Version control and track changes

Git, GitHub, Gitlab

An introduction to version control, easy to share/reproduce code, and more!

You can find it as a scrollable RevealJS presentation here.

By: L. Darmet and JJ. Torre

Are you in this picture? Or in this one ?

Version control can be a solution !

Use cases

• Keep track of file changes (also with Matlab..!) 🖥️
• Synchronize changes among team members 🤝
• Share the code along your publication: open science and open data 📡
  • Yes you are ashamed to share your code but it would put a strain on you for better code (cleaner, clearer, etc) 🥲
  • Sharing only data is sometimes harsh if you don’t provide an example on how to use them 🙏
• Maintain a code library 📚 to share existing code with new interns, PhD, collaborators,…
  • Avoid developing again and again the same tools for experimental protocol, pre-processing, data visualization…
  • Standard pipelines
  • We have created a COPHY organization on GitHub to centralize code
• Manage and maintain the $LATEX$ code of your thesis 🤓
• Overleaf supports direct sync with GitHub to import existing repos or create one based on current project. > This direct sync also allows to backup your Overleaf projects

Git + GitHub is the most common version control system

What are the differences between the two ?

• Git is an open-source distributed version control tool
• It follows the evolution of a set of files in your computer, called a repository or repo
• Created by Linus Torvalds (creator of Linux and Android) in 2005 and maintaned by the Linux Foundation

• Github is an online hosting service for git repos
• Startup created in 2008, acquired by Microsoft in 2018
• The repos can be either private or public
• Additionnal features:
  • Features requests, issues and pull request: ask for new functionnality and merge new functionnality to the exisiting code after review by the owner
  • A wiki for each project
  • Continuous integration tools (run automatic tests to check if additions in the code don’t alter the expected outputs)
  • Host your personnal website
• Cute cat/octopus mascot
• Follow people and explore their code database

Personnal static website

• There exists other online hosting services such as Bitbucket (also private company) or Gitlab (open-source).
• We have a self-hosted Gitlab in CRNL..! 💫
  

  

  

Get GitHub for free

GitHub is free but you may encounter limitations if you do not suscribe to GitHub Pro (4$ per month 💸)

Because of your academic or student status you can get Github Pro for free.

Apply here: https://education.github.com/benefits

Or use the Gitlab of CRNL 🤯

1. Open a ticket to ask access to the GitLab
2. Sign in and connect in: http://10.69.168.17/users/sign_in

Terminology

• Create a repository or repo and clone it
• Commit your changes (locally) and then push (remote) $\to$ keep track of changes/addition
• Pull to get latest changes from other people
• Going back to a previous commit
• Solve merge conflicts
• Use branch to develop features in parallel

Code example to start using Gitub 👩‍💻

Install Git on your machine

• On Linux from a terminal:

sudo apt update
sudo apt install git-all

• On Windows:
  • Download it from https://git-scm.com/download/win
  • Run the installer

Create a local repo from scratch

Enter commands in GitBash for Windows and on terminal for Linux

mkdir mynewrepo && cd mynewrepo
git init 
ECHO >> README.md
git add README.md
git commit -m "Add README"

Connect your machine with GitHub

First you need to create an account on https://github.com
Then we will need SSH key to have a secure and authentified connection

1. In terminal or GitBash, generate SSH keys:
   

ssh-keygen -t rsa -C "your_email@example.com"

Use same email as registred on GitHub. Then press Enter two times (no need to set a password).

2. Then open the generated (public) key to share it with GitHub:

notepad ~/.ssh/id_rsa.pub

3. On GitHub website go to: Settings > SSH and GPG Keys. Click on New SSH key and enter a title.

4. In the field Key paste all the contents of the file id_rsa.pub that you have just opened, beginning at ssh-ras ... up to your email (including it). You can copy with a terminal utility (such as xclip) if copying by hand does not work

5. Click Add SSH key

Connect your local repo to GitHub

As you have setup a secured SSH key, no need for password

Go back to you terminal where you have initialized your local repo:

git remote add origin git@github.com:username/new_repo
git push -u origin master

Or use a GUI for simpler interactions 🤓

• GitHub Desktop: from Github directly
• Gitkraken: the most comprehensive (requires GitHub Pro)

They also handle the SSH keys for you

Thank you for your attention!

Questions ❓