feat: Update titlepage

- Hide links in glossary entries

figures/tag-definition-figure.tex

@@ -0,0 +1,3 @@
+\caption[Tandemly Arrayed Genes (TAG) definitions]{
+  Tandemly Arrayed Genes (TAG) definitions.
+}

figures/tag-definition.tex

@@ -0,0 +1,48 @@
+% TAG definitions
+% Figure inspired from fig. 1 Charles 2023 internship report
+
+\documentclass[tikz]{standalone}
+
+\usepackage{tikz}
+
+
+\begin{document}
+\usetikzlibrary{positioning}
+\usetikzlibrary{decorations.pathreplacing}
+
+  \tikzset{
+    dot/.style={fill=black, circle, inner sep=1.5pt},
+    nod/.style={sloped, at start, xshift=3mm, font=\scriptsize, above},
+}
+\begin{tikzpicture}[node distance=0.25]
+  \newcommand{\geneLength}{1}
+  \newcommand{\geneHalfHeight}{0.25}
+  % DNA line
+  \draw[-,very thick] (-6,0) to (6,0);
+  % Gene blocks
+  \node[rectangle,fill=orange,minimum height=0.5cm, minimum width=1cm] (orange1) at (-5,0) {};
+  \node[rectangle,fill=green,minimum height=0.5cm, minimum width=1cm] (green1) [right=of orange1] {};
+  \node[rectangle,fill=red,minimum height=0.5cm, minimum width=1cm] (red1) [right=of green1] {};
+  \node[rectangle,fill=green,minimum height=0.5cm, minimum width=1cm] (green2) [right=of red1] {};
+  \node[rectangle,fill=green,minimum height=0.5cm, minimum width=1cm] (green3) [right=of green2] {};
+  \node[rectangle,fill=green,minimum height=0.5cm, minimum width=1cm] (green4) [right=of green3] {};
+  \node[rectangle,fill=blue,minimum height=0.5cm, minimum width=1cm] (blue1) [right=of green4] {};
+  \node[rectangle,fill=blue,minimum height=0.5cm, minimum width=1cm] (blue2) [right=of blue1] {};
+  \node[rectangle,fill=orange,minimum height=0.5cm, minimum width=1cm] (orange2) [right=of blue2] {};
+
+  % Homology links
+
+  \draw[-,orange, bend left=40] (orange1) to coordinate[dot] node[nod] {$\mathrm{TAG}_7$} (orange2);
+
+  \draw[-,green,bend right=40] (green1) to (green2)
+  (green2) to (green3)
+  (green3) to (green4);
+  \draw[-,green,bend left=40] (green1) to (green3)
+  (green1) to coordinate[dot] node[nod] {$\mathrm{TAG}_3$}(green4);
+  \draw[-,green,bend right=40] (green1) to (green2)
+  (green2) to (green4);
+
+  \draw[-,blue, bend left=40] (blue1) to  coordinate[dot] node[nod] {$\mathrm{TAG}_0$} (blue2);
+\end{tikzpicture}
+
+\end{document}

report.org

@@ -1,8 +1,8 @@
 #+title: Further development on FTAG Finder, a pipeline to identify Gene Families and Tandemly Arrayed Genes
 #+author: Samuel Ortion
 #+date: 2023-2024
-#+LATEX_CLASS: scientific-project
-#+LATEX_CLASS_OPTIONS: [twoside=false]
+#+LATEX_CLASS: lamme2024
+#+LATEX_CLASS_OPTIONS: [twoside=true]
 #+LATEX_HEADER: \usepackage{sty/lamme2024}
 
 #+bibliography: references.bib
@@ -12,8 +12,10 @@
 #+MACRO: conditional-header (eval (concat "#+header: :results output " (print-to-string org-export-current-backend)))
 # ref. conditional-header https://emacs.stackexchange.com/a/64340/41374
 
