Package: ipycytoscape
ipycytoscapeA widget enabling interactive graph visualization withcytoscape.jsin JupyterLab and the Jupyter notebook.Try it out using binder:or install and try out theexamples.Supports:Conversion from NetworkX seeexample1,example2Conversion from Pandas DataFrame seeexampleConversion from neo4j seeexampleInstallationWithmamba:mamba install -c conda-forge ipycytoscapeWithconda:conda install -c conda-forge ipycytoscapeWithpip:pipinstallipycytoscapePandas installationYou can install the Pandas dependencies foripycytoscapewith pip:pip install pandasOr conda-forge:mamba install pandasNeo4j installationYou can install the neo4j dependencies foripycytoscapewith pip:pip install -e ".[neo4j]"Or conda-forge:mamba install py2neo neotimeFor jupyterlab 1.x or 2.x:If you are using JupyterLab 1.x or 2.x then you will also need to installnodejsand thejupyterlab-managerextension. You can do this like so:# installing nodejscondainstall-cconda-forgenodejs# install jupyterlab-manager extensionjupyterlabextensioninstall@jupyter-widgets/jupyterlab-manager@2.0--no-build# if you have previously installed the manager you still to run jupyter lab buildjupyterlabbuildFor Jupyter Notebook 5.2 and earlierYou may also need to manually enable the nbextension:jupyternbextensionenable--py[--sys-prefix|--user|--system]ipycytoscapeFor a development installation:(requires npm)While not required, we recommend creating a conda environment to work in:condacreate-nipycytoscape-cconda-forgejupyterlabnodejs
condaactivateipycytoscape# clone repogitclonehttps://github.com/cytoscape/ipycytoscape.gitcdipycytoscapeInstall python package for developmentThis willrun npm installandnpm run build.
This command will also install the test suite and thedocslocally:pip install jupyter_packaging==0.7.9
pip install -e ".[test, docs]"

jupyter labextension develop . --overwriteoptionally install the pre-commit hooks with:pre-commitinstallOr for classic notebook, you can run:jupyter nbextension install --sys-prefix --symlink --overwrite --py ipycytoscape
jupyter nbextension enable --sys-prefix --py ipycytoscapeNote that the--symlinkflag doesn't work on Windows, so you will here have to run
theinstallcommand 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 changesTypescript:To continuously monitor the project for changes and automatically trigger a rebuild, start watching the ipycytoscape code:npmrunwatchAnd in a separate terminal start JupyterLab normally:jupyterlabonce 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 locallyInstall necessary dependencies with pip:pip install -e ".[test]"Or with conda/mamba:mamba -c conda-forge install networkx pandas nbval pytestAnd to run it:pytestHow to build the docscd docsInstall dependencies:conda env update --file doc_environment.ymlAnd build them:make htmlAcknowledgementsThe ipycytoscape project was started byMariana MeirelesatQuantStack. This initial development was funded as part of thePLASMAproject, which is led by Claire Vandiedonck, Pierre Poulain, and Sandrine Caburet.LicenseWe 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 theLICENSEfile for details.