\documentclass[12pt,a4paper,oneside]{book}
% Use 'twoside' for double-sided printing

% Essential packages
\usepackage[utf8]{inputenc}
\usepackage[T1]{fontenc}
\usepackage{lmodern}
\usepackage[english]{babel}
\usepackage{csquotes}

% Page layout
\usepackage[
    top=2.5cm,
    bottom=2.5cm,
    left=3.5cm,
    right=2.5cm,
    headsep=10mm,
    footskip=12mm
]{geometry}

% Graphics and figures
\usepackage{graphicx}
\usepackage{subcaption}
\usepackage{float}
\usepackage{rotating}

% Tables
\usepackage{booktabs}
\usepackage{multirow}
\usepackage{longtable}
\usepackage{array}
\newcolumntype{L}[1]{>{\raggedright\arraybackslash}p{#1}}
\newcolumntype{C}[1]{>{\centering\arraybackslash}p{#1}}
\newcolumntype{R}[1]{>{\raggedleft\arraybackslash}p{#1}}

% Mathematics
\usepackage{amsmath,amssymb,amsthm}
\usepackage{mathtools}

% Bibliography
\usepackage[
    backend=biber,
    style=authoryear,
    sorting=nyt,
    natbib=true,
    maxbibnames=99,
    maxcitenames=2,
    uniquelist=false,
    doi=true,
    isbn=false,
    url=false
]{biblatex}
\addbibresource{references.bib}

% Cross-references
\usepackage{hyperref}
\hypersetup{
    colorlinks=true,
    linkcolor=blue,
    citecolor=blue,
    urlcolor=blue,
    pdftitle={Your Thesis Title},
    pdfauthor={Your Name},
    pdfkeywords={keyword1, keyword2, keyword3}
}
\usepackage{cleveref}

% Headers and footers
\usepackage{fancyhdr}
\pagestyle{fancy}
\fancyhf{}
\fancyhead[R]{\nouppercase{\leftmark}}
\fancyfoot[C]{\thepage}
\renewcommand{\headrulewidth}{0.4pt}

% Chapter style
\usepackage{titlesec}
\titleformat{\chapter}[display]
{\normalfont\huge\bfseries}{\chaptertitlename\ \thechapter}{20pt}{\Huge}
\titlespacing*{\chapter}{0pt}{0pt}{40pt}

% Line spacing
\usepackage{setspace}
\onehalfspacing % or \doublespacing for double

% Custom commands
\newcommand{\university}{Your University Name}
\newcommand{\degree}{Doctor of Philosophy}
\newcommand{\department}{Department of Your Field}
\newcommand{\supervisor}{Prof. Supervisor Name}

% Theorem environments
\theoremstyle{definition}
\newtheorem{definition}{Definition}[chapter]
\newtheorem{theorem}{Theorem}[chapter]
\newtheorem{lemma}[theorem]{Lemma}
\newtheorem{proposition}[theorem]{Proposition}
\newtheorem{corollary}[theorem]{Corollary}

\theoremstyle{remark}
\newtheorem{remark}{Remark}[chapter]
\newtheorem{example}{Example}[chapter]

% Document begins
\begin{document}

% Front matter
\frontmatter

% Title page
\input{frontmatter/titlepage}

% Abstract
\input{frontmatter/abstract}

% Dedication (optional)
\input{frontmatter/dedication}

% Acknowledgments
\input{frontmatter/acknowledgments}

% Table of contents
\tableofcontents
\clearpage

% List of figures
\listoffigures
\clearpage

% List of tables
\listoftables
\clearpage

% List of abbreviations (optional)
\input{frontmatter/abbreviations}

% Main matter
\mainmatter

% Chapters
\input{chapters/introduction}
\input{chapters/literature-review}
\input{chapters/methodology}
\input{chapters/results}
\input{chapters/discussion}
\input{chapters/conclusion}

% Back matter
\backmatter

% Bibliography
\printbibliography[heading=bibintoc,title={References}]

% Appendices
\appendix
\input{appendices/appendix-a}
\input{appendices/appendix-b}

\end{document}

\begin{titlepage}
\centering
\vspace*{2cm}

% University logo (optional)
\includegraphics[width=0.3\textwidth]{university-logo.png}\\[1cm]

% University name
{\scshape\LARGE \university \par}
\vspace{0.5cm}
{\scshape\Large \department \par}
\vspace{2cm}

% Thesis title
{\huge\bfseries Your Thesis Title: \par}
{\huge\bfseries A Comprehensive Study of Something Important \par}
\vspace{2cm}

% Author name
{\Large\itshape Your Full Name \par}
\vfill

% Thesis type
A thesis submitted in fulfillment of the requirements\par
for the degree of \degree \par
\vspace{1cm}

% Supervisor
Supervised by:\par
\supervisor \par
\vspace{1cm}

% Date
{\large \today\par}

\end{titlepage}

\chapter*{Abstract}
\addcontentsline{toc}{chapter}{Abstract}

This thesis investigates [your research topic]. The primary objective is to 
[state your main goal]. 

