initial commit, import all templates

Thesis/Appendices/app-AppendixA.tex

@@ -0,0 +1,9 @@
+\chapter{Title for first appendix}
+\chaptermark{Title for first appendix in header}
+\label{app:annexeA}
+%\adjustmtc
+\minitoc
+
+\section{Section 1}
+
+...

Thesis/Appendices/app-Glossary.tex

@@ -0,0 +1,4 @@
+\chapter*{Glossary}
+\chaptermark{Glossary}
+\markboth{GLOSSARY}{PUBLICATIONS}
+\addcontentsline{toc}{chapter}{Glossary}

Thesis/Appendices/app-Publications.tex

@@ -0,0 +1,17 @@
+\chapter*{List of Publications}
+\chaptermark{List of Publications}
+\markboth{LIST OF PUBLICATIONS}{LIST OF PUBLICATIONS}
+\addcontentsline{toc}{chapter}{List of Publications}
+
+%%% Add all relevant publications to ./papers.bib
+%%% Define \firstauth{Name} and \addboldnames{{Name, I.},{Name, First-Name}} in PhDThesisED182.cls
+%%% Will go through all references, add categories based on First Author, Second Author or Contributor
+%%% Can also add conference talks and posters as non-articles
+
+\begin{refsection}
+    \nocite{*}%
+    \printbibliography[keyword={first},check=JoPR,type=article,heading=subbibliography,title={First Author}]%
+    \printbibliography[keyword={main},check=JoPR,type=article,heading=subbibliography,title={Main contribution}]%
+    \printbibliography[keyword={collab},check=JoPR,type=article,heading=subbibliography,title={Collaborator}]%
+    \printbibliography[nottype=article,heading=subbibliography,title={Conferences}]%
+\end{refsection}

Thesis/Chapters/ch-Abstract.tex

@@ -0,0 +1,6 @@
+\chapter*{Abstract}
+\chaptermark{Abstract}
+\markboth{ABSTRACT}{ABSTRACT}
+\addcontentsline{toc}{chapter}{Abstract}
+
+...

Thesis/Chapters/ch-Acknowledgements.tex

@@ -0,0 +1,5 @@
+\chapter*{Acknowledgements}
+\chaptermark{Acknowledgements}
+\markboth{ACKNOWLEDGEMENTS}{ACKNOWLEDGEMENTS}
+
+...

Thesis/Chapters/ch-Chapter1.tex

@@ -0,0 +1,28 @@
+\chapter{Chapter 1 title}
+\chaptermark{Chapter 1 title in header}
+\label{ch:chapter1}
+%\adjustmtc
+\minitoc
+
+\section{First Section of first chapter}
+\subsection{Let's talk about A}
+
+I must quote \citet{FavoriteAuthor} because they did a great job.
+
+\subsection{And now B}
+
+...
+
+\section{But what about this}
+
+\begin{figure}[ht]
+    \centering
+    \includegraphics[]{example-image-a}
+    \caption{Image A.}
+\end{figure}
+
+\begin{figure}[ht]
+    \centering
+    \includegraphics[]{example-image-b}
+    \caption{Image B.}
+\end{figure}

Thesis/Chapters/ch-Chapter2.tex

@@ -0,0 +1,14 @@
+\chapter{Chapter 2 title}
+\chaptermark{Chapter 2 title in header}
+\label{ch:chapter2}
+%\adjustmtc
+\minitoc
+
+
+\section{This is a work in progress}
+
+\subsection{Don't look at my notes}
+
+\begin{notes}
+    This text is only visible with the "ShowNotes" class option
+\end{notes}

Thesis/Chapters/ch-Chapter3.tex

@@ -0,0 +1,17 @@
+\chapter{Chapter 3 title}
+\chaptermark{Chapter 3 title in header}
+\label{ch:chapter3}
+%\adjustmtc
+\minitoc
+
+\section{Look at this Table}
+
+\begin{table}[ht]
+    \centering
+    \begin{tabular}{c|c}
+        First col & Second col \\
+        wow & right
+    \end{tabular}
+    \caption{Omg much data}
+    \label{tab:greattable}
+\end{table}

Thesis/Chapters/ch-Conclusion.tex

@@ -0,0 +1,7 @@
+\chapter*{Conclusion}
+\chaptermark{Conclusion}
+\markboth{CONCLUSION}{CONCLUSION}
+\addcontentsline{toc}{chapter}{Conclusion}
+\label{ch:Conclusion}
+
+...

Thesis/Chapters/ch-Introduction.tex

@@ -0,0 +1,7 @@
+\chapter*{Introduction}
+\chaptermark{Introduction}
+\markboth{INTRODUCTION}{INTRODUCTION}
+\addcontentsline{toc}{chapter}{Introduction}
+\label{ch:Introduction}
+
+We start slowly ok

Thesis/Chapters/ch-Remerciements.tex

@@ -0,0 +1,5 @@
+\chapter*{Remerciements}
+\chaptermark{Remerciements}
+\markboth{REMERCIEMENTS}{REMERCIEMENTS}
+
+...

Thesis/Chapters/ch-Résumé.tex

@@ -0,0 +1,6 @@
+\chapter*{R\'esum\'e}
+\chaptermark{R\'esum\'e}
+\markboth{R\'ESUM\'E}{R\'ESUM\'E}
+\addcontentsline{toc}{chapter}{R\'esum\'e}
+
+...

