commit 5c2d7a9c6bf10421842512fb1c4b80360bf8675f Author: Samuel Ortion Date: Wed Mar 20 12:19:56 2024 +0100 Initial commit - Base layout trying to follow instructions - Figure on left side, text on right side - Strange behavior: too much blank pages in the end. diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..d8d4037 --- /dev/null +++ b/.gitignore @@ -0,0 +1,311 @@ +*.gls-abr +*.glo-abr +*.glg-abr +*.ist + + +build/ +main.tex +*.html + +## 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 diff --git a/.latexmkrc b/.latexmkrc new file mode 100644 index 0000000..7da747c --- /dev/null +++ b/.latexmkrc @@ -0,0 +1,35 @@ +$hash_calc_ignore_pattern{aux} = +'^\\\\gdef\\\\minted@oldcachelist\{,' + . '|^\s*default\.pygstyle,' + . '|^\s*[[:xdigit:]]+\.pygtex'; + +$pdflatex = +'lualatex -shell-escape -file-line-error -interaction=nonstopmode -synctex=1 -output-directory=build %O ' + . '\'\PassOptionsToPackage{outputdir=build}{minted}\input{%S}\''; +$aux_dir = 'build'; +$bibtex_use = 2; + +# Amend cleaned extensions +$clean_ext .= " fdb_latexmk run.xml synctex.gz"; + +# Make latexmk quiet +$latexmk_silent = 1; + +# Makeglossaries +add_cus_dep( 'acn', 'acr', 0, 'makeglossaries' ); +add_cus_dep( 'glo', 'gls', 0, 'makeglossaries' ); +$clean_ext .= " acr acn alg glo gls glg"; + +sub makeglossaries { + my ( $base_name, $path ) = fileparse( $_[0] ); + my @args = ( "-q", "-d", $path, $base_name ); + if ($silent) { unshift @args, "-q"; } + return system "makeglossaries", "-d", $path, $base_name; +} + +sub biber { + my ( $base_name, $path ) = fileparse( $_[0] ); + my @args = ( "--output-directory", $path, $base_name ); + return system "biber", @args; +} + diff --git a/Makefile b/Makefile new file mode 100755 index 0000000..0011af3 --- /dev/null +++ b/Makefile @@ -0,0 +1,16 @@ +OPTIONS=-shell-escape -file-line-error -synctex=1 +SOURCE=main + +all: latexmk bib glossaries latexmk + +build: + lualatex $(OPTIONS) $(SOURCE) + +latexmk: + latexmk -gg -pdf $(SOURCE) + +bib: + biber --output-directory=build $(SOURCE) + +glossaries: + makeglossaries $(SOURCE) diff --git a/glossary.tex b/glossary.tex new file mode 100644 index 0000000..e69de29 diff --git a/main.pdf b/main.pdf new file mode 100644 index 0000000..b263fc2 Binary files /dev/null and b/main.pdf differ diff --git a/media/logo/logo-lamme.pdf b/media/logo/logo-lamme.pdf new file mode 100644 index 0000000..1956eb0 Binary files /dev/null and b/media/logo/logo-lamme.pdf differ diff --git a/media/logo/logo-lamme.svg b/media/logo/logo-lamme.svg new file mode 100644 index 0000000..70321f8 --- /dev/null +++ b/media/logo/logo-lamme.svg @@ -0,0 +1,98 @@ + + + \ No newline at end of file diff --git a/media/logo/logo-psaclay.pdf b/media/logo/logo-psaclay.pdf new file mode 100644 index 0000000..8534124 Binary files /dev/null and b/media/logo/logo-psaclay.pdf differ diff --git a/media/logo/logo-ueve.pdf b/media/logo/logo-ueve.pdf new file mode 100644 index 0000000..7dd25bc Binary files /dev/null and b/media/logo/logo-ueve.pdf differ diff --git a/sty/floatlefttextright.sty b/sty/floatlefttextright.sty new file mode 100644 index 0000000..0e44bfa --- /dev/null +++ b/sty/floatlefttextright.sty @@ -0,0 +1,31 @@ +% https://www.developpez.net/forums/d910711/autres-langages/autres-langages/latex/mise-forme/texte-recto-figures-verso/ +% Solution by Martigan on Developpez.net + +\RequirePackage{afterpage} +\RequirePackage{caption} +\newcommand\@addfig{\relax} +\newcommand\addfig[1]{\global\long\def\@addfig{#1}} +\newcommand\@putfig{\@addfig\addfig{\relax}} +\newcommand\blankpage{% + \null + \vfill + \captionsetup{type=figure} % Warning: this could be faulty if tables are required + \@putfig% + \vfill + \thispagestyle{empty}% + \clearpage% + \addtocounter{page}{-1} + \afterpage{\blankpage} +} + + +\iffalse + % Example + \addfig{% + + \centering + \includegraphics[scale=1]{Image1} + \caption{Test} + \label{Ima1} + } +\fi diff --git a/sty/lamme2024.sty b/sty/lamme2024.sty new file mode 100644 index 0000000..f383b87 --- /dev/null +++ b/sty/lamme2024.sty @@ -0,0 +1,70 @@ + +\usepackage{graphicx} +\usepackage{tikz} +\usepackage{xcolor} +\usepackage{hyperref} + +\usepackage{fontspec} +\setmainfont{TeX Gyre Termes} % Times New Roman alternative +\usepackage{setspace} +\onehalfspacing % 1.5 interline spacing +\defaultfontfeatures[\rmfamily,\sffamily]{Ligatures=TeX} +\addtokomafont{disposition}{\rmfamily} + +% Force text on right side, float on left side +\usepackage{sty/floatlefttextright} + +% Font +\RequirePackage{polyglossia} +\setmainlanguage{english} +%\setotherlanguage{french} + + +% Float +\RequirePackage{graphicx} +\RequirePackage{float} +\RequirePackage{caption} +\RequirePackage{subcaption} +\RequirePackage{xcolor} + +% Math +\RequirePackage{amsmath} +\RequirePackage{amsthm} +\RequirePackage{amssymb} + + +\usepackage{enumitem} + +\usepackage{lipsum} + +% References +\usepackage[ + maxcitenames=2, + style=authoryear-comp, + backend=biber, + citestyle=authoryear-comp, + natbib=true +]{biblatex} +\RequirePackage{doi} +\RequirePackage{xurl} + +\RequirePackage{orcidlink} + +\RequirePackage[ + type={CC}, + modifier={by-sa}, + version={4.0}, +]{doclicense} + +\RequirePackage[ + nameinlink, + noabbrev +]{cleveref} + + +\usepackage[ + abbreviations, % create "abbreviations" glossary + %nomain, % don't create "main" glossary + stylemods=longbooktabs, % do the adjustments for the longbooktabs styles, + automake +]{glossaries-extra} diff --git a/summary.tex b/summary.tex new file mode 100644 index 0000000..e69de29 diff --git a/titlepage.tex b/titlepage.tex new file mode 100644 index 0000000..a3b18fe --- /dev/null +++ b/titlepage.tex @@ -0,0 +1,43 @@ +\begin{titlepage} + + \includegraphics[height=2cm]{media/logo/logo-psaclay.pdf} + \hfill + \includegraphics[height=2cm]{media/logo/logo-ueve.pdf} + + \begin{center} + \Huge Scientific Project + + \Large Master GENIOMHE + + \Large 2023--2024 + + \hfill + + \Huge Samuel ORTION \orcidlink{0009-0001-0971-497X} + + \vfill + + \Huge + + Development of a Nextflow\footnote{We still need to decide which workflow manager to choose: Nextflow or Snakemake} pipeline for FTAG Finder, a duplicate gene detection tool, and improvement of the existing Galaxy implementation + + \vfill + \normalsize + \begin{minipage}{15em} + \textbf{Advisors}:\\ + Carène RIZZON \\ + Franck SAMSON \\ + Laboratoire de Mathématiques et Modélisation d'Évry \\ + \href{mailto:carene.rizzon@univ-evry.fr}{carene.rizzon@univ-evry.fr} \\ + \href{mailto:franck.samson@inrae.fr}{franck.samson@inrae.fr} \\ + +33~(0)~1~64~85~35~40 \\ + IBGBI \\ + 23 Bd. de France \\ + 91037 Évry Cedex + \end{minipage} + \hfill + \includegraphics[height=2cm]{media/logo/logo-ueve.pdf} + \hfill + \includegraphics[height=2cm]{media/logo/logo-lamme.pdf} + \end{center} +\end{titlepage}