main.tex

%% LLT: Turn off some annoying warnings...
\RequirePackage{silence}
\WarningFilter{titlesec}{Non standard sectioning command}
\WarningFilter{scrreprt}{Usage of package}
\WarningFilter{scrreprt}{Activating an ugly workaround}

% **************************************************
% Document Class Definition
% **************************************************
\documentclass[%
	paper=A4,							% paper size
	twoside=true,					% onesite or twoside printing
	openright,						% doublepage cleaning ends up right side
	parskip=full,					% spacing value / method for paragraphs
	chapterprefix=true,		% prefix for chapter marks
	11pt,									% font size
	headings=normal,			% size of headings
	bibliography=totoc,		% include bib in toc
	listof=totoc,					% include listof entries in toc
	titlepage=on,					% own page for each title page
	captions=tableabove,	% display table captions above the float env
	draft=false,					% value for draft version
]{scrreprt}%

% **************************************************
% Debug LaTeX Information
% **************************************************
%\listfiles

% **************************************************
% Information and Commands for Reuse
% **************************************************
\newcommand{\thesisTitle}{Content and frequency of dream reports. Psychological and neurophysiological correlates.}
\newcommand{\thesisName}{Raphael Vallat}
\newcommand{\thesisSubject}{Neuroscience}
\newcommand{\thesisKeywords}{Dream, sleep, awakening, memory, magnetic resonance imaging, electroencephalography, brain networks, software development}
\newcommand{\thesisDate}{December 8\textsuperscript{th}, 2017}
\newcommand{\thesisVersion}{Draft}

\newcommand{\thesisUniversity}{\protect{Lyon 1 University}}
\newcommand{\thesisUniversityDepartment}{Department of Biology}
\newcommand{\thesisUniversityInstitute}{Lyon Neuroscience Research Center}
\newcommand{\thesisUniversityGroup}{Brain Dynamics and Cognition}
\newcommand{\thesisUniversityCity}{Lyon}
\newcommand{\thesisUniversityStreetAddress}{43 Boulevard du 11 Novembre 1918}
\newcommand{\thesisUniversityPostalCode}{69100 Villeurbanne}

% **************************************************
% Load and Configure Packages
% **************************************************
\usepackage[utf8]{inputenc}
\usepackage{booktabs}							% Better looking table
\usepackage{tabularx}							% Allow better control of column width in tables
\usepackage{rotating}							% Allow landscape figures
\usepackage{ltxtable}							% Allow multi-pages long table
\usepackage{placeins}							% Allow command \FloatBarrier
\usepackage[split=false]{enotez}	% Allow command \endnote{}
\usepackage{multicol}
\usepackage[english]{babel} 			% babel system, adjust the language of the content
\usepackage{pdfpages}
\usepackage[											% clean thesis style
	figuresep=colon,
	sansserif=false,
	hangfigurecaption=true,
	hangsection=true,
	hangsubsection=true,
	colorize=reduced,
	colortheme=bluemagenta,
	% LLT: Use biber if using UTF8 encoding
	% bibsys=biber,
	bibsys=bibtex,
	bibfile=bib-refs,
	bibstyle=authoryear,
]{cleanthesis}

\hypersetup{							% setup the hyperref-package options
	pdftitle={\thesisTitle},				% 	- title (PDF meta)
	pdfsubject={\thesisSubject},		% 	- subject (PDF meta)
	pdfauthor={\thesisName},				% 	- author (PDF meta)
	pdfkeywords={\thesisKeywords},	% 	- keywords (PDF meta)
	plainpages=false,								% 	-
	colorlinks=false,								% 	- colorize links?
	pdfborder={0 0 0},							% 	-
	breaklinks=true,								% 	- allow line break inside links
	bookmarksnumbered=true,					%
	bookmarksopen=true							%
}
% Font serif (default monospace) for \url{}
\urlstyle{same}

% Increase padding within table
\renewcommand{\arraystretch}{1.2}

% **************************************************
% Document CONTENT
% **************************************************
\begin{document}

% --------------------------
% rename document parts
% --------------------------
\renewcaptionname{english}{\figurename}{Fig.}

% --------------------------
% Front matter
% --------------------------
\pagenumbering{roman}						% roman page numbing (invisible for empty page style)
\pagestyle{empty}								% no header or footers

% \input{content/front-garde-fr}				% Page de garde français + composante
% \cleardoublepage

\input{content/front-garde-en}				% Title page english
\cleardoublepage

\input{content/front-grandville}

\pagestyle{plain}							% display just page numbers

\input{content/front-abstract}				% INCLUDE: the abstracts (english and french)
\cleardoublepage

\input{content/front-acknowledgement} 		% INCLUDE: acknowledgement
\cleardoublepage

\input{content/front-acronyms} 				% INCLUDE: acronyms
\cleardoublepage

\input{content/front-cv} 					% INCLUDE: short CV
\cleardoublepage

% \input{content/front-publications} 			% INCLUDE: publications
% \cleardoublepage

% Remove titles from TOC / LOF / LOT
\makeatletter
\let\@cftmaketoctitle\relax
\let\@cftmakeloftitle\relax
\let\@cftmakelottitle\relax
\makeatother

% Table of contents
\setcounter{tocdepth}{1}		% define depth of toc
\addchap{Table of contents}
\vspace*{-10mm}
\tableofcontents
\cleardoublepage

% List of figures
\addchap{List of figures}
\vspace*{-10mm}
\listoffigures
\cleardoublepage

% List of tables
\addchap{List of tables}
\vspace*{-10mm}
\listoftables
\cleardoublepage

\input{content/front-quote}

% --------------------------
% Body matter
% --------------------------
\pagenumbering{arabic}						% Arabic page numbering
\setcounter{page}{1}							% set page counter
\pagestyle{maincontentstyle} 			% fancy header and footer
%
\part{GENERAL INTRODUCTION}
\input{content/intro-1-dream-research}
\input{content/intro-2-dream-recall}
\input{content/intro-3-dream-content}
\input{content/intro-4-dream-function}
\input{content/intro-5-problematic}
%
\part{METHODS}
\input{content/method-1-eeg}
\input{content/method-2-fMRI}
%
\cleardoublepage
\part{EXPERIMENTAL RESULTS}
\input{content/results-1-arousal}
\input{content/results-2-inertia}
\input{content/results-3-dmn-crea}
\input{content/results-4-survey}
\input{content/results-5-wle}
\input{content/results-6-software}
%
\cleardoublepage
\part{GENERAL DISCUSSION}
\input{content/discussion}
%
\cleardoublepage
%
% --------------------------
% Back matter
% --------------------------
\part{REFERENCES} \cleardoublepage
%
% Notes + translation
\DeclareInstance{enotez-list}{custom}{paragraph}
{
heading   = \chapter{#1},
notes-sep = 0.5\baselineskip,
format    = \normalfont,
number    = \textsuperscript{#1}
}
\setenotez{list-name={Translations}}
\printendnotes[custom] \cleardoublepage
%
% Bibliography
\chapter{Bibliography}
{
\setstretch{1}
\renewcommand{\bibfont}{\normalfont\small}
\setlength{\biblabelsep}{0.2pt}
\setlength{\bibitemsep}{0.5\baselineskip plus 0.5\baselineskip}
\printbibliography[nottype=online, heading=none]
}
%
\cleardoublepage
\input{content/back-colophon}
%
% **************************************************
% End of Document CONTENT
% **************************************************
\cleardoublepage
\end{document}