{ "info": { "author": "Peter Kerpedjiev", "author_email": "pkerpedjiev@gmail.com", "bugtrack_url": null, "classifiers": [ "Development Status :: 4 - Beta", "Intended Audience :: Developers", "Intended Audience :: Science/Research", "Programming Language :: Python :: 3", "Programming Language :: Python :: 3.3", "Programming Language :: Python :: 3.4", "Programming Language :: Python :: 3.5", "Programming Language :: Python :: 3.6", "Programming Language :: Python :: 3.7", "Topic :: Multimedia :: Graphics" ], "description": "# HiGlass Python\n\n[![HiGlass](https://img.shields.io/badge/higlass-\ud83d\udc4d-red.svg?colorB=45afe5)](http://higlass.io)\n[![Docs](https://img.shields.io/badge/docs-\ud83c\udf89-red.svg?colorB=6680ff)](https://higlass.io/docs/python_api.html)\n[![Python](https://img.shields.io/badge/python-\ud83d\ude0d-red.svg?colorB=af80ff)](https://higlass.io/docs/python_api.html)\n[![Build Status](https://travis-ci.org/higlass/higlass-python.svg?branch=master)](https://travis-ci.org/higlass/higlass-python)\n\nPython bindings to the HiGlass for tile serving, view config generation, and Jupyter Notebook + Lab integration.\n\nThis package provide access to:\n- server: a lightweight flask server\n- tilesets: tileset API\n- client: an API for generating view configs\n- viewer: an API for launching HiGlass in Jupyter Notebook or Lab\n\n## Installation\n\n#### Requirements\n\n- Python >= 3.7\n- [FUSE](https://github.com/libfuse/libfuse) or [MacFuse](https://osxfuse.github.io/)\n- Jupyter Notebook >= 5.7\n- Jupyter Lab >= 0.35 & < 1.0\n- ipywidgets <= 7.4.2\n\n#### Install package\n\nFirst install `higlass-python` via pip:\n\n```bash\npip install higlass-python\n```\n\n#### Jupyter Notebook integration\n\nOpen a terminal and execute the following code to activate the integration:\n\n```bash\n# The following is only required if you have not enabled the ipywidgets nbextension yet\njupyter nbextension enable --py --sys-prefix widgetsnbextension\njupyter nbextension install --py --sys-prefix higlass\njupyter nbextension enable --py --sys-prefix higlass\n```\n\n#### Jupyter Lab integration\n\nOpen a terminal and execute the following code to activate the integration:\n\n```bash\n# The following is only required if you have not enabled the jupyterlab manager yet\njupyter labextension install @jupyter-widgets/jupyterlab-manager\njupyter labextension install higlass-jupyter\n```\n\n## Getting started\n\nTake a look at [notebooks/Examples.ipynb](notebooks/Examples.ipynb) on how to get started.\n\n## Development\n\n* Install the package in _editable_ mode. (The module will be imported from the development directory, rather than copied to `site-packages`).\n\n ```bash\n pip install -e .\n ```\n\n* 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.)\n\n ```bash\n python setup.py jsdeps\n jupyter nbextension enable --py --sys-prefix widgetsnbextension\n jupyter nbextension install --py --symlink --sys-prefix higlass\n jupyter nbextension enable --py --sys-prefix higlass\n ```\n\n* Uninstall the Jupyter Notebook Extension\n\n ```bash\n jupyter nbextension uninstall --py --sys-prefix higlass\n ```\n\n* Experimental: install the Jupyter Lab Extension\n\n ```bash\n cd js && jupyter labextension link .\n ```\n\n## Troubleshooting\n\n- 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. 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