Finish cff_read()

CITATION.cff

@@ -138,9 +138,6 @@ references:
     email: [email protected]
     orcid: https://orcid.org/0000-0002-4035-0289
   year: '2024'
-  identifiers:
-  - type: url
-    value: https://arxiv.org/abs/1403.2805
   version: '>= 1.7.2'
 - type: software
   title: jsonvalidate

NAMESPACE

@@ -20,6 +20,7 @@ export(cff_parse_person_bibtex)
 export(cff_read)
 export(cff_read_bib)
 export(cff_read_cff_citation)
+export(cff_read_citation)
 export(cff_read_description)
 export(cff_schema_definitions_entity)
 export(cff_schema_definitions_person)

R/cff_read.R

@@ -27,10 +27,33 @@
 #' @param authors_roles Roles to be considered as authors of the package when
 #'   generating the [`cff`][cff-class] object.
 #' @param encoding Encoding to be assumed for `path`. See [readLines()].
+#' @param meta A list of package metadata as obtained by
+#'   [utils::packageDescription()] or `NULL` (the default). See **Details**.
 #' @param ... Arguments to be passed to other functions.
 #'
-#' @return A [`cff`][cff-class] object.
+#' @return
+#' A [`cff`][cff-class] object. In the case of [cff_read_cff_citation()] and
+#' [cff_read_description()] a full and (potentially) valid `cff` object.
 #'
+#' In the case of [cff_read_bib()] and [cff_read_citation()], the result is
+#' the `cff` version of a [bibentry()] object (i.e. a bibliographic reference),
+#' that can be used to complement another `cff` object.
+#'
+#'
+#' @references
+#'
+#' R Core Team (2023). _Writing R Extensions_.
+#' <https://cran.r-project.org/doc/manuals/r-release/R-exts.html>
+#'
+#' @details
+#'
+#' Section 1.9 CITATION files of *Writing R Extensions* (R Core Team 2023)
+#' specifies how to create dynamic `CITATION` files using `meta` object, hence
+#' the `meta` argument in [cff_read_citation()] may be needed for reading
+#' some files correctly.
+#'
+#' @examples
+#' TODO
 #'
 cff_read <- function(path, ...) {
   if (length(path) > 1) {
@@ -53,6 +76,7 @@ cff_read <- function(path, ...) {
     "cff_citation" = cff_read_cff_citation(path, ...),
     "description" = cff_read_description(path, ...),
     "bib" = cff_read_bib(path, ...),
+    "citation" = cff_read_citation(path, ...),
     NULL
   )
 
@@ -62,6 +86,15 @@ cff_read <- function(path, ...) {
 #' @export
 #' @rdname cff_read
 cff_read_cff_citation <- function(path, ...) {
+  if (!file.exists(path)) {
+    cli::cli_abort(
+      paste(
+        "{.file {path}} does not exist. ",
+        "Check the {.file {dirname(path)}} directory"
+      )
+    )
+  }
+
   cffobj <- yaml::read_yaml(path)
   new_cff(cffobj)
 }
@@ -71,6 +104,15 @@ cff_read_cff_citation <- function(path, ...) {
 cff_read_description <- function(path, cff_version = "1.2.0",
                                  gh_keywords = TRUE,
                                  authors_roles = c("aut", "cre"), ...) {
+  if (!file.exists(path)) {
+    cli::cli_abort(
+      paste(
+        "{.file {path}} does not exist. ",
+        "Check the {.file {dirname(path)}} directory"
+      )
+    )
+  }
+
   pkg <- desc::desc(path)
   pkg$coerce_authors_at_r()
 
@@ -108,14 +150,71 @@ cff_read_description <- function(path, cff_version = "1.2.0",
 
