Merge branch 'syarra' into 'develop'

Pass over all slides.

See merge request !14

index.html

@@ -81,6 +81,16 @@
                 
                     
                         
+    <section data-separator="^\n\n\n"
+             data-vertical="^\n\n"
+             data-background="../img/whiteBG.jpg" data-markdown="slides/why_use_git.md"></section>
+
+
+                    
+                    
+                
+                    
+                        
     <section data-separator="^\n\n\n"
              data-vertical="^\n\n"
              data-background="../img/whiteBG.jpg" data-markdown="slides/installation.md"></section>
@@ -149,6 +159,16 @@
                     
                     
                 
+                    
+                        
+    <section data-separator="^\n\n\n"
+             data-vertical="^\n\n"
+             data-background="../img/whiteBG.jpg" data-markdown="slides/ready.md"></section>
+
+
+                    
+                    
+                
             </div>
 
         </div>

slides/best_practices.md

@@ -6,23 +6,23 @@
 * Do **not push** to `master` or `develop`, but **submit a PR**
 * Get your code **reviewed** by your peers (submit a PR!)
 * Do **not** combine `git` commands
-```sh
-$ git commit -am "myMessage" # do not do this
-```
+   ```bash
+   $ git commit -am "myMessage" # do not do this
+   ```
 * Stage only 1 file at once using
-```sh
-$ git add myFile.txt
-```
+   ```bash
+   $ git add myFile.txt
+   ```
 
 
 * Commit **only a few files** at once (after multiple separate `git add` commands)
 * Always **sync your fork** before starting to work
-```sh
-$ 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 (!)
-```
+   ```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>

slides/branches.md

@@ -2,14 +2,14 @@
 
 Branch-off within the same repository in order to stay safe!
 
-The master branch:
+<br><br>The master branch
 <img src="img/branch-master.png" class="branch-master" />
 
 
 ## One branch per feature
 
 Assume that you want to work on a function for a matrix-vector operation.
-```sh
+```bash
 $ git checkout -b matrix_vect_mult_myName
 # creates the branch locally
 ```
@@ -18,13 +18,13 @@ The `-b` flag creates the branch.
 <img src="img/branch-create.png" class="branch-create" />
 
 Push the branch to the remote repository
-```sh
+```bash
 $ git push
 ```
 
 
-If you do that, `git` will complain
-```sh
+If you do that, `git` might complain
+```bash
 fatal: The current branch matrix_vect_mult_myName has no upstream branch.
 To push the current branch and set the remote as upstream, use
 
@@ -32,8 +32,8 @@ To push the current branch and set the remote as upstream, use
 ```
 
 <br>
-Follow the advice and do:
-```sh
+Follow the advice and do
+```bash
 $ git push --set-upstream origin matrix_vect_mult_myName
 ```
 
@@ -43,21 +43,21 @@ $ git push --set-upstream origin matrix_vect_mult_myName
 In your terminal, you may see the name of the branch you are on.
 
 List available branches of the repository
-```sh
+```bash
 $ git branch --list
 ```
 
 <div class="fragment">
 <br>
 Checkout another branch
-```sh
+```bash
 $ git checkout <branch_name>
 ```
 
 <div class="fragment">
 <br>
 You can switch back to the `master` branch with
-```sh
+```bash
 $ git checkout master
 ```
 
@@ -85,8 +85,9 @@ Once merged, you can delete the branch via the interface.
 
 
 ## Gitlab interface
+<img src="https://gitlab.com/gitlab-com/gitlab-artwork/raw/master/logo/logo.png" alt="GitLab" style="width: 100px;"/>
 
-Detailed information is [docs.gitlab.com/ce/gitlab-basics/add-merge-request.html](https://docs.gitlab.com/ce/gitlab-basics/add-merge-request.html).
+Detailed information is on [docs.gitlab.com/ce/gitlab-basics/add-merge-request.html](https://docs.gitlab.com/ce/gitlab-basics/add-merge-request.html).
 
