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%% TOP Reference Manual
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%% Preamble
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%% Document layout
\documentclass[draft]{scrreport}

%% Custom style (.sty)
\usepackage{../../global/packages}
\hypersetup{
  pdftitle={Tracers in Ocean Paradigm (TOP) -- The NEMO passive tracers engine},
  pdfauthor={NEMO TOP Working Group},
  colorlinks
}

%% Include references and index for single subfile compilation
\newcommand{\biblio}{\bibliography{../main/TOP_manual}}
\newcommand{\pindex}{\printindex}

\makeindex

%% End of common preamble between main and sub-files
\begin{document}
\pagenumbering{gobble}

%% Override custom cmds for full manual compilation
\renewcommand{\biblio}{}
\renewcommand{\pindex}{}


%% Frontmatter
%% ==============================================================================

\title{Tracer in Ocean Paradigm (TOP) -- The NEMO passive tracer engine}
%  \small{\textcolor{red}{First draft documentation. Needs completion and rewriting.}}
}
\author{NEMO TOP Working Group\thanks{
    \'{E}th\'{e} Christian, Lovato Tomas, Aumont Olivier, Palmi\'{e}ri Julien,
    Mouchet Anne, Nurser Georges, Yool Andrew
  }
}
\date{\today}

%% Title and information pages
\input{../../global/frontpages}

%% Citation embedded
\textsf{
``{\bfseries Tracer in Ocean Paradigm (TOP) -- The NEMO passive tracer engine}'', 
NEMO TOP Working Group, 
{\em Scientific Notes of Climate Modelling Center (28)}, ISSN 1288-1619, 
Institut Pierre-Simon Laplace (IPSL), 
\href{http://doi.org/10.5281/zenodo.1471700}{doi:10.5281/zenodo.1471700}
}

\newpage
%\frontmatter   %% Chapter numbering off and Roman numerals for page numbers
\pagenumbering{roman}

\subfile{../subfiles/foreword}            %% Foreword


%% ToC i.e. Table of Contents
\newpage
\dominitoc
\tableofcontents

\clearpage

%% Mainmatter
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%\mainmatter   %% Chapter numbering on, page numbering is reset with Arabic numerals
\pagenumbering{arabic}

\graphicspath{{../../figures/TOP/}}

\subfile{../subfiles/introduction}
\subfile{../subfiles/model_description}
\subfile{../subfiles/model_setup}
\subfile{../subfiles/miscellaneous}

%% Appendix
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%\appendix   % Chapter numbering is reset with letters now


%% Backmatter
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%\backmatter   %% Chapter numbering off

%% Bibliography
\phantomsection
\addcontentsline{toc}{chapter}{Bibliography}
\bibliography{../main/TOP_manual}

%% Index
\clearpage
\phantomsection
\addcontentsline{toc}{chapter}{Index}
\printindex

\end{document}