env_dissertation.mkiv

\startenvironment env_dissertation
\usepath[{parts}]

\enableregime[utf-8]
\mainlanguage[en]
\setuplanguage[en][spacing=packed] % no double space after sentences

% Interoperability: Unifying/connecting methods through frameworks
% Discoverability: Best practice tools pre-selected
% Stabilization: Focus on interpretation by having reproducibility and frameworks instead of glue code
% “Frameworks of interpretation”
% “Codifying the tools of the trade”
\def\doctitle{Frameworks of interpretation: stabilizing scRNA-Seq data processing for discovery}
\def\author{Philipp J.G.F. Angerer}
\def\kindofwork{Ph.D. Thesis}
\def\topicofwork{Computational Biology}

% Page layout
\setuplayout[
	alternative=doublesided,
	width=middle,
	headerdistance=0cm,
	header=1cm,
	footerdistance=0cm,
	footer=0cm,
]
% Page numbering
\setuppagenumbering[
	state=start,
	alternative=singlesided,
	location={header, right},
	style=sans,
	way=bypart,
	sectionnumber=no,
	strut=yes,
]
% Headers & footers
\setupheader[text][after=\vskip 4pt \hrule]
\setupheadertexts
	[{\userpagenumber}]
	[{\getmarking[chapternumber]\ \getmarking[chapter]}]
	[{\userpagenumber}]
	[{\getmarking[chapternumber]\ \getmarking[chapter]}]

% Allow colors
\setupcolors[state=start]
\setupbar[color=black]
% Links & document metadata
\setupinteraction[
	state=start,
	color=,
	contrastcolor=,
	% Document metadata
	title=\doctitle,
	subtitle={\kindofwork\ in \topicofwork},
	author=\author,
	% Don’t switch to fit page mode on link click
	focus=standard,
]
% \setupsynctex[state=start] % Takes time and doesn’t seem to work in Kile
% keep track of the number but don’t show it
\setuphead[title][incrementnumber=yes, number=no]
% Make all section titles interactive, and show titles too
\setupcombinedlist[content][interaction=all,list={chapter,section,subsection,subsubsection,title}]

% Which PDF bookmarks to create and which ones to open
\placebookmarks[chapter,title,section,subsection,subsubsection][chapter,title,section][force=yes]
\setupinteractionscreen[option=bookmark]
\enabledirectives[interaction.identity.preroll]  % prevent TeX from appering in title metadata
\enabledirectives[references.bookmarks.preroll]  % prevent TeX from appering in PDF bookmarks

% % Vim syntax highlighting
%\usemodule[vim]
%\definevimtyping[python][syntax=python, strip=yes, lines=split, escape=on]
%\definevimtyping[R][syntax=r, strip=yes]

% Typography settings
\setupalign[hz, hanging, tolerant] % Breaks: Font expansion, Protruding punct., tolerance
\definefontfeature[default][default][ % https://docs.microsoft.com/en-us/typography/opentype/spec/features_ae
	liga=yes, tlig=yes, ccmp=yes, % ligatures and glyph composition/decomposition
	kern=yes, % kerning
	onum=yes, % oldstyle numbers
	expansion=quality, protrusion=quality,
	trep=no, mode=node, % text replacement like '→’
]
\setupbodyfontenvironment[default][em=italic] %italic instead of slanted
\setupindenting[yes, medium] % Indent paragraph starts
\setbreakpoints[compound] % Allow breaking after dashes

% hyphenation
\hyphenation{chan-ges}
\hyphenation{u-bi-qui-tous}
\hyphenation{me-thy-la-tion}
\hyphenation{he-te-ro-ge-ne-i-ty}
\hyphenation{mar-kers}

% Font settings, need to be after typography
%\usetypescriptfile[type-imp-euler.mkiv]
%\usetypescript[eulernova]
%\usetypescriptfile[type-luxi]
%\usetypescript[type-luxi]
\definefontfamily[myfonts][serif][TeX Gyre Pagella] % Palatino
\definefontfamily[myfonts][math][TeX Gyre Pagella Math] % AMS Euler or TeX Gyre Pagella Math or XITS Math
\definefontfamily[myfonts][sans][TeX Gyre Heros]   %Helvetica
\definefontfamily[myfonts][mono][Luxi Mono][rscale=0.86]  % or: Tex Gyre Cursor
\setupbodyfont[myfonts, 12pt]

% small caps
\def\n#1{\smallcaps{#1}}

% Heading style
\setuphead[chapter]      [style=\ss\bfc, align=flushleft]
\setuphead[section]      [style=\ss\bfb, align=flushleft]
\setuphead[subsection]   [style=\ss\bfa, align=flushleft]
\setuphead[subsubsection][style=\ss\bf,  align=flushleft]
\setuplabeltext[en][appendix=Appendix~]
\define[2]\AppendixHeader
  {\framed[frame=off,width=broad,align=flushleft]{\ss\bfc#1\crlf#2}}
\startsectionblockenvironment[appendix]
\setuphead[chapter][command=\AppendixHeader]
\stopsectionblockenvironment

