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https://github.com/cytoscape/ipycytoscape

A Cytoscape Jupyter widget
https://github.com/cytoscape/ipycytoscape

binder cytoscape jupyter-notebook

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A Cytoscape Jupyter widget

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README 

        
# ipycytoscape



[![Tests](https://github.com/cytoscape/ipycytoscape/actions/workflows/test.yml/badge.svg)](https://github.com/cytoscape/ipycytoscape/actions/workflows/test.yml) [![Documentation Status](https://readthedocs.org/projects/ipycytoscape/badge/?version=master)](https://ipycytoscape.readthedocs.io/en/latest/?badge=master) [![StackOverflow](https://img.shields.io/badge/stackoverflow--orange.svg)](https://stackoverflow.com/questions/tagged/ipycytoscape) [![Join the chat at https://gitter.im/QuantStack/Lobby](https://badges.gitter.im/Join%20Chat.svg)](https://gitter.im/QuantStack/Lobby?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)



A widget enabling interactive graph visualization with [cytoscape.js](https://js.cytoscape.org/) in JupyterLab and the Jupyter notebook.



Try it out using binder: [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/cytoscape/ipycytoscape/HEAD?filepath=examples) or install and try out the [examples](examples).



![cytoscape screencast](https://user-images.githubusercontent.com/17600982/76328068-bbbbcf00-62e2-11ea-93ed-01ba392ac50c.gif)



#### Supports:



* Conversion from NetworkX see [example1](https://github.com/cytoscape/ipycytoscape/blob/master/examples/Test%20NetworkX%20methods.ipynb), [example2](https://github.com/cytoscape/ipycytoscape/blob/master/examples/NetworkX%20Example.ipynb)

* Conversion from Pandas DataFrame see [example](https://github.com/cytoscape/ipycytoscape/blob/master/examples/pandas.ipynb)

* Conversion from neo4j see [example](https://github.com/cytoscape/ipycytoscape/blob/master/examples/Neo4j_Example.ipynb)



## Installation



With `mamba`:



```

mamba install -c conda-forge ipycytoscape

```



With `conda`:



```

conda install -c conda-forge ipycytoscape

```



With `pip`:



```bash

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:



```bash

# installing nodejs

conda install -c conda-forge nodejs



# install jupyterlab-manager extension

jupyter labextension install @jupyter-widgets/[email protected] --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:

```bash

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:

```bash

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](https://ipycytoscape.readthedocs.io/en/latest/) locally:



```

pip install jupyter_packaging==0.7.9

pip install -e ".[test, docs]"



jupyter labextension develop . --overwrite

```



optionally install the pre-commit hooks with:



```bash

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:

```bash

npm run watch

```

And in a separate terminal start JupyterLab normally:

```bash

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](https://github.com/marimeireles) at [QuantStack](https://quantstack.net). This initial development was funded as part of the [PLASMA](https://plasmabio.org) 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](LICENSE) file for details.