\documentclass[a4paper,10pt,titlepage]{report}
%\linespread{1.3}
%\usepackage{setspace}
%\onehalfspacing 
 \parskip 10pt           % sets spacing between paragraphs
 %\renewcommand{\baselinestretch}{1.5} 	% Uncomment for 1.5 spacing between lines
 %\parindent 0pt		  % sets leading space for paragraphs


%\usepackage{natbib}
\usepackage{makeidx}
\usepackage{graphicx}
\usepackage{caption}
%\usepackage{subfigure}
\usepackage{rotating}
%\usepackage{lscape}
\usepackage{pdflscape} % Needed for landscaping - in pdf viewer
\usepackage{verbatim}
\usepackage{amsmath, amsthm,amssymb}
\usepackage{mathrsfs}
\usepackage{hyperref}

\usepackage{epstopdf}
\usepackage{float}
\usepackage[compact]{titlesec}
\titlespacing{\chapter}{0pt}{0pt}{0pt}
\titleformat{\chapter}
{\normalfont\LARGE\bfseries}{\thechapter.}{1em}{}

\usepackage[usenames,dvipsnames]{color}
\usepackage{listings} % For code snippets

\definecolor{darkgray}{rgb}{0.95,0.95,0.95}
\definecolor{darkred}{rgb}{0.75,0,0}
\definecolor{darkblue}{rgb}{0,0,0.75}
\definecolor{pink}{rgb}{1,0.5,0.5}
\lstset{language=Java}
\lstset{backgroundcolor=\color{darkgray}}
\lstset{numbers=left, numberstyle=\tiny, stepnumber=1, numbersep=5pt}
\lstset{keywordstyle=\color{darkred}\bfseries}
\lstset{commentstyle=\color{darkblue}}
%\lstset{stringsyle=\color{red}}
\lstset{showstringspaces=false}
\lstset{basicstyle=\small}



\newtheorem{theorem}{Theorem}[section]
\newtheorem{lemma}[theorem]{Lemma}
\theoremstyle{definition}\newtheorem{definition}[theorem]{Definition}
\newtheorem{proposition}[theorem]{Proposition}
\newtheorem{corollary}[theorem]{Corollary}
\newtheorem{example}{Example}
\theoremstyle{remark}\newtheorem*{remark}{Remark}

\newcommand{\Phid}[0]{\dot{\Phi}}
\newcommand{\Phib}[0]{\bar{\Phi}}

\newcommand{\de}[0]{\delta}
\newcommand{\deb}[0]{\bar{\delta}}

\newcommand{\that}[0]{\hat{\theta}}

\newcommand{\vect}[1]{\boldsymbol{#1}} % Draw a vector
\newcommand{\divg}[1]{\nabla \cdot #1} % divergence
\newcommand{\curl}[1]{\nabla \times #1} % curl
\newcommand{\grad}[1]{\nabla #1} %gradient
\newcommand{\pd}[3][ ]{\frac{\partial^{#1} #2}{\partial #3^{#1}}} %partial derivative
\newcommand{\der}[3][ ]{\frac{d^{#1} #2}{d #3^{#1}}} %full derivative
\newcommand{\phasor}[1]{\tilde{#1}} % make a phasor
\newcommand{\laplacian}[1]{\nabla^2 {#1}} % The laplacian operator



% Reference things in GitHub
\newcommand{\gitref}[2]{\href{https://github.com/szmoore/MCTX3420/blob/master/#1/#2}{  \textcolor{blue}{\emph{#2}}}}
% Refer to API commands
\newcommand{\api}[1]{  ``\textcolor{black}{\texttt{/api/#1}}''}

% To make underscores printable without escaping them
\usepackage[T1]{fontenc}
\catcode`\_=12

% Refer to code (can change each one as needed)
\newcommand{\funct}[1]{  \texttt{#1}}
\newcommand{\var}[1]{  \texttt{#1}}
\newcommand{\type}[1]{  \texttt{#1}}
\newcommand{\code}[1]{  \texttt{#1}}


%\usepackage{endfloat}
%\nomarkersintext
\pagestyle{plain}
\topmargin -0.6true in
\textwidth 15true cm
\textheight 9.5true in
\oddsidemargin 0.25true in
\evensidemargin 0.25true in
\headsep 0.4true in

\usepackage{fancyheadings}
\pagestyle{fancy}
\addtolength{\headheight}{2.5pt}
\renewcommand{\chaptermark}[1]{\markboth{\thechapter~~#1}{}}
\renewcommand{\sectionmark}[1]{\markright{\thesection~~#1}{}}
\ifthenelse{\boolean{@twoside}}
{
        \rhead[\bfseries \rightmark]{\bfseries \thepage}
        \lhead[\bfseries \leftmark]{\bfseries \thepage}
        \addtolength{\headwidth}{\marginparsep}
        \addtolength{\headwidth}{\marginparwidth}
}{
        \lhead{\bfseries \leftmark}
        \rhead{\bfseries \thepage}
}
\cfoot{}

%---------------------------------------------------------
%---------------------------------------------------------
\begin{document}

\include{titlepage/Titlepage}               % This is who you are

%\newpage

%\include{acknowledgments/Acknowledgments}   % This is who you thank

%\newpage

%\include{abstract/Abstract}          % This is your thesis abstract

\pagenumbering{roman}
\newpage
%---------------------------------------------------------
% Do the table of Contents and lists of figures and tables
%---------------------------------------------------------
\linespread{0.8}
\tableofcontents
\markboth{}{}
\linespread{1.0}
\newpage

\pagenumbering{arabic}
%---------------------------------------------------------
%---------------------------------------------------------
%Include the chapters!

\include{chapters/Introduction}

\include{chapters/Design}           % This is chapter 1

%\include{chapters/Approach}          % This is chapter 2

\include{chapters/Results}
%\newpage
%---------------------------------------------------------
\renewcommand{\bibname}{References}
\bibliography{references/refs}
\bibliographystyle{ieeetr}  
\addcontentsline{toc}{part}{References}
%---------------------------------------------------------

% Appendices
\appendix
\include{appendices/glossary}
\include{appendices/figures}
%\include{proposal/proposal.tex}
%\renewcommand\chaptername{Appendix}
%\chapter{Appendix} 
%\include{appendices/electron_optics}
%\include{appendices/electron_gun_circuit}
%\include{appendices/tcs_noise}
%\include{appendices/data_aquisition}


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

\end{document}

