JupyterLab Python docker stack

Multi-arch (linux/amd64, linux/arm64/v8) docker images:

• glcr.b-data.ch/jupyterlab/python/base
• glcr.b-data.ch/jupyterlab/python/scipy

Images considered stable for Python versions ≥ 3.10.5.

:microscope: Check out jupyterlab/python/scipy at https://demo.jupyter.b-data.ch.

Build chain

base → scipy

Features

• JupyterLab: A web-based interactive development environment for Jupyter notebooks, code, and data. The images include
  • code-server: VS Code in the browser without MS branding/telemetry/licensing.
  • Git: A distributed version-control system for tracking changes in source code.
  • Git LFS: A Git extension for versioning large files.
  • Pandoc: A universal markup converter.
  • Python: An interpreted, object-oriented, high-level programming language with dynamic semantics.
  • Quarto: A scientific and technical publishing system built on Pandoc.
    :information_source: scipy image
  • TinyTeX: A lightweight, cross-platform, portable, and easy-to-maintain LaTeX distribution based on TeX Live.
    :information_source: scipy image
  • Zsh: A shell designed for interactive use, although it is also a powerful scripting language.

:point_right: See the Version Matrix for detailed information.

The following extensions are pre-installed for code-server:

• .gitignore Generator
• Black Formatter
  :information_source: devtools subtags
• Docker
  :information_source: docker subtags
• EditorConfig for VS Code (3.11.3+)
• ESLint
  :information_source: devtools subtags
• Git Graph
• GitHub Pull Requests and Issues (3.11.5+)
• GitLab Workflow
• GitLens — Git supercharged
  :information_source: Pinned to version 11.7.0 due to unsolicited AI content (3.11.4+)
• Excel Viewer
• hadolint
  :information_source: docker subtags (3.11.4+)
• Jupyter
• LaTeX Workshop
  :information_source: scipy image
• markdownlint (3.11.6+)
• Path Intellisense
• Prettier - Code formatter
  :information_source: devtools subtags
• Project Manager
• Python
• Quarto
  :information_source: scipy image
• Resource Monitor (3.11.4+)
• ShellCheck
  :information_source: devtools and docker subtags (3.11.4+)
• YAML

Subtags

• {PYTHON_VERSION,latest}-root (versions ≥ 3.10.5): Container runs as root
• {PYTHON_VERSION,latest}-devtools (versions ≥ 3.10.5): Includes the requirements according to
  • coder/code-server > Docs > Contributing
  • microsoft/vscode-python > Wiki > Coding
• {PYTHON_VERSION,latest}-devtools-root: The combination of both
• {PYTHON_VERSION,latest}-docker (versions ≥ 3.10.11, versions ≥ 3.11.2): Includes
  • docker-ce-cli
  • docker-buildx-plugin
  • docker-compose-plugin
  • docker-scan-plugin (amd64 only)
• {PYTHON_VERSION,latest}-docker-root: The combination of both
• {PYTHON_VERSION,latest}-devtools-docker: The combination of both
• {PYTHON_VERSION,latest}-devtools-docker-root: The combination of all three

Table of Contents

• Prerequisites
• Install
• Usage
• Similar projects
• Contributing
• Support
• License

Prerequisites

This projects requires an installation of docker.

Install

To install docker, follow the instructions for your platform:

• Install Docker Engine | Docker Documentation > Supported platforms
• Post-installation steps for Linux

Usage

Build image (base)

latest:

cd base && docker build \
  --build-arg PYTHON_VERSION=3.12.2 \
  -t jupyterlab/python/base \
  -f latest.Dockerfile .

version:

cd base && docker build \
  -t jupyterlab/python/base:MAJOR.MINOR.PATCH \
  -f MAJOR.MINOR.PATCH.Dockerfile .

For MAJOR.MINOR.PATCH ≥ 3.10.5.