Thesis/Covers/BackCover.tex

@@ -0,0 +1,49 @@
+\thispagestyle{empty}
+\pagenumbering{gobble}
+
+\setlength\oddsidemargin{\dimexpr(\paperwidth-\textwidth)/2 - 1in\relax}
+\setlength\evensidemargin{\oddsidemargin}
+
+\makeatletter
+\begin{changemargin}{-15mm}{-5mm}
+    \noindent%
+    \vspace*{-20mm}%
+    \begin{center}%
+        \includegraphics[keepaspectratio, height=8mm, trim={0 8mm 0 0}]{\@UniversityLogo}%
+        \hfill%
+        {\Large\bf \@Firstname\, \MakeUppercase{\@Lastname}}%
+        \hfill%
+        \includegraphics[keepaspectratio, height=8mm, trim={0 8mm 0 0}]{\ifdefempty{\@LaboLogo}{\@DoctoralSchoolLogo}{\@LaboLogo}}%
+    \end{center}%
+\end{changemargin}\vspace*{1cm}%
+
+\begin{changemargin}{-10mm}{0mm}
+    \begin{center}
+        {\LARGE\bf \@TitreThese}%
+    \end{center}
+    \begin{mybox}
+        {\Large\textbf{Résumé}}\vspace*{5mm}
+    
+        \@resume
+        
+        \vspace*{5mm}
+        \textbf{Mots-clés}: \@motscles
+    \end{mybox}\vspace*{5mm}
+    
+    \begin{center}
+        {\LARGE\bf \@ThesisTitle}%
+    \end{center}
+    \begin{mybox}
+        {\Large\textbf{Abstract}}\vspace*{5mm}
+        
+        \@abstract
+        
+        \vspace*{5mm}
+        \textbf{Keywords}: \@keywords
+    \end{mybox}
+\end{changemargin}
+\makeatother
+
+% go back to default geometry settings
+\setlength\oddsidemargin{\defaultOddsidemargin}
+\setlength\evensidemargin{\defaultEvensidemargin}

Thesis/Covers/FrontCover.tex

@@ -0,0 +1,69 @@
+%%% Note: Adjust the number of \bigskip to fit everything in one page
+\thispagestyle{empty}
+\pagenumbering{gobble}
+
+\setlength\oddsidemargin{\dimexpr(\paperwidth-\textwidth)/2 - 1in\relax}
+\setlength\evensidemargin{\oddsidemargin}
+
+\makeatletter
+\begin{changemargin}{-15mm}{-5mm}
+    \noindent
+    \vspace*{-25mm}%
+    \begin{center}%
+        \includegraphics[keepaspectratio, height=1.5cm]{\@UniversityLogo}%
+        \ifdefempty{\@LaboLogo}{}{\hfill\includegraphics[keepaspectratio, height=1.5cm]{\@LaboLogo}}%
+        \hfill%
+        \includegraphics[keepaspectratio, height=1.8cm, trim={0 3.0mm 0 0}]{\@DoctoralSchoolLogo}\\\vspace{5mm}
+        {\ifdefempty{\@LaboLogo}{\vspace{-15mm}}{}\Large\bf \MakeUppercase{\@UniversityName}}\\\vspace{10mm}
+        {\large\bf\textit{\MakeUppercase{\@DoctoralSchoolName}}}\\\vspace{5mm}
+        {\bf \@LaboName}
+    \end{center}
+\end{changemargin}
+\vfill%
+\begin{changemargin}{-10mm}{0mm}
+    \begin{center}
+        \huge \textbf{TH\`ESE} \large pr\'esent\'ee par\\\vspace{5mm}
+        {\LARGE\bf\@Firstname\, \MakeUppercase{\@Lastname}}\\\vspace{5mm}
+        {\large soutenue le: \bfseries \@ThesisDate}\vspace{5mm}
+
+        \begin{tabular}{rl}
+         pour obtenir le grade de:  & \textbf{Docteur de l'\@UniversityName} \\
+         Discipline/Sp\'ecialit\'e: & \@Discipline \ifdefempty{\@Speciality}{}{/\@Speciality}
+        \end{tabular}\vspace{1cm}%
+
+        \begin{mybox}%
+            \Huge\centering{\bfseries \@TitreThese}\\
+            \ifdefempty{\@SousTitreThese}
+                {}
+                {\Large\centering{\bfseries \@SousTitreThese}}
+        \end{mybox}%
+    \end{center}%
+\end{changemargin}%
+\vfill%
+\begin{changemargin}{-15mm}{-5mm}
+    {\large\bfseries THÈSE dirigée par}:\vspace{2mm}
+
+    \begin{tabular}{p{7cm}p{10cm}}%
+        \@directeurs
+    \end{tabular}\vspace{3mm}
+
+    {\large\bfseries RAPPORTEURS}:\vspace{2mm}
+
+    \begin{tabular}{p{7cm}p{10cm}}
+        \@rapporteurs
+    \end{tabular}\vspace{3mm}
+
+    \noindent\makebox[\linewidth]{\rule{0.83\paperwidth}{0.4pt}}\vspace{3mm}
+
+    {\large\bfseries AUTRES MEMBRES DU JURY}:\vspace{2mm}
+
+    \begin{tabular}{p{7cm}p{10cm}}
+        \@jury
+    \end{tabular}\vspace{3mm}
+    
+\end{changemargin}
+\makeatother
+
+% go back to default geometry settings
+\setlength\oddsidemargin{\defaultOddsidemargin}
+\setlength\evensidemargin{\defaultEvensidemargin}

