Initial commit

.gitignore

@@ -0,0 +1,315 @@
+## Core latex/pdflatex auxiliary files:
+*.aux
+*.lof
+*.log
+*.lot
+*.fls
+*.out
+*.toc
+*.fmt
+*.fot
+*.cb
+*.cb2
+.*.lb
+
+## Intermediate documents:
+*.dvi
+*.xdv
+*-converted-to.*
+# these rules might exclude image files for figures etc.
+# *.ps
+# *.eps
+# *.pdf
+
+## Generated if empty string is given at "Please type another file name for output:"
+.pdf
+
+## Bibliography auxiliary files (bibtex/biblatex/biber):
+*.bbl
+*.bcf
+*.blg
+*-blx.aux
+*-blx.bib
+*.run.xml
+
+## Build tool auxiliary files:
+*.fdb_latexmk
+*.synctex
+*.synctex(busy)
+*.synctex.gz
+*.synctex.gz(busy)
+*.pdfsync
+
+## Build tool directories for auxiliary files
+# latexrun
+latex.out/
+
+## Auxiliary and intermediate files from other packages:
+# algorithms
+*.alg
+*.loa
+
+# achemso
+acs-*.bib
+
+# amsthm
+*.thm
+
+# beamer
+*.nav
+*.pre
+*.snm
+*.vrb
+
+# changes
+*.soc
+
+# comment
+*.cut
+
+# cprotect
+*.cpt
+
+# elsarticle (documentclass of Elsevier journals)
+*.spl
+
+# endnotes
+*.ent
+
+# fixme
+*.lox
+
+# feynmf/feynmp
+*.mf
+*.mp
+*.t[1-9]
+*.t[1-9][0-9]
+*.tfm
+
+#(r)(e)ledmac/(r)(e)ledpar
+*.end
+*.?end
+*.[1-9]
+*.[1-9][0-9]
+*.[1-9][0-9][0-9]
+*.[1-9]R
+*.[1-9][0-9]R
+*.[1-9][0-9][0-9]R
+*.eledsec[1-9]
+*.eledsec[1-9]R
+*.eledsec[1-9][0-9]
+*.eledsec[1-9][0-9]R
+*.eledsec[1-9][0-9][0-9]
+*.eledsec[1-9][0-9][0-9]R
+
+# glossaries
+*.acn
+*.acr
+*.glg
+*.glo
+*.gls
+*.glsdefs
+*.lzo
+*.lzs
+*.slg
+*.slo
+*.sls
+
+# uncomment this for glossaries-extra (will ignore makeindex's style files!)
+# *.ist
+
+# gnuplot
+*.gnuplot
+*.table
+
+# gnuplottex
+*-gnuplottex-*
+
+# gregoriotex
+*.gaux
+*.glog
+*.gtex
+
+# htlatex
+*.4ct
+*.4tc
+*.idv
+*.lg
+*.trc
+*.xref
+
+# hyperref
+*.brf
+
+# knitr
+*-concordance.tex
+# TODO Uncomment the next line if you use knitr and want to ignore its generated tikz files
+# *.tikz
+*-tikzDictionary
+
+# listings
+*.lol
+
+# luatexja-ruby
+*.ltjruby
+
+# makeidx
+*.idx
+*.ilg
+*.ind
+
+# minitoc
+*.maf
+*.mlf
+*.mlt
+*.mtc[0-9]*
+*.slf[0-9]*
+*.slt[0-9]*
+*.stc[0-9]*
+
+# minted
+_minted*
+*.pyg
+
+# morewrites
+*.mw
+
+# newpax
+*.newpax
+
+# nomencl
+*.nlg
+*.nlo
+*.nls
+
+# pax
+*.pax
+
+# pdfpcnotes
+*.pdfpc
+
+# sagetex
+*.sagetex.sage
+*.sagetex.py
+*.sagetex.scmd
+
+# scrwfile
+*.wrt
+
+# svg
+svg-inkscape/
+
+# sympy
+*.sout
+*.sympy
+sympy-plots-for-*.tex/
+
+# pdfcomment
+*.upa
+*.upb
+
+# pythontex
+*.pytxcode
+pythontex-files-*/
+
+# tcolorbox
+*.listing
+
+# thmtools
+*.loe
+
+# TikZ & PGF
+*.dpth
+*.md5
+*.auxlock
+
+# titletoc
+*.ptc
+
+# todonotes
+*.tdo
+
+# vhistory
+*.hst
+*.ver
+
+# easy-todo
+*.lod
+
+# xcolor
+*.xcp
+
+# xmpincl
+*.xmpi
+
+# xindy
+*.xdy
+
+# xypic precompiled matrices and outlines
+*.xyc
+*.xyd
+
+# endfloat
+*.ttt
+*.fff
+
+# Latexian
+TSWLatexianTemp*
+
+## Editors:
+# WinEdt
+*.bak
+*.sav
+
+# Texpad
+.texpadtmp
+
+# LyX
+*.lyx~
+
+# Kile
+*.backup
+
+# gummi
+.*.swp
+
+# KBibTeX
+*~[0-9]*
+
+# TeXnicCenter
+*.tps
+
+# auto folder when using emacs and auctex
+./auto/*
+*.el
+
+# expex forward references with \gathertags
+*-tags.tex
+
+# standalone packages
+*.sta
+
+# Makeindex log files
+*.lpz
+
+# xwatermark package
+*.xwm
+
+# REVTeX puts footnotes in the bibliography by default, unless the nofootinbib
+# option is specified. Footnotes are the stored in a file with suffix Notes.bib.
+# Uncomment the next line to have this generated file ignored.
+#*Notes.bib
+
+*.auxlock
+
+*.pdf
+!figures/*.pdf
+!figures/*/*_stdl.pdf
+!Couverture-these/*.pdf
+
+*.ist
+
+Couverture-these/resume.pdf
+Couverture-these/titlepage.pdf
+
+

.latexmkrc

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+$pdflatex = 'lualatex -shell-escape -interaction=nonstopmode -file-line-error -synctex=1';
+$pdf_mode = 1;        # tex -> pdf
+
+@default_files = ('main.tex');
+
+# add_cus_dep('glo', 'gls', 0, 'makeglo2gls');
+# sub makeglo2gls {
+#     system("makeglossaries main");
+# }

Acknowledgement/acknowledgement.tex

@@ -0,0 +1,13 @@
+\documentclass[../main.tex]{subfiles}
+
+\begin{document}
+
+\chapter*{Remerciements}
+
+\selectlanguage{french}
+
+Je tiens à remercier \dots
+
+J'adresse également toute ma reconnaissance à \dots
+
+\end{document}

Appendices/appendix_A.tex

@@ -0,0 +1,27 @@
+\documentclass[../main.tex]{subfiles}
+
+\makeatletter
+\def\input@path{{\subfix{../}}}
+%or: \def\input@path{{/path/to/folder/}{/path/to/other/folder/}}
+\makeatother
+
+\graphicspath{{\subfix{../}}}
+
+\hypersetup{
+    pdfauthor   = {Author},
+    pdftitle    = {Appendix: A},
+    pdfsubject  = {Appendix: A},
+%    pdfkeywords = {mots-cl\'{e}s},
+}
+
+
+
+
+\begin{document}
+
+\section{Appendix A} \label{appendix:A}
+
+Interesting things about A.
+
+\end{document}
+

Appendices/appendix_B.tex

@@ -0,0 +1,23 @@
+\documentclass[../main.tex]{subfiles}
+
+\makeatletter
+\def\input@path{{\subfix{../}}}
+%or: \def\input@path{{/path/to/folder/}{/path/to/other/folder/}}
+\makeatother
+
+\graphicspath{{\subfix{../}}}
+
+\hypersetup{
+    pdfauthor   = {Author},
+    pdftitle    = {Appendix: B},
+    pdfsubject  = {Appendix: B},
+%    pdfkeywords = {mots-cl\'{e}s},
+}
+
+\begin{document}
+
+\section{Appendix B} \label{appendix:B}
+
+Interesting things about B.
+
+\end{document}

