Github <> JupyterHub

Github account

Scispot account with JupyterHub enabled

Scispot account with Github integration enabled

Some linux terminal command knowledge (Optional)

Customers with JupyterHub access have the option to sync scripts stored in JupyterHub with a Github repository

This article will go through setting up the SSH authentication for Github as well as using the Git GUI extension for JupyterLab, but using the terminal to run git commands is also supported for more advanced Git usage

We will first configure the ssh key for github authentication. First login to your jupyterlab and click on the terminal
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Run the following commands in the terminal by copying and pasting:

This will remove any previously created ssh keys

rm -r .ssh

You may receive an error if the folder doesn't exist, you can safely ignore this error:
​rm: cannot remove '.ssh': No such file or directory

Now create the ssh directory

mkdir -p ~/.ssh

Set permission on the newly created directory
​chmod 700 ~/.ssh

Generate the ssh public and private key

ssh-keygen -t ed25519 -C "scispot_jupyter_ssh" -f ~/.ssh/id_ed25519
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You will receive the following, passphrase is optional, simply type the passphrase you would like to use (or leave it blank) and press enter for each line
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Generating public/private ed25519 key pair.

Set permissions on the ssh public and private key

chmod 600 ~/.ssh/id_ed25519

chmod 644 ~/.ssh/id_ed25519.pub

Add github to known_hosts

ssh-keyscan github.com >> ~/.ssh/known_hosts

Set permissions on known_hosts

chmod 644 ~/.ssh/known_hosts

Reveal the public key and copy the ENTIRE SSH key displayed in the console

cat ~/.ssh/id_ed25519.pub

This is what the response will look like that you would need to copy

ssh-ed25519 AAAAC3NzaC1lZDI1NTE5AAAAILQNgvhF0wGnrsQlSgOOvPgCwwvG5Z9zlSLc7hbTYuWa scispot_jupyter_ssh

In your Github account, click the Github account settings icon in the top right corner

Click the settings page

Click the SSH and GPG keys page

Click new SSH key to your Github account

Name the SSH key "Scispot" and paste the ssh key into the key input. After, click "Add SSH key"

Confirm SSH key creation with your Github account password

Create a new private Github repo in your GIthub account or go to an existing one.

Once setup, go click on "Code" and switch to the "SSH" tab. Copy the SSH URL.

Now swap to JupyterLab and open up the terminal

In the terminal type "git clone " and paste (hotkey: shift + ins) the SSH URL you've copied earlier

This will clone the Github repo into a new folder, in this example it is the scispot-jupyterlab-scripts folder. Navigate to this folder then click on the Git extension tab on the left to open up the Git GUI.

Now after making some changes we can click this "+" button to stage our changes, add a commit message and then commit the change

If it's your first time commiting, you'll be prompted to add a name and email for this commit. This will be saved for any subsequent commit, but can be changed using Git commands

Now after commiting we can then click on this button to push to remote

You should then receive a notification on the bottom right of your screen with a success message.

Checking on Github you will then see the user that was setup from before pushing changes

We can also pull changed from remote using this button

Note: This is simply a tutorial on using the Git GUI. Any git commands are also available using the terminal.