%!TEX root = thesis.tex

\usepackage[english]{babel} % Load characters and hyphenation
\usepackage{csquotes}  % English quotes mess with biblatex quotes
\usepackage{ccicons}
\usepackage{todonotes}
\usepackage{blindtext}
\usepackage{amsmath,amssymb}
\usepackage{textgreek}
\usepackage{tikz}
\usepackage{tocloft}
\usepackage{siunitx}
\usepackage{float}
\usepackage{microtype}
\usepackage{booktabs}
\usepackage{texshade}
\usepackage{morefloats}
\usepackage{hyperref}
\usepackage{hypcap}
\usepackage{enumitem}
\usepackage{xspace}
\usepackage{hyphenat}
\usepackage[most]{tcolorbox}
\usepackage[noabbrev,nameinlink]{cleveref}

% required for certain inkscape exports
\usepackage{xcolor}

\xspaceaddexceptions{]\}}

\usetikzlibrary{shapes,arrows,shapes.multipart}


\sisetup{separate-uncertainty,range-units=single,group-separator = {,}}

% show a black bar when overfull 
% \overfullrule=2cm  

% nonbreaking namerefs
% \AtBeginDocument{
% \let\oldnameref\nameref
% \renewcommand\nameref[1]{\ref{#1}~\oldnameref{#1}}
% }

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Disable warnings                                           
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\usepackage{silence}
\WarningFilter{biblatex}{Patching footnotes}
\WarningFilter{biblatex}{Name format 'last-first' deprecated}
\WarningFilter{latex}{Marginpar on page}
\WarningFilter{latexfont}{Font shape}
\WarningFilter{latexfont}{Some font}
\WarningFilter{latexfont}{Font shape}
\WarningFilter{biblatex}{No driver for entry type 'software'}
\WarningFilter{latex}{`!h' float specifier changed to `!ht'}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Acronyms                                           
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\usepackage[nogroupskip,nopostdot,acronym,style=super,nonumberlist,nohypertypes={acronym},automake]{glossaries}
\renewcommand*{\glsnamefont}[1]{#1}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% fonts                                           
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\usepackage{fontspec}
% \setmainfont{TeX Gyre Pagella}
% \usepackage[libertine,cmintegrals,cmbraces,vvarbb]{newtxmath}
% \setmainfont{ETBembo}[
    % SmallCapsFont={Bembo Small Caps & Oldstyle Fig}
% ]
\setmainfont{Vollkorn}
\setsansfont{Gillius ADF No2}
% \setmonofont

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% hyperlinks                                           
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\definecolor{hyperrefcolor}{rgb}{0.2, 0.5, 0.8} % matches pymol slate
\hypersetup{
colorlinks, 
allcolors=hyperrefcolor,
}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% TOC Style                                             
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% hide something from toc
\newcommand{\changelocaltocdepth}[1]{%
  \addtocontents{toc}{\protect\setcounter{tocdepth}{#1}}%
  \setcounter{tocdepth}{#1}%
}

% allows to specifically place chapters outside of parts
\makeatletter
\newcommand{\ChaptersOutsidePart}{%
    \addtocontents{toc}{\bigskip}
    \def\toclevel@chapter{-1}\def\toclevel@section{0}\def\toclevel@subsection{1}}
\newcommand{\ChaptersInsidePart}{%
    \def\toclevel@chapter{0}\def\toclevel@section{1}\def\toclevel@subsection{2}}
\makeatother

% TOC style
\setlength{\cftbeforechapskip}{0pt}
\setlength{\cftbeforepartskip}{10pt}
\renewcommand\cftpartfont{\sc\bfseries}
\renewcommand\cftchapfont{\small\sc}
\renewcommand\cftsecfont{\small}
\renewcommand\cftsubsecfont{\small}
\renewcommand\cftsubsubsecfont{\small}

