Update bibliography_entries() lua filter and internals for pandoc change

Resolves #246

NEWS.md

@@ -1,5 +1,8 @@
 # vitae (development version)
 
+* Fixed `bibliography_entries()` failing to render PDF outputs with recent 
+  versions of pandoc (#246).
+
 # vitae 0.5.3
 
 Small release to resolve CRAN checks and removed dependency on the unmaintained 

R/bibliography.R

@@ -101,17 +101,16 @@ knit_print.vitae_bibliography <- function(x, options = knitr::opts_current$get()
   endlabel <- x %@% "endlabel"
 
   # Convert file separator to format expected by citeproc
-  file <- gsub("\\", "/", file, fixed = TRUE)
+  # file <- gsub("\\", "/", file, fixed = TRUE)
 
   out <- glue(
     '
 
-    ::: {#bibliography}
-    << file >>
+    ::: {#refs-<< rlang::hash_file(file) >>}
     :::
 
     ',
     .open = "<<", .close = ">>"
   )
-  knitr::asis_output(out, meta = list(structure(x$id, class = "vitae_nocite")))
+  knitr::asis_output(out, meta = list(structure(list(file = file, id = x$id), class = "vitae_nocite")))
 }

R/cv_document.R

@@ -16,20 +16,8 @@ cv_document <- function(..., pandoc_args = NULL, pandoc_vars = NULL,
     pandoc_args <- c(pandoc_args, rmarkdown::pandoc_variable_arg(names(pandoc_vars)[[i]], pandoc_vars[[i]]))
   }
 
-  # Inject multiple-bibliographies lua filter
-  mult_bib <- file.path(tempdir(), "multiple-bibliographies.lua")
-  if(rmarkdown::pandoc_version() <= package_version("2.7.3")) {
-    warn(sprintf("Detected pandoc version %s, which may cause issues with bibliography_entries().
-Please update pandoc if you have any issues knitting bibliographies (this can be done by updating RStudio).", rmarkdown::pandoc_version()))
-  }
-  cat(
-    gsub("<<PANDOC_PATH>>", rmarkdown::find_pandoc()$dir, fixed = TRUE,
-         readLines(system.file("multiple-bibliographies.lua", package = "vitae", mustWork = TRUE), encoding = "UTF-8")),
-    file = mult_bib, sep = "\n"
-  )
-
   pandoc_args <- c(
-    c(rbind("--lua-filter", mult_bib)),
+    c(rbind("--lua-filter", system.file("multiple-bibliographies.lua", package = "vitae", mustWork = TRUE))),
     pandoc_args
   )
 
@@ -41,8 +29,15 @@ Please update pandoc if you have any issues knitting bibliographies (this can be
                files_dir, output_dir)
 
     # Add citations to front matter yaml, there may be a better way to do this.
+    # For example, @* wildcard. Keeping as is to avoid unintended side effects.
     meta_nocite <- vapply(knit_meta, inherits, logical(1L), "vitae_nocite")
-    metadata$nocite <- c(metadata$nocite, paste0("@", do.call(c, knit_meta[meta_nocite]), collapse = ", "))
+
+    bib_files <- lapply(knit_meta[meta_nocite], function(x) x$file)
+    names(bib_files) <- vapply(bib_files, rlang::hash_file, character(1L))
+    metadata$bibliography <- bib_files
+
+    bib_ids <- unique(unlist(lapply(knit_meta[meta_nocite], function(x) x$id)))
+    metadata$nocite <- c(metadata$nocite, paste0("@", bib_ids, collapse = ", "))
     if(is.null(metadata$csl)) metadata$csl <- system.file("vitae.csl", package = "vitae", mustWork = TRUE)
 
     body <- partition_yaml_front_matter(xfun::read_utf8(input_file))$body

inst/multiple-bibliographies.lua

@@ -1,8 +1,7 @@
 --[[
-multiple-bibliographies – create multiple bibliographies
+multibib – create multiple bibliographies
 
