From 1bcb211e40d9f2777eaacd5845f6315e15d31089 Mon Sep 17 00:00:00 2001
From: Samuel Ortion <samuel+git@ortion.fr>
Date: Wed, 17 Apr 2024 08:07:39 +0200
Subject: [PATCH] feat: Add some colors and title formatting

- Hide links in glossary entries
---
 report.org        |  2 +-
 report.pdf        |  4 +--
 sty/lamme2024.sty | 81 +++++++++++++++++++++++++++++++++++++++++++----
 3 files changed, 77 insertions(+), 10 deletions(-)

diff --git a/report.org b/report.org
index 3391403..2f92aff 100644
--- a/report.org
+++ b/report.org
@@ -33,7 +33,7 @@
 | 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  |
diff --git a/report.pdf b/report.pdf
index ecc374f..2573e69 100644
--- a/report.pdf
+++ b/report.pdf
@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:d87e7035c51051c9357085f06e80d00a175aee5b7d93370d117dd0250c51200c
-size 180869
+oid sha256:a33b17a4dc21bd767ab98a233be1903c840c806cedb9a4ddc50a99e35a23b70a
+size 185000
diff --git a/sty/lamme2024.sty b/sty/lamme2024.sty
index 0c365ad..f814e80 100644
--- a/sty/lamme2024.sty
+++ b/sty/lamme2024.sty
@@ -12,9 +12,17 @@
 \RequirePackage{float}
 \RequirePackage{caption}
 \RequirePackage{subcaption}
-\RequirePackage{xcolor}
 \RequirePackage{csquotes}
 \RequirePackage[english]{babel}
+
+% 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}
@@ -47,7 +55,8 @@
 \RequirePackage[
 	nameinlink,
 	noabbrev
-]{cleveref}
+	]{cleveref}
+
 
 
 \usepackage[
@@ -59,16 +68,41 @@
 \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}}
 
@@ -82,4 +116,37 @@
 	\fi
   }
 
-\usepackage{scrhack}
+  \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}%
+}
+% Adapted to KOMA-Script (and to my preferences):
+\renewcommand*{\sectionformat}{\thesection\filright\hspace{1ex}}
+\addtokomafont{subsection}{\color{primary}}
+\fi
+
+\usepackage{titlesec}
+\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}{}