% \renewcommand\cftpartafterpnum{\vspace{-10pt}}

% Titles of TOC, LOF, LOT
\renewcommand\cfttoctitlefont{\vspace{-2.5cm}\relax\huge\rmfamily}
\renewcommand\cftaftertoctitle{\vspace{0.35em}}
\renewcommand\cftloftitlefont{\vspace{-2.5cm}\relax\huge\rmfamily}
\renewcommand\cftafterloftitle{\vspace{0.35em}}
\renewcommand\cftlottitlefont{\relax\huge\rmfamily}
\renewcommand\cftafterlottitle{\vspace{0.35em}}


\hypersetup{linktocpage} % TOC link on page number

\setcounter{tocdepth}{1} % number of sections in the toc

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% biblatex                                             
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\usepackage{hyphenat} % required bc. biblatex uses \nohyphenations
\usepackage[
    backend=biber,
    style=authoryear,
    maxnames=3,
    minbibnames=6,
    maxbibnames=6,
    sorting=nyt,
    isbn=false,
    doi=true,
    url=false,
    backref,
    giveninits=true, % initials for first names
    uniquelist=true,
    uniquename=init,
    dashed=false, % do not use dashes for same author names
]{biblatex}
\addbibresource{biblio.bib}
\addbibresource{publications.bib}

% environment with supressed letters after the year for my reference section
% https://tex.stackexchange.com/questions/63500/suppress-year-label-letter-in-biblatex-author-year-styles-on-a-per-bibliography
\defbibenvironment{nodis}
  {\list
     {}
     {\setlength{\leftmargin}{\bibhang}%
      \setlength{\itemindent}{-\leftmargin}%
      \setlength{\itemsep}{\bibitemsep}%
      \setlength{\parsep}{\bibparsep}}}
  {\endlist}
  {\clearfield{extradate}\item}


% my papers section settings
\DeclareRefcontext{mypaper}{sorting=none}

% Reverse names for all authors
\DeclareNameAlias{sortname}{last-first}

% Make title in bibliography link to the doi
\newbibmacro{string+doi}[1]{%
  \iffieldundef{doi}{#1}{\href{http://dx.doi.org/\thefield{doi}}{#1}}}
% \DeclareFieldFormat{title}{\usebibmacro{string+doi}{\mkbibemph{#1}}}
\DeclareFieldFormat{title}{\usebibmacro{string+doi}{#1}}
\DeclareFieldFormat[article]{title}{\usebibmacro{string+doi}{#1}}

% newline after author (year)
\DeclareDelimFormat[bib]{nametitledelim}{\newline\bibsentence}

% spacing between entries
\setlength\bibitemsep{1.5\itemsep}

% Only years for dates
\AtEveryBibitem{\clearfield{month}}
\AtEveryBibitem{\clearfield{day}}

% No pmid
\AtEveryBibitem{\clearfield{eprint}}

% No editors, translators, ...
\renewbibmacro*{byeditor+others}{}

% Supress the in: in references
\renewbibmacro{in:}{}

% Annotate authors
% last name
\renewcommand*{\mkbibnamefamily}[1]{
\ifitemannotation{highlight}
  {\textbf{#1}}%
  {\ifitemannotation{highfirst}
    {\textbf{#1}}%
    {#1}%
  }
}%%
% first name
\renewcommand*{\mkbibnamegiven}[1]{
\ifitemannotation{highlight}
  {\textbf{#1}}%
  {\ifitemannotation{highfirst}
    {\textbf{#1}}%
    {#1}
  }%
\ifitemannotation{first}
  {*}
  {\ifitemannotation{highfirst}
    {\textbf{*}}
    {}
  }%
}%%

% backreference string
\DefineBibliographyStrings{english}{%
  backrefpage = {cited on p\adddot},%
  backrefpages = {cited on pp\adddot}%
}

% no header for bibleography
\defbibheading{secbib}[\bibname]{%
  \section*{#1}%
  \markboth{#1}{#1}}

% marginnnote with a reduced citing format:
% Authors (year), Title. Year links to bibliography
\DeclareCiteCommand{\customcite}
  {\boolfalse{citetracker}% precode
   \boolfalse{pagetracker}%
   \usebibmacro{prenote}}
  {\ifciteindex % loopcode (the actual formatting)
     {\indexnames{labelname}%
      \indexfield{indextitle}}
     {}%
   \printtext{%
       \printnames{labelname}%
       \setunit{\addspace}
       \printtext[parens]{\printfield[bibhyperref]{year}}% year links to references
       % \setunit{\labelnamepunct}%
       % \printfield[citetitle]{labeltitle}%
     }%
   }
  {\multicitedelim} % sepcode: a comma usually
  {\usebibmacro{postnote}\printtext{\adddot}} % endcode: finish with a dot