Create home directory

Create an empty directory using docker:

docker run --rm \
  -v "${PWD}/jupyterlab-jovyan":/dummy \
  alpine chown 1000:100 /dummy

It will be bind mounted as the JupyterLab user's home directory and automatically populated.
:exclamation: Bind mounting a subfolder of the home directory is only possible for images with Python version ≥ 3.12.2.

Run container

self built:

docker run -it --rm \
  -p 8888:8888 \
  -u root \
  -v "${PWD}/jupyterlab-jovyan":/home/jovyan \
  -e NB_UID=$(id -u) \
  -e NB_GID=$(id -g) \
  -e CHOWN_HOME=yes \
  -e CHOWN_HOME_OPTS='-R' \
  jupyterlab/python/base[:MAJOR.MINOR.PATCH]

from the project's GitLab Container Registries:

docker run -it --rm \
  -p 8888:8888 \
  -u root \
  -v "${PWD}/jupyterlab-jovyan":/home/jovyan \
  -e NB_UID=$(id -u) \
  -e NB_GID=$(id -g) \
  -e CHOWN_HOME=yes \
  -e CHOWN_HOME_OPTS='-R' \
  IMAGE[:MAJOR[.MINOR[.PATCH]]]

IMAGE being one of

• glcr.b-data.ch/jupyterlab/python/base
• glcr.b-data.ch/jupyterlab/python/scipy

The use of the -v flag in the command mounts the empty directory on the host (${PWD}/jupyterlab-jovyan in the command) as /home/jovyan in the container.

-e NB_UID=$(id -u) -e NB_GID=$(id -g) instructs the startup script to switch the user ID and the primary group ID of ${NB_USER} to the user and group ID of the one executing the command.

-e CHOWN_HOME=yes -e CHOWN_HOME_OPTS='-R' instructs the startup script to recursively change the ${NB_USER} home directory owner and group to the current value of ${NB_UID} and ${NB_GID}.
:information_source: This is only required for the first run.

The server logs appear in the terminal.

Using Podman (rootless mode, 3.11.6+)

Create an empty home directory:

mkdir "${PWD}/jupyterlab-root"

Use the following command to run the container as root:

podman run -it --rm \
  -p 8888:8888 \
  -u root \
  -v "${PWD}/jupyterlab-root":/home/root \
  -e NB_USER=root \
  -e NB_UID=0 \
  -e NB_GID=0 \
  -e NOTEBOOK_ARGS="--allow-root" \
  IMAGE[:MAJOR[.MINOR[.PATCH]]]

Using Docker Desktop

Creating a home directory might not be required. Also

docker run -it --rm \
  -p 8888:8888 \
  -v "${PWD}/jupyterlab-jovyan":/home/jovyan \
  IMAGE[:MAJOR[.MINOR[.PATCH]]]

might be sufficient.

Credential storage

:exclamation: Keyring services are not available due to the difficulties of setting them up in containers.
Therefore, provide login credentials for the following extensions as environment variables (-e):

[^1]: Device activation may require a one-time login from the extension's sidebar.

Similar projects

• jupyter/docker-stacks
• geocompx/docker

What makes this project different:

1. Multi-arch: linux/amd64, linux/arm64/v8
   :information_source: Runs on Apple M series using Docker Desktop.
2. Base image: Debian instead of Ubuntu
   :information_source: CUDA-enabled images are Ubuntu-based.
3. IDE: code-server next to JupyterLab
   :information_source: code-server = VS Code in the browser.
4. Just Python – no Conda / Mamba

See Notes for tweaks, settings, etc.

Contributing

PRs accepted.

This project follows the Contributor Covenant Code of Conduct.

Support

For commercial support, please contact b-data by email: [email protected].

b-data tailors the JupyterLab images to your needs, e.g.

• Integration of self-signed CA certificates to enable communication with web services on the intranet.
• Setting up the necessary environment variables so that everything works behind a corporate proxy server.

Additionally, the JupyterHub setup can be customised to allow

• authentication with AD/LDAP
• mounting CIFS/SMB file shares

and much more.

License

MIT © 2022 b-data GmbH