Update docs and lint

ropensci · Aug 2, 2023 · 50930ce · 50930ce
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diff --git a/R/assertions.R b/R/assertions.R
@@ -57,7 +57,7 @@ is.cff <- function(x) {
 #' Check if a object is cff file
 #' @param x object to be evaluated
 #' @noRd
-is.cff.file <- function(x) {
+is.cff_file <- function(x) {
   if (!inherits(x, "character")) {
     return(FALSE)
   }

diff --git a/R/cff_create.R b/R/cff_create.R
@@ -7,7 +7,7 @@
 #'
 #' @return A [`cff`] list object.
 #'
-#' @family core functions
+#' @family Core functions
 #'
 #' @export
 #'
@@ -60,8 +60,8 @@
 #' for additional details.
 #'
 #' If `x` is a path to a DESCRIPTION file or `inst/CITATION`, is not present on
-#' your package, **cffr** would auto-generate a `preferred-citation` key using
-#' the information provided on that file.
+#' your package, \CRANpkg{cffr} would auto-generate a `preferred-citation` key
+#' using the information provided on that file.
 #'
 #' By default, only persons whose role in the DESCRIPTION file of the package
 #' is author (`"aut"`) or maintainer (`"cre"`) are considered to be authors

diff --git a/R/cff_from_bibtex.R b/R/cff_from_bibtex.R
@@ -12,16 +12,16 @@
 #' @param encoding Encoding to be assumed for `x`. See [readLines()].
 #' @param ... Other arguments passed to [bibtex::read.bib()].
 #'
-#' @family bibtex
+#' @family BibTeX helpers
 #'
 #' @return A [`cff`] object ready to be used on [cff_create()].
 #'
 #' @export
 #'
 #' @details
 #'
-#' This function requires the package **bibtex** (>= 0.5.0), that is listed
-#' as `Suggested` by  **cffr**.
+#' This function requires the package \CRANpkg{bibtex} (>= 0.5.0), that is
+#' listed as `Suggested` by \CRANpkg{cffr}.
 #'
 #' @seealso
 #'

diff --git a/R/cff_gha_update.R b/R/cff_gha_update.R
@@ -24,7 +24,7 @@
 #' }
 #' @export
 #'
-#' @family git
+#' @family Git helpers
 cff_gha_update <- function(path = ".",
                            overwrite = FALSE) {
   destdir <- file.path(path, ".github", "workflows")

diff --git a/R/cff_git_hook.R b/R/cff_git_hook.R
@@ -8,7 +8,7 @@
 #'
 #' @name cff_git_hook
 #'
-#' @family git
+#' @family Git helpers
 #'
 #' @export
 #'
@@ -85,7 +85,9 @@ cff_git_hook_remove <- function() {
   hookfile <- file.path(".git", "hooks", "pre-commit")
 
   if (file.exists(hookfile)) {
-    cli::cli_alert_info("Removing git pre-commit hook (was on {.path {hookfile}})")
+    cli::cli_alert_info(
+      "Removing git pre-commit hook (was on {.path {hookfile}})"
+    )
     unlink(hookfile, force = TRUE)
   }
 

diff --git a/R/cff_parse_citation.R b/R/cff_parse_citation.R
@@ -6,7 +6,7 @@
 #'
 #' @export
 #'
-#' @family parsers
+#' @family Parsers
 #'
 #' @param bib A `bibentry` object, either created with [bibentry()]
 #'   (preferred) or [citEntry()].
@@ -188,8 +188,7 @@ cff_parse_citation <- function(bib) {
 
   # Remove non-valid names
   validnames <- cff_schema_definitions_refs()
-  parse_cit <- parse_cit[names(parse_cit) %in%
-    c(validnames)]
+  parse_cit <- parse_cit[names(parse_cit) %in% validnames]
 
   parse_cit <- drop_null(parse_cit)
   parse_cit_result <- as.cff(parse_cit)

diff --git a/R/cff_parse_person.R b/R/cff_parse_person.R
@@ -9,7 +9,7 @@
 #'
 #' @export
 #'
-#' @family parsers
+#' @family Parsers
 #'
 #' @param person A `person` object created with [person()] or a
 #'   character string. See **Details**.
@@ -83,8 +83,10 @@ cff_parse_person <- function(person) {
   # Special case for R Core Team
 
 
-  if (is.substring(clean_str(person$given), "R Core") &&
-    is.substring(person$family, "Team")) {
+  if (all(
+    is.substring(clean_str(person$given), "R Core"),
+    is.substring(person$family, "Team")
+  )) {
     person <- person(
       given = paste(
         clean_str(person$given),
@@ -157,8 +159,7 @@ cff_parse_person <- function(person) {
   } else {
     cff_schema_definitions_person()
   }
-  parsed_person <- parsed_person[names(parsed_person) %in%
-    definition]
+  parsed_person <- parsed_person[names(parsed_person) %in% definition]
 
   parsed_person <- as.cff(parsed_person)
   parsed_person

diff --git a/R/cff_read.R b/R/cff_read.R
@@ -9,7 +9,7 @@
 #' A `cff` object. Under the hood, a `cff` object is a regular [`list`] object
 #' with a special [print()] method.
 #'
-#' @family core functions
+#' @family Core functions
 #'
 #' @param path The path to a `CITATION.cff` file.
 #' @param ... Named arguments to be used for creating a [`cff`] object. See

diff --git a/R/cff_to_bibtex.R b/R/cff_to_bibtex.R
@@ -36,7 +36,7 @@
 #'   - `all`: A combination of the previous two options. This would extract
 #'      both the preferred citation info and the references.
 #'
-#' @family bibtex
+#' @family BibTeX helpers
 #'
 #' @return A `bibentry` object or a list of `bibentry` objects. This could
 #' be parsed to BibTeX using [toBibtex()]
@@ -91,7 +91,7 @@ cff_to_bibtex <- function(x,
     return(NULL)
   }
 
-  if (is.cff.file(x)) {
+  if (is.cff_file(x)) {
     x <- cff_read(x)
   }
 
@@ -195,8 +195,10 @@ cff_bibtex_parser <- function(x) {
   # Check if it may be an incollection
   # Hint: is misc with collection-title and publisher
 
-  if (tobibentry$bibtype == "misc" && !is.null(x$`collection-title`) &&
-    !is.null(x$publisher)) {
+  if (all(
+    tobibentry$bibtype == "misc", !is.null(x$`collection-title`),
+    !is.null(x$publisher)
+  )) {
     tobibentry$bibtype <- "incollection"
   }
 
@@ -225,8 +227,7 @@ cff_bibtex_parser <- function(x) {
   ))
 
   # As a fallback, use also location
-  if (is.null(tobibentry$address) &&
-    !is.null(x$location)) {
+  if (is.null(tobibentry$address) && !is.null(x$location)) {
     tobibentry$address <- x$location$name
   }
 

diff --git a/R/cff_validate.R b/R/cff_validate.R
@@ -13,7 +13,7 @@
 #' ```
 #' @export
 #'
-#' @family core functions
+#' @family Core functions
 #'
 #' @seealso
 #' ```{r, echo=FALSE, results='asis'}

diff --git a/R/cff_write.R b/R/cff_write.R
@@ -9,7 +9,7 @@
 #' function is basically a wrapper around [cff_create()] to both create the
 #' [`cff`] object and writes it out to a YAML-formatted file in one command.
 #'
-#' @family core functions
+#' @family Core functions
 #'
 #' @param x The source that would be used for generating
 #'   the `CITATION.cff` file. It could be:

diff --git a/R/parse_description.R b/R/parse_description.R
@@ -49,13 +49,12 @@ parse_desc_contacts <- function(pkg) {
 parse_desc_date_released <- function(pkg) {
   # See https://cran.r-project.org/doc/manuals/R-exts.html#The-DESCRIPTION-file
   date1 <- pkg$get("Date")
-  # CRAN/BioConductor
+  # This is for CRAN/BioConductor packages
   date2 <- pkg$get("Date/Publication")
   # R-universe
   date3 <- pkg$get("Packaged")
   # Work with vector
   alldates <- unname(c(date1, date2, date3))
-  x <- alldates[3]
   clean_dates <- lapply(alldates, function(x) {
     if (is.na(x) || is.null(x)) {
       return(NULL)

diff --git a/R/utils-bibtex.R b/R/utils-bibtex.R
@@ -7,7 +7,7 @@
 #'
 #' @param x A string, possibly encoded in UTF-8 encoding system.
 #'
-#' @family bibtex
+#' @family BibTeX helpers
 #'
 #' @seealso [tools::encoded_text_to_latex()]
 #'

diff --git a/R/utils-schema.R b/R/utils-schema.R
@@ -33,7 +33,7 @@
 #'
 #' ```
 #'
-#' @family schema
+#' @family Schemas
 #'
 #' @export
 #'

diff --git a/R/utils.R b/R/utils.R
@@ -138,8 +138,12 @@ fuzzy_keys <- function(keys) {
     ))
 
     # Message
-    ll <- paste0("{.dt ", names_fuzzy, "}{.dl ", keys_match, "}\n", collapse = "")
-    cli::cli_alert_warning(paste0("Found misspelled keys. Trying to map:\n", ll))
+    ll <- paste0("{.dt ", names_fuzzy, "}{.dl ", keys_match, "}\n",
+      collapse = ""
+    )
+    cli::cli_alert_warning(
+      paste0("Found misspelled keys. Trying to map:\n", ll)
+    )
 