 1. Click on **New merge request**
 
@@ -105,8 +106,9 @@ Detailed information is [docs.gitlab.com/ce/gitlab-basics/add-merge-request.html
 
 
 ## Github interface
+<img src="https://assets-cdn.github.com/images/modules/logos_page/GitHub-Mark.png" alt="GitHub" style="width: 100px;"/>
 
-Detailed information is [help.github.com/articles/creating-a-pull-request/](https://help.github.com/articles/creating-a-pull-request/).
+Detailed information is on [help.github.com/articles/creating-a-pull-request/](https://help.github.com/articles/creating-a-pull-request/).
 
 1. Click on **New pull request**
 

slides/essential_commands.md

@@ -8,7 +8,7 @@
 
 <br>
 or in other words (remember these!):
-```shell
+```bash
 $ git pull
 $ git status
 $ git add myFile.txt # example
@@ -20,18 +20,18 @@ $ git push
 ## Pull the latest version of an existing repository
 
 First, browse to the cloned directory (`git clone [...]`):
-```sh
+```bash
 $ cd practice
 ```
 
 Then, pull the latest revision:
-```sh
+```bash
 $ git pull
 # Already up to date
 ```
 
 Verify its `status` with:
-```sh
+```bash
 $ git status
 ```
 
@@ -51,15 +51,15 @@ Then, uncomment the line
 
 <br>
 Save and rename the file by adding your name
-```sh
-mv firstCommit/addTwoNumbers.m firstCommit/addTwoNumbers_myName.m
+```bash
+$ mv firstCommit/addTwoNumbers.m firstCommit/addTwoNumbers_myName.m
 ```
 
 
 ## Add your file to the stage
 
 First, check the repository status
-```sh
+```bash
 $ git status
 # uncommitted changes (displayed in red)
 ```
@@ -67,7 +67,7 @@ $ git status
 <div class="fragment">
 <br>
 Now, add the file (bring it on stage)
-```sh
+```bash
 $ git add firstCommit/addTwoNumbers_myName.m
 # returns the same as before, generally in green (means staged)
 ```
@@ -75,7 +75,7 @@ $ git add firstCommit/addTwoNumbers_myName.m
 <div class="fragment">
 <br>
 **ADVANCED**: see your changes in the terminal
-```sh
+```bash
 $ git diff
 ```
 exit with `:q`
@@ -83,34 +83,34 @@ exit with `:q`
 
 ## Add a commit message
 
-```shell
+```bash
 $ git commit -m "Uncommented line for adding 2 numbers"
 $ git status
 ```
 
 <br>
 You can pull, even at this stage, new possible changes
-```sh
+```bash
 $ git pull
 ```
 
 
 ## Push your file to the repository
 
-```sh
+```bash
 $ git push
 ```
 
 <div class="fragment">
 <br>
 **ADVANCED**: see the log of all the commits (and your last one) in the terminal
-```sh
+```bash
 $ git log
 ```
 exit with `:q`
 
 
-## Do it yourself:
+## Do it yourself
 
 * Modify and rename `secondCommit/multiplyTwoNumbers.m`
 * Push the file `secondCommit/multiplyTwoNumbers_myName.m`
@@ -118,7 +118,7 @@ exit with `:q`
 <div class="fragment">
 <br>
 Commands:
-```sh
+```bash
 $ git pull
 $ git diff # optional
 $ git add secondCommit/multiplyTwoNumbers_myName.m

slides/forks.md

@@ -2,6 +2,7 @@
 
 You **fork** when you want to work on a public repository or a protected repository.
 
+<br><br>
 Remember:
 
 - A **fork** is your own **copy** of a repository.
@@ -11,21 +12,21 @@ Remember:
 
 ## Fork via interface
 
-Browse to the original repository and click on the button `Fork`:
+Browse to the original repository and click on the button `Fork`
 
 ![Fork the repo](https://help.github.com/assets/images/help/repository/fork_button.jpg)
 
 
 ## Clone your fork
 
-Clone first:
-```sh
+Clone first
+```bash
 $ git clone https://git-r3lab.uni.lu/myGroup/myRepo.git forkMyRepo
 ```
 