 #' @export
 #' @rdname cff_read
-cff_read_cff_citation <- function(path, ...) {
-  cffobj <- yaml::read_yaml(path)
-  new_cff(cffobj)
+cff_read_citation <- function(path, meta = NULL, ...) {
+  if (!file.exists(path)) {
+    cli::cli_abort(
+      paste(
+        "{.file {path}} does not exist. ",
+        "Check the {.file {dirname(path)}} directory"
+      )
+    )
+  }
+
+  if (!any(is.null(meta), inherits(meta, "packageDescription"))) {
+    # nolint start
+    # Object for cli only
+    ex <- packageDescription("cffr")
+    # nolint end
+
+    cli::cli_alert_warning(
+      paste0(
+        "{.arg meta} should be {.val NULL} or {.obj_type_friendly {ex}}",
+        " not {.obj_type_friendly {meta}}. Using {.arg meta = NULL}"
+      )
+    )
+    meta <- NULL
+  }
+
+  new_meta <- clean_package_meta(meta)
+  the_cit <- try(utils::readCitationFile(path, meta = new_meta), silent = TRUE)
+
+  # If error then new try
+  if (inherits(the_cit, "try-error")) {
+    cli::cli_alert_warning(
+      paste0(
+        "It was not possible to read {.file {path}} with the {.arg meta} ",
+        "provided. Trying with {.code packageDescription('base')}"
+      )
+    )
+    new_meta <- packageDescription("base")
+    the_cit <- try(utils::readCitationFile(path, meta = new_meta),
+      silent = TRUE
+    )
+    # nocov start
+    if (inherits(the_cit, "try-error")) {
+      cli::cli_alert_danger(
+        "Can't read {.file path}, returning {.val NULL}"
+      )
+      return(NULL)
+    }
+    # nocov end
+  }
+  tocff <- cff_parse_citation(the_cit)
+  new_cff(tocff)
 }
 
 #' @export
 #' @rdname cff_read
 cff_read_bib <- function(path, encoding = "UTF-8", ...) {
+  if (!file.exists(path)) {
+    cli::cli_abort(
+      paste(
+        "{.file {path}} does not exist. ",
+        "Check the {.file {dirname(path)}} directory"
+      )
+    )
+  }
+
   # nocov start
   if (!requireNamespace("bibtex", quietly = TRUE)) {
     msg <- paste0(
@@ -156,3 +255,53 @@ guess_type_file <- function(path) {
     )
   )
 }
+
+#' Parse and clean data from DESCRIPTION to create metadata
+#' @noRd
+clean_package_meta <- function(meta) {
+  if (!inherits(meta, "packageDescription")) {
+    return(NULL)
+  }
+
+  # Convert to a desc object
+
+  # First write to a dcf file
+  tmp <- tempfile("DESCRIPTION")
+  meta_unl <- unclass(meta)
+  write.dcf(meta_unl, tmp)
+  pkg <- desc::desc(tmp)
+  pkg$coerce_authors_at_r()
+  # Extract package data
+  meta <- pkg$get(desc::cran_valid_fields)
+
+  # Clean missing and drop empty fields
+  meta <- drop_null(lapply(meta, clean_str))
+
+  # Check encoding
+  if (!is.null(meta$Encoding)) {
+    meta <- lapply(meta, iconv, from = meta$Encoding, to = "UTF-8")
+  } else {
+    meta$Encoding <- "UTF-8"
+  }
+  unlink(tmp, force = TRUE)
+  meta
+}
+
+# For testing, packageDescription object from desc
+test_meta <- function(x) {
+  src <- x
+  my_meta <- desc::desc(src)
+
+  # As list
+  my_meta_l <- my_meta$get(desc::cran_valid_fields)
+  my_meta_l <- as.list(my_meta_l)
+  v_nas <- vapply(my_meta_l, is.na, logical(1))
+
+  my_meta_l <- my_meta_l[!v_nas]
+  meta_proto <- packageDescription("cffr")
+
+  class(my_meta_l) <- class(meta_proto)
+  attr(my_meta_l, "file") <- x
+
+  my_meta_l
+}

README.md

@@ -72,7 +72,7 @@ file and the `CITATION` file (if present) of your package. Note that
 **cffr** works best if your package pass
 `R CMD check/devtools::check()`.
 