Thesis/NAME_Thesis.tex

@@ -0,0 +1,110 @@
+%\documentclass{PhDThesisED182}
+\documentclass[showNotes, showLineNumbers]{PhDThesisED182}
+%\modulolinenumbers[5] % Change line numbering every N lines
+
+%\renewcommand{\familydefault}{\sfdefault} % Uncomment to default to sans serif font
+
+%%%%%%%%%%%%%%%% Fill in for Front and Back Covers %%%%%%%%%%%%%%%%
+% Author
+\Firstname{Firstname}
+\Lastname{Lastname}
+% University
+\UniversityName{Universit\'e de Strasbourg}
+\UniversityLogo{Images/Covers/Logo\_StrasbourgUni.pdf}
+% Labo
+\LaboName{Observatoire Astronomique de Strasbourg (UMR 7550)}
+\LaboLogo{Images/Covers/Logo\_ObAS.pdf}
+% Doctoral school
+\DoctoralSchoolName{\'Ecole Doctorale de physique et chimie-physique}
+\DoctoralSchoolLogo{Images/Covers/logo\_ED182.pdf}
+% Thesis
+\ThesisDate{XX mois 20XX}
+\TitreThese{Le titre de la thèse en français.}
+\SousTitreThese{Un sous titre.}
+\ThesisTitle{Title of the thesis in english.}
+\ThesisSubTitle{A subtitle.}
+\resume{1000 caract\`eres maximum}
+\motscles{Mot-clé1, Mot-clé2, Mot-clé3}
+\abstract{1000 letters max}
+\keywords{Keyword1, Keyword2, Keyword3}
+% Discipline
+\Discipline{Physique}
+\Speciality{}
+% Directeurs
+\directeurs{
+    \person{Civ.}{Lastname}{Firstname}{Pos.}{Affiliation}
+    \person{Civ.}{Lastname}{Firstname}{Pos.}{Affiliation}
+}
+% Rapporteurs
+\rapporteurs{
+    \person{Civ.}{Lastname}{Firstname}{Pos.}{Affiliation}
+    \person{Civ.}{Lastname}{Firstname}{Pos.}{Affiliation}
+}
+% Jury
+\jury{
+    \person{Civ.}{Lastname}{Firstname}{Pos.}{Affiliation}
+    \person{Civ.}{Lastname}{Firstname}{Pos.}{Affiliation}
+    \person{Civ.}{Lastname}{Firstname}{Pos.}{Affiliation}
+}
+% Define first author and name(s) to be put in bold face in the List of publications
+\firstauth{Name}
+\addboldnames{{Name, Firstname},{Name, I.}}
+
+%%%%%%%%%%%%%%%% Document begin %%%%%%%%%%%%%%%%
+\begin{document}
+
+    \include{Covers/FrontCover}
+    
+    \cleardoublepage
+    \pagenumbering{roman}
+    
+    \dominitoc % use a mini table of contents for each chapter
+    
+    \ifshowLineNumbers\linenumbers\fi % show line numbers if switched on
+    \adjustmtc  % to avoid minitoc position issue in the following chapters
+    \include{Chapters/ch-Abstract}
+    \include{Chapters/ch-Résumé}
+    
+    \adjustmtc
+    \include{Chapters/ch-Acknowledgements}
+    \include{Chapters/ch-Remerciements}
+    
+    \tableofcontents
+    
+    \adjustmtc
+    \include{Appendices/app-Glossary}
+    
+    \adjustmtc
+    \include{Appendices/app-Publications}
+    
+    \newpage
+    \listoffigures \mtcaddchapter    % do not forget "\mtcaddchapter" (ohterwise, conflict with minitoc)
+    
+    \newpage
+    \listoftables \mtcaddchapter
+    
+    \cleardoublepage
+    \pagenumbering{arabic}
+    
+    \adjustmtc
+    \include{Chapters/ch-Introduction}
+    
+    \include{Chapters/ch-Chapter1}
+    \include{Chapters/ch-Chapter2}
+    \include{Chapters/ch-Chapter3}
+    
+    \adjustmtc
+    \include{Chapters/ch-Conclusion}
+    
+    \begin{appendices}
+        \include{Appendices/app-AppendixA}
+    \end{appendices}
+    
+    \resetboldnames % Remove bold font on \firstauth for global bibliography
+    \printbibliography
+    \addcontentsline{toc}{chapter}{Bibliography}
+    
+    \cleardoublepage
+    \include{Covers/BackCover}
+
+\end{document}

