copy of git course from previous

2020/2020-03-30_basicGitTraining/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+- Documentation will become outdated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>
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2020/2020-03-30_basicGitTraining/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*
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2020/2020-03-30_basicGitTraining/slides/syncFork.md

+# Synchronize your fork
+
+![bulb](slides/img/bulb.png) Remember, we have to regularly update our own copy of the code.
+
+
+Add the `upstream` address (original/protected repository)
+```bash
+$ git remote add upstream git@github.com:LCSB-BioCore/basic-git-practice.git
+```
+
+![bulb](slides/img/bulb.png) Note the change in the URL.
+
+
+You can then check whether the remote address is set correctly
+```bash
+$ git remote -v
+```
+
+<div class="fragment">
+
+Fetch the changes from upstream (similar to pull)
+```bash
+$ git fetch upstream
+```
+
+
+
+
+Merge the retrieved changes on the `master` branch:
+```bash
+$ git checkout master
+$ git merge upstream/master
+$ git push origin master
+```
+
+<div class="fragment">
+
+Do the same for the `develop` branch.
+
+<img src="slides/img/icon-live-demo.png" height="100px">
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2020/2020-03-30_basicGitTraining/slides/thanks.md

+# Let's refresh our memories
+
+<div class="fragment">
+
+- What is a **fork**?
+
+<div class="fragment">
+
+- What are **branches**?
+
+<div class="fragment">
+
+- Can I have **multiple branches** in my fork?
+
+<div class="fragment">
+
+- What is a good **development scheme**?
+
+<div class="fragment">
+
+- What are the **5 essential commands**?
+
+
+
+# References & Cheat sheet
+
+[1]: Git Book: https://git-scm.com/book/en/v2
+
+[2]: GitHub training services: https://services.github.com/training/
+
+[3]: Cheat sheet: http://rogerdudler.github.io/git-guide
+
+
+
+# Thank you.
+
+<img src="slides/img/r3-training-logo.png" height="200px">
+
+Contact us if you need help:
+
+r3lab.core@uni.lu
+

2020/2020-03-30_basicGitTraining/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

2020/2020-03-30_basicGitTraining/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
+```bash
+cesar@myComputer>
+```
+
+Often written, for covenience, as
+```bash
+$
+```
+
+When you open your terminal (shell), you are located
+in your home directory (unless otherwise configured), denoted as `~/`.
+
+
+
+# Essential Linux commands
+
+List the contents of a directory
+```bash
+$ ls #-lash
+```
+
+Create a directory
+```bash
+$ mkdir myNewDirectory
+```
+
+Change the directory to a specific folder
+```bash
+$ cd myNewDirectory
+```
+
+Change the directory 1 level and 2 levels up
+```bash
+$ cd ..
+# 1 level up
+
+$ cd ../..
+# 2 levels up
+```
+
+
+
+Move a file or a directory
+```bash
+$ mv myFile.m myNewDirectory/.
+```
+
+
+Rename a file or a directory
+```bash
+$ mv myFile.m myNewFile.m
+$ mv myNewDirectory myDirectory
+```
\ No newline at end of file

2020/2020-03-30_basicGitTraining/slides/what_is_git.md

+# What is `git`?
+
+<!-- ![](slides/img/git_definition.png) -->
+
+`git` is a **version control system** (VCS) for tracking changes in computer files and coordinating work on those files among multiple people [1].
+
+Designed and implemented in 2005 by **Linus Torvalds**
+
+<div align="center">
+<img src="slides/img/linus.jpg">
+</div>
+
+[1] *https://en.wikipedia.org/wiki/Git*
+
+
+
+# The inventor of `git`
+
+<div align="center">
+<img src="slides/img/git_definition.png">
+</div>
+
+`I'm an egotistical bastard, and I name all my projects after myself.
+First Linux, now git.`
+Linus Torvald (2007-06-14)
+
+
+
+# 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**)
+* Allows you to **backtrack** (if necessary) and undo unwanted changes
+* Easily **add contributions** of your collaborators to the main code base
+
+note:
+
+Other points to mention:
+* git shall not be considered as a nuisance, but as a tool that should help to track and trace the code.
+* git is not to track performance. Not using it shows exactly the opposite.

2020/2020-03-30_basicGitTraining/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>

2020/2020-03-30_basicGitTraining/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>
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2020/2020-03-30_basicGitTraining/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**