higlass-python 0.1.11

Python bindings 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

Requirements

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

Installation

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 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 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.

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 .