Added rjournal_article as preferred alias to rjournal_web_article

DESCRIPTION

@@ -34,6 +34,7 @@ Description: Create an 'R Journal' 'Rmarkdown' template article, that will
 License: MIT + file LICENSE
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.2.3
 Imports: 
     distill,
     stringr,
@@ -63,4 +64,3 @@ VignetteBuilder: knitr
 URL: https://github.com/rjournal/rjtools
 BugReports: https://github.com/rjournal/rjtools/issues
 Config/testthat/edition: 3
-RoxygenNote: 7.2.3

NAMESPACE

@@ -17,6 +17,7 @@ export(create_article)
 export(get_orcid)
 export(initial_check_article)
 export(prepare_submission)
+export(rjournal_article)
 export(rjournal_pdf_article)
 export(rjournal_pdf_issue)
 export(rjournal_web_article)

NEWS.md

@@ -1,5 +1,7 @@
 # rjtools 1.0.12
 
+* 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

R/rj_article.R

@@ -0,0 +1,326 @@
+#' R Markdown output formats for R Journal articles
+#'
+#' The R Journal is built upon the distill framework with some modifications.
+#' This output format behaves almost identically to the
+#' `distill::distill_article()` format, with some formatting and structural
+#' changes. The `rjournal_article()` format will produce both HTML and PDF
+#' outputs, while the `rjournal_pdf_article()` produces only the PDF output.
+#'
+#' @param ... Arguments passed to `distill::distill_article()` for web articles,
+#'   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, ...) {
+  args <- c()
+  base_format <- distill::distill_article(
+    self_contained = self_contained, toc = toc, ...
+  )
+
+  # Remove distill RStudio validation checks
+  base_format$on_exit <- function(){}
+
+  distill_post_knit <- base_format$post_knit
+
+  rmd_path <- NULL
+  render_pdf <- NULL
+  article_metadata <- NULL
+
+  base_format$post_knit <- function(metadata, input_file, runtime, ...) {
+    # Modify YAML metadata for pre-processor
+    render_env <- rlang::caller_env(n = 2)
+    metadata <- replace_names(metadata, c("abstract" = "description"))
+    metadata$title <- strip_macros(metadata$title)
+    metadata$description <- strip_macros(metadata$description %||% paste0('"', metadata$title, '" published in The R Journal.'))
+    for(i in seq_along(metadata$author)) {
+      metadata$author[[i]] <- replace_names(metadata$author[[i]], c("orcid" = "orcid_id"))
+    }
+
+    metadata$journal <- list(
+      title = metadata$journal$title %||% "The R Journal",
+      issn = metadata$journal$issn %||% "2073-4859",
+      firstpage = metadata$journal$firstpage %||% metadata$pages[1] %||% 1,
+      lastpage = metadata$journal$lastpage %||% metadata$pages[2]
+    )
+    metadata$slug <- metadata$slug %||% xfun::sans_ext(basename(input_file))
+    metadata$pdf_url <- xfun::with_ext(metadata$slug, "pdf")
+    if(metadata$journal$title == "The R Journal") {
+      has_parent_dir <- function(path, nm){
+        if(basename(path) == nm) return(TRUE)
+        if(path == dirname(path)) return(FALSE)
+        has_parent_dir(dirname(path), nm)
+      }
+      is_repo <- has_parent_dir(normalizePath(input_file), "rjournal.github.io")
+      if(is_repo) {
+        if(has_parent_dir(normalizePath(input_file), "_articles")) {
+          # Use article DOIs
+          metadata$citation_url <- paste0("https://doi.org/10.32614/", metadata$slug)
+          metadata$doi <- paste0("10.32614/", metadata$slug)
+        } else {
+          # News don't have DOIs
+          metadata$citation_url <- paste0("https://journal.r-project.org/news/", metadata$slug)
+        }
+      }
+    }
+    metadata$creative_commons <- metadata$creative_commons %||% "CC BY"
+    if(is.null(metadata$date)) {
+      if(!is.null(metadata$volume) && !is.null(metadata$issue)) {
+        issue_freq <- if(metadata$volume < 14) 6 else 3
+        metadata$date <- paste0(2008 + metadata$volume, "-", issue_freq * metadata$issue, "-01")
+      } else {
+        warning("A date must be provided for your article. Defaulting to today's date.")
+        metadata$date <- format(Sys.Date())
+      }
+    }
+    if(is.null(metadata$packages)) {
+      input <- xfun::read_utf8(input_file)
+      pkgs <- gregexpr("\\\\(CRAN|BIO)pkg\\{.+?\\}", input)
+      pkgs <- mapply(
+        function(pos, line) {
+          if(pos[1] == -1) return(NULL)
+          substr(rep_len(line, length(pos)), pos, pos + pos%@%"match.length" - 1)
