Merge branch 'main' of github.com:rjournal/rjtools

NEWS.md

@@ -1,14 +1,17 @@
 # rjtools 1.0.12
 
+* Updates for accessibility based on updates in distill package.
+* File structure for template article is now cleaner, with data, figures, scripts, motivation-letter, folders. 
 * Added `rjournal_article()` as a preferred alias to `rjournal_web_article()`
   since this output format generally produces both HTML and PDF outputs.
-* check functions updated, including DOIs in references, title case in bib file, existence of csl file
-* reference to new web site in the documentation
-* new function to assist authors prepare for a release
-* style to better adhere to accessibility standards
-* remove link to twitter/x
-* handling of longtable
-* utilise system sty file, not author supplied
+* This is reflected in the change in the YAML header to be `rjtools::rjournal_article`. This generates both html and pdf. `rjtools::rjournal_web_article`, which will now only generate the html. `rjtools::rjournal_pdf_article` now only generates the pdf.
+* Check functions updated, including DOIs in references, title case in bib file, existence of csl file
+* Reference to new web site in the documentation.
+* New function to assist authors prepare for a release.
+* Style to better adhere to accessibility standards.
+* Remove link to twitter/x.
+* Handling of longtable.
+* Utilise system sty file, not author supplied.
 
 # rjtools 1.0.11
 

R/rj_article.R

@@ -10,13 +10,12 @@
 #'   and `rticles::rjournal_article()` for pdf articles.
 #' @inheritParams distill::distill_article
 #' @param legacy_pdf whether an article is from the past and only have pdf version
-#' @param web_only additional param for embedding PDF or using Rmd to produce HTML
 #' @importFrom rlang caller_env env_poke
 #' @return the rendered R Journal article
 #' @export
 #' @rdname rjournal_article
 rjournal_article <- function(toc = FALSE, self_contained = FALSE,
-                             legacy_pdf = FALSE, web_only = !legacy_pdf, ...) {
+                             legacy_pdf = FALSE, ...) {
   args <- c()
   base_format <- distill::distill_article(
     self_contained = self_contained, toc = toc, ...
@@ -34,9 +33,14 @@ rjournal_article <- function(toc = FALSE, self_contained = FALSE,
   base_format$post_knit <- function(metadata, input_file, runtime, ...) {
     # Modify YAML metadata for pre-processor
     render_env <- rlang::caller_env(n = 2)
+    # FIXME: renames abstract to description and then later hacks around it by creating
+    # a d-abstract html element by hand in JS (rjdistill.html). This
+    # is incredibly fragile, because the element has no idenficiation tag,
+    # so this should be cleaned up so we can have distill create d-abstract directly...
     metadata <- replace_names(metadata, c("abstract" = "description"))
     metadata$title <- strip_macros(metadata$title)
-    metadata$description <- strip_macros(metadata$description %||% paste0('"', metadata$title, '" published in The R Journal.'))
+    if (is.null(metadata$subtitle)) ## the tools don't support both abstract and subtitle
+      metadata$description <- strip_macros(metadata$description %||% paste0('"', metadata$title, '" published in The R Journal.'))
     for(i in seq_along(metadata$author)) {
       metadata$author[[i]] <- replace_names(metadata$author[[i]], c("orcid" = "orcid_id"))
     }
@@ -106,7 +110,7 @@ rjournal_article <- function(toc = FALSE, self_contained = FALSE,
         ctvs <- local_cache$get("ctv")
       } else {
         ctvs <- readRDS(
-          gzcon(url("https://cran.r-project.org/src/contrib/Views.rds", open = "rb"))
+          gzcon(url(.cran("/src/contrib/Views.rds"), open = "rb"))
         )
         local_cache$add(ctvs, "ctv")
       }
@@ -148,8 +152,13 @@ rjournal_article <- function(toc = FALSE, self_contained = FALSE,
   pre_processor <- function(metadata, input_file, runtime, knit_meta, files_dir,
                             output_dir) {
 
-    # Add embedded PDF
-    embed_pdf <- if(! web_only){
+    input <- xfun::read_utf8(input_file)
+    front_matter_delimiters <- grep("^(---|\\.\\.\\.)\\s*$", input)
+    body <- input[(front_matter_delimiters[2]+1):length(input)]
+
+    # Add embedded PDF to HTML stubs
+    is_stub <- !any(grepl("^\\s*#+\\s*.*", body))
+    embed_pdf <- if(isTRUE(metadata$tex_native) || (legacy_pdf && is_stub)) {
       whisker::whisker.render(
         '<div class="l-page">
   <embed src="{{slug}}.pdf" type="application/pdf" height="955px" width="100%">
@@ -184,7 +193,7 @@ rjournal_article <- function(toc = FALSE, self_contained = FALSE,
         data <- c(data, list(BIOC = BIOC))
       }
     }
-    if (web_only && legacy_pdf) {
+    if (FALSE && legacy_pdf) {
       TEXOR <- "This article is converted from a Legacy LaTeX article using the
                 [texor](https://cran.r-project.org/package=texor) package.
                 The pdf version is the official version. To report a problem with the html,
@@ -195,16 +204,13 @@ rjournal_article <- function(toc = FALSE, self_contained = FALSE,
     template <- xfun::read_utf8(system.file("appendix.md", package = "rjtools"))
     appendix <- whisker::whisker.render(template, data)
 
-    input <- xfun::read_utf8(input_file)
-    front_matter_delimiters <- grep("^(---|\\.\\.\\.)\\s*$", input)
-
     xfun::write_utf8(
       c(
         "---",
         yaml::as.yaml(metadata),
         "---",
         "",
-        if(! web_only) embed_pdf else input[(front_matter_delimiters[2]+1):length(input)],
+        c(embed_pdf, body),
         "",
         appendix
       ),
@@ -330,3 +336,13 @@ rjournal_article <- function(toc = FALSE, self_contained = FALSE,
     base_format = base_format
   )
 }
+
+.cran <- function(path="") {
+  cran <- "http://cran.R-project.org"
+  rep <- getOption("repos")
+  if ("CRAN" %in% names(rep)) {
+    opt <- rep["CRAN"]
+    if (opt != "@CRAN@") cran <- opt
+  }
+  paste0(cran, path)
+}

R/rj_pdf_article.R

@@ -32,7 +32,7 @@ rjournal_pdf_article <- function(..., self_contained = FALSE) {
   }
   pre_processor <- fmt$pre_processor
   fmt$pre_processor <- function(front_matter, input, ...) {
-    if(!is.null(front_matter$bibliography)) {
+    if(!is.null(front_matter$bibliography) && !isTRUE(front_matter$tex_native)) {
       xfun::write_utf8(
         c(xfun::read_utf8(input), "\n# References\n"),
         input
@@ -51,7 +51,6 @@ rjournal_pdf_article <- function(..., self_contained = FALSE) {
       file.rename(filename, filename2)
       filename <- filename2
     }
-
     # Copy purl-ed R file with the correct name
     dest_file <- xfun::with_ext(filename, "R")
     our_file <- TRUE
@@ -79,6 +78,16 @@ rjournal_pdf_article <- function(..., self_contained = FALSE) {
     temp_tex <- xfun::read_utf8(output_file)
     # Add author line
     temp_tex <- post_process_authors(temp_tex)
+    ## remove CLS references if we are using native ones
+    ## coversely, if CLS is already included, don't add TeX ones
+    if (isTRUE(metadata$tex_native)) {
+        cls.b <- grep("^\\\\begin\\{CSLReferences\\}", temp_tex)
+        cls.e <- grep("^\\\\end\\{CSLReferences\\}", temp_tex)
+        if (length(cls.b) == 1 && length(cls.e) == 1 && cls.b < cls.e)
+            temp_tex <- temp_tex[-(cls.b:cls.e)]
+    } else if (length(grep("^\\\\begin\\{CSLReferences\\}", temp_tex)) &&
+               length(bil <- grep("^\\\\bibliography", temp_tex)))
+	temp_tex <- temp_tex[-bil]
     xfun::write_utf8(temp_tex, output_file)
 