% marginnnote with a reduced citing format:
% Authors (year), Title. Year links to bibliography
\DeclareCiteCommand{\inlinecite}
  {\boolfalse{citetracker}% precode
   \boolfalse{pagetracker}%
   \usebibmacro{prenote}}
  {\ifciteindex % loopcode (the actual formatting)
     {\indexnames{labelname}%
      \indexfield{indextitle}}
     {}%
   \printtext{%
       \printnames{labelname}%
       \setunit{\addspace}
       \printtext[parens]{\printfield[bibhyperref]{year}}% year links to references
       % \setunit{\labelnamepunct}%
       % \printfield[citetitle]{labeltitle}%
     }%
   }
  {\multicitedelim} % sepcode: a comma usually
  {\usebibmacro{postnote}\printtext{}} % endcode: finish with a dot


% normal citation -> margin
\renewcommand{\cite}[2][0pt]{\sidenote[][#1]{\customcite{#2}}}
% inline citation
\newcommand{\icite}[2][]{\customcite[#1]{#2}}

% explanation of a word/phrase
\newcommand{\explanation}[2][0pt]{*\marginnote[#1]{*#2}}

% easier sub and superscripts
\newcommand{\sups}[1]{\textsuperscript{#1}}
\newcommand{\subs}[1]{\textsubscript{#1}}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Utility functions                                         
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%% include tex with embedded pdf
\newcommand{\pdftex}[2][0.975\textwidth]{
\scriptsize\sffamily\selectfont
\def\svgwidth{#1}
\input{#2}
}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% headings                                         
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% headline
\newcommand\HUGE{\fontsize{26}{26}\selectfont}
\newcommand\CHAPTERSIZE{\fontsize{16}{10}\selectfont}
\titleformat{\chapter}%
  [display]% shape
  {\vspace{-2.5cm}\relax\begin{fullwidth}}% format applied to label+text
  {\CHAPTERSIZE \rmfamily\scshape Chapter \thechapter}% label
  {-1em}% horizontal separation between label and title body
  {\HUGE\rmfamily}% before the title body
  [\end{fullwidth}\vspace{-2em}]% after the title body

% Indent for section number number
\titlespacing*{\section}{0pt}{0pt}{0pt}
\titleformat{\section}%
  [hang]% shape
  {\normalfont\scshape}% format applied to label+text
  {\thesection\hfill}
  {1em}% horizontal separation between label and title body
  {\normalfont\scshape}% before the title body
  []% after the title body

\titlespacing*{\subsection}{0pt}{0pt}{0pt}  
\titleformat{\subsection}%
  [hang]% shape
  {\normalfont\scshape}% format applied to label+text
  {\thesubsection\hfill}% label
  {1em}% horizontal separation between label and title body
  {\normalfont}% before the title body
  []% after the title body

\titleformat{\paragraph}
  [hang]
  {\normalfont}
  {\thesubsubsection} 
  {0em}
  {\normalfont}
  [\vspace{-1em}]

% number of sections that become a counter
\setcounter{secnumdepth}{2}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Ref Names                                       
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\creflabelformat{equation}{#2\textup{#1}#3}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Page Style                                             
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% remove paragraph indentation
\makeatletter
% Paragraph indentation and separation for normal text
\renewcommand{\@tufte@reset@par}{%
  \setlength{\RaggedRightParindent}{0.0pc}%
  \setlength{\JustifyingParindent}{0.0pc}%
  \setlength{\parindent}{0pc}%
  \setlength{\parskip}{\baselineskip}%
}
\@tufte@reset@par

% Paragraph indentation and separation for marginal text
\renewcommand{\@tufte@margin@par}{%
  \setlength{\RaggedRightParindent}{0.0pc}%
  \setlength{\JustifyingParindent}{0.0pc}%
  \setlength{\parindent}{0.0pc}%
  \setlength{\parskip}{10pt}%
}
\makeatother

