First commit

.gitignore

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+## 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
+*.rubbercache
+rubber.cache
+
+## 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
+
+# hypdoc
+*.hd
+
+# 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

chapter1.tex

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+\addtocounter{customchapter}{1}
+\chapter{Un premier chapitre méga chouette}
+
+Et on fait même des citations \cite{kundakovicSexHormoneFluctuation2022} !

chapter2.tex

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+\addtocounter{customchapter}{1}
+\chapter{Second chapitre, t'y as capté}
+
+Et ouais deux chapitres mon pote

intro.tex

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+\chapter*{Introduction super cool}
+\pagestyle{intro}
+
+Ici du blabla introductif

page-garde.tex

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+\begin{titlepage}
+
+    %\thispagestyle{empty}
+
+    \newgeometry{left=7.5cm,bottom=2cm, top=1cm, right=1cm}
+
+    % Le bandeau sur le côté
+    \begin{tikzpicture}[remember picture,overlay]
+        \fill [pruneps] (-4,-28.3) rectangle (-8.15, 1.4);
+
+        \foreach \x  in {-8.1, -7.9, -7.6, -7.2}
+        \draw[white, line width=0.5mm] (\x, -28.3) -- (\x, 1.4);
+
+        \node[inner sep=0pt, rotate=90, font=\fontfamily{fvs}\fontseries{b}\fontsize{26}{26}\selectfont, text=white] (rapport) at (-6.3, -22.4) {Rapport de stage};
+        \node[inner sep=0pt, opacity=1] (logo-UPS) at (-0.85,0) {\includegraphics{logo/Logotype_UPSaclay_CMJN.eps}};
+    \end{tikzpicture}
+
+    % fonte sans empattement pour la page de titre
+    \fontfamily{fvs}\fontseries{m}\selectfont
+
+
+
+    %*****************************************************
+    %**  LOGO  ÉTABLISSEMENT PARTENAIRE SI COTUTELLE
+    %**  CHANGER L'IMAGE PAR DÉFAUT **
+    %*****************************************************
+    \vspace{-10mm} % à ajuster en fonction de la hauteur du logo
+    \flushright\includegraphics[scale=0.3]{logo/APT_Logo_RVB_Positif}
+    \flushright\includegraphics[scale=0.3]{logo/X-IPparis-RVB.eps}
+
+
+
+    %*****************************************************
+    %******************** TITRE **************************
+    %*****************************************************
+    \flushright
+    \vspace{10mm} % à régler éventuellement
+    \color{pruneps}
+    \fontfamily{fvs}\fontseries{m}\fontsize{22}{26}\selectfont
+    \thetitle
+
+    %*****************************************************
+
+    %\fontfamily{fvs}\fontseries{m}\fontsize{8}{12}\selectfont
+    \normalsize
+    \vspace{1.5cm}
+
+    \color{black}
+    \textbf{Stage de M2 Mathématiques pour les Sciences du vivant}
+
+    \vspace{15mm}
+
+    \footnotesize Unité de recherche: Math\'ematiques et informatique appliqu\'ees \\(AgroParisTech), UMR 518 INRAE\\
+    \footnotesize Référent: Camille Coron\\
+    \vspace{15mm}
+
+    \textbf{par}\\
+    \bigskip
+    \Large {\color{pruneps} \textbf{\theauthor}}
+
+
+    %************************************
+    \vspace{\fill} % ALIGNER LE TABLEAU EN BAS DE PAGE
+    %************************************
+
+    \flushleft \small \textbf{Encadrement du stage :}
+    \bigskip
+
+    \scriptsize
+    \begin{tabular}{|p{8cm}l}\arrayrulecolor{pruneps}
+        \textbf{Michèle Unetelle} & Co-encadrante \\
+        \textbf{Sandra Truc}      & Co-encadrante
+        %		\textbf{Prénom Nom} &   Coencadrante\\ 
+        %		Titre, Affiliation  &   \\ 
+        %		\textbf{Prénom Nom} &  Invité \\ 
+        %		Titre, Affiliation  &   \\ 
+    \end{tabular}
+
+
+\end{titlepage}

