eshernan/scijava-jupyter-kernel

Write SciJava scripts in Jupyter notebook!

scijava-jupyter-kernel

scijava-jupyter-kernel aims to be a polyglot Jupyter kernel. It uses the Scijava scripting languages to execute the code in Jupyter client and it's possible to use different languages in the same notebook.

Some of the supported languages are Groovy (default), Python, Beanshell, Clojure, Java, Javascript, Ruby and Scala.

The kernel has been originally created to work with ImageJ. See here for more details.

Under the hood scijava-jupyter-kernel uses the Beaker base kernel.

Binder Usage

• ImageJ notebook
• JupyterLab

Documentation

A documentation is available as a series of notebooks here.

Installation

• Install Anaconda
• Install scijava-jupyter-kernel with :

# Add the conda-forge channel
conda config --add channels conda-forge

# Create an isolated environment called `java_env` and install the kernel
conda create --name java_env scijava-jupyter-kernel

• Usage :

# Activate the `java_env` environment
source activate java_env

# Check the kernel has been installed
jupyter kernelspec list

# Launch your favorite Jupyter client
jupyter notebook

# or
jupyter lab

Note : It is strongly suggested to install the kernel in an isolated Conda environment (not in the root environment).

Development

• CI with Travis makes sure the project builds without errors for each new commit.
• A test notebook is executed during CI with nbconvert.
• A Conda package is built for each new release.

License

Under Apache 2.0 license. See LICENSE.

Authors

• Hadrien Mary [email protected]