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]"
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 thevitessce
package itselfvitessce-python-notebooks
(defined in docs/notebooks/environment.yml) is used for running the example notebooks in thedocs/notebooks/
directory (seedocs/notebooks/README.md
for 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
Formatting
One file:
autopep8 --in-place --aggressive ./path/to/file.py
All .py
files:
find . -name '*.py' -exec autopep8 --in-place --aggressive '{}' \;
Documentation
make html
Deployment
To deploy a new version, increment the version of the Python package in setup.py
.
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 package to PyPI.
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.
Project details
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