rapport.tex

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+\documentclass[12pt,a4paper,twoside]{report}
+%====En-tête====
+% Ajout des packages
+\usepackage[french,english]{babel} % pour dire que le texte est en francais
+\usepackage{csquotes}
+\usepackage{a4} % pour la taille
+\usepackage[T1]{fontenc} % pour les font postscript
+\usepackage[cyr]{aeguill} % Police vectorielle TrueType, guillemets francais
+\usepackage{epsfig} % pour gérer les images
+\usepackage{amsmath,amsthm, mathtools} % très bon mode mathématique
+\usepackage{amsfonts,amssymb,bm, bbold}% permet la definition des ensembles
+\usepackage{algorithm2e} % pour les algorithmes
+\usepackage{algpseudocode} % pour les algorithmes
+\usepackage{float} % pour le placement des figure
+\usepackage{url} % pour une gestion efficace des url
+\usepackage[citecolor=blueind,urlcolor=blueps,bookmarks=false,hypertexnames=true]{hyperref}  % pour les hyperliens dans le document
+\usepackage{tocbibind} % Pour avoir des index pour table des matières, biblio
+\usepackage{geometry}
+\usepackage{tikz} % For graph plots
+\usepackage[outline]{contour}
+\usepackage[super]{nth}
+
+
+\usepackage{caption} % Figures
+\usepackage{subcaption} % And Subfigures
+
+
+\usepackage{longtable}
+\usepackage{colortbl}
+
+\usepackage{titling}
+
+\usepackage{rotating} % For allowing to rotate figures
+\usepackage{float} % To allow Pandoc to control figure placement
+\usepackage{booktabs} % For good tables
+
+% FancyHDR
+\usepackage{fancyhdr}
+\pagestyle{fancy}
+\fancyhf{}
+\renewcommand{\chaptermark}[1]{\markboth{#1}{#1}}
+\fancyhead[lo]{\slshape\nouppercase{\rightmark}}
+\fancyhead[re]{\slshape\nouppercase{\leftmark}}
+\fancyhead[ro,le]{\thepage}
+
+\fancypagestyle{intro}{%
+    \fancyhf{}
+    \fancyfoot[C]{\thepage}
+    \renewcommand{\headrulewidth}{0pt}
+    \renewcommand{\footrulewidth}{0pt}
+}
+
+
+% Images
+\graphicspath{{img/}}
+
+% Figure placement
+\floatplacement{figure}{H}
+
+%% Tikz Related
+\usetikzlibrary{calc,shapes,backgrounds,arrows,automata,shadows,positioning,
+arrows,shapes,positioning,shadows,trees,calc,backgrounds,
+automata,positioning}
+
+
+% Couleurs
+%% Couleur Paris-Saclay
+\definecolor{pruneps}{RGB}{99,0,60}
+\definecolor{bluefonceps}{RGB}{0,78,125}
+\definecolor{blueps}{RGB}{14,135,201}
+\definecolor{cyanps}{RGB}{70,195,210}
+\definecolor{vertps}{RGB}{64,183,105}
+
+% Pour la biblio
+\usepackage[style=apa, sorting=none, backend=biber]{biblatex}
+\addbibresource{references.bib}
+\AtEveryCite{\color{bluefonceps}}
+
+% Pour avoir les chapitres stylés
+\newcounter{customchapter}
+
+% Pour arrêter de colorer après le contenu principal
+\newcounter{maincontentend}
+
+
+% Important : modifie ici le nombre de chapitres que tu as.
+% A savoir que cela correspond aux nombres de labels du bandeau sur le côté.
+% Le bandeau est automatiquement mis à jour pour correspondre à la valeur de la 
+% variable customchapter, avec 0 = pas de label.
+\newcommand\ChapNum{5}
+
+%%%%%% Debut code onglets
+
+\usepackage{background}
+\usepackage{changepage}
+\usepackage{sectsty}
+\newcommand\DeactivateBG{\backgroundsetup{contents={}}}
+\newcommand\ActivateBG{\backgroundsetup{
+		scale=1,
+		angle=0,
+		opacity=0.5,
+		contents={
+            \ifnum\value{maincontentend}=0
+			\ifnum\value{customchapter}>0
+			\checkoddpage
+			\ifoddpage
+			\begin{tikzpicture}[remember picture,overlay]
+			\node[rotate=90,minimum width=\paperheight,minimum height=0.5cm,fill=gray!40,font=\large\bfseries,text=white,anchor=south west] at ($(current page.south east)$) {};
+			\node[rotate=90,minimum width=1/\ChapNum*\paperheight,minimum height=0.5cm,fill=\BoxColor,font=\large\bfseries,text=white,anchor=south west] at ([yshift=(\ChapNum-\thecustomchapter)/\ChapNum*\paperheight]$(current page.south east)$) {\chaptername~\thechapter}; 
+			\end{tikzpicture}
+			\else
+			\begin{tikzpicture}[remember picture,overlay]
+			\node[rotate=90,minimum width=\paperheight,minimum height=0.5cm,fill=gray!40,font=\large\bfseries,text=white,anchor=south west] at ([xshift=-\paperwidth+0.5cm]$(current page.south east)$) {};
+			\node[rotate=270,minimum width=1/\ChapNum*\paperheight,minimum height=0.5cm,fill=\BoxColor,font=\large\bfseries,text=white,anchor=south west] at ([yshift=(\ChapNum-\thecustomchapter+1)/\ChapNum*\paperheight,xshift=-\paperwidth]$(current page.south east)$) {\chaptername~\thechapter};
+			\end{tikzpicture}
+			\fi
+            \fi
+			\fi
+}
+}
+}
+
+\definecolor{bleuvert}{RGB}{102, 255, 204}
+\definecolor{greenAgro}{HTML}{028887}
+\newcommand\BoxColor{%
+	\ifcase\thecustomchapter greenAgro!40!black\or green!40!black\or blue!40!black\or  orange!70!black\or violet!60!black\or teal!60!black\or red!40!black\or blue!40!black\else greenAgro!40!black
+    \fi}
+% \newcommand\ChapterTitle{%
+% 	\ifcase\thecustomchapter {\thechapter} \else {}
+%     \fi
+%     }
+
+\sectionfont{\color{\BoxColor}}
+\subsectionfont{\color{\BoxColor}}
+\subsubsectionfont{\color{\BoxColor}}
+
+%%%% End onglets
+
+%%%%%%%%%%%%%% En-tête de chapitre %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+\makeatletter
+\def\thickhrulefill{\leavevmode \leaders \hrule height 1ex \hfill \kern \z@}
+\def\@makechapterhead#1{%
+	\vspace*{-30\p@}%
+	{
+		\parindent \z@ \raggedleft \reset@font
+		\scshape 
+		\color{\BoxColor}{\@chapapp{} {\fontsize{100pt}{12pt}\selectfont{\textbf{\thechapter}}}}
+		\par\nobreak
+		\interlinepenalty\@M
+		\Huge \bfseries {\color{\BoxColor}{#1}}\par\nobreak
+		\vspace*{-20\p@}%
+		{\color{\BoxColor}\hrulefill}
+		\par\nobreak
+		\vskip 10\p@
+}}
+\def\@makeschapterhead#1{%
+	\vspace*{-30\p@}%
+	{
+		\parindent \z@ \raggedleft \reset@font
+		\scshape \vphantom{\@chapapp{} \thechapter}
+		\par\nobreak
+		\interlinepenalty\@M
+		\Huge \bfseries {\color{\BoxColor}{#1}}\par\nobreak
+		\vspace*{-20\p@}%
+		\hrulefill
+		\par\nobreak
+		\vskip 10\p@
+}}
+\makeatother
+
+% Nouvelles commandes
+\newcommand{\Tau}{\mathcal{T}}
+\newcommand{\eps}[1][]{\ensuremath{\epsilon_{#1}}}
+
+
+% titre et auteur
+\title{Un titre qui claque}
+\author{Un.e auteur.e}
+\begin{document}
+
+% Pour désactiver le fond (background)
+\DeactivateBG
+\include{page-garde}
+% Pour activer les onglets
+\ActivateBG
+\begin{selectlanguage}{french}
+	% \maketitle
+	\pagenumbering{roman}
+	\tableofcontents
+	\include{remerciements}
+	\include{intro}
+\end{selectlanguage}
+
+\begin{selectlanguage}{english}
+	\pagenumbering{arabic}
+	\include{chapter1}
+
+	\include{chapter2}
+
+
+	% On marque la fin du contenu principal
+	\addtocounter{maincontentend}{1}
+	% On incrémente le compteur pour changer de couleurs quand même
+	\addtocounter{customchapter}{1}
+	\printbibliography
+\end{selectlanguage}
+\begin{selectlanguage}{french}
+	\listoffigures
+	\listoftables
+\end{selectlanguage}
+
+\end{document}

