pymotif 0.0.1.dev0

jupyter widget bindings for the motif library

motif

Jupyter widget bindings for the motif library

Installation

You can install using pip:

pip install pymotif

If you use jupyterlab:

// Add the pymotif jupyter lab extension
jupyter labextension install @jupyter-widgets/jupyterlab-manager

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] pymotif

Try

Demo notebooks can be found in the examples folder.

Sample code:

from pymotif import Motif
import networkx as nx

gml1 = 'karate.gml'
g1 = nx.read_gml(gml1)
motif = Motif(nx_graph=g1, title='karate')
motif.plot()

More documentation coming soon...

Development

For a more thorough walkthrough check out the official guide:
https://ipywidgets.readthedocs.io/en/latest/examples/Widget%20Custom.html

Create a new conda environment with the dependencies

To create the environment, execute the following command:

conda create -n motif -c conda-forge jupyterlab nodejs python

Then activate the environment with:

conda activate motif

Build and install the widget for development

Since the widget contains a Python part, you need to install the package in editable mode:

python -m pip install -e .

If you are using JupyterLab:

jupyter labextension develop --overwrite .

If you are using the Classic Notebook:

jupyter nbextension install --sys-prefix --symlink --overwrite --py pymotif
jupyter nbextension enable --sys-prefix --py pymotif

Installing the js dependencies:

npm install

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 start

After a change wait for the build to finish and then refresh your browser and the changes should take effect.

If you make a change to the python code then you will need to restart the notebook kernel to have it take effect.

Publishing

1. Update the version in package.json
2. Relase the @cylynx/pymotif packages:

npm login
npm publish

3. Bundle the python package: python setup.py sdist bdist_wheel
4. Update the version in pymotif/_version.py
5. If frontend version dependency has changed, update pymotif/_frontend.py
6. Publish the package to PyPI:

pip install twine
twine upload dist/pymotif*