+
 # ref. https://write.as/dani/writing-a-phd-thesis-with-org-mode
 
+
 #+name: acronyms
 | key        | abbreviation | full form                                  |
 |------------+--------------+--------------------------------------------|
@@ -27,11 +29,11 @@
 |----------------------+----------------------+-------------------------------------------------------------------------------------------------------------------------------|
 | singleton            | singleton            | A gene with a single copy                                                                                                     |
 | polyploidisation     | polyploidisation     | Mechanism leading to the acquisition of at least three versions of the same original genome in a species                      |
-| pseudogene           | pseudogene           | A gene like sequence that lost its capacity to transcribe                                                                     |
+| pseudogene           | pseudogene           | A gene-like sequence that lost its capacity to transcribe                                                                     |
 | segment_duplcation   | segment duplication  | Long stretches of DNA sequences with high identity score                                                                      |
 | retroduplication     | retroduplication     | Duplication of a gene through retro-transcription of its RNA transcript                                                       |
 | autopolyploidisation | autopolyploidisation | Polyploidisation within the same species                                                                                      |
-| allopolyploidisation | allopolyploidisation | Polyploidisation with genetic material comming from a diverged species                                                        |
+| allopolyploidisation | allopolyploidisation | Polyploidisation with genetic material coming from a diverged species                                                         |
 | polyspermy           | polyspermy           | Fertilization of an egg by more than one sperm                                                                                |
 | segment_duplication  | segment duplication  | DNA sequences present in multiple locations within a genome that share high level of sequence identity                        |
 | subfunctionalization | subfunctionalization | Fate of a duplicate gene which gets a part of the original gene function, the function being shared among multiple duplicates  |
@@ -92,23 +94,24 @@ Duplicate genes offers a pool of genetic material available for further experime
 Multiple mechanisms may lead to a gene duplication. Their effect ranges from the duplication of the whole genome to the duplication of a fragment of a gene.
 
 *** Whole genome duplication and polyploidisation
-In an event of gls:WGD, the entire set of genes present on the chromosomes is duplicated ([[cref:fig:gene-duplication-mechanisms]] (A)).
+During an event of gls:WGD, the entire set of genes present on the chromosomes is duplicated ([[cref:fig:gene-duplication-mechanisms]] (A)).
 gls:WGD can occur thanks to gls:polyspermy or in case of a non-reduced gamete.
 Gls:polyploidisation is a mechanism leading to a species with at least three copies of an initial genome.
-A striking example is probably /Triticum aestivum/ (wheat) which is hexaploid\footenote{An hexaploid cell have three pairs of homologous chromosomes} due to several hybridisation events [cite:@golovninaMolecularPhylogenyGenus2007a].
+A striking example is probably /Triticum aestivum/ (wheat) which is hexaploid[fn:hexaploid: An hexaploid cell have three pairs of homologous chromosomes.] due to several hybridisation events [cite:@golovninaMolecularPhylogenyGenus2007a].
+
 We distinguish two kinds of glspl:polyploidisation, based on the origin of the duplicate genome: (i) Gls:allopolyploidisation occurs when the supplementary chromosomes come from a divergent species. This is the case for /Triticum aestivum/ hybridisation, which consisted in the union of the chromosome set of a /Triticum/ species with those of an /Aegilops/ species. (ii) Gls:autopolyploidisation consists in the hybridisation or duplication of the whole genome within the same species.
 
 *** Unequal crossing-over
-Another source of gene duplication relies on unequal crossing-over. During cell division, a crossing-over occurs when two chromatids exchange fragments of chromosome. If the cleavage of the two chromatids occurs at different positions, the shared fragments may have different lengths. Homologous recombination of such uneven crossing-over results in the incorporation of a duplicate region, as depicted in cref:fig:gene-duplication-mechanisms (B, C).
+Another source of gene duplication relies on unequal crossing-over. During cell division, a crossing-over occurs when two chromatids exchange fragments of chromosome. If the cleavage of the two chromatids occurs at different positions, the shared fragments may have different lengths. Homologous recombination of such uneven crossing-over leads to the incorporation of a duplicate region, as depicted in cref:fig:gene-duplication-mechanisms (B, C).
 This mechanism leads to the duplication of the whole set of genes present in the fragment. These duplicate genes locate one set after the other: we call them gls:TAG. Gls:TAG are the kind of gene duplication we will be particularly interested in during this internship.
 