Conclusion/.latexmkrc

@@ -0,0 +1,4 @@
+$pdflatex = 'lualatex -shell-escape -interaction=nonstopmode -file-line-error -synctex=1';
+$pdf_mode = 1;        # tex -> pdf
+
+@default_files = ('conclusion.tex');

Conclusion/conclusion.tex

@@ -0,0 +1,46 @@
+\documentclass[../main.tex]{subfiles}
+
+\makeatletter
+\@ifundefined{fromRoot}{%
+  \newcommand{\fromRoot}[1]{../#1}
+  
+  \usepackage{xr}
+  \externaldocument{../main}
+}{}
+
+\def\input@path{{\subfix{../}}}
+%or: \def\input@path{{/path/to/folder/}{/path/to/other/folder/}}
+\makeatother
+
+\graphicspath{{\subfix{../}}}
+
+\hypersetup{
+    pdfauthor   = {Author},
+    pdftitle    = {Th\`{e}se (Conclusion)},
+    pdfsubject  = {Th\`{e}se (Conclusion)},
+%    pdfkeywords = {mots-cl\'{e}s},
+}
+
+
+\begin{document}
+
+\selectlanguage{english}
+
+\setmainfont{Latin Modern Roman}
+\setmonofont{Latin Modern Math}
+
+\chapter{Conclusion} \label{chapter:conclusion}
+\chaptermark{Conclusion}
+
+\section{Synthesis}
+
+\section{Perspectives}
+
+
+\begin{sidewaysfigure}
+  \includegraphics[width=\linewidth]{figures/pgfplots/score_demo_raw_stdl.pdf}
+  \caption{A sidewaysfigure}
+\end{sidewaysfigure}
+
+\end{document}
+

Couverture-these/.latexmkrc

@@ -0,0 +1,4 @@
+$pdflatex = 'lualatex -shell-escape -interaction=nonstopmode -file-line-error -synctex=1';
+$pdf_mode = 1;        # tex -> pdf
+
+@default_files = ('pagedegarde.tex');

Couverture-these/README.md

@@ -0,0 +1,212 @@
+
+### 3M - École doctorale Matière, Molécules Matériaux
+
+Spécialités & unités de recherche:
+https://ed-3m.doctorat-bretagneloire.fr/fr/7_presentation
+
+```
+\ecoledoctorale{3M}
+
+\etablissement{ENSCR} % École Nationale Supérieure de Chimie Rennes
+\etablissement{IMTA}  % IMT Atlantique
+\etablissement{INSA}  % Institut National des Sciences Appliquées Rennes
+\etablissement{LMU}   % Le Mans Université
+\etablissement{UA}    % Université d'Angers
+\etablissement{UBO}   % Université de Bretagne Occidentale
+\etablissement{UN}    % Université de Nantes
+\etablissement{UR1}   % Université de Rennes 1
+```
+
+
+### ALL - École doctorale Arts Lettres Langues
+
+
+Spécialités & unités de recherche: https://ed-all.doctorat-bretagneloire.fr/fr/3_presentation
+
+```
+\ecoledoctorale{ALL}
+
+\etablissement{LMU}       % Le Mans Université
+\etablissement{UA}        % Université d'Angers
+\etablissement{UBO}       % Université de Bretagne Occidentale
+\etablissement{UBS}       % Université de Bretagne Sud
+\etablissement{UN}        % Université de Nantes
+\etablissement{UR2}       % Université de Rennes 2
+\etablissement{UR2-ENSAB} % Délivrance conjointe - Joint degrees
+```
+
+
+### BS - École doctorale Biologie Santé
+
+Spécialités & unités de recherche: https://ed-bs.doctorat-bretagneloire.fr/fr/4_presentation
+
+```
+\ecoledoctorale{BS}
+
+\etablissement{EHESP}   % École des Hautes Études en Santé Publique de Rennes
+\etablissement{ENS}     % École Normale Supérieure de Rennes
+\etablissement{Oniris}  % Oniris
+\etablissement{UA}      % Université d'Angers
+\etablissement{UBO}     % Université de Bretagne Occidentale
+\etablissement{UN}      % Université de Nantes
+\etablissement{UR1}     % Université de Rennes 1
+\etablissement{UR1-UR2} % Délivrance conjointe - Joint degrees
+```
+
+
+### DSP - École doctorale Droit et Science politique
+
+Spécialités & unités de recherche: https://ed-dsp.doctorat-bretagneloire.fr/fr/6_presentation
+
+```
+\ecoledoctorale{DSP}
+
+\etablissement{LMU}       % Le Mans Université
+\etablissement{UA}        % Université d'Angers
+\etablissement{UBO}       % Université de Bretagne Occidentale
+\etablissement{UBS}       % Université de Bretagne Sud
+\etablissement{UN}        % Université de Nantes
+\etablissement{UR1}       % Université de Rennes 1
+\etablissement{UR1-EHESP} % Délivrance conjointe - Joint degrees
+\etablissement{UR1-UR2}   % Délivrance conjointe - Joint degrees
+```
+
+
+### EDGE - École doctorale sciences Économiques et sciences De Gestion
+
+Spécialités & unités de recherche: https://ed-edge.doctorat-bretagneloire.fr/fr/10_presentation
+
+```
+\ecoledoctorale{EDGE}
+
+\etablissement{IMTA}         % IMT Atlantique
+\etablissement{InstitutAgro} % Institut Agro - AgroCampus Ouest
+\etablissement{LMU}          % Le Mans Université
+\etablissement{UA}           % Université d'Angers
+\etablissement{UBO}          % Université de Bretagne Occidentale
+\etablissement{UBS}          % Université de Bretagne Sud
+\etablissement{UN}           % Université de Nantes
+\etablissement{UR1}          % Université de Rennes 1
+\etablissement{UR1-EHESP}    % Délivrance conjointe - Joint degrees
+```
+
+
+### EGAAL - École doctorale Écologie, Géosciences, Agronomie et Alimentation
+
+Spécialités & unités de recherche: https://ed-egaal.doctorat-bretagneloire.fr/fr/5_presentation
+
+```
+\ecoledoctorale{EGAAL}
+
+\etablissement{InstitutAgro} % Institut Agro - AgroCampus Ouest
+\etablissement{Oniris}       % Oniris
+\etablissement{UA}           % Université d'Angers
+\etablissement{UA-LMU}       % Délivrance conjointe - Joint degrees
+\etablissement{UBO}          % Université de Bretagne Occidentale
+\etablissement{UN}           % Université de Nantes
+\etablissement{UR1}          % Université de Rennes 1
+```
+
+
+### ELICC - École doctorale Education, Langages, Interactions, Cognition, Clinique
+
+Spécialités & unités de recherche: https://ed-elicc.doctorat-bretagneloire.fr/fr/2_presentation
+
+```
+\ecoledoctorale{ELICC}
+
+\etablissement{LMU} % Le Mans Université
+\etablissement{UA}  % Université d'Angers
+\etablissement{UBO} % Université de Bretagne Occidentale
+\etablissement{UBS} % Université de Bretagne Sud
+\etablissement{UN}  % Université de Nantes
+\etablissement{UR1} % Université de Rennes 1
+\etablissement{UR2} % Université de Rennes 2
+```
+
+
+### MathSTIC - École doctorale MathSTIC
+
+Spécialités & unités de recherche: https://ed-mathstic.doctorat-bretagneloire.fr/fr/8_presentation
+
+```
+\ecoledoctorale{MathSTIC}
+
+\etablissement{CS}               % CentraleSupélec
+\etablissement{ECN}              % École Centrale de Nantes
+\etablissement{ENIB}             % École Nationale d'Ingénieurs de Brest
+\etablissement{ENSAI}            % École Nationale de la Statistique et de l'Analyse de l'Information
+\etablissement{ENS}              % École Normale Supérieure de Rennes
+\etablissement{ENSTA}            % École Nationale Supérieure de Techniques Avancées Bretagne
+\etablissement{IMTA}             % IMT Atlantique
+\etablissement{INSA}             % Institut National des Sciences Appliquées Rennes
+\etablissement{LMU}              % Le Mans Université
+\etablissement{UA}               % Université d'Angers
+\etablissement{UBO}              % Université de Bretagne Occidentale
+\etablissement{UBS}              % Université de Bretagne Sud
+\etablissement{UN}               % Université de Nantes
+\etablissement{UR1}              % Université de Rennes 1
+\etablissement{UR1-InstitutAgro} % Délivrance conjointe - Joint degrees
+\etablissement{UR1-UR2}          % Délivrance conjointe - Joint degrees
+```
+
+
+### SML - École doctorale Sciences de la Mer et du Littoral
+
+Spécialités & unités de recherche: https://ed-sml.doctorat-bretagneloire.fr/fr/9_presentation
+
+```
+\ecoledoctorale{SML}
+
+\etablissement{InstitutAgro} % Institut Agro - AgroCampus Ouest
+\etablissement{LMU}          % Le Mans Université
+\etablissement{UA}           % Université d'Angers
+\etablissement{UBO}          % Université de Bretagne Occidentale
+\etablissement{UBO-IMTA}     % Délivrance conjointe - Joint degrees
+\etablissement{UBS}          % Université de Bretagne Sud
+\etablissement{UN}           % Université de Nantes
+```
+
+
+### SPI - École doctorale Sciences pour l'Ingénieur
+
+Spécialités & unités de recherche: https://ed-spi.doctorat-bretagneloire.fr/fr/11_presentation
+
+```
+\ecoledoctorale{SPI}
+
+\etablissement{ECN}       % École Centrale de Nantes
+\etablissement{ECN-ENSA}  % Délivrance conjointe - Joint degrees
+\etablissement{ENS}       % École Normale Supérieure de Rennes
+\etablissement{ENSTA}     % École Nationale Supérieure de Techniques Avancées Bretagne
+\etablissement{IMTA}      % IMT Atlantique
+\etablissement{INSA}      % Institut National des Sciences Appliquées Rennes
+\etablissement{LMU}       % Le Mans Université
+\etablissement{UA}        % Université d'Angers
+\etablissement{UBO}       % Université de Bretagne Occidentale
+\etablissement{UBO-ENIB}  % Délivrance conjointe - Joint degrees
+\etablissement{UBS}       % Université de Bretagne Sud
+\etablissement{UN}        % Université de Nantes
+\etablissement{UN-Oniris} % Délivrance conjointe - Joint degrees
+\etablissement{UR1}       % Université de Rennes 1
+```
+
+
+### STT - École doctorale Sociétés, temps, territoires
+
+Spécialités & unités de recherche: https://ed-stt.doctorat-bretagneloire.fr/fr/12_acteurs-du-doctorat
+
+```
+\ecoledoctorale{STT}
+
+\etablissement{EHESP}     % École des Hautes Études en Santé Publique de Rennes
+\etablissement{ENSA-UN}   % Délivrance conjointe - Joint degrees
+\etablissement{LMU}       % Le Mans Université
+\etablissement{UA}        % Université d'Angers
+\etablissement{UBO}       % Université de Bretagne Occidentale
+\etablissement{UBS}       % Université de Bretagne Sud
+\etablissement{UN}        % Université de Nantes
+\etablissement{UR1}       % Université de Rennes 1
+\etablissement{UR2}       % Université de Rennes 2
+\etablissement{UR2-ENSAB} % Délivrance conjointe - Joint degrees
+```

