rticles::rjournal_article() is now defunct (#597)

* rticles::rjournal_article() is now defunct

Remove ressources which will help reduce package size and allow cran release

* remove from other docs and vignette

* Update test

* Other removal

Author: cderv

DESCRIPTION

@@ -108,5 +108,5 @@ Config/Needs/website: magick, pdftools, gifski, tidyverse/tidytemplate,
 Config/testthat/edition: 3
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3
 SystemRequirements: GNU make

NAMESPACE

@@ -37,7 +37,6 @@ export(peerj_article)
 export(pihph_article)
 export(plos_article)
 export(pnas_article)
-export(rjournal_article)
 export(rsos_article)
 export(rss_article)
 export(sage_article)

R/rjournal_article.R

@@ -3,169 +3,12 @@
 #' @description
 #' `r lifecycle::badge('deprecated')`
 #'
-#' This function is now deprecated in favor of the [**rjtools**](https://rjournal.github.io/rjtools/) package
-#' which is now officialy recommanded by R Journal <https://rjournal.github.io/submissions.html>. See below for document
+#' This function is now defunct in favor of the [**rjtools**](https://rjournal.github.io/rjtools/) package
+#' which is now officialy recommanded by R Journal <https://rjournal.github.io/submissions.html>.
 #'
-#' @details # About this format and the R Journal requirements
-#'
-#' Format for creating R Journal articles. Adapted from
-#' <https://journal.r-project.org/submissions.html>.
-#'
-#' This file is only a basic article template. For full details of _The R
-#' Journal_ style and information on how to prepare your article for submission,
-#' see the [Instructions for Authors](https://journal.r-project.org/share/author-guide.pdf)
-#'
-
-#'
-#' `rticles::rjournal_article` will help you build the correct files requirements:
-#'
-#' - A R file will be generated automatically using `knitr::purl` - see
-#' https://bookdown.org/yihui/rmarkdown-cookbook/purl.html for more information.
-#' - A tex file will be generated from this Rmd file and correctly included in
-#' `RJwapper.tex` as expected to build `RJwrapper.pdf`.
-#' - All figure files will be kept in the default rmarkdown `*_files` folder. This
-#' happens because `keep_tex = TRUE` by default in `rticles::rjournal_article`
-#' - Only the bib filename is to be modified. An example bib file is included in the
-#' template (`RJreferences.bib`) and you will have to name your bib file as the
-#' tex, R, and pdf files.
-#'
-#' # About YAML header fields
-#'
-#' This section documents some of the YAML fields that can be used with this
-#' formats.
-#'
-#' ## The `author` field in the YAML header
-#'
-#' | FIELD  | TYPE | DESCRIPTION |
-#' | ------ | ---- | ----------- |
-#' | `name` | *required* | name and surname of the author |
-#' | `affiliation` | *required* | name of the author's affiliation |
-#' | `address` | *required* | at least one address line for the affiliation |
-#' | `url` | *optional* | an additional url for the author or the main affiliation |
-#' | `orcid` | *optional* | the authors ORCID if available |
-#' | `email` | *required* | the author's e-mail address |
-#' | `affiliation2` | *optional* | name of the author's 2nd affiliation |
-#' | `address2` | *optional* | address lines belonging to the author's 2nd affiliation |
-#'
-#' *Please note: Only one `url`, `orcid` and `email` can be provided per author.*
-#'
-#' ## Other YAML fields
-#'
-#' | FIELD | TYPE | DESCRIPTION |
-#' | ----- | ---- | ----------- |
-#' | `bibliography` | *with default* | the BibTeX file with the reference entries |
-#'
-#' @inheritParams rmarkdown::pdf_document
-#' @param ... Arguments to [rmarkdown::pdf_document()].
-#' @export
+#' @keywords internal
 rjournal_article <- function(..., keep_tex = TRUE, citation_package = "natbib") {
 
-  lifecycle::deprecate_warn("0.25", "rjournal_article()", "rjtools::rjournal_pdf_article()", details = "See official recommandation at https://rjournal.github.io/submissions.html")
-  rmarkdown::pandoc_available("2.2", TRUE)
-
-  base <- pdf_document_format(
-    "rjournal",
-    highlight = NULL, citation_package = citation_package,
-    keep_tex = keep_tex, ...
-  )
-
-  # Render will generate tex file, post-knit hook gerenates the R file,
-  # post-process hook generates appropriate RJwrapper.tex and
-  # use pandoc to build pdf from that
-  base$pandoc$to <- "latex"
-  base$pandoc$ext <- ".tex"
-
-  # Generates R file expected by R journal requirement.
-  # We do that in the post-knit hook do access input file path.
-  pk <- base$post_knit
-  output_R <- NULL
-  base$post_knit <- function(metadata, input_file, runtime, ...) {
-    # run post_knit it exists
-    if (is.function(pk)) pk(metadata, input_file, runtime, ...)
-
-    # purl the Rmd file to R code per requirement
-    temp_R <- tempfile(fileext = ".R")
-    output_R <<- knitr::purl(input_file, temp_R, documentation = 1, quiet = TRUE)
-    # Add magic comment about '"do not edit" (rstudio/rstudio#2082)
-    xfun::write_utf8(c(
-      "# Generated by `rjournal_article()` using `knitr::purl()`: do not edit by hand",
-      sprintf("# Please edit %s to modify this file", input_file),
-      "",
-      xfun::read_utf8(output_R)
-    ), output_R)
-
-    NULL
-  }
-
-  base$post_processor <- function(metadata, utf8_input, output_file, clean, verbose) {
-    filename <- basename(output_file)
-    # underscores in the filename will be problematic in \input{filename};
-    # pandoc will escape underscores but it should not, i.e., should be
-    # \input{foo_bar} instead of \input{foo\_bar}
-    if (filename != (filename2 <- gsub("_", "-", filename))) {
-      file.rename(filename, filename2)
-      filename <- filename2
-    }
-
-    # Copy purl-ed R file with the correct name
-    dest_file <- xfun::with_ext(filename, "R")
-    our_file <- TRUE
-    if (file.exists(dest_file)) {
-      # we check this file is generated by us
-      # otherwise we leave it as is and warn
-      current_r <- xfun::read_utf8(dest_file)
-      our_file <- grepl("Generated.*rjournal_article.*do not edit by hand", current_r[1])
-      if (!our_file) {
-        warning(
-          sprintf("R file with name '%s' already exists.", dest_file),
-          "\nIt will not be overwritten by the one generated",
-          " during rendering using `knitr::purl()`.",
-          "\nRemove the existing file to obtain the generated one.",
-          call. = FALSE
-        )
-      }
-    }
-    if (our_file) {
-      # we only overwrite if it is our file
-      file.copy(output_R, xfun::with_ext(filename, "R"), overwrite = TRUE)
-    }
-    unlink(output_R)
-
-    # post process TEX file
-    temp_tex <- xfun::read_utf8(filename)
-    temp_tex <- post_process_authors(temp_tex)
-    xfun::write_utf8(temp_tex, filename)
-
-    # check bibliography name
-    bib_filename <- metadata$bibliography
-    if (length(bib_filename) == 1 &&
-      xfun::sans_ext(bib_filename) != xfun::sans_ext(filename)) {
-      msg <- paste0(
-        "Per R journal requirement, bibliography file and tex file should",
-        " have the same name. Currently, you have a bib file ", bib_filename,
-        " and a tex file ", filename, ". Don't forget to rename and change",
-        " the bibliography field in the YAML header."
-      )
-      warning(msg, call. = FALSE)
-    }
-
-    # Create RJwrapper.tex per R Journal requirement
-    m <- list(filename = xfun::sans_ext(filename))
-    h <- get_list_element(metadata, c("output", "rticles::rjournal_article", "includes", "in_header"))
-    h <- c(h, if (length(preamble <- unlist(metadata[c("preamble", "header-includes")]))) {
-      f <- tempfile(fileext = ".tex")
-      on.exit(unlink(f), add = TRUE)
-      xfun::write_utf8(preamble, f)
-      f
-    })
-    t <- find_resource("rjournal", "RJwrapper.tex")
-    template_pandoc(m, t, "RJwrapper.tex", h, verbose)
-
-    tinytex::latexmk("RJwrapper.tex", base$pandoc$latex_engine, clean = clean)
-  }
-
-  # Mostly copied from knitr::render_sweave
-  base$knitr$opts_chunk$comment <- "#>"
+  lifecycle::deprecate_stop("0.25", "rjournal_article()", "rjtools::rjournal_pdf_article()", details = "See official recommandation at https://rjournal.github.io/submissions.html")
 
-  set_sweave_hooks(base)
 }

R/utils.R

@@ -5,7 +5,7 @@
 #' These names can be useful in two ways:
 #'
 #' * You can add `_article` suffix to get the name of the output format (e.g.,
-#' [rjournal_article()]).
+#' [jss_article()]).
 #'
 #' * You can use the name directly in the `template` argument of
 #' [rmarkdown::draft()].
@@ -47,13 +47,6 @@ merge_list <- function(x, y) {
 #' @param output Path to save output.
 #' @param in_header Paths to files to include in the header.
 #' @return (Invisibly) The path of the generate file.
-#' @examples
-#' x <- rticles:::template_pandoc(
-#'   list(preamble = "%abc", filename = "wickham"),
-#'   rticles:::find_resource("rjournal", "RJwrapper.tex"),
-#'   tempfile()
-#' )
-#' if (interactive()) file.show(x)
 #' @noRd
 template_pandoc <- function(metadata, template, output,
                             in_header = NULL, verbose = FALSE) {