main.tex

\documentclass[
    paper=240mm:170mm,
    paper=portrait,
    parskip=half,
    cleardoublepage=plain,
    toc=chapterentrywithdots,
    chapterprefix=true,
    captions=tableheading,
    fontsize=10pt,
    mpinclude=true,
    DIV=13,
    BCOR=15mm
]{scrbook}


\usepackage{fontspec}
\setmainfont{sourceserifpro}
\renewcommand*\sectfont{\normalcolor\bfseries}

\setmonofont[Scale=MatchLowercase]{Droid Sans Mono}

\usepackage[english]{babel}

% Het formaat van een doctoraat is "proefschrift B5".
% Een lichte afwijking tegenover ISO B5. B5 = 176x250mm
% Wij gebruiken 170x240mm.
% 1/9th of height = 28mm
% 1/9th of width = 19mm
% top = 1/9th + 1/18th
\usepackage[paperwidth=17cm, paperheight=24cm, heightrounded, top=2.6cm, bottom=5.3cm, right=3.8cm]{geometry} % left=1.9cm, total right 3.8, so 2.3
\addtolength{\marginparwidth}{1.5cm}

% \usepackage[
%   % set width and height to width and height + 4mm
%   width=18.4truecm, height=25.4truecm,
%   % use any combination of these options to add different cut markings
%   cam,
%   % set the type of TeX renderer you use
%   lualatex,
%   % center the contents
%   center
% ]{crop}

% We want more margins
% \addtolength{\marginparwidth}{1.5cm}
\usepackage{graphicx} % Required for inserting images
\usepackage{natbib} % probably should've done biblatex
\usepackage{hyperref}
\usepackage[sectionbib]{chapterbib}
\usepackage{float}
\usepackage{amsfonts} % checkmark
\usepackage{wasysym} % partial bullet
\usepackage{microtype}
\usepackage{xr}
\usepackage{transparent}
\usepackage[utf8]{inputenc}
\usepackage{epigraph}

\newcommand{\hidetitlepar}[1]{\par}
\usepackage{svg}

\usepackage{xurl}
\usepackage{listings}

\usepackage{afterpage}

\newcommand\blankpage{%
    \null
    \thispagestyle{empty}%
    \addtocounter{page}{-1}%
    \newpage}

\renewcommand{\bibname}{References}

\usepackage{babel}%.................. Language setup
    \addto{\captionsenglish}{\renewcommand{\bibname}{References}}

\usepackage{xcolor}


% Listings 
\definecolor{codegreen}{rgb}{0,0.6,0}
\definecolor{codegray}{rgb}{0.5,0.5,0.5}
\definecolor{kwordblue}{HTML}{00769E}
\definecolor{basiccolor}{HTML}{003B4F}
\definecolor{stringgreen}{HTML}{20794D}
\definecolor{background}{RGB}{233,236,239}

\lstdefinestyle{mystyle}{
  backgroundcolor=\color{background},   
  commentstyle=\color{codegreen},
  keywordstyle=\color{kwordblue},
  numberstyle=\tiny\color{codegray},
  stringstyle=\color{stringgreen},
  basicstyle=\ttfamily\footnotesize\color{basiccolor},
  breakatwhitespace=false,         
  breaklines=true,                 
  captionpos=t,                    
  keepspaces=true,                 
  numbers=left,                    
  numbersep=8pt,                  
  showspaces=false,                
  showstringspaces=false,
  showtabs=false,                  
  frame=single,                    
  rulecolor=\color{black},         
  xleftmargin=2pt,
  xrightmargin=2pt,
  framextopmargin=0pt,             % <-- Increased top margin
  framexbottommargin=0pt,
  framexleftmargin=0pt,
  framexrightmargin=0pt,
  framesep=2pt,                    % <-- Set to 0pt so code and frame touch            
}

\lstset{style=mystyle}
\usepackage{caption}

\renewcommand*{\captionformat}{~}
\setkomafont{captionlabel}{\small\bfseries}
\setkomafont{caption}{\small}
\setcapindent{1em}