-As per 2024-02-16 there are at least 240 repos on GitHub using **cffr**.
+As per 2024-02-19 there are at least 261 repos on GitHub using **cffr**.
 [Check them out
 here](https://github.com/search?q=cffr%20path%3A**%2FCITATION.cff&type=code).
 
@@ -385,9 +385,6 @@ test <- cff_create("rmarkdown")
         email: [email protected]
         orcid: https://orcid.org/0000-0002-4035-0289
       year: '2024'
-      identifiers:
-      - type: url
-        value: https://arxiv.org/abs/1403.2805
     - type: software
       title: knitr
       abstract: 'knitr: A General-Purpose Package for Dynamic Report Generation in R'
@@ -753,18 +750,6 @@ test <- cff_create("rmarkdown")
         given-names: Davis
         email: [email protected]
       year: '2024'
-    - type: software
-      title: cleanrmd
-      abstract: 'cleanrmd: Clean Class-Less ''R Markdown'' HTML Documents'
-      notes: Suggests
-      url: https://pkg.garrickadenbuie.com/cleanrmd/
-      repository: https://CRAN.R-project.org/package=cleanrmd
-      authors:
-      - family-names: Aden-Buie
-        given-names: Garrick
-        email: [email protected]
-        orcid: https://orcid.org/0000-0002-7111-0077
-      year: '2024'
     - type: software
       title: withr
       abstract: 'withr: Run Code ''With'' Temporarily Modified Global State'
@@ -903,9 +888,9 @@ for more info.
 
 <div id="ref-codemeta" class="csl-entry">
 
-Boettiger, Carl, and Maëlle Salmon. 2021a. *<span
-class="nocase">codemeta</span>: A Smaller <span
-class="nocase">codemetar</span> Package*.
+Boettiger, Carl, and Maëlle Salmon. 2021a.
+*<span class="nocase">codemeta</span>: A Smaller
+<span class="nocase">codemetar</span> Package*.
 <https://CRAN.R-project.org/package=codemeta>.
 
 </div>
@@ -926,8 +911,8 @@ Among Citation Formats*.
 
 <div id="ref-citation22" class="csl-entry">
 
-Dietrich, Jan Philipp, and Waldir Leoncio. 2022. *<span
-class="nocase">citation</span>: Software Citation Tools*.
+Dietrich, Jan Philipp, and Waldir Leoncio. 2022.
+*<span class="nocase">citation</span>: Software Citation Tools*.
 
 </div>
 

codemeta.json

@@ -14,7 +14,7 @@
     "name": "R",
     "url": "https://r-project.org"
   },
-  "runtimePlatform": "R version 4.3.2 (2023-10-31)",
+  "runtimePlatform": "R version 4.3.2 (2023-10-31 ucrt)",
   "provider": {
     "@id": "https://cran.r-project.org",
     "@type": "Organization",
@@ -200,7 +200,7 @@
   },
   "isPartOf": "https://ropensci.org",
   "keywords": ["attribution", "citation", "credit", "citation-files", "cff", "metadata", "r", "r-package", "citation-file-format", "rstats", "ropensci", "cran"],
-  "fileSize": "1030.282KB",
+  "fileSize": "918.861KB",
   "citation": [
     {
       "@type": "ScholarlyArticle",

inst/schemaorg.json

@@ -26,6 +26,6 @@
     "name": "Comprehensive R Archive Network (CRAN)",
     "url": "https://cran.r-project.org"
   },
-  "runtimePlatform": "R version 4.3.2 (2023-10-31)",
+  "runtimePlatform": "R version 4.3.2 (2023-10-31 ucrt)",
   "version": "0.5.0.9000"
 }