joss-template.latex

\documentclass[10pt,a4paper,onecolumn]{article}
\usepackage{marginnote}
\usepackage{graphicx}
\usepackage{xcolor}
\usepackage{authblk,etoolbox}
\usepackage{titlesec}
\usepackage{calc}
\usepackage{tikz}
\usepackage{hyperref}
\hypersetup{colorlinks,breaklinks,
            urlcolor=[rgb]{0.0, 0.5, 1.0},
            linkcolor=[rgb]{0.0, 0.5, 1.0}}
\usepackage{caption}
\usepackage{tcolorbox}
\usepackage{amssymb,amsmath}
\usepackage{ifxetex,ifluatex}
\usepackage{seqsplit}
\usepackage{xstring}

\usepackage{float}
\let\origfigure\figure
\let\endorigfigure\endfigure
\renewenvironment{figure}[1][2] {
    \expandafter\origfigure\expandafter[H]
} {
    \endorigfigure
}

\usepackage{fixltx2e} % provides \textsubscript
\usepackage[
  backend=biber,
%  style=alphabetic,
%  citestyle=numeric
]{biblatex}
\bibliography{$bibliography$}

% --- Splitting \texttt --------------------------------------------------

\let\textttOrig=\texttt
\def\texttt#1{\expandafter\textttOrig{\seqsplit{#1}}}
\renewcommand{\seqinsert}{\ifmmode
  \allowbreak
  \else\penalty6000\hspace{0pt plus 0.02em}\fi}


% --- Pandoc does not distinguish between links like [foo](bar) and
% --- [foo](foo) -- a simplistic Markdown model.  However, this is
% --- wrong:  in links like [foo](foo) the text is the url, and must
% --- be split correspondingly.
% --- Here we detect links \href{foo}{foo}, and also links starting
% --- with https://doi.org, and use path-like splitting (but not
% --- escaping!) with these links.
% --- Another vile thing pandoc does is the different escaping of
% --- foo and bar.  This may confound our detection.
% --- This problem we do not try to solve at present, with the exception
% --- of doi-like urls, which we detect correctly.


\makeatletter
\let\href@Orig=\href
\def\href@Urllike#1#2{\href@Orig{#1}{\begingroup
    \def\Url@String{#2}\Url@FormatString
    \endgroup}}
\def\href@Notdoi#1#2{\def\tempa{#1}\def\tempb{#2}%
  \ifx\tempa\tempb\relax\href@Urllike{#1}{#2}\else
  \href@Orig{#1}{#2}\fi}
\def\href#1#2{%
  \IfBeginWith{#1}{https://doi.org}%
  {\href@Urllike{#1}{#2}}{\href@Notdoi{#1}{#2}}}
\makeatother

$if(csl-refs)$
\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}
  % 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}
  \fi
 }%
 {}
\usepackage{calc}
\newcommand{\CSLBlock}[1]{#1\hfill\break}
\newcommand{\CSLLeftMargin}[1]{\parbox[t]{\csllabelwidth}{#1}}
\newcommand{\CSLRightInline}[1]{\parbox[t]{\linewidth - \csllabelwidth}{#1}}
\newcommand{\CSLIndent}[1]{\hspace{\cslhangindent}#1}
$endif$

% --- Page layout -------------------------------------------------------------
\usepackage[top=3.5cm, bottom=3cm, right=1.5cm, left=1.0cm,
            headheight=2.2cm, reversemp, includemp, marginparwidth=4.5cm]{geometry}

% --- Default font ------------------------------------------------------------
% \renewcommand\familydefault{\sfdefault}

% --- Style -------------------------------------------------------------------
\renewcommand{\bibfont}{\small \sffamily}
\renewcommand{\captionfont}{\small\sffamily}
\renewcommand{\captionlabelfont}{\bfseries}

% --- Section/SubSection/SubSubSection ----------------------------------------
\titleformat{\section}
  {\normalfont\sffamily\Large\bfseries}
  {}{0pt}{}
\titleformat{\subsection}
  {\normalfont\sffamily\large\bfseries}
  {}{0pt}{}
\titleformat{\subsubsection}
  {\normalfont\sffamily\bfseries}
  {}{0pt}{}
\titleformat*{\paragraph}
  {\sffamily\normalsize}