Thesis/PhDThesisED182.cls

@@ -0,0 +1,184 @@
+%%% File: PhDThesisED182.cls
+%%% Brief: Document class template for ED182 thesis manuscript
+%%% Use: \documentclass[showNotes, showLineNumbers, showWatermark]{PhDThesisED182}
+%%% Author: Alexandre BIGOT, alexandre.bigot@iphc.cnrs.fr
+%%% Tweaks: Thibault BARNOUIN, thibault.barnouin@astro.unistra.fr
+
+%% Identification
+%% The class identifies itself and the LaTeX version needed
+\NeedsTeXFormat{LaTeX2e}
+\ProvidesClass{PhDThesisED182}[2024-02-28 Minimal class for PhD thesis manuscript in ED182]
+
+%% Load the article class file
+\LoadClass[a4paper,twoside,12pt]{report}
+
+%%%%%%%%%%%%%%%% Commands and default values for Covers %%%%%%%%%%%%%%%%
+% Author name
+\newcommand{\Firstname}[1]{\gdef\@Firstname{#1}}
+\Firstname{Firstname}
+\newcommand{\Lastname}[1]{\gdef\@Lastname{#1}}
+\Lastname{Lastname}
+% University name and logo
+\newcommand{\UniversityName}[1]{\gdef\@UniversityName{#1}}
+\UniversityName{Universit\'e de Strasbourg}
+\newcommand{\UniversityLogo}[1]{\gdef\@UniversityLogo{#1}}
+\UniversityLogo{Images/Covers/Logo\_StrasbourgUni.pdf}
+% Labo name and logo
+\newcommand{\LaboName}[1]{\gdef\@LaboName{#1}}
+\LaboName{My Laboratory}
+\newcommand*{\LaboLogo}[1]{\gdef\@LaboLogo{#1}}
+\LaboLogo{}
+% Doctoral school name and logo
+\newcommand{\DoctoralSchoolName}[1]{\gdef\@DoctoralSchoolName{#1}}
+\DoctoralSchoolName{\'Ecole Doctorale de physique et chimie-physique}
+\newcommand{\DoctoralSchoolLogo}[1]{\gdef\@DoctoralSchoolLogo{#1}}
+\DoctoralSchoolLogo{Images/Covers/logo\_ED182}
+% Thesis title and subtitle in French and English
+\newcommand{\TitreThese}[1]{\gdef\@TitreThese{#1}}
+\TitreThese{Le titre de la thèse en français.}
+\newcommand*{\SousTitreThese}[1]{\gdef\@SousTitreThese{#1}}
+\SousTitreThese{}
+\newcommand{\resume}[1]{\gdef\@resume{#1}}
+\resume{1000 caract\`eres maximum}
+\newcommand{\motscles}[1]{\gdef\@motscles{#1}}
+\motscles{...}
+\newcommand{\ThesisTitle}[1]{\gdef\@ThesisTitle{#1}}
+\ThesisTitle{Title of the thesis in english.}
+\newcommand*{\ThesisSubTitle}[1]{\gdef\@ThesisSubTitle{#1}}
+\ThesisSubTitle{}
+\renewcommand{\abstract}[1]{\gdef\@abstract{#1}}
+\abstract{1000 letters max}
+\newcommand{\keywords}[1]{\gdef\@keywords{#1}}
+\keywords{...}
+\newcommand{\ThesisDate}[1]{\gdef\@ThesisDate{#1}}
+\ThesisDate{XX mois 20XX}
+% Discipline
+\newcommand{\Discipline}[1]{\gdef\@Discipline{#1}}
+\Discipline{Physique}
+\newcommand*{\Speciality}[1]{\gdef\@Speciality{#1}}
+\Speciality{}
+%%% Members of the jury title, name, position and affiliation
+\newcommand{\person}[5]{\hspace{2mm}\bfseries{#1\, \MakeUppercase{#2}\, #3} & {#4, #5}\\}
+% Directeurs
+\newcommand{\directeurs}[1]{\gdef\@directeurs{#1}}
+\directeurs{
+    \person{Civ.}{Lastname}{Firstname}{Pos.}{Affiliation}
+    \person{Civ.}{Lastname}{Firstname}{Pos.}{Affiliation}
+}
+% Rapporteurs
+\newcommand{\rapporteurs}[1]{\gdef\@rapporteurs{#1}}
+\rapporteurs{
+    \person{Civ.}{Lastname}{Firstname}{Pos.}{Affiliation}
+    \person{Civ.}{Lastname}{Firstname}{Pos.}{Affiliation}
+}
+% Jury
+\newcommand{\jury}[1]{\gdef\@jury{#1}}
+\jury{
+    \person{Civ.}{Lastname}{Firstname}{Pos.}{Affiliation}
+    \person{Civ.}{Lastname}{Firstname}{Pos.}{Affiliation}
+    \person{Civ.}{Lastname}{Firstname}{Pos.}{Affiliation}
+}
+
+%% Load packages
+\PassOptionsToPackage{pdftitle={\@ThesisTitle}, pdfauthor={\@Firstname \@Lastname}, pdfcreator={PdfLaTeX}, pdfkeywords={\@keywords}, pdfsubject={Thesis Manuscript}}{hyperref}\RequirePackage{hyperref} % Extensive support for hypertext
+\makeatother
+\PassOptionsToPackage{a4paper,inner=25mm,outer=15mm,top=25mm,bottom=20mm}{geometry}\RequirePackage{geometry} % Flexible and complete interface to document dimensions
+\PassOptionsToPackage{T1}{fontenc}\RequirePackage{fontenc} % Standard package for selecting font encodings
