twocol.tex

\documentclass[10pt]{article}

$if(small_margin)$
\RequirePackage[top=0.6in,left=0.6in,right=0.6in,bottom=0.3in,includefoot]{geometry}
$else$
\RequirePackage[top=0.8in,left=0.8in,right=0.8in,bottom=0.3in,includefoot]{geometry}
$endif$ 

% Include a series of generic definitions and usepackage commands
\input{mediabuilder.tex}

% \usepackage{microtype}

% Need this for the \Letter glyph, envelope, for corresponding author.
\usepackage[misc,geometry]{ifsym} 


\usepackage{authblk}

\renewcommand{\rmdefault}{bch} % Charter
\renewcommand{\sfdefault}{bch} % Charter


% used for twocol flush balance end on last page
\usepackage{flushend}
\usepackage{pdfpages}


\usepackage[skip=2pt, font=footnotesize, format=plain, labelfont=it, textfont=it, tableposition=below]{caption}
%  This code to use {caption} will wipe out the ability of pandoc-crossref
%  to prepend the "Figure" reference to the caption.
\DeclareCaptionLabelFormat{nolabel}{}
\captionsetup{labelformat=nolabel}
\usepackage{amssymb,amsmath}
\usepackage{ifxetex,ifluatex}

% colors
\definecolor{bluehaze}{RGB}{54,95,145}
\definecolor{maroonhaze}{RGB}{148,54,52}
\definecolor{orangehaze}{RGB}{227,108,10}
\definecolor{black}{RGB}{0,0,0}
\definecolor{bluetint}{RGB}{0,50,100}
\definecolor{bluetint2}{RGB}{0,30,60}
\definecolor{graytint}{RGB}{175,175,175}
\definecolor{graybit}{RGB}{245,245,245}
\definecolor{lightblack}{RGB}{75,75,75}
\definecolor{brickred}{rgb}{0.8, 0.25, 0.33}
%  This is used to allow Shaded environment
$if(highlighting-macros)$
$highlighting-macros$
$endif$


% Start column longtable hack
% Allows tables to be used in two-column documents with pandoc
% Credit: https://tex.stackexchange.com/a/224096/161489
\makeatletter
\let\oldlt\longtable
\let\endoldlt\endlongtable

\def\longtable{\@ifnextchar[\longtable@i \longtable@ii}
\def\longtable@i[#1]{\begin{figure}[H]
\onecolumn
\begin{minipage}{0.5\textwidth}
\oldlt[#1]
}
\def\longtable@ii{\begin{figure}[H]
\onecolumn
\begin{minipage}{0.5\textwidth}
\oldlt
}
\def\endlongtable{\endoldlt
\end{minipage}
\twocolumn
\end{figure}}
\makeatother
% End column longtable hack


\ifxetex
  \usepackage{fontspec,xltxtra,xunicode}
  \defaultfontfeatures{Mapping=tex-text,Scale=MatchLowercase}
\else
  \ifluatex
    \usepackage{fontspec}
    \defaultfontfeatures{Mapping=tex-text,Scale=MatchLowercase}
  \else
    \usepackage[utf8]{inputenc}
  \fi
\fi

$if(natbib)$
\usepackage{natbib}
\bibliographystyle{plainnat}
$endif$
$if(biblatex)$
\usepackage{biblatex}
$if(biblio-files)$
\bibliography{$biblio-files$}
$endif$
$endif$
$if(lhs)$
\usepackage{listings}
\lstnewenvironment{code}{\lstset{language=Haskell,basicstyle=\small\ttfamily}}{}
$endif$
$if(verbatim-in-note)$
\usepackage{fancyvrb}
$endif$
$if(fancy-enums)$
% Redefine labelwidth for lists; otherwise, the enumerate package will cause
% markers to extend beyond the left margin.
\makeatletter\AtBeginDocument{%
  \renewcommand{\@listi}
    {\setlength{\labelwidth}{4em}}
}\makeatother


$endif$
$if(tables)$
\usepackage{ctable}
\usepackage{float} % provides the H option for float placement
$endif$
$if(url)$
\usepackage{url}
$endif$


