From c9f0b05230567aff9d6c9f5f342a4128824bac09 Mon Sep 17 00:00:00 2001
From: laurentheirendt <laurent.heirendt@uni.lu>
Date: Wed, 2 Oct 2019 09:33:57 +0200
Subject: [PATCH] add slides from basic training to siu training
---
.../slides/best_practices.md | 20 ++++
.../slides/branches.md | 98 +++++++++++++++++++
.../slides/cloneRepo.md | 14 +++
.../slides/configuration.md | 46 +++++++++
.../slides/essential_commands.md | 98 +++++++++++++++++++
.../slides/forks.md | 79 +++++++++++++++
.../slides/github_gitlab.md | 18 ++++
.../slides/index.md | 19 ++++
.../slides/installation.md | 45 +++++++++
.../slides/list.json | 65 ++++++++++++
.../slides/merge.md | 13 +++
.../slides/overview.md | 17 ++++
.../slides/qualityCode.md | 34 +++++++
.../slides/repro_crisis.md | 7 ++
.../slides/syncFork.md | 40 ++++++++
.../slides/thanks.md | 42 ++++++++
.../slides/the_editor.md | 10 ++
.../slides/the_terminal.md | 81 +++++++++++++++
.../slides/what_is_git.md | 40 ++++++++
.../slides/whatiscode.md | 15 +++
.../slides/wheel.md | 20 ++++
.../slides/whyCare.md | 33 +++++++
22 files changed, 854 insertions(+)
create mode 100644 2019/2019-10-03_basicGitTraining-SIU/slides/best_practices.md
create mode 100644 2019/2019-10-03_basicGitTraining-SIU/slides/branches.md
create mode 100644 2019/2019-10-03_basicGitTraining-SIU/slides/cloneRepo.md
create mode 100644 2019/2019-10-03_basicGitTraining-SIU/slides/configuration.md
create mode 100644 2019/2019-10-03_basicGitTraining-SIU/slides/essential_commands.md
create mode 100644 2019/2019-10-03_basicGitTraining-SIU/slides/forks.md
create mode 100644 2019/2019-10-03_basicGitTraining-SIU/slides/github_gitlab.md
create mode 100644 2019/2019-10-03_basicGitTraining-SIU/slides/index.md
create mode 100644 2019/2019-10-03_basicGitTraining-SIU/slides/installation.md
create mode 100644 2019/2019-10-03_basicGitTraining-SIU/slides/list.json
create mode 100644 2019/2019-10-03_basicGitTraining-SIU/slides/merge.md
create mode 100644 2019/2019-10-03_basicGitTraining-SIU/slides/overview.md
create mode 100644 2019/2019-10-03_basicGitTraining-SIU/slides/qualityCode.md
create mode 100644 2019/2019-10-03_basicGitTraining-SIU/slides/repro_crisis.md
create mode 100644 2019/2019-10-03_basicGitTraining-SIU/slides/syncFork.md
create mode 100644 2019/2019-10-03_basicGitTraining-SIU/slides/thanks.md
create mode 100644 2019/2019-10-03_basicGitTraining-SIU/slides/the_editor.md
create mode 100644 2019/2019-10-03_basicGitTraining-SIU/slides/the_terminal.md
create mode 100644 2019/2019-10-03_basicGitTraining-SIU/slides/what_is_git.md
create mode 100644 2019/2019-10-03_basicGitTraining-SIU/slides/whatiscode.md
create mode 100644 2019/2019-10-03_basicGitTraining-SIU/slides/wheel.md
create mode 100644 2019/2019-10-03_basicGitTraining-SIU/slides/whyCare.md
diff --git a/2019/2019-10-03_basicGitTraining-SIU/slides/best_practices.md b/2019/2019-10-03_basicGitTraining-SIU/slides/best_practices.md
new file mode 100644
index 00000000..dea55fee
--- /dev/null
+++ b/2019/2019-10-03_basicGitTraining-SIU/slides/best_practices.md
@@ -0,0 +1,20 @@
+# Best practices
+
+* `pull` before `push`
+* Work on your <font color="red">own</font> branch (in your own fork), and **not** on `master` and **not** on `develop`
+* Do **not push** to `master`, but **submit a PR**
+* Get your code **reviewed** by your peers (submit a PR!)
+* Submit a PR **often**!
+* `clone` a repository, do not download the `.zip` file.
+* Do **not** combine `git` commands
+ ```bash
+ $ git commit -am "myMessage" # do not do this
+ ```
+* Stage only 1 file at once using
+ ```bash
+ $ git add myFile.md
+ ```
+* Commit **only a few files** at once (after multiple separate `git add` commands)
+* `Push` often - avoid conflicts
+
+Remember: **A `push` a day keeps conflicts away!**
diff --git a/2019/2019-10-03_basicGitTraining-SIU/slides/branches.md b/2019/2019-10-03_basicGitTraining-SIU/slides/branches.md
new file mode 100644
index 00000000..0c91358c
--- /dev/null
+++ b/2019/2019-10-03_basicGitTraining-SIU/slides/branches.md
@@ -0,0 +1,98 @@
+# Development scheme
+
+
+Generally, in a repository, there are guidelines for contributing.
+
+<div class="fragment">
+
+A common development scheme is dual with a:
+
+- **development** version of the code on `develop`
+- **stable** version of the code on `master`
+
+
+A **version** of the code is referred to as a **branch**.
+
+<div class="fragment">
+
+<img src="slides/img/icon-live-demo.png" height="100px">
+
+
+<font color="red">In the practice repository, the development branch is called `develop`!</font>
+
+<div class="fragment">
+
+ Use this dual development scheme for your own repositories!
+
+
+
+# Branches
+
+A **version** of the code (i.e., a **branch**) is made up of a sequence of code changes.
+
+<div class="fragment">
+
+These individual code changes are called **commits**.
+
+
+For instance, the `master` and `develop` branches can be represented as a timeline:
+<img src="slides/img/branch-master.png" class="branch-master" height="500em"/>
+
+
+
+# Switch between branches
+
+List all branches of the repository with
+```bash
+$ git branch -a
+```
+
+Exit by typing `q`. The branch with the * is the current branch.
+
+<div class="fragment">
+
+Checkout another branch
+```bash
+$ git checkout <branchName>
+```
+
+<div class="fragment">
+
+You can switch to the `develop` branch with
+```bash
+$ git checkout develop
+```
+If the local branch does not exist but the remote does, it is created automatically.
+
+<div class="fragment">
+
+<img src="slides/img/icon-live-demo.png" height="100px">
+
+
+
+# Create your own version
+
+Assume that you want to work on a file:
+
+<div class="fragment">
+
+<font color="red">Create a new **branch**!</font>
+
+```bash
+$ git checkout -b myBranch
+```
+The `-b` flag creates the branch. Locally, you have your own version now:
+<img src="slides/img/branch-create.png" class="branch-create" height="500em"/>
+
+
+
+
+Push your version to your fork:
+```bash
+$ git push origin myBranch
+```
+
+
+<div class="fragment">
+
+<img src="slides/img/icon-live-demo.png" height="100px">
diff --git a/2019/2019-10-03_basicGitTraining-SIU/slides/cloneRepo.md b/2019/2019-10-03_basicGitTraining-SIU/slides/cloneRepo.md
new file mode 100644
index 00000000..887a6e08
--- /dev/null
+++ b/2019/2019-10-03_basicGitTraining-SIU/slides/cloneRepo.md
@@ -0,0 +1,14 @@
+# How do I start working on a repository?
