first round of cleanup

2019/2019-10-03_basicGitTraining-SIU/slides/configuration.md

-# How to configure `git`?
-
-```bash
-$ git config --global user.name "Firstname Lastname"
-$ git config --global user.email "first.last@uni.lu"
-```
-
-Test whether your username and email have been registered
-
-```bash
-$ git config --list
-```
-
-This should list the configuration with `user.name` and `user.email`.
-
-Exit by typing `q`.
-
-
-
-# What is an SSH key?
-
-An SSH key is a secure access credential.
-
-**Principle**: <br><br>
-Communicate **securely** with Github/Gitlab **without** entering the username/password.
-
-
-
-# How do I get and set my SSH key?
-
-Check if you already have an SSH key:
-
-```bash
-$ ls -al ~/.ssh
-```
-
-If there are 2 files named `id_rsa`, you have an SSH key.
-
-If you don’t have yet an SSH key, you have to generate one:
-```bash
-$ ssh-keygen -t rsa # -b 4096
-```
-
-Then, add the SSH key to Github/Gitlab.
-
-<img src="slides/img/icon-live-demo.png" height="100px">
\ No newline at end of file

2019/2019-10-03_basicGitTraining-SIU/slides/index.md

 # R3.school
 
-## June 11th, 2019
+## October 3rd, 2019
 
 <div style="top: 6em; left: 0%; position: absolute;">
     <img src="theme/img/lcsb_bg.png">
@@ -9,11 +9,11 @@
 <div style="top: 5em; left: 60%; position: absolute;">
     <img src="slides/img/r3-training-logo.png" height="200px">
     <br><br><br>
-    <h1>git training for absolute beginners</h1>
+    <h1>Basic git training</h1>
     <br><br><br><br>
     <h4>
-        Laurent Heirendt, Ph.D.<br><br>
-        laurent.heirendt@uni.lu<br><br>
+        Laurent Heirendt, Ph.D.<br>
+        laurent.heirendt@uni.lu<br>
         <i>Luxembourg Centre for Systems Biomedicine</i>
     </h4>
 </div>

2019/2019-10-03_basicGitTraining-SIU/slides/installation.md

-# Installation of `git`
-
-<img src="slides/img/github_app.png" class="as-is" height="200" />
-
-**macOS**
-
-Install *Xcode Command Line Tools*
-
-
-**Windows**
-
-Install Git Bash: <br>`https://git-scm.com/download/win`
-
-
-**Linux (Ubuntu)**
-
-```bash
-$ sudo apt-get install git-all
-```
-
-
-
-# How to get started?
-
-**macOS**
-
-Start the `Terminal` or `iTerm`.
-
-
-**Windows**
-
-Start `GUI Bash`.
-
-
-**Linux (Ubuntu)**
-
-Start the `Terminal` or `Terminator`.
-
-
-**Is `git` properly installed?**
-
-```bash
-$ git --version
-# git version 2.10.0
-```
\ No newline at end of file

2019/2019-10-03_basicGitTraining-SIU/slides/list.json

 [
-    {
-        "filename": "index.md"
-    },
-    {
-        "filename": "overview.md"
-    },
-    {
-        "filename": "wheel.md"
-    },
-    {
-        "filename": "repro_crisis.md"
-    },
-    {
-        "filename": "whatiscode.md"
-    },
-    {
-        "filename": "whyCare.md"
-    },
-    {
-        "filename": "qualityCode.md"
-    },
-    {
-        "filename": "what_is_git.md"
-    },
-    {
-        "filename": "the_terminal.md"
-    },
-    {
-        "filename": "the_editor.md"
-    },
-    {
-        "filename": "installation.md"
-    },
-    {
-        "filename": "github_gitlab.md"
-    },
-    {
-        "filename": "configuration.md"
-    },
-    {
-        "filename": "cloneRepo.md"
-    },
-    {
-        "filename": "forks.md"
-    },
-    {
-        "filename": "branches.md"
-    },
-    {
-        "filename": "essential_commands.md"
-    },
-    {
-        "filename": "merge.md"
-    },
-    {
-        "filename": "syncFork.md"
-    },
-    {
-        "filename": "best_practices.md"
-    },
-    {
-        "filename": "thanks.md"
-    }
+    { "filename": "index.md" },
+    { "filename": "overview.md" },
+    { "filename": "what_is_git.md" },
+    { "filename": "the_terminal.md" },
+    { "filename": "github_gitlab.md" },
+    { "filename": "cloneRepo.md" },
+    { "filename": "forks.md" },
+    { "filename": "branches.md" },
+    { "filename": "essential_commands.md" },
+    { "filename": "merge.md" },
+    { "filename": "syncFork.md" },
+    { "filename": "best_practices.md" },
+    { "filename": "thanks.md" }
 ]

2019/2019-10-03_basicGitTraining-SIU/slides/overview.md

 # Overview
 
-1. **PART I**: Quality of computer code.
-2. **PART II**: Basic git course
-    1. The terminal
-    2. The editor
-    3. What is `git`? What is the use of `git`? <!--(5 min)//-->
-    4. Installation of `git`
-    5. GitHub and GitLab <!--(5min)//-->
-    6. How do I configure `git`? <!--(5min)//-->
-    7. Where and how to start? <!--(5min)//-->
-    8. What is a fork? <!--(5min)//-->
-    9. What are branches?
-    10. The 5 essential commands (`pull` / `status` / `add` / `commit` / `push`)
-    11. What are merge/pull requests? <!--(10 min)//-->
-    12. How do I synchronize my fork?
+1. The terminal
+2. The editor
+3. What is `git`? What is the use of `git`? <!--(5 min)//-->
+4. Installation of `git`
+5. GitHub and GitLab <!--(5min)//-->
+6. How do I configure `git`? <!--(5min)//-->
+7. Where and how to start? <!--(5min)//-->
+8. What is a fork? <!--(5min)//-->
+9. What are branches?
+10. The 5 essential commands (`pull` / `status` / `add` / `commit` / `push`)
+11. What are merge/pull requests? <!--(10 min)//-->
+12. How do I synchronize my fork?
+13. Best practices
\ No newline at end of file
-    13. Best practices
\ No newline at end of file

