Thesis.tex

% MARK: Preamble
\documentclass{thesis}

\usepackage{geometry}
\geometry{a4paper, margin=25mm}

\usepackage[utf8]{inputenc}
\usepackage[T1]{fontenc}

% MARK: Supress Warnings
\usepackage{silence}

% Warnings from keywords seperated by $-$
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% Warnings from combining sc, it, and bf font variations
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% Table 2.2 sfrac fontsize warning
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\WarningFilter{latexfont}{Size substitutions with differences}

% Set paragraph seperation and indentation
\usepackage[%
    skip=1.0\baselineskip plus2pt,
    indent=20pt
]{parskip}
% Remove lineskip in itemize environment
\usepackage{enumitem}
\setlist[itemize]{nosep}

% Allow text coloring
% https://www.overleaf.com/learn/latex/Using_colours_in_LaTeX
% https://www.overleaf.com/learn/latex/Environments
\usepackage{xcolor}
\definecolor{mylinkcolor}{HTML}{313e80}
\definecolor{mycitecolor}{HTML}{179b7d}%{0f4636}

% Set the styling of captions
\usepackage[%
    hypcap=true,
    font=scriptsize,
    labelfont=bf,
    figurename=Figure,
    tablename=Table,
]{caption}
\usepackage{subcaption}

% MARK: Math packages
% Add: \degree and \micro, etc.
\usepackage{textcomp, gensymb}
% To get matrixes
% \usepackage{amsmath}
% Add additional math support, eg.: \lesssim
\usepackage{amssymb}
\usepackage{comment}
% \usepackage{mathtools}
\usepackage{siunitx}
% Provide sfrac command: $\sfrac{a}{b}$ -> a/b
\usepackage{xfrac}

% MARK: Graphics packages
% Include tikz figures
\usepackage{tikz}
\usetikzlibrary{shapes.geometric, arrows}
\tikzset{font=\footnotesize}
% Include svg figures
\usepackage{svg}
% Convert eps figures to pdf
% \usepackage{epstopdf}
% Allow custom in-text plots
\usepackage{pgfplots}
\pgfplotsset{compat=1.15}
% Include pdf documents in latex. Eg. for publications included in the appendix
\usepackage{pdfpages}
% Allows you to work with graphics 
\usepackage{graphicx}
\graphicspath{%
    {chapter_0/figures/}%
    {chapter_1/figures/}%
    {chapter_2/figures/}%
    {chapter_3/figures/}%
    {chapter_4/figures/}%
    {chapter_5/figures/}%
    {chapter_6/figures/}%
}
% Add support for floats, i.e., floating
% \usepackage{float}
% programmatic-like interface to create highly customizable subfloats/subfigures
% \usepackage[farskip=0pt]{subfig}
% Needed for `Python pandas` tables
\usepackage{booktabs}
% Allow figure text wrapping
% \usepackage{wrapfig}
% Allow rotation of tables
% \usepackage{rotating}
% Enhanced table setup
% \usepackage{ctable}
% Create tables that may continue to the next page
% \usepackage{longtable}

% Section depth, e.g.: \S 1.1.1.1
% \setcounter{secnumdepth}{5}

% MARK: hyperref
% Looks for hyperref.cfg
\usepackage[lowtilde]{url}
\usepackage{hyperref}
% Define keywords for use in the document
% Redefine \autoref{} defaults
\renewcommand\chapterautorefname{Chapter}
\renewcommand\sectionautorefname{\S}
\renewcommand\subsectionautorefname{\S}
\renewcommand\subsubsectionautorefname{\S}
\renewcommand\pageautorefname{p.}
% \renewcommand\pagesautorefname{pp.}
\newcommand\mykeywords{\GetDocumentProperties{hyperref/pdfkeywords}}

% MARK: Title constants
\title{\textbf{\GetDocumentProperties{hyperref/pdftitle}}}
\author{\GetDocumentProperties{hyperref/pdfauthor}}
\Cdegree{B.Sc. (Hons) \textit{cum laude}}
\Sdegree{Master of Science in Astrophysics} % \SDegree{Magister Scienti\ae}
\department{Department of Physics}
\faculty{Faculty of Natural and Agricultural Sciences}
\university{University of the Free State}
\country{South Africa}
\degreedate{\monthyear\today}
\supervisor{Prof. B. van Soelen}

% MARK: Other packages
% Add support to split a table cell into multiple rows
\usepackage{multirow}
% Format tabular environments. Used by math and table packages
\usepackage{array}
% Allow strikethrough, eg.: \sout{example strikethrough text}
\usepackage{ulem}

\usepackage{datetime}
\newdateformat{monthyear}{\monthname[\THEMONTH] \THEYEAR}

% Control footnote layouts
% \usepackage[bottom, hang, flushmargin]{footmisc}
% Upright greek letters
% \usepackage{upgreek}
% 'robusify' the \subref command so it doesn't break on a whim
% \robustify{\subref}