+
+You have to `clone` it first:
+
+```bash
+$ git clone git@github.com:userName/myRepo.git myRepo
+```
+
+If you did not configure your SSH key, clone using HTTPS:
+```bash
+$ git clone https://github.com/userName/myRepo.git myRepo
+```
+
+You will be prompted to enter your credentials.
diff --git a/2019/2019-10-03_basicGitTraining-SIU/slides/configuration.md b/2019/2019-10-03_basicGitTraining-SIU/slides/configuration.md
new file mode 100644
index 00000000..0b07cc41
--- /dev/null
+++ b/2019/2019-10-03_basicGitTraining-SIU/slides/configuration.md
@@ -0,0 +1,46 @@
+# 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
diff --git a/2019/2019-10-03_basicGitTraining-SIU/slides/essential_commands.md b/2019/2019-10-03_basicGitTraining-SIU/slides/essential_commands.md
new file mode 100644
index 00000000..0fa56f47
--- /dev/null
+++ b/2019/2019-10-03_basicGitTraining-SIU/slides/essential_commands.md
@@ -0,0 +1,98 @@
+# The 5 essential commands
+
+
+**Yes**, you only need 5 commands!
+
+`pull, status, add, commit, push`
+
+or in other words (remember these!):
+```bash
+$ git pull <remote> <branch>
+$ git status
+$ git add myFile.md # example
+$ git commit -m "myMessage" # example
+$ git push <remote> <branch>
+```
+
+
+
+# Pull the latest version of an existing branch
+
+Pull the latest revision on branch `myBranch`:
+```bash
+$ git pull origin myBranch
+# Already up to date
+```
+
+<div class="fragment">
+
+Verify its `status` with:
+```bash
+$ git status
+```
+
+
+
+# Modify a file
+
+Copy the file `template.md` in the folder `_attendees` and rename it with your firstname:
+
+```bash
+$ cd _attendees
+$ cp template.md myName.md
+```
+
+Then, make your changes with your favorite editor!
+
+
+
+# Add your file to the stage
+
+First, check the repository status
+```bash
+$ git status
+# uncommitted changes (displayed in red)
+```
+
+
+<div class="fragment">
+
+Now, add the file (bring it on stage)
+```bash
+$ git add myName.md # replace myName
+$ git status
+#Â returns the same as before, generally in green (means staged)
+```
+
+<div class="fragment">
+
+**ADVANCED**: If there have been more changes after the file has been added, you can see your changes in the terminal
+```bash
+$ git diff
+```
+exit with `q`
+
+
+
+# Add a commit message
+
+```bash
+$ git commit -m "Add the profile of <myName>"
+$ git status
+```
+
+
+
+# Push your file to your fork
+
+```bash
+$ git push origin myBranch
+```
+
+<div class="fragment">
+
+**ADVANCED**: see the log of all the commits (and your last one) in the terminal
+```bash
+$ git log
+```
+exit by typing `q`.
\ No newline at end of file
diff --git a/2019/2019-10-03_basicGitTraining-SIU/slides/forks.md b/2019/2019-10-03_basicGitTraining-SIU/slides/forks.md
new file mode 100644
index 00000000..3a4f61cd
--- /dev/null
+++ b/2019/2019-10-03_basicGitTraining-SIU/slides/forks.md
@@ -0,0 +1,79 @@
+# 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 ...
+
+<img src="slides/img/fork-crossed.png" class="as-is" height="500em"/>
+
+
+
+# What is a `fork`?
+
+In general, when contributing to a repository, you only have **read** access.
+
+In other words, you can only **pull** (unless it is your own repository or access has been granted).
+
+In general, you **cannot write** changes. In other words, you do not have **push** access.
+
+You have to work on your **own copy**.
+
+In other words, you have to work on your own <font color="red">**fork**</font>.
+
+
+
+# How to get a fork?
+
+Browse to the original repository and click on the button `Fork`:
+
+
+
+<img src="slides/img/icon-live-demo.png" height="100px">
+
+
+
+# Time to practice!
+
+Fork the practice repository: <br><br>
+https://github.com/LCSB-BioCore/basic-git-practice
+
+Then, clone your fork to your home directory!
