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


% --- 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]{\footnotesize{\sffamily $citation_author$, ($year$). $title$. \textit{$journal_name$}, $volume$($issue$), $page$. \href{https://doi.org/$formatted_doi$}{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}}
\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}}{}
$endif$
$if(verbatim-in-note)$
\usepackage{fancyvrb}
\VerbatimFootnotes % allows verbatim text in footnotes
$endif$
$if(graphics)$
\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}
}
$endif$
\setlength{\emergencystretch}{3em}  % prevent overfull lines
$if(numbersections)$
\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
$endif$

$if(highlighting-macros)$
% Pandoc syntax highlighting
$highlighting-macros$
$endif$

% tightlist command for lists without linebreak
\providecommand{\tightlist}{%
  \setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}}

$if(tables)$
% From pandoc table feature
\usepackage{longtable,booktabs,array}
$if(multirow)$
\usepackage{multirow}
$endif$
\usepackage{calc} % for calculating minipage widths
% Correct order of tables after \paragraph or \subparagraph
\usepackage{etoolbox}
\makeatletter
\patchcmd\longtable{\par}{\if@noskipsec\mbox{}\fi\par}{}{}
\makeatother
% Allow footnotes in longtable head/foot
\IfFileExists{footnotehyper.sty}{\usepackage{footnotehyper}}{\usepackage{footnote}}
\makesavenoteenv{longtable}
$endif$

$if(csl-refs)$
% Pandoc citation processing
\newlength{\cslhangindent}
\setlength{\cslhangindent}{1.5em}
\newlength{\csllabelwidth}
\setlength{\csllabelwidth}{3em}
\newlength{\cslentryspacingunit} % times entry-spacing
\setlength{\cslentryspacingunit}{\parskip}
% for Pandoc 2.8 to 2.10.1
\newenvironment{cslreferences}%
  {$if(csl-hanging-indent)$\setlength{\parindent}{0pt}%
  \everypar{\setlength{\hangindent}{\cslhangindent}}\ignorespaces$endif$}%
  {\par}
% For Pandoc 2.11+
\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
  \let\oldpar\par
  \def\par{\hangindent=\cslhangindent\oldpar}
  \fi
  % set entry spacing
  \setlength{\parskip}{#2\cslentryspacingunit}
 }%
 {}
\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}
$endif$

$for(header-includes)$
$header-includes$
$endfor$

$if(title)$
\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{
  %\hrule
  \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{http://creativecommons.org/licenses/by/4.0/}{\color{linky}{CC-BY}}).
}

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

$endfor$
$if(toc)$
{
$if(colorlinks)$
\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}
