<commit_before>%%%%%%%%%%%%%%%%%%%%%%%%%
% PACKAGES              %
%%%%%%%%%%%%%%%%%%%%%%%%%
\documentclass[]{report} % book|article|…

\usepackage[utf8x]{inputenc}    % accents
\usepackage{geometry}           % marges
\usepackage[francais]{babel}    % langue
\usepackage{graphicx}           % images
\usepackage{verbatim}           % texte préformaté
\usepackage{fancyhdr}           % fancy
\usepackage{filecontents}       % write file directly
\usepackage{csvsimple}          % csv reader
\usepackage{lastpage}	        % get number of last page
\usepackage{listings}           % source code 
\usepackage{url}                % clickable urls 
\usepackage{float}              % exact placing of figures
\usepackage{amsmath}            % fancy matrices
\usepackage{xkeyval}            % keywords arguments for newcommand
\usepackage{xifthen}            % provides \isempty test

% packages for graphics
\usepackage{fancybox}         
\usepackage{pgfplots}        
\usepackage{pgfplotstable}
\usepgfplotslibrary{dateplot}
\usepackage{pgfplots}

\definecolor{Gene0}{RGB}{250, 164, 1}
\definecolor{Gene1}{RGB}{128, 0, 128}
\definecolor{Gene2}{RGB}{255, 0, 0}
\definecolor{Gene3}{RGB}{58, 242, 75}
\definecolor{Gene4}{RGB}{8, 81, 156}
\definecolor{Diversity}{RGB}{0, 0, 0}

\pgfplotscreateplotcyclelist{list}{
        {Gene0},
        {Gene1},
        {Gene2},
        {Gene3},
        {Gene4},
        {Diversity}
}




%%%%%%%%%%%%%%%%%%%%%%%%%
% SIMULATION COMMAND    %
%%%%%%%%%%%%%%%%%%%%%%%%%
%This is needed for encapsulating.
%changes the catcode of @ so it
%can be used freely (not needed
%when writing a package)
\makeatletter

\define@cmdkey [SIMPAR] {fam} {generations} {}
\define@cmdkey [SIMPAR] {fam} {popsize}     {}
\define@cmdkey [SIMPAR] {fam} {parents}     {}
\define@cmdkey [SIMPAR] {fam} {seed}        {}
\define@cmdkey [SIMPAR] {fam} {mutationrate}{}
\define@cmdkey [SIMPAR] {fam} {initialpheno}{}
\define@cmdkey [SIMPAR] {fam} {link}        {}
 
\presetkeys [SIMPAR] {fam} {generations  = 200,
                            popsize      = 300,
                            parents      = 2,
                            seed         = 4223,
                            mutationrate = $10^{-4}$,
                            initialpheno = 11111,
                            link         = ?,
                           }{}

\newcommand{\simulationParameters}[1]{%
        \setkeys[SIMPAR]{fam}{#1}
        \begin{center}
                \begin{tabular}{|l|c||l|c|}
                \hline
                \textbf{Generations computed}   & \cmdSIMPAR@fam@generations    & \textbf{Population size}      & \cmdSIMPAR@fam@popsize        \\ \hline
                \textbf{Parent number}          & \cmdSIMPAR@fam@parents        & \textbf{Mutation rate}        & \cmdSIMPAR@fam@mutationrate   \\ \hline
                \textbf{Seed}                   & \cmdSIMPAR@fam@seed           & \textbf{Initial Phenotype}    & \cmdSIMPAR@fam@initialpheno   \\ \hline
                \textbf{Figure}                 & \ref{fig:\cmdSIMPAR@fam@link} & \textbf{Matrix}               & \ref{mat:\cmdSIMPAR@fam@link} \\ \hline
                \end{tabular}
        \end{center}
}

%Change again the @ catcode
%to normal
\makeatother




%%%%%%%%%%%%%%%%%%%%%%%%%
% PRÉAMBULE             %
%%%%%%%%%%%%%%%%%%%%%%%%%
%\title{Genomat\\PRJ Project Report}
%\author{<NAME> and <NAME>}
% laisser vide pour date de compilation
%\date{} 