     # Modify names
     names[!is_valid_key] <- keys_match

diff --git a/R/write_bib.R b/R/write_bib.R
@@ -1,6 +1,6 @@
-#' Create a .bib file
+#' Create a `.bib` file
 #'
-#' Creates a .bib file from a `bibentry` object(s)
+#' Creates `a .bib` file from a `bibentry` object(s)
 #'
 #' @param x A `bibentry` object created with:
 #'    - [cff_to_bibtex()]
@@ -13,7 +13,7 @@
 #' @param ascii Whether to write the entries using ASCII characters only or not.
 #'
 #' @export
-#' @family bibtex
+#' @family BibTeX helpers
 #'
 #' @return Writes an `.bib` file specified on `file` parameter and the
 #' equivalent `Bibtex` object created with [utils::toBibtex()]. It also
@@ -26,9 +26,9 @@
 #'
 #' @seealso `vignette("bibtex_cff", "cffr")`, [knitr::write_bib()] and the
 #' following packages:
-#' - [bibtex](https://github.com/ropensci/bibtex) package.
-#' - [RefManageR](https://github.com/ropensci/RefManageR) package.
-#' - [rbibutils](https://github.com/GeoBosh/rbibutils/)
+#' - \CRANpkg{bibtex}.
+#' - \CRANpkg{RefManageR}
+#' - \CRANpkg{rbibutils}
 #'
 #' @examples
 #'
@@ -53,11 +53,9 @@ write_bib <- function(x,
 
   if (ascii) {
     # Base encoding as per file()
-    encoding <- getOption("encoding")
     btex <- encoded_utf_to_latex(btex)
     class(btex) <- "Bibtex"
   } else {
-    encoding <- "UTF-8"
     btex <- enc2utf8(btex)
   }
 

diff --git a/R/write_citation.R b/R/write_citation.R
@@ -20,7 +20,7 @@
 #' @inheritDotParams cff_to_bibtex
 #'
 #' @export
-#' @family bibtex
+#' @family BibTeX helpers
 #'
 #' @return Writes an `inst/CITATION` file and (invisibly) returns the
 #' `bibentry` object that has been written to the file.

diff --git a/README.md b/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 2023-08-02 there are at least 204 repos on GitHub using **cffr**.
+As per 2023-08-02 there are at least 202 repos on GitHub using **cffr**.
 [Check them out
 here](https://github.com/search?q=cffr%20path%3A**%2FCITATION.cff&type=code).
 
@@ -566,25 +566,6 @@ test <- cff_create("rmarkdown")
       - family-names: Attali.
         given-names: Dean
       year: '2023'
-    - type: software
-      title: dygraphs
-      abstract: 'dygraphs: Interface to ''Dygraphs'' Interactive Time Series Charting
-        Library'
-      notes: Suggests
-      url: https://github.com/rstudio/dygraphs
-      repository: https://CRAN.R-project.org/package=dygraphs
-      authors:
-      - family-names: Vanderkam
-        given-names: Dan
-      - family-names: Allaire
-        given-names: JJ
-      - family-names: Owen
-        given-names: Jonathan
-      - family-names: Gromer
-        given-names: Daniel
-      - family-names: Thieurmel
-        given-names: Benoit
-      year: '2023'
     - type: software
       title: fs
       abstract: 'fs: Cross-Platform File System Operations Based on ''libuv'''
@@ -601,26 +582,6 @@ test <- cff_create("rmarkdown")
         given-names: Gábor
         email: [email protected]
       year: '2023'
-    - type: software
-      title: rsconnect
-      abstract: 'rsconnect: Deploy Docs, Apps, and APIs to ''Posit Connect'', ''shinyapps.io'',
-        and ''RPubs'''
-      notes: Suggests
-      url: https://github.com/rstudio/rsconnect
-      repository: https://CRAN.R-project.org/package=rsconnect
-      authors:
-      - family-names: Atkins
-        given-names: Aron
-        email: [email protected]
-      - family-names: Allen
-        given-names: Toph
-      - family-names: Wickham
-        given-names: Hadley
-      - family-names: McPherson
-        given-names: Jonathan
-      - family-names: Allaire
-        given-names: JJ
-      year: '2023'
     - type: software
       title: downlit
       abstract: 'downlit: Syntax Highlighting and Automatic Linking'
@@ -633,19 +594,6 @@ test <- cff_create("rmarkdown")
         email: [email protected]
       year: '2023'
       version: '>= 0.4.0'
-    - type: software
-      title: katex
-      abstract: 'katex: Rendering Math to HTML, ''MathML'', or R-Documentation Format'
-      notes: Suggests
-      url: https://docs.ropensci.org/katex/
-      repository: https://CRAN.R-project.org/package=katex
-      authors:
-      - family-names: Ooms
-        given-names: Jeroen
-        email: [email protected]
-        orcid: https://orcid.org/0000-0002-4035-0289
-      year: '2023'
-      version: '>= 1.4.0'
     - type: software
       title: sass
       abstract: 'sass: Syntactically Awesome Style Sheets (''Sass'')'
@@ -757,18 +705,6 @@ test <- cff_create("rmarkdown")
         given-names: Davis
         email: [email protected]
       year: '2023'
-    - 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: '2023'
     - type: software
       title: withr
       abstract: 'withr: Run Code ''With'' Temporarily Modified Global State'