+
+<img src="slides/img/icon-live-demo.png" height="100px">
+
+```bash
+$ git clone git@github.com:<yourName>/basic-git-practice.git
+```
+
+Change to the practice directory with:
+```bash
+$ cd basic-git-practice
+```
+
+
+
+# A note on shortcuts ...
+
+<font color="red">
+Any other rudimentary method such as
+
+*'I simply download the `.zip` and unzip it - works like a charm!'*
+
+shall **be avoided**!
+</font>
+
+**Why?**
+
+
+
+# How to update my fork?
+
+As you have your own fork, it will not automatically update once the original repository is update.
+
+ You have to update it yourself!
+
+**More on that later!**
+
diff --git a/2019/2019-10-03_basicGitTraining-SIU/slides/github_gitlab.md b/2019/2019-10-03_basicGitTraining-SIU/slides/github_gitlab.md
new file mode 100644
index 00000000..84930c39
--- /dev/null
+++ b/2019/2019-10-03_basicGitTraining-SIU/slides/github_gitlab.md
@@ -0,0 +1,18 @@
+# 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;"/>
+
+GitHub and GitLab are VCS systems.
+
+GitHub/Gitlab are both **publicly available**, but GitLab can be **on-premise**.
+
+Positive point: GitHub and GitLab are (almost) the same.
+
+
+<img src="slides/img/icon-live-demo.png" height="100px">
+
+
+- **GitHub**: [https://github.com](https://github.com)
+- Public GitLab: [https://gitlab.com](https://gitlab.com)
+- LCSB specific: [https://git-r3lab.uni.lu](https://git-r3lab.uni.lu)
\ No newline at end of file
diff --git a/2019/2019-10-03_basicGitTraining-SIU/slides/index.md b/2019/2019-10-03_basicGitTraining-SIU/slides/index.md
new file mode 100644
index 00000000..a2726fc4
--- /dev/null
+++ b/2019/2019-10-03_basicGitTraining-SIU/slides/index.md
@@ -0,0 +1,19 @@
+# R3.school
+
+## June 11th, 2019
+
+<div style="top: 6em; left: 0%; position: absolute;">
+ <img src="theme/img/lcsb_bg.png">
+</div>
+
+<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>
+ <br><br><br><br>
+ <h4>
+ Laurent Heirendt, Ph.D.<br><br>
+ laurent.heirendt@uni.lu<br><br>
+ <i>Luxembourg Centre for Systems Biomedicine</i>
+ </h4>
+</div>
diff --git a/2019/2019-10-03_basicGitTraining-SIU/slides/installation.md b/2019/2019-10-03_basicGitTraining-SIU/slides/installation.md
new file mode 100644
index 00000000..506be614
--- /dev/null
+++ b/2019/2019-10-03_basicGitTraining-SIU/slides/installation.md
@@ -0,0 +1,45 @@
+# 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
diff --git a/2019/2019-10-03_basicGitTraining-SIU/slides/list.json b/2019/2019-10-03_basicGitTraining-SIU/slides/list.json
new file mode 100644
index 00000000..e06ee227
--- /dev/null
+++ b/2019/2019-10-03_basicGitTraining-SIU/slides/list.json
@@ -0,0 +1,65 @@
+[
+ {
+ "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"
+ }
+]
diff --git a/2019/2019-10-03_basicGitTraining-SIU/slides/merge.md b/2019/2019-10-03_basicGitTraining-SIU/slides/merge.md
new file mode 100644
index 00000000..5b59e684
--- /dev/null
+++ b/2019/2019-10-03_basicGitTraining-SIU/slides/merge.md
@@ -0,0 +1,13 @@
+# 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.
+
+Use the **interface** to make use of your peers to review your code!
+<img src="slides/img/branch-merge.png" class="branch-merge" height="500em"/>
+
+Once merged, you can delete the branch via the interface.