Couverture-these/liste-ecoles-etablissements.tex

@@ -0,0 +1,372 @@
+
+%%% Switch case in latex
+%%% https://tex.stackexchange.com/a/343306
+\makeatletter
+\newcommand\addcase[3]{\expandafter\def\csname\string#1@case@#2\endcsname{#3}}
+\newcommand\makeswitch[2][]{%
+  \newcommand#2[1]{%
+    \ifcsname\string#2@case@##1\endcsname\csname\string#2@case@##1\endcsname\else#1\fi%
+  }%
+}
+\makeatother
+
+%%%% Il faut adapter la taille des logos dans certains cas (e.g., EGAAL, 2 etablissements)
+\newcommand\hauteurlogos[3]{
+  \hauteurlogoecole{#1}
+  \hauteurlogoetablissementA{#2}
+  \hauteurlogoetablissementB{#3}
+}
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%%%%%%%%%%%%%% ECOLES DOCTORALES %%%%%%%%%%%%%%%%
+
+%%%% #1: dossier des images, #2: numero ED, #3: couleur ED, #4-#5: nom complet sur plusieurs lignes
+\newcommand\addecoledoctorale[5]{\direcole{#1}\numeroecole{#2}\definecolor{color-ecole}{RGB}{#3}\nomecoleA{#4}\nomecoleB{#5}}
+
+\makeswitch[default]\ecoledoctorale{}
+
+\addcase\ecoledoctorale{3M}{\addecoledoctorale
+{3M}
+{596}
+{193,192,183}
+{Mati\`{e}re, Mol\'{e}cules, Mat\'{e}riaux}
+{}
+}
+\addcase\ecoledoctorale{ALL}{\addecoledoctorale
+  {ALL}
+  {595}
+  {240,209,134}
+  {Arts, Lettres, Langues}
+  {}
+}
+\addcase\ecoledoctorale{BS}{\addecoledoctorale
+{BS}
+{605}
+{163,219,208}
+{Biologie, Sant\'{e}}
+{}
+}
+\addcase\ecoledoctorale{DSP}{\addecoledoctorale
+  {DSP}
+  {599}
+  {188,208,220}
+  {Droit et Science politique}
+  {}
+}
+\addcase\ecoledoctorale{EDGE}{\addecoledoctorale
+{EDGE}
+{597}
+{216,178,210}
+{Sciences \'{E}conomiques et sciences De Gestion}
+{}
+}
+\addcase\ecoledoctorale{EGAAL}{\addecoledoctorale
+{EGAAL}
+{600}
+{146,213,182}
+{\'{E}cologie, G\'{e}osciences, Agronomie et Alimentation}
+{}
+\hauteurlogos{2cm}{2cm}{2cm}
+}
+\addcase\ecoledoctorale{ELICC}{\addecoledoctorale
+{ELICC}
+{603}
+{249,201,188}
+{\'{E}ducation, Langages, Interactions, Cognition, Clinique}
+{}
+\hauteurlogos{2cm}{2cm}{2cm}
+}
+\addcase\ecoledoctorale{MathSTIC}{\addecoledoctorale
+{MathSTIC}
+{601}
+{236,115,127}
+{Math\'{e}matiques et Sciences et Technologies}
+{de l'Information et de la Communication}
+}
+\addcase\ecoledoctorale{SML}{\addecoledoctorale
+  {SML}
+  {598}
+  {162,225,230}
+  {Sciences de la Mer et du Littoral}
+  {}
+}
+\addcase\ecoledoctorale{SPI}{\addecoledoctorale
+{SPI}
+{602}
+{159,182,217}
+{Sciences pour l'Ing\'{e}nieur}
+{}
+}
+\addcase\ecoledoctorale{STT}{\addecoledoctorale
+{STT}
+{604}
+{172,184,192}
+{Soci\'{e}t\'{e}s, temps, territoires}
+{}
+}
+
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%%%%%%%%%%%%%% ETABLISSEMENTS %%%%%%%%%%%%%%%%
+
+%%%% #1 nom du logo, #2-#4: nom complet sur plusieurs lignes
+\newcommand\addetablissement[4]{\logoetablissementB{#1}\nometablissementC{#2}\nometablissementD{#3}\nometablissementE{#4}}
+
+\makeswitch[default]\etablissement{}
+
+\addcase\etablissement{CS}{\addetablissement
+{CS}
+{}
+{}
+{CENTRALESUP\'{E}LEC}
+}
+\addcase\etablissement{ECN}{\addetablissement
+{ECN}
+{}
+{}
+{L'\'{E}COLE CENTRALE DE NANTES}
+}
+\addcase\etablissement{EHESP}{\addetablissement
+{EHESP}
+{}
+{L'\'{E}COLE DES HAUTES \'{E}TUDES}
+{EN SANT\'{E} PUBLIQUE DE RENNES}
+}
+\addcase\etablissement{ENIB}{\addetablissement
+{ENIB}
+{}
+{L'\'{E}COLE NATIONALE}
+{D'ING\'{E}NIEURS DE BREST}
+}
+\addcase\etablissement{ENS}{\addetablissement
+{ENS}
+{}
+{L'\'{E}COLE NORMALE}
+{SUP\'{E}RIEURE RENNES}
+}
+\addcase\etablissement{ENSA}{\addetablissement
+{ENSA}
+{}
+{L'\'{E}COLE NORMALE SUP\'{E}RIEURE}
+{D'ARCHITECTURE DE NANTES}
+}
+\addcase\etablissement{ENSAB}{\addetablissement
+{ENSAB}
+{}
+{L'\'{E}COLE NORMALE SUP\'{E}RIEURE}
+{D'ARCHITECTURE DE BRETAGNE}
+}
+\addcase\etablissement{ENSAI}{\addetablissement
+{ENSAI}
+{}
+{L'\'{E}COLE NATIONALE DE LA STATISTIQUE}
+{ET DE L'ANALYSE DE L'INFORMATION}
+}
+\addcase\etablissement{ENSCR}{\addetablissement
+{ENSCR}
+{}
+{L'\'{E}COLE NATIONALE SUP\'{E}RIEURE}
+{DE CHIMIE RENNES}
+}
+\addcase\etablissement{ENSTA}{\addetablissement
+{ENSTA}
+{}
+{L'\'{E}COLE NATIONALE SUP\'{E}RIEURE}
+{DE TECHNIQUES AVANC\'{E}ES BRETAGNE}
+}
+\addcase\etablissement{IMTA}{\addetablissement
+{IMTA}
+{L'\'{E}COLE NATIONALE SUP\'{E}RIEURE}
+{MINES-T\'{E}L\'{E}COM ATLANTIQUE BRETAGNE}
+{PAYS-DE-LA-LOIRE - IMT ATLANTIQUE}
+}
