adapt training slides to new theme

2019/2019-06-11_gitTraining/slides/best_practices.md

-## Best practices
+# Best practices
 
 * `pull` before `push`
 

2019/2019-06-11_gitTraining/slides/branches.md

-## Development scheme
+# Development scheme
 
 
 Generally, in a repository, there are guidelines for contributing.
@@ -26,7 +26,7 @@ A **version** of the code is referred to as a **branch**.
 
 
 
-## Branches
+# Branches
 
 A **version** of the code (i.e., a **branch**) is made up of a sequence of code changes.
 
@@ -40,7 +40,7 @@ For instance, the `master` and `develop` branches can be represented as a timeli
 
 
 
-## Switch between branches
+# Switch between branches
 
 List all branches of the repository with
 ```bash
@@ -70,7 +70,7 @@ If the local branch does not exist but the remote does, it is created automatica
 
 
 
-## Create your own version
+# Create your own version
 
 Assume that you want to work on a file:
 

2019/2019-06-11_gitTraining/slides/cloneRepo.md

-## How do I start working on a repository?
+# How do I start working on a repository?
 
 You have to `clone` it first:
 

2019/2019-06-11_gitTraining/slides/configuration.md

-## How to configure `git`?
+# How to configure `git`?
 
 ```bash
 $ git config --global user.name "Firstname Lastname"
@@ -17,7 +17,7 @@ Exit by typing `q`.
 
 
 
-## What is an SSH key?
+# What is an SSH key?
 
 An SSH key is a secure access credential.
 
@@ -26,7 +26,7 @@ Communicate **securely** with Github/Gitlab **without** entering the username/pa
 
 
 
-## How do I get and set my SSH key?
+# How do I get and set my SSH key?
 
 Check if you already have an SSH key:
 

2019/2019-06-11_gitTraining/slides/essential_commands.md

-## The 5 essential commands
+# The 5 essential commands
 
 
 **Yes**, you only need 5 commands!
@@ -16,7 +16,7 @@ $ git push <remote> <branch>
 
 
 
-## Pull the latest version of an existing branch
+# Pull the latest version of an existing branch
 
 Pull the latest revision on branch `myBranch`:
 ```bash
@@ -33,7 +33,7 @@ $ git status
 
 
 
-## Modify a file
+# Modify a file
 
 Copy the file `template.md` in the folder `_attendees` and rename it with your firstname:
 
@@ -46,7 +46,7 @@ Then, make your changes with your favorite editor!
 
 
 
-## Add your file to the stage
+# Add your file to the stage
 
 First, check the repository status
 ```bash
@@ -74,7 +74,7 @@ exit with `q`
 
 
 
-## Add a commit message
+# Add a commit message
 
 ```bash
 $ git commit -m "Add the profile of <myName>"
@@ -83,7 +83,7 @@ $ git status
 
 
 
-## Push your file to your fork
+# Push your file to your fork
 
 ```bash
 $ git push origin myBranch

2019/2019-06-11_gitTraining/slides/forks.md

-
-## What is a `fork`?
+# What is a `fork`?
 
 <img src="slides/img/fork.jpg" class="as-is" height="500em"/>
 <!--http://www.cndajin.com/data/wls/246/22302193.jpg-->
 
 
 
-## Not really ...
+# Not really ...
 
 <img src="slides/img/fork-crossed.png" class="as-is" height="500em"/>
 
 
 
-## What is a `fork`?
+# What is a `fork`?
 
 In general, when contributing to a repository, you only have **read** access.
 
@@ -26,7 +25,7 @@ In other words, you have to work on your own <font color="red">**fork**</font>.
 
 
 
-## How to get a fork?
+# How to get a fork?
 
 Browse to the original repository and click on the button `Fork`:
 
@@ -36,7 +35,7 @@ Browse to the original repository and click on the button `Fork`:
 
 
 
-## Time to practice!
+# Time to practice!
 
 Fork the practice repository: <br><br>
 https://github.com/LCSB-BioCore/basic-git-practice
@@ -56,7 +55,7 @@ $ cd basic-git-practice
 
 
 
-## A note on shortcuts ...
+# A note on shortcuts ...
 
 <font color="red">
 Any other rudimentary method such as
@@ -70,7 +69,7 @@ shall **be avoided**!
 
 
 
-## How to update my fork?
+# How to update my fork?
 
 As you have your own fork, it will not automatically update once the original repository is update.
 

