main.tex

\documentclass[12pt,openright]{book}

%%% Packages

% Setting up page
\usepackage[a4paper,top=1in,right=1in,bottom=1in,left=40mm]{geometry}
\usepackage{emptypage}

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

% Fonts and typesetting
\usepackage{./fonts}
\usepackage{datetime}
    \newdateformat{monthyeardate}{\THEYEAR}
\usepackage{setspace}
    \onehalfspacing%
\usepackage{enumerate}  % Roman numerals in lists

% Page headers and footers
\usepackage{fancyhdr}
\usepackage{etoolbox}

\renewcommand{\chaptermark}[1]{%
    \markboth{\MakeUppercase{\thechapter.\ #1}}{}  % Number and title only
}

\renewcommand{\sectionmark}[1]{%
    \markright{\MakeUppercase{\thesection.\ #1}}{}  % Number and title only
}

\fancypagestyle{normal}{  % Used for most pages
    \fancyhf{}
    \fancyhead[LE]{\slshape\leftmark}  % Show chapter title on left outer leaf
    \fancyhead[RO]{\slshape\rightmark}  % Show section title on right outer leaf
    \fancyfoot[C]{\thepage}  % Show page number on outer leaf
    \renewcommand{\headrulewidth}{1pt}
}

\fancypagestyle{chapterstyle}{  % For chapter pages (no need for a header)
    \fancyhf{}
    \fancyfoot[C]{\thepage}
    \renewcommand{\headrulewidth}{0pt}% Line at the header invisible
}

\patchcmd{\chapter}{\thispagestyle{plain}}{\thispagestyle{chapterstyle}}{}{}

\fancypagestyle{appendixstyle}{  % For appendices
    \fancyhf{}
    \fancyhead[LE,RO]{\slshape\rightmark}
    \fancyfoot[LE,RO]{\thepage}
}

% Images, lists and tables
\usepackage{booktabs}
    \renewcommand{\arraystretch}{1.3}
\usepackage{graphicx}
\usepackage{interval}
    \intervalconfig{soft open fences}
\usepackage{pgf}
\usepackage{rotating}
\usepackage{standalone}
\usepackage{tikz}
    \usetikzlibrary{%
        arrows,
        backgrounds,
        decorations.pathreplacing,
        shapes.geometric,
        positioning,
    }

% Bibliography, appendices and links
\usepackage{appendix}
\usepackage{float}  % Force hyperref to patch float [for minted]
\usepackage{hyperref}
\usepackage{nameref}
\usepackage[numbers]{natbib}
    \bibliographystyle{abbrvurl}

% Algorithms and code blocks
\usepackage[ruled,algochapter,linesnumbered]{algorithm2e}
\usepackage{xcolor}
\usepackage{tcolorbox}
\usepackage[newfloat,chapter]{minted}

% Captions, floats and subfigures
\usepackage{caption}
\usepackage{subcaption}
\usepackage{pdflscape}
\usepackage{afterpage}


%%% Settings

% Page stuff
\setcounter{tocdepth}{2}

% Maths stuff
\DeclareMathOperator*{\argmin}{arg\,min}
{\theoremstyle{definition}\newtheorem{definition}{Definition}[chapter]}
{\theoremstyle{plain}\newtheorem{theorem}{Theorem}[chapter]}
\DeclarePairedDelimiter\abs{\lvert}{\rvert}%
\DeclarePairedDelimiter\norm{\lVert}{\rVert}%

% Lengths
\newlength{\imgwidth}
\setlength{\imgwidth}{.95\textwidth}
\newlength{\tabwidth}
\setlength{\tabwidth}{.9\textwidth}
\newlength{\hierheight}
\setlength{\hierheight}{.2\paperheight}

\makeatletter
\renewcommand*\l@algocf{\l@figure}
\makeatother

% Colours
\definecolor{linenums}{HTML}{4c566a}
\definecolor{sourcebg}{HTML}{d8dee9}
\definecolor{sourcefr}{HTML}{b2bdd1}
\definecolor{usagebg}{HTML}{fdf6e3}
\definecolor{usagefr}{HTML}{eee8d5}
\definecolor{myurl}{HTML}{5e81ac}