+
+<div class="fragment">
+
+<img src="slides/img/icon-live-demo.png" height="100px" >
\ No newline at end of file
diff --git a/2019/2019-10-03_basicGitTraining-SIU/slides/overview.md b/2019/2019-10-03_basicGitTraining-SIU/slides/overview.md
new file mode 100644
index 00000000..569ee378
--- /dev/null
+++ b/2019/2019-10-03_basicGitTraining-SIU/slides/overview.md
@@ -0,0 +1,17 @@
+# 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?
+ 13. Best practices
\ No newline at end of file
diff --git a/2019/2019-10-03_basicGitTraining-SIU/slides/qualityCode.md b/2019/2019-10-03_basicGitTraining-SIU/slides/qualityCode.md
new file mode 100644
index 00000000..24abf2c8
--- /dev/null
+++ b/2019/2019-10-03_basicGitTraining-SIU/slides/qualityCode.md
@@ -0,0 +1,34 @@
+# 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
diff --git a/2019/2019-10-03_basicGitTraining-SIU/slides/repro_crisis.md b/2019/2019-10-03_basicGitTraining-SIU/slides/repro_crisis.md
new file mode 100644
index 00000000..8e411c3b
--- /dev/null
+++ b/2019/2019-10-03_basicGitTraining-SIU/slides/repro_crisis.md
@@ -0,0 +1,7 @@
+# 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
diff --git a/2019/2019-10-03_basicGitTraining-SIU/slides/syncFork.md b/2019/2019-10-03_basicGitTraining-SIU/slides/syncFork.md
new file mode 100644
index 00000000..a9088695
--- /dev/null
+++ b/2019/2019-10-03_basicGitTraining-SIU/slides/syncFork.md
@@ -0,0 +1,40 @@
+# Synchronize your fork
+
+ 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
+```
+
+ 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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diff --git a/2019/2019-10-03_basicGitTraining-SIU/slides/thanks.md b/2019/2019-10-03_basicGitTraining-SIU/slides/thanks.md
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@@ -0,0 +1,42 @@
+# 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
+
diff --git a/2019/2019-10-03_basicGitTraining-SIU/slides/the_editor.md b/2019/2019-10-03_basicGitTraining-SIU/slides/the_editor.md
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+# 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
diff --git a/2019/2019-10-03_basicGitTraining-SIU/slides/the_terminal.md b/2019/2019-10-03_basicGitTraining-SIU/slides/the_terminal.md
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@@ -0,0 +1,81 @@
+# PART II
+
+<br><br><h1>Basic git course</h1>
+
+
+
+# The terminal (shell)
+
+**macOS users:**
+
+Start the Terminal from your `/Applications` directoy.
+
+ Install iTerm2: `https://www.iterm2.com`
+
+**Windows users:**
+
+Install Git Bash: <br>`https://git-scm.com/download/win`
+
+**Linux users:**
+
+Launch default terminal.<br>
+ 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
diff --git a/2019/2019-10-03_basicGitTraining-SIU/slides/what_is_git.md b/2019/2019-10-03_basicGitTraining-SIU/slides/what_is_git.md
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+# What is `git`?
+
+<!--  -->
+
+`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.
diff --git a/2019/2019-10-03_basicGitTraining-SIU/slides/whatiscode.md b/2019/2019-10-03_basicGitTraining-SIU/slides/whatiscode.md
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+# 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>
diff --git a/2019/2019-10-03_basicGitTraining-SIU/slides/wheel.md b/2019/2019-10-03_basicGitTraining-SIU/slides/wheel.md
new file mode 100644
index 00000000..789873bc
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@@ -0,0 +1,20 @@
+# 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
diff --git a/2019/2019-10-03_basicGitTraining-SIU/slides/whyCare.md b/2019/2019-10-03_basicGitTraining-SIU/slides/whyCare.md
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index 00000000..75d3c6b4
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@@ -0,0 +1,33 @@
+# 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**
--
GitLab