my-thesis-main.tex

\documentclass[
12pt,
a4paper, 
%oneside, % Uncomment this for digital
twoside,  % Use twoside for printing.
openright, % Uncomment this for printing
]{book}
% ]{scrbook}

% Ragged bottom prevents variable spacing text and floats (done usually to keep last lines in both pages same in book format.)
\raggedbottom

% Fonts
\usepackage[english]{babel}
\usepackage{fontspec}
\usepackage{parskip}

% Bibliography
\usepackage[round]{natbib}
\usepackage[sectionbib]{chapterbib} %References on each chapter
\usepackage{chapterbib}

% Graphics and other packages for text and figures
\usepackage{graphicx}
\graphicspath{ {figures/cropped/} }
\usepackage[dvipsnames]{xcolor}
\usepackage{enumitem, siunitx, mathtools, amsfonts}
\usepackage[font=small, labelfont=bf, singlelinecheck=false, width=.95\textwidth, labelsep=colon]{caption}
\usepackage[rightFloats, CaptionBefore]{styles/fltpage}
\newtagform{brackets}{[}{]}
\usetagform{brackets}
\newcommand{\figuretitle}{}
\DeclareCaptionFormat{myformat}{#1 #2 \textbf{\figuretitle} \\ #3}
\captionsetup{format=myformat}
\captionsetup[FPfigure]{format=myformat}
\newenvironment{Mfigure}[1]
	{\renewcommand{\figuretitle}{#1}
	\begin{figure}[htbp]}
	{\end{figure}}
\newenvironment{MFPfigure}[1]
	{\renewcommand{\figuretitle}{#1}
	\begin{FPfigure}}
	{\end{FPfigure}}
\newenvironment{Mtable}[1]
	{\renewcommand{\figuretitle}{#1}
	\begin{table}[htbp]}
	{\end{table}}	
\usepackage{subcaption}

% Packages to make the thesis beautiful.
\usepackage{standalone} % load only in the main file
\usepackage{fancyhdr} %For header
\usepackage{emptypage} % Removes header from empty pages
\usepackage{longtable} % Multipage Tables
\usepackage{makeidx} %To make index page
\usepackage[totoc]{idxlayout} %To get index into TOC
\usepackage[acronym,toc]{glossaries} %Acronyms, TOC option will add it to TOC
\usepackage[titletoc,title]{appendix} %For Appendix
% \raggedbottom
% \setlength{\parskip}{1em plus .1em minus 1.em}

% Short chapter and section headings
\newcommand{\markedchapter}[2]{\chapter[#2]{#2%
\chaptermark{#1}}
\chaptermark{#1}}
\newcommand{\markedsection}[2]{\section[#2]{#2%
\sectionmark{#1}}
\sectionmark{#1}}

% Need to remove section numbers of appendix from TOC
\usepackage{etoolbox}
\appto\appendix{\addtocontents{toc}{\protect\setcounter{tocdepth}{0}}}
% reinstate the correct level for list of tables and figures
\appto\listoffigures{\addtocontents{lof}{\protect\setcounter{tocdepth}{1}}}
\appto\listoftables{\addtocontents{lot}{\protect\setcounter{tocdepth}{1}}}

%Create new style to add header on each page
\pagestyle{fancy}
\fancyhf{}
\renewcommand{\chaptermark}[1]{\markboth{#1}{}}
% \newcommand{\mymark}{\chaptername\ \thechapter.\ \ \leftmark}
\makeatletter
\fancyhead[RO]{\if@mainmatter \slshape\nouppercase{\leftmark} \else \slshape\nouppercase{\leftmark} \fi}
\fancyhead[LE]{\if@mainmatter \slshape\nouppercase{\rightmark} \else \slshape\nouppercase{\leftmark} \fi}
\makeatother
\cfoot{\fancyplain{}{\thepage}}
\setlength{\headheight}{15pt}

% Footnote related command
\newcommand\pubnote[1]{%
	\begingroup
	\renewcommand\thefootnote{}\footnote{#1}%
	\addtocounter{footnote}{-1}%
	\endgroup
}

% Author, title information
\author{C.M.O.T Dibbler}
\usepackage[
pdfauthor={C.M.O.T Dibbler},
pdftitle ={The chronicles of Blind Io},
pdfsubject={Theology},
pdfkeywords={preach, time, faith, disbelief, bargain}, hidelinks]{hyperref} %References and hyperlinks

% Comment following Hypersetup during printing
\hypersetup{ 
	colorlinks   = true, %Colours links instead of ugly boxes
	urlcolor     = blue, %Colour for external hyperlinks
	linkcolor    = BurntOrange, %Colour of internal links
	citecolor   = teal %Colour of citations
}

% \makeindex %Makes index file.
% \makeglossaries %Make glossary file

\begin{document}

	\frontmatter
	\input{front_matter/cover_page}
	\input{front_matter/declaration}
	\input{front_matter/certificate}
	\input{front_matter/publications}
	\input{front_matter/acknowledgment}
	\input{front_matter/dedication}

	\printglossary[type=\acronymtype,title={Abbreviations}, style=alttree]
	\phantomsection
	\addcontentsline{toc}{chapter}{\listfigurename}
	\listoffigures
	\phantomsection
	\addcontentsline{toc}{chapter}{\listtablename}
	\listoftables
	\tableofcontents

	\chapter{Acknowledgements}
	I would like to thank my supervisors, Professor Someone. This
	research was funded by the Imaginary Research Council.

	\chapter{Abstract}
	A brief summary of the project goes here.
	% A glossary and list of acronyms may go here
	% or may go in the back matter.

	\mainmatter
	%% \input{scrivener-input.tex} %% This line is required to properly autogenerate tex files.

	% acronymns etc
	\input{helpers/acronym} %Include add acronyms
	\printindex

	% The bibliography will go here
	%\bibliographystyle{plainnat}
	%\bibliography{literature}

\end{document}