root.tex

% This template was originally by R. Jacob Vogelstein
% Updated on March 1, 2010 by Noah J. Cowan
% Updated in late 2016 by Jonathan Bohren ME'17

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Font size:        10pt, 11pt, 12pt
% Paper size:       letter
% Margin ordering:  oneside, twoside
% Draft mode:       draft (no figures), final
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\documentclass[12pt,letterpaper,oneside,final]{thesis}

% use this to create PDF/A that supports PDF 1.6 %
% PDF/A is required by JHU ETD system
\usepackage[a-3b]{pdfx}

% layout %
\showboxdepth=5
\showboxbreadth=5
\usepackage{fancyhdr}

% fonts %
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\usepackage{lmodern} \normalfont
\DeclareFontShape{T1}{lmr}{bx}{sc} { <-> ssub * cmr/bx/sc }{}
\usepackage{amsmath,amsfonts}

% logistics %
\usepackage{import}
\usepackage{verbatim}

% citations %
\usepackage[numbers]{natbib}

% references %
\usepackage{hyperref}

% graphics packages %
\usepackage{graphicx}
\usepackage{adjustbox}
\usepackage{array}
\usepackage{wrapfig} % wrapfig is fragile: use sparingly
\usepackage{float}
\usepackage{framed}
\usepackage[font=singlespacing, labelfont=bf]{caption}
\usepackage{subcaption}

\graphicspath{{./figs/}}

% typesetting
\usepackage{upgreek}
\usepackage{setspace}
\usepackage{csquotes}
\usepackage{mathtools}
\usepackage{hyphenat}

% tables %
\usepackage{booktabs}
\usepackage{multirow}
\usepackage{longtable}
\usepackage{tabularx}
\usepackage{tabulary}

% algorithms %
\usepackage[vlined]{algorithm2e}

% lists %
\usepackage{enumitem}
\newlist{inlinelist}{enumerate*}{1}
\setlist*[inlinelist,1]{%
  label=(\arabic*),
}

% colors %
\usepackage{xcolor}

% glossary % 
\usepackage[acronym, toc]{glossaries-prefix}
\renewcommand{\glossarypreamble}{\ssp{}}
\makeglossaries

% todos %
\usepackage[backgroundcolor=white, bordercolor=red]{todonotes}
\reversemarginpar
\setlength{\marginparwidth}{2cm}
\usepackage{silence}
\WarningFilter*{latex}{Marginpar on page \thepage\space moved}
\newcounter{todoListItems}
\input{todo_macros.tex}
%   usage: \todoin[time]{short}{long}
%   usage: \todocite{}
%   usage: \todoref{}

% Define the header/footer style
\pagestyle{fancy}
\fancyhf{}
\setlength{\headheight}{15pt}
\lhead{\leftmark}
\cfoot{\thepage}
\renewcommand{\headrulewidth}{0pt}
\fancypagestyle{plain}{% Redefine ``plain'' style for chapter boundaries
\fancyhf{} % clear all header and footer fields
\fancyfoot[C]{\thepage} % except the center
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\renewcommand{\footrulewidth}{0pt}}
\def\newblock{\hskip .11em plus .33em minus .07em}

% indicies of terms
\input{terms_acronyms}
\input{terms_glossary}

\begin{document}

% add separate files for each chapter
\include{chapter0}
\include{chapter1}

\clearpage \markboth{Appendix}{Appendix}
\include{appendix}

% references

\bibliographystyle{abbrv}
\bibliography{thesis}

\begin{vita}

\begin{wrapfigure}{l}{0pt}
\includegraphics[width=2in,height=2.5in,clip,keepaspectratio]{headshot.jpg}
\end{wrapfigure}

David R. Jones studied art, music and design, including layout and typesetting. After Terry Burns, his half-brother, introduced him to modern jazz, his enthusiasm for players like Charles Mingus and John Coltrane led his mother to give him a plastic alto saxophone in 1961; he was soon receiving lessons from a local musician.

\end{vita}
\end{document}