neurolibrenew.tex

\documentclass[10pt,a4paper,onecolumn]{article}
\usepackage{marginnote}
\usepackage{graphicx}
\usepackage[rgb]{xcolor}
\usepackage{authblk,etoolbox}
\usepackage{titlesec}
\usepackage{calc}
\usepackage{tikz}
\usepackage[pdfa]{hyperref}
\usepackage{hyperxmp}
\usepackage{awesomebox}
\hypersetup{%
    unicode=true,
    pdfapart=3,
    pdfaconformance=B,
$if(title-meta)$
    pdftitle={$title-meta$},
$endif$
$if(author-meta)$
    pdfauthor={$author-meta$},
$endif$
$if(keywords)$
    pdfkeywords={$for(keywords)$$keywords$$sep$; $endfor$},
$endif$
    pdfpublication={$journal.title$},
    pdfpublisher={NeuroLibre},
    pdfpubtype={journal}
$if(article.doi)$
    pdfdoi={$article.doi$},
$endif$
$if(author-meta)$
    pdfcopyright={Copyright (c) $year$, $author-meta$},
$endif$
    pdflicenseurl={http://creativecommons.org/licenses/by/4.0/},
$if(colorlinks)$
    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
}
% https://tex.stackexchange.com/a/535849
% Create an OutputIntent in order to correctly specify colours
% \immediate\pdfobj stream attr{/N 3} file{sRGB.icc}
% \pdfcatalog{%
%   /OutputIntents [
%     <<
%       /Type /OutputIntent
%       /S /GTS_PDFA1
%       /DestOutputProfile \the\pdflastobj\space 0 R
%       /OutputConditionIdentifier (sRGB)
%       /Info (sRGB)
%     >>
%   ]
% }
\pdfvariable omitcidset=1
\usepackage{caption}
\usepackage{orcidlink}
\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

$if(csl-refs)$
\newlength{\cslhangindent}
\setlength{\cslhangindent}{1.5em}
\newlength{\csllabelwidth}
\setlength{\csllabelwidth}{3em}
\newenvironment{CSLReferences}[2] % #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}\break}
\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{\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 $self-citation$}.}}


\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}}
\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\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}
    \usepackage{fontspec}

  \else
    \usepackage{fontspec}
  \fi
  \defaultfontfeatures{Scale=MatchLowercase}
  \defaultfontfeatures[\sffamily]{Ligatures=TeX}
  \defaultfontfeatures[\rmfamily]{Ligatures=TeX,Scale=1}

\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
}{}

%% Font settings
\usepackage{fontsetup} % Lazy way to get proper Greek lowercase glyphs

% Use Hack https://sourcefoundry.org/hack/
\setmonofont{Hack}

$if(colorlinks)$
\PassOptionsToPackage{usenames,dvipsnames}{color} % color is loaded by hyperref
$endif$
\urlstyle{same}  % don't use monospace font for urls
$if(lang)$
\ifLuaTeX
\usepackage[bidi=basic]{babel}
\else
\usepackage[bidi=default]{babel}
\fi
\babelprovide[main,import]{$babel-lang$}
$for(babel-otherlangs)$
\babelprovide[import]{$babel-otherlangs$}
$endfor$
% get rid of language-specific shorthands (see #6817):
\let\LanguageShortHands\languageshorthands
\def\languageshorthands#1{}
$endif$
$if(natbib)$
\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,array}
$endif$
$-- add watermark and linenumbers unless this is the final (non-draft) version
$if(draft)$
\usepackage{lineno}
\linenumbers
\usepackage{draftwatermark}
$endif$

$if(graphics)$
\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}
}
$endif$
$if(strikeout)$
$-- also used for underline
\usepackage{soul}
$endif$
\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
$endif$
$for(header-includes)$
$header-includes$
$endfor$
\ifLuaTeX
  \usepackage{selnolig}  % disable illegal ligatures
\fi

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

% ------------- This section is executed for maketitle if 
% the number of authors are < 10. Default joss \maketitle
$if(noMoreThanTenAuthors)$
$for(authors)$
\author[$for(authors.affiliation)$$authors.affiliation$$sep$,$endfor$%
$if(authors.equal-contrib)$*$endif$%
$if(authors.cor-id)$\ensuremath\mathparagraph$endif$]{$authors.name$%
$if(it.orcid)$
  \,\orcidlink{${it.orcid}}\,%
$endif$
$if(it.note)$
  \thanks{$it.note$}%
$endif$
}
$endfor$

