Python bindings for the HiGlass viewer
Project description
# HiGlass Python
[](http://higlass.io) [](https://higlass.io/docs/python_api.html) [](https://higlass.io/docs/python_api.html)
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](https://github.com/libfuse/libfuse) or [MacFuse](https://osxfuse.github.io/)
Jupyter Notebook >= 5.7
Jupyter Lab >= 0.35
### Installation
First install higlass-python via pip:
`bash pip install higlass-python `
#### Jupyter notebook integration
Open a terminal and execute the following code to activate the integration:
`bash # 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:
`bash # 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](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).
`bash 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.)
`bash 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
`bash jupyter nbextension uninstall --py --sys-prefix higlass `
Experimental: install the Jupyter Lab Extension
`bash cd js && jupyter labextension link . `
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