Updated slides

essential_commands.md

 ## The 5 essential commands
 
-`pull, status, add, commit, push`
-
-note:
-    Put your speaker notes here.
-    You can see them pressing 's'.
-    Fullscreen can be activated by typing 'f'.
+<br>
+**Yes**, you only need 5 commands!
 
+<br>
+`pull, status, add, commit, push`
 
+<br>
+or in other words (more technically)
 ```shell
-$ git init
+$ git pull
 $ git status
-$ git add
-$ git diff
-$ git commit
-$ git log
+$ git add myFile.txt
+$ git commit -m "myMessage"
+$ git push
 ```
-note:
-  Voici les commandes que nous allons apprendre
 
 
 ## Nouveau projet : Listes
 
-<div class="fragment">
 Créer l'espace de travail
 
 ```shell
@@ -31,7 +27,6 @@ $ mkdir workspace
 $ cd workspace
 ```
 
-<div class="fragment">
 Puis le dossier du nouveau projet
 
 ```shell

forks.md

-## Remote
-
-Parlons de dépôt *distant*
-
+## Fork
 
 <img src="img/remote-0-master.png" class="as-is" />
 
-
 <img src="img/remote-1-remote.png" class="as-is" />
 
-
-## Héberger un dépôt distant ?
-Github (Ou [BitBucket](https://bitbucket.org/))
-
-
 ## Ajouter une _remote_
 
 ```shell
@@ -41,12 +32,30 @@ $ git pull origin master  # Récupérer le travail
 Terminologie de l'application GitHub
 
 
-## Conflits
+## Avoid conflicts
 
+Good practice:
 
-## Pull Requests
-Ou comment utiliser GitHub pour vos revues de code
+<large>**PULL**</large> before you **push**!
+
+Do **not** combine `git` commands
+```sh
+$ git commit -am "myMessage" # do not do this
+```
 
+Verify to have the right remote set on your fork
+```sh
+$ git remote -v
+```
 
-## Fork
-Contribuez à l'open source
+Keep your fork up-to-date
+```sh
+$ git fetch upstream
+$ git merge upstream/master
+$ git push origin master # do not do git push (!)
+```
+
+
+## Pull Requests
+
+How to submit a Pull Request (PR)

github_gitlab.md

@@ -11,3 +11,9 @@ Positive point: GitHub and GitLab are (almost) the same.
 
 
 ## GitLab
+
+
+
+## Good practices
+
+Always `clone` a repository, do not download the `.zip` file.

index.md

 <img src="img/Git-Logo-Black.png" class="as-is" height="100px">training
 <br><br>
-**SBG and MSP groups**
+**SBG & MSP groups**
 
 <img src="img/logoLCSB.png" class="as-is" height="100px">
 
@@ -46,3 +46,7 @@ PR, issues (on a dummy test repo)
 - Task 2: Push to forked repo and create a PR
 - Bonus Task: Fork the cobratoolbox and update
 - Friday: 1h debriefing
+
+    Put your speaker notes here.
+    You can see them pressing 's'.
+    Fullscreen can be activated by typing 'f'.

installation.md

@@ -26,19 +26,19 @@ Follow instructions on *[git-for-windows.github.io](https://git-for-windows.gith
 
 **Linux (Ubuntu)** and **macOS**
 
-Start the terminal
+Start the terminal (or any other shell)
+
 <br>
 **Windows**
 
-Start `GUI Bash` or, if installed, `MobaXTerm`.
+Start `GUI Bash` or `MobaXTerm`.
 
 
-## Configuration
+## How to configure `git`?
 
 ```shell
 $ git config --global user.name "Firstname Lastname"
 $ git config --global user.email "first.last@uni.lu"
-$ git config -l
 ```
 
 
@@ -48,3 +48,30 @@ $ git config -l
 $ git --version
 # git version 2.10.0
 ```
+
+
+## Test the configuration
+
+Test whether your username and email have been registered
+
+```sh
+$ git config -l
+```
+
+<br>
+This should list the configuration with `user.name` and `user.email`.
+
+
+## I need to get `The COBRAToolbox` - How?
+
+Simply `clone` the repository (i.e., retrieve a copy)
+
+```sh
+$ git clone https://github.com/opencobra/cobratoolbox.git cobratoolbox
+```
+
+Any other rudimentary method such as
+
+*'I simply download the `.zip` un unzip it - works like a charm!'*
+
+shall **be avoided**!

the_terminal.md

@@ -2,7 +2,7 @@
 
 Starting the terminal presents itself with a line where you can enter a command:
 ```sh
-michael@myComputer>
+cesar@myComputer>
 ```
 Often written, for covenience, as:
 ```sh

what_is_git.md

@@ -2,10 +2,10 @@
 
 ![](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**
 
 ![](img/linus.jpg)
 
-`git` is a **version control system** (VCS) for tracking changes in computer files and coordinating work on those files among multiple people [1].
-
 <div align="left"><small>[1] *https://en.wikipedia.org/wiki/Git*</small></div>