 *** Retroduplication
-Transposable elements plays a major role in genome plasticity, and enable gene duplication too.
+Transposable elements play a major role in genome plasticity, and enable gene duplication too.
 Retrotransposons, or RNA transposons are one type of transposable elements.
 They share similar structure and replication mechanisms with retroviruses.
 Retrotransposons replicate in the genome through a mechanism known as "copy-and-paste".
-These transposons typically contain a reverse transcriptase gene. This enzyme proceed in the reverse transcription of an mRNA transcript into its reverse, complementary DNA sequence which can then insert elsewhere in the genome.
-More generally, gls:retroduplication refers to the duplication of a sequence through reverse transcription of a RNA transcript. Gene duplicated through retroduplication lose their intronic sequences and bring a polyA tail with them in their new locus (cref:fig:gene-duplication-mechanisms (D)).
+These transposons typically contain a reverse transcriptase gene. This enzyme proceeds in the reverse transcription of an mRNA transcript into its reverse complementary DNA sequence which can then insert elsewhere in the genome.
+More generally, gls:retroduplication refers to the duplication of a sequence through reverse transcription of a RNA transcript. Genes duplicated through retroduplication lose their intronic sequences and bring a polyA tail with them in their new locus (cref:fig:gene-duplication-mechanisms (D)).
 
 *** Transduplication
 DNA transposons are another kind of transposable elements whose transposition mechanism can also lead to gene duplication.
@@ -117,7 +120,7 @@ A typical DNA transposon contains a transposase gene. This enzyme recognizes two
 
 *** Segment duplication
 Finally, glspl:segment_duplication, also called /low copy repeats/ are long stretches of DNA with high identity score ([[cref:fig:gene-duplication-mechanisms]] (F)). Their exact duplication mechanism remains unclear [cite:@lallemandOverviewDuplicatedGene2020]. They may come from an accidental replication, distinct from an uneven cross-over or a double stranded breakage.
-Transposable elements may well be involved in the mechanism, as a high enrichment of transposable elements has been found at duplicate segments extremities, in /Drosophila/ [cite:@lallemandOverviewDuplicatedGene2020].
+Transposable elements may well be involved in the mechanism, as a high enrichment of transposable elements is found next to duplicate segment extremities, in /Drosophila/ [cite:@lallemandOverviewDuplicatedGene2020].
 
 ** Fate of duplicate genes in genome evolution
 In his book /Evolution by Gene Duplication/, Susumu [[latex:textsc][Ohno]] proposed that gene duplication plays a major role in species evolution [cite:@ohnoEvolutionGeneDuplication1970], because it provides new genetic materials to build on new phenotypes while keeping a backup gene for the previous function.
@@ -127,13 +130,13 @@ Indeed, duplicate genes may evolve after duplication: they may be inactivated, b
 Duplicate genes may be inactivated and become pseudogenes. These pseudogenes keep a gene-like structure, which degrades as and when further genome modifications occur. However, they are no longer expressed.
 *** Neofunctionalization
 Duplicate genes may be conserved and gain a new function.
-For instance, in the set of olfactory receptor genes result from several duplication and deletion events (in /Drosophila/: [cite:@nozawaEvolutionaryDynamicsOlfactory2007]), after which the duplicate may specialize in the detection of a particular chemical compound.
+For instance, the current set of olfactory receptor genes result from several duplication and deletion events (in /Drosophila/: [cite/t:@nozawaEvolutionaryDynamicsOlfactory2007]), after which the duplicate olfactory genes specialized in the detection of particular chemical compounds.
 *** Subfunctionalization
 Two duplicate genes with the same original function may encounter a gls:subfunctionalization by which each gene conserves only one part of the function.
 *** Functional redundancy
-The two gene copies may keep the ancestral function: in this case the organism may increase the quantity of gene product.
+The two gene copies may keep the ancestral function: in this case the quantity of gene product may increase.
 ** Methods to identify duplicate genes
-[cite:@lallemandOverviewDuplicatedGene2020] review the different methods used to detect duplicate genes. These methods depend on the type of duplicate genes they target and vary on computation burden as well as ease of use [cite:@lallemandOverviewDuplicatedGene2020].
+ [[latex:textsc][Lallemand]] et al. review the different methods used to detect duplicate genes. These methods depend on the type of duplicate genes they target and vary on computation burden as well as ease of use [cite:@lallemandOverviewDuplicatedGene2020].
 