\hypersetup{breaklinks=true, pdfborder={0 0 0}, colorlinks=true, urlcolor=bluehaze, linkcolor=bluehaze, citecolor=bluehaze, anchorcolor=bluehaze}
$if(strikeout)$
\usepackage[normalem]{ulem}
% avoid problems with \sout in headers with hyperref:
\pdfstringdefDisableCommands{\renewcommand{\sout}{}}
$endif$
$if(subscript)$
\newcommand{\textsubscr}[1]{\ensuremath{_{\scriptsize\textrm{#1}}}}
$endif$
$if(listings)$
\usepackage{listings}
$endif$
$if(numbersections)$
$else$
\setcounter{secnumdepth}{0}
$endif$
$if(verbatim-in-note)$
\VerbatimFootnotes % allows verbatim text in footnotes
$endif$
$for(header-includes)$
$header-includes$
$endfor$

$if(title)$
\title{$title$}
$endif$
% $if(author)$
% \author{$for(author)$$author$$sep$ \and $endfor$}
% $endif$
$if(date)$
\date{$date$}
$endif$



$if(linespread)$\linespread{$linespread$}$else$
\linespread{1.0}
$endif$

% Fancy page numbering ---------------------------------------------------------

%\pagestyle{fancy}
%\fancyhead[RO]{Sheffield \thepage}
\usepackage{fancyhdr}
\fancyhead{} % empty
\fancyfoot{} % empty out the default, which is page number in center
\def\middot{\textperiodcentered~}
\lfoot{\scriptsize \thepage \middot $short_title$ $if(journal_tagline)$\middot \textit{$journal_tagline$} $endif$ $if(date)$ \middot \textsl{$date$} $endif$ $if(copyright)$ \middot \textcopyright $copyright$ $endif$}
\pagestyle{fancy}


% Fancy abstract box styling ---------------------------------------------------

\usepackage{mdframed}   % for framing
\newmdenv[linecolor=white, fontcolor=bluetint, backgroundcolor=graybit, leftmargin=8, rightmargin=8, innertopmargin=8, innerbottommargin=8, innerleftmargin=12, innerrightmargin=12, roundcorner=10pt, font=\normalsize]{infobox}



% Title spacing, size, and color ------------------------------------------------------
\usepackage{titlesec}
\usepackage{xcolor}% http://ctan.org/pkg/xcolor

\titleformat{\section}
  {\normalfont\fontfamily{phv}\fontsize{11pt}{11pt}
    \selectfont\color{bluetint}\bfseries}{\thesection}{1em}{}

\titleformat{\subsection}
  {\normalfont\fontfamily{phv}\fontsize{9pt}{9pt}
    \selectfont\color{black}\bfseries}{\thesubsection}{1em}{}

\titleformat{\subsubsection}
  {\normalfont\fontfamily{phv}\fontsize{1em}{1em}
    \selectfont\color{black}}{\thesubsubsection}{1em}{}



% use amsthm for addpunct, to add periods to the end of non-punctuated
% paragraph titles (header level 4; ####)
\usepackage{amsthm}
\makeatletter
\newcommand{\addperiod}[1]{#1\@addpunct{.}}
\makeatother
% use runin to specify no newline
\titleformat{\paragraph}[runin]
  {\normalfont\color{lightblack}\itshape}{\theparagraph}{}{\addperiod}

% \titlespacing{command}{left spacing}{before spacing}{after spacing}[right]
\titlespacing\section{0pt}{12pt plus 2pt minus 2pt}{-2pt plus 2pt minus 2pt}
\titlespacing\subsection{0pt}{11pt plus 2pt minus 2pt}{-2pt plus 2pt minus 2pt}
\titlespacing\subsubsection{0pt}{4pt plus 2pt minus 2pt}{-2pt plus 2pt minus 2pt}

\titlespacing{\paragraph}{0pt}{1pt plus 4pt minus 2pt}{6pt plus 2pt minus 2pt}


% The maximum part of the top or bottom of a text page that can be
% occupied by floats. This is set so that at least four lines of text 
% fit on the page.
% \renewcommand\topfraction{.9}
% \renewcommand\bottomfraction{.9}
% % The minimum amount of a text page that must be occupied by text.
% % This should accomodate four lines of text.
% \renewcommand\textfraction{.06}
% % The minimum amount of a float page that must be occupied by floats.
% \renewcommand\floatpagefraction{.94}

% % The same parameters repeated for double column output
% \renewcommand\dbltopfraction{.9}
% \renewcommand\dblfloatpagefraction{.9}