+\addcase\etablissement{INSA}{\addetablissement
+{INSA}
+{}
+{L'INSTITUT NATIONAL DES}
+{SCIENCES APPLIQU\'{E}ES RENNES}
+}
+\addcase\etablissement{InstitutAgro}{\addetablissement
+{InstitutAgro}
+{L'INSTITUT NATIONAL D'ENSEIGNEMENT SUP\'{E}RIEUR}
+{POUR L'AGRICULTURE, L'ALIMENTATION ET}
+{L'ENVIRONNEMENT - ECOLE INTERNE AGROCAMPUS OUEST}
+}
+\addcase\etablissement{LMU}{\addetablissement
+{LMU}
+{}
+{}
+{LE MANS UNIVERSIT\'{E}}
+}
+\addcase\etablissement{Oniris}{\addetablissement
+  {Oniris}
+  {}
+  {}
+  {ONIRIS}
+}
+\addcase\etablissement{UA}{\addetablissement
+{UA-couleur}
+{}
+{}
+{L'UNIVERSIT\'{E} D'ANGERS}
+}
+\addcase\etablissement{UB}{\addetablissement
+{UB}
+{}
+{}
+{L'UNIVERSIT\'{E} DE BREST}
+}
+\addcase\etablissement{UBO}{\addetablissement
+{UBO}
+{}
+{}
+{L'UNIVERSIT\'{E} DE BRETAGNE OCCIDENTALE}
+}
+\addcase\etablissement{UBS}{\addetablissement
+{UBS}
+{}
+{}
+{L'UNIVERSIT\'{E} DE BRETAGNE SUD}
+}
+\addcase\etablissement{UN}{\addetablissement
+{UN-noir}
+{}
+{}
+{L'UNIVERSIT\'{E} DE NANTES}
+}
+\addcase\etablissement{UR1}{\addetablissement
+{UR1-noir}
+{}
+{}
+{L'UNIVERSIT\'{E} DE RENNES 1}
+}
+\addcase\etablissement{UR2}{\addetablissement
+{UR2}
+{}
+{}
+{L'UNIVERSIT\'{E} DE RENNES 2}
+}
+
+
+%%%% #1-#2: nom des deux logos, #3-#7: nom complet de la double affiliation sur plusieurs lignes
+\newcommand\addpairetablissements[7]{
+  \logoetablissementA{#1}
+  \logoetablissementB{#2}
+  \nometablissementA{#3}
+  \nometablissementB{#4}
+  \nometablissementC{#5}
+  \nometablissementD{#6}
+  \nometablissementE{#7}
+}
+
+% ALL, STT: UR2-ENSAB
+\addcase\etablissement{UR2-ENSAB}{\addpairetablissements
+{ENSAB}
+{UR2}
+{}
+{L'\'{E}COLE NORMALE SUP\'{E}RIEURE}
+{D'ARCHITECTURE DE BRETAGNE}
+{D\'{E}LIVR\'{E}E CONJOINTEMENT AVEC}
+{L'UNIVERSIT\'{E} DE RENNES 2}
+\hauteurlogos{2cm}{1.2cm}{2cm}
+}
+% BS, DSP, MathSTIC: UR1-UR2
+\addcase\etablissement{UR1-UR2}{\addpairetablissements
+{UR2}
+{UR1-noir}
+{}
+{}
+{L'UNIVERSIT\'{E} DE RENNES 2}
+{D\'{E}LIVR\'{E}E CONJOINTEMENT AVEC}
+{L'UNIVERSIT\'{E} DE RENNES 1}
+\hauteurlogos{2cm}{2cm}{2cm}
+}
+% DSP, EDGE: UR1-EHESP
+\addcase\etablissement{UR1-EHESP}{\addpairetablissements
+{EHESP}
+{UR1-noir}
+{}
+{L'UNIVERSIT\'{E} DE RENNES 1}
+{D\'{E}LIVR\'{E}E CONJOINTEMENT AVEC}
+{L'\'{E}COLE DES HAUTES \'{E}TUDES}
+{EN SANT\'{E} PUBLIQUE DE RENNES}
+\hauteurlogos{2cm}{2cm}{2cm}
+}
+% EGAAL: UA-LMU
+\addcase\etablissement{UA-LMU}{\addpairetablissements
+{LMU}
+{UA-couleur}
+{}
+{}
+{LE MANS UNIVERSIT\'{E}}
+{D\'{E}LIVR\'{E}E CONJOINTEMENT AVEC}
+{L'UNIVERSIT\'{E} D'ANGERS}
+\hauteurlogos{2cm}{1cm}{2cm}
+}
+% MathSTIC: UR1-InstitutAgro
+\addcase\etablissement{UR1-InstitutAgro}{\addpairetablissements
+{InstitutAgro}
+{UR1-noir}
+{L'INSTITUT NATIONAL D'ENSEIGNEMENT SUP\'{E}RIEUR}
+{POUR L'AGRICULTURE, L'ALIMENTATION ET}
+{L'ENVIRONNEMENT - ECOLE INTERNE AGROCAMPUS OUEST}
+{D\'{E}LIVR\'{E}E CONJOINTEMENT AVEC}
+{L'UNIVERSIT\'{E} DE RENNES 1}
+\hauteurlogos{1.8cm}{1.3cm}{1.5cm}
+}
+% SML: UBO-IMTA
+\addcase\etablissement{UBO-IMTA}{\addpairetablissements
+{IMTA}
+{UBO}
+{L'\'{E}COLE NATIONALE SUP\'{E}RIEURE}
+{MINES-T\'{E}L\'{E}COM ATLANTIQUE BRETAGNE}
+{PAYS-DE-LA-LOIRE - IMT ATLANTIQUE}
+{D\'{E}LIVR\'{E}E CONJOINTEMENT AVEC}
+{L'UNIVERSIT\'{E} DE BRETAGNE OCCIDENTALE}
+\hauteurlogos{2cm}{1.8cm}{1.8cm}
+}
+% SPI: ECN-ENSA
+\addcase\etablissement{ECN-ENSA}{\addpairetablissements
+{ENSA}
+{ECN}
+{}
+{L'\'{E}COLE NORMALE SUP\'{E}RIEURE}
+{D'ARCHITECTURE DE NANTES}
+{D\'{E}LIVR\'{E}E CONJOINTEMENT AVEC}
+{L'\'{E}COLE CENTRALE DE NANTES}
+\hauteurlogos{2cm}{1.8cm}{1.8cm}
+}
+% SPI: UBO-ENIB
+\addcase\etablissement{UBO-ENIB}{\addpairetablissements
+{ENIB}
+{UBO}
+{}
+{L'\'{E}COLE NATIONALE}
+{D'ING\'{E}NIEURS DE BREST}
+{D\'{E}LIVR\'{E}E CONJOINTEMENT AVEC}
+{L'UNIVERSIT\'{E} DE BRETAGNE OCCIDENTALE}
+\hauteurlogos{2cm}{1.8cm}{1.6cm}
+}
+% SPI: UN-Oniris
+\addcase\etablissement{UN-Oniris}{\addpairetablissements
+{Oniris}
+{UN-noir}
+{}
+{}
+{ONIRIS}
+{D\'{E}LIVR\'{E}E CONJOINTEMENT AVEC}
+{L'UNIVERSIT\'{E} DE NANTES}
+\hauteurlogos{2cm}{2cm}{2cm}
+}
+% STT: ENSA-UN
+\addcase\etablissement{ENSA-UN}{\addpairetablissements
+{ENSA}
+{UN-noir}
+{}
+{L'\'{E}COLE NORMALE SUP\'{E}RIEURE}
+{D'ARCHITECTURE DE NANTES}
+{D\'{E}LIVR\'{E}E CONJOINTEMENT AVEC}
+{L'UNIVERSIT\'{E} DE NANTES}
+\hauteurlogos{2cm}{2cm}{2cm}
+}