 *** Paralog detection
 Paralogs are homologous genes derived from a duplication event. We can identify them as homologous genes coming from the same genome, or as homologous genes between different species once we filtered out gls:orthologues (homologous genes derived from a speciation event).
@@ -157,7 +160,13 @@ We apply a graph clustering algorithm on the graph in order to infer the gene fa
 FTAG Finder proposes three clustering algorithm alternatives: single linkage, Markov Clustering [cite:@vandongenNewClusterAlgorithm1998] or Walktrap [cite:@ponsComputingCommunitiesLarge2005].
 **** Detection of TAGs
 The final step of FTAG Finder consists in the identification of gls:TAG from the gene families and the positions of genes.
-For a given chromosome, the tool seeks genes belonging to the same family and located close to each other. The tool allows a maximal number of genes between the homologous genes, with a parameter set by the user.
+For a given chromosome, the tool seeks genes belonging to the same family and located close to each other. The tool allows a maximal number of genes between the homologous genes, with a parameter set by the user. Ref:fig:tag-definitions is a schematic representation of some possible gls:TAG positioning on a genome associated with their definition in FTAG Finder /Find Tags/ step.
+#+begin_export latex
+\fladdfig{
+	\includegraphics[width=.9\linewidth]{./figures/tag-definition.pdf}
+	\caption[Schematic representation of TAG definitions]{\label{fig:tag-definitions} Schematic representation of TAG definitions. Several genes are represented on a linear chromosome. The red box represent a singleton gene. Orange boxes represent a TAG with two duplicate genes seperated by 7 other genes ($\mathrm{TAG}_7$). Four green boxes constitute a TAG, the gene at the extremities are seperated by three genes ($\mathrm{TAG}_3$. The two blue boxes represents a TAG with two genes next to each other $\mathrm{TAG}_0$. The bended edges represents the homology links between each pair of genes of a TAG.}}
+#+end_export
+
 * Objectives for the internship
 ** Scientific questions
 The underlying question of FTAG Finder is the study of the evolutionary fate of duplicate genes in Eukaryotes.
@@ -183,7 +192,9 @@ The two main options being Snakemake and Nextflow. Snakemake is a python powered
 
 #+begin_export latex
 \cleartoleftpage
+\clearpairofpagestyles
 #+end_export
+
 ** Summary
 :PROPERTIES:
 :UNNUMBERED: t
@@ -205,3 +216,16 @@ Principle: construct vertex communities based on where an agent would get stuck
 
