Contributing

This page is the docs-site entry point for contributors.

If you want the full contributor guide used on GitHub, see the repository file as well. Within the docs site, this page keeps the contribution path discoverable without breaking site navigation.

Getting Started

# Fork and clone
git clone https://github.com/YOUR_USERNAME/ChatSpatial.git
cd ChatSpatial

# Create environment and install
python3 -m venv venv && source venv/bin/activate
pip install -e ".[dev]"

# Verify
pytest tests/unit/ -x

Prerequisites: Python 3.11-3.13, Git. For R-based methods (RCTD, CellChat, SPARK-X, etc.): R 4.4+ and rpy2.

Contribution Paths

Documentation

  • clarify terminology

  • reduce duplicated guidance

  • improve examples and workflows

  • keep method/reference docs aligned with schemas

Code

Common areas:

  • chatspatial/ — package source

  • tests/ — automated verification

  • docs/ — user-facing documentation

New analysis methods

Follow the existing pattern:

  • add a parameter model in models/data.py

  • add a result model in models/analysis.py

  • implement the tool in tools/

  • register it in server.py

  • add unit/integration tests

Quality Gate

black chatspatial/
isort chatspatial/
ruff check chatspatial/ --fix
mypy chatspatial/
pytest tests/unit/

Submitting Changes

  1. Create a branch

  2. Make focused changes

  3. Run tests and linting

  4. Open a PR against main

Suggested commit styles:

feat: add new spatial analysis method
fix: handle edge case in deconvolution
docs: update methods reference
test: add integration test for trajectory

More Detail

For the full contributor guide, open CONTRIBUTING.md.

For user-facing docs, return to: