JupyterLab Requirements

This is a JupyterLab extension for dependency management and optimization created to guarantee reproducibility of Jupyter notebooks.

About

This extension provides management of dependencies for JupyterLab notebooks.

The main goals of the project are the following:

• manage notebook requirements without leaving the notebook
• provide a unique and optimized environment for each notebook

NOTE: The requirements are optimized using the Thoth resolution engine.

Installation

This extension requires:

• JupyterLab >= 3.1.0

The extension can be installed via pip or Pipenv from PyPI:

pip install jupyterlab-requirements

You can initialize JupyterLab and start using it.

jupyter lab

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

Usage

There are 3 ways to interact with this extension:

• %horus magic commands directly in your notebook's cells.
• horus CLI from terminal or integrated in pipelines.
• jupyterlab-requirements UI accessible through Manage Dependencies button that appears in the notebook when it is opened in JupyteLab.

Resolution engines

There are currently two resolution engines available in the extension:

• Thoth
• Pipenv

NOTE: Thoth is used by default and Pipenv can be triggered with flags or run as backup automatically.

NOTE: Currently this extension supports only Python kernels.

Thoth

Using the Thoth resolution engine you can request an optimized software stack that satisfies your requirements.

Thoth: recommendation type

You can choose the type of recommendation that better fits your needs:

• latest (default)
• performance
• security
• stable
• testing

You can find more information and updates here.

Thoth: runtime environment

Thoth resolution engine is able to provide an optimized software stack based on the runtime environment you are using (several inputs are used, if you want to know more, have a look here here).

In general different runtime environment will provide different effect on you application (e.g. more performance), therefore we include these information in the notebook metadata so that other can find out what runtime environment has been used to run a certain notebook.

You can select the runtime environment to be used for the recommendation selecting:

• Operating System Name
• Operating System Version
• Python Interpreter Version

NOTE: Those parameters are autodiscovered by the extension and assigned to your environment, you can customize them if you are interested.

Dependencies installation

Once lock file is created using any of available resolution engines, the dependencies will be installed in the virtualenv using micropipenv.

Virtual environment for you dependencies

The virtual environment created and assigned to the kernel to be used for your notebook according to your dependencies requirements can be checked using the following command from a terminal:

cat ~/.local/share/thoth/kernels/{kernel_name}

Overlays directory

The dependencies stored in the notebook metadata can be also stored into overlays folder using the kernel name by default. If you want to know more about the use of overlays, have a look micropipenv. If you want to see a practical example on the use of overlays and how to create them from your notebook, you can check this tutorial.

Delete kernels

If you have too many kernels, you can remove them directly from the JupyterLab menu under Kernel Section. This plugin is provided from this extension.

Reproducibility

You can use this extension for each of your notebook to guarantee they have the correct dependencies files required for reproducibility and shareability. In this way, all the dependencies information required to repeat the environment are shipped with the notebook. In the notebook metadata you will find:

key	notes
requirements	All packages required (direct dependencies).
requirements	All packages (direct and transitive dependencies) locked with all hashes (Pipfile.lock).
dependency resolution engine	Currently two resolution engine are enabled.
configuration file	Only for Thoth resolution engine.

All this information can allow reproducibility of the notebook.

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.

1. Fork this repository
2. Clone the origin repo to your local environment

git clone [email protected]:thoth-station/jupyterlab-requirements.git

3. Change directory to the jupyterlab-requirements directory
4. Create new virtualenv

pipenv install --dev

5. Enter environment.

pipenv shell

All following commands needs to be run from the virtualenv created and accessed with command in point 5.

6. Install package in development mode

pip install -ve . --no-cache-dir

7. Link your development version of the extension with JupyterLab

jupyter labextension develop . --overwrite

jupyter serverextension enable --py jupyterlab-requirements --sys-prefix

8. 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.

The following command watch the source directory in one terminal, automatically rebuilding when needed.

jlpm run watch

The following command 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

9. Run tests using the command

python3 setup.py test

When all tests passed and you are ready with a new contribution open a Pull Request!! We are very happy to receive contributions from the community!

Demo development status and new features

• v0.13.0 [Nov 22 2021]
• v0.11.0 [Sep 13 2021]
• v0.10.4 [Aug 10 2021]
• v0.9.2 [Jul 19 2021]
• v0.8.0 [Jul 9 2021]
• v0.7.4 [Jun 22 2021]
• v0.5.0 [Mar 15 2021]
• v0.3.7 [Feb 10 2021]
• v0.1.0 [Dec 8 2020]

Uninstall

pip uninstall jupyterlab-requirements