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Contributing to amber-codon-scanner

Thank you for your interest in contributing!

Reporting bugs

Please open an issue on GitHub with:

  • A description of the bug
  • A minimal reproducible example (DNA sequence and expected output)
  • Your Python version and operating system

Suggesting features

Open an issue describing:

  • The feature you would like
  • The biological use case it addresses
  • Any relevant literature on pyrrolysine or amber codon biology

Contributing code

  1. Fork the repository
  2. Create a new branch: git checkout -b my-feature
  3. Make your changes
  4. Run the tests: pytest
  5. Push your branch and open a pull request

Development setup

git clone https://github.com/CameronCat/amber-codon-scanner
cd amber-codon-scanner
pip install -e ".[dev]"
pytest

Code style

  • Follow PEP 8
  • Add docstrings to new functions
  • Add tests for new functionality
  • Keep biological claims grounded in published literature with citations
  • Be explicit about heuristic vs validated methods

Questions

Open an issue on GitHub.