A jupyterLab extension for the fairly package, and the seamless integration of Jupyter-based research environments and research data repositories.
This extension is composed of a Python package named jupyter_fairly
for the server extension and a NPM package named jupyter-fairly
for the frontend extension.
- JupyterLab >= 3.0 < 4
- fairly == 0.4.1
This is the last version that supports JupyterLab 3.x.
To install the extension, execute:
pip install jupyter_fairlyConfigurations are stored in .fairly/config.json in the user's home directory. This is where the extension stores access tokens for data repositories.
To add an access tokens, use the Fairly menu in the JupyterLab main menu bar.
To remove the extension, execute:
pip uninstall jupyter_fairlyIf you are seeing the frontend extension, but it is not working, check that the server extension is enabled:
jupyter server extension listIf the server extension is installed and enabled, but you are not seeing the frontend extension, check the frontend extension is installed:
jupyter labextension listNote: You will need NodeJS to build the extension package.
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
# Change directory to the jupyter_fairly directory
# Install package in development mode
pip install -e ".[test]"
# Link your development version of the extension with JupyterLab
jupyter labextension develop . --overwrite
# Server extension must be manually installed in develop mode
jupyter server extension enable jupyter_fairly
# Rebuild extension Typescript source after making changes
jlpm buildYou can watch the source directory and run JupyterLab at the same time in different terminals to watch for changes in the extension's source and automatically rebuild the extension.
# Watch the source directory in one terminal, automatically rebuilding when needed
jlpm watch
# Run JupyterLab in another terminal
jupyter labWith the watch command running, every saved change will immediately be built locally and available in your running JupyterLab. Refresh JupyterLab to load the change in your browser (you may need to wait several seconds for the extension to be rebuilt).
By default, the jlpm build command generates the source maps for this extension to make it easier to debug using the browser dev tools. To also generate source maps for the JupyterLab core extensions, you can run the following command:
jupyter lab build --minimize=False# Server extension must be manually disabled in develop mode
jupyter server extension disable jupyter_fairly
pip uninstall jupyter_fairlyIn development mode, you will also need to remove the symlink created by jupyter labextension develop
command. To find its location, you can run jupyter labextension list to figure out where the labextensions
folder is located. Then you can remove the symlink named jupyter-fairly within that folder.
This extension is using Pytest for Python code testing.
Install test dependencies (needed only once):
pip install -e ".[test]"
# Each time you install the Python package, you need to restore the front-end extension link
jupyter labextension develop . --overwriteTo execute them, run:
pytest -vv -r ap --cov jupyter_fairlyThis extension is using Jest for JavaScript code testing.
To execute them, execute:
jlpm
jlpm testThis extension uses Playwright for the integration tests (aka user level tests). More precisely, the JupyterLab helper Galata is used to handle testing the extension in JupyterLab.
More information are provided within the ui-tests README.
See RELEASE
Please cite this software using as follows:
Garcia Alvarez, M., Girgin, S., & Urra Llanusa, J., Jupyter-fairly: a JupyterLab extension for the fairly pacakage [Computer software]
This research is funded by the Dutch Research Council (NWO) Open Science Fund, File No. 203.001.114.
Project members: