thesis.tex

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\usepackage{nameref}
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\usepackage{grffile}
\usepackage{graphicx}
\usepackage[font=footnotesize]{caption}
\usepackage[superscript,biblabel,nomove,ref]{cite}
%\usepackage[superscript,biblabel,noadjust]{cite}
\usepackage[toc,page]{appendix}
\usepackage{lineno}


\usepackage[xetex,
pdfauthor={Quentin Geissmann},
pdftitle={High-throughput Recording, Analysis and Manipulation of Sleep in Drosophila},
pdfsubject={Computational biology},
pdfkeywords={Drosophila, behaviour, sleep, high-throughput},
pdfproducer={Latex with hyperref},
pdfcreator={XeTex}]{hyperref}

%todo remove
%\usepackage{hyperref}
%\usepackage[utf8]{inputenc}
%end todo


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\usepackage{gensymb}

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\usepackage{parskip} % Spaces between paragraphs

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% add binding margins

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\usepackage{sidecap}
\usepackage{epigraph}

\usepackage{etoolbox}
\usepackage{titlesec}
\usepackage{fancyhdr}
\pagestyle{fancy}
\fancyhf{}
%\fancyhead[C]{\rule{.5\textwidth}{4\baselineskip}}% Add something BIG in the header

%todo remove
%\usepackage[none]{hyphenat}
%todo uncoment
\fancyhead[EL]{\nouppercase\leftmark}
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\fancyhead[ER,OL]{\thepage}

\setlength{\headheight}{62,5pt}% ...at least 51.60004pt

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\usepackage{titlesec, blindtext, color}

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\titleformat{\chapter}[hang]{\Huge\bfseries}{\thechapter\hsp\textcolor{gray75}{|}\hsp}{0pt}{\Huge\bfseries}


\preto\chapter\glsresetall

\makeglossaries

%~ \renewcommand*\abstractname{Summary}

% http://www.tex.ac.uk/cgi-bin/texfaq2html?label=altabcr
\setcounter{MaxMatrixCols}{50}

% package name:
\newcommand{\py}{\texttt{python}}
\newcommand{\re}{\texttt{rethomics}}
\newcommand{\ctit}{\emph}
\newcommand{\ptit}{\emph}
\newcommand{\eg}{\emph{e.g.}}
\newcommand{\ie}{\emph{i.e.}}
\newcommand{\droso}{\emph{Drosophila}}
\newcommand{\dmel}{\emph{Drosophila melanogaster}}

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\sloppy

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\newcommand{\emd}{\,---\,}

%\newcommand{\sectionbreak}{\clearpage}

\usepackage{pgfpages}
%\pgfpagesuselayout{4 on 1}[a4paper]
%\pgfpagesuselayout{2 on 1}[a4paper,landscape]
\begin{document}

\input{title-abstract}
\setcounter{page}{1}
\pagenumbering{arabic}
\onehalfspacing

%\linenumbers

\input{1-intro/1-intro}
\input{2-ethoscopes/2-ethoscopes}
\input{3-rethomics/3-rethomics}
\input{4-baseline/4-baseline}
\input{5-sleep-deprivation/5-sleep-deprivation}
\input{6-discussion/6-discussion}
\newpage
\singlespacing
%\bibliographystyle{apalike} 
\bibliographystyle{cj}

{\footnotesize
\bibliography{thesis.bib}{}}




\end{document}