% FORMAT PAGES         
\pagestyle{fancy} % nom du rendu (définit les lignes suivantes)
        \lhead{M1 BIG} % left head
        \chead{Genomat} % center head
        \rhead{2014/2015} % right head
        \lfoot{} % left foot
        \cfoot{\thepage/\pageref{LastPage}} % center foot
        \rfoot{} % right foot






%%%%%%%%%%%%%%%%%%%%%%%%%
% BEGIN                 %
%%%%%%%%%%%%%%%%%%%%%%%%%
\begin{document}
\begin{titlepage}
\newcommand{\HRule}{\rule{\linewidth}{0.5mm}}
\center
\textsc{\LARGE University of Rennes 1}\\[1.5cm]
\textsc{\large Master 1}\\[0.5cm] 
\textsc{\Large Bioinformatics and Genomics}\\[0.5cm] 

%----------------------------------------------------------------------------------------
%	TITLE SECTION
%----------------------------------------------------------------------------------------

\HRule \\[0.4cm]
{ \huge \bfseries Genomat}\\[0.4cm] % Title of your document
\HRule \\[1.5cm]
 
%----------------------------------------------------------------------------------------
%	AUTHOR SECTION
%----------------------------------------------------------------------------------------

\begin{minipage}{0.4\textwidth}
\begin{flushleft} \large
\emph{Authors:}\\
Lucas \textsc{Bourneuf}\\
Ostiane	\textsc{D'Augustin}
\end{flushleft}
\end{minipage}
~
\begin{minipage}{0.4\textwidth}
\begin{flushright} \large
\emph{Supervisors:} \\
Olivier \textsc{Dameron}
Yann \textsc{<NAME>}\\
\end{flushright}<commit_msg>line jump<commit_after>%%%%%%%%%%%%%%%%%%%%%%%%%
% PACKAGES              %
%%%%%%%%%%%%%%%%%%%%%%%%%
\documentclass[]{report} % book|article|…

\usepackage[utf8x]{inputenc}    % accents
\usepackage{geometry}           % marges
\usepackage[francais]{babel}    % langue
\usepackage{graphicx}           % images
\usepackage{verbatim}           % texte préformaté
\usepackage{fancyhdr}           % fancy
\usepackage{filecontents}       % write file directly
\usepackage{csvsimple}          % csv reader
\usepackage{lastpage}	        % get number of last page
\usepackage{listings}           % source code 
\usepackage{url}                % clickable urls 
\usepackage{float}              % exact placing of figures
\usepackage{amsmath}            % fancy matrices
\usepackage{xkeyval}            % keywords arguments for newcommand
\usepackage{xifthen}            % provides \isempty test

% packages for graphics
\usepackage{fancybox}         
\usepackage{pgfplots}        
\usepackage{pgfplotstable}
\usepgfplotslibrary{dateplot}
\usepackage{pgfplots}

\definecolor{Gene0}{RGB}{250, 164, 1}
\definecolor{Gene1}{RGB}{128, 0, 128}
\definecolor{Gene2}{RGB}{255, 0, 0}
\definecolor{Gene3}{RGB}{58, 242, 75}
\definecolor{Gene4}{RGB}{8, 81, 156}
\definecolor{Diversity}{RGB}{0, 0, 0}

\pgfplotscreateplotcyclelist{list}{
        {Gene0},
        {Gene1},
        {Gene2},
        {Gene3},
        {Gene4},
        {Diversity}
}




%%%%%%%%%%%%%%%%%%%%%%%%%
% SIMULATION COMMAND    %
%%%%%%%%%%%%%%%%%%%%%%%%%
%This is needed for encapsulating.
%changes the catcode of @ so it
%can be used freely (not needed
%when writing a package)
\makeatletter

