add slides

2020/2020-01-31_gitTrainingBioTech/slides/best_practices.md

+# Best practices
+
+* Fetch the upstream before creating a new branch.
+* Work on your <font color="red">own</font> branch (in your own fork), and **not** on `master` and **not** on `develop`
+* Get your code **reviewed** by your peers (submit a PR!)
+* Submit a PR **often**!
+* `Push` often - avoid conflicts
+
+Remember: **A `push` a day keeps conflicts away!**

2020/2020-01-31_gitTrainingBioTech/slides/branches.md

+# Development scheme
+
+
+Generally, in a repository, there are guidelines for contributing.
+
+<div class="fragment">
+
+A common development scheme is dual with a:
+
+- **development** version of the code on `develop`
+- **stable** version of the code on `master`
+
+
+A **version** of the code/text is referred to as a **branch**.
+
+<div class="fragment">
+
+<font color="red">In the `howto-cards-internal` repository, the development branch is called `develop`!</font>
+
+<div class="fragment">
+
+![bulb](slides/img/bulb.png) Use this dual development scheme for your own repositories!
+
+
+
+# Branches
+
+A **version** of the code (i.e., a **branch**) is made up of a sequence of code changes.
+
+<div class="fragment">
+
+These individual code changes are called **commits**.
+
+
+For instance, the `master` and `develop` branches can be represented as a timeline:
+<img src="slides/img/branch-master.png" class="branch-master" height="500em"/>
+
+
+
+# Switch between branches
+
+<img src="slides/img/icon-live-demo.png" height="100px">
+
+
+
+# Create your own version
+
+Assume that you want to work on a file:
+
+<div class="fragment">
+
+<font color="red">Create a new **branch** and start editing!</font>
+
+
+<img src="slides/img/icon-live-demo.png" height="100px">
+
+<img src="slides/img/branch-create.png" class="branch-create" height="500em"/>

2020/2020-01-31_gitTrainingBioTech/slides/configuration.md

+# How to configure `git`?
+
+```bash
+$ git config --global user.name "Firstname Lastname"
+$ git config --global user.email "first.last@uni.lu"
+```
+
+Test whether your username and email have been registered
+
+```bash
+$ git config --list
+```
+
+This should list the configuration with `user.name` and `user.email`.
+
+
+
+
+# What is an SSH key?
+
+An SSH key is a secure access credential.
+
+**Principle**: <br><br>
+Communicate **securely** with Github/Gitlab **without** entering the username/password.
+
+
+
+# How do I get and set my SSH key?
+
+Check if you already have an SSH key:
+
+```bash
+$ ls -al ~/.ssh
+```
+
+If there are 2 files named `id_rsa`, you have an SSH key.
+
+If you don’t have yet an SSH key, you have to generate one:
+```bash
+$ ssh-keygen -t rsa # -b 4096
+```
+
+Then, add the SSH key to your profile on git-r3lab.
+
+On Windows, please unmount `P:\` (your personal atlas folder) first.
+
+<img src="slides/img/icon-live-demo.png" height="100px">
\ No newline at end of file

2020/2020-01-31_gitTrainingBioTech/slides/forks.md

+# What is a `fork`?
+
+<br><br>
+<center><img src="slides/img/fork.jpg" class="as-is" height="500em"/></center>
+<!--http://www.cndajin.com/data/wls/246/22302193.jpg-->
+
+
+
+# Not really ...
+
+<br><br>
+<center><img src="slides/img/fork-crossed.png" class="as-is" height="500em"/></center>
+
+
+
+# What is a `fork`?
+
+- In general, when contributing to a repository, you only have **read** access.
+
+- In other words, you can only **pull** (unless it is your own repository or access has been granted).
+
+- In general, you **cannot write** changes. In other words, you do not have **push** access.
+
+- You have to work on your **own copy**.
+
+- In other words, you have to work on your own <font color="red">**fork**</font>.
+
+<br>
+<h2>How to get a fork?</h1>
+
+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)
+
+
+
+
+# How to update my fork?
+
+As you have your own fork, it will not automatically be updated once the original repository is updated.
+
+![bulb](slides/img/bulb.png) You have to update it yourself!
+
+<img src="slides/img/icon-live-demo.png" height="100px">
+
+**More on that during the demo!**
+
+
+
+
+# Time to practice!
+
+Fork the howto-cards (internal) repository: <br><br>
+https://git-r3lab.uni.lu/R3-core/howto-cards-internal/
+
+<img src="slides/img/icon-live-demo.png" height="100px">
\ No newline at end of file

2020/2020-01-31_gitTrainingBioTech/slides/github_gitlab.md

+# GitHub and GitLab
+
+<img src="https://github.githubassets.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 online platforms for developing code using the version control system (VCS) `git`.
+
+Positive point: GitHub and GitLab are (almost) the same.
+
+
+<img src="slides/img/icon-live-demo.png" height="100px">
+
+
+- **GitHub**: [https://github.com](https://github.com)
+- **GitLab**: [https://gitlab.com](https://gitlab.com)
+
+At the LCSB, we use our own instance of Gitlab: [https://git-r3lab.uni.lu](https://git-r3lab.uni.lu)
\ No newline at end of file

2020/2020-01-31_gitTrainingBioTech/slides/index.md

@@ -9,7 +9,7 @@
 <div style="top: 5em; left: 60%; position: absolute;">
     <img src="slides/img/r3-training-logo.png" height="200px">
     <br><br><br>
-    <h1>git training for Biotech team</h1>
+    <h1>git training for biotech team</h1>
     <br><br><br><br>
     <h4>
         Laurent Heirendt, Ph.D.<br>

2020/2020-01-31_gitTrainingBioTech/slides/merge.md

+# Merge requests
+
+If you want your changes to be reflected on the `develop` or `master` branches,
+**submit a MR** via the Gitlab interface.
+
+Use the **interface** to make use of your peers to review your code!
+<img src="slides/img/branch-merge.png" class="branch-merge" height="500em"/>
+
+Once merged, you can delete the branch via the interface.
+
+<div class="fragment">
+
+<img src="slides/img/icon-live-demo.png" height="100px" >
\ No newline at end of file

2020/2020-01-31_gitTrainingBioTech/slides/overview.md

 # Overview
 
-0. Subject 1
-1. Subject 2
+1. Introduction 📚
+    1. What is `git`? What is the use of `git`? 📚
+    2. GitHub and GitLab 📚
+2. Installation & set up
+    - Configure git 💻
+    - Configure an SSH key 💻
+3. Before starting to contribute to a repository
+    - What is a fork? 📚
+    - Create and clone a fork 💻
+4. Contributing to a repository
+    - What are branches? 📚
+    - Create a branch 💻
+    - Create and edit a new card 💻
+5. Submit the contribution for review
+    - What is a merge request? 📚
+    - Submit a merge request 💻
+    - Review a merge request 💻
+6. Summary 📚
\ No newline at end of file

2020/2020-01-31_gitTrainingBioTech/slides/thanks.md

+# Let's refresh our memories
+
+<div class="fragment">
+
+- What is a **fork**?
+
+<div class="fragment">
+
+- What are **branches**?
+
+<div class="fragment">
+
+- Can I have **multiple branches** in my fork?
+
+<div class="fragment">
+
+- What is a good **development scheme**?
+
+
+
+
 # Thank you.
 
-<center><img src="slides/img/r3-training-logo.png" height="200px"></center>
+<img src="slides/img/r3-training-logo.png" height="200px">
 
 Contact us if you need help:
 
-<a href="mailto:r3lab.core@uni.lu">r3lab.core@uni.lu</a>
+r3lab.core@uni.lu
 

2020/2020-01-31_gitTrainingBioTech/slides/what_is_git.md

+# What is `git`? (i)
+
+<!-- ![](slides/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**
+
+<div align="center">
+<img src="slides/img/linus.jpg">
+</div>
+
+[1] *https://en.wikipedia.org/wiki/Git*
+
+
+
+# What is `git`? (ii)
+
+<div align="center">
+<img src="slides/img/git_definition.png">
+</div>
+
+`I'm an egotistical bastard, and I name all my projects after myself.
+First Linux, now git.`
+<br>
+Linus Torvald (2007-06-14)
+
+
+
+# What is the use of `git`?
+
+* `git` can be used for code or text documents, such as markdown language
+
+* No need to fully rewrite code/text; **reuse code/text** and **save time**
+
+* Keep the changes you made over time (**history**)
+
+* Allows you to **backtrack** (if necessary) and undo unwanted changes
+
+* Easily **add contributions** of your collaborators to the main repository
+
+<br>
+Other points:
+
+- `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.