date_revised	2022/06/15
revised_by	wfordwfu

WFBMI Jupyter Lab Devcontainer

A Jupyter devcontainer datascience solution based on the Jupyter/Docker-Stacks solution.

• WFBMI Jupyter Lab Devcontainer
  • Getting Started
    • Tools to install locally
  • Useful Docker commands to know
  • Jupyter commands
  • Other helpful things:
  • Jupyter Magics
  • Issues
  • Reference

Getting Started

Access Jupyter Lab

• Make sure server is running jupyter server list
• From shell run ./jupyter.sh or go to http://localhost:8888/lab

Tools to install locally

• Docker Desktop - Ideally install from Software Center
• VS Code
• VS Code Remote Containers Extension

Useful Docker commands to know (Run outside VS Code)

These are useful if you JupyterLab instance has locked up

• docker ps list running containers
• docker kill $(docker ps -q) stop any running containers
• docker rm $(docker ps -aq) remove any stopped containers
• docker logs wfbmi-dev If you need to get the url\token to log back into your instance

Jupyter commands

Start here: How to use Jupyter Lab (YouTube)

Think of a jupyter notebook interface like VIM lite. You can use your mouse, but you can navigate jupyter via keyboard much faster.

• To enter a cell: enter
• To run a cell: ctrl-enter
• To run a cell and create a new one: shift-enter
• To exit a cell back to command mode: escape

When in command mode you have commands like this:

• Basic navigation: enter, shift-enter, up/k, down/j
• Saving the notebook: s
• Change Cell types: y, m, 1-6, t
• Cell creation: a, b
• Cell editing: x, c, v, d, z
• Kernel operations: i, 0 (press twice)

Other helpful things:

• If you need a package and it's not installed, you can run pip install x directly within a code cell. Jupyter will know what to do.
• If you need help with a function you can type it into a cell followed by ? and run print?
• While writing code, hitting Tab will display hints

Jupyter Magics

Lots to learn here, but this is a good starting list

• %lsmagic list of magic commands.
• %run <file name>.py to run an external python file within your jupyter notebook.
• %%time at the top of a code block will return the execution time
• %who list all the current variables in a notebook
• %pinfo <variable> query specifics about a given variable in a notebook
• %env list all the environment variables
• %env FOO=Bar set the value of a new environment variable

There's lots more to explore about Jupyter:

• Check out the help menu in JupyterLab
• Jupyter lab docs
• Jupyter Docker Stacks
• jupyter notebook docs
• jupyter docker stacks
• Example Notebooks

Issues

• nbconvert changed a value in version 6.0 and many jupyter related packages haven't updated
  • Example error "Config option template_path not recognized by *. Did you mean one of: extra_template_paths, template_name, template_paths?"

Reference

• Devcontainer Spec
• Based on the Microsoft provided mod of datascience jupyter stack
• Devcontainer/CLI

Feature Ideas

• xeus-sqlite
  • conda install xeus-sqlite jupyterlab -c conda-forge