main.tex

\documentclass[12pt,a4paper,twoside,openright,pdftex]{book}
                              % Reproservice prints on G4, which is about 80% of A4.
                              % With this scale, 12pt font becomes 9.6pt.
                              % https://www.chalmers.se/insidan/SV/arbetsredskap/kommunikation/tryck-och-layout/mallar-for-trycksaker/avhandlingens-utformning

\synctex=1                    % instead of "pdflatex -synctex=1 main"

\usepackage{lipsum}           % generating fill-in text for this thesis template

\usepackage{ifthen}           % if-then-else (to choose PhD/Lic titles)

\usepackage[utf8]{inputenc}   % unicode letters in the input tex document

\usepackage[T1]{fontenc}      % unicode letters in the output pdf

\usepackage{amssymb, amsmath} % math symbols

\usepackage{lmodern}          % better font

\usepackage{microtype}        % micro typesetting (on errors use draft to disable)

\usepackage{booktabs}         % better table formatting

\usepackage[pdftex]{graphicx} % images

\usepackage{tikz}             % simply amazing graphics library for LaTeX
\usetikzlibrary{calc}

\usepackage[%                 %
  a4paper%
  ,twoside                    %
  ,inner=2.5cm                % inner margin
  ,outer=2.5cm                % outer margin
  ,bindingoffset=1cm       % additional binding offset on the inner side
  ,bottom=3cm
]{geometry}                   % Adjust the margins

\usepackage{fancyhdr}         % fine-tuning of headers
\pagestyle{fancy}

\usepackage{emptypage}        % no page numbers in headers/footers of blank pages between chapters

\usepackage{setspace}         % for \setstretch in captions

\usepackage[%
    margin=0.75cm,            % make captions narrower than the main text
    font={small,stretch=0.80}%%
  ]{caption}                  % captions

\usepackage{subcaption}       % subcaption -- subfigures (replaces subfig)

\usepackage{url}              % handles URLs correctly (e.g. DOI, software links)

\usepackage[%
  url=true,%                  % print URLs in references, except for the ones removed below
  backend=biber,%             % use biber instead of bibtex
  style=authoryear,%          % cite as: (Author 2008)
  maxbibnames=10,%            % max names in bibliography
  maxcitenames=2,%            % max names in citation
  mincitenames=1,%            % if there are more than maxcitenames, shrink to this
  backref=true,%              % prints page numbers (wrong with \frontmatter and hypertexnames=false)
  dashed=false                % do not replace repeated author with a dash in bibliography
]{biblatex}                   % Modern bibtex replacement (bibliography mgmt)

\usepackage[%
   pdftex%
  ,hidelinks%
  ,linktoc=all%               % part of a ToC entry to be made into a link (section/page/all)
  ,unicode%
  ,bookmarksopen=true%
  ,bookmarksopenlevel=0
  ,bookmarksnumbered=true
  %,hypertexnames=false,%     % Correct ToC hyperlinks even with chapter counter reset, but broken biblatex backref.
                              % Instead of using hypertexnames=false, use \renewcommand on \theHchapter, 
                              % see http://tex.stackexchange.com/a/6099
  %,draft                     % draft can be used to avoid some strange links errors
]{hyperref}                   % links in pdf document

\usepackage{bookmark}         % Create pdf bookmarks in one go


% % % Biblatex

\addbibresource{library.bib}  % Bibliography file
\renewcommand{\cite}{\parencite}

% Remove URLs from common (easy-to-find) entries.
\AtEveryBibitem{%
  \ifboolexpr%
    {%
      test { \ifentrytype{book} }
      or
      test { \ifentrytype{inbook} }
      or
      test { \ifentrytype{inproceedings} }
      or
      test { \ifentrytype{incollection} }
      or
      test { \ifentrytype{article} }
    }
    {\clearfield{url}}
    {}%
}
% End Biblatex


% % % New environments

% \newenvironment{env-name}[optional-number-of-args]{insert-before}{insert-after}

