Version control and track changes

L. Darmet
JJ. Torre

Git, GitHub, Gitlab

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

By: L. Darmet and JJ. Torre

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Are you in this picture?
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Or in this one ?
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Version control can be a solution !

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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
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  • 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 ?

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  • 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

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  • 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

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

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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

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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
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Terminology

  • Create a repository or repo and clone it
  • Commit your changes (locally) and then push (remote) \(\rightarrow\) 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
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Code example to start using Gitub 👩‍💻

Install Git on your machine

  • On Linux from a terminal:
sudo apt update
sudo apt install git-all

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).

  1. Then open the generated (public) key to share it with GitHub:
notepad ~/.ssh/id_rsa.pub

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

  2. 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

  3. 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)
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They also handle the SSH keys for you

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Thank you for your attention!


Questions ❓


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