Registry / data / ipycytoscape

ipycytoscape

library1.3.3pypypi✓ verified 84d ago

ipycytoscape is a Python library that provides a Cytoscape widget for Jupyter notebooks and JupyterLab environments. It allows users to visualize and interact with complex networks directly within their Jupyter workflows, leveraging the powerful rendering capabilities of Cytoscape.js. The current version is 1.3.3, with minor releases occurring every few months for bug fixes and compatibility updates.

data web-framework

pip install ipycytoscape

github ↗package ↗homepage ↗

INSTALL

IMPORT

SIG · IPYCYTOSCAPE

ipycytoscape

datapythonv1.3.3

Install

5.7s avg

Import

1861ms

Disk

84MB

Pass rate

10/ 10

Env Coverage10 / 10

glibc

3.9–3.13

musl

3.9–3.13

Install & Compatibility

Where this runs

tested against v1.3.3 · pip install

no network on importno background threads

Install × environment matrix

Each cell = how many times install + import succeeded across repeated harness runs. Partial = flaky.
glibc = Debian/Ubuntu slim · musl = Alpine Linux

musl

py 3.10–3.910 runs

installs and imports cleanly · install 0.0s · import 1.960s · 92.1MB

glibc

py 3.10–3.910 runs

installs and imports cleanly · install 5.7s · import 1.761s · 93MB

84MB installed

● package 84MB

Code

Verified usage

Verified import paths — ran on the pinned version, not inferred.

CytoscapeWidget

✓ from ipycytoscape import CytoscapeWidget

This quickstart demonstrates how to create a Cytoscape widget, populate it with data from a NetworkX graph, apply a layout, and display it in a Jupyter environment. The `set_layout()` call is essential for proper rendering.

import ipycytoscape import networkx as nx # Create a Cytoscape widget instance cy = ipycytoscape.CytoscapeWidget() # Create a simple graph using NetworkX G = nx.Graph() G.add_edge('A', 'B') G.add_edge('B', 'C') G.add_node('D') # Add the graph data to the widget cy.graph.add_graph_from_networkx(G, directed=False) # Set a layout; this is crucial for the graph to display properly cy.set_layout(name='cose') # Other options: 'cola', 'grid', 'circle', etc. # Display the widget cy

Debug

Known issues

breakingVersion 1.2.0 significantly changed how ipycytoscape integrates with JupyterLab. Prior to 1.2.0, an explicit `jupyter lab build` step and Node.js were often required. Version 1.2.0+ no longer requires these for JupyterLab 3 and above.

fix

Ensure you are using `ipycytoscape>=1.2.0` for JupyterLab 3+ compatibility without a build step. If upgrading from an older version, remove any manual `jupyter lab build` steps from your workflow. Consider `pip install --upgrade ipycytoscape`.

affects: <1.2.0 to 1.2.0+

gotchaGraphs may not display properly (nodes overlapping at the center) if a layout is not explicitly set using `cy.set_layout()`. Cytoscape.js requires a layout algorithm to arrange nodes and edges.

fix

Always call `cy.set_layout(name='some_layout_name')` after adding graph data to the widget. Common layout names include 'cola', 'cose', 'grid', 'circle', 'random'.

affects: All versions

gotchaWhen using `ipycytoscape` in classic Jupyter Notebook (not JupyterLab), you might need to ensure the nbextension is enabled, especially if the widget does not render.

fix

Run `jupyter nbextension enable --py --sys-prefix ipycytoscape` from your terminal if widgets fail to load in classic Jupyter Notebook.

affects: All versions (less common with recent JupyterLab)

Errors

Common errors & fixes

Widget not found. This usually happens when the widgets JavaScript hasn't been run.

The Jupyter environment (JupyterLab or classic Notebook) has not correctly loaded the ipycytoscape frontend extension.

fix

For JupyterLab 3+, ensure `ipycytoscape>=1.2.0` is installed. No manual build should be needed. For classic Notebook, try `jupyter nbextension enable --py --sys-prefix ipycytoscape`. Restart your kernel and browser.

TraitError: The 'layout' trait of a CytoscapeWidget instance must be a dict or None, but a value of type <class 'str'> was specified.

You passed a string directly to `cy.layout` instead of using the `set_layout` method, or the `set_layout` method was used with an invalid parameter type.

fix

Use the `set_layout` method with the `name` parameter, e.g., `cy.set_layout(name='cola')`. If you need custom layout options, provide a dictionary: `cy.set_layout(name='cose', options={'padding': 10})`.

ModuleNotFoundError: No module named 'ipycytoscape'

The `ipycytoscape` package is not installed in the Python environment where Jupyter is running.

fix

Install the package: `pip install ipycytoscape`. Ensure you are installing into the correct Python environment if you use virtual environments or conda environments.

Upgrade

Version history

1.3.3latest on PyPI · released Apr 4, 2022

Audit

Dependencies

py2neooptionalUsed in examples for integrating with Neo4j graphs, but not a core dependency.

Agent activity

4 hits · last 30 days

node

Resources

githubhttps://github.com/cytoscape/ipycytoscape ↗

packagehttps://pypi.org/project/ipycytoscape/ ↗

homepagehttps://cytoscape.org ↗