     # Bookdown post-processing, silently capture error as it will attempt to

R/rj_web_article.R

@@ -1,3 +1,9 @@
 #' @export
 #' @rdname rjournal_article
-rjournal_web_article <- rjournal_article
+rjournal_web_article <- function(toc = FALSE, self_contained = FALSE, ...) {
+  base_format <- rjournal_article(
+    self_contained = self_contained, toc = toc, ...
+  )
+  base_format$on_exit <- function() {}
+  base_format
+}

R/rj_web_issue.R

@@ -110,6 +110,12 @@ rjournal_web_issue <- function(toc = FALSE, self_contained = FALSE, rnews = FALS
     args
   }
 
+  args <- c(
+    rmarkdown::pandoc_include_args(
+      in_header = system.file("rjdistill.html", package = "rjtools")
+    )
+  )
+
   on_exit <- function() {
     # Deactivate for now as I am not sure to understand what should be built
     # if (!is.null(render_pdf) && !legacy_pdf) {
@@ -124,7 +130,13 @@ rjournal_web_issue <- function(toc = FALSE, self_contained = FALSE, rnews = FALS
 
   rmarkdown::output_format(
     knitr = NULL, # use base one
-    pandoc = list(),
+
+    pandoc = list(
+      args = args,
+      lua_filters = c(
+        system.file("latex-pkg.lua", package = "rjtools")
+      )
+    ),
     keep_md = NULL, # use base one
     clean_supporting = NULL, # use base one
     pre_knit = NULL,
@@ -140,7 +152,7 @@ list_issue_articles <- function(volume, issue, rnews = FALSE) {
   prefix <- if(rnews) "RN" else "RJ"
   articles <- list.files(
     list.dirs("../../_articles", recursive = FALSE),
-    paste0(prefix, "-\\d{4}-\\d{3}\\.(r|R)md"),
+    paste0(prefix, "-\\d{4}-\\d{3}\\.[Rr]md$"),
     full.names = TRUE
   )
 
@@ -194,7 +206,7 @@ news_entry <- function(art) {
     art$author <- vapply(art$author, function(z) z$name %||% paste(z$first_name, z$last_name), character(1L))
   }
   stringr::str_glue(
-    "[{art$title}](../../news/{art$slug})<br>{glue::glue_collapse(art$author, sep = ', ', last = ' and ')} {art$journal$firstpage %||% art$pages[1] %||% \"\"}\n\n"
+    "[{art$title}](../../news/{art$slug}/)<br>{glue::glue_collapse(art$author, sep = ', ', last = ' and ')} {art$journal$firstpage %||% art$pages[1] %||% \"\"}\n\n"
   )
 }
 
@@ -219,7 +231,7 @@ article_entry <- function(art) {
   }
 
   stringr::str_glue(
-    "[{art$title}](../../articles/{art$slug})<br>{glue::glue_collapse(art$author, sep = ', ', last = ' and ')} {art$journal$firstpage %||% art$pages[1] %||% \"\"}\n\n"
+    "[{art$title}](../../articles/{art$slug}/)<br>{glue::glue_collapse(art$author, sep = ', ', last = ' and ')} {art$journal$firstpage %||% art$pages[1] %||% \"\"}\n\n"
   )
 }
 

R/submit-rjournal.R

@@ -1,8 +1,8 @@
 #' Submit a paper to the R Journal
 #'
-#' This is a last-minute self-serve  check function, similar to
-#' [devtools::release()], for handling R Journal styling that can be difficult
-#'  with automatic checks.
+#' This is a final self-check function, similar to
+#' that runs through a checklist on your submission
+#' that cannot be done automatically.
 #' @importFrom utils browseURL
 #' @export
 submit_rjournal <- function(){

cran-comments.md

@@ -1,13 +1,32 @@
-This revision is to fix a problem identified by CRAN maintainers.
+This revision has some changes to fix some errors, and streamline usage and submission operations.
 