references.bib

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+@article{kundakovicSexHormoneFluctuation2022,
+  title = {Sex Hormone Fluctuation and Increased Female Risk for Depression and Anxiety Disorders: From Clinical Evidence to Molecular Mechanisms},
+  shorttitle = {Sex Hormone Fluctuation and Increased Female Risk for Depression and Anxiety Disorders},
+  author = {Kundakovic, Marija and Rocks, Devin},
+  date = {2022-07},
+  journaltitle = {Front Neuroendocrinol},
+  volume = {66},
+  eprint = {35716803},
+  eprinttype = {pmid},
+  pages = {101010},
+  issn = {0091-3022},
+  doi = {10.1016/j.yfrne.2022.101010},
+  url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9715398/},
+  urldate = {2024-05-29},
+  abstract = {Women are at twice the risk for anxiety and depression disorders as men are, although the underlying biological factors and mechanisms are largely unknown. In this review, we address this sex disparity at both the etiological and mechanistic level. We dissect the role of fluctuating sex hormones as a critical biological factor contributing to the increased depression and anxiety risk in women. We provide parallel evidence in humans and rodents that brain structure and function vary with naturally-cycling ovarian hormones. This female-unique brain plasticity and associated vulnerability are primarily driven by estrogen level changes. For the first time, we provide a sex hormone-driven molecular mechanism, namely chromatin organizational changes, that regulates neuronal gene expression and brain plasticity but may also prime the (epi)genome for psychopathology. Finally, we map out future directions including experimental and clinical studies that will facilitate novel sex- and gender-informed approaches to treat depression and anxiety disorders.},
+  pmcid = {PMC9715398},
+  file = {/home/polarolouis/Zotero/storage/EJQQPIA3/Kundakovic et Rocks - 2022 - Sex hormone fluctuation and increased female risk .pdf}
+}

remerciements.tex

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+\newpage
+\chapter*{Remerciements}
+\addcontentsline{toc}{chapter}{Remerciements}
+
+Ici on remercie correctement les gens