Python API and Jupyter widget facilitating interactive visualization of spatial single-cell data with Vitessce.
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
Explore our example notebooks. These contain demos of different use cases and integrations with single-cell data analysis packages.
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.
cd tests
python -m unittest
make html
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.
- ipywidget docs: Building a Custom Widget
- ipywidget docs: Low Level Widget Tutorial
- ipywidget example: ipyleaflet
- ipywidget example (with React): ipymaterialui
- ipywidget example (with React): higlass-python
- ipywidget cookiecutter
- Sphinx: Getting Started
- Read the Docs Sphinx Theme
- jupyter server proxy