https://github.com/cytoscape/ipycytoscape

A Cytoscape Jupyter widget

Science Score: 36.0%

This score indicates how likely this project is to be science-related based on various indicators:

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CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
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DOI references
○
Academic publication links
✓
Committers with academic emails
2 of 33 committers (6.1%) from academic institutions
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Institutional organization owner
○
JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (10.1%) to scientific vocabulary

Keywords

binder cytoscape jupyter-notebook

Keywords from Contributors

ipython jupyterlab notebooks visualizations closember visualisation dataviz wx tk qt

Last synced: 5 months ago · JSON representation

Repository

A Cytoscape Jupyter widget

Basic Info

Host: GitHub
Owner: cytoscape
License: bsd-3-clause
Language: Python
Default Branch: master
Homepage: https://ipycytoscape.readthedocs.io/en/master/
Size: 2.75 MB

Statistics

Stars: 282
Watchers: 28
Forks: 63
Open Issues: 74
Releases: 4

Topics

binder cytoscape jupyter-notebook

Created about 6 years ago · Last pushed 8 months ago

Metadata Files

Readme License

ipycytoscape

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.

cytoscape screencast

Supports:

Conversion from NetworkX see example1, example2
Conversion from Pandas DataFrame see example
Conversion from neo4j see example

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/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: 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 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 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.

Owner

Name: Cytoscape Consortium
Login: cytoscape
Kind: organization

Website: http://www.cytoscape.org/
Repositories: 153
Profile: https://github.com/cytoscape

GitHub Events

Total

Watch event: 11
Issue comment event: 2
Push event: 5
Pull request event: 1
Fork event: 2

Last Year

Watch event: 11
Issue comment event: 2
Push event: 5
Pull request event: 1
Fork event: 2

Committers

Last synced: 9 months ago

All Time

Total Commits: 547
Total Committers: 33
Avg Commits per committer: 16.576
Development Distribution Score (DDS): 0.581

Past Year

Commits: 0
Committers: 0
Avg Commits per committer: 0.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
Mariana Meireles	m**a@p**e	229
ianhi	i**k@g**m	112
Peter Rose	p**e@u**u	49
joseberlines	3****s	43
Jens H. Nielsen	j**n@g**m	15
dependabot[bot]	4****]	13
Mridul Seth	s**l@g**m	11
Sylvain Corlay	s**y@g**m	10
Stefan Countryman	s**n@g**m	6
Nicholas Bollweg	n**g@g**m	5
martinRenou	m**u@g**m	5
vaniisgh	v**h@l**k	5
Sven Schiffer	s**n@s**g	5
Jeremy Tuloup	j**p@g**m	5
Jay Donnell	j**l@g**m	4
Cagtay Fabry	4****y	4
pre-commit-ci[bot]	6****]	3
sandertyu	n**s@u**u	3
Jose Ferro	j**e@J**x	2
Mridul Seth	s**b@g**m	2
Michał Krassowski	5****i	2
Tim Paine	t**4@g**m	2
vinh	n**0@g**m	2
Andre LaBranche	d**e@m**m	1
Daniel Himmelstein	d**n@g**m	1
Kozo Nishida	k**a@g**m	1
Maarten A. Breddels	m**s@g**m	1
Max Klein	t****n	1
Ryan Morshead	r**d@g**m	1
Sevickson	s**n@o**m	1
and 3 more...

Committer Domains (Top 20 + Academic)

arrival.com: 1 mac.com: 1 joses-mbp.fritz.box: 1 ucdavis.edu: 1 schiffner.org: 1 live.co.uk: 1 ucsd.edu: 1 psychonautgirl.space: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 53
Total pull requests: 54
Average time to close issues: 3 months
Average time to close pull requests: about 1 month
Total issue authors: 27
Total pull request authors: 11
Average comments per issue: 2.66
Average comments per pull request: 1.89
Merged pull requests: 35
Bot issues: 0
Bot pull requests: 22

Past Year

Issues: 0
Pull requests: 1
Average time to close issues: N/A
Average time to close pull requests: N/A
Issue authors: 0
Pull request authors: 1
Average comments per issue: 0
Average comments per pull request: 1.0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

marimeireles (8)
ianhi (5)
shadiakiki1986 (5)
fpom (4)
joseberlines (4)
pwrose (3)
davidbrochart (2)
ktaletsk (1)
jenshnielsen (1)
koertkuipers (1)
Phocion (1)
gt-eq-1998 (1)
hbalp (1)
leilakany (1)
AlexejPenner (1)

Pull Request Authors

dependabot[bot] (19)
marimeireles (9)
ianhi (8)
jenshnielsen (8)
pre-commit-ci[bot] (3)
timkpaine (3)
vaniisgh (1)
pwrose (1)
bollwyvl (1)
donbr (1)
dreness (1)

Top Labels

Issue Labels

enhancement (14) question (10) documentation (4) bug (3) good first issue (3) help wanted (2) mentored (2) hacktoberfest (1) python (1)

Pull Request Labels

dependencies (19)

Packages

Total packages: 2
Total downloads:
- npm 33 last-month
- pypi 36,313 last-month
Total docker downloads: 5,650

