Merge branch 'lh-changes-git-part-1' into 'develop'

Changes for git part 1

See merge request !126

2022/2022-05-31_git-trilogy-part-1/slides/best_practices.md

 
-# Wrap-up
+# Summary
 
-* Git makes things separated but interlinked!
-    * separation of changes into commits - compare with standard "versioning" of dropbox/onedrive/owncloud or labeling v1.2 manually
-    * separation of work into branches - compare with standard work in parallel - making copy of file and renaming, then "putting it together"
-    * separation of work into forks - compare with "I will make my own copy of the whole folder"
+GitLab creates a convenient and efficient working environment
+  - merge requests
+  - issues
+  - assignments
+  - much much more...
 
 
-<div class="fragment">
 
-* GitLab creates a convenient working environment
-  * merge requests
-  * issues
-  * assignements
-  * and much much more...
-
-
-   <div style="position:absolute;left:55%;top:55%">
-   <img src="slides/img/fox.png">
-   https://pixabay.com/images/id-5236832/
-   </div>
-</div>
-
-
-
-
-# Wrap-up
-## Glossary
-* git
-* repository
-* fork
-* commit
-* branch
-* merge
-* merge/pull request
-
-## Best practices
+# Best practices
 
 * Work on your <font color="red">own</font> branch (in your own fork), and **not** on `master` and **not** on `develop`
 * Do **not commit** to `master`/`develop`, but **submit a merge request (MR)**

2022/2022-05-31_git-trilogy-part-1/slides/branches.md

 # New term:  <font color="color:red">branch</font>
 
-* A sequence of commits (changes) is referred to as **branch**.
-* A new branch can be created by __branching off__ from a commit.
-* A **branch** can be understood as a named **version** of your repository.
+* A sequence of commits (changes) is referred to as *branch*.
+* A new branch can be created by *branching off* from a commit on another branch.
+* A *branch* can be understood as a named *version* of your repository.
 
 <div style="position:absolute;left:50%;top:1em">
 <img src="slides/img/branch_branch-off_detail.png" class="as-is" height="800px"/>
@@ -14,7 +14,7 @@
 
 Generally, in a repository, there are guidelines for contributing.
 
-<div class="fragment">
+<br>
 
 A common development scheme is dual with a:
 
@@ -48,33 +48,39 @@ Best practice is to <font color="red">create a new **branch**!</font>
 <img src="slides/img/branch_my-branch.png" height="800em"/>
 </div>
 
-<br> 
+<br>
 
 Using branches ensures:
-* your changes are made separately from other changes
-* your version won't be affected by others
-* all related changes are aggregated on one place
+* your changes are made separately from other (unrelated) changes
+* your version will not be affected by other contributors
+* all related changes are aggregated in one place
 * work can continue if the development of one feature gets stuck
 
+<br>
 Are you working on more features in parallel?
 
-<font color="red">Create a new **branch**!</font> for each of them :)
+<font color="red">Create a new **branch**!</font> for each of them!
+
+
 
 
 
+# Quick recap
 
+What is the difference between a *fork* and a *branch*?
 
-# Time to practice!
+<div class="fragment">
+<br><br><br>
+<div align="center">
+<img src="slides/img/forking_detail-with-branches.png" height="500em"/>
+</div>
 
-1. What is the difference between **fork** and **branch**?
-    <div class="fragment fade-in-then-out">
-    <div style="position:absolute;left:10%;top:8em">
-    <img src="slides/img/forking_detail-with-branches.png" height="500em"/>
-    </div>
 
-2. Why is best practice to branch off from `develop`?
-3. Switch between branches
-    <div class="fragment fade-in-then-out">
-    <div style="position:absolute;left:10%;top:8em">
-    <img src="slides/img/branch_GUI_switch.png" height="500em"/>
-    </div>
+
+# How to switch between branches?
+
+<div style="position:absolute;left:10%;top:8em">
+<img src="slides/img/branch_GUI_switch.png" height="500em"/>
+</div>
+
+Why is best practice to branch off from `develop`?
\ No newline at end of file

2022/2022-05-31_git-trilogy-part-1/slides/commit.md

@@ -4,17 +4,18 @@
 * Every change moves the repository to a new state.
 * Every change added to the sequence of changes is called **commit**.
 * Every commit has:
-  * message - why
-  * author - who
-  * timestamp - when
-  * unique identifier
+  * content - what?
+  * a message - why?
+  * an author - who?
+  * a timestamp - when?
+  * unique identifier - tracking number
 
 <div style="position:absolute;left:60%;top:1em">
 <img src="slides/img/commit_history-diagram.png" class="as-is" height="800px"/>
 </div>
 
