%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Thesis Configuration File
%
% The main lines to change in this file are in the DOCUMENT VARIABLES
% section, the rest of the file is for advanced configuration.
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%----------------------------------------------------------------------------------------
%	DOCUMENT VARIABLES
%	Fill in the lines below to enter your information into the thesis template
%	Each of the commands can be cited anywhere in the thesis
%----------------------------------------------------------------------------------------

% Remove drafting to get rid of the '[ Date - classicthesis version 4.0 ]' text at the bottom of every page
\PassOptionsToPackage{eulerchapternumbers,listings,pdfspacing, subfig,dottedtoc,floatperchapter}{classicthesis}
% Available options: drafting parts nochapters linedheaders eulerchapternumbers beramono eulermath pdfspacing minionprospacing tocaligned dottedtoc manychapters listings floatperchapter subfig
% Adding 'dottedtoc' will make page numbers in the table of contents flushed right with dots leading to them
%eulermath was nice but had missing plus sign (gl)

\newcommand{\myTitle}{Managing understory light to maintain \\ the coexistence of forest tree species \\ with different shade tolerances\xspace}
\newcommand{\mySubtitle}{Essai pr\'esent\'e en vue de l'obtention du grade \\ de docteur en sciences agronomiques et ing\'enierie biologique
\xspace}
\newcommand{\myDegree}{Ing.\xspace}
\newcommand{\myName}{Gauthier LIGOT\xspace}
\newcommand{\myProf}{Philippe LEJEUNE\xspace}
%\newcommand{\myOtherProf}{Hugues CLAESSENS\xspace}
\newcommand{\myFaculty}{Gembloux Agro-Bio Tech\xspace}
\newcommand{\myDepartment}{Gestion des Ressources foresti\`eres et des Milieux naturels\xspace}
\newcommand{\myUni}{Universit\'e de Li\`ege\xspace}
\newcommand{\myLocation}{Gembloux\xspace}
\newcommand{\myTime}{2014\xspace}
\newcommand{\myVersion}{version 1.0\xspace}

%----------------------------------------------------------------------------------------
%	USEFUL COMMANDS
%----------------------------------------------------------------------------------------
\newcounter{dummy} % Necessary for correct hyperlinks (to index, bib, etc.)
\providecommand{\mLyX}{L\kern-.1667em\lower.25em\hbox{Y}\kern-.125emX\@}

%----------------------------------------------------------------------------------------
%	PACKAGES
%----------------------------------------------------------------------------------------
\usepackage{geometry} %to manage margin in some sections - gl
\usepackage{pdflscape} %to put table in page with landscape orientation - gl
\usepackage{lipsum} % Used for inserting dummy 'Lorem ipsum' text into the template

%------------------------------------------------
 
\PassOptionsToPackage{utf8}{inputenc}
\usepackage{inputenc}
 
 %------------------------------------------------

\PassOptionsToPackage{american}{babel}  % Change this to your language(s)
% Spanish languages need extra options in order to work with this template
%\PassOptionsToPackage{spanish,es-lcroman}{babel}
\usepackage{babel}

%------------------------------------------------			

\PassOptionsToPackage{round}{natbib} 
 \usepackage{natbib}
 
 %------------------------------------------------

\PassOptionsToPackage{fleqn}{amsmath} % Math environments and more by the AMS 
 \usepackage{amsmath}
 
 %------------------------------------------------
%\renewcommand*\familydefault{\ttdefault} %% Only if the base font of the document is to be typewriter style
\PassOptionsToPackage{T1}{fontenc} % T2A for cyrillics
\usepackage{fontenc}

%------------------------------------------------

\usepackage{xspace} % To get the spacing after macros right

%------------------------------------------------

\usepackage{mparhack} % To get marginpar right

%------------------------------------------------

\usepackage{fixltx2e} % Fixes some LaTeX stuff 

%------------------------------------------------

\PassOptionsToPackage{smaller}{acronym} % Include printonlyused in the first bracket to only show acronyms used in the text
\usepackage{acronym} % nice macros for handling all acronyms in the thesis

%------------------------------------------------

%\renewcommand*{\acsfont}[1]{\textssc{#1}} % For MinionPro
\renewcommand{\bflabel}[1]{{#1}\hfill} % Fix the list of acronyms

%------------------------------------------------

\PassOptionsToPackage{pdftex}{graphicx}
\usepackage{graphicx} 

%----------------------------------------------------------------------------------------
%	Gauthier's modifications
% 	change in the order of package loading seems to cause compilation errors
%----------------------------------------------------------------------------------------

\usepackage{siunitx} % SI units
\usepackage{varwidth} 
%\usepackage{enumitem}  %does not work ... too bad
%\usepackage[figure,table]{totalcount} %does not work ... too bad
\usepackage{lastpage}


%----------------------------------------------------------------------------------------
%	FLOATS: TABLES, FIGURES AND CAPTIONS SETUP
%----------------------------------------------------------------------------------------

\usepackage{tabularx} % Better tables
\setlength{\extrarowheight}{3pt} % Increase table row height
\newcommand{\tableheadline}[1]{\multicolumn{1}{c}{\spacedlowsmallcaps{#1}}}
\newcommand{\myfloatalign}{\centering} % To be used with each float for alignment
\usepackage{caption}
\captionsetup{format=hang,font=small}
\usepackage{subfig}  

%----------------------------------------------------------------------------------------
%	CODE LISTINGS SETUP
%----------------------------------------------------------------------------------------

\usepackage{listings} 
%\lstset{emph={trueIndex,root},emphstyle=\color{BlueViolet}}%\underbar} % for special keywords
\lstset{language=[LaTeX]Tex, % Specify the language for listings here
keywordstyle=\color{RoyalBlue}, % Add \bfseries for bold
basicstyle=\small\ttfamily, % Makes listings a smaller font size and a different font
%identifierstyle=\color{NavyBlue}, % Color of text inside brackets
commentstyle=\color{Green}\ttfamily, % Color of comments
stringstyle=\rmfamily, % Font type to use for strings
numbers=left, % Change left to none to remove line numbers
numberstyle=\scriptsize, % Font size of the line numbers
stepnumber=5, % Increment of line numbers
numbersep=8pt, % Distance of line numbers from code listing
showstringspaces=false, % Sets whether spaces in strings should appear underlined
breaklines=true, % Force the code to stay in the confines of the listing box
%frameround=ftff, % Uncomment for rounded frame
frame=single, % Frame border - none/leftline/topline/bottomline/lines/single/shadowbox/L
belowcaptionskip=.75\baselineskip % Space after the "Listing #: Desciption" text and the listing box
}

%----------------------------------------------------------------------------------------
%	HYPERREFERENCES
%----------------------------------------------------------------------------------------

\PassOptionsToPackage{pdftex,hyperfootnotes=false,pdfpagelabels}{hyperref}
\usepackage{hyperref}  % backref linktocpage pagebackref
\pdfcompresslevel=9
\pdfadjustspacing=1

\hypersetup{
% Uncomment the line below to remove all links (to references, figures, tables, etc)
%draft, 
colorlinks=true, linktocpage=true, pdfstartpage=3, pdfstartview=FitV,
% Uncomment the line below if you want to have black links (e.g. for printing black and white)
%colorlinks=false, linktocpage=false, pdfborder={0 0 0}, pdfstartpage=3, pdfstartview=FitV, 
breaklinks=true, pdfpagemode=UseNone, pageanchor=true, pdfpagemode=UseOutlines,
plainpages=false, bookmarksnumbered, bookmarksopen=true, bookmarksopenlevel=1,
hypertexnames=true, pdfhighlight=/O, urlcolor=webbrown, linkcolor=RoyalBlue, citecolor=webgreen,
%hypertexnames=true, pdfhighlight=/O, urlcolor=Gray, linkcolor=Gray, citecolor=Gray,
%------------------------------------------------
% PDF file meta-information
pdftitle={\myTitle},
pdfauthor={\textcopyright\ \myName, \myUni, \myFaculty},
pdfsubject={},
pdfkeywords={},
pdfcreator={pdfLaTeX},
pdfproducer={LaTeX with hyperref and classicthesis}
%------------------------------------------------
}   

%----------------------------------------------------------------------------------------
%	BACKREFERENCES
%----------------------------------------------------------------------------------------

\usepackage{ifthen} % Allows the user of the \ifthenelse command
\newboolean{enable-backrefs} % Variable to enable backrefs in the bibliography
\setboolean{enable-backrefs}{false} % Variable value: true or false

\newcommand{\backrefnotcitedstring}{\relax} % (Not cited.)
\newcommand{\backrefcitedsinglestring}[1]{(Cited on page~#1.)}
\newcommand{\backrefcitedmultistring}[1]{(Cited on pages~#1.)}
\ifthenelse{\boolean{enable-backrefs}} % If backrefs were enabled
{
\PassOptionsToPackage{hyperpageref}{backref}
\usepackage{backref} % to be loaded after hyperref package 
\renewcommand{\backreftwosep}{ and~} % separate 2 pages
\renewcommand{\backreflastsep}{, and~} % separate last of longer list
\renewcommand*{\backref}[1]{}  % disable standard
\renewcommand*{\backrefalt}[4]{% detailed backref
\ifcase #1 
\backrefnotcitedstring
\or
\backrefcitedsinglestring{#2}
\else
\backrefcitedmultistring{#2}
\fi}
}{\relax} 

%----------------------------------------------------------------------------------------
%	AUTOREFERENCES SETUP
%	Redefines how references in text are prefaced for different 
%	languages (e.g. "Section 1.2" or "section 1.2")
%----------------------------------------------------------------------------------------

\makeatletter
\@ifpackageloaded{babel}
{
\addto\extrasamerican{
\renewcommand*{\figureautorefname}{Figure}
\renewcommand*{\tableautorefname}{Table}
\renewcommand*{\partautorefname}{Part}
\renewcommand*{\chapterautorefname}{Chapter}
\renewcommand*{\sectionautorefname}{Section}
\renewcommand*{\subsectionautorefname}{Section}
\renewcommand*{\subsubsectionautorefname}{Section}
}
\addto\extrasngerman{
\renewcommand*{\paragraphautorefname}{Absatz}
\renewcommand*{\subparagraphautorefname}{Unterabsatz}
\renewcommand*{\footnoteautorefname}{Fu\"snote}
\renewcommand*{\FancyVerbLineautorefname}{Zeile}
\renewcommand*{\theoremautorefname}{Theorem}
\renewcommand*{\appendixautorefname}{Anhang}
\renewcommand*{\equationautorefname}{Gleichung}
\renewcommand*{\itemautorefname}{Punkt}
}
\providecommand{\subfigureautorefname}{\figureautorefname} % Fix to getting autorefs for subfigures right
}{\relax}
\makeatother

%----------------------------------------------------------------------------------------

\usepackage{classicthesis} 

%----------------------------------------------------------------------------------------
%	CHANGING TEXT AREA 
%----------------------------------------------------------------------------------------

%\linespread{1.05} % a bit more for Palatino
%\areaset[current]{312pt}{761pt} % 686 (factor 2.2) + 33 head + 42 head \the\footskip
%\setlength{\marginparwidth}{7em}%
%\setlength{\marginparsep}{2em}%

%----------------------------------------------------------------------------------------
%	USING DIFFERENT FONTS
%----------------------------------------------------------------------------------------

%I chose font to avoid old style numbers contrary to what the author of ClassicThessis suggested


%\usepackage{kpfonts}
%\usepackage[oldstylenums]{kpfonts} % oldstyle notextcomp
%http://tex.stackexchange.com/questions/114331/lining-figures-in-tables-and-math-old-style-figures-in-text
\usepackage{libertine}
\usepackage[cmintegrals, cmbraces, libertine]{newtxmath} %libertine
%\usepackage[version=3]{mhchem}
%\mhchemoptions{textfontcommand=\libertineLF}
%\makeatletter
%\AtBeginDocument{\def\libertine@figurealign{}\libertineOsF}
%\newcommand\libertineTabular{\def\libertine@figurealign{T}\libertineLF}
%\makeatother

%\usepackage{hfoldsty} % Computer Modern with osf
%\usepackage[light,condensed,math]{iwona}
%\renewcommand{\sfdefault}{iwona}
%\usepackage{lmodern} % <-- no osf support :-(
%\usepackage[urw-garamond]{mathdesign} <-- no osf support :-(


%----------------------------------------------------------------------------------------
%	change chapter format
%----------------------------------------------------------------------------------------
%\renewcommand{\thechapter}{\Roman{chapter}}
%\titleformat{\chapter}[display]
%{\bfseries\Large}
%{\filleft\MakeUppercase{\chaptertitlename} \Huge\thechapter}
%{4ex}
{%\titlerule
%\vspace{2ex}%
%\filleft}
%[\vspace{2ex}%
%\titlerule
%\vspace{10ex}]

%\titleformat{\chapter}[display]
%{\relax}{\raggedleft\color{halfgray}\chapterNumber\thechapter}{0pt}%
%        {\vspace{2ex}\raggedleft\spacedallcaps}[\normalsize\vspace*{.8\baselineskip}\titlerule
%        \vspace{10ex}]% 
       
%figure location
\graphicspath{{gfx/}}

%----------------------------------------------------------------------------------------
%	Gauthier's modifications
%----------------------------------------------------------------------------------------
\usepackage{afterpage}
\DeclareSIUnit\year{year}
