Merge pull request #549 from rstudio/fix/new-citeproc-support

rstudio · Nov 2, 2023 · 058e404 · 058e404
2 parents 8dd188a + eddb999
commit 058e404
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diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -32,10 +32,11 @@ jobs:
       matrix:
         config:
           # testing R release with last shipped pandoc version in RStudio IDE and new pandoc
-          - {os: windows-latest, pandoc: '3.1.1',    r: 'release'}
-          - {os: macOS-latest,   pandoc: '3.1.1',    r: 'release'}
+          - {os: windows-latest, pandoc: '3.1.9',    r: 'release'}
+          - {os: macOS-latest,   pandoc: '3.1.9',    r: 'release'}
           - {os: ubuntu-latest,  pandoc: 'devel',    r: 'release'}
           # testing older pandoc versions
+          - {os: ubuntu-latest,  pandoc: '3.1.7',   r: 'release'} # special citeproc change
           - {os: ubuntu-latest,  pandoc: '2.19.2',   r: 'release'}
           - {os: ubuntu-latest,  pandoc: '2.18',     r: 'release'}
           - {os: ubuntu-latest,  pandoc: '2.17.1.1', r: 'release'}
@@ -74,8 +75,7 @@ jobs:
         shell: Rscript {0}
 
 
-      - uses: r-lib/actions/setup-tinytex@v2-branch 
-        # special branch required for TeX Live 2023 fix
+      - uses: r-lib/actions/setup-tinytex@v2
         env:
           # install full prebuilt version
           TINYTEX_INSTALLER: TinyTeX
@@ -89,7 +89,7 @@ jobs:
         with:
           extra-packages: any::rcmdcheck
           needs: check
-          
+
       - name: Remove default installed Pandoc
         if: runner.os == 'Linux'
         run: sudo dpkg -r pandoc

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Type: Package
 Package: rticles
 Title: Article Formats for R Markdown
-Version: 0.25.2
+Version: 0.25.3
 Authors@R: c(
     person("JJ", "Allaire", , "jj@posit.co", role = "aut"),
     person("Yihui", "Xie", , "xie@yihui.name", role = "aut",
@@ -99,7 +99,7 @@ Suggests:
     withr,
     covr,
     testit,
-    testthat (>= 3.0.0),
+    testthat (>= 3.2.0),
     xtable
 Config/Needs/website: magick, pdftools, gifski, tidyverse/tidytemplate,
     rstudio/quillt

diff --git a/NEWS.md b/NEWS.md
@@ -2,6 +2,14 @@
 
 - `elsevier_article()` Rmd skeleton is now updated to show different available bibliostyle file (i.e `*.bst` for _natbib_) with `elsearticle` document class. `biblio-style: elsarticle-harv` is set by default to correctly work with the `authoryear` classoption already set (thanks, @pepijn-devries, #545).
 
+- Update `ajs_article()` resources for the template.
+
+- Update `frontiers_article()` to version 3.4 from 2022. 
+  - New document class file (.cls) and new bibliography style file (.bst)
+  - LaTeX template is also updated
+  - The format is now only compatible with `natbib` citation processor when Pandoc 3.1.7+ is used, because Frontiers documentclass requires usage of `natbib` and it conflicts with pandoc Citeproc.
+
+- Update `mnras_article()` and `lncs_article()` to work with the Pandoc 3.1.7+ citeproc change.
 # rticles 0.25
 
 ## BREAKING CHANGES

diff --git a/R/article.R b/R/article.R
@@ -195,8 +195,12 @@ elsevier_article <- function(..., keep_tex = TRUE,
 #'   <https://www.frontiersin.org/about/author-guidelines>.
 #' @export
 #' @rdname article
-frontiers_article <- function(..., keep_tex = TRUE) {
-  pdf_document_format("frontiers", keep_tex = keep_tex, ...)
+frontiers_article <- function(..., keep_tex = TRUE, citation_package = "natbib") {
+  # check all arguments for format's default
+  if (citation_package != "natbib" && rmarkdown::pandoc_available("3.1.7")) {
+    stop("Frontiers template only supports 'natbib' for citation processing. Pandoc citeproc is no more compatible with the Frontier documentclass.")
+  }
+  pdf_document_format("frontiers", keep_tex = keep_tex, citation_package = citation_package,...)
 }
 