 <br>
-then, you can change to the directory:
-```sh
+then, you can change to the directory
+```bash
 $ cd forkMyRepo
 ```
 
@@ -33,13 +34,13 @@ $ cd forkMyRepo
 ## Add the address of the original repository
 
 Add the `upstream` address (original/protected repository)
-```sh
+```bash
 $ git remote add upstream https://git-r3lab.uni.lu/origGroup/origRepo.git
 ```
 
 <br>
-You can then check whether the remote address is set correctly:
-```sh
+You can then check whether the remote address is set correctly
+```bash
 $ git remote -v
 ```
 <!-- <img src="img/remote-0-master.png" class="as-is" /> //-->
@@ -49,7 +50,7 @@ $ git remote -v
 
 ## Synchronize your fork
 
-```sh
+```bash
 $ git checkout master
 $ git status
 ```
@@ -57,21 +58,21 @@ $ git status
 <div class="fragment">
 <br>
 Fetch the changes from upstream (similar to pull)
-```sh      
+```bash      
 $ git fetch upstream
 ```
 
 <div class="fragment">
 <br>
 Merge the retrieved changes
-```sh
+```bash
 $ git merge upstream/master
 ```
 
 <div class="fragment">
 <br>
-Push the changes to your own fork:
-```sh
+Push the changes to your own fork
+```bash
 $ git push origin master
 ```
 

slides/github_gitlab.md

 ## GitHub and GitLab
 
+<img src="https://assets-cdn.github.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 is **public**, whereas GitLab is **restricted/private**.
@@ -10,11 +13,13 @@ Positive point: GitHub and GitLab are (almost) the same.
 ## GitHub (Live Demo)
 
 [www.github.com](www.github.com)
+<br><img src="https://assets-cdn.github.com/images/modules/logos_page/GitHub-Mark.png" alt="GitHub" style="width: 200px;"/>
 
 
 ## GitLab (Live Demo)
 
 [https://git-r3lab.uni.lu](https://git-r3lab.uni.lu)
+<br><img src="https://gitlab.com/gitlab-com/gitlab-artwork/raw/master/logo/logo-extra-whitespace.png" alt="GitLab" style="width: 200px;"/>
 
 
 ## Open an issue (Live Demo)

slides/installation.md

@@ -4,8 +4,8 @@
 
 **Linux (Ubuntu)**
 
-```sh
-sudo apt-get install git-all
+```bash
+$ sudo apt-get install git-all
 ```
 <br>
 **macOS**
@@ -36,7 +36,7 @@ Start `GUI Bash` or `MobaXTerm`.
 
 ## How to configure `git`?
 
-```shell
+```bash
 $ git config --global user.name "Firstname Lastname"
 $ git config --global user.email "first.last@uni.lu"
 ```
@@ -44,7 +44,7 @@ $ git config --global user.email "first.last@uni.lu"
 
 ## Does it work?
 
-```sh
+```bash
 $ git --version
 # git version 2.10.0
 ```
@@ -54,7 +54,7 @@ $ git --version
 
 Test whether your username and email have been registered
 
-```sh
+```bash
 $ git config --list
 ```
 
@@ -65,7 +65,7 @@ This should list the configuration with `user.name` and `user.email`.
 ## I need `The COBRAToolbox`?
 
 Simply `clone` the repository (i.e., retrieve a copy)
-```sh
+```bash
 $ git clone https://github.com/opencobra/cobratoolbox.git cobratoolbox
 ```
 
@@ -79,15 +79,15 @@ shall **be avoided**!
 
