Migrating to org-mode

.gitattributes

@@ -0,0 +1 @@
+main.pdf filter=lfs diff=lfs merge=lfs -text

.latexmkrc

@@ -1,3 +1,9 @@
+sub createFolderStructure{
+   system("bash ./folder-structure.sh");
+}
+
+createFolderStructure();
+
 $hash_calc_ignore_pattern{aux} =
 '^\\\\gdef\\\\minted@oldcachelist\{,'
   . '|^\s*default\.pygstyle,'

folder-structure.sh

@@ -0,0 +1,8 @@
+#!/bin/sh
+
+find ./content -type d > folder_list.txt
+
+mkdir -p build
+cd build
+cat ../folder_list.txt | xargs mkdir -p
+rm ../folder_list.txt

glossary.tex

@@ -0,0 +1 @@
+\newabbreviation{TAG}{TAGs}{Tandem Arrayed Genes}

report.org

@@ -0,0 +1,44 @@
+#+title: Further development on FTAG Finder, a pipeline to identify Tandem Arrayed Genes
+#+subtitle: Scientific project
+#+author: Samuel Ortion
+#+date: 2023-2024
+#+LATEX_CLASS: lamme2024
+#+LATEX_HEADER: \usepackage{sty/lamme2024}
+#+bibliography: ../references.bib
+#+exclude_tags: noexport
+
+# ref. https://write.as/dani/writing-a-phd-thesis-with-org-mode
+
+#+begin_export latex
+\hypersetup{
+	pdfauthor={Samuel Ortion},
+	pdftitle={},
+	pdfkeywords={duplicate genes, workflow management systems, pipeline},
+	pdfsubject={},
+	pdflang={English}}
+{
+\pagenumbering{roman}
+\hypersetup{hidelinks}
+\tableofcontents
+\printglossaries
+}
+#+end_export
+
+#+begin_center
+duplicate genes, tandem arrayed genes, pipeline
+
+#+end_center
+
+* Context
+** Duplicate genes
+*** Duplication mechanism
+*** Role in genome evolution
+** Identification of duplicate genes
+** FTAG Finder, a method to identify Families and Tandem Arrayed Genes
+* Objectives
+
+* Tips :noexport:
+
+To export:
+C-c C-e C-b l l
+

report.tex

@@ -0,0 +1,23 @@
+% Created 2024-03-21 Thu 19:34
+% Intended LaTeX compiler: lualatex
+\documentclass{scrreprt}
+                                \usepackage{sty/lamme2024}
+\author{Samuel Ortion}
+\date{2023-2024}
+\title{Further development on FTAG Finder, a pipeline to identify Tandem Arrayed Genes\\\medskip
+\large Scientific project}
+\hypersetup{
+ pdfauthor={Samuel Ortion},
+ pdftitle={Further development on FTAG Finder, a pipeline to identify Tandem Arrayed Genes},
+ pdfkeywords={},
+ pdfsubject={},
+ pdfcreator={Emacs 29.2 (Org mode 9.7)}, 
+ pdflang={English}}
+\usepackage{biblatex}
+\addbibresource{../references.bib}
+\begin{document}
+
+\maketitle
+\tableofcontents
+
+\end{document}

sty/floatlefttextright.sty

@@ -1,31 +1,47 @@
 % https://www.developpez.net/forums/d910711/autres-langages/autres-langages/latex/mise-forme/texte-recto-figures-verso/
 % Solution by Martigan on Developpez.net
 
+\iffalse
 \RequirePackage{afterpage}
 \RequirePackage{caption}
 \newcommand\@addfig{\relax}
 \newcommand\addfig[1]{\global\long\def\@addfig{#1}}
 \newcommand\@putfig{\@addfig\addfig{\relax}}
-\newcommand\blankpage{%
+\newcommand\flblankpage{%
 	\null
 	\vfill
+	\begin{figure}[H]
 	\captionsetup{type=figure} % Warning: this could be faulty if tables are required
 	\@putfig%
+	\end{figure}
 	\vfill
 	\thispagestyle{empty}%
 	\clearpage%
-	\addtocounter{page}{-1}
+	%\addtocounter{page}{-1}
-	\afterpage{\blankpage}
+	\afterpage{\flblankpage}
 }
 
 
+
 \iffalse
 	% Example
-	\addfig{%
 
+	% Add this at the beggining of the document:
+	\afterpage{\flblankpage}
+
+	\addfig{%
 		\centering
 		\includegraphics[scale=1]{Image1}
 		\caption{Test}
 		\label{Ima1}
 	}
 \fi
+
+\fi
+
+\def\@floatplacement{\global\@topnum\c@topnumber
+   \global\@toproom \topfraction\@colht
+   \global\@botnum  \c@bottomnumber
+   \global\@botroom \bottomfraction\@colht
+   \global\@colnum  \ifodd\c@page\c@totalnumber\else\z@\fi%<<<<<<<
+   \@fpmin   \floatpagefraction\@colht}

sty/lamme2024.sty

@@ -1,23 +1,10 @@
 
-\usepackage{graphicx}
+% Font
-\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
@@ -26,13 +13,13 @@
 \RequirePackage{caption}
 \RequirePackage{subcaption}
 \RequirePackage{xcolor}
-
+\RequirePackage{csquotes}
+\RequirePackage[english]{babel}
 % Math
 \RequirePackage{amsmath}
 \RequirePackage{amsthm}
 \RequirePackage{amssymb}
 
-
 \usepackage{enumitem}
 
 \usepackage{lipsum}
@@ -45,8 +32,8 @@
 	citestyle=authoryear-comp,
 	natbib=true
 ]{biblatex}
-\RequirePackage{doi}
+%\RequirePackage{doi}
-\RequirePackage{xurl}
+%\RequirePackage{xurl}
 
 \RequirePackage{orcidlink}
 
@@ -68,3 +55,13 @@
 	stylemods=longbooktabs, % do the adjustments for the longbooktabs styles,
 	automake
 ]{glossaries-extra}
+
+\usepackage{hyperref}
+
+% Force text on right side, float on left side
+% \usepackage{sty/floatlefttextright}
+
+
+\makeglossaries
+\makeindex
+\renewcommand\maketitle{\include{titlepage}}

sty/test_figurelefttextright.tex

@@ -0,0 +1,19 @@
+\documentclass{book}
+
+\usepackage{floatlefttextright}
+\usepackage{lipsum}
+\usepackage{graphicx}
+
+\begin{document}
+
+	\afterpage{\blankpage}
+\lipsum{100}
+
+
+\addfig{
+  \includegraphics[width=\textwidth]{example-image-a}
+  \caption{Test figure}
+  \label{fig:Test figure}
+}
+
+\end{document}

titlepage.tex

@@ -11,13 +11,13 @@
 
 		\Large 2023--2024
 
-		\hfill
+		\vfill
 
-		\Huge Samuel ORTION \orcidlink{0009-0001-0971-497X}
+	\Large Samuel ORTION \orcidlink{0009-0001-0971-497X}
 
 		\vfill
 
-		\Huge
+		\LARGE
 
 		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