 

diff --git a/R/utils.R b/R/utils.R
@@ -140,6 +140,9 @@ render_draft <- function(journal, output_options = NULL, quiet = FALSE) {
 
 # Use to create variables command for Pandoc from a named vector
 list_to_pandoc_variable_args <- function(v_args) {
+  # v_args must be named
+  # stopifnot(length(names(v_args) > 0)
+
   truthy <- which(sapply(v_args, isTRUE))
   truthy_arg <- NULL
   if (length(truthy) > 0) {
@@ -152,6 +155,12 @@ list_to_pandoc_variable_args <- function(v_args) {
     v_args <- v_args[-truthy]
   }
 
+  # remove named args which are false
+  falsy <- sapply(v_args, isFALSE)
+  if (any(falsy)) {
+    v_args <- v_args[-which(falsy)]
+  }
+
   # Convert to pandoc arguments
   pandoc_arg_list <-  c(
     mapply(
@@ -211,13 +220,23 @@ string_to_table <- function(x, n, split_regex = ", ?") {
 pdf_document_format <- function(format,
                                 template = find_resource(format, "template.tex"),
                                 ...) {
+
   fmt <- rmarkdown::pdf_document(..., template = template)
   fmt$inherits <- "pdf_document"
 
   ## Set some variables to adapt template based on Pandoc version
   args <- list_to_pandoc_variable_args(list(
-    pandoc3 = rmarkdown::pandoc_available("3")
+    pandoc3 = rmarkdown::pandoc_available("3"),
+    pandoc317 = rmarkdown::pandoc_available("3.1.7"), # new citeproc command
+    pandoc318 = rmarkdown::pandoc_available("3.1.8") # revised citeproc command
   ))
   fmt$pandoc$args <- c(fmt$pandoc$args, args)
   fmt
 }
+
+
+is_citeproc_pandoc_args <- function(args) {
+  "--citeproc" %in% args || "--natbib" %notin% args || "--biblatex" %notin% args
+}
+
+`%notin%` <- Negate(`%in%`)
diff --git a/inst/rmarkdown/templates/acm/resources/template.tex b/inst/rmarkdown/templates/acm/resources/template.tex
@@ -85,6 +85,60 @@
 