% List environments
\definedescription[desc][
	headstyle=bold, style=normal,
	align=justify, alternative=hanging,
	width=broad, margin=1cm,
]

% Floating environments
\setupcombinations[location=top, alternative=text]
\definefloat[listing][listings]
\setupcaption[figure][hang=yes, indentnext=no]
\definefloat[subfigure][subfigures]
\setupfloat[subfigure][local=yes]
\setupcaption[subfigure][number=yes, numberconversion=a, style=bold, location=right]
\setuplabeltext[subfigure=]
\appendvalue{stopplacefigure}{\resetcounter[subfigure]}
\definefloat[narrowfigure][figures][figure]
\setupcaption[narrowfigure][location=right, hang=no]

% Tables
\setupTABLE[c][each][align={middle,lohi},frame=off]

\usemodule[database]
\defineseparatedlist
	[TSV]
	[separator=tab,first=\bTR,last=\eTR,left=\bTD,right=\eTD]
\defineseparatedlist
	[CSV]
	[separator=comma,first=\bTR,last=\eTR,left=\bTD,right=\eTD]

%\startseparatedlist[TSV]
%\startTSV
%\processseparatedfile[TSV][filename]

% references
\setupreferencing[left=, right=]

% Citations/Bibliography
% http://pragma-ade.nl/general/manuals/mkiv-publications.pdf
\definebtxdataset[main]
\usebtxdataset[main][bib/\jobname.bib]
\setupbtx[dataset=main] % make \cite use this by default
\setupbtx[default:cite][alternative=authoryear] % default so the shortcut \cite[ref] can be used
\usebtxdefinitions[apa] % load apa styles for bib entry and \cite rendering
\setupbtx[apa:cite][otherstext={ et al.}, etallimit=3]
\setupbtx[apa:list][etallimit=, etaldisplay=]

\definebtxrendering[main][apa][dataset=main, pagestate=start] % define a bib entry rendering to use with \placebtxrendering (sorting, numbering=no, …)
% \newbibfield[timestamp]
% \setuppublicationlayout[electronic]{%
% 	\insertauthors{}{. }{}%
% 	\inserttitle{}{ }{}%
% 	\inserturl{\bgroup\tt}{\egroup\ }{}%
% 	\inserttimestamp{accessed:}{ }{}%
% 	\insertnote{ }{.}{}%
% }
\def\inlinecite[#1]{\cite[authoryears][#1]}
\def\inbracecite[#1]{\cite[authoryear,left=,right=][#1]}

% command to extract titles
\startluacode
local luadata = publications.datasets.main.luadata
--for tag, entry in next, luadata do
--    if entry.title then
--        logs.report("btx", "tag: %a, title: %a", entry.tag, entry.title)
--    end
--end

userdata = userdata or {}

function userdata.cite_title(tag)
    tex.print(luadata[tag].title)
end
\stopluacode

\def\placecitationtitle#1{\ctxlua{userdata.cite_title([==[#1]==])}}

\def\titlecite#1{\placecitationtitle{#1} \cite[#1]}

\def\embedappendix{\dosingleempty\doEmbedappendix}
\def\doEmbedappendix[#1]#2{\page[odd]
\startchapter[title={\titlecite{#2}}, #1]
\cite[alternative=entry, left=, right=][#2]
\page
\copypages[publications/#2.pdf][][scale=900]
\stopchapter}

% \usemodule[res-08] \setups[rl:manipulate]
\setupexternalfigures[directory=imgs,conversion=pdf]
% Modules
%\usemodule[newmat]
%\usemodule[chemic]

\usemodule[tikz]

\usemodule[pgfplots] % needs to be before \usetikzlibrary calls
\pgfplotsset{compat=1.14}
% \usepgfplotslibrary[groupplots]
\unexpanded\def\startgroupplot{\groupplot}
\unexpanded\def\stopgroupplot{\endgroupplot}
% \usemodule[pgfplotstable]
%\usepgfplotslibrary[groupplots]

% https://tikz.dev/pgfplots/pgfplotstable-load-data
% Applies to both `\pgfplotstableread` and `\addplot table`
\pgfplotsset{
	table/search path={data},
}

\usetikzlibrary[positioning] % needs to be after pgfplots
\usetikzlibrary[decorations.pathreplacing]
\usetikzlibrary[backgrounds] %\tikz[framed] for debugging
\usetikzlibrary[shapes]
%\usetikzlibrary[shadings]
\usetikzlibrary[arrows.meta]
\usetikzlibrary[fadings]
\usetikzlibrary[calc]
%\usetikzlibrary[external]
%\tikzexternalize[prefix=imgs/]