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Quick fix for xelatex (authors forgot it in tufte)
% see https://tex.stackexchange.com/questions/200722/xetex-seems-to-break-headers-in-tufte-handout                                          
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\ifxetex
  \renewcommand{\textls}[2][5]{%
    \begingroup\addfontfeatures{LetterSpace=#1}#2\endgroup
  }
  \renewcommand{\allcapsspacing}[1]{\textls[15]{#1}}
  \renewcommand{\smallcapsspacing}[1]{\textls[10]{#1}}
  \renewcommand{\allcaps}[1]{\textls[15]{\MakeTextUppercase{#1}}}
  \renewcommand{\smallcaps}[1]{\smallcapsspacing{\scshape\MakeTextLowercase{#1}}}
  \renewcommand{\textsc}[1]{\smallcapsspacing{\textsmallcaps{#1}}}
\fi

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Custom title page
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\makeatletter
\newcommand{\fb}[1]{
  \def\@fb{#1}
}
\newcommand{\university}[1]{
  \def\@university{#1}
}
\newcommand{\refereeA}[1]{
  \def\@refereeA{#1}
}
\newcommand{\refereeB}[1]{
  \def\@refereeB{#1}
}
\newcommand{\location}[1]{
  \def\@location{#1}
}

\usepackage{linegoal}% http://ctan.org/pkg/linegoal
\usepackage{xparse}% http://ctan.org/pkg/xparse
\NewDocumentCommand{\centerrule}{O{0.5ex} O{0.4pt}}{%
  \leavevmode\rule[#1]{\linegoal}{#2}
}

\renewcommand{\maketitlepage}{
\begin{fullwidth}
\sffamily
\centering
{% top
    \includegraphics[width=3.5cm]{athene}\\
    \vspace{2pc}
    \centerrule
    \fontsize{24}{26}\selectfont\textcolor{darkgray}{\allcaps{\textrm{\thanklesstitle}}}\\
    \centerrule
}
\vspace{1pc}
\doublespacing
{% center
    \fontsize{14}{14}\selectfont
    \par
    dem Fachbereich \@fb\\
    der \@university\\
    \vspace{1.5pc}
    zur Erlangung des Grades\\
    Doctor rerum naturalium (Dr. rer. nat.)\\
    \vspace{2pc}
    vorgelegte Dissertation von\\
    \vspace{1pc}
    \Huge\selectfont\hspace{0.4cm}\textcolor{darkgray}{\allcaps{\textrm{\@author}}}
}
~\vfill
{% bottom 
\begin{tabular}{ll}
\fontsize{14}{14}\selectfont\par\noindent{Erstgutachter:}  & \fontsize{14}{14}\selectfont\par\noindent{\@refereeA} \\
\fontsize{14}{14}\selectfont\par\noindent{Zweitgutachter:} & \fontsize{14}{14}\selectfont\par\noindent{\@refereeB} \\
\end{tabular}
% \vspace{1pc}
\fontsize{14}{14}\selectfont\par\noindent\allcaps{\@location~\the\year}
}
\end{fullwidth}
\thispagestyle{empty}
\clearpage
}

\newcommand{\plainsubtitle}{}
\newcommand{\subtitle}[1]{%
  \gdef\@subtitle{#1}%
  \renewcommand{\plainsubtitle}{#1}% use provided plain-text title
  \ifthenelse{\isundefined{\hypersetup}}%
    {}% hyperref is not loaded; do nothing
    {\hypersetup{pdftitle={\plaintitle: \plainsubtitle{}}}}% set the PDF metadata title
}
\makeatother

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% My page style
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\usepackage{fancyhdr}
% pagestyle that does not print anything
\fancypagestyle{nothing}{
    \lhead{}
    \fancyhead[LE]{}
    \fancyhead[RO]{}
}

% no numbers on part pages
\patchcmd{\part}{\thispagestyle{plain}}{\thispagestyle{empty}}
  {}{\errmessage{Cannot patch \string\part}}
\fancypagestyle{plain}{}