2019/2019-06-11_gitTraining/slides/github_gitlab.md

-## GitHub and GitLab
+# GitHub and GitLab
 
 <img src="https://github.githubassets.com/images/modules/logos_page/GitHub-Mark.png" alt="GitHub" style="width: 200px;"/>
 <img src="https://gitlab.com/gitlab-com/gitlab-artwork/raw/master/logo/logo-extra-whitespace.png" alt="GitLab" style="width: 200px;"/>

2019/2019-06-11_gitTraining/slides/index.md

-## R3.school
-<br><br>
-#### June 11th, 2019
+# R3.school
+
+## June 11th, 2019
 
 <div style="top: 6em; left: 0%; position: absolute;">
     <img src="theme/img/lcsb_bg.png">
@@ -8,8 +8,8 @@
 
 <div style="top: 5em; left: 60%; position: absolute;">
     <img src="slides/img/r3-training-logo.png" height="200px">
-    <br><br><br><br>
-    <h3>git training for absolute beginners</h3>
+    <br><br><br>
+    <h1>git training for absolute beginners</h1>
     <br><br><br><br>
     <h4>
         Laurent Heirendt, Ph.D.<br><br>

2019/2019-06-11_gitTraining/slides/installation.md

-## Installation of `git`
+# Installation of `git`
 
 <img src="slides/img/github_app.png" class="as-is" height="200" />
 
@@ -20,7 +20,7 @@ $ sudo apt-get install git-all
 
 
 
-## How to get started?
+# How to get started?
 
 **macOS**
 

2019/2019-06-11_gitTraining/slides/merge.md

-## Pull and merge requests
+# Pull and merge requests
 
 If you want your changes to be reflected on the `develop` or `master` branches,
 **submit a PR** via the Github interface.

2019/2019-06-11_gitTraining/slides/overview.md

-## Overview
+# Overview
 
 1. **PART I**: Quality of computer code.
 2. **PART II**: Basic git course

2019/2019-06-11_gitTraining/slides/qualityCode.md

-## Quality of computer code is relevant for everyone.
+# Quality of computer code is relevant for everyone.
 
 `This does not concern me – I am only writing documentation or a script for generating a figure that I want to publish!`
 [Anonymous researcher]
@@ -19,7 +19,7 @@
 
 
 
-## Attributes of high-quality computer code
+# Attributes of high-quality computer code
 
 **Quality** of computer code can be seen as a **group of various attributes**.
 

2019/2019-06-11_gitTraining/slides/repro_crisis.md

-## Reproducibility crisis
+# Reproducibility crisis
 
 <div align="center">
 <img src="slides/img/reproCrisis.png">

2019/2019-06-11_gitTraining/slides/syncFork.md

-## Synchronize your fork
+# Synchronize your fork
 
 ![bulb](slides/img/bulb.png) Remember, we have to regularly update our own copy of the code.
 

2019/2019-06-11_gitTraining/slides/thanks.md

-## Let's refresh our memories
+# Let's refresh our memories
 
 <div class="fragment">
 
@@ -22,7 +22,7 @@
 
 
 
-## References & Cheat sheet
+# References & Cheat sheet
 
 [1]: Git Book: https://git-scm.com/book/en/v2
 
@@ -32,7 +32,7 @@
 
 
 
-## Thank you.
+# Thank you.
 
 <img src="slides/img/r3-training-logo.png" height="200px">
 

2019/2019-06-11_gitTraining/slides/the_editor.md

-## The editor(s)
+# The editor(s)
 
 Recommended editors:
 

2019/2019-06-11_gitTraining/slides/the_terminal.md

-## PART II
+# PART II
 
 <br><br><h1>Basic git course</h1>
 
 
 
-## The terminal (shell)
+# The terminal (shell)
 
 **macOS users:**
 
@@ -23,7 +23,7 @@ Launch default terminal.<br>
 
 
 
-## First steps in the terminal
+# First steps in the terminal
 
 Starting the terminal presents itself with a line where you can enter a command
 ```bash
@@ -40,7 +40,7 @@ in your home directory (unless otherwise configured), denoted as `~/`.
 
 
 
-## Essential Linux commands
+# Essential Linux commands
 
 List the contents of a directory
 ```bash

2019/2019-06-11_gitTraining/slides/what_is_git.md

-## What is `git`?
+# What is `git`?
 
 <!-- ![](slides/img/git_definition.png) -->
 
@@ -14,7 +14,7 @@ Designed and implemented in 2005 by **Linus Torvalds**
 
 
 
-## The inventor of `git`
+# The inventor of `git`
 
 <div align="center">
 <img src="slides/img/git_definition.png">
@@ -26,7 +26,7 @@ Linus Torvald (2007-06-14)
 
 
 
-## What is the use of `git`?
+# What is the use of `git`?
 
 * No need to fully rewrite code; **reuse code** and **save time**
 * Keep the changes you made over time (**history**)

2019/2019-06-11_gitTraining/slides/whatiscode.md

-## What is computer code?
+# What is computer code?
 
 **Computer code**: Set of instructions executed by a computer
 

2019/2019-06-11_gitTraining/slides/wheel.md

-## PART I
+# PART I
 
 <br><br><h1>Quality of computer code.</h1><br>
 <h1>Should you care? What if you didn't?</h1>
 
 
 
-## A true story ...
+# A true story ...
 
 <div align="center">
 <img src="slides/img/wheel.png">