2019/2019-10-03_basicGitTraining-SIU/slides/qualityCode.md

-# 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]
-
-<div class="fragment">
-
-**Great**, but ...
-
-- Figure may not be reproducible
-- Figure looks different when the input data changes
-- Documentation will become outdated
-
-… actually, **EVERYONE** writing documentation, a script, or code is concerned!
-
-<div align="center">
-<img src="slides/img/snoopy.png" height="400px">
-</div>
-
-
-
-# Attributes of high-quality computer code
-
-**Quality** of computer code can be seen as a **group of various attributes**.
-
-High-quality computer code should be:
-
-1. <font color="#A52A2A">**Versioned**</font>: incremental code
-2. <font color="#FFA500">**Well-written**</font> (formatted, documented, commented): easy to read by a human
-3. <font color="#008931">**Tested**</font>: extensively tested code
-
-<div align="center">
-<img src="slides/img/qualitybadge.png">
-</div>
\ No newline at end of file

2019/2019-10-03_basicGitTraining-SIU/slides/repro_crisis.md

-# Reproducibility crisis
-
-<div align="center">
-<img src="slides/img/reproCrisis.png">
-</div>
-
-*Baker, M., <a href="https://www.nature.com/news/1-500-scientists-lift-the-lid-on-reproducibility-1.19970">1,500 scientists lift the lid on reproducibility</a>, Nature 533, 452–454, 2016. doi:10.1038/533452a*
\ No newline at end of file

2019/2019-10-03_basicGitTraining-SIU/slides/the_editor.md

-# The editor(s)
-
-Recommended editors:
-
-- **Visual Studio Code** (https://code.visualstudio.com)
-- **Atom** (https://atom.io)
-
-*Note*: Other editors such as IntelliJ IDEA (https://www.jetbrains.com/idea) or Sublime Text (https://www.sublimetext.com) can, of course, also be used.
-
-<img src="slides/img/icon-live-demo.png" height="100px">
\ No newline at end of file

2019/2019-10-03_basicGitTraining-SIU/slides/the_terminal.md

-# PART II
-
-<br><br><h1>Basic git course</h1>
-
-
-
-# The terminal (shell)
-
-**macOS users:**
-
-Start the Terminal from your `/Applications` directoy.
-
-![bulb](slides/img/bulb.png) Install iTerm2: `https://www.iterm2.com`
-
-**Windows users:**
-
-Install Git Bash: <br>`https://git-scm.com/download/win`
-
-**Linux users:**
-
-Launch default terminal.<br>
-![bulb](slides/img/bulb.png) Install Terminator: `https://launchpad.net/terminator`
-
-
-
 # First steps in the terminal
 
 Starting the terminal presents itself with a line where you can enter a command

2019/2019-10-03_basicGitTraining-SIU/slides/whatiscode.md

-# What is computer code?
-
-**Computer code**: Set of instructions executed by a computer
-
-**Programming language:**: Style of writing the set of instructions (e.g., C, C++, Fortran, Python, R, Matlab, Julia, …)
-
-**Example:**
-
-<div align="center">
-<img src="slides/img/computerCode.png">
-</div>
-
-<div class="fragment">
-
-<div align="center"><font color="#A52A2A"><span class="fas fa-arrow-right"></span> Maybe this is not so relevant … or even, why should I care?</font></div>

2019/2019-10-03_basicGitTraining-SIU/slides/wheel.md

-# PART I
-
-<br><br><h1>Quality of computer code.</h1><br>
-<h1>Should you care? What if you didn't?</h1>
-
-
-
-# A true story ...
-
-<div align="center">
-<img src="slides/img/wheel.png">
-</div>
-
-<table style="width:100%">
-  <tr>
-    <th width="33%" align="center">Researcher who cares about<br>quality of his code</th>
-    <th width="33%" align="center">Fellow researcher</th>
-    <th width="33%" align="center">Pi or Manager</th>
-  </tr>
-</table>
\ No newline at end of file

2019/2019-10-03_basicGitTraining-SIU/slides/whyCare.md

-# Why you should care (1)
-
-<div align="center">
-<video width="40%" controls>
-  <source src="slides/img/arianeLaunch.mov" type="video/mp4">
-Your browser does not support the video tag.
-</video>
-</div>
-
-**Aerospace Application**: First launch of Ariane 5, 1996
-
-<font color="#A52A2A"><span class="fas fa-times-circle"></span></font> **Problem**: Rocket exploded shortly after liftoff.
-
-<font color="#FFA500"><span class="fas fa-exclamation-triangle"></span></font> **Root cause of disaster - Software error:**
-
-Horizontal velocity of the rocket exceeded the limits of the 16-bit signed integer value and led to overflow
-Ariane 5 launched with the same software as Ariane 4 - **the code had not been tested**
-
-
-
-# Why you should care (2)
-
-<div align="center">
-<img src="slides/img/therac.png">
-</div>
-
-**Biotechnology Application**: Therac-25 – computer controlled radiation therapy machine
-
-<font color="#A52A2A"><span class="fas fa-times-circle"></span></font> **Problem**: Device malfunctions and delivers a lethal dose of radiation - several patients died.
-
-<font color="#FFA500"><span class="fas fa-exclamation-triangle"></span></font> **Root cause of disaster - Software error:**
-
-**No testing** of software before release, **lack of documentation**