% --- Header / Footer ---------------------------------------------------------
\usepackage{fancyhdr}
\pagestyle{fancy}
\fancyhf{}
%\renewcommand{\headrulewidth}{0.50pt}
\renewcommand{\headrulewidth}{0pt}
\fancyhead[L]{\hspace{-0.75cm}\includegraphics[width=5.5cm]{$logo_path$}}
\fancyhead[C]{}
\fancyhead[R]{}
\renewcommand{\footrulewidth}{0.25pt}

\fancyfoot[L]{\parbox[t]{0.98\headwidth}{\footnotesize{\sffamily $citation_author$, ($year$). $title$. \textit{$journal_name$}, $volume$($issue$), $page$. \url{https://doi.org/$formatted_doi$}}}}


\fancyfoot[R]{\sffamily \thepage}
\makeatletter
\let\ps@plain\ps@fancy
\fancyheadoffset[L]{4.5cm}
\fancyfootoffset[L]{4.5cm}

% --- Macros ---------

\definecolor{linky}{rgb}{0.0, 0.5, 1.0}

\newtcolorbox{repobox}
   {colback=red, colframe=red!75!black,
     boxrule=0.5pt, arc=2pt, left=6pt, right=6pt, top=3pt, bottom=3pt}

\newcommand{\ExternalLink}{%
   \tikz[x=1.2ex, y=1.2ex, baseline=-0.05ex]{%
       \begin{scope}[x=1ex, y=1ex]
           \clip (-0.1,-0.1)
               --++ (-0, 1.2)
               --++ (0.6, 0)
               --++ (0, -0.6)
               --++ (0.6, 0)
               --++ (0, -1);
           \path[draw,
               line width = 0.5,
               rounded corners=0.5]
               (0,0) rectangle (1,1);
       \end{scope}
       \path[draw, line width = 0.5] (0.5, 0.5)
           -- (1, 1);
       \path[draw, line width = 0.5] (0.6, 1)
           -- (1, 1) -- (1, 0.6);
       }
   }

% --- Title / Authors ---------------------------------------------------------
% patch \maketitle so that it doesn't center
\patchcmd{\@maketitle}{center}{flushleft}{}{}
\patchcmd{\@maketitle}{center}{flushleft}{}{}
% patch \maketitle so that the font size for the title is normal
\patchcmd{\@maketitle}{\LARGE}{\LARGE\sffamily}{}{}
% patch the patch by authblk so that the author block is flush left
\def\maketitle{{%
  \renewenvironment{tabular}[2][]
    {\begin{flushleft}}
    {\end{flushleft}}
  \AB@maketitle}}
\makeatletter
\renewcommand\AB@affilsepx{ \protect\Affilfont}
%\renewcommand\AB@affilnote[1]{{\bfseries #1}\hspace{2pt}}
\renewcommand\AB@affilnote[1]{{\bfseries #1}\hspace{3pt}}
\renewcommand{\affil}[2][]%
   {\newaffiltrue\let\AB@blk@and\AB@pand
      \if\relax#1\relax\def\AB@note{\AB@thenote}\else\def\AB@note{#1}%
        \setcounter{Maxaffil}{0}\fi
        \begingroup
        \let\href=\href@Orig
        \let\texttt=\textttOrig
        \let\protect\@unexpandable@protect
        \def\thanks{\protect\thanks}\def\footnote{\protect\footnote}%
        \@temptokena=\expandafter{\AB@authors}%
        {\def\\{\protect\\\protect\Affilfont}\xdef\AB@temp{#2}}%
         \xdef\AB@authors{\the\@temptokena\AB@las\AB@au@str
         \protect\\[\affilsep]\protect\Affilfont\AB@temp}%
         \gdef\AB@las{}\gdef\AB@au@str{}%
        {\def\\{, \ignorespaces}\xdef\AB@temp{#2}}%
        \@temptokena=\expandafter{\AB@affillist}%
        \xdef\AB@affillist{\the\@temptokena \AB@affilsep
          \AB@affilnote{\AB@note}\protect\Affilfont\AB@temp}%
      \endgroup
       \let\AB@affilsep\AB@affilsepx
}
\makeatother
\renewcommand\Authfont{\sffamily\bfseries}
\renewcommand\Affilfont{\sffamily\small\mdseries}
\setlength{\affilsep}{1em}


