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https://github.com/vitessce/vitessce-python
Python API and Jupyter widget for Vitessce
https://github.com/vitessce/vitessce-python
data-visualization gehlenborglab hidivelab ipywidget jupyter-widget jupyterlab-extension kharchenkolab single-cell vitessce
Last synced: 6 days ago
JSON representation
Python API and Jupyter widget for Vitessce
- Host: GitHub
- URL: https://github.com/vitessce/vitessce-python
- Owner: vitessce
- License: mit
- Created: 2020-09-01T21:11:52.000Z (about 4 years ago)
- Default Branch: main
- Last Pushed: 2024-10-28T13:46:00.000Z (9 days ago)
- Last Synced: 2024-10-28T17:02:59.310Z (9 days ago)
- Topics: data-visualization, gehlenborglab, hidivelab, ipywidget, jupyter-widget, jupyterlab-extension, kharchenkolab, single-cell, vitessce
- Language: Python
- Homepage: https://python-docs.vitessce.io
- Size: 34.8 MB
- Stars: 40
- Watchers: 6
- Forks: 7
- Open Issues: 101
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- License: LICENSE
Awesome Lists containing this project
README
# vitessce-python
[](https://pypi.org/project/vitessce)
[](https://vitessce.github.io/vitessce-python/)
[](https://mybinder.org/v2/gh/vitessce/vitessce-python/main?filepath=docs/notebooks/widget_pbmc.ipynb)
[](https://colab.research.google.com/github/vitessce/vitessce-python/blob/main/docs/notebooks/widget_on_colab.ipynb)
Python API and Jupyter widget facilitating interactive visualization of spatial single-cell data with [Vitessce](https://github.com/vitessce/vitessce).
## Installation
To install with pip:
$ pip install vitessce[all]
## Getting started
Explore our [example notebooks](./docs/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,docs,all]"
### Conda environments
In this repository, there are multiple conda environments for different purposes:
- `vitessce-python-dev` (defined in [environment.yml](./environment.yml)) is used for the development of the `vitessce` package itself
- `vitessce-python-notebooks` (defined in [docs/notebooks/environment.yml](./docs/notebooks/environment.yml)) is used for running the example notebooks in the `docs/notebooks/` directory (see [`docs/notebooks/README.md`](./docs/notebooks#readme) for more information)
- `vitessce-python-binder` (defined in [binder/environment.yml](./binder/environment.yml)) is the environment used by Binder upon opening notebooks from this repository
## Linting and testing
```sh
flake8
pytest
```
### Formatting
One file:
```sh
autopep8 --in-place --aggressive ./path/to/file.py
```
All `.py` files:
```sh
find . -name '*.py' -exec autopep8 --in-place --aggressive '{}' \;
```
## Documentation
```sh
make html
```
## Deployment
To deploy a new version, increment the version of the Python package in [`pyproject.toml`](./pyproject.toml).
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.
## Troubleshooting
### Check JavaScript console
Check the JavaScript console in the web browser for error messages. To do so, shift+right click in Jupyter, then click Inspect element. You may need to enable your browser's develop mode in its preferences for this option to appear when you right-click.
### Check your Python environment
Check that you have activated the correct conda or other virtual environment as you expect.
When sharing errors, it can be helpful to share the current versions of packages in the environment, e.g., by `conda list` or `pip list`.
### Restart Kernel and Clear All Outputs, then refresh the browser tab
To ensure that older widget JavaScript output is not causing conflicts with newer JavaScript output (which may persist via notebook outputs even without running notebook cells), clear old outputs by Kernel -> Restart Kernel and Clear All Outputs. Then refresh the browser tab (containing Jupyter) to ensure all JavaScript outputs are fresh.
This is also typically required when running `!pip install vitessce[all]` from within a Jupyter notebook cell in the same session as running `vc.widget()` for the first time.
The Kernel restart/Output clearing is required when a new Jupyter widget is installed in the environment, otherwise Jupyter will not yet recognize the newly-installed widget (as the notebook was opened with a different set of Jupyter widgets installed, and widget discovery is performed only at certain stages in the notebook lifecycle).
### Check the widget configuration
If the widget renders successfully, you can get its current configuration by
```py
vw = vc.widget()
vw
```
```py
vw.config
```
### Usage when Jupyter is running on a remote machine
If Jupyter is running on a remote machine, then use `proxy=True`. You may need to specify `host_name` as well (`widget` should be able to detect this but the plain `display` cannot).
```py
vw = vc.widget(proxy=True)
vw
```
or
```py
vc.display(proxy=True, host_name="http://localhost:8888")
```
### Ensure that Vitessce and Jupyter are installed in the same environment
With the environment activated, run `pip list` on the command line:
```
Package Version
----------------------------- -----------
...
jupyterlab 3.x.x
...
vitessce 3.x.x
```
## Resources
- [ipywidget docs: Building a Custom Widget](https://ipywidgets.readthedocs.io/en/stable/examples/Widget%20Custom.html)
- [ipywidget docs: Low Level Widget Tutorial](https://ipywidgets.readthedocs.io/en/latest/examples/Widget%20Low%20Level.html)
- [ipywidget example: ipyleaflet](https://github.com/jupyter-widgets/ipyleaflet)
- [ipywidget example (with React): ipymaterialui](https://github.com/maartenbreddels/ipymaterialui)
- [ipywidget example (with React): higlass-python](https://github.com/higlass/higlass-python)
- [ipywidget cookiecutter](https://github.com/jupyter-widgets/widget-cookiecutter)
- [Sphinx: Getting Started](https://www.sphinx-doc.org/en/master/usage/quickstart.html)
- [Read the Docs Sphinx Theme](https://github.com/readthedocs/sphinx_rtd_theme)
- [jupyter server proxy](https://jupyter-server-proxy.readthedocs.io/en/latest/arbitrary-ports-hosts.html)
## Getting/Offering Help
If you have a specific bug or feature request, please feel free to open an [issue](https://github.com/vitessce/vitessce-python/issues/new). Otherwise our [discussions](https://github.com/vitessce/vitessce-python/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.