 <div class="fragment">
-Gitlab UI:
+Gitlab:
 <div style="position:absolute">
 <img src="slides/img/commit_GUI_1.png" class="as-is" height="350px"/>
 </div>
@@ -23,9 +24,10 @@ Gitlab UI:
 
 
 # New term: <font color="color:red">commit</font>
-## Time to practice!
 
-1. Notice last commit on files
+<img src="slides/img/icon-live-demo.png" height="100px">
+
+1. Notice last commits that modified files/folders
 <!-- .element: class="fragment" data-fragment-index="1" -->
 1. Review history of your repository
 <!-- .element: class="fragment" data-fragment-index="2" -->
@@ -45,10 +47,5 @@ Gitlab UI:
 <img src="slides/img/commit_GUI_click-on-commit.png" class="as-is" height="75px"/>
 </div>
 <div class="fragment fade-in-then-out" data-fragment-index="3">
-<img src="slides/img/commit_changes.png" class="as-is" height="600px"/>
+<img src="slides/img/commit_changes.png" class="as-is" width="90%"/>
 </div>
-
-What is this
-
-Notes:
-Congrats! Now you have reviewed recent changes in your repository!
\ No newline at end of file

2022/2022-05-31_git-trilogy-part-1/slides/forks.md

@@ -20,18 +20,15 @@
 # New term:  <font color="color:red">fork</font>
 ## What is a `fork`?
 
-- In general, by default you can only **read** files in a repository.
-- In general, by default you **cannot write** changes.
+- In general, by default, you can only **read** files in a repository. You **cannot write**.
 
 <div class="fragment">
 <img src="slides/img/forking.png" height="400px">
 
 
-- You have to work on your **own copy** of the repository
+- You have to work on your **own copy** of the repository in order to make changes.
 - In other words, you have to work on your own <font color="red">**fork**</font>.
-<br>
 
-## Why?
 
 
 
@@ -39,7 +36,9 @@
 
 Browse to the original repository and click on the button `Fork`:
 
-<img src="https://docs.gitlab.com/ee/user/project/repository/img/forking_workflow_fork_button_v13_10.png" height="250px">
+<div align="center">
+<img src="https://docs.gitlab.com/ee/user/project/repository/img/forking_workflow_fork_button_v13_10.png" height="150">
+</div>
 
 <br>
 
@@ -48,19 +47,19 @@ Browse to the original repository and click on the button `Fork`:
 
 ## Time to practice!
 
-1. Fork the practice repository: <br><br>
-TODO<br><br>
+1. Fork the training repository  [https://gitlab.lcsb.uni.lu/R3/school/git/basic-practice-pages](https://gitlab.lcsb.uni.lu/R3/school/git/basic-practice-pages)
+
+
+Congrats! Now you have your own **fork**!
 
-Congrats! Now you have your own **fork**! 
 
 
+# How to update my fork?
 
-# How to update my fork? - TODO: move to the end or delete
-\
-As you have your own fork, it will not automatically be updated once the original repository is updated.
+As you have your own copy (fork), it will not automatically be updated once the original repository is updated.
 
 ![bulb](slides/img/bulb.png) You have to update it yourself!
 
 <br>
 
-**More on that later!**
+**More on that later - time permitting**

2022/2022-05-31_git-trilogy-part-1/slides/gitlab.md

 # Git repository hosting platforms
+
 <div style="position:absolute; left:70%">
 <img src="https://gitlab.com/gitlab-com/gitlab-artwork/raw/master/logo/logo-extra-whitespace.png" alt="GitLab" style="width: 500px;"/>
 </div>
@@ -22,22 +23,15 @@ Another popular platforms:
 
 
 
-# Time to practice!
-
-<img src="slides/img/icon-live-demo.png" height="100px">
+# Login and report and issue
 
 1. Login to [https://gitlab.lcsb.uni.lu](https://gitlab.lcsb.uni.lu)
    * use your LUMS credentials
-2. browse the existing repositories
-   * Explore ->
-   * navigate to the training repository
+2. Browse the existing repositories
+   * Explore and Search
+   * Navigate to the training repository [https://gitlab.lcsb.uni.lu/R3/school/git/basic-practice-pages](https://gitlab.lcsb.uni.lu/R3/school/git/basic-practice-pages)
 3. Inspect project/repository folder structure
-4. Discover an issue (see README.md) and report it
+4. Report an issue
 
-<div class="fragment">
-
-Congrats! You are a **reporter** :)
-</div>
+<img src="slides/img/icon-live-demo.png" height="100px">
 
-notes:
-- reporter is very important role

2022/2022-05-31_git-trilogy-part-1/slides/index.md

-# Trilogy of Git Part 1
+# R3.school
 
 ## May 31st, 2022
 
@@ -8,12 +8,13 @@
 
 <div style="top: 5em; left: 60%; position: absolute;">
     <img src="slides/img/r3-training-logo.png" height="200px">
-    <br><br><br>
-    <h1>Contribute using Gitlab</h1>
+    <br><br><br><br>
+    <h1>Trilogy of git - Part I</h1>
+    <h2>Contribute using Gitlab</h2>
     <br><br><br>
     <h4>
-        Laurent Heirendt<br><br>
-        laurent.heirendt@uni.lu<br><br>
+        Laurent Heirendt, Ph.D.<br>
+        R3 Team - <a href="mailto:lcsb-r3@uni.lu">lcsb-r3@uni.lu</a><br>
         <i>Luxembourg Centre for Systems Biomedicine</i>
     </h4>
-</div>
+</div>
\ No newline at end of file

2022/2022-05-31_git-trilogy-part-1/slides/merge.md

 # New term: <font color="color:red">merge</font>
 
 * You have made changes on your branch
-* Now you want your changes to be reflected on another branch </br>(most probably `develop` or `master`)
+* Now you want your changes to be reflected on another branch </br>(most probably `develop`)
 
-<div style="position:absolute;left:60%;top:1em">
+<div style="position:absolute;left:70%;top:1em">
 <img src="slides/img/branch_merge-detail.png" height="800px" >
 </div>
 
 You have to <font color="color:red">merge</font> the branches.
 
-**Remarks**: merging is directional - *Merge branch A to branch B*
+- Merging is directional - *Merge branch A to branch B*
+- Merging of branches is a process that is initiated via a so called **merge request** (MR):
+- Your peers can comment on your changes in a merge request **review**!
 
-### The merge is initiated via so called **merge request**
-* *Requesting* someone (from the original repository) to *merge* your changes.
-* *merge request* is commonly abreviated as **MR**
 
-Your peers can comment on your changes in a merge request **review**!
 
+# What happened in the background?
 
-
-# Our state at the moment?
-
-<div style="position:absolute;top:2em" >
+<div style="position:absolute;top:2em" class="fragment fade-in-then-out" data-fragment-index="1">
 <img src="slides/img/fork_branch-diagram-after-commit.png" height="600px" >
 </div>
 
+
 <div style="position:absolute;top:2em" class="fragment fade-in-then-out" data-fragment-index="1">
 <img src="slides/img/fork_branch-diagram-after-commit-with-back-arrow.png" height="600px" >
 </div>
 
 
 
-# Time to practice!
+# Merge request (MR)
 
-* After hitting the Commit button, you get redirected to the submission page for your merge request
-* Please make sure that you see that you are proposing to merge your branch (version) into the develop branch. This is shown at the top of the page:
-<!-- .element: class="fragment" data-fragment-index="1" -->
-* Fill your merge request submission form and select an Assignee.
-<!-- .element: class="fragment" data-fragment-index="3" -->
-* Good practice is to select Delete source branch when merge request is accepted. (Why?)
-<!-- .element: class="fragment" data-fragment-index="4" -->
-* Under Changes tab, you can see your... changes :)
-<!-- .element: class="fragment" data-fragment-index="5" -->
+<img src="slides/img/icon-live-demo.png" height="100px">
 
+After hitting the *Commit* button, you get redirected to the submission page for your *merge request (MR)*
 
-<div style="position:absolute;left:30%;top:4em" class="fragment fade-in-then-out" data-fragment-index="1">
-<img src="slides/img/merge_GUI_detail.png" height="720px" >
-</div>
-
-<div style="position:absolute;left:30%;top:6em" class="fragment fade-in-then-out" data-fragment-index="2">
-<img src="slides/img/merge_branch-to-branch.png" height="100px" >
-</div>
+* Propose to merge your branch into the *development branch*. This is shown at the top of the page.
+* Fill your merge request submission form and select an *Assignee*.
+* Under Changes tab, you can see your changes
 
-<div style="position:absolute;left:5%;top:10em" class="fragment fade-in-then-out" data-fragment-index="5">
-<img src="slides/img/merge_changes.png" height="400px" >
-</div>
+![bulb](slides/img/bulb.png) Good practice is to select *Delete source branch when merge request is accepted*. Why?