\definecolor{grey}{RGB}{134, 134, 134}
\definecolor{cyan}{RGB}{0, 164, 216}
\definecolor{magenta}{RGB}{226, 62, 138}
\definecolor{deepblue}{RGB}{0,0,150}
\definecolor{deepred}{RGB}{200,0,0}
\definecolor{deepgreen}{RGB}{0,150,0}

\definecolor{blue}{HTML}{0072B2}
\definecolor{green}{HTML}{009E73}
\definecolor{orange}{HTML}{D55E00}
\definecolor{pink}{HTML}{CC79A7}

% Code snippet stuff
\usemintedstyle{friendly}
\setminted{fontsize=\scriptsize, breaklines=true, framerule=\linewidth}
\setmintedinline{fontsize=\small}

%%% Commands and environments

% URLs
\hypersetup{
    colorlinks=true,
    citecolor=deepgreen,
    linkcolor=deepred,
    urlcolor=myurl,
}

\renewcommand*{\UrlFont}{\ttfamily\small\relax}

\newcommand{\arxiv}[1]{%
    \href{https://arxiv.org/abs/#1}{\small\nolinkurl{arXiv:#1}}%
}

\newcommand{\doi}[1]{%
    \href{https://doi.org/#1}{\small\nolinkurl{doi:#1}}%
}

\newcommand{\github}[1]{%
    \href{https://github.com/#1}{\small\nolinkurl{github:#1}}%
}

% Line rule
\newcommand{\myrule}{%
    \begin{center}\noindent\rule[0.5ex]{.8\linewidth}{1pt}\end{center}
}

% Checkmarks
\newcommand{\cmark}{\ding{51}}%
\newcommand{\xmark}{\ding{55}}%

% Code snippets
\SetupFloatingEnvironment{listing}{%
  name={Snippet},
  fileext=lol%
}

\renewcommand{\theFancyVerbLine}{%
    \color{linenums}{%
        \scriptsize%
        \oldstylenums{%
            \usefont{T1}{DejaVuSansMono-TLF}{m}{n}\selectfont%
            \arabic{FancyVerbLine}
        }
    }%
}

\newenvironment{sourcepy}{%
    \VerbatimEnvironment%
    \begin{tcolorbox}[%
        colback=sourcebg,
        colframe=sourcefr,
        left=2em,
        right=2em,
    ]%
    \begin{minted}[%
        bgcolor=sourcebg,
        linenos=true,
        numbersep=0ex,
    ]{python}%
}{\end{minted}\end{tcolorbox}}

\newenvironment{sourceyml}{%
    \VerbatimEnvironment%
    \begin{tcolorbox}[%
        colback=sourcebg,
        colframe=sourcefr,
        left=2em,
        right=2em,
    ]%
    \begin{minted}[%
        bgcolor=sourcebg,
        linenos=true,
        numbersep=0ex,
    ]{yaml}%
}{\end{minted}\end{tcolorbox}}

\newenvironment{usagepy}{%
    \VerbatimEnvironment%
    \begin{tcolorbox}[%
        colback=usagebg,
        colframe=usagefr,
    ]%
    \begin{minted}[bgcolor=usagebg]{python}%
}{\end{minted}\end{tcolorbox}}

\newenvironment{usagesh}{%
    \VerbatimEnvironment%
    \begin{tcolorbox}[
        colback=usagebg,
        colframe=usagefr,
    ]%
    \begin{minted}[bgcolor=usagebg]{console}%
}{\end{minted}\end{tcolorbox}}

% Inputting source
\newcommand{\tikzpath}{}
\newcommand{\inputtikz}[3][\tikzpath]{%
    \begin{figure}[htbp]
        \centering
        \resizebox{\imgwidth}{!}{%
            \input{#1/#2}
        }
        \caption{#3}\label{fig:#2}
    \end{figure}
}

\newcommand{\texpath}{}

\newcommand{\algpath}{}
\newcommand{\inputalg}[2][\algpath]{\input{#1/#2}}

\newcommand{\balg}[1][htbp]{\begin{algorithm}[#1]\DontPrintSemicolon}
\newcommand{\ealg}{\end{algorithm}}


%%% Tikz stuff
\usetikzlibrary{%
    arrows.meta,
    decorations.pathreplacing,
    decorations.text,
    patterns,
    shapes.arrows,
    shapes.geometric
}

% TikZ styles, commands and settings
\pgfdeclarelayer{background}
\pgfsetlayers{background,main}

