Updates for Citeproc and new latex

Makefile

@@ -13,7 +13,7 @@ TEMPLATE_DIR = Template
 TEMPLATE_FILE = $(TEMPLATE_DIR)/disso.latex
 
 #Report Export Options
-PDF_PANDOC_OPTIONS = --filter=pandoc-citeproc --template=$(TEMPLATE_FILE) --top-level-division=chapter --filter=pandoc-include
+PDF_PANDOC_OPTIONS =  --filter=pandoc-include --filter=pandoc-citeproc --template=$(TEMPLATE_FILE) --top-level-division=chapter 
 
 TEX_PANDOC_OPTIONS = --template=$(TEMPLATE_FILE) --top-level-division=chapter --biblatex --filter=pandoc-include
 

Template/disso.latex

@@ -1,16 +1,98 @@
-\PassOptionsToPackage{unicode=true}{hyperref} % options for packages loaded elsewhere
+% Options for packages loaded elsewhere
+\PassOptionsToPackage{unicode$for(hyperrefoptions)$,$hyperrefoptions$$endfor$}{hyperref}
 \PassOptionsToPackage{hyphens}{url}
 $if(colorlinks)$
 \PassOptionsToPackage{dvipsnames,svgnames*,x11names*}{xcolor}
 $endif$
+$if(dir)$
+$if(latex-dir-rtl)$
+\PassOptionsToPackage{RTLdocument}{bidi}
+$endif$
+$endif$
+$if(CJKmainfont)$
+\PassOptionsToPackage{space}{xeCJK}
+$endif$
 %
-\documentclass[$if(fontsize)$$fontsize$,$endif$$if(lang)$$babel-lang$,$endif$$if(papersize)$$papersize$paper,$endif$$if(beamer)$ignorenonframetext,$if(handout)$handout,$endif$$if(aspectratio)$aspectratio=$aspectratio$,$endif$$endif$$for(classoption)$$classoption$$sep$,$endfor$]{$documentclass$}
-
-%DG - Remove font familty stuff
+\documentclass[
+$if(fontsize)$
+  $fontsize$,
+$endif$
+$if(lang)$
+  $babel-lang$,
+$endif$
+$if(papersize)$
+  $papersize$paper,
+$endif$
+$if(beamer)$
+  ignorenonframetext,
+$if(handout)$
+  handout,
+$endif$
+$if(aspectratio)$
+  aspectratio=$aspectratio$,
+$endif$
+$endif$
+$for(classoption)$
+  $classoption$$sep$,
+$endfor$
+]{$documentclass$}
+$if(beamer)$
+$if(background-image)$
+\usebackgroundtemplate{%
+  \includegraphics[width=\paperwidth]{$background-image$}%
+}
+$endif$
+\usepackage{pgfpages}
+\setbeamertemplate{caption}[numbered]
+\setbeamertemplate{caption label separator}{: }
+\setbeamercolor{caption name}{fg=normal text.fg}
+\beamertemplatenavigationsymbols$if(navigation)$$navigation$$else$empty$endif$
+$for(beameroption)$
+\setbeameroption{$beameroption$}
+$endfor$
+% Prevent slide breaks in the middle of a paragraph
+\widowpenalties 1 10000
+\raggedbottom
+$if(section-titles)$
+\setbeamertemplate{part page}{
+  \centering
+  \begin{beamercolorbox}[sep=16pt,center]{part title}
+    \usebeamerfont{part title}\insertpart\par
+  \end{beamercolorbox}
+}
+\setbeamertemplate{section page}{
+  \centering
+  \begin{beamercolorbox}[sep=12pt,center]{part title}
+    \usebeamerfont{section title}\insertsection\par
+  \end{beamercolorbox}
+}
+\setbeamertemplate{subsection page}{
+  \centering
+  \begin{beamercolorbox}[sep=8pt,center]{part title}
+    \usebeamerfont{subsection title}\insertsubsection\par
+  \end{beamercolorbox}
+}
+\AtBeginPart{
+  \frame{\partpage}
+}
+\AtBeginSection{
+  \ifbibliography
+  \else
+    \frame{\sectionpage}
+  \fi
+}
+\AtBeginSubsection{
+  \frame{\subsectionpage}
+}
+$endif$
+$endif$
+$if(beamerarticle)$
+\usepackage{beamerarticle} % needs to be loaded first
+$endif$
 $if(fontfamily)$
 \usepackage[$for(fontfamilyoptions)$$fontfamilyoptions$$sep$,$endfor$]{$fontfamily$}
 $else$
-\usepackage{cmodern}
+\usepackage{lmodern}
 $endif$
 
