Jupyter widget facilitating interactive visualization of spatial single-cell data with Vitessce
Project description
vitessce-python
Python API and Jupyter widget facilitating interactive visualization of spatial single-cell data with Vitessce.
Installation
To install with pip:
$ pip install vitessce[all]
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 NodeJS and NPM),
$ git clone https://github.com/vitessce/vitessce-python.git
$ cd vitessce-python
$ conda env create -f environment.yml
$ conda activate vitessce-python-dev
$ pip install -e ".[dev]"
$ jupyter nbextension install --py --symlink --overwrite --sys-prefix vitessce
$ jupyter nbextension enable --py --sys-prefix vitessce
When actively developing your extension for JupyterLab, run the command:
$ jupyter labextension develop --overwrite vitessce
For the JS codebase, install nvm
and then run nvm install to get the correct version of Node.
To rebuild the JS when you make a code change:
$ cd js
$ npm run build
You then need to refresh the JupyterLab page when your javascript changes.
Conda environments
In this repository, there are multiple conda environments for different purposes:
vitessce-python-dev(defined in environment.yml) is used for the development of thevitesscepackage itselfvitessce-python-notebooks(defined in docs/notebooks/environment.yml) is used for running the example notebooks in thedocs/notebooks/directory (seedocs/notebooks/README.mdfor more information)vitessce-python-binder(defined in binder/environment.yml) is the environment used by Binder upon opening notebooks from this repository
Linting and testing
flake8
pytest
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:
cd js
npm version patch
Then, when you push or merge the code with the incremented versions to main, the GitHub Action deploy.yml workflow will build and push the packages to PyPI and NPM.
Resources
- 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
Getting/Offering Help
If you have a specific bug or feature request, please feel free to open an issue. Otherwise our discussions section is a great place to get help or offer it. If you aren't sure if something is a bug or not, don't have all the reproduction steps, or just have a general question, feel free to open a discussion post.
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