% arara: makechapters: {items: [titlepage, frontmatter, toc, introduction, preliminaries, design_space, basic_constraints, problem, local_search, mining, towards_general, applications, conclusion, bibliography, summary, samenvatting, cv, acknowledgements, glossaries]}
\documentclass{book}
\usepackage{afterpage}
%\usepackage[textsize=tiny,prependcaption,backgroundcolor=red!20]{todonotes}
\usepackage[disable,textsize=tiny,prependcap
tion,backgroundcolor=red!20]{todonotes}
\setlength{\marginparwidth}{2.2cm}
\reversemarginpar
%\usepackage{showframe} % Show margins
%\usepackage[]{glossaries}
\usepackage[b5paper,margin=2cm,inner=2.5cm,top=3cm,bottom=3cm,footskip=1.25cm]{geometry}
\usepackage[acronym,toc,nonumberlist,ucmark=true,symbols,nogroupskip,automake]{glossaries-extra}
\setglossarystyle{altlist}
\usepackage[nottoc,numbib]{tocbibind}
\usepackage{amsfonts}
\usepackage{bm}
\usepackage{enumitem}
\usepackage[labelfont=bf,textfont=small]{caption}
\usepackage[labelfont=bf,textfont=small]{subcaption}
\usepackage[percent]{overpic}
\usepackage{booktabs}
\usepackage{algpseudocode,algorithm,algorithmicx}
\usepackage{mathtools}
\usepackage{siunitx}
\usepackage{amssymb}
\usepackage{amsthm}
\usepackage{centernot}
\usepackage{import}
\usepackage[subpreambles=true]{standalone}% requires -shell-escape
\usepackage{tikz}
\usetikzlibrary{positioning,shapes.misc}
% \usetikzlibrary{external}
% \tikzexternalize[prefix=tikz/]
\usepackage{fancyhdr}
\setlength{\headheight}{15.2pt}
\pagestyle{fancy}
\renewcommand{\chaptermark}[1]{ \markboth{#1}{} }
\renewcommand{\sectionmark}[1]{ \markright{#1} }
\lhead[\textbf{\nouppercase{\rightmark}}]{}
\rhead[]{\textbf{\nouppercase{\leftmark}}}
\usepackage{setspace}
%\usepackage{hyperref}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Base PhD Thesis for PhD's at LIACS %
% Based on the thesis by Koen van der Blom %
% Cleaned up and made generic by Sander van Rijn %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\DeclareMathOperator{\sgn}{sgn}
%\usepackage[style=numeric]{biblatex}
%\addbibresource{thesis.bib}
%\DeclareFieldFormat*{author}{\mkbibbold{#1}}
%\renewcommand*{\mkbibnamegiven}[1]{%
% \ifitemannotation{highlight}
% {\textbf{#1}}
% {#1}}
%
%\renewcommand*{\mkbibnamefamily}[1]{%
% \ifitemannotation{highlight}
% {\textbf{#1}}
% {#1}}
% Horizontal alignment for fixed width table columns
\newcolumntype{L}[1]{>{\raggedright\arraybackslash\hspace{0pt}}m{#1}}
\newcolumntype{C}[1]{>{\centering\arraybackslash\hspace{0pt}}m{#1}}
\newcolumntype{R}[1]{>{\raggedleft\arraybackslash\hspace{0pt}}m{#1}}
\usepackage{bibentry}
%\nobibliography*
\theoremstyle{definition}
\newtheorem{definition}{Definition}[chapter]
\newtheorem{constraint}{Constraint}
\renewcommand{\theconstraint}{C\arabic{constraint}}
\makeglossaries
\input{glossary}
\input{acronyms}
\input{symbols}
\renewcommand*{\glossarypreamble}{%
\label{\currentglossary}%
}
% Define acknowledgement box and box title style
\tikzset{northround/.style={append after command={
\pgfextra
\draw[sharp corners, fill=#1, draw=none, very thick]%
(\tikzlastnode.west)%
[rounded corners=5pt] |- (\tikzlastnode.north)%
[rounded corners=5pt] -| (\tikzlastnode.east)%
[rounded corners=0pt] |- (\tikzlastnode.south)%
[rounded corners=0pt] -| (\tikzlastnode.west);
\endpgfextra}}}
\definecolor{myturq}{RGB}{79,205,207}
\tikzstyle{mybox} = [draw=myturq, fill=blue!0, very thick,
inner sep=10pt, inner ysep=10pt]
\tikzstyle{fancytitle} =[northround=myturq, text width=.94\textwidth, inner xsep=10.42pt]
%\onehalfspacing
\begin{document}
%\listoftodos[Notes]
% Frontpage, contents
\frontmatter
\include{titlepage}
\onehalfspacing
\include{frontmatter}
\include{toc}
% Chapters
%\mainmatter
\include{introduction}
\include{preliminaries}
\include{content_0}
\include{content_1}
\include{content_2}
\include{content_3}
\include{content_4}
\include{content_5}
\include{content_6}
\include{conclusion}\clearpage\newpage\newpage
% Appendix, bibliography, summary, samenvatting, CV, acknowledgements
\appendix
%\backmatter
\include{bibliography}
%\include{summary}
\include{samenvatting}
\include{cv}
%\include{acknowledgements}
% Glossaries
\begin{singlespace}
\include{glossaries}
\end{singlespace}
\end{document}
