embl-tools-jl

Copyright (c) 2020, Dr. Nandor Poka

Distributed under the terms of the 3-clause BSD License.

An extension adding Launcher shortcuts to JupyterLab for EMBL Tools.

This extension is composed of a Python package named embl_tools_jl for the server extension and a NPM package named embl-tools-jl for the frontend extension.

Preview

Requirements

• JupyterLab >= 2.0

Scanning for the tools can take long and thus delay the startup of JupyterLab. It is recommended to put EMBL-Tools in the root of your regular work directory you use JupyterLab in. If the scan does not find the EMBL-Tools in the current Jupyter Lab working dir root, the extension will copy the supplied version for temporary use. This copy will be removed at the next startup.

Quick Install

Note: You will need NodeJS to install the extension.

pip install embl_tools_jl
jupyter lab build

Troubleshoot

If you are seeing the frontend extension but it is not working, check that the server extension is enabled:

jupyter serverextension list

If the server extension is installed and enabled but you are not seeing the frontend, check the frontend is installed:

jupyter labextension list

If it is installed, try:

jupyter lab clean
jupyter lab build

Contributing

Install

The jlpm command is JupyterLab's pinned version of yarn that is installed with JupyterLab. You may use yarn or npm in lieu of jlpm below.

# Clone the repo to your local environment
# Move to embl-tools-jl directory

# Install server extension
pip install -e .
# Register server extension
jupyter serverextension enable --py embl_tools_jl

# Install dependencies
jlpm
# Build Typescript source
jlpm build
# Link your development version of the extension with JupyterLab
jupyter labextension link .
# Rebuild Typescript source after making changes
jlpm build
# Rebuild JupyterLab after making any changes
jupyter lab build

You can watch the source directory and run JupyterLab in watch mode to watch for changes in the extension's source and automatically rebuild the extension and application.

# Watch the source directory in another terminal tab
jlpm watch
# Run jupyterlab in watch mode in one terminal tab
jupyter lab --watch

Uninstall

pip uninstall embl_tools_jl

jupyter labextension uninstall embl-tools-jl