Couverture-these/pagedegarde.tex

@@ -0,0 +1,82 @@
+% La page de garde est en français
+% The front cover is in French
+\selectlanguage{french}
+
+% Inclure les infos de chaque établissement
+% Include each institution data
+\input{./Couverture-these/liste-ecoles-etablissements.tex}
+
+% Inclure infos de l'école doctorale
+% Include doctoral school data
+% (3M ALL BS DSP EDGE EGAAL ELICC MathSTIC SML SPI STT)
+\ecoledoctorale{MathSTIC}
+
+% Inclure infos de l'établissement
+% Include institution data
+\etablissement{UBS}
+
+%Inscrivez ici votre sp\'{e}cialit\'{e} (voir liste des sp\'{e}cialit\'{e}s sur le site de votre \'{e}cole doctorale)
+%Indicate the domain (see list of domains in your ecole doctorale)
+\spec{Électronique}
+
+%Attention : le pr\'{e}nom doit être en minuscules (Jean) et le NOM en majuscules (BRITTEF) 
+%Attention : the first name in small letters and the name in Capital letters 
+\author{Author}
+
+% Donner le titre complet de la th\`{e}se, \'{e}ventuellement le sous titre, si n\'{e}cessaire sur plusieurs lignes 
+%Give the complete title of the thesis, if necessary on several lines
+\title{Titre}
+\lesoustitre{Sous-titre}
+
+%Indiquer la date et le lieu de soutenance de la th\`{e}se 
+%indicates the date and the place of the defense 
+\date{DD/MM/YYYY}
+\lieu{Lieu}
+
+%Indiquer le nom du (ou des) laboratoire (s) dans le(s)quel(s) le travail de th\`{e}se a \'{e}t\'{e} effectu\'{e}, indiquer aussi si souhait\'{e} le nom de la (les) facult\'{e}(s) (UFR, \'{e}cole(s), Institut(s), Centre(s)...), son (leurs) adresse(s)... 
+%Indicates the name (or names) of research laboratories where the work has been done as well as (if desired) the names of faculties (UFR, Schools, institution...
+\uniterecherche{Laboratoire --- UMR XXXX CNRS, Université de XXXX}
+
+%Indiquer le Numero de th\`{e}se, si cela est opportun, ou laisser vide pour faire disparaitre cet ligne de la couverture
+%Indicate the number of the thesis if there is one. otherwise leave empty so the line disappeurs on the cover
+\numthese{} % \numthese{}
+
+%Indiquer le Pr\'{e}nom en minuscules et le Nom en majuscules, le titre de la personne et l’\'{e}tablissement dans lequel il effectue sa recherche  
+%Indicates the first name on small letters and the Names on capital letters, the person's title and the institution where he/she belongs to.
+%Exemples :  Examples :
+%%%- Professeur, Universit\'{e} d’Angers 
+%%%- Chercheur, CNRS, \'{e}cole Centrale de Nantes 
+%%%-  Professeur d’universit\'{e} – Praticien Hospitalier, Universit\'{e} Paris V  
+%%%-  Maitre de conf\'{e}rences, Oniris 
+%%%- Charg\'{e} de recherche, INSERM, HDR, Universit\'{e} de Tours  
+%S’il n’y a pas de co-direction, faire disparaitre cet item de la couverture  
+%In there is no co-director, remove the item from the cover
+\jury{
+{\normalTwelve \textbf{Rapporteurs avant soutenance :}}\\ \newline
+\footnotesizeTwelve
+\begin{tabular}{@{}ll}
+  Prénom NOM & Fonction (établissement d'exercice) \\
+  Prénom NOM & Fonction (établissement d'exercice)
+\end{tabular}
+
+\vspace{\baselineskip}
+{\normalTwelve \textbf{Composition du Jury :}}\\
+{\fontsize{9.5}{11}\selectfont {\textcolor{red}{\textit{Attention, en cas d’absence d’un des membres du Jury le jour de la soutenance, la composition du jury doit être revue pour s’assurer qu’elle est conforme et devra être répercutée sur la couverture de thèse}}}}\\ \newline
+\footnotesizeTwelve
+\begin{tabular}{@{}lll}
+
+  Pr\'{e}sident :    & Prénom NOM & Fonction (établissement d'exercice) \textit{(à préciser après la soutenance)} \\
+  Examinateurs :     & Prénom NOM & Fonction (établissement d'exercice)                                           \\
+                     & Prénom NOM & Fonction (établissement d'exercice)                                           \\
+  Dir. de thèse :    & Prénom NOM & Fonction (établissement d'exercice)                                           \\
+  Co-Enc. de thèse : & Prénom NOM & Fonction (établissement d'exercice)                                           \\
+\end{tabular}
+
+\vspace{\baselineskip}
+{\normalTwelve \textbf{Invité(.e.s) :}}\\ \newline
+\footnotesizeTwelve
+\begin{tabular}{@{}ll}
+  Prénom NOM & Fonction (établissement d'exercice) \\
+  Prénom NOM & Fonction (établissement d'exercice)
+\end{tabular}
+}