+%\PassOptionsToPackage{comma,square,numbers,sort&compress}{natbib}\RequirePackage{natbib} % Flexible bibliography support
+\PassOptionsToPackage{main=english,french}{babel}\RequirePackage{babel} % Multilingual support
+\RequirePackage{lmodern} % Make sure thesis is ready for printing
+\RequirePackage{graphicx} % Enhanced support for graphics
+\RequirePackage{amsmath} % AMS mathematical facilities
+\RequirePackage{amsfonts} % TeX fonts from the American Mathematical Society
+\RequirePackage{xcolor} % Driver-independent color extensions
+\RequirePackage{fancyhdr} % Extensive control of page headers and footers
+\RequirePackage{etoolbox} % Extended conditional commands
+\PassOptionsToPackage{most}{tcolorbox}\RequirePackage{tcolorbox} % Coloured boxes
+\PassOptionsToPackage{nottoc}{tocbibind}\RequirePackage{tocbibind}  % Add bibliography/index/contents to Table of Contents
+\RequirePackage{minitoc} % Produce a table of contents for each chapter, part or section
+\PassOptionsToPackage{title}{appendix}\RequirePackage{appendix} % Extra control of appendices
+\PassOptionsToPackage{modulo}{lineno}\RequirePackage{lineno} % Line numbers on paragraphs
+\RequirePackage{macros} % Personal macros for bibliography
+
+\addbibresource[glob]{*.bib}
+
+%% Define my colours
+\definecolor{DarkBlue}{rgb}{0.0, 0.0, 0.55}
+\definecolor{DarkRed}{rgb}{0.55, 0.0, 0.0}
+\definecolor{DarkGreen}{rgb}{0.0, 0.2, 0.13}
+\definecolor{DodgerBlue}{rgb}{0.12, 0.56, 1.0}
+\colorlet{DodgerBlue2}{DodgerBlue!80}
+
+%% Color commands
+\newcommand{\mycolor}[2]{\color{#1}#2\color{black}\xspace}
+\newcommand{\red}[1]{\color{red}#1\color{black}\xspace}
+
+%% Change hyperlinks style
+\hypersetup
+{
+    colorlinks=true,
+    linkcolor=black,
+    linktocpage=false, % to have the link on the page number in toc
+    filecolor=magenta,
+    urlcolor=DodgerBlue,
+    citecolor=DodgerBlue,
+}
+
+%% Fonts substitutions for non existing bold small caps in lmodern
+\rmfamily
+\DeclareFontShape{T1}{lmr}{b}{sc}{<->ssub*cmr/b/sc}{}
+\DeclareFontShape{T1}{lmr}{bx}{sc}{<->ssub*cmr/bx/sc}{}
+
+\sffamily
+\DeclareFontShape{T1}{lmss}{m}{sc} { <-> ssub * phv/m/sc }{}
+\DeclareFontShape{T1}{lmss}{bx}{sc} { <-> ssub * phv/bx/sc }{}
+
+%% Table of contents configuration
+\setcounter{minitocdepth}{3}
+\setlength{\mtcindent}{24pt}
+\renewcommand{\mtcfont}{\small}
+\renewcommand{\mtifont}{\large\bf}
+\renewcommand{\mtcSfont}{\small\bf}
+\renewcommand{\mtcSSfont}{\small}
+%\renewcommand{\mtctitle}{Contents}
+
+%% Section configuration | Change the numerotations of sections
+    % \renewcommand{\thesection}{\Roman{section})}
+    % \renewcommand{\thesubsection}{\Roman{section}.\arabic{subsection})}
+    % \renewcommand{\thesubsubsection}{\Roman{section}.\arabic{subsection}.\alph{subsubsection})}
+
+%% A simple box
+\newenvironment{mybox}[0]{%
+    \tcolorbox[opacityback=0., standard jigsaw,breakable]}%
+    {\endtcolorbox}
+
+%% Change left and right margins (used in front and back covers)
+\newenvironment{changemargin}[2]{%
+    \begin{list}{}{%
+        \setlength{\topsep}{0pt}%
+        \setlength{\leftmargin}{#1}%
+        \setlength{\rightmargin}{#2}%
+        \setlength{\listparindent}{\parindent}%
+        \setlength{\itemindent}{\parindent}%
+        \setlength{\itemsep}{\parskip}%
+        \setlength{\parsep}{\parskip}%
+    }%
+    \item[]
+}{\end{list}}
+
+%% Save deault margin lengths
+\newlength{\defaultOddsidemargin}
+\setlength{\defaultOddsidemargin}{\oddsidemargin}
+\newlength{\defaultEvensidemargin}
+\setlength{\defaultEvensidemargin}{\evensidemargin}
+
+%% Switches
+\newif\ifshowNotes
+    \newenvironment{notes}[1]{\ifshowNotes #1\fi}
+
+\newif\ifshowLineNumbers
+%
+%% Class options
+\DeclareOption{showNotes}{\showNotestrue}
+\DeclareOption{showLineNumbers}{\showLineNumberstrue}
+\ProcessOptions\relax % to process options