2022/2022-05-31_git-trilogy-part-1/slides/syncFork.md

 # Synchronize your fork
 
-<!-- TODO: do we need this slide? -->
-<!-- Should it contain steps for deleting a branch -->
+As mentioned earlier, your fork has been created a certain moment in time.
+
\ No newline at end of file
+How to keep it updated?
+
+## Easy way
+
+Delete your fork and re-create it!
+
+- Go to `Settings > General`
+- Scroll down to the `Advanced` section and expand it
+- Click on `Delete this project` and follow the on-screen instructions
+
+![bulb](slides/img/bulb.png) Before you do this, please make sure that all your merge requests have been accepted.
+
+## Automatic way
+
+Follow the instructions on the How-To card: [https://howto.lcsb.uni.lu/?contribute:mirror-fork](https://howto.lcsb.uni.lu/?contribute:mirror-fork)
\ No newline at end of file

2022/2022-05-31_git-trilogy-part-1/slides/versioning.md

-# Using versioning system?
+# Why use a version control system?
+
 Basic feature:
-* Ability to recover old versions
 
+* Ability to recover old versions
 
-<div class="fragment">
 <div style="position:absolute; left:50%">
 <img src="slides/img/version-history_OneDrive.png" height="650px">
 </div>
@@ -11,20 +11,22 @@ Basic feature:
 Common tools you are already using supporting "version control":
 - Owncloud
 - OneDrive
-- DropBox
 - ...
 
-Its clear **who** changed **which file** and **when** :) Huray!
+From the list of files, it is clear *who* changed which file and *when*.
+
 
 <div class="fragment">
 
-### But something is missing, right?
-- **What exactly** was changed? (which section or row?)
-- **Why** it was changed?
+But some information is missing:
 
+- *What exactly* was changed? (which section or row?)
+- *Why* was it changed?
 
 
-# Using versioning system?
+
+# Why use a version control system?
+
 ## Manual file versioning + CHANGELOG
 
 <br>
@@ -73,7 +75,9 @@ note: overhead for doing this manually is huge
 
 
 # Using versioning system?
-What happens if **3** people contribute?
+
+What happens when **3** people contribute?
+
 ```
 my-document_v01_AK.docx
 my-document_v01_AK_BP.docx
@@ -87,14 +91,4 @@ CHANGELOG.txt
 
 <div class="fragment">
 
-What happens when **10** people contribute?
-```
+What happens when **10** people contribute?
\ No newline at end of file
-          _ ._  _ , _ ._
-        (_ ' ( `  )_  .__)
-      ( (  (    )   `)  ) _)
-     (__ (_   (_ . _) _) ,__)
-         `~~`\ ' . /`~~`
-              ;   ;
-              /   \
-_____________/_ __ \_____________
-```

2022/2022-05-31_git-trilogy-part-1/slides/web-ide.md

-# Time to practice!
+# Workflow - Web IDE
+
 To change content of a file:
 
+* Browse to *your fork*
 * Open Web IDE
 <!-- .element: class="fragment" data-fragment-index="1" -->
-* Select a branch you want to work on
+* Select the development branch
 <!-- .element: class="fragment" data-fragment-index="2" -->
 * Edit file content
 <!-- .element: class="fragment" data-fragment-index="3" -->
 * Commit
 <!-- .element: class="fragment" data-fragment-index="4" -->
-  * Hit Commit
-  * Select **Create a new branch** and type your branch name
-  * Leave the **Start a new merge request** checked
-  * Hit Commit
+  * Click Commit
+  * Select **Create a new branch**
+  * Type your branch name (optional, but recommended)
+  * Check **Start a new merge request**
+  * Click Commit
 
 
-<div style="position:absolute;left:40%;top:1em" class="fragment fade-in-then-out" data-fragment-index="1">
-<img src="slides/img/commit_GUI_web-ide.png" height="600px" >
+<div style="position:absolute;left:30%;top:1em" class="fragment fade-in-then-out" data-fragment-index="1">
+<img src="slides/img/commit_GUI_web-ide.png" width="90%" >
 </div>
 
 <div style="position:absolute;left:40%;top:1em" class="fragment fade-in-then-out" data-fragment-index="2">
-<img src="slides/img/web-ide_select-branch.png" height="600px" >
+<img src="slides/img/web-ide_select-branch.png" width="90%" >
 </div>
 
 <div style="position:absolute;left:33%;top:1em" class="fragment fade-in-then-out" data-fragment-index="3">
-<img src="slides/img/web-ide_edit-file.png" height="400px" >
+<img src="slides/img/web-ide_edit-file.png" width="90%" >
 </div>
 
 <div style="position:absolute;left:50%;top:1em" class="fragment fade-in-then-out" data-fragment-index="4">
-<img src="slides/img/web-ide_commit-button.png" height="200px" >
+<img src="slides/img/web-ide_commit-button.png" width="90%" >
 </div>
 
 <div style="position:absolute;left:50%;top:10em" class="fragment fade-in-then-out" data-fragment-index="4">
-<img src="slides/img/web-ide_commit-detail.png" height="400px" >
-</div>
-
-
-
-# What have we done?
-
-<div style="position:absolute;top:2em" class="fragment fade-in-then-out" data-fragment-index="1">
-<img src="slides/img/fork_branch-diagram-after-commit.png" height="600px" >
+<img src="slides/img/web-ide_commit-detail.png" width="90%" >
 </div>