Jupyter Environment Management for Dummies

Andrew Bolster

Senior R&D Manager (Data Science) at Synopsys Software Integrity Group and Treasurer @ Bsides Belfast and NI OpenGovernment Network

This is another one of those “I kept googling the same thing over and over again” things that needed a post, except this time I made an issue to make a post and then started to repeatedly refer to that.

TL;DR

When you want to spin up an experimental environment and get it tied in to your Jupyter environment of choice (I actually quite like JupyterLab Desktop these days…), you need two steps.

# Create the conda environment with $NAME and ipykernel as the main dependency
conda create --name $NAME ipykernel && conda activate

# Once you're in the new environment, add it to the _global_ (There may be a better `kernelspec` way to do this but I haven't done it yet.)
ipython kernel install --name=$CONDA_DEFAULT_ENV --user

... Do real work here ...

# If you messed up and need to nuke it from orbit without wiping out the rest of your env;
jupyter kernelspec uninstall $NAME

BTW it can sometimes take a few minutes/interactions to coax Jupyterlab into identifying the new kernel.

Aside on Kernel Names

There’s also a trick to getting the current kernel name in a Notebook that doesn’t abuse any magic functions

import sys
import os
kernel_name = os.path.basename(sys.executable.replace("/bin/python",""))

But what does abuse the magic string is then using that in-kernel python variable to do the out of kernel invocation of the ‘correct’ install incantation;

Reminder:

  • !command runs the command in shell of the jupyterlab runner (so you can install jupyter extensions etc from a running notebook.)
    • e.g. !which python which give you the system python of the runtime the jupyterlab runner is executing in, not the notebook kernel
  • %command are a small subset of magic commands for interacting with the notebook kernel
    • e,g. %conda install -y -q <requirement> or %pip install -yq <requirement> DON’T COPY PASTE THESE YET

However some environment setups (particularly conda related ones) cause a bit of mayhem, so for instance when you run the magic of %conda env list, you may get a response back that has a * beside the ‘base’ environment, which is a bit wrong coming from a notebook we just created above.

To be sure that you’re actually installing things in the right environment, this works;

import sys
import os
kernel_name = os.path.basename(sys.executable.replace("/bin/python",""))
%conda install -y -n $kernel_name magicalpackagenamethatsdefinitelynotahallucination

Published: January 17 2024

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