Final changes to slides

best_practices.md

 ## Best practices
 
-* `clone` a repository, do not download the `.zip` file.
 * `pull` before `push`
-* Work on your **own** branch (in your own fork)
+
+* 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` or `develop`, 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.txt
@@ -16,13 +24,15 @@
 
 
 * Commit **only a few files** at once (after multiple separate `git add` commands)
-* Always **sync your fork** before starting to work
+
+* Always **sync your fork** before starting to work on a new branch
    ```bash
    $ git remote -v # verify to have the right remote set
    $ git fetch upstream
    $ git merge upstream/master
    $ git push origin master # do not do git push (!)
    ```
+
 * `Push` often - avoid conflicts
 
 <br><br>

essential_commands.md

@@ -53,7 +53,7 @@ Uncomment the line
 ```
 
 <br>
-Save and rename the file by adding your name
+Save and rename the file by <font color="red">adding your name</font>
 ```bash
 $ mv firstCommit/addTwoNumbers.m firstCommit/addTwoNumbers_myName.m
 ```
@@ -110,13 +110,18 @@ $ git push
 ```bash
 $ git log
 ```
-exit with `:q`
+exit by typing `q`
+
+<div class="fragment">
+<br><br>
+You just pushed to `master`. This is **not a good** practice (more later!).
 
 
 ## Do it yourself
 
 * Modify and rename `secondCommit/multiplyTwoNumbers.m`
 * Push the file `secondCommit/multiplyTwoNumbers_myName.m`
+* Don't forget to add <font color="red">`_myName`</font>
 
 <div class="fragment">
 <br>

forks.md

@@ -9,6 +9,9 @@ Remember:
 - A **fork** can have multiple **branches**.
 - A **fork** is not a **branch**, but can have multiple **branches**.
 
+<br><br>
+A **fork** is only useful when you want to contribute, e.g., to The COBRAToolbox.
+
 
 ## Fork via interface
 

homework.md

-## Homework
+## Homework on GitLab
 
 *This exercise has to be done on your lab computer on which `Matlab` **is** installed. Don't forget to properly configure `git` with your username and email, as we explained in the training slides.*
 
-During the training, you committed to the `https://git-r3lab.uni.lu/git-training/practice` repository.
+<br>
+During the training, you committed to the
+<br>
+[https://git-r3lab.uni.lu/git-training/practice](https://git-r3lab.uni.lu/git-training/practice)
+repository.
 
+<br>
 Your task is to create a fork of this repository, commit some code and create a merge request on `GitLab`.
 
 
-## Instructions
+## Homework: instructions
 
-- First, fork the `https://git-r3lab.uni.lu/git-training/practice` repository.
+- First, fork the [https://git-r3lab.uni.lu/git-training/practice](https://git-r3lab.uni.lu/git-training/practice) repository.
 
-- Create the new branch `your_name`
+- Create the new branch `homework_myName`.
 
-- Implement a new function called `sqrt_myName` that computes the square root of a number.
+- Implement a new function (create a new file `sqrt_myName.m`) called `sqrt_myName(x)` that computes the square root of `x`.
 
 - Copy the `test.m` file to `test_myName.m` and change the names of the functions accordingly.
 
@@ -29,4 +34,5 @@ Your task is to create a fork of this repository, commit some code and create a
 
 - Assign either Laurent (@laurent.heirendt) or Sylvain (@sylvain.arreckx) depending on your group and your merge-request will be reviewed by one of us.
 
+<br>
 That's it!

installation.md

@@ -62,13 +62,23 @@ $ git config --list
 This should list the configuration with `user.name` and `user.email`.
 
 
-## I need `The COBRAToolbox`?
+## How do I `clone` a repository?
 
-Simply `clone` the repository (i.e., retrieve a copy)
+You can clone a repository with
 ```bash
-$ git clone https://github.com/opencobra/cobratoolbox.git cobratoolbox
+$ git clone https://github.com/userName/myRepo.git myRepo
 ```
 
+<div class="fragment">
+<br>
+Clone the training repository with
+```bash
+$ git clone https://git-r3lab.uni.lu/git-training/practice.git practice
+```
+<br>
+You may be prompted to enter your credentials.
+
+<div class="fragment">
 <br>
 Any other rudimentary method such as
 
@@ -77,17 +87,12 @@ Any other rudimentary method such as
 shall **be avoided**!
 
 
-## How do I generally `clone` a repository?
+## I need `The COBRAToolbox`?
 
-You can clone any other repository with
+Simply `clone` the repository (i.e., retrieve a copy)
 ```bash
-$ git clone https://github.com/userName/myRepo.git myRepo
+$ git clone https://github.com/opencobra/cobratoolbox.git cobratoolbox
 ```
 
-<div class="fragment">
-<br>
-Clone the training repository with
-```bash
-$ git clone https://git-r3lab.uni.lu/git-training/practice.git practice
-```
-Note: You may be prompted to enter your credentials.
+<br><br>
+**Do not** do it right now! Thank you.

overview.md

@@ -5,7 +5,7 @@
 2. GitHub and GitLab <!--(5min)//-->
 3. Installation of `git`
 4. The 5 essential commands <!--(10 min)//-->
-    * `clone/pull` / `status` / `add` / `commit` / `push`
+    * `pull` / `status` / `add` / `commit` / `push`
 5. Branches <!--(10 min)//-->
 6. Forks <!--(10 min)//-->
 7. Best practices

the_terminal.md

@@ -26,12 +26,19 @@ $ ls
 
 <div class="fragment">
 <br>
-Change the directory to a specific folder
+Create a directory
 ```bash
-$ cd myDirectory
+$ mkdir myNewDirectory
 ```
 
 <div class="fragment">
+<br>
+Change the directory to a specific folder
+```bash
+$ cd myNewDirectory
+```
+
+
 <br>
 Change the directory 1 level and 2 levels up
 ```bash
@@ -42,18 +49,11 @@ $ cd ../..
 # 2 levels up
 ```
 
-
-<br>
-Create a directory
-```bash
-$ mkdir myNewDirectory
-```
-
 <div class="fragment">
 <br>
 Move a file or a directory
 ```bash
-$ mv myFile.m myDirectory/.
+$ mv myFile.m myNewDirectory/.
 ```
 
 <div class="fragment">
@@ -61,4 +61,5 @@ $ mv myFile.m myDirectory/.
 Rename a file or a directory
 ```bash
 $ mv myFile.m myNewFile.m
+$ mv myNewDirectory myDirectory
 ```