book preambles.tex

\documentclass[a4paper, 11pt]{book}

%\usepackage[center]{titlesec}

\usepackage{amsfonts, amssymb, amsmath, amsthm, amsxtra}

\usepackage{foekfont}

\usepackage{MnSymbol}

\usepackage{pdfrender, xcolor}
%\pdfrender{StrokeColor=black,LineWidth=.4pt,TextRenderingMode=2}

\usepackage{minitoc}
\setcounter{tocdepth}{5}
\setcounter{minitocdepth}{5}
\setcounter{secnumdepth}{5}

\usepackage{graphicx}

\usepackage[english]{babel}
\usepackage[utf8]{inputenc}
%\usepackage{mathpazo}
%\usepackage{euler}
\usepackage{eucal}
\usepackage{bbm}
\usepackage{bm}
\usepackage{csquotes}
\usepackage[nottoc]{tocbibind}
\usepackage{appendix}
\usepackage{float}
\usepackage[T1]{fontenc}
\usepackage[
    left = \flqq{},% 
    right = \frqq{},% 
    leftsub = \flq{},% 
    rightsub = \frq{} %
]{dirtytalk}

\usepackage{imakeidx}
\makeindex

%\usepackage[dvipsnames]{xcolor}
\usepackage{hyperref}
    \hypersetup{
        colorlinks=true,
        linkcolor=teal,
        filecolor=pink,      
        urlcolor=teal,
        citecolor=magenta
    }
\usepackage{comment}

% You would set the PDF title, author, etc. with package options or
% \hypersetup.

\usepackage[backend=biber, style=alphabetic, sorting=nty]{biblatex}
    \addbibresource{bibliography.bib}

\raggedbottom

\usepackage{mathrsfs}
\usepackage{mathtools} 
\mathtoolsset{showonlyrefs} 
%\usepackage{amssymb}
%\usepackage{amsthm}
\renewcommand\qedsymbol{$\blacksquare$}
\usepackage{tikz-cd}
\tikzcdset{scale cd/.style={every label/.append style={scale=#1},
    cells={nodes={scale=#1}}}}
\usepackage{tikz}
\usepackage{setspace}
\usepackage[version=3]{mhchem}
\parskip=0.1in
\usepackage[margin=25mm]{geometry}

\usepackage{listings, lstautogobble}
\lstset{
	language=matlab,
	basicstyle=\scriptsize\ttfamily,
	commentstyle=\ttfamily\itshape\color{gray},
	stringstyle=\ttfamily,
	showstringspaces=false,
	breaklines=true,
	frameround=ffff,
	frame=single,
	rulecolor=\color{black},
	autogobble=true
}

\usepackage{todonotes,tocloft,xpatch,hyperref}

% This is based on classicthesis chapter definition
\let\oldsec=\section
\renewcommand*{\section}{\secdef{\Sec}{\SecS}}
\newcommand\SecS[1]{\oldsec*{#1}}%
\newcommand\Sec[2][]{\oldsec[\texorpdfstring{#1}{#1}]{#2}}%

\newcounter{istodo}[section]

% http://tex.stackexchange.com/a/61267/11984
\makeatletter
%\xapptocmd{\Sec}{\addtocontents{tdo}{\protect\todoline{\thesection}{#1}{}}}{}{}
\newcommand{\todoline}[1]{\@ifnextchar\Endoftdo{}{\@todoline{#1}}}
\newcommand{\@todoline}[3]{%
	\@ifnextchar\todoline{}
	{\contentsline{section}{\numberline{#1}#2}{#3}{}{}}%
}
\let\l@todo\l@subsection
\newcommand{\Endoftdo}{}

\AtEndDocument{\addtocontents{tdo}{\string\Endoftdo}}
\makeatother

\usepackage{lipsum}

%   Reduce the margin of the summary:
\def\changemargin#1#2{\list{}{\rightmargin#2\leftmargin#1}\item[]}
\let\endchangemargin=\endlist 

%   Generate the environment for the abstract:
\newcommand\summaryname{Abstract}
\newenvironment{abstract}%
    {\small\begin{center}%
    \bfseries{\summaryname} \end{center}}

\newtheorem{theorem}{Theorem}[section]
    \numberwithin{theorem}{subsection}
\newtheorem{proposition}{Proposition}[section]
    \numberwithin{proposition}{subsection}
\newtheorem{lemma}{Lemma}[section]
    \numberwithin{lemma}{subsection}
\newtheorem{claim}{Claim}[section]
    \numberwithin{claim}{subsection}

\theoremstyle{definition}
    \newtheorem{definition}{Definition}[section]
        \numberwithin{definition}{subsection}

\theoremstyle{remark}
    \newtheorem{remark}{Remark}[section]
        \numberwithin{remark}{subsection}
    \newtheorem{example}{Example}[section]
        \numberwithin{example}{subsection}    
    \newtheorem{convention}{Convention}[section]
        \numberwithin{convention}{subsection}
    \newtheorem{corollary}{Corollary}[section]
        \numberwithin{corollary}{subsection}