\documentclass[12pt]{book}

\input{header}

\setcounter{maxexercise}{1000}  % show listings up to exercise maxexercise

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\begin{document} 

\hypersetup{pageanchor=false}
\maketitle
\hypersetup{pageanchor=true}

\frontmatter

\tableofcontents
\listoffigures
\lstlistoflistings
\listofexercisefs
\listofiboxfs


\mainmatter

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\part{Programming basics}

\graphicspath{{programming/lecture/}{programming/images/}}
\lstset{inputpath=programming/code}
\include{programming/lecture/programming}

\graphicspath{{debugging/lecture/}{debugging/lecture/figures/}}
\lstset{inputpath=debugging/code}
\include{debugging/lecture/debugging}

\graphicspath{{plotting/lecture/}{plotting/lecture/images/}}
\lstset{inputpath=plotting/code/}
\include{plotting/lecture/plotting}

\graphicspath{{programmingstyle/lecture/}{programmingstyle/lecture/figures/}}
\lstset{inputpath=programmingstyle/code/}
\include{programmingstyle/lecture/programmingstyle}

\graphicspath{{designpattern/lecture/}{designpattern/lecture/figures/}}
\lstset{inputpath=designpattern/code}
\include{designpattern/lecture/designpattern}


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\part{Data analysis}

\graphicspath{{statistics/lecture/}{statistics/lecture/figures/}}
\lstset{inputpath=statistics/code}
\include{statistics/lecture/statistics}

\graphicspath{{bootstrap/lecture/}{bootstrap/lecture/figures/}}
\lstset{inputpath=bootstrap/code}
\include{bootstrap/lecture/bootstrap}

\graphicspath{{regression/lecture/}{regression/lecture/figures/}}
\lstset{inputpath=regression/code}
\include{regression/lecture/regression}

\graphicspath{{likelihood/lecture/}{likelihood/lecture/figures/}}
\lstset{inputpath=likelihood/code}
\include{likelihood/lecture/likelihood}

\graphicspath{{pointprocesses/lecture/}{pointprocesses/lecture/figures/}}
\lstset{inputpath=pointprocesses/code/}
\renewcommand{\texinputpath}{pointprocesses/lecture/}
\include{pointprocesses/lecture/pointprocesses}

\graphicspath{{spectral/lecture/}{spectral/lecture/figures/}}
\lstset{inputpath=spectral/code/}
\renewcommand{\texinputpath}{spectral/lecture/}
%\include{spectral/lecture/spectral}

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%\part{Tools}
% Latex
% markdown
% Makefile
% version control (git and github) only put source files into repository!
% distributed computing (ssh and grid engines)
% data handling (structure, data bases, storage (rsync), backup)
% data annotation, meta data

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%\part{Appendix}

%\chapter{Cheat-Sheet}

\backmatter

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\printindex[term]

\printindex[determ]    % for english text
% \printindex[enterm]    % for german text

%\setindexprenote{Some explanations.}
%\printindex[pcode]
\printindex[mcode]

\end{document}