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README.md

vitessce-python

Binder

Python API and Jupyter widget facilitating interactive visualization of spatial single-cell data with Vitessce.

Installation

To install with pip:

$ pip install vitessce
$ jupyter nbextension install --py vitessce
$ jupyter nbextension enable --py vitessce

To enable the widget for Jupyter Lab run the following additional lines:

$ jupyter labextension install @jupyter-widgets/jupyterlab-manager
$ jupyter labextension install vitessce-jupyter

Getting started

Explore our example notebooks. These contain demos of different use cases and integrations with single-cell data analysis packages.

Development

For a development installation (requires npm),

$ git clone https://github.com/vitessce/vitessce-python.git
$ cd vitessce-python
$ conda env create -f environment.yml
$ conda activate vitessce-jupyter-dev
$ pip install -e .
$ jupyter nbextension install --py --symlink --sys-prefix vitessce
$ jupyter nbextension enable --py --sys-prefix vitessce
$ cd js
$ jupyter labextension install @jupyter-widgets/jupyterlab-manager
$ jupyter labextension install

When actively developing your extension, build Jupyter Lab with the command:

$ jupyter lab --watch

This takes a minute or so to get started, but then automatically rebuilds JupyterLab when your javascript changes.

Note on first jupyter lab --watch, you may need to touch a file to get Jupyter Lab to open.

Testing

cd tests
python -m unittest

Documentation

make html

Deployment

To deploy a new version, increment the version of the Python package in vitessce/_version.py and the JS package in js/package.json.

Then, when you push or merge the code with the incremented versions to master, the GitHub Action deploy.yml workflow will build and push the packages to PyPI and NPM.

Resources