%% Follow comments to support use.

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% STEP 1: Choose options for MSc / BSc / seminar layout and your bibliographic style
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%%  Language: 
%%      finnish, swedish, or english
%%  Pagination (use twoside by default)  
%%      oneside or twoside,
%%  Study programme / kind of report
%%      csm  = Master's thesis in Computer Science Master's Programme;
%%      tkt = Bachelor's thesis in Computer Science Bachelor's Programme;
%%      seminar = seminar report
%%  For Master's thesis choose your line or track:
%%      (30 cr thesis, 2020 onwards, Master's Programme in Computer Science = csm)
%%      software-track-2020 = Software study track
%%      algorithms-track-2020 = Algorithms study track
%%      networking-track-2020 = Networking study track

\documentclass[english,twoside,censored,csm,software-track-2020]{HYthesisML} 


% If wanted, open new chapters only at right page.
% By default, "openany".
%\PassOptionsToClass{openright,twoside,a4paper}{report}
\PassOptionsToClass{openany,twoside,a4paper}{report}

\usepackage{csquotes}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% REFERENCES
%% Some notes on bibliography usage and options:
%% natbib -> you can use, e.g., \citep{} or \parencite{} for (Einstein, 1905); with APA \cite -> Einstein, 1905 without ()
%% maxcitenames=2 -> only 2 author names in text citations, if more -> et al. is used
%% maxbibnames=99 as no great need to suppress the biliography list in a thesis
%% for more information see biblatex package documentation, e.g., from https://ctan.org/pkg/biblatex 

%% Reference style: select one 
%% for APA = Harvard style = authoryear -> (Einstein, 1905) use:
\usepackage[style=authoryear,bibstyle=authoryear,backend=biber,natbib=true,maxnames=99,maxcitenames=2,uniquelist=minyear,giveninits=true,uniquename=mininit]{biblatex}
%% for numeric = Vancouver style -> [1] use:
%\usepackage[style=numeric,bibstyle=numeric,backend=biber,natbib=true,maxbibnames=99,giveninits=true,uniquename=init]{biblatex}
%% for alpahbetic -> [Ein05] use:
%\usepackage[style=alphabetic,bibstyle=alphabetic,backend=biber,natbib=true,maxbibnames=99,giveninits=true,uniquename=init]{biblatex}
%

\addbibresource{bibliography.bib}
% in case you want the final delimiter between authors & -> (Einstein & Zweistein, 1905) 
% \renewcommand{\finalnamedelim}{ \& }
% List the authors in the Bibilipgraphy as Lastname F, Familyname G,
\DeclareNameAlias{sortname}{family-given}
% remove the punctuation between author names in Bibliography 
%\renewcommand{\revsdnamepunct}{ }

% Asked chat.openai.com: I'm using biblatex package, but it prints odd format volume.number in reference list, while this should be volume (number). How to fix this?
%Answer (shortened):
% Redefine the volume and number format
%\DeclareFieldFormat[article]{volume}{\mkbibbold{#1}}
%\DeclareFieldFormat[article]{number}{\mkbibparens{#1}}
% Please remove the boldface from the volume and number fields:
\DeclareFieldFormat[article]{volume}{#1}
\DeclareFieldFormat[article]{number}{\mkbibparens{#1}}
% Now this generated format volume.(number). How to remove the dot? (and so on with some adjustments):
\renewbibmacro*{volume+number+eid}{%
  \setunit{\addcomma\space}% 
  \printfield{volume}%
  %\setunit*{\addnbspace\addthinspace}% <-- Adjust spacing here
  \printfield{number}%
  \setunit{\addcomma\space}%
  \printfield{eid}}


%% Block of definitions for fonts and packages for picture management.
%% In some systems, the figure packages may not be happy together.
%% Choose the ones you need.

%\usepackage[utf8]{inputenc} % For UTF8 support, in some systems. Use UTF8 when saving your file.

