LaTeX

\documentclass[11pt, twoside, openright, final]{thesis}
% \documentclass[11pt, twoside, openright, draft]{thesis}

%% Modification to the thesis style
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\geometry{
  %% Space for the binding can be taken into account with bindingoffset
  % bindingoffset=0.5cm,
  %% Text width should be adjust such that there are 60 to 90 characters per
  %% line.
  textwidth=13cm,
  vmargin={3cm,3cm},
}

\thesisset{
  %% Adjust the logo
}

%% Adjust the primary colour
% \definecolor{primary}{cmyk}{1,0.57,0,0.40}

\usepackage{setspace}
\onehalfspacing

%% Language
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\usepackage[UKenglish]{babel} % Set up the language
\usepackage{csquotes}
\usepackage{siunitx}          % Provides \SI{1}{\metre}, also \ang{90}

\sisetup{
  range-units=single,
  list-units=single,
}

%% Formatting
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\usepackage{enumitem}  % Allows for easy modifications to lists

%% Graphics & Figure
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\usepackage{graphicx}   % Allow graphics to be included
\usepackage{subcaption} % Subfigures inside a figure

% Keep all pictures in the './images/' sub-directory
\graphicspath{{./images/}}

\usepackage{tikz}       % Powerful drawing language
\usepackage{pgfplots}   % Plotting with LaTeX
\pgfplotsset{compat=1.14}

%% Math Packages
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\usepackage{amsmath}   % The core math package
\usepackage{amssymb}   % Defines additional math fonts
\usepackage{mathtools} % Various extra maths functions
% \usepackage{autonum}   % Only number referenced equations (must be loaded after cleverref)

%% Define \withnumber which forces the line to have number
\newcommand{\withnumber}{\refstepcounter{equation}\tag{\theequation}}

%% Allows page breaks in math (1 = avoid if possible, 4 = whenever)
%% Page breaks can be avoided at particular places by using \\*
\allowdisplaybreaks[2]

%% Tables
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\usepackage{tabularx}  % Improved tabular environment
\usepackage{longtable} % Multipage tables
\usepackage{array}     % New column types, including >x<
\usepackage{booktabs}  % Provides nicer horizontal lines
\usepackage{multirow}  % Allows cells to span multiple rows
%\usepackage{longtable} % Allows for tables to span multiple pages

%% Define the maths version of clr columns
\newcolumntype{C}{>{\(}c<{\)}}
\newcolumntype{L}{>{\(}l<{\)}}
\newcolumntype{R}{>{\(}r<{\)}}

%% Inline Code
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\usepackage{minted}

%% Other Packages
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\usepackage[version=4]{mhchem}     % Chemistry formatting
\usepackage{pageslts}              % Reference the last page
\usepackage[perpage]{footmisc}     % Customize footnotes

%% The following packages must be loaded in a specific order
\usepackage{hyperref}    % Automatically inserts hyperlinks
\usepackage{cleveref}    % Use `\cref` to reference anything
\usepackage{autonum}     % Only enumerate referenced equations

%% Bibliography
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%% hyperref should be loaded first
\usepackage[
    autocite=inline,
    backend=biber,
    biblabel=brackets,
    doi=true,
    eprint=true,
    maxbibnames=2,
    maxcitenames=4,
    style=phys,
]{biblatex}

\addbibresource{references.bib}

\defbibheading{bibliography}[\bibname]
{%
  \chapter{\bibname}
}

\renewcommand\bibfont{\small}

%% Other modifications
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%% MWE provides a lot of useful command for minimal working examples
\usepackage{mwe}

%% Don't display subsections in the Table of Contents
% \setcounter{tocdepth}{1}

%% Documentation-specific
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% The following section is used for the documentatino and is not otherwise
%% needed.  It should be deleted if you do not use it.