\ifnum 0\ifxetex 1\fi\ifluatex 1\fi=0 % if pdftex
  \usepackage[$if(fontenc)$$fontenc$$else$T1$endif$]{fontenc}
  \usepackage[utf8]{inputenc}

\else % if luatex or xelatex
  \ifxetex
    \usepackage{mathspec}
  \else
    \usepackage{fontspec}
  \fi
  \defaultfontfeatures{Ligatures=TeX,Scale=MatchLowercase}

\fi
% use upquote if available, for straight quotes in verbatim environments
\IfFileExists{upquote.sty}{\usepackage{upquote}}{}
% use microtype if available
\IfFileExists{microtype.sty}{%
\usepackage{microtype}
\UseMicrotypeSet[protrusion]{basicmath} % disable protrusion for tt fonts
}{}

\usepackage{hyperref}
$if(colorlinks)$
\PassOptionsToPackage{usenames,dvipsnames}{color} % color is loaded by hyperref
$endif$
\hypersetup{unicode=true,
$if(title-meta)$
            pdftitle={$title-meta$},
$endif$
$if(author-meta)$
            pdfauthor={$author-meta$},
$endif$
$if(keywords)$
            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$,
$else$
            pdfborder={0 0 0},
$endif$
            breaklinks=true}
\urlstyle{same}  % don't use monospace font for urls
$if(lang)$
\ifnum 0\ifxetex 1\fi\ifluatex 1\fi=0 % if pdftex
  \usepackage[shorthands=off,$for(babel-otherlangs)$$babel-otherlangs$,$endfor$main=$babel-lang$]{babel}
$if(babel-newcommands)$
  $babel-newcommands$
$endif$
\else
  \usepackage{polyglossia}
  \setmainlanguage[$polyglossia-lang.options$]{$polyglossia-lang.name$}
$for(polyglossia-otherlangs)$
  \setotherlanguage[$polyglossia-otherlangs.options$]{$polyglossia-otherlangs.name$}
$endfor$
\fi
$endif$
$if(natbib)$
\usepackage{natbib}
\bibliographystyle{$if(biblio-style)$$biblio-style$$else$plainnat$endif$}
$endif$
$if(biblatex)$
\usepackage$if(biblio-style)$[style=$biblio-style$]$endif${biblatex}
$if(biblatexoptions)$\ExecuteBibliographyOptions{$for(biblatexoptions)$$biblatexoptions$$sep$,$endfor$}$endif$
$for(bibliography)$
\addbibresource{$bibliography$}
$endfor$
$endif$
$if(listings)$
\usepackage{listings}
$endif$
$if(lhs)$
\lstnewenvironment{code}{\lstset{language=Haskell,basicstyle=\small\ttfamily}}{}
$endif$
$if(highlighting-macros)$
$highlighting-macros$
$endif$
$if(verbatim-in-note)$
\usepackage{fancyvrb}
\VerbatimFootnotes % allows verbatim text in footnotes
$endif$
$if(tables)$
\usepackage{longtable,booktabs}
$endif$

% --- We redefined \texttt, but in sections and captions we want the
% --- old definition
\let\addcontentslineOrig=\addcontentsline
\def\addcontentsline#1#2#3{\bgroup
  \let\texttt=\textttOrig\addcontentslineOrig{#1}{#2}{#3}\egroup}
\let\markbothOrig\markboth
\def\markboth#1#2{\bgroup
  \let\texttt=\textttOrig\markbothOrig{#1}{#2}\egroup}
\let\markrightOrig\markright
\def\markright#1{\bgroup
  \let\texttt=\textttOrig\markrightOrig{#1}\egroup}