 $if(linestretch)$
@@ -23,8 +105,8 @@ $endif$
 \ifnum 0\ifxetex 1\fi\ifluatex 1\fi=0 % if pdftex
   \usepackage[$if(fontenc)$$fontenc$$else$T1$endif$]{fontenc}
   \usepackage[utf8]{inputenc}
-  \usepackage{textcomp} % provides euro and other symbols
-\else % if luatex or xelatex
+  \usepackage{textcomp} % provide euro and other symbols
+\else % if luatex or xetex
 $if(mathspec)$
   \ifxetex
     \usepackage{mathspec}
@@ -34,19 +116,20 @@ $if(mathspec)$
 $else$
   \usepackage{unicode-math}
 $endif$
-  \defaultfontfeatures{Ligatures=TeX,Scale=MatchLowercase}
-$for(fontfamilies)$
-  \newfontfamily{$fontfamilies.name$}[$fontfamilies.options$]{$fontfamilies.font$}
-$endfor$
+  \defaultfontfeatures{Scale=MatchLowercase}
+  \defaultfontfeatures[\rmfamily]{Ligatures=TeX,Scale=1}
 $if(mainfont)$
-    \setmainfont[$for(mainfontoptions)$$mainfontoptions$$sep$,$endfor$]{$mainfont$}
+  \setmainfont[$for(mainfontoptions)$$mainfontoptions$$sep$,$endfor$]{$mainfont$}
 $endif$
 $if(sansfont)$
-    \setsansfont[$for(sansfontoptions)$$sansfontoptions$$sep$,$endfor$]{$sansfont$}
+  \setsansfont[$for(sansfontoptions)$$sansfontoptions$$sep$,$endfor$]{$sansfont$}
 $endif$
 $if(monofont)$
-    \setmonofont[Mapping=tex-ansi$if(monofontoptions)$,$for(monofontoptions)$$monofontoptions$$sep$,$endfor$$endif$]{$monofont$}
+  \setmonofont[$for(monofontoptions)$$monofontoptions$$sep$,$endfor$]{$monofont$}
 $endif$
+$for(fontfamilies)$
+  \newfontfamily{$fontfamilies.name$}[$for(fontfamilies.options)$$fontfamilies.options$$sep$,$endfor$]{$fontfamilies.font$}
+$endfor$
 $if(mathfont)$
 $if(mathspec)$
   \ifxetex
@@ -79,49 +162,58 @@ $endif$
 