\tikzstyle{every picture} += [remember picture]
\tikzstyle{na} = [baseline=-.5ex]

\tikzset{%
    column/.pic={%
        code{%
            \draw[line width=1pt] (0, 0) rectangle (-2cm, 4cm);
            \foreach \val in {0, ..., #1}{%
                \draw[rotate=90] ([xshift=-\val*10pt] 4cm, 2cm) -- ++(0, -2cm);
            };
            \node at (-1cm, 1.25) {$\vdots$};
            \foreach \val in {1, 2}{%
                \draw (0, \val * 10pt) -- ++(-2cm, 0);
            };
        }
    }
}

\tikzset{%
    fullcolumn/.pic={%
        code{%
            \draw[line width=1pt] (0, 0) rectangle (-2cm, #1*10pt);
            \foreach \val in {0, ..., #1}{%
                \draw[rotate=90] ([xshift=-\val*10pt] #1*10pt, 2cm) -- ++(0, -2cm);
            };
        }
    }
}

\tikzset{%
    queue/.pic={%
        code{%
            \node (rect) at (38.5mm, 10mm) {};
            \draw[thick] (0, 0) -- ++(40mm, 0) -- ++(0, 20mm) -- ++(-40mm, 0);
            \foreach \val in {0, ..., #1}{%
                \draw[thick] ([xshift=-\val*5mm] 40mm, 20mm) -- ++(0, -20mm);
            };

            \foreach \val/\lab/\size in {%
                0/1/\scriptsize,
                1/2/\scriptsize,
                3/c-1/\tiny,
                4/c/\scriptsize%
            }{%
                \node[draw, circle, thick, minimum size=9.5mm] (\lab)
                    at (55mm, 29mm - \val * 9.5mm) {\size$\lab$};
                \draw[-latex, thick] (rect.east) -- (\lab.west);
            };

            \node at (55mm, 11mm) {$\vdots$};
            \node at (5mm, 10mm) {$\cdots$};
        };
    },
    myarrow/.style={%
        line width=2mm,
        draw=gray!50,
        -triangle 60,
        postaction={draw=gray!50, line width=4mm, shorten >=6mm, -},
    },
    double -latex/.style args={#1 colored by #2 and #3}{%
        -latex,
        line width=#1,
        #2,
        postaction={%
            draw,
            -latex,
            #3,
            line width=(#1)/3,
            shorten <=(#1)/4,
            shorten >=4.5*(#1)/3
        },
    },
    mypointer/.style={%
        double -latex=1mm colored by gray!50 and gray!50,
    }
}

%% Shortcuts

\newcommand{\ciw}{\mintinline{console}{ciw}}
\newcommand{\ctmuhb}{Cwm Taf Morgannwg UHB}
\newcommand{\edo}{\mintinline{console}{edo}}
\newcommand{\edolab}{\mintinline{console}{edolab}}
\newcommand{\kmodes}{\mintinline{console}{kmodes}}
\newcommand{\matching}{\mintinline{console}{matching}}
\newcommand{\matchingr}{\mintinline{console}{MatchingR}}
\newcommand{\pip}{\mintinline{console}{pip}}
\newcommand{\pytest}{\mintinline{console}{pytest}}
\newcommand{\pytestcov}{\mintinline{console}{pytest-cov}}


%%% DOCUMENT %%%

\begin{document}

%TC:ignore
\input{title.tex}
\pagestyle{chapterstyle}

% Preamble
\frontmatter%
\input{preamble/abstract}
\input{preamble/acknowledgements}
\input{preamble/dissemination}

\addtocontents{toc}{\vspace{1em}\par\noindent\protect\myrule\par}

{
  \hypersetup{hidelinks}

    \tableofcontents%
    \listoffigures%
    \listoftables%
    \listofalgorithms%
    \listoflisting%
}
%TC:endignore

% Main text
\mainmatter%
\pagestyle{normal}
\input{chapters/intro/main}
\input{chapters/lit/main}
\input{chapters/edo/main}
\input{chapters/kmodes/main}
\input{chapters/copd/main}
\input{chapters/conclusion}

\addtocontents{toc}{\vspace{1em}\par\noindent\protect\myrule\par}

% Post-text
%TC:ignore
\bibliography{bibliography.bib}
\input{appendix/main}
%TC:endignore

\end{document}