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tvb-ext-unicore

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TVB Widgets - A Unicore Lab extension

This jupyter extension offers a UI component to monitor HPC jobs through Unicore interface. It allows users to easily switch between computing sites, retrieve details about the jobs, and also cancel them.

The package is composed of a Python module named tvb_ext_unicore for the server extension and a NPM package named tvb-ext-unicore for the frontend extension.

As the extension provides access to different EBRAINS HPC sites, it needs your EBRAINS authentication token in order to work.

There are 2 options to use this extension:

  1. Directly in EBRAINS Lab: in this case, your token will be retrieved automatically (as you had to login for accessing the extension).
  2. Outside EBRAINS Lab: you will need to manually copy your authentication token from EBRAINS Lab and keep it in an environment variable called CLB_AUTH.

Requirements

  • JupyterLab version >= 4
  • pyunicore >= 1.0

Install

To install the extension, execute:

pip install tvb-ext-unicore

Uninstall

To remove the extension, execute:

pip uninstall tvb-ext-unicore

Troubleshoot

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

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:

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.

# Install external dependencies
pip install pyunicore

# Clone the tvb-ext-unicore repo to your local environment
# Change directory to the tvb-ext-unicore directory
cd tvb-ext-unicore
# Install package in development mode
pip install -e .
# 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 tvb_ext_unicore

# Define CLB_AUTH environment variable holding your EBRAINS token
export CLB_AUTH=${ebrains_token}

# Rebuild extension Typescript source after making changes
jlpm run 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.

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

Development uninstall

# Server extension must be manually disabled in develop mode
jupyter server extension disable tvb_ext_unicore
pip uninstall tvb-ext-unicore

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 tvb-ext-unicore within that folder.

Testing the extension

Server tests

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 . --overwrite

To execute them, run:

pytest -vv -r ap --cov tvb_ext_unicore

Frontend tests

This extension is using Jest for JavaScript code testing.

To execute them, execute:

jlpm
jlpm test

Packaging the extension

See RELEASE

Acknowledgments

This project has received funding from the European Union’s Horizon 2020 Framework Programme for Research and Innovation under the Specific Grant Agreement No. 945539 (Human Brain Project SGA3).

This project has received funding from the European Union’s Horizon Europe Programme under the Specific Grant Agreement No. 101147319 (EBRAINS 2.0 Project).