This lesson is being piloted (Beta version)

JupyterLab git extension


Teaching: 30 min
Exercises: 30 min
  • How to use JupyterLab git extension?

  • How to manage your research project with JupyterLab?

  • Learn about Jupyterlab git extension

  • Learn to create a git and github repository for your research project

JupyterLab git extension is already installed in the Resbaz VM. If you want to install this extension to your local JupyterLab, follow installation instructions at

Check availability of JupyterLab git extension

A tab labeled “Git” as well as “Git panel” are available once JupyterLab git extension is properly installed, as shown on the figure below:

Jupyterlab git extension

Git setup

This section is taken from the Software Carpentry Git lesson. It has be shortened as we are using a Linux VM but feel free to go through the entire Software Carpentry lesson if you need to install and use git on your laptop.

When we use Git on a new computer for the first time, we need to configure a few things. Below are a few examples of configurations we will set as we get started with Git:

Save and close your Jupyter notebook so you can start a terminal from the JupyterLab Launcher:

JupyterLab Terminal


  • Another way to open a Git Terminal is to use the “Git” Tab -> “Open Terminal”
  • The copy/paste menu is “hidden” so to get it:
    • copy: select the text to copy with your mouse then SHIFT and right-click with your mouse so the copy menu will appear.
    • paste: SHIFT and right click to get the paste menu.

On a command line, Git commands are written as git verb options, where verb is what we actually want to do and options is additional optional information which may be needed for the verb. So here is how Dracula sets up his new laptop:

$ git config --global "Vlad Dracula"
$ git config --global "vlad@tran.sylvan.ia"

Please use your own name and email address instead of Dracula’s. This user name and email will be associated with your subsequent Git activity, which means that any changes pushed to GitHub, BitBucket, GitLab or another Git host server in a later lesson will include this information.

Line Endings

As with other keys, when you hit Return on your keyboard, your computer encodes this input as a character. Different operating systems use different character(s) to represent the end of a line. (You may also hear these referred to as newlines or line breaks.) Because Git uses these characters to compare files, it may cause unexpected issues when editing a file on different machines. Though it is beyond the scope of this lesson, you can read more about this issue on this GitHub page.

You can change the way Git recognizes and encodes line endings using the core.autocrlf command to git config. The following settings are recommended:

On macOS and Linux:

$ git config --global core.autocrlf input

For these lessons, we will be interacting with GitHub and so the email address used should be the same as the one used when setting up your GitHub account. If you are concerned about privacy, please review GitHub’s instructions for keeping your email address private.

If you select to use a private email address with GitHub, then use that same email address for the value, e.g. replacing username with your GitHub one. You can change the email address later on by using the git config command again.

The commands we just ran above only need to be run once: the flag --global tells Git to use the settings for every project, in your user account, on this computer.

You can check your settings at any time:

$ git config --list

You can change your configuration as many times as you want.

Manage your research project with JupyterLab and Git/Github

To make publication ready scientific reports and presentations, we would need to share our research with Github.

In this section we will learn:

Later in this workshop, we will see how to publish our research work using MyBinder and Zenodo.

Create a new local git repository

Create a new folder

jupyterlab folder

For our example, we will be moving the jupyter notebook we created (called example.ipynb).

Create a new Git repository

As you are in the ResearchBazaarJupyterLab2019 repository, click on the Git Tab and select Init.

jupyterlab git init

A window will pop-up, aksing for confirmation. Select YES.

jupyterlab git init confirmation

It does not look like anything happened but you have now created a new git repository. Let’s now add our research work to this repository.

Add your research work in your newly created repository

On the left hand side of the JupyterLab panel, click on the “Git Icon” as shown on the figure below:

jupyterlab git icon

If you are familiar with Git, you will recognize the interface and steps we use for staging and committing files into git.

jupyterlab git track

jupyterlab git commit

You are done! However, make sure you stage and commit your notebooks and related research work every time you make changes and are willing to keep track of these changes!

Share your research work online using Github

In anticipation of our next lesson on sharing using the capability of Binder, we need to share the notebook that we have been working on.

One step consists in sharing your local git repository on Github. For this, you would need a Github account.


GitHub is a development platform where we “can host and review code, manage projects, and build software.” GitHub hosts source code for 75+ million projects including the pandas package we have been using among many others.

Make sure you have a (free) account otherwise follow our setup instructions.

1. Create a new repository


Create a new repository:

  • Add a repository name. We choose to name our repository research-bazaar-jupyter-2019.
  • Add a description, for instance: “Repository for the Research Bazaar workshop on publishing jupyter notebooks”
  • Personal GitHub accounts require that projects be public.
  • DO NOT Check the Initialize this repository with a README option.
  • ** DO NOT add a license**. We will add it afterwards.
  • Click the green Create repository button.

If everything went fine, you should be re-directed to a page giving you sime information on the next steps, as shown in the figure below:

github new repository.png

Congratulations!! We now have created our repository for hosting our research work!

As we already have a local repository, we will push our existing repository from the command line. Open a Terminal (Git tab –> Open Terminal):

git remote add origin
git push -u origin master

3. Add a LICENSE

Choosing a license may be tricky and is out of scope of this workshop. However, without a license, sharing our work is meaningless.

We will be adding an MIT license to our github repository. To get more information on which license to choose, follow this link.

Choose a license

You will be re-directed to your Github repository research-bazaar-jupyter-2019 and the current date and your name will be automatically suggested.

Review and Submit


If you choose to Create a new branch for this commit and start a pull request, follow the steps to start a pull request and merge your contribution to the master branch.

4. Add a README file

As suggested, add a README file from the Github interface.

github README file.png

5. Authoring & Citation

In addition to LICENSE, it is recommended to add:

List of authors

A GitHub repository is very often created by an individual user so adding the list of authors is very important.

Add a new file AUTHORS in your repository

  • Go to your repository in your web browser
  • Click on “Create new file” and name your file AUTHORS
  • Add the list of authors/contributors and commit your changes

Sync your local git repository

We have done a number of changes to our Github repository but if you go back to your jupyterLab instance, you will see that none of them are reported yet.

To synchronize your local git repository, go back to your Jupyterlab:

Sync with remote


You can also pull from a Git Terminal; make sure you are in the ResearchBazaarJupyterLab2019 repository.


And then pull the remote changes:

git pull 

Where to find more about GitHub

To learn more about GitHub you can review one or more of these additional (external) resources:

More about Git version control

If you would like to learn about source code version control using the git software, the git in GitHub, please see these resources:

  • Try this 15 minute interactive git tutorial
  • Try some additional git exercises here

Key Points

  • jupyterlab git extension