\documentclass{mimosis}

\usepackage{metalogo}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Some of my favourite personal adjustments
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% These are the adjustments that I consider necessary for typesetting
% a nice thesis. However, they are *not* included in the template, as
% I do not want to force you to use them.

% This ensures that I am able to typeset bold font in table while still aligning the numbers
% correctly.
\usepackage{etoolbox}

\usepackage[binary-units=true]{siunitx}
\DeclareSIUnit\px{px}

\sisetup{%
  detect-all           = true,
  detect-family        = true,
  detect-mode          = true,
  detect-shape         = true,
  detect-weight        = true,
  detect-inline-weight = math,
}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Hyperlinks & bookmarks
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\usepackage[%
  colorlinks = true,
  citecolor  = RoyalBlue,
  linkcolor  = RoyalBlue,
  urlcolor   = RoyalBlue,
  unicode,
  ]{hyperref}

\usepackage{bookmark}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Bibliography
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% I like the bibliography to be extremely plain, showing only a numeric
% identifier and citing everything in simple brackets. The first names,
% if present, will be initialized. DOIs and URLs will be preserved.

\usepackage[%
  autocite     = plain,
  backend      = biber,
  doi          = true,
  url          = true,
  giveninits   = true,
  hyperref     = true,
  maxbibnames  = 99,
  maxcitenames = 99,
  sortcites    = true,
  style        = numeric,
  ]{biblatex}

\input{bibliography-mimosis}
\addbibresource{Thesis.bib}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Fonts
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\ifxetexorluatex
  \setmainfont{Minion Pro}
\else
  \usepackage[lf]{ebgaramond}
  \usepackage[oldstyle,scale=0.7]{sourcecodepro}
  \singlespacing
\fi

\renewcommand{\th}{\textsuperscript{\textup{th}}\xspace}

\newacronym[description={Principal component analysis}]{PCA}{PCA}{principal component analysis}
\newacronym                                            {SNF}{SNF}{Smith normal form}
\newacronym[description={Topological data analysis}]   {TDA}{TDA}{topological data analysis}

\newglossaryentry{LaTeX}{%
  name        = {\LaTeX},
  description = {A document preparation system},
  sort        = {LaTeX},
}

\newglossaryentry{Real numbers}{%
  name        = {$\real$},
  description = {The set of real numbers},
  sort        = {Real numbers},
}

\makeindex
\makeglossaries

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Incipit
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\title{\texttt{latex-mimosis}}
\subtitle{A minimal, modern \LaTeX{} package for typesetting your thesis}
\author{Bastian Rieck}

\begin{document}

\frontmatter
  \include{Sources/Title}
  \include{Sources/Abstract}

  \tableofcontents

\mainmatter

  \include{Sources/Introduction}

% This ensures that the subsequent sections are being included as root
% items in the bookmark structure of your PDF reader.
\bookmarksetup{startatroot}
\backmatter

  \begingroup
    \let\clearpage\relax
    \glsaddall
    \printglossary[type=\acronymtype]
    \newpage
    \printglossary
  \endgroup

  \printindex
  \printbibliography

\end{document}