\usepackage{lmodern}         % Font package, again in some systems.
\usepackage{textcomp}        % Package for special symbols
\usepackage[pdftex]{color, graphicx} % For pdf output and jpg/png graphics
\usepackage{epsfig}
\usepackage{subfigure}
\usepackage[pdftex, plainpages=false]{hyperref} % For hyperlinks and pdf metadata
\usepackage{fancyhdr}        % For nicer page headers
\usepackage{tikz}            % For making vector graphics (hard to learn but powerful)
%\usepackage{wrapfig}        % For nice text-wrapping figures (use at own discretion)
\usepackage{amsmath, amssymb} % For better math

\singlespacing               %line spacing options; normally use single

\fussy
%\sloppy                      % sloppy and fussy commands can be used to avoid overlong text lines
% if you want to see which lines are too long or have too little stuff, comment out the following lines
% \overfullrule=1mm
% to see more info in the detailed log about under/overfull boxes...
% \showboxbreadth=50 
% \showboxdepth=50



%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% STEP 2:
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Set up personal information for the title page and the abstract form.
%% Replace parameters with your information.
\title{Title}

\author{Firstname Lastname}
\date{\today}

% Set supervisors, use the titles according to the thesis language
% in English Prof. or Dr., or in Finnish toht. or tri or FT, TkT, Ph.D. or in Swedish... 
\supervisors{Prof.~D.U.~Mind, Dr.~O.~Why}

\keywords{algorithms, data structures}
\additionalinformation{\translate{\track}}

%% For seminar reports:
%%\additionalinformation{Name of the seminar}

%% Provide classification terms, to appear on the abstract page.
%% Replace the classification terms below with the ones that match your work.
%% ACM Digital library provides a taxonomy and a tool for classification
%% in computer science. Use 1-3 paths, and use right arrows between the
%% about three levels in the path; each path requires a new line.

\classification{\protect{\ \\
\  General and reference $\rightarrow$ Document types  $\rightarrow$ Surveys and overviews\  \\
\  Applied computing  $\rightarrow$ Document management and text processing  $\rightarrow$ Document management $\rightarrow$ Text editing
}}

%% If you want to quote someone special. You can comment this line out and there will be nothing on the document.
%\quoting{Bachelor's degrees make pretty good placemats if you get them laminated.}{Jeph Jacques}


%% OPTIONAL STEP: Set up properties and metadata for the pdf file that pdfLaTeX makes.
%% Your name, work title, and keywords are recommended.
\hypersetup{
    unicode=true,           % to show non-Latin characters in Acrobat’s bookmarks
    pdftoolbar=true,        % show Acrobat’s toolbar?
    pdfmenubar=true,        % show Acrobat’s menu?
    pdffitwindow=false,     % window fit to page when opened
    pdfstartview={FitH},    % fits the width of the page to the window
    pdftitle={},            % title
    pdfauthor={},           % author
    pdfsubject={},          % subject of the document
    pdfcreator={},          % creator of the document
    pdfproducer={pdfLaTeX}, % producer of the document
    pdfkeywords={something} {something else}, % list of keywords for
    pdfnewwindow=true,      % links in new window
    colorlinks=true,        % false: boxed links; true: colored links
    linkcolor=black,        % color of internal links
    citecolor=black,        % color of links to bibliography
    filecolor=magenta,      % color of file links
    urlcolor=cyan           % color of external links
}

%%-----------------------------------------------------------------------------------

\begin{document}

% Generate title page.
\maketitle

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% STEP 3:
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Write your abstract in the separate file, to be positioned here.
%% You can make several abstract pages (if you want it in different languages),
%% in which case you should also define the language of the abstract,
%% as below.

\include{Ch.00_Abstract}

% Place ToC
%\newpage
\mytableofcontents

\mainmatter

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% STEP 4: Write the thesis.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Your actual text starts here. You shouldn't mess with the code above the line except
%% to change the parameters. Removing the abstract and ToC commands will mess up stuff.
%%
%% Command \include{file} includes the file of name file.tex.
%% A new page will be created at every \include command, 
%% which makes it appropriate to use it for large entities such as book chapters. Cannot be nested.
%% It is useful for a big project, as changing one of the include targets 
%% won't force the regeneration of the outputs of all the rest.
%% Alternatively, \input is a more lower level macro 
%% which simply inputs the content of the given file like it was copy&pasted there manually.

\include{Ch.10_Introduction}
\include{Ch.20_Methods}
\include{Ch.30_Results}
\include{Ch.40_Discussion}
\include{Ch.50_Conclusions}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%\cleardoublepage                          %fixes the position of bibliography in bookmarks
%\phantomsection
\addcontentsline{toc}{chapter}{\bibname}  % This lines adds the bibliography to the ToC
\printbibliography

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\backmatter
\begin{appendices}

%% A sample Appendix
\include{Ch.90_Appendix_1}
%% another appendix
\include{instructions/instructions_english}
%% yet another appendix
\include{instructions/instructions_finnish}

% BSc instructions
%\include{instructions/bsc_finnish_contents}
%\include{instructions/bsc_english_contents}


\end{appendices}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\end{document}