$for(affiliations)$
\affil[$affiliations.index$]{$affiliations.name$}
$endfor$
$if(article.author-notes.corresp)$
\affil[$$\mathparagraph$$]{Corresponding author}
$endif$
$if(article.has-equal-contributors)$
\affil[*]{$if(message.equal-contrib)$$message.equal-contrib$$else$These authors contributed equally.$endif$}
$endif$
$endif$

\date{\vspace{-2.5ex}}

\begin{document}

% Authblk behaves awkwardly when there are too many authors 
% NeuroLibre lua filter handles that. Therefore, the default \maketitle 
% gets executed when there are equal or less than 10 authors.
$if(noMoreThanTenAuthors)$
$if(title)$
\maketitle
$endif$
$endif$

$if(moreThanTenAuthors)$
{\begin{flushleft} \LARGE\sffamily $title$ \end{flushleft}}

\vspace{1em}

{\begin{flushleft} $authorsWithAffiliations$ \end{flushleft} }

$if(article.has-equal-contributors)$
{$if(message.equal-contrib)$$message.equal-contrib$$else$* These authors contributed equally.$endif$}
$endif$

$endif$



\marginpar{

  \begin{flushleft}
  %\hrule
  \sffamily\small

  \vspace{-3.5cm}

  {\bfseries DOI:} \href{https://doi.org/$article.doi$}{\color{red}{$article.doi$}}

   \vspace{2mm}

    {\bfseries Interactive Version}
  \begin{itemize}
    \setlength\itemsep{0em}
    \item \href{$book_exec_url$}{\color{red}{Living Preprint}} \ExternalLink
  \end{itemize}

  \vspace{2mm}
  
  {\bfseries Code}
  \begin{itemize}
    \setlength\itemsep{0em}
    \item \href{$software_review_url$}{\color{red}{Technical Screening}} \ExternalLink
    \item \href{$software_repository_url$}{\color{red}{Submitted Repository}} \ExternalLink
  \end{itemize}

   \vspace{2mm}

    {\bfseries Reproducibility Assets}
  \begin{itemize}
    \setlength\itemsep{0em}
    $if(include_repository_doi)$
    \item \href{https://doi.org/$repository_doi$}{\color{red}{Repository}} \ExternalLink
    $endif$
    $if(include_data_doi)$
    \item \href{https://doi.org/$data_doi$}{\color{red}{Dataset}} \ExternalLink
    $endif$
    $if(include_book_doi)$
    \item \href{https://doi.org/$book_doi$}{\color{red}{Living Preprint}} \ExternalLink
    $endif$
    $if(include_docker_doi)$
    \item \href{https://doi.org/$docker_doi$}{\color{red}{Container}} \ExternalLink
$endif$
  \end{itemize}

  \vspace{1mm}

  \par\noindent\hrulefill\par

  \vspace{2mm}

  {\bfseries Moderator:} \href{$editor.url$}{$editor.name$} \ExternalLink
  \vspace{1mm}
  $if(reviewers)$
  {\bfseries Screener(s):}
  \begin{itemize}
  \setlength\itemsep{0em}
  $for(reviewers)$
  \item \href{https://github.com/$reviewers$}{@$reviewers$}
  $endfor$
  \end{itemize}
  $endif$
  \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{red}{CC BY 4.0}}).

  $if(aas-doi)$
  \vspace{4mm}
  {\bfseries In partnership with}\\
  \vspace{2mm}
  \includegraphics[width=4cm]{$aas_logo_path$}
  \vspace{2mm}
  \newline
  This article and software are linked with research article DOI \href{https://doi.org/$aas-doi$}{\color{linky}{$aas-doi$}}, published in the $aas-journal$.
  $endif$

  $if(europar-doi)$
  \vspace{4mm}
  {\bfseries In partnership with}\\
  \vspace{2mm}
  \includegraphics[width=4cm]{$europar_logo_path$}
  \vspace{2mm}
  \newline
  JOSS Special Issue for Euro-Par 2022 Artefacts \href{https://doi.org/$europar-doi$}{\color{linky}{$europar-doi$}}
  $endif$

  \end{flushleft}
}

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

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

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

\subsection*{Disclaimer}
\awesomebox[red]{2pt}{\faRocket}{red}{\textbf{This pdf is intended for content registration purposes only! For full access and interactive reading of this publication, please visit \href{https://preprint.neurolibre.org/$article.doi$}{the live version}.}}

$body$


$if(moreThanTenAuthors)$
\section{Affiliations}

{\Affilfont $affiliationsList$}

$endif$

$if(natbib)$
$if(bibliography)$
$if(biblio-title)$
$if(book-class)$
\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}