The research employs [methodology] to examine [what you're examining]. 
Data was collected from [sources] and analyzed using [methods].

Key findings include:
\begin{itemize}
\item First major finding with brief explanation
\item Second significant result and its importance
\item Third contribution to the field
\end{itemize}

The results demonstrate that [main conclusion]. This work contributes to 
[field] by [specific contribution]. Future research directions include 
[suggestions].

\vspace{1cm}
\noindent\textbf{Keywords:} keyword1, keyword2, keyword3, keyword4, keyword5

\chapter{Chapter Title}
\label{chap:chapter-label}

% Chapter abstract (optional)
\begin{abstract}
Brief summary of what this chapter covers, main findings, and how it 
relates to the overall thesis narrative.
\end{abstract}

\section{Introduction}
\label{sec:chapter-intro}

Introduce the specific focus of this chapter and its objectives. Explain 
how it builds on previous chapters and contributes to your thesis.

\section{Background}
\label{sec:chapter-background}

Provide necessary context specific to this chapter's content. Reference 
relevant literature using \textcite{author2023} or \parencite{author2023}.

\section{Methodology}
\label{sec:chapter-method}

Describe methods specific to this chapter's work. Use subsections for clarity:

\subsection{Data Collection}
Details about how data was gathered...

\subsection{Analysis Approach}
Explanation of analytical methods...

\section{Results}
\label{sec:chapter-results}

Present your findings clearly with appropriate figures and tables:

\begin{figure}[htbp]
\centering
\includegraphics[width=0.8\textwidth]{figures/result-plot.pdf}
\caption{Descriptive caption explaining what the figure shows.}
\label{fig:result-plot}
\end{figure}

As shown in \cref{fig:result-plot}, the results indicate...

\begin{table}[htbp]
\centering
\caption{Summary of experimental results}
\label{tab:results-summary}
\begin{tabular}{lccr}
\toprule
Parameter & Method A & Method B & Improvement \\
\midrule
Accuracy & 0.85 & 0.92 & +8.2\% \\
Speed & 120ms & 95ms & -20.8\% \\
Memory & 512MB & 480MB & -6.3\% \\
\bottomrule
\end{tabular}
\end{table}

\section{Discussion}
\label{sec:chapter-discussion}

Interpret your results in the context of existing knowledge. Address:
\begin{itemize}
\item How findings relate to your hypotheses
\item Comparison with previous work
\item Limitations and their impact
\item Implications for the field
\end{itemize}

\section{Conclusion}
\label{sec:chapter-conclusion}

Summarize the chapter's key contributions and link to the next chapter.

\chapter{Literature Review}
\label{chap:lit-review}

\section{Introduction}
This chapter critically examines existing research in [field], identifying 
gaps that this thesis addresses.

\section{Theoretical Foundations}
\subsection{Classical Theories}
Early work by \textcite{pioneer1950} established... Subsequently, 
\textcite{researcher1970} expanded this framework...

\subsection{Modern Developments}
Recent advances include:
\begin{itemize}
\item \textcite{author2020} demonstrated...
\item The work of \textcite{team2021} showed...
\item \textcite{group2022} challenged existing assumptions...
\end{itemize}

\section{Current State of Research}
\subsection{Approach A: Traditional Methods}
Several studies \parencite{study1,study2,study3} have used traditional 
approaches...

\subsection{Approach B: Novel Techniques}
Emerging methods include:

\begin{table}[htbp]
\centering
\caption{Comparison of methodological approaches}
\begin{tabular}{L{3cm}L{4cm}L{4cm}}
\toprule
Method & Advantages & Limitations \\
\midrule
Traditional & Well-established, Validated & Limited scalability \\
Machine Learning & Adaptive, Scalable & Requires large datasets \\
Hybrid & Best of both & Complex implementation \\
\bottomrule
\end{tabular}
\end{table}

\section{Research Gaps}
Despite extensive research, several gaps remain:
\begin{enumerate}
\item Limited understanding of...
\item No comprehensive framework for...
\item Lack of empirical evidence regarding...
\end{enumerate}

\section{Summary}
This review reveals that while significant progress has been made, 
opportunities exist for contributions in [specific areas]. This thesis 
addresses these gaps by...