% MARK: 'include' files
\includeonly{%
    chapter_0/Abstract,
    chapter_0/Acknowledgements,
    chapter_0/Appendix_reduction,
    chapter_0/Appendix_code,
    chapter_1/Introduction,
    chapter_2/SALT_RSS_pipeline,
    chapter_3/Developed_tools,
    chapter_4/Testing_Application,
    chapter_5/Conclusions,
}

% Allow directory `tree' structures
\usepackage{dirtree}
% Allow relative font resizing.
\usepackage{relsize}

% MARK: My listings
\usepackage{mylistings}
% \usepackage[path=G:/STOPS/]{mylistings}

% MARK: Custom cmd's
\newcommand\todo[1]{{\noindent}\textcolor{red}{\textbf{TODO: #1}}}
% Hide TODO's
% \renewcommand\todo[1]{}
\newcommand{\Chapter}[2]{\chapter[#1]{#1:\\ \smallskip {\smaller[1] #2}}}

\newcommand{\arcmin}{\hbox{$^\prime$} }
\newcommand{\arcsec}{\hbox{$^{\prime\prime}$} }
\newcommand{\avg}[1]{\left< #1 \right> }
\newcommand{\matr}[1]{\mathbf{#1}}
% \newcommand{\degr}{\hbox{$^\circ$}}

% Use numeric counting for footnotes
\renewcommand{\thefootnote}{\arabic{footnote}}

\newcommand{\super}[1]{\textsuperscript{#1}}
\newcommand{\rmn}[1]{{\mathrm{#1}}}

% Shorthand for blank line after a paragraph
% \newcommand{\prgph}%{}%{\vspace{\baselineskip}}

% \renewcommand{\arraystretch}{0.8}
% \renewcommand{\floatpagefraction}{.9}

% https://www.overleaf.com/learn/latex/Page_numbering
% Page numbering alteration
% \pagenumbering{Roman}

% MARK: My Glossary
\usepackage{myglossary}

% Set the bibliography references
\usepackage[%
    round,
    colon,
    authoryear,
    sort&compress
]{natbib}
% Add bibliography to ToC
\usepackage[nottoc]{tocbibind}
% Set NASA ADS journal abbrevation macros
\usepackage{journal_macros}

% Fix Bibliography Underfull \hbox (badness 10000)
\usepackage{etoolbox}
\apptocmd{\sloppy}{\hbadness 10000\relax}{}{}

% Remnants from Hanno commands
% \newcolumntype{P}[1]{>{\centering\arraybackslash}p{#1}}


% MARK: Main document
\begin{document}

% MARK: Front matter
\frontmatter
\maketitle
\clearpage

\include{chapter_0/Abstract}
\include{chapter_0/Acknowledgements}

\tableofcontents

% \printglossaries
% Longest abbreviation so the column width can be set
% \glssetwidest{\gls{STOPS}}
\printglossary[%
    type=\acronymtype,
    style=super,
    title={List of Acronyms and Symbols}
]

% \printglossary[%
%     type=main,
%     title={Glossary}
% ]

% Reset all acronyms to their full form
\glsresetall

% MARK: Main matter
\mainmatter
\include{chapter_1/Introduction}
\include{chapter_2/SALT_RSS_pipeline}
\include{chapter_3/Developed_tools}
\include{chapter_4/Testing_Application}
\include{chapter_5/Conclusions}

% MARK: Back matter
{
    % No chapter count type
    \backmatter
    \bibliographystyle{plainnat}
    \bibliography{references}
}

% MARK: Appendix
% New chapter count type
\appendix
% Roman numerals for Appendix numbering
% \renewcommand{\thechapter}{\Roman{chapter}}
\include{chapter_0/Appendix_reduction}
\include{chapter_0/Appendix_code}

\chapter{Proceedings} \label{app:papers}

Development of \stops\ and it's application to spectropolarimetric observations was presented at conferences, with the following proceedings included here.

\begin{itemize}
    \item \glsxtrshort{HEASA} $2021$ -- \citet*{Cooper_HEASA2021}
    \item \glsxtrshort{HEASA} $2022$ -- \citet*{Cooper_HEASA2022}
\end{itemize}

\includepdf[pages=-]{chapter_4/papers/Cooper_HEASA2021.pdf}
\includepdf[pages=-]{chapter_4/papers/Cooper_HEASA2022.pdf}

% \chapter{Supplementary Information} \label{app:supp}

% Specific versions as used throughout this thesis were used and are included here for reference.

% \begin{itemize}
%     \item \polsalt\ v0.2.dev144
%     \item PySALT v0.5dev%
%     \footnote{PySALT version date: 1 October 2014}
%     \item PyRAF v1.8.1
%     \item \iraf\ v2.14
%     \item specpolfinalstokes -- $20171226$
%     \item specpolcorrect -- $20191123 | 20191210$%
%     \footnote{Multiple versions are noted in the `extract_sc' source file.}
%     \item specpolspectrum_sc -- $20191123$
%     \item specpolrawstokes -- $20191111$
%     \item specpolwavmap -- $20180804$
%     \item specpolextract_dev -- $20180524$
%     \item specpolrawstokes_dev -- $20171226$
% \end{itemize}

\end{document}