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Contributing to BioPAT

We welcome contributions to the BioPAT project! As an open science effort, your input helps advance the state of biomedical IR.

How to Contribute

  1. Bug Reports: Open an issue on GitHub describing the bug and steps to reproduce.
  2. Feature Requests: Discuss new features in the GitHub Issues.
  3. Pull Requests:
    • Fork the repository.
    • Create a new branch.
    • Ensure all tests pass (pytest).
    • Update CHANGELOG.md with your changes.
    • Submit the PR.

Code Standards

  • Use Black for formatting.
  • Use isort for imports.
  • Include type hints for all new functions.
  • Add tests for new functionality in the tests/ directory.

Reproducibility Priority

BioPAT is an academic benchmark. Any changes to the data processing pipeline must be strictly deterministic and documented.