Thesis/biblio.bib

@@ -0,0 +1,10 @@
+@article{FavoriteAuthor,
+    author = {{Another-Name}, I. and {Another-Name}, J. and {Another-Name}, K. and {Another-Name},
+              L.},
+    title = "{Some really interesting article I didn't even write}",
+    journal = {Nature},
+    year = 2005,
+    month = oct,
+    adsurl = {https://ui.adsabs.harvard.edu/abs/},
+    adsnote = {Provided by the SAO/NASA Astrophysics Data System},
+}

Thesis/macros.sty

@@ -0,0 +1,180 @@
+%----------------------------------------------------------------------------------------
+%	DEFINE BIBLIOGRAPHY STYLE
+%----------------------------------------------------------------------------------------
+\usepackage{csquotes}
+\usepackage[backend=biber,natbib=true,style=authoryear,uniquename=init,giveninits=true,isbn=false,url=false,doi=false,maxcitenames=3,minbibnames=6,maxbibnames=50,sorting=ynt]{biblatex}
+\addbibresource[glob]{papers.bib}
+\makeatletter
+\def\nhblx@bibfile@name{papers-sort.bib}
+\newwrite\nhblx@bibfile
+\immediate\openout\nhblx@bibfile=\nhblx@bibfile@name
+
+\immediate\write\nhblx@bibfile{%
+  @comment{Auto-generated file}\blx@nl}
+
+\newcounter{nhblx@name}
+\setcounter{nhblx@name}{0}
+
+\newcommand*{\nhblx@writenametobib}[1]{%
+  \stepcounter{nhblx@name}%
+  \edef\nhblx@tmp@nocite{%
+    \noexpand\AfterPreamble{%
+      \noexpand\setbox0\noexpand\vbox{%
+        \noexpand\nhblx@getmethehash{nhblx@name@\the\value{nhblx@name}}}}%
+  }%
+  \nhblx@tmp@nocite
+  \immediate\write\nhblx@bibfile{%
+    @misc{nhblx@name@\the\value{nhblx@name}, author = {\unexpanded{#1}}, %
+          options = {dataonly=true},}%
+  }%
+}
+
+\AtEndDocument{%
+  \closeout\nhblx@bibfile}
+
+\addbibresource{\nhblx@bibfile@name}
+
+\newcommand*{\nhblx@boldhashes}{}
+\DeclareNameFormat{nhblx@hashextract}{%
+  \xifinlist{\thefield{hash}}{\nhblx@boldhashes}
+    {}
+    {\listxadd{\nhblx@boldhashes}{\thefield{hash}}}}
+
+\DeclareCiteCommand{\nhblx@getmethehash}
+  {}
+  {\printnames[nhblx@hashextract][1-999]{author}}
+  {}
+  {}
+
+\newcommand*{\nhblx@writefirsttokey}[1]{%
+    \DeclareSourcemap{
+        \maps[datatype=bibtex,overwrite=true]{
+            \map{
+                \perdatasource{papers.bib}
+                \step[fieldsource=author, match=\regexp{^{#1}}, final]
+                \step[fieldset=keywords, fieldvalue={, first},append]
+            }
+            \map{
+                \perdatasource{papers.bib}
+                \step[fieldsource=author, match=\regexp{^(?>\{[^\}]+\}\,\s[\w\-\.]+\sand\s){1}\{#1\}}, final]
+                \step[fieldset=keywords, fieldvalue={, main},append]
+            }
+            \map{
+                \perdatasource{papers.bib}
+                \step[fieldsource=author, match=\regexp{^(?:.+?\sand\s){2}.*?\{#1\}}, final]
+                \step[fieldset=keywords, fieldvalue={, collab},append]
+            }
+        }
+    }
+}
+
+\newcommand*{\addboldnames}{\forcsvlist\nhblx@writenametobib}
+\newcommand*{\resetboldnames}{\def\nhblx@boldhashes{}}
+\newcommand*{\firstauth}{\forcsvlist\nhblx@writefirsttokey}
+
+\newcommand*{\ifhashinboldlist}{%
+  \xifinlist{\thefield{hash}}{\nhblx@boldhashes}}
+\makeatother
+
+\newcommand*{\mkboldifhashinlist}[1]{%
+  \ifhashinboldlist
+    {\mkbibbold{#1}}
+    {#1}}
+
+\DeclareNameWrapperFormat{boldifhashinlist}{%
+  \renewcommand*{\mkbibcompletename}{\mkboldifhashinlist}%
+  #1}
+
+\DeclareNameWrapperAlias{sortname}{default}
+\DeclareNameWrapperAlias{default}{boldifhashinlist}
+
+\defbibcheck{noJoPR}{%
+  \iffieldequalstr{journaltitle}{arXiv e-prints}
+    {}
+    {\skipentry}
+}
+\defbibcheck{JoPR}{%
+  \iffieldequalstr{journaltitle}{arXiv e-prints}
+    {\skipentry}
+    {}
+}
+
+%----------------------------------------------------------------------------------------
+%	DEFINE ADS ACRONYMS
+%----------------------------------------------------------------------------------------
+
+\makeatletter
+\let\jnl@style=\rm
+\def\ref@jnl#1{{\jnl@style#1}}
+
+\def\aj{\ref@jnl{AJ}}                   % Astronomical Journal
+\def\actaa{\ref@jnl{Acta Astron.}}      % Acta Astronomica
