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# 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 is referred to as a **branch**.
<div class="fragment">
<img src="slides/img/icon-live-demo.png" height="100px">
<font color="red">In the practice 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
List all branches of the repository with
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You have to `clone` it first:
```bash
$ git clone git@github.com:LCSB-BioCore/basic-git-practice.git
$ git clone ssh://git@gitlab.lcsb.uni.lu:8022/R3/school/git/basic-practice-pages.git
```
If you did not configure your SSH key, clone using HTTPS:
```bash
$ git clone https://github.com/LCSB-BioCore/basic-git-practice.git
$ git clone https://gitlab.lcsb.uni.lu/R3/school/git/basic-practice-pages
```
You will be prompted to enter your credentials.
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This should list the configuration with `user.name` and `user.email`.
Exit by typing `q`.
# 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
```
If you set a password to your key (recommended), add it to the `ssh-agent`:
```bash
$ eval "$(ssh-agent -s)"
$ ssh-add -K ~/.ssh/id_rsa
```
Then, add the SSH key to Github/Gitlab.
<img src="slides/img/icon-live-demo.png" height="100px">
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# What is a `fork`?
<center>
<img src="slides/img/fork.jpg" class="as-is" height="500em"/>
</center>
<!--http://www.cndajin.com/data/wls/246/22302193.jpg-->
# Not really ...
<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>.
# How to get a 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)
<img src="slides/img/icon-live-demo.png" height="100px">
# Time to practice!
Fork the practice repository: <br><br>
https://github.com/LCSB-BioCore/basic-git-practice<br><br>
Then, clone your fork to your home directory!
<img src="slides/img/icon-live-demo.png" height="100px">
```bash
$ git clone git@github.com:<yourName>/basic-git-practice.git
```
Change to the practice directory with:
```bash
$ cd basic-git-practice
```
<img src="slides/img/icon-live-demo.png" height="100px">
If you did not configure your SSH key, clone using HTTPS:
```bash
$ git clone https://github.com/<yourName>/basic-git-practice.git
```
# A note on shortcuts ...
<font color="red">
Any other rudimentary method such as
*'I simply download the `.zip` and unzip it - works like a charm!'*
shall **be avoided**!
</font>
<br>
**Why?**
# 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!
<br>
**More on that later!**
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# 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 VCS systems.
GitHub/Gitlab are both **publicly available**, but GitLab can be **on-premise**.
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)
- Public GitLab: [https://gitlab.com](https://gitlab.com)
- LCSB specific: [https://gitlab.lcsb.uni.lu](https://gitlab.lcsb.uni.lu)
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# Elixir-LU training (R3.school)
## October 20th, 2021
<div style="top: 6em; left: 0%; position: absolute;">
<img src="theme/img/lcsb_bg.png">
</div>
<div style="top: 5em; left: 60%; position: absolute;">
<img src="slides/img/elixir.png" height="200px">
<img src="slides/img/r3-training-logo.png" height="200px">
<br><br><br><br>
<h1>Basic git training</h1>
<br><br><br><br>
<h4>
Laurent Heirendt, Ph.D.<br>
laurent.heirendt@uni.lu<br>
<i>ELIXIR/LU, Luxembourg Centre for Systems Biomedicine</i>
</h4>
</div>
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[
{ "filename": "index.md" },
{ "filename": "overview.md" },
{ "filename": "what_is_git.md" },
{ "filename": "github_gitlab.md" },
{ "filename": "installation.md" },
{ "filename": "the_terminal.md" },
{ "filename": "the_editor.md" },
{ "filename": "configuration.md" },
{ "filename": "cloneRepo.md" },
{ "filename": "forks.md" },
{ "filename": "branches.md" },
{ "filename": "essential_commands.md" },
{ "filename": "merge.md" },
{ "filename": "syncFork.md" },
{ "filename": "best_practices.md" },
{ "filename": "advanced.md" },
{ "filename": "thanks.md" }
]
]
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# Pull (merge) requests
If you want your changes to be reflected on the `develop` or `master` branches,
**submit a PR** via the Github 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" >
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# Overview
1. What is `git`? What is the use of `git`?
2. GitHub and GitLab
3. The terminal
4. Installation of `git`
5. The editor
6. How do I configure `git`?
7. Where and how to start?
8. What is a fork?
9. What are branches?
10. The 5 essential commands (`pull` / `status` / `add` / `commit` / `push`)
11. What are merge/pull requests?
12. How do I synchronize my fork?
13. Best practices
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# Overview
0. Subject 1
1. Subject 2
1. The terminal
2. Installation of `git`
3. How do I configure `git`?
4. Where and how to start?
5. The 5 essential commands (`pull` / `status` / `add` / `commit` / `push`)
6. How do I synchronize my fork?
7. What if things go wrong?
8. Best practices
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# The editor(s)
Recommended editors:
- **Visual Studio Code** [https://code.visualstudio.com](https://code.visualstudio.com)
- **Atom** [https://atom.io](https://atom.io)
*Note*: Other editors can, of course, also be used. Examples:
- IntelliJ IDEA [https://www.jetbrains.com/idea](https://www.jetbrains.com/idea)
- Sublime Text [https://www.sublimetext.com](https://www.sublimetext.com)
<img src="slides/img/icon-live-demo.png" height="100px">
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# First steps in the terminal
Starting the terminal presents itself with a line where you can enter a command
```bash
cesar@myComputer>
```
Often written, for covenience, as
```bash
$
```
When you open your terminal (shell), you are located
in your home directory (unless otherwise configured), denoted as `~/`.
<br>
**Is `git` properly installed?**
```bash
$ git --version
# git version 2.33.1
```
# Essential Linux commands
List the contents of a directory
```bash
$ ls
```
You can list more details with:
```bash
$ ls -lah
```
Create a directory
```bash
$ mkdir myNewDirectory
```
Change the directory to a specific folder
```bash
$ cd myNewDirectory
```
Change the directory 1 level and 2 levels up
```bash
$ cd ..
# 1 level up
$ cd ../..
# 2 levels up
```
Move a file or a directory
```bash
$ mv myFile.m myNewDirectory/.
```
Rename a file or a directory
```bash
$ mv myFile.m myNewFile.m
$ mv myNewDirectory myDirectory
```
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# What is `git`?
<!-- ![](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*
# The inventor of `git`
<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.`
Linus Torvald (2007-06-14)
# What is the use of `git`?
* No need to fully rewrite code; **reuse code** 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 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.
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