Couverture-these/resume.tex

@@ -0,0 +1,43 @@
+\documentclass[../main.tex]{subfiles}
+
+\begin{document}
+
+\markboth{}{}
+% Plus petite marge du bas pour la quatrième de couverture
+% Shorter bottom margin for the back cover
+\newgeometry{inner=30mm,outer=20mm,top=40mm,bottom=20mm}
+
+%insertion de l'image de fond du dos (resume)
+%background image for resume (back)
+\backcoverheader
+
+% Switch font style to back cover style
+\selectfontbackcover{ % Font style change is limited to this page using braces, just in case
+
+\selectlanguage{french}
+
+\titleFR{Titre en français.}
+
+\keywordsFR{Quelques,
+Mots,
+Clefs}
+
+\abstractFR{Un résumé en français ($\approx 1000 \backsim 1500$ mots).}
+
+
+\selectlanguage{english}
+
+\titleEN{Title in english.}
+
+\keywordsEN{Few,
+  keywords}
+
+\abstractEN{An abstract in english ($\approx 1000 \backsim 1500$ words).}
+
+}
+
+% Rétablit les marges d'origines
+% Restore original margin settings
+\restoregeometry
+
+\end{document}

Couverture-these/titlepage.tex

@@ -0,0 +1,12 @@
+\documentclass[../main.tex]{subfiles}
+
+\makeatletter
+\def\input@path{{\subfix{../}}}
+%or: \def\input@path{{/path/to/folder/}{/path/to/other/folder/}}
+\makeatother
+
+\graphicspath{{\subfix{../}}}
+
+\begin{document}
+\maketitle
+\end{document}

Introduction/.latexmkrc

@@ -0,0 +1,4 @@
+$pdflatex = 'lualatex -shell-escape -interaction=nonstopmode -file-line-error -synctex=1';
+$pdf_mode = 1;        # tex -> pdf
+
+@default_files = ('introduction.tex');

Introduction/introduction.tex

@@ -0,0 +1,54 @@
+\documentclass[../main.tex]{subfiles}
+
+\makeatletter
+\@ifundefined{fromRoot}{%
+  \newcommand{\fromRoot}[1]{../#1}
+  
+  \usepackage{xr}
+  \externaldocument{../main}
+}{}
+
+\def\input@path{{\subfix{../}}}
+%or: \def\input@path{{/path/to/folder/}{/path/to/other/folder/}}
+\makeatother
+
+\graphicspath{{\subfix{../}}}
+
+\hypersetup{
+    pdfauthor   = {Author},
+    pdftitle    = {Th\`{e}se (Introduction)},
+    pdfsubject  = {Th\`{e}se (Introduction)},
+%    pdfkeywords = {mots-cl\'{e}s},
+}
+
+\begin{document}
+
+\chapter{Introduction}
+\chaptermark{Introduction}
+
+
+\textbf{Une boite magique : }
+
+\boitemagique{Titre de la boite}{
+  Praesent placerat, ante at venenatis pretium, diam turpis faucibus arcu, nec vehicula quam lorem ut leo. Sed facilisis, augue in pharetra dapibus, ligula justo accumsan massa, eu suscipit felis ipsum eget enim.
+}
+
+\section*{Foreword / Avant-propos}
+
+Financement, collaboration, etc.
+
+\section{Compile the thesis}
+
+To make this work, you need to compile the figures independently. For that purpose, a Makefile is available. Just run ``\emph{make figures}'' and see the files being compiled. You can use ``\emph{make -j figures}'' to enable parallel compilation.
+
+If you are not on Linux, nor MacOS, nor a BSD system, do not panic. You can still directly open the figures '.tex' files and compile them directly, it will work.
+
+Apart from figures, this project works on overleaf or on any platform that uses \textbf{latexmk} and \textbf{lualatex}. All chapters are \emph{subfiles}, that can be compiled independently of each others, to fasten compilation and focus on writing.
+
+\section{Introduction}
+
+Here, let us cite art1 \cite{art1}. You can also cite art2 \cite{art2}.\\Or, you may cite them together \cite{art1, art2}.
+
+
+\end{document}
+

Makefile

@@ -0,0 +1,123 @@
+
+MAKE = make
+
+.PHONY: all clean clear
+all: main
+	@echo
+	@echo Main file generated.
+	@echo
+
+clean:
+	cd figures/tikzpicture && $(MAKE) clean
+	cd figures/pgfplots && $(MAKE) clean
+
+clear:
+	cd figures/tikzpicture && $(MAKE) clear
+	cd figures/pgfplots && $(MAKE) clear
+
+## To compile all subfiles
+
+subfiles: introduction conclusion stateoftheart
+	@echo
+	@echo Subfiles generated
+	@echo
+
+
+## To compile the complete thesis
+
+main: figures main.pdf main.gls main.acr
+	makeglossaries main
+	latexmk main.tex
+
+main.pdf: main.tex figures
+	latexmk main.tex
+
+main.gls main.acr: main.ist  main.glo main.acn
+	makeglossaries main
+
+
+## To compile all latex figures
+
+figures: tikzpictures pgfplots
+	@echo
+	@echo Figures generated.
+	@echo
+
+## To compile only tikz figures
+
+tikzpictures: figures/tikzpicture/.latexmkrc figures/tikzpicture/Makefile
+	cd figures/tikzpicture && $(MAKE) -B
+
+## To compile only PGFPlots figures
+
+pgfplots: figures/pgfplots/.latexmkrc figures/pgfplots/Makefile
+	cd figures/pgfplots && $(MAKE) -B
+
+## To compile the introduction alone
+
+introduction: Introduction/introduction.pdf Introduction/introduction.bbl
+	cd Introduction; lualatex -interaction=nonstopmode -file-line-error -synctex=1 introduction.tex
+
+Introduction/introduction.pdf: Introduction/introduction.tex figures
+	cd Introduction; lualatex -interaction=nonstopmode -file-line-error -synctex=1 introduction.tex
+
+Introduction/introduction.bbl: Introduction/introduction.pdf
+	biber --output-directory Introduction introduction.bcf
+
+
+## To compile the conclusion alone
+
+conclusion: Conclusion/conclusion.pdf Conclusion/conclusion.bbl
+	cd Conclusion; lualatex -interaction=nonstopmode -file-line-error -synctex=1 conclusion.tex
+
+Conclusion/conclusion.pdf: Conclusion/conclusion.tex figures
+	cd Conclusion; lualatex -interaction=nonstopmode -file-line-error -synctex=1 conclusion.tex
+
+Conclusion/conclusion.bbl: Conclusion/conclusion.pdf
+	biber --output-directory Conclusion conclusion.bcf
+
+
+## To compile the state of the art alone
+
+stateoftheart: StateOfTheArt/stateoftheart.pdf StateOfTheArt/stateoftheart.bbl
+	cd StateOfTheArt; lualatex -interaction=nonstopmode -file-line-error -synctex=1 stateoftheart.tex
+
+StateOfTheArt/stateoftheart.pdf: StateOfTheArt/stateoftheart.tex figures
+	cd StateOfTheArt; lualatex -interaction=nonstopmode -file-line-error -synctex=1 stateoftheart.tex
+
+StateOfTheArt/stateoftheart.bbl: StateOfTheArt/stateoftheart.pdf
+	biber --output-directory StateOfTheArt stateoftheart.bcf
+
+
+## To compile the chapter 1 alone
+
+chapter1: chapter1/chapter1.pdf chapter1/chapter1.bbl
+	cd chapter1; lualatex -interaction=nonstopmode -file-line-error -synctex=1 chapter1.tex
+
+chapter1/chapter1.pdf: chapter1/chapter1.tex figures
+	cd chapter1; lualatex -interaction=nonstopmode -file-line-error -synctex=1 chapter1.tex
+
+chapter1/chapter1.bbl: chapter1/chapter1.pdf
+	biber --output-directory chapter1 chapter1.bcf
+
+## To compile the chapter 2 alone
+
+chapter2: chapter2/chapter2.pdf chapter2/chapter2.bbl
+	cd chapter2; lualatex -interaction=nonstopmode -file-line-error -synctex=1 chapter2.tex
+
+chapter2/chapter2.pdf: chapter2/chapter2.tex figures
+	cd chapter2; lualatex -interaction=nonstopmode -file-line-error -synctex=1 chapter2.tex
+
+chapter2/chapter2.bbl: chapter2/chapter2.pdf
+	biber --output-directory chapter2 chapter2.bcf
+
+## To add others, uncomment and replace NAME by whatever you want
+
+# NAME: NAME/NAME.pdf NAME/NAME.bbl
+# 	cd NAME; lualatex -interaction=nonstopmode -file-line-error -synctex=1 NAME.tex
+
+# NAME/NAME.pdf: NAME/NAME.tex figures
+# 	cd NAME; lualatex -interaction=nonstopmode -file-line-error -synctex=1 NAME.tex
+
+# NAME/NAME.bbl: NAME/NAME.pdf
+# 	biber --output-directory NAME NAME.bcf