 $if(csl-refs)$
 % Pandoc citation processing
+$if(pandoc318)$
+%From Pandoc 3.1.8
+% definitions for citeproc citations
+\NewDocumentCommand\citeproctext{}{}
+\NewDocumentCommand\citeproc{mm}{%
+  \begingroup\def\citeproctext{#2}\cite{#1}\endgroup}
+\makeatletter
+ % allow citations to break across lines
+ \let\@cite@ofmt\@firstofone
+ % avoid brackets around text for \cite:
+ \def\@biblabel#1{}
+ \def\@cite#1#2{{#1\if@tempswa , #2\fi}}
+\makeatother
+\newlength{\cslhangindent}
+\setlength{\cslhangindent}{1.5em}
+\newlength{\csllabelwidth}
+\setlength{\csllabelwidth}{3em}
+\newenvironment{CSLReferences}[2] % #1 hanging-indent, #2 entry-spacing
+ {\begin{list}{}{%
+  \setlength{\itemindent}{0pt}
+  \setlength{\leftmargin}{0pt}
+  \setlength{\parsep}{0pt}
+  % turn on hanging indent if param 1 is 1
+  \ifodd #1
+   \setlength{\leftmargin}{\cslhangindent}
+   \setlength{\itemindent}{-1\cslhangindent}
+  \fi
+  % set entry spacing
+  \setlength{\itemsep}{#2\baselineskip}}}
+ {\end{list}}
+$else$$if(pandoc317)$
+% definitions for citeproc citations
+\NewDocumentCommand\citeproctext{}{}
+\NewDocumentCommand\citeproc{mm}{%
+  \begingroup\def\citeproctext{#2}\cite{#1}\endgroup}
+% avoid brackets around text for \cite:
+\makeatletter
+ \def\@biblabel#1{}
+ \def\@cite#1#2{{#1\if@tempswa , #2\fi}}
+\makeatother
+\newlength{\cslhangindent}
+\setlength{\cslhangindent}{1.5em}
+\newlength{\csllabelwidth}
+\setlength{\csllabelwidth}{3em}
+\newlength{\cslentryspacing}
+\setlength{\cslentryspacing}{0em}
+\usepackage{enumitem}
+\newlist{CSLReferences}{itemize}{1}
+\setlist[CSLReferences]{label={},
+  leftmargin=\cslhangindent,
+  itemindent=-1\cslhangindent,
+  parsep=\parskip,
+  itemsep=\cslentryspacing}
+$else$
 \newlength{\cslhangindent}
 \setlength{\cslhangindent}{1.5em}
 \newlength{\csllabelwidth}
@@ -109,6 +163,7 @@
   \setlength{\parskip}{#2\cslentryspacingunit}
  }%
  {}
+$endif$$endif$
 \usepackage{calc}
 \newcommand{\CSLBlock}[1]{#1\hfill\break}
 \newcommand{\CSLLeftMargin}[1]{\parbox[t]{\csllabelwidth}{#1}}

diff --git a/inst/rmarkdown/templates/acs/resources/template.tex b/inst/rmarkdown/templates/acs/resources/template.tex
@@ -97,6 +97,60 @@
 
 $if(csl-refs)$
 % Pandoc citation processing
+$if(pandoc318)$
+%From Pandoc 3.1.8
+% definitions for citeproc citations
+\NewDocumentCommand\citeproctext{}{}
+\NewDocumentCommand\citeproc{mm}{%
+  \begingroup\def\citeproctext{#2}\cite{#1}\endgroup}
+\makeatletter
+ % allow citations to break across lines
+ \let\@cite@ofmt\@firstofone
+ % avoid brackets around text for \cite:
+ \def\@biblabel#1{}
+ \def\@cite#1#2{{#1\if@tempswa , #2\fi}}
+\makeatother
+\newlength{\cslhangindent}
+\setlength{\cslhangindent}{1.5em}
+\newlength{\csllabelwidth}
+\setlength{\csllabelwidth}{3em}
+\newenvironment{CSLReferences}[2] % #1 hanging-indent, #2 entry-spacing
+ {\begin{list}{}{%
+  \setlength{\itemindent}{0pt}
+  \setlength{\leftmargin}{0pt}
+  \setlength{\parsep}{0pt}
+  % turn on hanging indent if param 1 is 1
+  \ifodd #1
+   \setlength{\leftmargin}{\cslhangindent}
+   \setlength{\itemindent}{-1\cslhangindent}
+  \fi
+  % set entry spacing
+  \setlength{\itemsep}{#2\baselineskip}}}
+ {\end{list}}
+$else$$if(pandoc317)$
+% definitions for citeproc citations
+\NewDocumentCommand\citeproctext{}{}
+\NewDocumentCommand\citeproc{mm}{%
+  \begingroup\def\citeproctext{#2}\cite{#1}\endgroup}
+% avoid brackets around text for \cite:
+\makeatletter
+ \def\@biblabel#1{}
+ \def\@cite#1#2{{#1\if@tempswa , #2\fi}}
+\makeatother
+\newlength{\cslhangindent}
+\setlength{\cslhangindent}{1.5em}
+\newlength{\csllabelwidth}
+\setlength{\csllabelwidth}{3em}
+\newlength{\cslentryspacing}
+\setlength{\cslentryspacing}{0em}
+\usepackage{enumitem}
+\newlist{CSLReferences}{itemize}{1}
+\setlist[CSLReferences]{label={},
+  leftmargin=\cslhangindent,
+  itemindent=-1\cslhangindent,
+  parsep=\parskip,
+  itemsep=\cslentryspacing}
+$else$
 \newlength{\cslhangindent}
 \setlength{\cslhangindent}{1.5em}
 \newlength{\csllabelwidth}
@@ -121,6 +175,7 @@
   \setlength{\parskip}{#2\cslentryspacingunit}
  }%
  {}
+$endif$$endif$
 \usepackage{calc}
 \newcommand{\CSLBlock}[1]{#1\hfill\break}
 \newcommand{\CSLLeftMargin}[1]{\parbox[t]{\csllabelwidth}{#1}}