% \newenvironment{env-name}[optional-number-of-args][default-args]{insert-before}{insert-after}

\newenvironment{abstract}{
  \begin{center}
    {\bfseries Abstract\par}  % \bfseries - some bold font, \par - end of paragraph (as empty line)
  \end{center}
  \quotation                  % extra indent from left and right
  \noindent
}
{\par\endquotation}

\newenvironment{keywords}%
{{\bfseries Keywords:}}%
{\par}%
% % % End new environments


% Begin page content adjustments for putting more text on pages.
\renewcommand{\topfraction}{.85}       % max fraction of floats at top
\renewcommand{\bottomfraction}{.7}     % max fraction of floats at bottom
\renewcommand{\textfraction}{.15}      % minimal text wrt. figs
\renewcommand{\floatpagefraction}{.66} % fraction for page of floats. floatpagefraction MUST be less than topfraction 
\renewcommand{\dbltopfraction}{.66}    % fit big float above 2-col. text
\renewcommand{\dblfloatpagefraction}{.66}
\setcounter{topnumber}{9}
\setcounter{bottomnumber}{9}
\setcounter{totalnumber}{20}
\setcounter{dbltopnumber}{9}
\widowpenalty=300                             % widow (at the beginning of page)
\clubpenalty=300                              % orphans (at the end of page)
\setlength{\parskip}{0ex plus 0.5ex}  % space between paragraphs
% End page content adjustments

% % %
% Begin remove page numbers from the "Part I" pages
\fancypagestyle{veryempty}{% no headers, no page numbers
  \fancyhf{} % remove everything
  \fancyfoot{}
  \renewcommand{\headrulewidth}{0pt} % remove lines as well
  \renewcommand{\footrulewidth}{0pt}
}
\makeatletter
\renewcommand\part{%
  \if@openright
    \cleardoublepage
  \else
    \clearpage
  \fi
  \thispagestyle{veryempty}%
  \if@twocolumn
    \onecolumn
    \@tempswatrue
  \else
    \@tempswafalse
  \fi
  \null\vfil
  \secdef\@part\@spart}
\makeatother
% End remove page numbers from the "Part I" pages


% % % % %

\input{frontmatter/common-basic-info}     % author, title, etc

\title{\thesistitle}
\author{\thesisauthor}

\pdfinfo{%
  /Title (\thesistitle)
  /Author (\thesisauthor)
}

% Compression options
\pdfminorversion=5
\pdfobjcompresslevel=3  % compression requires \pdfminorversion at least 5
\pdfcompresslevel=9     % compression requires \pdfminorversion at least 5


\begin{document}

\input{frontmatter/standard-cover-page}

\frontmatter                  % roman page numbers

\input{frontmatter/standard-title-page}

\input{frontmatter/standard-copyrights-page}

\input{frontmatter/dedications-page}

% Add abstract to the ToC
\cleardoublepage              % advance the pages
\phantomsection               % put pdf anchor
\addcontentsline{toc}{chapter}{Abstract}  % add toc line with target at the last anchor
\chapter*{Abstract}
\vspace*{-1cm}                % More space for abstract text
\input{frontmatter/abstract}

\cleardoublepage              % advance the pages
\phantomsection               % put pdf anchor
\addcontentsline{toc}{chapter}{Acknowledgments}  % add toc line with target at the last anchor
\chapter*{Acknowledgments}
\input{frontmatter/acknowledgments}

\cleardoublepage              % advance the pages
\phantomsection               % put pdf anchor
\addcontentsline{toc}{chapter}{List of Publications}  % add toc line with target at the last anchor
\chapter*{List of Publications}
\input{frontmatter/publications-list}

\cleardoublepage              % advance the pages
\phantomsection               % put pdf anchor
\addcontentsline{toc}{chapter}{List of Acronyms}  % add toc line with target at the last anchor
\chapter*{List of Acronyms}
\input{frontmatter/acronyms}

