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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,docs,all]"

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 the vitessce package itself
vitessce-python-notebooks (defined in docs/notebooks/environment.yml) is used for running the example notebooks in the docs/notebooks/ directory (see docs/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 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

vw = vc.widget()
vw

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).

vw = vc.widget(proxy=True)
vw

or

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

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.

	install_requires=[
	'ipywidgets>=7.0.0',
	'hypercorn>=0.11.0',
	'ujson>=4.0.1',
	'aiofiles>=0.6.0',
	'starlette==0.14.0',
	'zarr>=2.5.0',
	'numcodecs>=0.5.7',
	'scipy>=1.2.1',
	'negspy>=0.2.24',
	'generate-tiff-offsets>=0.1.7'
	],

	# Add each dataset from the incoming config.
	for d in config["datasets"]:
	new_dataset = vc.add_dataset(uid=d["uid"], name=d["name"])
	for f in d["files"]:
	new_file = new_dataset.add_file(
	url=f["url"],
	data_type=f["type"],
	file_type=f["fileType"]
	)

	cluster_ids = adata.obs['CellType'].unique().tolist()
	cell_cluster_ids = adata.obs['CellType'].values.tolist()

vitessce / vitessce-python Goto Github PK

vitessce-python's Introduction

vitessce-python

Installation

Getting started

Development

Conda environments

Linting and testing

Formatting

Documentation

Deployment

Troubleshooting

Check JavaScript console

Check your Python environment

Restart Kernel and Clear All Outputs, then refresh the browser tab

Check the widget configuration

Usage when Jupyter is running on a remote machine

Ensure that Vitessce and Jupyter are installed in the same environment

Resources

Getting/Offering Help

vitessce-python's People

Contributors

Stargazers

Watchers

Forkers

vitessce-python's Issues

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what I attempted with vitessce-python

the error:

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