
       "preferred-citation",
       "repository",
       "repository-artifact",
       "repository-code",
+      "commit",
       "url",
       "date-released",
       "contact",
       "keywords",
       "references",
-      "commit",
-      "identifiers",
       "license-url"
     )
   }