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A Cytoscape widget for Jupyter

Project description

ipycytoscape

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A widget enabling interactive graph visualization with cytoscape.js in JupyterLab and the Jupyter notebook.

Try it out using binder: Binder or install and try out the examples.

cytoscape screencast

Supports:

Installation

With mamba:

mamba install -c conda-forge ipycytoscape

With conda:

conda install -c conda-forge ipycytoscape

With pip:

pip install ipycytoscape

Pandas installation

You can install the Pandas dependencies for ipycytoscape with pip:

pip install pandas

Or conda-forge:

mamba install pandas

Neo4j installation

You can install the neo4j dependencies for ipycytoscape with pip:

pip install -e ".[neo4j]"

Or conda-forge:

mamba install py2neo neotime

For jupyterlab 1.x or 2.x:

If you are using JupyterLab 1.x or 2.x then you will also need to install nodejs and the jupyterlab-manager extension. You can do this like so:

# installing nodejs
conda install -c conda-forge nodejs


# install jupyterlab-manager extension
jupyter labextension install @jupyter-widgets/jupyterlab-manager@2.0 --no-build

# if you have previously installed the manager you still to run jupyter lab build
jupyter lab build

For Jupyter Notebook 5.2 and earlier

You may also need to manually enable the nbextension:

jupyter nbextension enable --py [--sys-prefix|--user|--system] ipycytoscape

For a development installation:

(requires npm)

While not required, we recommend creating a conda environment to work in:

conda create -n ipycytoscape -c conda-forge jupyterlab nodejs
conda activate ipycytoscape

# clone repo
git clone https://github.com/cytoscape/ipycytoscape.git
cd ipycytoscape

Install python package for development

This will run npm install and npm run build. This command will also install the test suite and the docs locally:

pip install jupyter_packaging==0.7.9
pip install -e ".[test, docs]"

jupyter labextension develop . --overwrite

optionally install the pre-commit hooks with:

pre-commit install

Or for classic notebook, you can run:

jupyter nbextension install --sys-prefix --symlink --overwrite --py ipycytoscape
jupyter nbextension enable --sys-prefix --py ipycytoscape

Note that the --symlink flag doesn't work on Windows, so you will here have to run the install command every time that you rebuild your extension. For certain installations you might also need another flag instead of --sys-prefix, but we won't cover the meaning of those flags here.

How to see your changes

Typescript:

To continuously monitor the project for changes and automatically trigger a rebuild, start watching the ipycytoscape code:

npm run watch

And in a separate terminal start JupyterLab normally:

jupyter lab

once the webpack rebuild finishes refresh the JupyterLab page to have your changes take effect.

Python:

If you make a change to the python code then you need to restart the notebook kernel to have it take effect.

How to run tests locally

Install necessary dependencies with pip:

pip install -e ".[test]"

Or with conda/mamba:

mamba -c conda-forge install networkx pandas nbval pytest

And to run it:

pytest

How to build the docs

cd docs

Install dependencies:

conda env update --file doc_environment.yml

And build them:

make html

Acknowledgements

The ipycytoscape project was started by Mariana Meireles at QuantStack. This initial development was funded as part of the PLASMA project, which is led by Claire Vandiedonck, Pierre Poulain, and Sandrine Caburet.

License

We use a shared copyright model that enables all contributors to maintain the copyright on their contributions.

This software is licensed under the BSD-3-Clause license. See the LICENSE file for details.

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