\define@cmdkey [SIMPAR] {fam} {generations} {}
\define@cmdkey [SIMPAR] {fam} {popsize}     {}
\define@cmdkey [SIMPAR] {fam} {parents}     {}
\define@cmdkey [SIMPAR] {fam} {seed}        {}
\define@cmdkey [SIMPAR] {fam} {mutationrate}{}
\define@cmdkey [SIMPAR] {fam} {initialpheno}{}
\define@cmdkey [SIMPAR] {fam} {link}        {}
 
\presetkeys [SIMPAR] {fam} {generations  = 200,
                            popsize      = 300,
                            parents      = 2,
                            seed         = 4223,
                            mutationrate = $10^{-4}$,
                            initialpheno = 11111,
                            link         = ?,
                           }{}

\newcommand{\simulationParameters}[1]{%
        \setkeys[SIMPAR]{fam}{#1}
        \begin{center}
                \begin{tabular}{|l|c||l|c|}
                \hline
                \textbf{Generations computed}   & \cmdSIMPAR@fam@generations    & \textbf{Population size}      & \cmdSIMPAR@fam@popsize        \\ \hline
                \textbf{Parent number}          & \cmdSIMPAR@fam@parents        & \textbf{Mutation rate}        & \cmdSIMPAR@fam@mutationrate   \\ \hline
                \textbf{Seed}                   & \cmdSIMPAR@fam@seed           & \textbf{Initial Phenotype}    & \cmdSIMPAR@fam@initialpheno   \\ \hline
                \textbf{Figure}                 & \ref{fig:\cmdSIMPAR@fam@link} & \textbf{Matrix}               & \ref{mat:\cmdSIMPAR@fam@link} \\ \hline
                \end{tabular}
        \end{center}
}

%Change again the @ catcode
%to normal
\makeatother




%%%%%%%%%%%%%%%%%%%%%%%%%
% PRÉAMBULE             %
%%%%%%%%%%%%%%%%%%%%%%%%%
%\title{Genomat\\PRJ Project Report}
%\author{<NAME> and <NAME>}
% laisser vide pour date de compilation
%\date{} 

% FORMAT PAGES         
\pagestyle{fancy} % nom du rendu (définit les lignes suivantes)
        \lhead{M1 BIG} % left head
        \chead{Genomat} % center head
        \rhead{2014/2015} % right head
        \lfoot{} % left foot
        \cfoot{\thepage/\pageref{LastPage}} % center foot
        \rfoot{} % right foot






%%%%%%%%%%%%%%%%%%%%%%%%%
% BEGIN                 %
%%%%%%%%%%%%%%%%%%%%%%%%%
\begin{document}
\begin{titlepage}
\newcommand{\HRule}{\rule{\linewidth}{0.5mm}}
\center
\textsc{\LARGE University of Rennes 1}\\[1.5cm]
\textsc{\large Master 1}\\[0.5cm] 
\textsc{\Large Bioinformatics and Genomics}\\[0.5cm] 

%----------------------------------------------------------------------------------------
%	TITLE SECTION
%----------------------------------------------------------------------------------------

\HRule \\[0.4cm]
{ \huge \bfseries Genomat}\\[0.4cm] % Title of your document
\HRule \\[1.5cm]
 
%----------------------------------------------------------------------------------------
%	AUTHOR SECTION
%----------------------------------------------------------------------------------------

\begin{minipage}{0.4\textwidth}
\begin{flushleft} \large
\emph{Authors:}\\
Lucas \textsc{Bourneuf}\\
Ostiane	\textsc{D'Augustin}
\end{flushleft}
\end{minipage}
~
\begin{minipage}{0.4\textwidth}
\begin{flushright} \large
\emph{Supervisors:} \\
Olivier \textsc{Dameron}\\
Yann \textsc{<NAME>}
\end{flushright}
{'fraction_non_alphanumeric': 0.23754631535611362, 'fraction_numerical': 0.019761218608480857, 'mean_word_length': 1.8462214411247804, 'pattern_counts': {'":': 0, '<': 9, '<?xml version=': 0, '>': 9, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 2, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '4389234', 'n_tokens_mistral': 3190, 'n_tokens_neox': 2870, 'n_words': 574}