%% LaTeX Documentations
\usepackage{doc}
\usepackage{makeidx}

%% The doc package overwrites \maketitle, so we restore it to use the thesis
%% class' title.
\makeatletter
\renewcommand*\maketitle{\thesis@maketitle}
\makeatother

%% The \marg, \oarg and \parg functions are defined by the `ltxdoc` class, but
%% not the `doc` package, so they have to be defined here.
\providecommand\marg[1]{%
  {\ttfamily\char`\{}\meta{#1}{\ttfamily\char`\}}}
\providecommand\oarg[1]{%
  {\ttfamily[}\meta{#1}{\ttfamily]}}
\providecommand\parg[1]{%
  {\ttfamily(}\meta{#1}{\ttfamily)}}

%% Load the pgfmanual macros
\IfFileExists{pgfmanual-en-macros}{
  \let\attribute\relax
  \input{pgfmanual-en-macros}
}{
  \PackageError{thesis-documentation}{
    This document requires the file pgfmanual-en-macros.tex (distributed with
    pgf) to compile.  Please place a copy (or link) of that file in the current
    directory
  }{}
}

\makeindex

\pgfkeys{
  /pdflinks/search key prefixes in={/thesis/}
  /pdflinks/internal link prefix=/thesis,
  %
  /pdflinks/warnings=false,
  % for debugging:
  /pdflinks/show labels=false,
}

%% Center codeexample
\makeatletter
\let\codeexample@orig=\codeexample
\let\endcodeexample@orig=\endcodeexample
\def\codeexample{
  \begin{center}
    \codeexample@orig
}
\def\endcodeexample{
    \endcodeexample@orig
  \end{center}
}

%% Introduce a new font key
\newenvironment{fontkey}[1]{
  \begin{pgfmanualentry}
    \def\extrakeytext{font, }
    \extractkey#1\@nil%
    \pgfmanualbody
}{%
  \end{pgfmanualentry}
}
\newenvironment{fontkeylist}[2][]{%
  \begin{pgfmanualentry}
    \def\extrakeytext{font, }%
  \foreach \xx in {#2} {%
    \expandafter\insertpathifneeded\expandafter{\xx}{#1}%
    \expandafter\extractkey\mykey\@nil%
  }%
  \pgfmanualbody
}{%
  \end{pgfmanualentry}
}%


%% Adjust the Index to be a chapter
\def\index@prologue{\chapter{Index}}
\makeatother

\providecommand*\LuaLaTeX{Lua\LaTeX}

%% Document Information
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\logo{\includegraphics[width=0.2\paperwidth]{example-image-a}}
\university{The University of Templates}
\department{School of Theses}
\degreetitle{Doctor of Philosophy}

%%
\title{\texorpdfstring{%
    Thesis Template%
  }{%
    Thesis Template%
  }}
\subtitle{An example in practice}

\author{Joshua}{Ellis}
\orcid{0000-0003-2556-1536}
\supervisor{John}{Smith}
\supervisor{Jane}{Doe}

\subject{LaTeX thesis class}
\keywords{LaTeX class; template}

%% Include Only
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

% \includeonly{
%   chapters/documentation
% }

%% Document Start
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\begin{document}
\pagenumbering{Alph}

\maketitle

\cleardoublepage
\pagenumbering{roman}

%% Abstract
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\clearpage
\section*{Abstract}

\lipsum[1]

%% Acknowledgements
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\section*{Acknowledgements}

\lipsum[3]

%% Statement of Contribution
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\section*{Statement of Contribution}

\lipsum[10]

%% Table of Contents
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\cleardoublepage

\tableofcontents

%% Content
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\cleardoublepage
\pagenumbering{arabic}

\include{chapters/documentation}
\include{chapters/lorem}
\include{chapters/ipsum}

\appendix
\include{chapters/appendix}

%% Bibliography
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\cleardoublepage
\pagestyle{plain}
\twocolumn
\printbibliography

%% Index (for the documentation keys)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\cleardoublepage
\printindex


\end{document}