 % use upquote if available, for straight quotes in verbatim environments
 \IfFileExists{upquote.sty}{\usepackage{upquote}}{}
-% use microtype if available
-\IfFileExists{microtype.sty}{%
-\usepackage[$for(microtypeoptions)$$microtypeoptions$$sep$,$endfor$]{microtype}
-\UseMicrotypeSet[protrusion]{basicmath} % disable protrusion for tt fonts
+\IfFileExists{microtype.sty}{% use microtype if available
+  \usepackage[$for(microtypeoptions)$$microtypeoptions$$sep$,$endfor$]{microtype}
+  \UseMicrotypeSet[protrusion]{basicmath} % disable protrusion for tt fonts
 }{}
 $if(indent)$
 $else$
-\IfFileExists{parskip.sty}{%
-\usepackage{parskip}
-}{% else
-\setlength{\parindent}{0pt}
-\setlength{\parskip}{6pt plus 2pt minus 1pt}
-}
+\makeatletter
+\@ifundefined{KOMAClassName}{% if non-KOMA class
+  \IfFileExists{parskip.sty}{%
+    \usepackage{parskip}
+  }{% else
+    \setlength{\parindent}{0pt}
+    \setlength{\parskip}{6pt plus 2pt minus 1pt}}
+}{% if KOMA class
+  \KOMAoptions{parskip=half}}
+\makeatother
 $endif$
 $if(verbatim-in-note)$
 \usepackage{fancyvrb}
 $endif$
-$if(colorlinks)$
 \usepackage{xcolor}
-$endif$
-\usepackage{hyperref}
+\IfFileExists{xurl.sty}{\usepackage{xurl}}{} % add URL line breaks if available
+\IfFileExists{bookmark.sty}{\usepackage{bookmark}}{\usepackage{hyperref}}
 \hypersetup{
 $if(title-meta)$
-            pdftitle={$title-meta$}
+  pdftitle={$title-meta$},
 $endif$
 $if(author-meta)$
-            pdfauthor={$author-meta$},
+  pdfauthor={$author-meta$},
+$endif$
+$if(lang)$
+  pdflang={$lang$},
+$endif$
+$if(subject)$
+  pdfsubject={$subject$},
 $endif$
 $if(keywords)$
-            pdfkeywords={$for(keywords)$$keywords$$sep$, $endfor$},
+  pdfkeywords={$for(keywords)$$keywords$$sep$, $endfor$},
 $endif$
 $if(colorlinks)$
-            colorlinks=true,
-            linkcolor=$if(linkcolor)$$linkcolor$$else$Maroon$endif$,
-            citecolor=$if(citecolor)$$citecolor$$else$Blue$endif$,
-            urlcolor=$if(urlcolor)$$urlcolor$$else$Blue$endif$,
+  colorlinks=true,
+  linkcolor=$if(linkcolor)$$linkcolor$$else$Maroon$endif$,
+  filecolor=$if(filecolor)$$filecolor$$else$Maroon$endif$,
+  citecolor=$if(citecolor)$$citecolor$$else$Blue$endif$,
+  urlcolor=$if(urlcolor)$$urlcolor$$else$Blue$endif$,
 $else$
-            pdfborder={0 0 0},
+  hidelinks,
 $endif$
-            breaklinks=true}
-\urlstyle{same}  % don't use monospace font for urls
+  pdfcreator={LaTeX via pandoc}}
+\urlstyle{same} % disable monospaced font for URLs
 $if(verbatim-in-note)$
-\VerbatimFootnotes % allows verbatim text in footnotes
+\VerbatimFootnotes % allow verbatim text in footnotes
 $endif$
 $if(geometry)$
 \usepackage[$for(geometry)$$geometry$$sep$,$endfor$]{geometry}
@@ -130,6 +222,8 @@ $endif$
 $if(listings)$
 \usepackage{listings}
 \newcommand{\passthrough}[1]{#1}
+\lstset{defaultdialect=[5.3]Lua}
+\lstset{defaultdialect=[x86masm]Assembler}
 $endif$
 $if(lhs)$
 \lstnewenvironment{code}{\lstset{language=Haskell,basicstyle=\small\ttfamily}}{}
@@ -152,44 +246,42 @@ $if(graphics)$
 % margins by default, and it is still possible to overwrite the defaults
 % using explicit options in \includegraphics[width, height, ...]{}
 \setkeys{Gin}{width=\maxwidth,height=\maxheight,keepaspectratio}
+% Set default figure placement to htbp
+\makeatletter
+\def\fps@figure{htbp}
+\makeatother
 $endif$
 $if(links-as-notes)$
 % Make links footnotes instead of hotlinks:
 \DeclareRobustCommand{\href}[2]{#2\footnote{\url{#1}}}
 $endif$
 $if(strikeout)$
 \usepackage[normalem]{ulem}
-% avoid problems with \sout in headers with hyperref:
+% Avoid problems with \sout in headers with hyperref
 \pdfstringdefDisableCommands{\renewcommand{\sout}{}}
 $endif$
-\setlength{\emergencystretch}{3em}  % prevent overfull lines
+\setlength{\emergencystretch}{3em} % prevent overfull lines
 \providecommand{\tightlist}{%
   \setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}}
 $if(numbersections)$
 \setcounter{secnumdepth}{$if(secnumdepth)$$secnumdepth$$else$5$endif$}
 $else$
-\setcounter{secnumdepth}{0}
+\setcounter{secnumdepth}{-\maxdimen} % remove section numbering
 $endif$
 $if(subparagraph)$
 % Redefines (sub)paragraphs to behave more like sections
 \ifx\paragraph\undefined\else
-\let\oldparagraph\paragraph
-\renewcommand{\paragraph}[1]{\oldparagraph{#1}\mbox{}}
+  \let\oldparagraph\paragraph
+  \renewcommand{\paragraph}[1]{\oldparagraph{#1}\mbox{}}
 \fi
 \ifx\subparagraph\undefined\else
-\let\oldsubparagraph\subparagraph
-\renewcommand{\subparagraph}[1]{\oldsubparagraph{#1}\mbox{}}
+  \let\oldsubparagraph\subparagraph
+  \renewcommand{\subparagraph}[1]{\oldsubparagraph{#1}\mbox{}}
 \fi
 $endif$
 $if(pagestyle)$
 \pagestyle{$pagestyle$}
 $endif$
-
-% set default figure placement to htbp
-\makeatletter
-\def\fps@figure{htbp}
-\makeatother
-
 $for(header-includes)$
 $header-includes$
 $endfor$
@@ -236,9 +328,14 @@ $for(bibliography)$
 \addbibresource{$bibliography$}
 $endfor$
 $endif$
-
-%Allow PDF to be included
-\usepackage{pdfpages}
+$if(csl-refs)$
+\newlength{\cslhangindent}
+\setlength{\cslhangindent}{1.5em}
+\newenvironment{cslreferences}%
+  {$if(csl-hanging-indent)$\setlength{\parindent}{0pt}%
+  \everypar{\setlength{\hangindent}{\cslhangindent}}\ignorespaces$endif$}%
+  {\par}
+$endif$
 
 $if(title)$
 
@@ -316,11 +413,11 @@ $include-before$
 $endfor$
 $if(toc)$
 {
-  $if(colorlinks)$
-    \hypersetup{linkcolor=$if(toccolor)$$toccolor$$else$$endif$}
-  $endif$
-  \setcounter{tocdepth}{$toc-depth$}
-  \tableofcontents
+$if(colorlinks)$
+\hypersetup{linkcolor=$if(toccolor)$$toccolor$$else$$endif$}
+$endif$
+\setcounter{tocdepth}{$toc-depth$}
+\tableofcontents
 }
 $endif$
 $if(lot)$