Configure the shell environment for notebook kernels

While the terminal in the Notebook Aspect sources ~/.bashrc, Jupyter Notebook kernels do not. Instead, you can configure the environment for Jupyter notebooks with the ~/notebooks/.user_setups file. With this file, you can set up environment variables and even set up LSST Science Pipelines packages, for your Jupyter notebooks.

Export environment variables for notebooks

The ~/notebooks/.user_setups file is sourced by bash. This means you can include any valid bash syntax.

For example, you can define environment variables that are accessible from notebooks:

export MYVAR="My env var"

Note

Environment variables exported from ~/.bashrc are not accessible from notebooks. You need to export those variables from ~/notebooks/.user_setups instead.

Customizing the EUPS package set up

The main use for ~/notebooks/.user_setups is setting up a package that you’ve locally cloned and built. See Customizing the EUPS package setup (~/notebooks/.user_setups) for an example.

Updating ~/notebooks/.user_setups for a running notebook kernel

If you need to change package setups or environment variables for an already-opened notebook, follow these steps:

1. Edit and save the ~/notebooks/.user_setups file.

2. Return to your notebook’s tab and restart the kernel (Kernel → Restart Kernel).

You’ll need to rerun your notebook’s cells after restarting the kernel.

Tip: source ~/notebooks/.user_setups to verify it

Since ~/notebooks/.user_setups is a bash script, it’s sensitive to syntax errors. You won’t be alerted to syntax errors when you start a new notebook kernel, though.

The best way to check that your ~/notebooks/.user_setups file is correct is by sourcing it from a terminal:

source ~/notebooks/.user_setups

Note

If ~/notebooks/.user_setups includes a setup command, ensure that you have set up the LSST environment in the terminal first.