-Copyright © 2018-2020 Albert Krewinkel
-Modified 19/10/2020 by Mitchell O'Hara-Wild
+Copyright © 2018-2022 Albert Krewinkel
 
 Permission to use, copy, modify, and/or distribute this software for any
 purpose with or without fee is hereby granted, provided that the above
@@ -16,69 +15,63 @@ WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
 ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
 OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
 ]]
+PANDOC_VERSION:must_be_at_least '2.11'
+
 local List = require 'pandoc.List'
 local utils = require 'pandoc.utils'
 local stringify = utils.stringify
 local run_json_filter = utils.run_json_filter
 
+--- get the type of meta object
+local metatype = pandoc.utils.type or
+  function (v)
+    local metatag = type(v) == 'table' and v.t and v.t:gsub('^Meta', '')
+    return metatag and metatag ~= 'Map' and metatag or type(v)
+  end
+
 --- Collection of all cites in the document
 local all_cites = {}
 --- Document meta value
 local doc_meta = pandoc.Meta{}
 
---- Div used by pandoc-citeproc to insert the bibliography.
+--- Div used by citeproc to insert the bibliography.
 local refs_div = pandoc.Div({}, pandoc.Attr('refs'))
 
-local supports_quiet_flag = (function ()
-  -- We use pandoc instead of pandoc-citeproc starting with pandoc 2.11
-  if PANDOC_VERSION >= "2.11" then
-    return true
-  end
-  local version = pandoc.pipe('<<PANDOC_PATH>>/pandoc-citeproc', {'--version'}, '')
-  local major, minor, patch = version:match 'pandoc%-citeproc (%d+)%.(%d+)%.?(%d*)'
-  major, minor, patch = tonumber(major), tonumber(minor), tonumber(patch)
-  return major > 0
-    or minor > 14
-    or (minor == 14 and patch >= 5)
-end)()
+-- Div filled by citeproc with properties set according to
+-- the output format and the attributes of cs:bibliography
+local refs_div_with_properties
 
-local function run_citeproc(doc, quiet)
-  if PANDOC_VERSION >= "2.11" then
-    return run_json_filter(
-      doc,
-      '<<PANDOC_PATH>>/pandoc',
-      {'--from=json', '--to=json', '--citeproc', quiet and '--quiet' or nil}
-    )
-  else
-    -- doc = run_json_filter(doc, '<<PANDOC_PATH>>/pandoc-citeproc')
-    return run_json_filter(
-      doc,
-      '<<PANDOC_PATH>>/pandoc-citeproc',
-      {FORMAT, (quiet and supports_quiet_flag) and '-q' or nil}
-    )
+--- Run citeproc on a pandoc document
+local citeproc
+if utils.citeproc then
+  -- Built-in Lua function
+  citeproc = utils.citeproc
+else
+  -- Use pandoc as a citeproc processor
+  citeproc = function (doc)
+    local opts = {'--from=json', '--to=json', '--citeproc', '--quiet'}
+    return run_json_filter(doc, 'pandoc', opts)
   end
 end
 
-
 --- Resolve citations in the document by combining all bibliographies
 -- before running pandoc-citeproc on the full document.
 local function resolve_doc_citations (doc)
   -- combine all bibliographies
   local meta = doc.meta
-  local orig_bib = meta.bibliography
-  meta.bibliography = pandoc.MetaList{orig_bib}
-  for name, value in pairs(meta) do
-    if name:match('^bibliography_') then
-      table.insert(meta.bibliography, value)
+  local bibconf = meta.bibliography
+  meta.bibliography = pandoc.MetaList{}
+  if metatype(bibconf) == 'table' then
+    for _, value in pairs(bibconf) do
+      table.insert(meta.bibliography, stringify(value))
     end
   end
-  -- add dummy div to catch the created bibliography
+  -- add refs div to catch the created bibliography
   table.insert(doc.blocks, refs_div)
   -- resolve all citations
-  -- doc = run_json_filter(doc, '<<PANDOC_PATH>>/pandoc-citeproc')
-  doc = run_citeproc(doc)
-  -- remove catch-all bibliography
-  table.remove(doc.blocks)
+  doc = citeproc(doc)
+  -- remove catch-all bibliography and keep it for future use
+  refs_div_with_properties = table.remove(doc.blocks)
   -- restore bibliography to original value
   doc.meta.bibliography = orig_bib
   return doc
@@ -103,22 +96,37 @@ local function meta_for_pandoc_citeproc (bibliography)
   return new_meta
 end
 