% Attempt to smash lists together

\let\tightlist\relax
\providecommand{\tightlist}{%
  \setlength{\itemsep}{0pt}
  \setlength{\parskip}{3pt}
  \setlength{\topsep}{-6pt}
  }
\usepackage{enumerate}
\usepackage{enumitem}
\setlist[itemize]{topsep=0pt,parsep=2pt,itemindent=0pt,leftmargin=18pt}
% \def\labelitemi{\raisebox{0.5ex}{\tiny\textbullet}}


% Convert author/affiliations from yaml into latex -----------------------------

$for(author)$
$if(author.name)$
  $if(author.correspondence)$
    \author[$author.affiliation$,\Letter]{$author.name$}
  $else$
    \author[$author.affiliation$]{$author.name$}
  $endif$
$else$
\author{$author$}
$endif$
$endfor$

% institutions must come after \author definitions so that corresponding tag comes last.
$if(author)$
$for(institutions)$
$if(institutions.name)$
\affil[$institutions.key$]{$institutions.name$}
$endif$
$endfor$
$endif$

$for(author)$
  $if(author.correspondence)$
    \affil[ ]{\Letter \hspace{0.08cm}  Correspondence: \href{mailto:$author.correspondence$}{$author.correspondence$}}
$endif$
$endfor$


% bring affils a little closer to author.
\setlength{\affilsep}{0.5em}

\usepackage{titling}
\renewcommand{\headrulewidth}{0pt}
\renewcommand{\Affilfont}{\scriptsize}
\makeatletter

% Define the nice-looking title for the databio theme
\renewcommand{\maketitle}{
  $if(class)$
    \begin{flushright}{\huge{\color{graytint}\textbf{\MakeUppercase{$class$}}}}\end{flushright}\vspace{-0.4em}
    {\color{graytint}\hrule}\vspace{0.3em}
  $endif$
  \begin{raggedright} 
  \huge\textbf{\@title}
    \par\normalsize \vspace{0.5em}
    {    $if(author)$
    \ignorespaces\@author
    $endif$
    $if(permalink)$
      \newline\href{http://databio.org$permalink$}{http://databio.org$permalink$}
    $endif$
    \par}
    \vspace{0.2em}
    \end{raggedright}
} % end \maketitle
\makeatother

%\subsectionfont{\color{maroonhaze}}
%\subsubsectionfont{\color{orangehaze}}
% end colors

% this code uses titles.sty to make a pagebreak with every header 1
% so each section will begin on a new page.
%\newcommand{\sectionbreak}{\clearpage}



$if(csl-refs)$
\newlength{\cslhangindent}       % set up new length
\setlength{\cslhangindent}{$if(csl-hanging-indent)$2em$else$0em$endif$}
\newenvironment{cslreferences}%
  {\everypar{\setlength{\hangindent}{\cslhangindent}}}%
  {\par} % by default, this env does not change anything
$endif$






\begin{document}

$if(onecol)$
    $if(title)$
    \maketitle
    $endif$

    $if(abstract)$
    \begin{infobox}
    $abstract$
    \end{infobox}
    $endif$

    $for(include-before)$
    $include-before$

    $endfor$
    $if(toc)$
    \tableofcontents
    $endif$
$else$
\twocolumn[{%
  \begin{@twocolumnfalse}
    $if(title)$
    \maketitle
    $endif$

    $if(abstract)$
    \begin{infobox}
    $abstract$
    \end{infobox}
    $endif$

    $for(include-before)$
    $include-before$

    $endfor$
    $if(toc)$
    \tableofcontents
    $endif$
  \end{@twocolumnfalse}
}]
$endif$

$if(bodyfont)$
\$bodyfont$
$endif$

$body$

% make the references smaller, and sloppier

$if(natbib)$
$if(biblio-files)$
$if(biblio-title)$
$if(book-class)$
\renewcommand\bibname{$biblio-title$}
$else$
\renewcommand\refname{$biblio-title$}
$endif$
$endif$

{\footnotesize\sloppy\bibliography{$biblio-files$}}

$endif$
$endif$
$if(biblatex)$

{\footnotesize\sloppy\printbibliography$if(biblio-title)$[title=$biblio-title$]$endif$}

$endif$
$for(include-after)$
$include-after$

$endfor$

\end{document}