\DeclareCaptionFont{black}{\color{black}}
\DeclareCaptionFormat{listing}{%
  \parbox{\textwidth}{%
    \fcolorbox{black}{white}{%
      \parbox{\dimexpr\textwidth-2\fboxsep-2\fboxrule\relax}{#1#2#3}%
    }%
  }%
}
\captionsetup[lstlisting]{format=listing,labelfont=black,textfont=black}
\lstset{
  captionpos=t,
  belowcaptionskip=4pt,
  abovecaptionskip=0pt
}
\renewcommand{\lstlistingname}{\bfseries Listing}

% marginnotes
\usepackage{scrlayer-scrpage}
\usepackage{scrlayer-notecolumn}
\addtokomafont{notecolumn.marginpar}{\scriptsize\raggedright}
\newcommand*{\marginnote}{\makenote}
\newcommand*{\comment}[1]{\makenote{\textcolor{red}{#1}}}
\newcommand*{\inlinecomment}[1]{\textcolor{red}{#1}}
\newcommand{\https}[1]{\href{https://#1}{#1}}
\newcommand{\footlink}[1]{\footnote{\https{#1}}}
\makeatletter
\ModifyLayer[
    contents = {%
    \textheight = 2\textheight%
    \slnc@processnotes{marginpar}%
    }
]{notecolumn.marginpar}

% no dots after chapter title
\renewcommand*{\chapterformat}{%
  \mbox{\chapappifchapterprefix{\nobreakspace}\thechapter
  \IfUsePrefixLine{}{\enskip}}%
}

% Smaller dots for table
\newcommand\mydots{\ifmmode\ldots\else\makebox[1em][c]{.\hfil.\hfil.}\fi}
\def\thickhline{\noalign{\hrule height.8pt}}

\usepackage{pdfpages}

% \NewDocumentCommand \software {m}{\textsc{#1}}
\NewDocumentCommand \software {m}{#1}

\raggedbottom

% for linenumbers
\usepackage{lineno}
% \linenumbers

\begin{document}

\frontmatter

\pagestyle{empty}
\includepdf[pages=-, pagecommand={}]{titlepage2.pdf}

\pagestyle{plain}

\include{genai}

\epigraph{'t Kan verkeren.}{\textit{Bredero}}

\include{acknowledgements}

\include{0_summary}
\include{0_samenvatting}

\includepdf[pages=-, pagecommand={}]{pubs.pdf} 

\include{0_conferences}

\tableofcontents

\mainmatter

\include{1-introduction/1-introduction}

\part{Trajectory inference}
\include{2-trajectoriesoverview/2-trajectoriesoverview}
\include{3-dynchro/3-dynchro}

\part{Interoperability}

\setlength{\epigraphwidth}{0.7\textwidth}
\epigraph{
The big idea is ``messaging'' ... The Japanese have a small word - ma - for ``that which is in between'' - perhaps the nearest English equivalent is ``interstitial''.

The key in making great and growable systems is much more to design how its
modules communicate rather than what their internal properties and
behaviors should be.
}{\textit{Alan Kay, On Messaging}}
% https://wiki.c2.com/?AlanKayOnMessaging
% https://userpage.fu-berlin.de/~ram/pub/pub_jf47ht81Ht/doc_kay_oop_en
% https://news.ycombinator.com/item?id=19415983

\include{4-interoperability/4-interoperability}
\include{5-anndataR/5-anndataR}

\part{Visualization}

\include{6-funkyheatmap/6-funkyheatmap}

\part{Reflections}

% \epigraph{
% How we remember changes how we have lived.
% Time runs both ways. We make stories of our lives.
% }{\textit{Guy Gavriel Kay, Under Heaven}}

\include{7a-future/7a-future}
\include{7-discussion/7-discussion}

\setlength{\epigraphwidth}{0.45\textwidth}
\epigraph{\foreignlanguage{greek}{Θάλαττα! Θάλαττα!}}{\textit{Xenophon, Anabasis}}

% \phantomsection{}
\appendix

\part{Appendices}
% \addcontentsline{toc}{part}{Appendices}

\include{4-interoperability/4-4-appendix}

% \include{6-funkyheatmap/funkyheatmap_appendix}
\chapter{Getting started with funkyheatmap}
\label{app:funky}
\includepdf[pages=-, pagecommand={}]{6-funkyheatmap/funkyheatmap_customized.pdf}
% \includepdf[pages=-]{6-funkyheatmap/funkyheatmap_appendix.pdf} 

% \afterpage{\blankpage}
% \afterpage{\blankpage}

\end{document}