+local function remove_duplicates(classes)
+  local seen = {}
+  return classes:filter(function(x)
+      if seen[x] then
+        return false
+      else
+        seen[x] = true
+        return true
+      end
+  end)
+end
+
 --- Create a bibliography for a given topic. This acts on all divs whose
--- ID matches "bibliography", and uses the path contained within the div
+-- ID starts with "refs", followed by nothing but underscores and
+-- alphanumeric characters.
 local function create_topic_bibliography (div)
-
-  local is_bib = div.identifier == 'bibliography'
-  if not is_bib then
+  local name = div.identifier:match('^refs[-_]?([-_%w]*)$')
+  local bibfile = name and (doc_meta.bibliography or {})[name]
+  if not bibfile then
     return nil
   end
-  local bibfile = div.content[1].content[1].text
   local tmp_blocks = {pandoc.Para(all_cites), refs_div}
   local tmp_meta = meta_for_pandoc_citeproc(bibfile)
   local tmp_doc = pandoc.Pandoc(tmp_blocks, tmp_meta)
-  local res = run_citeproc(tmp_doc, true) -- try to be quiet
+  local res = citeproc(tmp_doc)
   -- First block of the result contains the dummy paragraph, second is
-  -- the refs Div filled by pandoc-citeproc.
+  -- the refs Div filled by citeproc.
   div.content = res.blocks[2].content
+  -- Set the classes and attributes as citeproc did it on refs_div
+  div.classes = remove_duplicates(refs_div_with_properties.classes)
+  div.attributes = refs_div_with_properties.attributes
   return div
 end
 

inst/rmarkdown/templates/awesomecv/resources/awesome-cv.tex

@@ -136,26 +136,41 @@
 $endfor$
 
 % Pandoc CSL macros
+$if(csl-refs)$
+% 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}{2em}
-\newenvironment{CSLReferences}[2] % #1 hanging-ident, #2 entry spacing
- {% don't indent paragraphs
-  \setlength{\parindent}{0pt}
+\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 \everypar{\setlength{\hangindent}{\cslhangindent}}\ignorespaces\fi
-  % set entry spacing
-  \ifnum #2 > 0
-  \setlength{\parskip}{#2\baselineskip}
+  \ifodd #1
+   \setlength{\leftmargin}{\cslhangindent}
+   \setlength{\itemindent}{-1\cslhangindent}
   \fi
- }%
- {}
+  % set entry spacing
+  \setlength{\itemsep}{#2\baselineskip}}}
+ {\end{list}}
 \usepackage{calc}
-\newcommand{\CSLBlock}[1]{#1\hfill\break}
-\newcommand{\CSLLeftMargin}[1]{\parbox[t]{\csllabelwidth}{\honortitlestyle{#1}}}
-\newcommand{\CSLRightInline}[1]{\parbox[t]{\linewidth - \csllabelwidth}{\honordatestyle{#1}}}
+\newcommand{\CSLBlock}[1]{\hfill\break\parbox[t]{\linewidth}{\strut\ignorespaces#1\strut}}
+\newcommand{\CSLLeftMargin}[1]{\parbox[t]{\csllabelwidth}{\strut#1\strut}}
+\newcommand{\CSLRightInline}[1]{\parbox[t]{\linewidth - \csllabelwidth}{\strut#1\strut}}
 \newcommand{\CSLIndent}[1]{\hspace{\cslhangindent}#1}
+$endif$
 