% add Contents to PDF bookmarks, but do not add it to the 'printed' Contents
\cleardoublepage
\phantomsection
% \pdfbookmark[level]{text-to-display-in-outline}{unique-pdf-anchor-name}, chapter is level 0
\pdfbookmark[0]{Contents}{Contents}
\tableofcontents

\mainmatter                   % normal arabic page numbers

\part{Introductory chapters}

% Headers, footers
\fancyfoot{}                  % clean all
\fancyhead[RE]{\textit{\nouppercase{\rightmark}}}
\fancyhead[RO]{\thepage}
\fancyhead[LE]{\thepage}
\fancyhead[LO]{\textit{\nouppercase{\leftmark}}}

  \begin{refsection}

    \include{kappa/body}

    \printbibliography[heading=bibintoc]

  \end{refsection}

\cleardoublepage

% % % Preparations before Part II. In this part one chapter = one paper

\renewcommand{\chaptername}{Paper}
                              % write 'Paper' instead of 'Chapter' in the title

\setcounter{chapter}{0}       % reset chapter numbers after Part I

% Fix hyperlinks to chapters/papers after chapter counter reset, see
% http://tex.stackexchange.com/a/6099
\renewcommand\theHchapter{appendedPaper.\arabic{chapter}}

\renewcommand{\thesection}{\arabic{section}}
                              % exclude chapter number from section number
                              % Figures, Tables, etc are still prefixed by chapter number.
                              % For algorithms numbering see definition of
                              % \newfloat{algorithm} above.

\newcommand{\paper}[7]
% #1 Paper Title
% #2 Short Title for page headers (ToC has the full title)
% #3 Label for later (or earlier) \ref:s
% #4 Authors
% #5 Where published
% #6 Comment (like "reprinted with a kind permission" and "reformatted for uniformity")
% #7 File to input
{
  \chapter{#1\label{#3}}      % Title as Chapter
  \chaptermark{#2}            % Short title for the page header
  \thispagestyle{empty}       % no page numbers
  {\Large #4}\par             % authors
  \vspace{1cm}
  \noindent\emph{\Large #5}\par % where published
  \vspace{3cm}
  \noindent\emph{\Large #6}   % Comment
  \cleardoublepage            % skip back side of the page
  \thispagestyle{plain}       % no header above paper title
  \begin{center}
    {\Large \bfseries Paper~\thechapter. #1}\par % title again
    \vspace{1pc}
    #4 \par                   % authors again
    \vspace{3pc}
  \end{center}
  \begin{refsection}          % start of biblatex's refsection for sub-bibliography
  \input{#7}                  % paper itself, starting from abstract (no title)
  \printbibliography[heading=subbibintoc] % biblatex bibliography
  \end{refsection}            % end of biblatex refsection
}

\newcommand{\reformatted}{The paper was reformatted for uniformity, but otherwise is unchanged.}

\part{Appended papers}        % in this part one chapter = one paper

% Example of using the command \paper defined above: 
\paper{SAT-solving in practice, with a tutorial example from supervisory control}
      {SAT-solving in practice, with a SCT example}
      {pap:supervisory}
      {Koen~Claessen, Niklas~Een, Mary~Sheeran, Niklas~Sörensson, Alexey~Voronov and Knut~Åkesson}
      {Journal of Discrete Event Dynamic Systems (2009), 19(4): 495--524.}
      {Reproduced with kind permission from Springer Science+Business Media. \reformatted}
      {paper-supervisory/body}

\paper{The same paper, inserted second time for illustration}
      {SAT-solving in practice, with a SCT example}
      {pap:another-one}
      {Koen~Claessen, Niklas~Een, Mary~Sheeran, Niklas~Sörensson, Alexey~Voronov and Knut~Åkesson}
      {Journal of Discrete Event Dynamic Systems (2009), 19(4): 495--524.}
      {Reproduced with kind permission from Springer Science+Business Media. \reformatted}
      {paper-supervisory/body}

\end{document}