| See the CUDA-enabled JupyterLab R docker stack for GPU accelerated docker images. |
|---|
Multi-arch (linux/amd64, linux/arm64/v8) docker images:
glcr.b-data.ch/jupyterlab/r/baseglcr.b-data.ch/jupyterlab/r/r-ver(4.0.4 ≤ version < 4.2.0)
glcr.b-data.ch/jupyterlab/r/tidyverseglcr.b-data.ch/jupyterlab/r/verseglcr.b-data.ch/jupyterlab/r/geospatialglcr.b-data.ch/jupyterlab/r/qgisprocess(versions ≥ 4.3.0)
Images considered stable for R versions ≥ 4.2.0.
👉 The current state may eventually be backported to versions ≥
4.0.4.
🔬 Check out jupyterlab/r/verse at
https://demo.jupyter.b-data.ch.
Build chain
base → tidyverse → verse → geospatial → qgisprocess
ℹ️ The term verse+ means verse or later in the build chain.
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.
- GRASS GIS: A free and open source Geographic Information System (GIS).
ℹ️ qgisprocess image - Orfeo Toolbox: An open-source project for state-of-the-art remote
sensing.
ℹ️ qgisprocess image (amd64 only) - Pandoc: A universal markup converter.
- Python: An interpreted, object-oriented, high-level programming language with dynamic semantics.
- QGIS: A free, open source, cross platform (lin/win/mac) geographical
information system (GIS).
ℹ️ qgisprocess image - Quarto: A scientific and technical publishing system built on Pandoc.
ℹ️ verse+ images - R: A language and environment for statistical computing and graphics.
- SAGA GIS: A Geographic Information System (GIS) software with immense
capabilities for geodata processing and analysis.
ℹ️ qgisprocess image - TinyTeX: A lightweight, cross-platform, portable, and easy-to-maintain
LaTeX distribution based on TeX Live.
ℹ️ verse+ images - Zsh: A shell designed for interactive use, although it is also a powerful scripting language.
👉 See the Version Matrix for detailed information.
The following extensions are pre-installed for code-server:
- .gitignore Generator
- Black Formatter
ℹ️ devtools subtags - Docker
ℹ️ docker subtags - EditorConfig for VS Code (4.3.0+)
- ESLint
ℹ️ devtools subtags - Git Graph
- GitHub Pull Requests and Issues (4.3.1+)
- GitLab Workflow
- GitLens — Git supercharged
ℹ️ Pinned to version 11.7.0 due to unsolicited AI content (4.3.1+) - hadolint
ℹ️ docker subtags (4.3.1+) - Excel Viewer
- Jupyter
- LaTeX Workshop
ℹ️ verse+ images - markdownlint (4.3.2+)
- Path Intellisense
- Prettier - Code formatter
ℹ️ devtools subtags - Project Manager
- Python
- Quarto
ℹ️ verse+ images - R
- Resource Monitor (4.3.0+)
- ShellCheck
ℹ️ devtools and docker subtags (4.3.1+) - YAML
Subtags
{R_VERSION,latest}-root(versions ≥ 4.2.0): Container runs asroot{R_VERSION,latest}-devtools(versions ≥ 4.2.2): Includes the requirements according to{R_VERSION,latest}-devtools-root: The combination of both{R_VERSION,latest}-docker(versions ≥ 4.2.2): Includesdocker-ce-clidocker-buildx-plugindocker-compose-plugindocker-scan-plugin(amd64 only)
{R_VERSION,latest}-docker-root: The combination of both{R_VERSION,latest}-devtools-docker: The combination of both{R_VERSION,latest}-devtools-docker-root: The combination of all three
This projects requires an installation of docker.
To install docker, follow the instructions for your platform:
- Install Docker Engine | Docker Documentation > Supported platforms
- Post-installation steps for Linux
latest:
cd base && docker build \
--build-arg R_VERSION=4.4.0 \
-t jupyterlab/r/base \
-f latest.Dockerfile .version:
cd base && docker build \
-t jupyterlab/r/base:MAJOR.MINOR.PATCH \
-f MAJOR.MINOR.PATCH.Dockerfile .For MAJOR.MINOR.PATCH ≥ 4.2.0.
Create an empty directory using docker:
docker run --rm \
-v "${PWD}/jupyterlab-jovyan":/dummy \
alpine chown 1000:100 /dummyIt will be bind mounted as the JupyterLab user's home directory and
automatically populated.
❗ Bind mounting a subfolder of the home directory is only possible
for images with R version ≥ 4.3.2.
self built:
docker run -it --rm \
-p 8888:8888 \
-u root \
-v "${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/r/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=$(id -g) \
-e CHOWN_HOME=yes \
-e CHOWN_HOME_OPTS='-R' \
IMAGE[:MAJOR[.MINOR[.PATCH]]]IMAGE being one of
glcr.b-data.ch/jupyterlab/r/baseglcr.b-data.ch/jupyterlab/r/tidyverseglcr.b-data.ch/jupyterlab/r/verseglcr.b-data.ch/jupyterlab/r/geospatialglcr.b-data.ch/jupyterlab/r/qgisprocess
The use of the -v flag in the command mounts the empty directory on the host
(${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 ${NB_GID}.
ℹ️ This is only required for the first run.
The server logs appear in the terminal.
Create an empty home directory:
mkdir "${PWD}/jupyterlab-root"Use the following command to run the container as root:
podman run -it --rm \
-p 8888:8888 \
-u root \
-v "${PWD}/jupyterlab-root":/home/root \
-e NB_USER=root \
-e NB_UID=0 \
-e NB_GID=0 \
-e NOTEBOOK_ARGS="--allow-root" \
IMAGE[:MAJOR[.MINOR[.PATCH]]]Creating a home directory might not be required. Also
docker run -it --rm \
-p 8888:8888 \
-v "${PWD}/jupyterlab-jovyan":/home/jovyan \
IMAGE[:MAJOR[.MINOR[.PATCH]]]might be sufficient.
❗ 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):
| Extension | Environment variable |
|---|---|
| GitHub Pull Requests and Issues | GITHUB_TOKEN: Personal access token with scopes repo and user.1 |
| GitLab Workflow | GITLAB_WORKFLOW_INSTANCE_URL: GitLab instance URL (e.g. https://gitlab.com).GITLAB_WORKFLOW_TOKEN: Personal access token with scopes api and read_user. |
What makes this project different:
- Multi-arch:
linux/amd64,linux/arm64/v8
👉 Since R 4.0.4 (2021-02-15)
ℹ️ Runs on Apple M series using Docker Desktop. - Base image: Debian instead of
Ubuntu
ℹ️ CUDA-enabled images are Ubuntu-based. - IDE: code-server instead of
RStudio
ℹ️ code-server = VS Code in the browser. - Just Python – no Conda / Mamba
See Notes for tweaks, settings, etc.
PRs accepted.
This project follows the Contributor Covenant Code of Conduct.
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.
Work partially funded by
MIT © 2020 b-data GmbH
Footnotes
-
Device activation may require a one-time login from the extension's sidebar. ↩
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