StateOfTheArt/.latexmkrc

@@ -0,0 +1,4 @@
+$pdflatex = 'lualatex -shell-escape -interaction=nonstopmode -file-line-error -synctex=1';
+$pdf_mode = 1;        # tex -> pdf
+
+@default_files = ('stateoftheart.tex');

StateOfTheArt/stateoftheart.tex

@@ -0,0 +1,76 @@
+\documentclass[../main.tex]{subfiles}
+
+\makeatletter
+\@ifundefined{fromRoot}{%
+  \newcommand{\fromRoot}[1]{../#1}
+  
+  \usepackage{xr}
+  \externaldocument{../main}
+}{}
+
+\def\input@path{{\subfix{../}}}
+%or: \def\input@path{{/path/to/folder/}{/path/to/other/folder/}}
+\makeatother
+
+\graphicspath{{\subfix{../}}}
+
+\hypersetup{
+    pdfauthor   = {Author},
+    pdftitle    = {Th\`{e}se (State of the Art)},
+    pdfsubject  = {Th\`{e}se (State of the Art)},
+%    pdfkeywords = {mots-cl\'{e}s},
+}
+
+
+\begin{document}
+
+\selectlanguage{english}
+
+\chapter{State of the Art} \label{chapter:state-of-the-art}
+\chaptermark{State of the Art}
+
+\etocsetnexttocdepth{4}
+\etocsettocstyle{{\large \hspace{-1.5 em} \textbf{Contents} \hfill}\vspace{-2.5 em}\\\par\noindent\rule{\linewidth}{1 pt}\vspace{-.2 em}}{\par\noindent\rule{\linewidth}{1 pt}\\}
+\localtableofcontents
+
+This chapter present the state of the art.
+
+It makes use of the \lstinline[language={[latex]tex}]{\acrfull} command for acronyms.
+
+like that for full: \acrfull{acr}, 
+
+with \emph{pl} for plural: \acrfullpl{acr}, 
+
+short for short: \acrshort{acr}, 
+
+long for long: \acrlong{acr}.
+
+You can also use glossary entry, like that: \gls{glos}.
+
+\section{Section 1}
+
+\subsection{Subsection 1}
+
+\begin{table}[b!]
+  \ra{1.6}
+  \centering
+  \caption{A table.}
+  \label{chapter:sota:tab:table1}
+  % \begin{noindent}
+  \begin{tabular}{@{}r@{\phantom{XXX}}r@{\phantom{XX}}r@{\phantom{XX}}r@{}}
+\toprule
+          & \textbf{Head A}   & \textbf{Head A}   & \textbf{Head C} \\ 
+\midrule
+
+Blah      & Gibberish         & Ohoho             & You fool        \\
+          \cmidrule{2-4}
+BlahBlah  & Interesting       & Ahaha             & You genius      \\
+ \bottomrule
+  \end{tabular}
+  % \end{noindent}
+  \ra{1}
+\end{table}
+
+\section{Section 2}
+
+\end{document}

acronyms.tex

@@ -0,0 +1,16 @@
+%%%%%%%%%%%%%%%%%%%%%%%%%
+% Glossary and acronyms file
+%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
+\makeglossaries
+
+\newglossaryentry{glos}{
+    name={Glossary Entry},
+    description={A glossary entry}
+}
+
+\setacronymstyle{long-short}
+
+\newacronym[]{acr}{ACR}{Acronym}
+

biblio/biblio.bib

@@ -0,0 +1,23 @@
+@article{art1,
+  title = {Article 1},
+  author = {{John Doe}},
+  year = {1337},
+  month = sep,
+  journal = {Proceedings of the IEEE},
+  volume = {104},
+  number = {9},
+  pages = {1711--1726},
+  doi = {10.1109/XXX}
+}
+
+@inproceedings{art2,
+  title = {Article 2},
+  author = {{Jane Smith}},
+  year = {2010},
+  month = sep,
+  journal = {Proceedings of the Springer},
+  volume = {104},
+  number = {9},
+  pages = {1711--1726},
+  doi = {10.1109/XXXY}
+}

chapter1/chapter1.tex

@@ -0,0 +1,40 @@
+\documentclass[../main.tex]{subfiles}
+
+\makeatletter
+\@ifundefined{fromRoot}{%
+  \newcommand{\fromRoot}[1]{../#1}
+  
+  \usepackage{xr}
+  \externaldocument{../main}
+}{}
+
+\def\input@path{{\subfix{../}}}
+%or: \def\input@path{{/path/to/folder/}{/path/to/other/folder/}}
+\makeatother
+
+\graphicspath{{\subfix{../}}}
+
+\hypersetup{
+    pdfauthor   = {Author},
+    pdftitle    = {Th\`{e}se (Chapitre 1)},
+    pdfsubject  = {Th\`{e}se (Chapitre 1)},
+%    pdfkeywords = {mots-cl\'{e}s},
+}
+
+
+\begin{document}
+
+\selectlanguage{english}
+
+\chapter{Name of chapter 1} \label{chapter:1}
+\chaptermark{Name of chapter 1}
+
+\etocsetnexttocdepth{4}
+\etocsettocstyle{{\large \hspace{-1.5 em} \textbf{Contents} \hfill}\vspace{-2.5 em}\\\par\noindent\rule{\linewidth}{1 pt}\vspace{-.2 em}}{\par\noindent\rule{\linewidth}{1 pt}\\}
+\localtableofcontents
+
+\section{Section 1}
+
+\section{Section 2}
+
+\end{document}

chapter2/chapter2.tex

@@ -0,0 +1,40 @@
+\documentclass[../main.tex]{subfiles}
+
+\makeatletter
+\@ifundefined{fromRoot}{%
+  \newcommand{\fromRoot}[1]{../#1}
+  
+  \usepackage{xr}
+  \externaldocument{../main}
+}{}
+
+\def\input@path{{\subfix{../}}}
+%or: \def\input@path{{/path/to/folder/}{/path/to/other/folder/}}
+\makeatother
+
+\graphicspath{{\subfix{../}}}
+
+\hypersetup{
+    pdfauthor   = {Author},
+    pdftitle    = {Th\`{e}se (Chapitre 2)},
+    pdfsubject  = {Th\`{e}se (Chapitre 2)},
+%    pdfkeywords = {mots-cl\'{e}s},
+}
+
+
+\begin{document}
+
+\selectlanguage{english}
+
+\chapter{Name of chapter 2} \label{chapter:2}
+\chaptermark{Name of chapter 2}
+
+\etocsetnexttocdepth{4}
+\etocsettocstyle{{\large \hspace{-1.5 em} \textbf{Contents} \hfill}\vspace{-2.5 em}\\\par\noindent\rule{\linewidth}{1 pt}\vspace{-.2 em}}{\par\noindent\rule{\linewidth}{1 pt}\\}
+\localtableofcontents
+
+\section{Section 1}
+
+\section{Section 2}
+
+\end{document}

