HOWTO: Use a Conda/Virtual Environment With Jupyter

The IPython kernel for a Conda/virtual environment* must be installed on Jupyter prior to use.

Install kernel

To perform the kernel installation, users should load the preferred version of Python*

module load python

and run one of the following commands, depending on how your Conda/virtual environment being created. Make sure to replace MYENV with the name of your conda environment or path to the environment.

if the Conda environment is created via conda create -n MYENV

~support/classroom/tools/create_jupyter_kernel conda MYENV

if the Conda environment is created via conda create -p /path/to/MYENV

~support/classroom/tools/create_jupyter_kernel conda /path/to/MYENV

if the Python virtual environment is created via python3 -m venv /path/to/MYENV

~support/classroom/tools/create_jupyter_kernel venv /path/to/MYENV

Install Jupyterlab Debugger kernel

According to Jupyterlab page, debugger requires ipykernel >= 6. Please create your own kernel with conda using the following commands:

$ module load miniconda
$ conda create -n jupyterlab-debugger -c conda-forge "ipykernel>=6" xeus-python
$ ~support/classroom/tools/create_jupyter_kernel conda jupyterlab-debugger

You should see a kernelspec 'conda_jupyterlab-debugger' created in home directory. Once the debugger kernel is done, you can use it:
1. go to OnDemand
2. request a JupyterLab app with kernel 3
3. open a notebook with the debugger kernel.
4. you can enable debug mode at upper-right kernel of the notebook

Remove kernel

If the envirnoment is rebuilt or renamed, users may want to erase any custom jupyter kernel installations.

rm -rf ~/.local/share/jupyter/kernels/${MYENV}

Manually install kernel

If the create_jupyter_kernel script does not work for you, try the following steps to manually install kernel:

# change to the proper version of python
module load python  

# replace with the name of conda env           
MYENV=useful-project-name

# Activate your conda/virtual environment
## For Conda environment
source activate $MYENV

# ONLY if you created venv instead of conda env
## For Python Virtual environment
source /path/to/$MYENV/bin/activate

# Install Jupyter kernel 
python -m ipykernel install --user --name $MYENV --display-name "Python ($MYENV)"