JupyterLab

Jupyter Startup

The container uses conda to manage environments. Jupyter is automatically started from jupyter_env.

All other dependencies for working in jupyter lab are installed in worker_env. You can extend this environment at runtime, or create your own environments using conda or venv.

The default is to choose worker_env as your Kernel after starting JupyterLab and creating a new notebook.

Also have a look at the excellent Jupyter Docs.

Takeaway:

  • There is a base environment prepared with the name worker_env. You can select this environment from the list of known kernels (e.g. from the top right corner in a JupyterLab notebook).

  • The Jupyter server is installed in a separate environment named jupyter_env.

Creating a custom environment

There are many ways to do this. One example is to use venv.

  1. Create a new empty environment somewhere from within a notebook cell
!python -m venv ./wikidata_venv

Note

the ! tells Jupyter to treat the cell code as bash instructions, not as Python.

  1. Install packages to the newly created venv
./wikidata_venv/bin/python -m pip install qwikidata ipykernel pandas
  1. Make the Kernel available in JupyterLab

In order to select the Kernel on the top-right corner in a Jupyter notebook, install (link) ipykernel to the venv.

./wikidata_venv/bin/python -m ipykernel install --user --name=qwikidata

See further information and alternatives under Task Guide: Updating packages and custom envs.

Tip

See an example in this notebook, where I added a further check to prevent re-installation, if the package or environment already exists.

In this notebook, a helper script pkginstall.sh is used to reduce the effort for maintaining environments and package installs. Find the tool in this repository.