+        },
+        pkgs, input,
+        SIMPLIFY = FALSE
+      )
+      pkgs <- unique(do.call(c, pkgs))
+      pkg_is_cran <- grepl("^\\\\CRAN", pkgs)
+      pkgs <- sub("\\\\(CRAN|BIO)pkg\\{(.+?)\\}$", "\\2", pkgs)
+      message(paste0(
+        "Detected the following packages from article:\n  ",
+        "CRAN: ", paste0(pkgs[pkg_is_cran], collapse = ", "), "\n  ",
+        "Bioconductor: ", paste0(pkgs[!pkg_is_cran], collapse = ", ")
+      ))
+      metadata$packages <- list(
+        cran = pkgs[pkg_is_cran],
+        bioc = pkgs[!pkg_is_cran]
+      )
+    }
+    if(is.null(metadata$CTV)) {
+      if(local_cache$exists("ctv")){
+        ctvs <- local_cache$get("ctv")
+      } else {
+        ctvs <- readRDS(
+          gzcon(url("https://cran.r-project.org/src/contrib/Views.rds", open = "rb"))
+        )
+        local_cache$add(ctvs, "ctv")
+      }
+      ctvs <- Filter(
+        function(taskview) {
+          any(metadata$packages$cran %in% taskview$packagelist$name)
+        },
+        ctvs
+      )
+      metadata$CTV <- vapply(ctvs, function(x) x[["name"]], character(1L))
+    }
+
+    if(!is.null(metadata$csl)) warning("Please do not use custom CSL formatting, if there is an issue with the default styling please contact [email protected]")
+    metadata$csl <- metadata$csl %||% system.file("rjournal.csl", package = "rjtools", mustWork = TRUE)
+
+    metadata$output <- replace_names(metadata$output, c("rjtools::rjournal_web_article" = "distill::distill_article"))
+
+    # Replace metadata with modified copy
+    article_metadata <<- metadata
+    rlang::env_poke(
+      render_env, nm = "front_matter", value = metadata,
+      inherit = TRUE, create = TRUE
+    )
+
+    # save Rmd path for later use
+    rmd_path <<- normalizePath(input_file)
+    render_pdf <<- !is.null(metadata$author)
+
+    # Pass updated metadata to distill's post_knit()
+    distill_post_knit(metadata, input_file, runtime, ...)
+  }
+
+  pre_processor <- function(metadata, input_file, runtime, knit_meta, files_dir,
+                            output_dir) {
+
+    # Add embedded PDF
+    embed_pdf <- if(! web_only){
+      whisker::whisker.render(
+        '<div class="l-page">
+  <embed src="{{slug}}.pdf" type="application/pdf" height="955px" width="100%">
+</div>', data = list(slug = metadata$slug)
+      )
+    } else {
+      NULL
+    }
+
+    # Add custom appendix
+    data <- list()
+    if(file.exists(suppl <- xfun::with_ext(metadata$slug, ".zip"))) {
+      # if (!is.null(metadata$supplementary_materials)) {
+      data <- c(data, list(supp = suppl))
+    }
+    if (!is.null(metadata$CTV)) {
+      if (length(metadata$packages$cran) > 0) {
+        CTV <- sprintf("[%s](https://cran.r-project.org/view=%s)", metadata$CTV, metadata$CTV)
+        CTV <- paste(CTV, collapse = ", ")
+        data <- c(data, list(CTV = CTV))
+      }
+    }
+    if (!is.null(metadata$packages)) {
+      if (length(metadata$packages$cran) != 0) {
+        CRAN <- sprintf("[%s](https://cran.r-project.org/package=%s)", metadata$packages$cran, metadata$packages$cran)
+        CRAN <- paste(CRAN, collapse = ", ")
+        data <- c(data, list(CRAN = CRAN))
+      }
+      if (length(metadata$packages$bioc) != 0) {
+        BIOC <- sprintf("[%s](https://www.bioconductor.org/packages/%s)", metadata$packages$bioc, metadata$packages$bioc)
+        BIOC <- paste(BIOC, collapse = ", ")
+        data <- c(data, list(BIOC = BIOC))
+      }
+    }
+    if (web_only && legacy_pdf) {
+      TEXOR <- "This article is converted from a Legacy LaTeX article using the
+                [texor](https://cran.r-project.org/package=texor) package.
+                The pdf version is the official version. To report a problem with the html,
+                refer to CONTRIBUTE on the R Journal homepage."
+      data <- c(data, list(TEXOR = TEXOR))
+    }
+
+    template <- xfun::read_utf8(system.file("appendix.md", package = "rjtools"))
+    appendix <- whisker::whisker.render(template, data)
+
+    input <- xfun::read_utf8(input_file)
+    front_matter_delimiters <- grep("^(---|\\.\\.\\.)\\s*$", input)
+
+    xfun::write_utf8(
+      c(
+        "---",
+        yaml::as.yaml(metadata),
+        "---",
+        "",
+        if(! web_only) embed_pdf else input[(front_matter_delimiters[2]+1):length(input)],
+        "",
+        appendix
