hkariti/higlass-python

Python bindings to and Jupyter Notebook+Lab integration for the HiGlass viewer

HiGlass Python

Python bindings to the HiGlass for tile serving, view config generation, and Jupyter Notebook + Lab integration.

This package provide access to:

• server: a lightweight flask server
• tilesets: tileset API
• client: an API for generating view configs
• viewer: an API for launching HiGlass in Jupyter Notebook or Lab

Installation

Requirements

• Python >= 3.7
• FUSE or MacFuse
• Jupyter Notebook >= 5.7
• Jupyter Lab >= 0.35

Install package

First install higlass-python via pip:

pip install higlass-python

Jupyter Notebook integration

Open a terminal and execute the following code to activate the integration:

# The following is only required if you have not enabled the ipywidgets nbextension yet
jupyter nbextension enable --py --sys-prefix widgetsnbextension
jupyter nbextension install --py --sys-prefix higlass
jupyter nbextension enable --py --sys-prefix higlass

Jupyter Lab integration

Open a terminal and execute the following code to activate the integration:

# The following is only required if you have not enabled the jupyterlab manager yet
jupyter labextension install @jupyter-widgets/jupyterlab-manager
jupyter labextension install higlass-jupyter

Getting started

Take a look at notebooks/Examples.ipynb on how to get started.

Documentation

There is more detailed documentation at docs-python.higlass.io.

Development

• Install the package in editable mode. (The module will be imported from the development directory, rather than copied to site-packages).

  pip install -e .

• Build and enable the Jupyter Notebook Extension. (With the --symlink option, the assets in higlass/static are linked to the extension registry rather than copied.)

  python setup.py jsdeps
  jupyter nbextension enable --py --sys-prefix widgetsnbextension
  jupyter nbextension install --py --symlink --sys-prefix higlass
  jupyter nbextension enable --py --sys-prefix higlass

• Uninstall the Jupyter Notebook Extension

  jupyter nbextension uninstall --py --sys-prefix higlass

• Experimental: install the Jupyter Lab Extension

  cd js && jupyter labextension link .

Editing the docs

To work on the docs, start the autoserver and edit the rst files in the docs directory:

cd docs
./serve.sh

Troubleshooting

• If you are running JupyterLab v1.x and ipywidgets v7.5 and the HiGlass widget is not being displayed! Then you might have an incompatible widget installed that makes all other widgets fail. Try to deinstall all other widgets to test HiGlass separately before submitting a ticket. For more information see jupyter-widgets/ipywidgets#2483 (comment)