 ## How do I generally `clone` a repository?
 
-You can clone any other repository with:
-```sh
+You can clone any other repository with
+```bash
 $ git clone https://github.com/userName/myRepo.git myRepo
 ```
 
 <div class="fragment">
 <br>
-Clone the training repository with:
-```sh
+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.

slides/list.json

@@ -23,6 +23,12 @@
           "data-background": "../img/whiteBG.jpg"
         }
     },
+    {
+        "filename": "why_use_git.md",
+        "attr": {
+          "data-background": "../img/whiteBG.jpg"
+        }
+    },
     {
         "filename": "installation.md",
         "attr": {
@@ -64,5 +70,11 @@
         "attr": {
           "data-background": "../img/whiteBG.jpg"
         }
+    },
+    {
+        "filename": "ready.md",
+        "attr": {
+          "data-background": "../img/whiteBG.jpg"
+        }
     }
 ]

slides/ready.md

+## Ready for a practice!!!
+
+<br>Go to https://github.com/uni-lu/group_members
+
+<br>And follow the `README` file.

slides/thanks.md

-## References
+### References
 
-[1]: **Git** Book: https://git-scm.com/book/en/v2
+[1]: **Git** Book:
+https://git-scm.com/book/en/v2
 
+<br>[2]: GitHub training services: https://services.github.com/training/
 
-## Acknowledgement
 
-Laurent Heirendt
+### Cheat sheet
+[Web](http://rogerdudler.github.io/git-guide/index.html) or [PDF](http://rogerdudler.github.io/git-guide/files/git_cheat_sheet.pdf)
 
-![](https://avatars0.githubusercontent.com/u/20812112?v=3&s=180)
-
-Sylvain Arreckx
-![](https://avatars1.githubusercontent.com/u/816318?v=3&s=180)
-
-Cheat sheet : [Web](http://rogerdudler.github.io/git-guide/index.html) or [PDF](http://rogerdudler.github.io/git-guide/files/git_cheat_sheet.pdf) prepared by [@rogerdudler](https://github.com/rogerdudler)

slides/the_terminal.md

 ## The Terminal (shell)
 
-Starting the terminal presents itself with a line where you can enter a command:
-```sh
+Starting the terminal presents itself with a line where you can enter a command
+```bash
 cesar@myComputer>
 ```
 
 <div class="fragment">
 <br>
-Often written, for covenience, as:
-```sh
+Often written, for covenience, as
+```bash
 $
 ```
 
@@ -20,21 +20,21 @@ in your home directory (unless otherwise configured), denoted as `~/`.
 ## Essential Linux commands
 
 List the contents of a directory
-```sh
+```bash
 $ ls
 ```
 
 <div class="fragment">
 <br>
 Change the directory to a specific folder
-```sh
+```bash
 $ cd myDirectory
 ```
 
 <div class="fragment">
 <br>
 Change the directory 1 level and 2 levels up
-```sh
+```bash
 $ cd ..
 # 1 level up
 
@@ -45,20 +45,20 @@ $ cd ../..
 
 <br>
 Create a directory
-```sh
+```bash
 $ mkdir myNewDirectory
 ```
 
 <div class="fragment">
 <br>
 Move a file or a directory
-```sh
+```bash
 $ mv myFile.m myDirectory/.
 ```
 
 <div class="fragment">
 <br>
 Rename a file or a directory
-```sh
+```bash
 $ mv myFile.m myNewFile.m
 ```

slides/what_is_git.md

 ## What is `git`?
 
-![](img/git_definition.png)
+<!-- ![](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**
+<br><br><br>Designed and implemented in 2005 by **Linus Torvalds**
 
 ![](img/linus.jpg)
 

slides/why_use_git.md

+# Why use git?
+
+* No need to fully rewrite code; reuse code and save time.
+* Keep the changes you made over time
+* Allow you to backtrack (if necessary) and undo those 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.