Jupyter Fairly

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.

Requirements

• JupyterLab >= 3.0 < 4
• fairly == 0.4.1

This is the last version that supports JupyterLab 3.x.

Install

To install the extension, execute:

bash pip install jupyter_fairly

Configurations 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.

Uninstall

To remove the extension, execute:

bash pip uninstall jupyter_fairly

Troubleshoot

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

bash jupyter server extension list

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

bash jupyter labextension list

Contributing

Development install

Note: 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.

```bash

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 build ```

You 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.

```bash

Watch the source directory in one terminal, automatically rebuilding when needed

jlpm watch

Run JupyterLab in another terminal

jupyter lab ```

With 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:

bash jupyter lab build --minimize=False

Development uninstall

```bash

Server extension must be manually disabled in develop mode

jupyter server extension disable jupyterfairly pip uninstall jupyterfairly ```

In 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.

Testing the extension

Server tests

This extension is using Pytest for Python code testing.

Install test dependencies (needed only once):

```sh pip install -e ".[test]"

Each time you install the Python package, you need to restore the front-end extension link

jupyter labextension develop . --overwrite ```

To execute them, run:

sh pytest -vv -r ap --cov jupyter_fairly

Frontend tests

This extension is using Jest for JavaScript code testing.

To execute them, execute:

sh jlpm jlpm test

Integration tests

This 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.

Packaging the extension

See RELEASE

Citation

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]

Acknowledgements

This research is funded by the Dutch Research Council (NWO) Open Science Fund, File No. 203.001.114.

Project members:

• Center of Expertise in Big Geodata Science, University of Twente, Faculty ITC
• Digital Competence Centre, TU Delft
• 4TU.ResearchData