 #  LocalWords:  speciation Subfunctionalization Neofunctionalization
 #  LocalWords:  Pseudogenization
+* Setup :noexport:
+
+#+name: startup
+#+begin_src emacs-lisp
+(org-babel-load-file "./setup.org")
+#+end_src
+
+#+RESULTS: startup
+: Loaded ./setup.el
+
+#  Local Variables:
+#  eval: (progn (org-babel-goto-named-src-block "startup") (org-babel-execute-src-block) (outline-hide-sublevels 1))
+#  End:

setup.org

@@ -0,0 +1,95 @@
+#+title: Standalone Emacs Config file for my report
+* I can set a variable at startup!
+
+Let's say I want this emacs-lisp code to be run at startup when I open my org file (say, for config purpose)
+#+begin_src emacs-lisp :tangle yes
+(setq lamme2024 "org powered")
+#+end_src
+
+#+RESULTS:
+: org powered
+
+To do so, add the following somewhere in your =report.org= file:
+#+begin_src org
+#+name: startup
+#+begin_src emacs-lisp
+(org-babel-load-file "./setup.org")
+#+end_src
+#+end_src
+
+And add the following at the end of your =report.org= file:
+
+#+begin_src org
+#  Local Variables:
+#  eval: (progn (org-babel-goto-named-src-block "startup") (org-babel-execute-src-block) (outline-hide-sublevels 1))
+#  End:
+#+end_src
+
+The next time you will open your file, you will be asked twice if org-babel should run the =startup= cell.
+
+See: [[https://emacs.stackexchange.com/a/41456/41374]]
+
+* Configure LaTeX template
+
+#+begin_src emacs-lisp :tangle yes
+(add-to-list 'org-latex-classes
+          '("lamme2024"
+             "\\documentclass{scrreprt}
+             [NO-DEFAULT-PACKAGES]
+             [EXTRA]
+                \\makeindex
+                \\makeglossaries          "
+             ;("\\part{%s}" . "\\part*{%s}")
+             ("\\chapter{%s}" . "\\chapter{%s}")
+             ("\\section{%s}" . "\\section*{%s}")
+             ("\\subsection{%s}" . "\\subsection*{%s}")
+             ("\\subsubsection{%s}" . "\\subsubsection*{%s}")
+             ("\\paragraph{%s}" . "\\paragraph*{%s}")
+             ("\\subparagraph{%s}" . "\\subparagraph*{%s}")))
+#+end_src
+
+#+RESULTS:
+| lamme2024 | \documentclass{scrreprt} |
+
+* Add latex: link for custom latex macro text wrapping
+
+#+begin_src emacs-lisp :tangle yes
+ (org-add-link-type
+  "latex" nil
+  (lambda (path desc format)
+   (cond
+    ((eq format 'html)
+     (format "<span class=\"%s\">%s</span>" path desc))
+    ((eq format 'latex)
+     (format "\\%s{%s}" path desc)))))
+#+end_src
+
+#+RESULTS:
+: Created latex link.
+
+#+begin_src emacs-lisp :tangle yes
+(org-add-link-type
+  "latex" nil
+  (lambda (path desc format)
+   (cond
+    ((eq format 'html)
+     (format "<span class=\"%s\">%s</span>" path desc))
+    ((eq format 'latex)
+     (format "\\%s{%s}" path desc)))))
+#+end_src
+
+#+RESULTS:
+: Created latex link.
+
+
+* Extend org reference system
+
+#+begin_src emacs-lisp :tangle yes
+(require 'org-ref)
+(require 'org-ref-refproc)
+(add-hook 'org-export-before-parsing-hook #'org-ref-acronyms-before-parsing)
+(add-hook 'org-export-before-parsing-hook #'org-ref-glossary-before-parsing)
+#+end_src
+
+#+RESULTS:
+| org-ref-glossary-before-parsing | org-ref-acronyms-before-parsing | org-attach-expand-links |

sty/lamme2024.sty

@@ -12,9 +12,27 @@
 \RequirePackage{float}
 \RequirePackage{caption}
 \RequirePackage{subcaption}
-\RequirePackage{xcolor}
 \RequirePackage{csquotes}
 \RequirePackage[english]{babel}
+%% Caption
+\captionsetup{
+    labelfont={color=black, bf},
+    figurename=Figure,
+    tablename=Table,
+    font={sf},
+    labelsep=period,
+    justification=raggedright,
+    singlelinecheck=false
+}
+
+% Colors
+\RequirePackage{xcolor}
+ \definecolor{lamme2024-blue}{HTML}{008682}
+ \colorlet{primary}{lamme2024-blue}
+ \colorlet{primaryLink}{primary!60!blue}
+ \colorlet{primaryCite}{red!70!primary}
+
+
 % Math
 \RequirePackage{amsmath}
 \RequirePackage{amsthm}
@@ -50,6 +68,7 @@
 	]{cleveref}
 
 
+
 \usepackage[
 	abbreviations,         % create "abbreviations" glossary
 	%nomain,                % don't create "main" glossary
@@ -59,16 +78,41 @@
 \setabbreviationstyle[acronym]{long-short}
 
 \usepackage{hyperref}
+\hypersetup{
+  colorlinks=true,
+  urlcolor=primaryLink,
+  linkcolor=primaryLink,
+  anchorcolor=primaryLink,
+  citecolor=primaryCite
+}
+\newcommand*{\glsplainhyperlink}[2]{%
+    \begingroup%
+      \hypersetup{hidelinks}%
+      \hyperlink{#1}{#2}%
+    \endgroup%
+  }
+
+\let\oldgls=\gls
+\renewcommand{\gls}[1]{{\hypersetup{hidelinks}%
+	\oldgls{#1}}}%
+
+\let\oldGls=\Gls
+\renewcommand{\Gls}[1]{{\hypersetup{hidelinks}%
+  \oldGls{#1}}}%
+
+
+%\renewcommand*{\glstextformat}[1]{\begingroup\hypersetup{hidelinks}#1\endgroup}
+%\renewcommand*{\glsdohyperlink}[2]{%
+% {\hypersetup{hidelinks=true}\hyperlink{#1}{#2}}}
+\renewcommand*{\glsentryfmt}{%
+  \hypersetup{hidelinks}\glshyperlink[\glsgenentryfmt]{\glslabel}%
+}
 
 % Force text on right side, float on left side (does not work well)
 \usepackage{sty/floatlefttextright}
 
 \renewcommand\maketitle{\include{titlepage}}
 
-\hypersetup{
-	hidelinks
-}
-
 \renewcommand*{\mkbibnamefamily}[1]{\textsc{#1}}
 \renewcommand*{\mkbibnameprefix}[1]{\textsc{#1}}
 
@@ -83,3 +127,121 @@
   }
 
   \usepackage{scrhack}
+% From S. Ivanov hdr preamble
+\iffalse
+\titleformat{\chapter}[frame]
+{\itshape\color{primary}}
+{\filright
+  \normalsize
+  \enspace Chapter \thechapter\enspace}
+{10mm}
+{\fontsize{35}{20}\selectfont\normalfont\bfseries\filright\hspace{1ex}}
+\titleformat{\section}{\Large\normalfont\bfseries\color{primary}}{\thesection \hspace{1ex}}{1ex}{}
+\titleformat{\subsection}{\large\normalfont\bfseries\color{primary}}{\thesubsection \hspace{1ex}}{1ex}{}
+\titleformat{\subsubsection}{\normalsize\normalfont\bfseries\color{primary}}{}{1ex}{}
+
+\newcommand{\changelocaltocdepth}[1]{%
+  \addtocontents{toc}{\protect\setcounter{tocdepth}{#1}}%
+  \setcounter{tocdepth}{#1}%
+}
+\fi
+
+%
+
+% \usepackage{sty/cleanthesis-extracts}
+
+\RequirePackage[manualmark]{scrlayer-scrpage}
+\renewcommand*\chaptermark[1]{%
+    \markboth{\Ifnumbered{chapter}{\chaptermarkformat}{}}{#1}% <- outdated macro replaced
+}
+\AfterTOCHead[toc]{\markboth{}{\contentsname}}
+
+\clearpairofpagestyles
+\clubpenalty = 10000
+\widowpenalty = 10000
+
+\automark[section]{part}
+\setlength{\footheight}{120pt}      % avoids scrlayer-scrpage warning:
+% footheight to low warning
+\setlength{\footskip}{185pt}        % BAD HACK that moves the foot downwards
+\KOMAoption{footwidth}{foot:53pt}   % BAD HACK that moves the foot towards
+\setkomafont{pagefoot}{\normalfont\footnotesize}
+\setkomafont{pagenumber}{\normalfont \fontfamily{\sfdefault}\selectfont \normalsize  \bfseries\color{black}}
+
+\renewcommand{\partmark}[1]{%
+    \markboth{%
+        % use \@chapapp instead of \chaptername to avoid
+        % 'Chapter A Appendix ...', thanks to @farbverlust (issue #47)
+        \fontfamily{\sfdefault}\selectfont
+        {\color{fgBlue}\textbf{\partname\ \thepart}}%
+        \quad%
+        \protect\begin{minipage}[t]{.65\textwidth}%
+            #1%
+            \protect\end{minipage}%
+    }{}%
+}
+
+\newlength{\lensectionnumber}
+\renewcommand{\sectionmark}[1]{%
+    \markright{%
+        \normalsize\fontfamily{\sfdefault}\selectfont\bfseries
+        \setlength{\lensectionnumber}{0em}
+        \settowidth{\lensectionnumber}{\textbf{\thesection}\quad}
+        \protect\begin{minipage}[t]{.72\textwidth}%
+            {\ }% bad hack to prevent a wrong baseline for the minipage
+            \protect\raggedleft%
+            \hangindent=\lensectionnumber%
+            {\color{black}\textbf{\fontfamily{\sfdefault}\selectfont\thesection}}%
+            \quad%
+            #1%
+            \protect\end{minipage}%
+    }%
+}
+
+\newcommand{\ctfooterline}{%
+    \color{black}\rule[-90pt]{1.25pt}{100pt}%
+}
+
+% Page number for odd (right) pages
+\newcommand{\ctfooterrightpagenumber}{%
+    \ctfooterline%
+    \hspace*{10pt}%
+    \begin{minipage}[b]{1.5cm}%
+        \pagemark\ %
+    \end{minipage}%
+}
+
+%% Page number for even (left) pages
+\newcommand{\ctfooterleftpagenumber}{%
+    \begin{minipage}[b]{1.5cm}%
+        \raggedleft\pagemark%
+    \end{minipage}%
+    \hspace*{10pt}%
+    \ctfooterline%
+}
+
+%% Defines the content for header and footer
+\lehead{}
+\cehead{}
+\rehead{}
+\lohead{}
+\cohead{}
+\rohead{}
+\lefoot[%   > plain
+    \ctfooterleftpagenumber%
+]{%         > srcheadings
+    \ctfooterleftpagenumber%
+    \hspace*{0.75cm}%
+    %\headmark%
+}
+\cefoot{}
+\refoot{}
+\lofoot{}
+\cofoot{}
+\rofoot[%   > plain
+    \ctfooterrightpagenumber%
+]{%         > srcheadings
+    %\headmark%
+    \hspace*{0.75cm}%
+    \ctfooterrightpagenumber%
+}

titlepage.tex

@@ -7,14 +7,10 @@
 	\begin{center}
 		\Huge Scientific Project
 
-		\Large Master GENIOMHE
+		\Large Master 1 GENIOMHE
 
 		\Large 2023--2024
 
-		\vspace{2cm}
-
-		\Large Samuel \textsc{Ortion} \orcidlink{0009-0001-0971-497X}
-
 		\vfill
 
 		\LARGE
@@ -22,6 +18,13 @@
 		\@title
 		\makeatother
 
+		\vspace{2em}
+
+		\Large Samuel \textsc{Ortion} \orcidlink{0009-0001-0971-497X}
+
+		\vfill
+
+
 		\vfill
 		\normalsize
 		\begin{minipage}{12.5em}