Use pandoc rather than distill framework for bibliography generation

Provides support for `csl` and `nocite` as well as use of multiple bibliographies (including non-BibTeX ones). Eliminates distill framework provided mouse-over citation display, but users seem to value the Pandoc features more than this one.

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: distill
 Title: 'R Markdown' Format for Scientific and Technical Writing
-Version: 0.8
+Version: 0.8.1
 Authors@R: c(
     person("JJ", "Allaire", role = c("aut", "cre"), email = "jj@rstudio.com"),
     person("Rich", "Iannone", role = c("aut")),

NEWS.md

@@ -1,3 +1,6 @@
+## distill v0.9 (Development)
+
+* Use pandoc rather than distill framewor for bibliography generation. Provides support for `csl` and `nocite` as well as use of multiple bibliographies (including non-BibTeX ones). Eliminates distill framework provided mouse-over citation display, but users seem to value the Pandoc features more than this one.
 
 ## distill v0.8 (CRAN)
 

R/appendices.R

@@ -3,28 +3,19 @@
 appendices_after_body_html <- function(input_file, site_config, metadata) {
 
   # write appendixes
+  references <- appendix_bibliography(metadata)
   updates_and_corrections <- appendix_updates_and_corrections(metadata)
   creative_commons <- appendix_creative_commons(metadata)
   citation <- appendix_citation(site_config, metadata)
   appendix <- tags$div(class = "appendix-bottom",
+                       references,
                        updates_and_corrections,
                        creative_commons,
                        citation)
 
-  # write bibliography
-  bibliography <- c()
-  if (!is.null(metadata$bibliography)) {
-    bibliography <- HTML(paste(c(
-      '<script id="distill-bibliography" type="text/bibtex">',
-      readLines(file.path(dirname(input_file), metadata$bibliography), warn = FALSE),
-      '</script>'
-    ), collapse = "\n"))
-  }
-
   # wrap in placeholder
   placeholder_html("appendices", tagList(
-    appendix,
-    bibliography
+    appendix
   ))
 }
 
@@ -70,6 +61,17 @@ appendix_updates_and_corrections <- function(metadata) {
   }
 }
 
+appendix_bibliography <- function(metadata) {
+  if (!is.null(metadata$bibliography)) {
+    list(
+      tags$h3(id = "references", "References"),
+      tags$div(id = "references-listing")
+    )
+  } else {
+    NULL
+  }
+}
+
 appendix_creative_commons <- function(metadata) {
 
   if (!is.null(metadata$creative_commons)) {

inst/rmarkdown/templates/distill_article/resources/distill.html

@@ -224,6 +224,16 @@
   color: rgba(0, 0, 0, 1.0);
 }
 
+/* Citations */
+
+d-article .citation {
+  color: inherit;
+  cursor: inherit;
+}
+
+div.hanging-indent{
+  margin-left: 1em; text-indent: -1em;
+}
 
 
 /* Tweak 1000px media break to show more text */
@@ -545,24 +555,9 @@
   // create d-appendix
   $('.d-appendix').changeElementType('d-appendix');
 
-  // create d-bibliography
-  var bibliography = $('<d-bibliography></d-bibliography>');
-  $('#distill-bibliography').wrap(bibliography);
-
   // flag indicating that we have appendix items
   var appendix = $('.appendix-bottom').children('h3').length > 0;
 
-  // replace citations with <d-cite>
-  $('.citation').each(function(i, val) {
-    appendix = true;
-    var cites = $(this).attr('data-cites').split(" ");
-    var dt_cite = $('<d-cite></d-cite>');
-    dt_cite.attr('key', cites.join());
-    $(this).replaceWith(dt_cite);
-  });
-  // remove refs
-  $('#refs').remove();
-
   // replace footnotes with <d-footnote>
   $('.footnote-ref').each(function(i, val) {
     appendix = true;
@@ -579,6 +574,9 @@
   // remove footnotes
   $('.footnotes').remove();
 
+  // move refs into #references-listing
+  $('#references-listing').replaceWith($('#refs'));
+
   $('h1.appendix, h2.appendix').each(function(i, val) {
     $(this).changeElementType('h3');
   });