Overview

This article describes how to add your mamba environments to Jupyter to use as a notebook kernel. You can learn about creating mamba environments in Managing Python Modules Through the Mamba Environment Manager.

Creating the Jupyter Kernel

The following command will create a jupyter kernel from an existing mamba environment:

This takes the environment called nobel and creates a Jupyter kernel for it. When creating a new notebook, it will have an Icon labeled nobel

Use the Environment in Jupyter Hub

In the web portal, create a new interactive session after selecting Jupyter from the server list. The new kernel is now available for driving notebooks!

Removing a Kernel from the Web App

From the terminal, execute the following commands (once again assuming a fresh shell session).

This will only remove the kernel entry in Jupyter and does not affect the environment.

Creating Kernels from a Data Directory

Since the command above only works for environments installed in the user’s home, to make a kernel from environments installed in /data directory:

1. If needed, re-create the env in this /data directory, then each user in your group can access this env and make a kernel from it.

2. Activate the env

3. Once the env is activated, install "ipykernel" with mamba: mamba install -c anaconda ipykernel

4. Then each user can make a kernel from this env for themselves: 

   1. They need to activate this env first by source activate ENV

   2. python -m ipykernel install --user --name=<exact name of the env>

Additional Help

If you require further assistance on this topic, please contact the Research Computing Team. To create a support ticket review our RTO Request Help page. For quick inquiries, reach out via our #rc-support Slack Channel or attend our office hours for live assistance.

We also offer a series of Educational Opportunities and Workshops.