\usemodule[logos]

\catcode`√=13\def√{\sqrt}
\catcode`∜=13\def∜{\sqrt[4]}
%\definemathfunction[cdf][mathlimits=auto]
%\definemathfunction[Cov][mathlimits=auto]
%\definemathfunction[Var][mathlimits=auto]
\definemathfunction[mean][mathlimits=auto]
\definemathfunction[argmin][mathlimits=auto]
\definemathfunction[argmax][mathlimits=auto]

\definemathfunction[LR][mathlimits=no]
\definemathfunction[GR][mathlimits=no]
\definemathfunction[rank][mathlimits=no]

% References
\definereferenceformat[ineq][text={Equation }] %left=(,right=),
\definereferenceformat[infig][text={Figure }]
\definereferenceformat[insec][text={Section }]
\definereferenceformat[andsec][text={and }]

% % http://tex.stackexchange.com/questions/60950/how-to-draw-cdf-of-normal-distribution-in-tikz
%\tikzset{
%	declare function={
%		normcdf(\x,\mu,\s)=1/(1 + exp(-0.07056*((\x-\mu)/\s)^3 - 1.5976*(\x-\mu)/\s));
%	}
%}

%\pgfmathdeclarefunction{gauss}{2}{%
%	\pgfmathparse{1/(#2*sqrt(2*pi))*exp(-((x-#1)^2)/(2*#2^2))}%
%}

% % for i in range(11): print('rgb({}mm)=({s[0]},{s[1]},{s[2]});'.format(i*8, s=Spectral(i, bytes=False)))
%\pgfplotsset{
%	every axis title/.style={at={(0.5,1)},above,yshift=6pt,font=\bold},
%	colormap={spectral}{%
%		rgb(0mm)=(0.61,0.0,0.25);
%		rgb(8mm)=(0.82,0.23,0.3);
%		rgb(16mm)=(0.95,0.42,0.26);
%		rgb(24mm)=(0.98,0.67,0.37);
%		rgb(32mm)=(0.99,0.87,0.54);
%		rgb(40mm)=(0.99,0.99,0.74);
%		rgb(48mm)=(0.9,0.96,0.59);
%		rgb(56mm)=(0.66,0.86,0.64);
%		rgb(64mm)=(0.4,0.76,0.64);
%		rgb(72mm)=(0.19,0.52,0.73);
%		rgb(80mm)=(0.36,0.3,0.63)},
%	colormap={purd}{%
%		rgb255=(103,0,31)
%		rgb255=(152,0,67)
%		rgb255=(206,18,86)
%		rgb255=(231,41,138)
%		rgb255=(223,101,176)
%		rgb255=(201,148,199)
%		rgb255=(212,185,218)
%		rgb255=(231,225,239)
%		rgb255=(247,244,249)},
%}

%\pgfplotsset{
%	% this transformation ensures that every input argument is
%	% transformed from -0.2 : 0.5 -> -0.5,0.5
%	% and every tick label is transformed back:
%	nonlinear colormap trafo/.code 2 args={
%		\def\nonlinearscalefactor{((#2)/(#1))}%
%		\pgfkeysalso{%
%			y coord trafo/.code={%
%				\pgfmathparse{##1 < 0 ? -1*##1*\nonlinearscalefactor : ##1}%
%			},
%			y coord inv trafo/.code={%
%				\pgfmathparse{##1 < 0 ? -1*##1/\nonlinearscalefactor : ##1}%
%			},
%		}%
%	},
%	nonlinear colormap around 0/.code 2 args={
%		\def\nonlinearscalefactor{((#2)/(#1))}%
%		\pgfkeysalso{
%			colorbar style={
%				nonlinear colormap trafo={#1}{#2},
%				%
%				% OVERRIDE this here. The value is *only* used to
%				% generate a nice axis, it does not affect the data.
%				% Note that these values will be mapped through the
%				% colormap trafo as defined above.
%				point meta min={#1},
%				point meta max={#2},
%			},
%			%
%			% this here is how point meta is computed for the plot.
%			% It means that a point meta of -0.2 will actually become -0.5
%			% Thus, the *real* point meta min is -0.5... but we
%			% override it above.
%			point meta={y < 0 ? -y*\nonlinearscalefactor : y},
%		}%
%	},
%}

% Front and body part definitions
\definestructureconversionset[frontpart:pagenumber][][romannumerals]
\definestructureconversionset[bodypart:pagenumber] [][numbers]
\setuplist[chapter][pageconversionset=pagenumber]
\startsectionblockenvironment[frontpart]
\setupuserpagenumber[numberconversion=romannumerals]
\setcounter[userpage][1]
\stopsectionblockenvironment
\startsectionblockenvironment[bodypart]
\setupuserpagenumber[numberconversion=numbers]
\setcounter[userpage][1]
\stopsectionblockenvironment

\stopenvironment