 \begin{document}
 

inst/rmarkdown/templates/hyndman/resources/hyndmantemplate.tex

@@ -270,26 +270,41 @@
 \setlength\LTright{0pt}
 
 % Pandoc CSL macros
+$if(csl-refs)$
+% 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}[3] % #1 hanging-ident, #2 entry spacing
- {% don't indent paragraphs
-  \setlength{\parindent}{0pt}
+\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 \everypar{\setlength{\hangindent}{\cslhangindent}}\ignorespaces\fi
-  % set entry spacing
-  \ifnum #2 > 0
-  \setlength{\parskip}{#2\baselineskip}
+  \ifodd #1
+   \setlength{\leftmargin}{\cslhangindent}
+   \setlength{\itemindent}{-1\cslhangindent}
   \fi
- }%
- {}
+  % set entry spacing
+  \setlength{\itemsep}{#2\baselineskip}}}
+ {\end{list}}
 \usepackage{calc}
-\newcommand{\CSLBlock}[1]{#1\hfill\break}
-\newcommand{\CSLLeftMargin}[1]{\parbox[t]{\csllabelwidth}{\hfill #1~}}
-\newcommand{\CSLRightInline}[1]{\parbox[t]{\linewidth - \cslhangindent - \csllabelwidth}{#1}\vspace{0.8ex}}
+\newcommand{\CSLBlock}[1]{\hfill\break\parbox[t]{\linewidth}{\strut\ignorespaces#1\strut}}
+\newcommand{\CSLLeftMargin}[1]{\parbox[t]{\csllabelwidth}{\strut#1\strut}}
+\newcommand{\CSLRightInline}[1]{\parbox[t]{\linewidth - \csllabelwidth}{\strut#1\strut}}
 \newcommand{\CSLIndent}[1]{\hspace{\cslhangindent}#1}
+$endif$
 
 
 \def\endfirstpage{\newpage}

inst/rmarkdown/templates/latexcv/resources/classic/main.tex

@@ -293,26 +293,41 @@
 
 
 % Pandoc CSL macros
+$if(csl-refs)$
+% 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}[3] % #1 hanging-ident, #2 entry spacing
- {% don't indent paragraphs
-  \setlength{\parindent}{0pt}
+\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 \everypar{\setlength{\hangindent}{\cslhangindent}}\ignorespaces\fi
-  % set entry spacing
-  \ifnum #2 > 0
-  \setlength{\parskip}{#2\baselineskip}
+  \ifodd #1
+   \setlength{\leftmargin}{\cslhangindent}
+   \setlength{\itemindent}{-1\cslhangindent}
   \fi
- }%
- {}
+  % set entry spacing
+  \setlength{\itemsep}{#2\baselineskip}}}
+ {\end{list}}
 \usepackage{calc}
-\newcommand{\CSLBlock}[1]{#1\hfill\break}
-\newcommand{\CSLLeftMargin}[1]{\parbox[t]{\csllabelwidth}{#1}}
-\newcommand{\CSLRightInline}[1]{\parbox[t]{\linewidth - \csllabelwidth}{#1}}
+\newcommand{\CSLBlock}[1]{\hfill\break\parbox[t]{\linewidth}{\strut\ignorespaces#1\strut}}
+\newcommand{\CSLLeftMargin}[1]{\parbox[t]{\csllabelwidth}{\strut#1\strut}}
+\newcommand{\CSLRightInline}[1]{\parbox[t]{\linewidth - \csllabelwidth}{\strut#1\strut}}
 \newcommand{\CSLIndent}[1]{\hspace{\cslhangindent}#1}
+$endif$
 
 
 %============================================================================%