-## Test environment
+## Test environment, using devtools::check_rhub()
 
-* local R installation: R version 4.2.1 (2022-06-23)
+* local R installation: R version 4.3.1 (2023-06-16)
 * Ubuntu Linux 20.04.1 LTS, R-release, GCC
-* Fedora Linux, R-devel, clang, gfortran
+* Fedora Fedora Linux, R-devel, clang, gfortran
 * Windows Server 2022, R-devel, 64 bit
 
-## R CMD check results
+── R CMD check results ──────────────────────────────────── rjtools 1.0.12 ────
+Duration: 29.9s
 
 0 errors ✔ | 0 warnings ✔ | 0 notes ✔
 
+With check_rhub, there are two notes, which I believe can be ignored.
+
+── rjtools 1.0.12: NOTE
+
+  Build ID:   rjtools_1.0.12.tar.gz-0420bebe3d074a298f5056193567f16e
+  Platform:   Windows Server 2022, R-devel, 64 bit
+  Submitted:  2h 53m 53.5s ago
+  Build time: 6m 12.7s
+
+❯ checking for non-standard things in the check directory ... NOTE
+  Found the following files/directories:
+    ''NULL''
+
+❯ checking for detritus in the temp directory ... NOTE
+  Found the following files/directories:
+    'lastMiKTeXException'
+
+0 errors ✔ | 0 warnings ✔ | 2 notes ✖

inst/rjdistill.html

@@ -32,13 +32,17 @@
     buttons.append('<a href="' + slug + '.pdf" class="dt-tag"><i class="fas fa-file-pdf"></i> PDF</a>')
     buttons.append('<a href="' + slug + '.zip" class="dt-tag"><i class="fas fa-file-zipper"></i> Supplement</a>')
 
-
-    const abstract = $('<d-abstract>')
-    abstract.append('<b>Abstract:</b><br>')
-    abstract.append($("d-title p:not(:empty)").first()) // Move description to d-abstract
-    $("d-title p:empty").remove() // Remove empty paragraphs after title
-    abstract.append(buttons)
-    abstract.insertAfter($('d-title')) // Add abstract section after title
+    // adds Abstract: in front of the first <p> in the title section --
+    // unless it happens to be the subtitle (FIXME: this is a bad hack - can't distill do this?)
+    var tpar = $("d-title p:not(:empty)").first();
+    if (tpar && ! tpar.hasClass("subtitle")) {
+      const abstract = $('<d-abstract>')
+      abstract.append('<b>Abstract:</b><br>')
+      abstract.append($("d-title p:not(:empty)").first()) // Move description to d-abstract
+      $("d-title p:empty").remove() // Remove empty paragraphs after title
+      abstract.append(buttons)
+      abstract.insertAfter($('d-title')) // Add abstract section after title */
+    }
 
     // tweak by-line
     var byline = $("d-byline div.byline")
@@ -142,4 +146,27 @@
     color: rgb(60, 60, 60);
   }
 
+  d-article h2 {
+    border-bottom: 0px solid rgba(0, 0, 0, 0.1);
+    padding-bottom: 0rem;
+  }
+  d-article h3 {
+    font-size: 20px;
+  }
+  d-article h4 {
+    font-size: 18px;
+    text-transform: none;
+  }
+
+  @media (min-width: 1024px) {
+    d-article h2 {
+      font-size: 32px;
+    }
+    d-article h3 {
+      font-size: 24px;
+    }
+    d-article h4 {
+      font-size: 20px;
+    }
+  }
 </style>

inst/tex/RJournal.sty

@@ -176,6 +176,7 @@
 % 
 \RequirePackage[sectionbib,round]{natbib}
 \bibliographystyle{abbrvnat}
+\renewcommand{\bibsection}{\section*{References}}
 
 % Equations, figures and tables are counted within articles, but we do
 % not show the article number. For equations it becomes a bit messy to avoid