% Main differences:
% \include{} - Starts new page, allows \includeonly
% \input{} - Inserts content inline, no page break

% For chapters (always starts new page anyway)
\include{chapters/introduction}
\include{chapters/methodology}

% For sections within chapters
\chapter{Results}
\input{chapters/results/experiment1}
\input{chapters/results/experiment2}

% Compile only specific chapters during writing
\includeonly{chapters/methodology,chapters/results}

% Use draft mode while writing
\documentclass[12pt,draft]{book}
% Shows boxes for bad spacing, loads figures as boxes

% Conditional compilation for figures
\newif\iffigures
\figurestrue % Set to \figuresfalse to skip figures

\iffigures
  \includegraphics[width=\textwidth]{complex-figure.pdf}
\else
  \framebox[\textwidth]{\rule{0pt}{5cm}Figure: complex-figure.pdf}
\fi

% Externalize TikZ figures
\usepackage{tikz}
\usetikzlibrary{external}
\tikzexternalize[prefix=tikz-cache/]

% Modern approach with BibLaTeX
\usepackage[
    backend=biber,              % Modern backend
    style=authoryear,           % Or numeric, apa, ieee
    sorting=nyt,                % Name-year-title
    natbib=true,               % Support natbib commands
    maxbibnames=99,            % Show all authors in bibliography
    maxcitenames=2,            % Use et al. after 2 in text
    uniquelist=false,          % Don't expand author lists
    doi=true,                  % Show DOIs
    isbn=false,                % Hide ISBNs
    url=false,                 % Hide URLs when DOI present
    eprint=false               % Hide arXiv info
]{biblatex}

% Multiple bibliography files
\addbibresource{references/primary.bib}
\addbibresource{references/secondary.bib}
\addbibresource{references/software.bib}

% Print bibliography by type
\printbibliography[type=article,title={Journal Articles}]
\printbibliography[type=book,title={Books}]
\printbibliography[type=inproceedings,title={Conference Papers}]

% Text citations
According to \textcite{smith2020}, the results show...
\textcite{jones2021} demonstrated that...

% Parenthetical citations
Recent studies \parencite{brown2019,wilson2020} indicate...
This finding \parencite[see][p.~45]{taylor2021} suggests...

% Multiple citations
Several researchers \parencite{study1,study2,study3} agree...

% Page numbers and notes
As noted by \textcite[p.~123]{author2020}...
This contradicts earlier work \parencite[cf.][]{previous2018}...

% Citing specific parts
\textcite[chap.~3]{book2019} discusses...
See \textcite[eq.~2.5]{paper2020} for details...

% Author only or year only
\citeauthor{reference2021} showed in \citeyear{reference2021} that...

% Subfigures
\begin{figure}[htbp]
\centering
\begin{subfigure}[b]{0.45\textwidth}
    \centering
    \includegraphics[width=\textwidth]{experiment-setup.pdf}
    \caption{Experimental setup}
    \label{fig:exp-setup}
\end{subfigure}
\hfill
\begin{subfigure}[b]{0.45\textwidth}
    \centering
    \includegraphics[width=\textwidth]{apparatus.pdf}
    \caption{Measurement apparatus}
    \label{fig:apparatus}
\end{subfigure}
\caption{Overview of experimental configuration showing (a) the complete 
setup and (b) detailed view of measurement apparatus.}
\label{fig:experiment-overview}
\end{figure}

% Wide figure spanning both columns (if using two-column)
\begin{figure*}[htbp]
\centering
\includegraphics[width=\textwidth]{timeline.pdf}
\caption{Project timeline showing all phases}
\label{fig:timeline}
\end{figure*}

% Rotated figure for landscape orientation
\begin{sidewaysfigure}
\centering
\includegraphics[width=\textwidth]{large-diagram.pdf}
\caption{Complex system diagram (rotated for clarity)}
\label{fig:rotated}
\end{sidewaysfigure}