$if(graphics)$
\usepackage{graphicx,grffile}
\makeatletter
\def\maxwidth{\ifdim\Gin@nat@width>\linewidth\linewidth\else\Gin@nat@width\fi}
\def\maxheight{\ifdim\Gin@nat@height>\textheight\textheight\else\Gin@nat@height\fi}
\makeatother
% Scale images if necessary, so that they will not overflow the page
% 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}
$endif$
$if(links-as-notes)$
% Make links footnotes instead of hotlinks:
\renewcommand{\href}[2]{#2\footnote{\url{#1}}}
$endif$
$if(strikeout)$
\usepackage[normalem]{ulem}
% avoid problems with \sout in headers with hyperref:
\pdfstringdefDisableCommands{\renewcommand{\sout}{}}
$endif$
$if(indent)$
$else$
\IfFileExists{parskip.sty}{%
\usepackage{parskip}
}{% else
\setlength{\parindent}{0pt}
\setlength{\parskip}{6pt plus 2pt minus 1pt}
}
$endif$
\setlength{\emergencystretch}{3em}  % prevent overfull lines
\providecommand{\tightlist}{%
  \setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}}
$if(numbersections)$
\setcounter{secnumdepth}{5}
$else$
\setcounter{secnumdepth}{0}
$endif$
$if(subparagraph)$
$else$
% Redefines (sub)paragraphs to behave more like sections
\ifx\paragraph\undefined\else
\let\oldparagraph\paragraph
\renewcommand{\paragraph}[1]{\oldparagraph{#1}\mbox{}}
\fi
\ifx\subparagraph\undefined\else
\let\oldsubparagraph\subparagraph
\renewcommand{\subparagraph}[1]{\oldsubparagraph{#1}\mbox{}}
\fi
$endif$
$if(dir)$
\ifxetex
  % load bidi as late as possible as it modifies e.g. graphicx
  $if(latex-dir-rtl)$
  \usepackage[RTLdocument]{bidi}
  $else$
  \usepackage{bidi}
  $endif$
\fi
\ifnum 0\ifxetex 1\fi\ifluatex 1\fi=0 % if pdftex
  \TeXXeTstate=1
  \newcommand{\RL}[1]{\beginR #1\endR}
  \newcommand{\LR}[1]{\beginL #1\endL}
  \newenvironment{RTL}{\beginR}{\endR}
  \newenvironment{LTR}{\beginL}{\endL}
\fi
$endif$
$for(header-includes)$
$header-includes$
$endfor$

$if(title)$
\title{$title$$if(thanks)$\thanks{$thanks$}$endif$}
$endif$
$if(subtitle)$
\providecommand{\subtitle}[1]{}
\subtitle{$subtitle$}
$endif$

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

$if(affiliations)$
  $for(affiliations)$
    \affil[$affiliations.index$]{$affiliations.name$}
  $endfor$
$endif$
\date{\vspace{-5ex}}

\begin{document}
$if(title)$
\maketitle
$endif$
$if(abstract)$
\begin{abstract}
$abstract$
\end{abstract}
$endif$

\marginpar{
  \sffamily\small

  {\bfseries DOI:} \href{https://doi.org/$formatted_doi$}{\color{linky}{$formatted_doi$}}

  \vspace{2mm}

  {\bfseries Software}
  \begin{itemize}
    \setlength\itemsep{0em}
    \item \href{$review_issue_url$}{\color{linky}{Review}} \ExternalLink
    \item \href{$repository$}{\color{linky}{Repository}} \ExternalLink
    \item \href{$archive_doi$}{\color{linky}{Archive}} \ExternalLink
  \end{itemize}

  \vspace{2mm}

  {\bfseries Submitted:} $submitted$\\
  {\bfseries Published:} $published$

  \vspace{2mm}
  {\bfseries License}\\
  Authors of papers retain copyright and release the work under a Creative Commons Attribution 4.0 International License (\href{https://creativecommons.org/licenses/by/4.0/}{\color{linky}{CC BY 4.0}}).
}

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

$endfor$
$if(toc)$
{
$if(colorlinks)$
\hypersetup{linkcolor=$if(toccolor)$$toccolor$$else$black$endif$}
$endif$
\setcounter{tocdepth}{$toc-depth$}
\tableofcontents
}
$endif$
$if(lot)$
\listoftables
$endif$
$if(lof)$
\listoffigures
$endif$
$body$

$if(natbib)$
$if(bibliography)$
$if(biblio-title)$
$if(book-class)$
\renewcommand\bibname{$biblio-title$}
$else$
\renewcommand\refname{$biblio-title$}
$endif$
$endif$
\bibliography{$for(bibliography)$$bibliography$$sep$,$endfor$}

$endif$
$endif$
$if(biblatex)$
\printbibliography$if(biblio-title)$[title=$biblio-title$]$endif$

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

$endfor$
\end{document}