+      ),
+      input_file
+    )
+
+    # Custom args
+    args <- c(
+      "--number-sections",
+      rmarkdown::pandoc_include_args(
+        in_header = system.file("rjdistill.html", package = "rjtools")
+      )
+    )
+
+    args
+  }
+
+  on_exit <- function() {
+    # TODO: This should be done in a temp directory
+    # and files produced moved back into the main dir.
+
+    # Skip rendering pdf for non-article pages
+    if(is.null(render_pdf)) return()
+
+    # Update legacy PDF metadata just by changing the wrapper
+    if (legacy_pdf) {
+      wrapper_path <- file.path(dirname(rmd_path), "RJwrapper.tex")
+      if(!file.exists(wrapper_path)) {
+        warning("Could not find wrapper for this legacy article, so the PDF could not be updated.")
+        return()
+      }
+
+      # Update wrapper with new metadata
+      wrapper <- xfun::read_utf8(wrapper_path)
+      has_parent_dir <- function(path, nm){
+        if(basename(path) == nm) return(TRUE)
+        if(path == dirname(path)) return(FALSE)
+        has_parent_dir(dirname(path), nm)
+      }
+      is_repo <- has_parent_dir(normalizePath(wrapper_path), "rjournal.github.io")
+      article_section <- if(is_repo) {
+        if(has_parent_dir(normalizePath(wrapper_path), "_articles")) {
+          "Contributed research article"
+        } else {
+          "News and notes"
+        }
+      } else {
+        "Contributed research article"
+      }
+
+      issue_months <- if(article_metadata$volume < 14) {
+        c("June", "December")
+      } else {
+        c("March", "June", "September", "December")
+      }
+      wrapper[str_which(wrapper, "^\\s*\\\\sectionhead")] <- sprintf("\\sectionhead{%s}", article_section)
+      wrapper[str_which(wrapper, "^\\s*\\\\volume")] <- sprintf("\\volume{%s}", article_metadata$volume)
+      wrapper[str_which(wrapper, "^\\s*\\\\volnumber")] <- sprintf("\\volnumber{%s}", article_metadata$issue)
+      wrapper[str_which(wrapper, "^\\s*\\\\year")] <- sprintf("\\year{%s}", 2008 + article_metadata$volume)
+      wrapper[str_which(wrapper, "^\\s*\\\\month")] <- sprintf("\\month{%s}", issue_months[article_metadata$issue])
+
+      # Set page count
+      wrapper_page_counter <- which(str_detect(wrapper, "^\\s*\\\\setcounter\\{page\\}\\{.+\\}"))
+      if(length(wrapper_page_counter) == 0) {
+        wrapper_page_counter <- which(str_detect(wrapper, "^\\s*\\\\month\\{.+\\}")) + 1
+        wrapper <- append(wrapper, "", wrapper_page_counter - 1)
+      }
+      wrapper[wrapper_page_counter] <- paste0("\\setcounter{page}{", article_metadata$journal$firstpage, "}")
+      if(identical(wrapper, xfun::read_utf8(wrapper_path))) return()
+      message("Detected changes to the article metadata, re-building PDF.")
+      xfun::write_utf8(wrapper, wrapper_path)
+
+      oldwd <- getwd()
+      on.exit(setwd(oldwd))
+      setwd(dirname(wrapper_path))
+      file.copy(
+        system.file("tex/RJournal.sty", package = "rjtools"),
+        "RJournal.sty"
+      )
+      on.exit(
+        file.remove("RJournal.sty"),
+        add = TRUE
+      )
+      pdf_path <- xfun::with_ext(article_metadata$slug, ".pdf")
+      tinytex::latexmk(
+        wrapper_path,
+        base_format$pandoc$latex_engine,
+        pdf_file = pdf_path,
+        clean = TRUE
+      )
+
+      # Update metadata with new page numbers
+      if(requireNamespace("pdftools", quietly = TRUE)) {
+        yml <- rmarkdown::yaml_front_matter(rmd_path)
+        yml$journal$lastpage <- yml$journal$firstpage + pdftools::pdf_length(pdf_path)
+        update_front_matter(yml, rmd_path)
+      }
+    } else {
+      callr::r(function(input){
+        rmarkdown::render(
+          input,
+          output_format = "rjtools::rjournal_pdf_article"
+        )
+      }, args = list(input = rmd_path))
+    }
+  }
+
+  rmarkdown::output_format(
+    knitr = NULL, # use base one
+    pandoc = list(
+      args = args,
+      lua_filters = c(
+        system.file("latex-pkg.lua", package = "rjtools"),
+        system.file("sec-depth.lua", package = "rjtools")
+      )
+    ),
+    keep_md = NULL, # use base one
+    clean_supporting = NULL, # use base one
+    pre_knit = NULL,
+    # post_knit = post_knit, # passed directly to base_format
+    pre_processor = pre_processor,
+    on_exit = on_exit,
+    base_format = base_format
+  )
+}