% Professional table with booktabs
\begin{table}[htbp]
\centering
\caption{Comparison of algorithmic approaches}
\label{tab:algorithm-comparison}
\begin{tabular}{@{}lcccc@{}}
\toprule
Algorithm & Time & Space & Accuracy & Scalability \\
         & Complexity & Complexity & (\%) & Rating \\
\midrule
Baseline & $O(n^2)$ & $O(n)$ & 78.3 & Low \\
Improved & $O(n\log n)$ & $O(n)$ & 85.7 & Medium \\
Proposed & $O(n)$ & $O(1)$ & 91.2 & High \\
\bottomrule
\end{tabular}
\end{table}

% Long table spanning multiple pages
\begin{longtable}{@{}llr@{}}
\caption{Comprehensive dataset characteristics} 
\label{tab:dataset} \\
\toprule
Dataset & Description & Size \\
\midrule
\endfirsthead
\multicolumn{3}{c}{\tablename\ \thetable{} -- continued from previous page} \\
\toprule
Dataset & Description & Size \\
\midrule
\endhead
\midrule
\multicolumn{3}{r}{Continued on next page} \\
\endfoot
\bottomrule
\endlastfoot
% Table content
Dataset A & Training data for model 1 & 10,000 \\
Dataset B & Validation set & 2,000 \\
Dataset C & Test set for evaluation & 2,500 \\
% ... many more rows ...
\end{longtable}

% Define theorem styles
\theoremstyle{plain} % Italic body
\newtheorem{theorem}{Theorem}[chapter]
\newtheorem{lemma}[theorem]{Lemma}
\newtheorem{proposition}[theorem]{Proposition}
\newtheorem{corollary}[theorem]{Corollary}

\theoremstyle{definition} % Roman body
\newtheorem{definition}[theorem]{Definition}
\newtheorem{example}[theorem]{Example}
\newtheorem{assumption}[theorem]{Assumption}

\theoremstyle{remark} % Roman body, no emphasis
\newtheorem{remark}[theorem]{Remark}
\newtheorem{note}[theorem]{Note}

% Usage with proof environment
\begin{theorem}[Convergence of Algorithm]
\label{thm:convergence}
Given assumptions A1-A3, the proposed algorithm converges to the global 
optimum with probability 1 as $t \to \infty$.
\end{theorem}

\begin{proof}
Let $X_t$ denote the state at iteration $t$. We show that 
$\{X_t\}_{t=1}^{\infty}$ forms a Cauchy sequence.

First, observe that:
\begin{equation}
\|X_{t+1} - X_t\| \leq \gamma_t \|G_t\|
\end{equation}
where $\gamma_t$ is the step size and $G_t$ is the gradient.

[... proof continues ...]

Therefore, the sequence converges, completing the proof.
\end{proof}

% Multi-line equation with alignment
\begin{align}
\mathcal{L}(\theta) &= \sum_{i=1}^{N} \log p(y_i | x_i, \theta) \\
                    &= \sum_{i=1}^{N} \left[ y_i \log h_\theta(x_i) + 
                       (1-y_i)\log(1-h_\theta(x_i)) \right] \\
                    &= -\frac{1}{N} \sum_{i=1}^{N} \mathcal{L}_i(\theta)
\end{align}

% System of equations
\begin{equation}
\begin{cases}
\frac{\partial f}{\partial x} = 2x + y \\
\frac{\partial f}{\partial y} = x + 2y \\
\nabla^2 f = 4 > 0
\end{cases}
\end{equation}

% Matrix equation
\begin{equation}
\mathbf{A} = \begin{bmatrix}
a_{11} & a_{12} & \cdots & a_{1n} \\
a_{21} & a_{22} & \cdots & a_{2n} \\
\vdots & \vdots & \ddots & \vdots \\
a_{m1} & a_{m2} & \cdots & a_{mn}
\end{bmatrix}_{m \times n}
\end{equation}

% Equation with conditions
\begin{equation}
f(x) = \begin{cases}
x^2 & \text{if } x \geq 0 \\
-x^2 & \text{if } x < 0
\end{cases}
\end{equation}

% Margins (check your university's requirements)
\usepackage[
    top=1in,        % Often 1-1.5 inches
    bottom=1in,     
    left=1.5in,     % Left often larger for binding
    right=1in,
    bindingoffset=0.5in  % Extra space for binding
]{geometry}

% Line spacing
\usepackage{setspace}
\doublespacing  % Many universities require double spacing
% \onehalfspacing  % Some allow 1.5 spacing
% \singlespacing   % Usually only for quotes/references

% Font requirements
\usepackage{times}  % Times New Roman if required
% \usepackage{arial}  % Arial if required
% Default LaTeX fonts are usually acceptable

