celldega

Documentation

https://broadinstitute.github.io/celldega/

Installation

pip install celldega

Note on VIPS Installation

If running on a new Terra.bio workspace you will need to install vips in a startup script (e.g., startup_script.sh) with the following

#!/bin/bash
apt update
apt install -y libvips
apt install -y libvips-tools
apt install -y libvips-dev

Please see Terra.bio documentation for more information.

Development installation

Create a virtual environment and and install celldega in editable mode with the optional development dependencies:

python -m venv .venv
source .venv/bin/activate
pip install -e ".[dev]"

You then need to install the JavaScript dependencies and run the development server.

npm install
npm run dev

Open example.ipynb in JupyterLab, VS Code, or your favorite editor to start developing. Changes made in js/ will be reflected in the notebook.

PyPI

Increment version in project.toml and

$ hatch build
$ hatch publish

Hatch Development

$ hatch env prune      # Remove old environments
$ hatch env create     # Create a new environment based on pyproject.toml
$ hatch shell          # Activate the new environment

NPM

Increment version in package.json and

$ npm run build
$ npm publish

Development Notes

May use older version of deck.gl 8.9.1 until bug with instanced layer is resolved using newer versions "^9.0.5".;