Merge branch 'april12' into 'develop'

Absolute Beginners workshop from April 12

See merge request R3.training/slides!22

index.html

@@ -121,16 +121,6 @@
                 
                     
                         
-    <section data-separator="^\n\n\n"
-             data-vertical="^\n\n"
-             data-background="../img/whiteBG.jpg" data-markdown="slides/forks.md"></section>
-
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-                    
-                    
-                
-                    
-                        
     <section data-separator="^\n\n\n"
              data-vertical="^\n\n"
              data-background="../img/whiteBG.jpg" data-markdown="slides/best_practices.md"></section>
@@ -149,26 +139,6 @@
                     
                     
                 
-                    
-                        
-    <section data-separator="^\n\n\n"
-             data-vertical="^\n\n"
-             data-background="../img/whiteBG.jpg" data-markdown="slides/ready.md"></section>
-
-
-                    
-                    
-                
-                    
-                        
-    <section data-separator="^\n\n\n"
-             data-vertical="^\n\n"
-             data-background="../img/whiteBG.jpg" data-markdown="slides/homework.md"></section>
-
-
-                    
-                    
-                
             </div>
 
         </div>

slides/best_practices.md

@@ -12,27 +12,20 @@
 
 * `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
    ```
 
-
 * Commit **only a few files** at once (after multiple separate `git add` commands)
 
-* 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>

slides/branches.md

@@ -84,36 +84,6 @@ Use the **interface** to make use of your peers to review your code!
 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 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**
-
-![New Merge Request](https://docs.gitlab.com/ee/gitlab-basics/img/merge_request_new.png)
-<br><br>
-2. Compare the branches
-
-![Compare branches](https://docs.gitlab.com/ee/gitlab-basics/img/merge_request_select_branch.png)
-
-
-<ol start="3">
-  <li>Assign your peer
-  <br>
-
-  ![Assigning a peer](https://gitlab.com/gitlab-org/gitlab-ce/uploads/6445f80f96d8cb85b320322d36d8bb0e/assigneesidebar.png)
-  </li>
-</ol>
-
-
-<ol start="4">
-  <li>Submit the MR
-
-  ![Submit MR](https://docs.gitlab.com/ee/gitlab-basics/img/merge_request_page.png)</li>
-</ol>
-
-
 ## Github interface
 <img src="https://assets-cdn.github.com/images/modules/logos_page/GitHub-Mark.png" alt="GitHub" style="width: 100px;"/>
 

slides/essential_commands.md

@@ -36,6 +36,15 @@ $ git status
 ```
 
 
+## Be safe and create a new branch 
+
+(more on branches in a few minutes)
+<br><br><br><br><br>
+```bash
+$ git checkout -b matrix_vect_mult_myName
+```
+
+
 ## Modify a file
 
 Modify and rename `addTwoNumbers.m` in the folder `firstCommit`
@@ -81,7 +90,7 @@ $ git add firstCommit/addTwoNumbers_myName.m
 ```bash
 $ git diff
 ```
-exit with `:q`
+exit with `q`
 
 
 ## Add a commit message
@@ -112,10 +121,6 @@ $ git log
 ```
 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
 

slides/github_gitlab.md

@@ -21,5 +21,3 @@ Positive point: GitHub and GitLab are (almost) the same.
 [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/index.md

-<img src="img/Git-Logo-Black.png" class="as-is" height="100px">training
-<br><br>
-**SBG & MSP groups**
+Absolute Beginners<br>
+<img src="img/Git-Logo-Black.png" class="as-is" height="100px"><br>Workshop
+<br>
 
 <img src="img/logoLCSB.png" class="as-is" height="100px">
 
 <br><br><br><br>
-<br><br><br><br>
+<br>
 
-January 19th, 2017
+April 12th, 2017
 
 Sylvain Arreckx & Laurent Heirendt
 
 <br><br><br><br>
-
-note:
-
-(**Tuesday**: verify that everybody has a working computer with git installed)
-
-Verify that everyone has a GitHub and a Gitlab account
-
-**Thursday**: interactive session
-˜/work/training/cobratoolbox
-
-1. Git (on GitHub and GitLab)
-
-Init (git-r3 / graphique)
-
-clone, add, commit, (diff, log), push and status
-
-branch, checkout (add commit push on a branch)
-
-Demo that if pushed to a branch, we will have a conflict -> submit a PR to DEVELOP from own branch to avoid that
-
-2. Github
-
-Explain interface
-
-Fork, update the fork
-
-PR, issues (on a dummy test repo)
-
-**Thursday**: Home exercise (30 min)
-- Task 1a: Create a function with documentation
-- Task 1b: test
-- 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'.

slides/installation.md

@@ -73,7 +73,7 @@ $ git clone https://github.com/userName/myRepo.git myRepo
 <br>
 Clone the training repository with
 ```bash
-$ git clone https://git-r3lab.uni.lu/git-training/practice.git practice
+$ git clone https://github.com/uni-lu/practice.git practice
 ```
 <br>
 You may be prompted to enter your credentials.
@@ -86,13 +86,3 @@ Any other rudimentary method such as
 
 shall **be avoided**!
 
-
-## I need `The COBRAToolbox`?
-
-Simply `clone` the repository (i.e., retrieve a copy)
-```bash
-$ git clone https://github.com/opencobra/cobratoolbox.git cobratoolbox
-```
-
-<br><br>
-**Do not** do it right now! Thank you.

slides/list.json

@@ -47,12 +47,6 @@
           "data-background": "../img/whiteBG.jpg"
         }
     },
-    {
-        "filename": "forks.md",
-        "attr": {
-          "data-background": "../img/whiteBG.jpg"
-        }
-    },
     {
         "filename": "best_practices.md",
         "attr": {
@@ -64,17 +58,5 @@
         "attr": {
           "data-background": "../img/whiteBG.jpg"
         }
-    },
-    {
-        "filename": "ready.md",
-        "attr": {
-          "data-background": "../img/whiteBG.jpg"
-        }
-    },
-    {
-        "filename": "homework.md",
-        "attr": {
-          "data-background": "../img/whiteBG.jpg"
-        }
     }
 ]

slides/overview.md

@@ -7,7 +7,4 @@
 4. The 5 essential commands <!--(10 min)//-->
     * `pull` / `status` / `add` / `commit` / `push`
 5. Branches <!--(10 min)//-->
-6. Forks <!--(10 min)//-->
 7. Best practices
-8. Practical session  <!--(40 min)//-->
-9. Evaluation <!--(10 min)//-->

slides/what_is_git.md

@@ -11,6 +11,17 @@
 <div align="left"><small>[1] *https://en.wikipedia.org/wiki/Git*</small></div>
 
 
+## Funny story
+
+![](img/git_definition.png)
+<br><br>
+```
+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**