+\def\araa{\ref@jnl{ARA\&A}}             % Annual Review of Astron and Astrophys
+\def\apj{\ref@jnl{ApJ}}                 % Astrophysical Journal
+\def\apjl{\ref@jnl{ApJ}}                % Astrophysical Journal, Letters
+\def\apjs{\ref@jnl{ApJS}}               % Astrophysical Journal, Supplement
+\def\ao{\ref@jnl{Appl.~Opt.}}           % Applied Optics
+\def\apss{\ref@jnl{Ap\&SS}}             % Astrophysics and Space Science
+\def\aap{\ref@jnl{A\&A}}                % Astronomy and Astrophysics
+\def\aapr{\ref@jnl{A\&A~Rev.}}          % Astronomy and Astrophysics Reviews
+\def\aaps{\ref@jnl{A\&AS}}              % Astronomy and Astrophysics, Supplement
+\def\azh{\ref@jnl{AZh}}                 % Astronomicheskii Zhurnal
+\def\baas{\ref@jnl{BAAS}}               % Bulletin of the AAS
+\def\bac{\ref@jnl{Bull. astr. Inst. Czechosl.}}
+                % Bulletin of the Astronomical Institutes of Czechoslovakia
+\def\caa{\ref@jnl{Chinese Astron. Astrophys.}}
+                % Chinese Astronomy and Astrophysics
+\def\cjaa{\ref@jnl{Chinese J. Astron. Astrophys.}}
+                % Chinese Journal of Astronomy and Astrophysics
+\def\icarus{\ref@jnl{Icarus}}           % Icarus
+\def\jcap{\ref@jnl{J. Cosmology Astropart. Phys.}}
+                % Journal of Cosmology and Astroparticle Physics
+\def\jrasc{\ref@jnl{JRASC}}             % Journal of the RAS of Canada
+\def\memras{\ref@jnl{MmRAS}}            % Memoirs of the RAS
+\def\mnras{\ref@jnl{MNRAS}}             % Monthly Notices of the RAS
+\def\na{\ref@jnl{New A}}                % New Astronomy
+\def\nar{\ref@jnl{New A Rev.}}          % New Astronomy Review
+\def\pra{\ref@jnl{Phys.~Rev.~A}}        % Physical Review A: General Physics
+\def\prb{\ref@jnl{Phys.~Rev.~B}}        % Physical Review B: Solid State
+\def\prc{\ref@jnl{Phys.~Rev.~C}}        % Physical Review C
+\def\prd{\ref@jnl{Phys.~Rev.~D}}        % Physical Review D
+\def\pre{\ref@jnl{Phys.~Rev.~E}}        % Physical Review E
+\def\prl{\ref@jnl{Phys.~Rev.~Lett.}}    % Physical Review Letters
+\def\pasa{\ref@jnl{PASA}}               % Publications of the Astron. Soc. of Australia
+\def\pasp{\ref@jnl{PASP}}               % Publications of the ASP
+\def\pasj{\ref@jnl{PASJ}}               % Publications of the ASJ
+\def\rmxaa{\ref@jnl{Rev. Mexicana Astron. Astrofis.}}%
+                % Revista Mexicana de Astronomia y Astrofisica
+\def\qjras{\ref@jnl{QJRAS}}             % Quarterly Journal of the RAS
+\def\skytel{\ref@jnl{S\&T}}             % Sky and Telescope
+\def\solphys{\ref@jnl{Sol.~Phys.}}      % Solar Physics
+\def\sovast{\ref@jnl{Soviet~Ast.}}      % Soviet Astronomy
+\def\ssr{\ref@jnl{Space~Sci.~Rev.}}     % Space Science Reviews
+\def\zap{\ref@jnl{ZAp}}                 % Zeitschrift fuer Astrophysik
+\def\nat{\ref@jnl{Nature}}              % Nature
+\def\iaucirc{\ref@jnl{IAU~Circ.}}       % IAU Cirulars
+\def\aplett{\ref@jnl{Astrophys.~Lett.}} % Astrophysics Letters
+\def\apspr{\ref@jnl{Astrophys.~Space~Phys.~Res.}}
+                % Astrophysics Space Physics Research
+\def\bain{\ref@jnl{Bull.~Astron.~Inst.~Netherlands}}
+                % Bulletin Astronomical Institute of the Netherlands
+\def\fcp{\ref@jnl{Fund.~Cosmic~Phys.}}  % Fundamental Cosmic Physics
+\def\gca{\ref@jnl{Geochim.~Cosmochim.~Acta}}   % Geochimica Cosmochimica Acta
+\def\grl{\ref@jnl{Geophys.~Res.~Lett.}} % Geophysics Research Letters
+\def\jcp{\ref@jnl{J.~Chem.~Phys.}}      % Journal of Chemical Physics
+\def\jgr{\ref@jnl{J.~Geophys.~Res.}}    % Journal of Geophysics Research
+\def\jqsrt{\ref@jnl{J.~Quant.~Spec.~Radiat.~Transf.}}
+                % Journal of Quantitiative Spectroscopy and Radiative Transfer
+\def\memsai{\ref@jnl{Mem.~Soc.~Astron.~Italiana}}
+                % Mem. Societa Astronomica Italiana
+\def\nphysa{\ref@jnl{Nucl.~Phys.~A}}   % Nuclear Physics A
+\def\physrep{\ref@jnl{Phys.~Rep.}}   % Physics Reports
+\def\physscr{\ref@jnl{Phys.~Scr}}   % Physica Scripta
+\def\planss{\ref@jnl{Planet.~Space~Sci.}}   % Planetary Space Science
+\def\procspie{\ref@jnl{Proc.~SPIE}}   % Proceedings of the SPIE
+\makeatother
+
+\let\astap=\aap
+\let\apjlett=\apjl
+\let\apjsupp=\apjs
+\let\applopt=\ao