% Page numbering
\pagenumbering{roman}  % i, ii, iii for front matter
\pagenumbering{arabic} % 1, 2, 3 for main matter

% Header/footer requirements
\pagestyle{plain}  % Only page numbers
% Some universities require chapter/section in headers
\pagestyle{fancy}
\fancyhf{}
\fancyhead[R]{\thepage}
\fancyhead[L]{\leftmark}

% myuniversity.cls
\NeedsTeXFormat{LaTeX2e}
\ProvidesClass{myuniversity}[2024/01/01 My University Thesis Class]

% Base on book class
\LoadClass[12pt,oneside]{book}

% University-specific packages and settings
\RequirePackage[margin=1in,left=1.5in]{geometry}
\RequirePackage{setspace}
\doublespacing

% Custom title page command
\newcommand{\makethesistitle}{%
  \begin{titlepage}
    \centering
    % University specific title page layout
    \vspace*{2cm}
    {\LARGE UNIVERSITY NAME \par}
    \vspace{4cm}
    {\huge\bfseries \@title \par}
    \vspace{2cm}
    {\Large \@author \par}
    \vfill
    A thesis submitted for the degree of\\
    Doctor of Philosophy\\
    \vspace{1cm}
    {\large \@date \par}
  \end{titlepage}
}

% Custom environments
\newenvironment{abstract}{%
  \chapter*{Abstract}
  \addcontentsline{toc}{chapter}{Abstract}
}{}

# Initialize repository
git init
git add .
git commit -m "Initial thesis structure"

# Create branches for chapters
git checkout -b chapter-methodology
# Work on chapter...
git add chapters/methodology.tex
git commit -m "Add methodology introduction"

# Create tags for milestones
git tag -a v1.0-first-draft -m "First complete draft"
git tag -a v2.0-post-feedback -m "After supervisor feedback"

# Useful .gitignore for LaTeX
cat > .gitignore << EOF
*.aux
*.bbl
*.bcf
*.blg
*.fdb_latexmk
*.fls
*.log
*.out
*.run.xml
*.synctex.gz
*.toc
*.lof
*.lot
thesis.pdf
EOF

% Track changes and comments
\usepackage{changes}
\definechangesauthor[color=blue]{YN}{Your Name}
\definechangesauthor[color=red]{SV}{Supervisor}

% Add comments
\added[id=YN]{New text added after review}
\deleted[id=SV]{Text removed per supervisor feedback}
\replaced[id=YN]{new text}{old text}

% Todo notes
\usepackage{todonotes}
\todo{Expand this section}
\todo[color=red]{Critical: Add citation}
\missingfigure{Add diagram of experimental setup}

% Draft watermark
\usepackage{draftwatermark}
\SetWatermarkText{DRAFT}
\SetWatermarkScale{1}
\SetWatermarkColor[gray]{0.9}

% Line numbers for review
\usepackage{lineno}
\linenumbers  % For supervisor review

% Quick referencing
\newcommand{\secref}[1]{Section~\ref{#1}}
\newcommand{\chapref}[1]{Chapter~\ref{#1}}
\newcommand{\figref}[1]{Figure~\ref{#1}}
\newcommand{\tabref}[1]{Table~\ref{#1}}
\newcommand{\eqref}[1]{Equation~(\ref{#1})}

% Common abbreviations
\newcommand{\ie}{i.e.,\ }
\newcommand{\eg}{e.g.,\ }
\newcommand{\cf}{cf.\ }
\newcommand{\etal}{et al.\ }
\newcommand{\vs}{vs.\ }

% Math shortcuts
\newcommand{\R}{\mathbb{R}}
\newcommand{\N}{\mathbb{N}}
\newcommand{\E}{\mathbb{E}}
\newcommand{\Var}{\mathrm{Var}}
\newcommand{\Cov}{\mathrm{Cov}}

% Consistent terminology
\newcommand{\ourmethod}{ProposedMethod}
\newcommand{\baseline}{BaselineApproach}

% For PDF/A compliance
\usepackage[a-1b]{pdfx}
\hypersetup{pdfstartview=}

% Metadata
\begin{filecontents*}{\jobname.xmpdata}
\Title{Your Thesis Title}
\Author{Your Name}
\Subject{PhD Thesis}
\Keywords{keyword1\sep keyword2\sep keyword3}
\Publisher{Your University}
\end{filecontents*}

% Compile with:
% pdflatex thesis
% biber thesis  
% pdflatex thesis
% pdflatex thesis