higlass-python














































higlass-python



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 https://github.com/jupyter-widgets/ipywidgets/issues/2483#issuecomment-508643088

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