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Contribute

We welcome all kinds of contributions to keep PyHealth growing and thriving: bug reports, feature proposals, new datasets, tasks, and models, bug fixes, and documentation improvements.

The full contributor guide lives in our documentation: How to Contribute (source: docs/how_to_contribute.rst). Please read it before opening a pull request. It covers:

  • Examples of great contributions and the review criteria we use
  • Setting up your development environment
  • Getting data access (MIMIC credentialing and open demo datasets)
  • Implementation requirements: file headers, code style, and docstrings
  • File checklists for contributing a dataset, task, or model
  • Test case requirements, including how to write fast tests with synthetic data
  • How to format your pull request description

Quick Start

  1. Fork the PyHealth repository

  2. Clone your fork and install it in editable mode:

    git clone https://github.com/your_username/PyHealth.git
cd PyHealth
pip install -e .

  3. Implement your change with tests and documentation

  4. Push to your fork and open a pull request against the master branch, with "Allow edits by maintainers" enabled

For trivial changes you can open a pull request directly. For non-trivial changes, please discuss them in an issue first.

Submit an Issue

Submit an issue on GitHub to report a bug or propose a new feature. For bug reports, please include:

  • A quick summary
  • Steps to reproduce (with sample code if possible)
  • What you expected to happen
  • What actually happens
  • Why you think this might be happening, and anything you tried that did not work

PR Contribution Rules (enforced in CI)

Any pull request that modifies a file under pyhealth/ must:

  • Keep newly added/modified lines free of ruff lint violations (ruff check, 88-char line length). Pre-existing lint issues elsewhere in a touched file are not blocked.
  • Give every new or modified top-level public class/function a >>> usage example in its docstring, so it renders as example code in the API docs.

These rules are checked by .github/workflows/pr_contribution_rules.yml, which runs tools/check_pr_rules.py. You can run the same check locally:

python tools/check_pr_rules.py --base <base_sha> --head HEAD

Community

Join our Slack workspace to ask questions, discuss ideas, and share your work.