commands.tex

@@ -0,0 +1,6 @@
+%%%%%%%%%%%%%%%%%%%%%%%%%
+% Commands file
+%%%%%%%%%%%%%%%%%%%%%%%%%
+
+%% To enlarge interline in tabulars
+\newcommand{\ra}[1]{\renewcommand{\arraystretch}{#1}}

data/score_famd_raw_m10db_sync.dat

@@ -0,0 +1,257 @@
+pfa             pmd             Nfa             Nmd             score           
+0.99999960      0.00000000      4               0               3236            
+0.99999920      0.00000000      4               0               3242            
+0.99999780      0.00000000      14              0               3248            
+0.99999390      0.00000000      39              0               3255            
+0.99998290      0.00000000      110             0               3261            
+0.99995390      0.00000000      290             0               3267            
+0.99988520      0.00000000      687             0               3274            
+0.99972140      0.00000000      1638            0               3280            
+0.99938580      0.00000000      3356            0               3287            
+0.99868260      0.00000000      7032            0               3293            
+0.99733130      0.00000000      13513           0               3299            
+0.99488800      0.00000000      24433           0               3306            
+0.99064670      0.00000000      42413           0               3312            
+0.98371770      0.00000000      69290           0               3318            
+0.97299840      0.00000000      107193          0               3325            
+0.95712570      0.00000000      158727          0               3331            
+0.93495280      0.00000000      221729          0               3337            
+0.90518160      0.00000000      297712          0               3344            
+0.86700580      0.00000000      381758          0               3350            
+0.82025430      0.00000000      467515          0               3357            
+0.76539630      0.00000000      548580          0               3363            
+0.70350350      0.00000000      618928          0               3369            
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+0.42450200      0.00000000      699786          0               3395            
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figures/pgfplots/.latexmkrc

@@ -0,0 +1,3 @@
+$pdflatex = 'lualatex -shell-escape -interaction=nonstopmode -file-line-error -synctex=1';
+$pdf_mode = 1;        # tex -> pdf
+

figures/pgfplots/Makefile

@@ -0,0 +1,25 @@
+MAKE = make
+SOURCES = $(wildcard *_stdl.tex)
+RESULTS = $(patsubst %.tex,%.pdf,$(SOURCES))
+
+
+all: echoing $(RESULTS) $(SOURCES)
+	@echo
+	@echo done
+	@echo
+
+%_stdl.pdf : %_stdl.tex
+	latexmk $<
+
+clean:
+	latexmk -c
+ 
+clear:
+	latexmk -C
+
+echoing:
+	@echo
+	@echo Calling latexmk to compile $(SOURCES)
+	@echo
+
+.PHONY: clean clear echoing

figures/pgfplots/score_demo_raw_stdl.tex

@@ -0,0 +1,64 @@
+%%%%%%%%%%%%
+%
+% @file: osi_layers_stdl.tex
+% @author: Camille Monière
+% @year: 2022
+% @license: CC-BY 4.0
+%
+% This file is licensed under the Creative Commons Attribution 4.0 International License. 
+% To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ or send a letter to Creative Commons, 
+% PO Box 1866, Mountain View, CA 94042, USA.
+%
+%%%%%%%%%%%%
+\documentclass[tikz,margin=0pt,dvipsnames,rgb]{standalone}
+
+\input{../stdl_preamble.tex}
+
+\begin{document}
+
+\pgfplotsset{yticklabel style={text width=3em,align=right}}
+
+\begin{tikzpicture}[
+    thin
+  ]
+  \tiny
+  \begin{semilogyaxis}
+    [
+      name = plot1,
+      height = 8 cm,
+      width  = 10cm,
+      % scaled y ticks = false,
+      % y tick label style={/pgf/number format/fixed,
+      % 		/pgf/number format/1000 sep = \thinspace},
+      % xmin=0, xmax=250,
+      ylabel={Normalized counting},
+      xlabel={Score},
+      ymin=10^-6, ymax=1,
+      ymajorgrids=true, xmajorgrids=true,
+      yminorgrids=true, xminorgrids=true,
+      legend pos = north east,
+      axis y line=left, axis x line=bottom,
+      legend columns = 1,
+      legend style={
+          % the /tikz/ prefix is necessary here...
+          % otherwise, it might end-up with `/pgfplots/column 2`
+          % which is not what we want. compare pgfmanual.pdf
+          % /tikz/column 2/.style={
+          %     column sep=5pt,
+          %   },
+          % /tikz/column 4/.style={
+          %     column sep=5pt,
+          %   },
+        },
+    ]
+
+    \addplot[ color=red,   thick ] table [ x=score, y=Nfa, y expr=\thisrow{Nfa}*1e-6 ] {\fromRoot{data/score_famd_raw_m10db_sync.dat}};
+    \addplot[ color=blue,  thick ] table [ x=score, y=Nmd, y expr=\thisrow{Nmd}*1e-6 ] {\fromRoot{data/score_famd_raw_m10db_sync.dat}};
+
+    \legend{
+      {Noise only},
+      {Frame $+$ noise}
+    }
+  \end{semilogyaxis}
+\end{tikzpicture}
+\end{document}

figures/stdl_preamble.tex

@@ -0,0 +1,49 @@
+%%%%%%%%%%%%
+%
+% @file: osi_layers_stdl.tex
+% @author: Camille Monière
+% @year: 2022
+% @license: CC-BY 4.0
+%
+% This file is licensed under the Creative Commons Attribution 4.0 International License. 
+% To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ or send a letter to Creative Commons, 
+% PO Box 1866, Mountain View, CA 94042, USA.
+%
+%%%%%%%%%%%%
+\usepackage{amsmath,amssymb,amsfonts}
+\usetikzlibrary{calc,
+fit,
+shapes.misc,
+shapes.geometric,
+arrows.meta,
+fadings,
+matrix,
+chains,
+scopes,
+positioning}
+
+\usepackage{pgfplots}
+\usepackage{pgfplotstable}
+\pgfplotsset{compat=1.18}
+
+\usepackage[]{fontspec}
+
+\setmainfont{Latin Modern Roman}
+\setmonofont{Latin Modern Math}
+
+%% To ensure math are printed correctly
+\renewcommand{\textsc}[1]{{\fontfamily{lmr}\selectfont \scshape #1}}
+
+%% To allow bold math symbols
+\usepackage[]{bm}
+
+
+%% To fix inputs of file within sub-files
+\makeatletter
+\@ifundefined{fromRoot}{\newcommand{\fromRoot}[1]{../../#1}}{}
+
+\def\input@path{{../..}{..}{.}{./svg}{./pgfplots}{./tikzpicture}}
+%or: \def\input@path{{/path/to/folder/}{/path/to/other/folder/}}
+\makeatother
+
+\input{commands.tex}

figures/tikzpicture/.latexmkrc

@@ -0,0 +1,2 @@
+$pdflatex = 'lualatex -shell-escape -interaction=nonstopmode -file-line-error -synctex=1';
+$pdf_mode = 1;        # tex -> pdf

figures/tikzpicture/Makefile

@@ -0,0 +1,25 @@
+MAKE = make
+SOURCES = $(wildcard *_stdl.tex)
+RESULTS = $(patsubst %.tex,%.pdf,$(SOURCES))
+
+
+all: echoing $(RESULTS) $(SOURCES)
+	@echo
+	@echo done
+	@echo
+
+%_stdl.pdf : %_stdl.tex
+	latexmk $<
+
+clean:
+	latexmk -c
+ 
+clear:
+	latexmk -C
+
+echoing:
+	@echo
+	@echo Calling latexmk to compile $(SOURCES)
+	@echo
+
+.PHONY: clean clear echoing