Python implementation of the graph visualization tool Cytoscape.
A widget enabling interactive graph visualization with cytoscape.js in JupyterLab and the Jupyter notebook.
Try it out using binder: or install and try out the examples.
conda install -c conda-forge ipycytoscape
pip install ipycytoscape
For jupyterlab users:
There is an aditional step if you're using JupyterLab:
jupyter labextension install @jupyter-widgets/jupyterlab-manager jupyter-cytoscape
If you are using Jupyter Notebook 5.2 or earlier, you may also need to enable the nbextension:
jupyter nbextension enable --py [--sys-prefix|--user|--system] ipycytoscape
For a development installation:
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/QuantStack/ipycytoscape.git cd ipycytoscape # Install python package for development, runs npm install and npm run build pip install -e .
When developing ipycytoscape, you need to manually enable the extension with the notebook / lab frontend. For lab, this is done by the command:
# install jupyterlab-manager and this extension jupyter labextension install @jupyter-widgets/jupyterlab-manager --no-build jupyter labextension install .
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
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
To continuously monitor the project for changes and automatically trigger a rebuild, start Jupyter in watch mode:
jupyter lab --watch
And in a separate session, begin watching the source directory for changes:
npm run watch
If you make a change to the python code then you need to restart the notebook kernel to have it take effect.
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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