Python bindings for the HiGlass viewer

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Project description

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

Project details

These details have not been verified by PyPI

Project links

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Release history Release notifications | RSS feed

1.2.0

Nov 12, 2024

1.1.2

Nov 12, 2024

1.1.1

Nov 9, 2024

1.1.0

Oct 3, 2023

1.0.3

Sep 19, 2023

1.0.2

Sep 19, 2023

1.0.1

Aug 22, 2023

1.0.0

May 28, 2023

1.0.0rc2 pre-release

Apr 20, 2023

1.0.0rc1 pre-release

Mar 9, 2023

This version

0.4.8

Mar 21, 2022

0.4.7

Dec 23, 2021

0.4.6

Dec 22, 2021

0.4.4

Jan 26, 2021

0.4.3

Aug 4, 2020

0.4.2

Aug 4, 2020

0.4.1

Jul 1, 2020

0.4.0

Jan 26, 2020

0.3.0

Nov 11, 2019

0.2.1

Sep 25, 2019

0.2.0

Sep 25, 2019

0.1.14

Sep 5, 2019

0.1.13

Jul 8, 2019

0.1.12

Jul 8, 2019

0.1.11

Jul 5, 2019

0.1.10

Jun 25, 2019

0.1.7

May 9, 2019

0.1.5

Mar 31, 2019

0.1.4

Mar 8, 2019

0.1.3

Mar 6, 2019

0.1.1

Jan 21, 2019

0.1.1rc4 pre-release

Dec 12, 2018

0.1.1rc3 pre-release

Dec 12, 2018

0.1.0

Dec 12, 2018

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