genepattern/lab repository overview

⁠nbtools for JupyterLab

nbtools is a framework for creating user-friendly Jupyter notebooks that are accessible to both programming and non-programming users. It is a core component of the GenePattern Notebook environment⁠. The package provides:

• A decorator which can transform any Python function into an interactive user interface.
• A toolbox interface for encapsulating and adding new computational steps to a notebook.
• Flexible theming and APIs to extend the nbtools functionality.
• A WYSIWYG editor for markdown cells (provided as part of the accompanying juptyter-wyswyg package and coming soon to JupyterLab).

Prerequisites

• JupyterLab >= 2.0.0
• ipywidgets >= 7.0.0

⁠Docker

A Docker image with nbtools and the full JupyterLab stack is available through DockerHub.

docker pull genepattern/lab
docker run --rm -p 8888:8888 genepattern/lab

⁠Installation

JupyterLab support is in beta. For now you will need to either install the specific prerelease version from pip or install from GitHub:

jupyter labextension install @jupyter-widgets/jupyterlab-manager
pip install nbtools==20.10a1
jupyter labextension install nbtools

OR

# Install ipywidgets, if you haven't already
jupyter nbextension enable --py widgetsnbextension
jupyter labextension install @jupyter-widgets/jupyterlab-manager

# Clone the nbtools repository
git clone https://github.com/genepattern/nbtools-lab-prototype.git
cd nbtools-lab-prototype

# Install the nbtools JupyterLab prototype
pip install .
jupyter labextension install .
jupyter nbextension install --py nbtools --sys-prefix
jupyter nbextension enable --py nbtools --sys-prefix

In the future you will be able to install using pip:

pip install nbtools

Or if you use jupyterlab:

pip install nbtools
jupyter labextension install @jupyter-widgets/jupyterlab-manager
jupyter labextension install @genepattern/nbtools

If you are using Jupyter Notebook 5.2 or earlier, you may also need to enable the nbextension:

jupyter nbextension enable --py [--sys-prefix|--user|--system] nbtools

⁠Development

For a development install (requires npm version 4 or later), do the following in the repository directory:

npm install
jupyter labextension link .

To rebuild the package and the JupyterLab app:

npm run build:all
jupyter lab build

⁠Getting Started

Let's start by writing a simple Hello World function and turning it into an interactive widget. Go ahead and install nbtools, launch Jupyter and open a new, blank notebook.

Once that's completed, let's write a basic function. The function below accepts a string and prints a brief message. By default, the message addresses the world. For good measure we will also add a docstring to document the function.

def say_hello(to_whom='World'):
    """Say hello to the world or whomever."""
    print('Hello ' + to_whom)

This is pretty basic Python and hopefully everything so far is familiar. Next, we will turn this function into an interactive widget with just an import statement and one line of code. Update your code to what is shown below and execute the cell.

import nbtools

@nbtools.build_ui
def say_hello(to_whom='World'):
    """Say hello to the world or whomever."""
    print('Hello ' + to_whom)

You should now see a widget containing a web form. This form will prompt for the value of the to_whom parameter. The docstring will also appear as a description near the top of the widget. Go ahead and change the to_whom value, then click the "Run" button. This will execute the function and print the results below. Meanwhile, the form will also collapse, making more room on your screen.

With the push of a button, you've run the say_hello function!

This is exciting, but it is far from the only feature of the nbtools package. You can edit markdown cells using a WYSIWYG editor, customize how your function displays, chain together multiple related functions, make widgets from existing third-party methods, create a library of interactive tools (just click the Tools button on the toolbar and you will see say_hello has already added itself) and more! Just see the documentation links below.

⁠Features

• UI Builder⁠
• UI Output⁠
• Tool Manager API⁠
• WYSWYG Editor⁠