Total dependent packages: 17
(may contain duplicates)
Total dependent repositories: 26
(may contain duplicates)
Total versions: 43
Total maintainers: 7

pypi.org: ipycytoscape

A Cytoscape widget for Jupyter

Homepage: https://github.com/cytoscape/ipycytoscape
Documentation: https://ipycytoscape.readthedocs.io/
License: BSD
Latest release: 1.3.3
published almost 4 years ago

Versions: 22
Dependent Packages: 16
Dependent Repositories: 26
Downloads: 36,313 Last month
Docker Downloads: 2,559

Rankings

Dependent packages count: 0.8%

Downloads: 1.7%

Docker downloads count: 1.9%

Average: 2.8%

Dependent repos count: 2.8%

Stargazers count: 4.2%

Forks count: 5.4%

Maintainers (4)

martinRenou Sylvain.Corlay ianhi marimeireles

Last synced: 6 months ago

npmjs.org: jupyter-cytoscape

A Cytoscape Jupyter Widget

Homepage: https://github.com/cytoscape/ipycytoscape
License: BSD-3-Clause
Latest release: 1.3.3
published almost 4 years ago

Versions: 21
Dependent Packages: 1
Dependent Repositories: 0
Downloads: 33 Last month
Docker Downloads: 3,091

Rankings

Docker downloads count: 0.6%

Forks count: 3.7%

Stargazers count: 3.8%

Downloads: 5.2%

Average: 8.6%

Dependent repos count: 18.8%

Dependent packages count: 19.5%

Maintainers (4)

sylvaincorlay martinrenou ianhuntisaak marimeireles

Last synced: 6 months ago

Dependencies

package-lock.json npm

1073 dependencies

package.json npm

@jupyterlab/builder ^3.0.0 development
@phosphor/application ^1.6.0 development
@phosphor/widgets ^1.6.0 development
@types/expect.js ^0.3.29 development
@types/mocha ^5.2.5 development
@types/node ^10.11.6 development
@types/webpack-env ^1.13.6 development
@typescript-eslint/eslint-plugin ^5.10.0 development
@typescript-eslint/parser ^5.10.0 development
css-loader ^3.2.0 development
eslint ^8.0.0 development
eslint-config-prettier ^6.11.0 development
eslint-plugin-prettier ^3.1.3 development
expect.js ^0.3.1 development
fs-extra ^7.0.0 development
karma ^6.0.0 development
karma-chrome-launcher ^2.2.0 development
karma-firefox-launcher ^1.1.0 development
karma-ie-launcher ^1.0.0 development
karma-mocha ^2.0.1 development
karma-mocha-reporter ^2.2.5 development
karma-typescript ^5.5.0 development
lint-staged ^10.2.2 development
mkdirp ^0.5.1 development
mocha ^9.2.2 development
npm-run-all ^4.1.3 development
prettier ^2.0.5 development
rimraf ^2.6.2 development
source-map-loader ^0.2.4 development
style-loader ^1.0.0 development
ts-loader ^5.2.1 development
typescript ~3.7.1 development
webpack ^5.0.0 development
webpack-cli ^4.0.0 development
@jupyter-widgets/base ^1.1.10 || ^2 || ^3 || ^4.0.0
@types/cytoscape ^3.8.8
cytoscape ^3.14.0
cytoscape-cola ^2.3.0
cytoscape-dagre ^2.2.2
cytoscape-klay ^3.1.3
cytoscape-popper ^1.0.6
tippy.js ^5.2.1

setup.py pypi

ipywidgets >=7.6.0
spectate >=1.0.0

.github/workflows/binder-on-pr.yml actions

actions/github-script v1 composite

.github/workflows/lint.yml actions

actions/checkout v2 composite
actions/setup-node v1 composite
actions/setup-python v2 composite
psf/black stable composite

.github/workflows/release.yml actions

actions/checkout v2 composite
actions/setup-node v1 composite
actions/setup-python v2 composite

.github/workflows/test.yml actions

actions/cache v2 composite
actions/checkout v2 composite
actions/setup-node v1 composite
actions/setup-python v2 composite

pyproject.toml pypi

docs/environment.yml conda

ipycytoscape >=1.0.3
jupyter_sphinx
jupyterlab 2.*
nbsphinx
nbsphinx-link
networkx
nodejs
pandas
python 3.7.*
sphinx
sphinx-copybutton
sphinx_rtd_theme

environment.yml conda

ipywidgets 7.*
jupyterlab 3.6.*
matplotlib-base
monotonic
networkx
nodejs 18.*
pandas
py2neo
spectate
traitlets

https://github.com/cytoscape/ipycytoscape

Science Score: 36.0%

Keywords

Keywords from Contributors

Repository

Basic Info

Statistics

Topics

Metadata Files

README.md

ipycytoscape

Supports:

Installation

Pandas installation

Neo4j installation

For jupyterlab 1.x or 2.x:

installing nodejs

install jupyterlab-manager extension

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

For Jupyter Notebook 5.2 and earlier

For a development installation:

clone repo

Install python package for development

How to see your changes

Typescript:

Python:

How to run tests locally

And to run it:

How to build the docs

Acknowledgements

License

Owner

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

pypi.org: ipycytoscape

Rankings

Maintainers (4)

npmjs.org: jupyter-cytoscape

Rankings

Maintainers (4)

Dependencies