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HiGlass Python

HiGlass Python Docs Build Status

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