Context
Ensuring seamless synchronization and backup of files is crucial for researchers, scientists, and data enthusiasts leveraging platforms like the WEkEO JupyterHub. With the integration of the JupyterHub GitHub Plugin, users gain a powerful solution to effortlessly synchronize their work on the JupyterHub environment with GitHub repositories. This seamless integration not only facilitates efficient collaboration but also provides a reliable backup mechanism, offering peace of mind in the face of potential data loss or system disruptions. Whether working on complex data analysis projects or collaborative research endeavors, the JupyterHub GitHub Plugin empowers users to maintain version control, enhance productivity, and safeguard their valuable work effectively.
⚠️ Please note, that the files which can be uploaded to GitHub are limited to 50 MB each. Therefore, we further recommend to store large files outside of the working folder (but be aware that they will not be backed up).
Tutorial
Step 1. create a GitHub Account
Log in to the site and follow the steps to create an account or log in to an existing account: GitHub.
Step 2. Create a new repository for the WEkEO JupyterHub backup
Access your repositories and create a new one
Create a file inside the repository to check the synchronization later
Step 3. Log into the WEkEO JupyterHub
From the WEkEO home page, log in to your WEkEO account, then launch the WEkEO JupyterHub via its icon in the top right-hand corner.
Step 4. Create an ssh key for authenticating with GitHub
Execute the following code in the terminal inside the WEkEO JupyterHub:
ssh-keygen -t ed25519 -C "email@email.com"
replace the email@email.com with the email address you used for setting up the github account
Step 5: Add the SSH key to you github account
Go here: SSH and GPG keys (github.com)
Copy the public key which is saved in your Jupyterhub files and enter it in the github page. You can execute the following code in the terminal inside the JupyterHub to see the key:
nano /home/jovyan/.ssh/id_ed25519.pub
where the path is the one in which your public key has been saved.
Check if the ssh set up was successful. Execute the following code in the terminal inside the WEkEO JupyterHub:
ssh -T git@github.com
You may see a warning like this:
> The authenticity of host 'github.com (IP ADDRESS)' can't be established.> ED25519 key fingerprint is SHA256:+DiY3wvvV6TuJJhbpZisF/zLDA0zPMSvHdkr4UvCOqU.
> Are you sure you want to continue connecting (yes/no)?Enter “yes”
You should now see a message like this in the terminal
Hi <username>! You've successfully authenticated, but GitHub does not provide shell access.
Step 6: Go to the Git Extension button and Clone the repository you set up in step 2
On the WEkEO JupyterHub on the left, you'll find the Git extension with its button. Then click on Clone a Repository.
Go to your Github repository on the GitHub site and copy the URL.
Then paste it into WEkEO JupyterHub.
Now the github repository appears in the JupyterHub working directory
Step 8. enable the ssh key for the repository
(you only should have to do this once for each repository)
In the terminal go to your repository
cd wekeo_backup
and type:
git remote set-url origin git@github.com:<gitaccount>/wekeo_backup.git
replace<gitaccount> with your actual gitHub account name
Step 9. Create a file in the WEkEOJupyterHub
In your cloned github repository create, for example, a new notebook:
Once the File is created you see that there are untracked changes in the git section:
Step 10. Sync the JupyterHub with GitHub
Method 1. Using the git extension graphical interface
Track changes by clicking the + when you slide the mouse over the “untracked” section
The changes will now appear in the section “Staged”
Commit the changes by filling out the “Summary” and a description of the changes in the bottom of the menu
Click on Commit
Enter your name and email
When the commit was successful, a confirmation will appear on the bottom of the page
Push the committed changes to your GitHub repository
You can now see that your repository version inside the JupyterHub is one commit ahead of the version in GitHub. Push the commits to GitHub to synchronize both versions by clicking on the button (
)
Because you set up the ssh connection this works now without your username and password
Method 2. Using git in the command line
Let's create another notebook called “test2_notebook.ipynb”
In the terminal go to the wekeo_backup folger and type
git status
You will get the untracked files here
On branch main
Your branch is up to date with 'origin/main'.
Untracked files:
(use git add <file>... to include in what will be committed)
.ipynb_checkpoints/test2_notebook-checkpoint.ipynb
test2_notebook.ipynb
nothing added to commit but untracked files present (use "git add" to track)
Next we stage the changes using (stace all changes by adding the -A )
git add -A
Next, we commit the changes and add a commit message
git commit -am "added additional notebook and push using command line"
Next, we push it in the command line using
git push
Step 11. Check if the push worked
We see that the notebooks are now available in our GitHub repository
That's it, you've successfully configured your GitHub with your WEkEO JupyterHub. You can now synchronize your files! 💪
What's next?
We are user-driven and we implement users' suggestions, so feel free to contact us:
through a chat session available in the bottom right corner of the page
via our contact webpage
via e-mail to our support team (supportATwekeo.eu)