Thesis/papers.bib

@@ -0,0 +1,116 @@
+@article{2024arXiv1,
+    author = {{Another-Name}, J. and {Name}, I. and {Another-Name}, K. and {Another-Name},
+              L.},
+    title = "{Some interesting article}",
+    journal = {\aap},
+    year = 2024,
+    month = oct,
+    adsurl = {https://ui.adsabs.harvard.edu/abs/},
+    adsnote = {Provided by the SAO/NASA Astrophysics Data System},
+}
+
+@article{2024arXiv2,
+    author = {{Name}, Firstname and {Another-Name}, First-FName and {
+              Another-Name}, Second-FName},
+    title = "{Another great article}",
+    journal = {\aap},
+    year = 2024,
+    month = nov,
+    adsurl = {https://ui.adsabs.harvard.edu/abs/},
+    adsnote = {Provided by the SAO/NASA Astrophysics Data System},
+}
+
+@article{2023MNRAS,
+    author = {{Another-Name}, First-FName and {Name}, Firstname and {Another-Name},
+              Second-FName and {Another-Name}, Third-FName and {Another-Name},
+              Fourth-FName and {Another-Name}, Fifth-FName and {Another-Name}, Sixth-FName},
+    title = "{This paper I did a lot of work for}",
+    journal = {\mnras},
+    year = 2023,
+    month = dec,
+    adsurl = {https://ui.adsabs.harvard.edu/abs/},
+    adsnote = {Provided by the SAO/NASA Astrophysics Data System},
+}
+
+@article{2023A&A1,
+    author = {{Name}, I. and {Another-Name}, F. and {Another-Name}, S. and {Another-Name}, T. and {Another-Name}, F.},
+    title = "{My first Paper}",
+    journal = {\aap},
+    year = 2023,
+    month = oct,
+    adsurl = {https://ui.adsabs.harvard.edu/abs/},
+    adsnote = {Provided by the SAO/NASA Astrophysics Data System},
+}
+
+@article{2023A&A2,
+    author = {{Another-Name}, F. and {Another-Name}, S. and {Another-Name}, T. and {Another-Name}, F. and {Another-Name}
+              , F. and {Name}, I. and {Another-Name}, S.},
+    title = "{This paper I had a small part in}",
+    journal = {\aap},
+    year = 2023,
+    month = may,
+    adsurl = {https://ui.adsabs.harvard.edu/abs/},
+    adsnote = {Provided by the SAO/NASA Astrophysics Data System},
+}
+
+@article{2022MNRAS,
+    author = {{Another-Name}, First and {Another-Name}, Second and {Name}, Firstname
+              and {Another-Name}, Fourth},
+    title = "{This is a paper I contributed to}",
+    journal = {\mnras},
+    year = 2022,
+    month = feb,
+    adsurl = {https://ui.adsabs.harvard.edu/abs/},
+    adsnote = {Provided by the SAO/NASA Astrophysics Data System},
+}
+
+@article{2022arXiv22,
+    author = {{Another-Name}, J. and {Name}, I. and {Another-Name}, K.},
+    title = "{Some main contribution by yours truly in non-refereed journal}",
+    journal = {arXiv e-prints},
+    year = 2022,
+    month = jan,
+    adsurl = {https://ui.adsabs.harvard.edu/abs/},
+    adsnote = {Provided by the SAO/NASA Astrophysics Data System},
+}
+
+@inproceedings{2021talk.conf.proceed,
+    author = {{Another-Name}, J. and {Name}, I. and {Another-Name}, K.},
+    title = "{A conference talk I contributed to}",
+    booktitle = {{This-Conf}: {This proceeding book Name}},
+    year = 2021,
+    editor = {Editors},
+    month = dec,
+    pages = {n-N},
+    adsurl = {https://ui.adsabs.harvard.edu/abs/},
+    adsnote = {Provided by the SAO/NASA Astrophysics Data System},
+}
+
+@unpublished{2022talk.conf,
+    author = {{Name}, I.},
+    title = "{Some talk that had no proceeding associated}",
+    note = {talk at {This-Conference}: {in this context}},
+    year = 2022,
+    month = jun,
+}
+
+@inproceedings{2024talk.conf.proceeds,
+    author = {{Name}, I. and {Another-Name}, J.},
+    title = "{Some proceeding published talk}",
+    booktitle = {{A Proceedings Books}},
+    year = 2024,
+    editor = {Editors},
+    month = dec,
+    pages = {n-N},
+    note = {talk at {This-Conference}: {that can be described like this}},
+    adsurl = {https://ui.adsabs.harvard.edu/abs/},
+    adsnote = {Provided by the SAO/NASA Astrophysics Data System},
+}
+
+@unpublished{2024poster.conf,
+    author = {{Name}, I.},
+    title = "{A nice poster presenting this}",
+    note = {poster at {That-Conf}: {also known as}},
+    year = 2024,
+    month = sep,
+}