diff --git a/inst/rmarkdown/templates/aea/resources/template.tex b/inst/rmarkdown/templates/aea/resources/template.tex
@@ -51,6 +51,60 @@
 
 $if(csl-refs)$
 % Pandoc citation processing
+$if(pandoc318)$
+%From Pandoc 3.1.8
+% definitions for citeproc citations
+\NewDocumentCommand\citeproctext{}{}
+\NewDocumentCommand\citeproc{mm}{%
+  \begingroup\def\citeproctext{#2}\cite{#1}\endgroup}
+\makeatletter
+ % allow citations to break across lines
+ \let\@cite@ofmt\@firstofone
+ % avoid brackets around text for \cite:
+ \def\@biblabel#1{}
+ \def\@cite#1#2{{#1\if@tempswa , #2\fi}}
+\makeatother
+\newlength{\cslhangindent}
+\setlength{\cslhangindent}{1.5em}
+\newlength{\csllabelwidth}
+\setlength{\csllabelwidth}{3em}
+\newenvironment{CSLReferences}[2] % #1 hanging-indent, #2 entry-spacing
+ {\begin{list}{}{%
+  \setlength{\itemindent}{0pt}
+  \setlength{\leftmargin}{0pt}
+  \setlength{\parsep}{0pt}
+  % turn on hanging indent if param 1 is 1
+  \ifodd #1
+   \setlength{\leftmargin}{\cslhangindent}
+   \setlength{\itemindent}{-1\cslhangindent}
+  \fi
+  % set entry spacing
+  \setlength{\itemsep}{#2\baselineskip}}}
+ {\end{list}}
+$else$$if(pandoc317)$
+% definitions for citeproc citations
+\NewDocumentCommand\citeproctext{}{}
+\NewDocumentCommand\citeproc{mm}{%
+  \begingroup\def\citeproctext{#2}\cite{#1}\endgroup}
+% avoid brackets around text for \cite:
+\makeatletter
+ \def\@biblabel#1{}
+ \def\@cite#1#2{{#1\if@tempswa , #2\fi}}
+\makeatother
+\newlength{\cslhangindent}
+\setlength{\cslhangindent}{1.5em}
+\newlength{\csllabelwidth}
+\setlength{\csllabelwidth}{3em}
+\newlength{\cslentryspacing}
+\setlength{\cslentryspacing}{0em}
+\usepackage{enumitem}
+\newlist{CSLReferences}{itemize}{1}
+\setlist[CSLReferences]{label={},
+  leftmargin=\cslhangindent,
+  itemindent=-1\cslhangindent,
+  parsep=\parskip,
+  itemsep=\cslentryspacing}
+$else$
 \newlength{\cslhangindent}
 \setlength{\cslhangindent}{1.5em}
 \newlength{\csllabelwidth}
@@ -75,6 +129,7 @@
   \setlength{\parskip}{#2\cslentryspacingunit}
  }%
  {}
+$endif$$endif$
 \usepackage{calc}
 \newcommand{\CSLBlock}[1]{#1\hfill\break}
 \newcommand{\CSLLeftMargin}[1]{\parbox[t]{\csllabelwidth}{#1}}