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Contributing to ProBioPred

Thank you for your interest in contributing to ProBioPred!

How to contribute

  1. Fork the repository on GitHub
  2. Clone your fork locally
  3. Create a branch for your changes: git checkout -b your-feature-name
  4. Make your changes and test them
  5. Commit with a clear message: git commit -m "Add/fix: description"
  6. Push to your fork: git push origin your-feature-name
  7. Open a Pull Request against the main branch

Development setup

conda create -n probiopred python=3.10
conda activate probiopred
conda install -c bioconda blast
conda install -c conda-forge libsvm
pip install -e .

You will also need RGI (Resistance Gene Identifier) for antibiotic resistance detection. See the main README for full installation instructions.

Code style

  • Use Python 3
  • Follow PEP 8 where practical
  • Add docstrings to new functions

Reporting issues

If you find a bug or have a suggestion, please open an issue on GitHub with:

  • A clear description of the problem
  • Steps to reproduce (for bugs)
  • Your environment (OS, Python version, etc.)

Questions

For questions about ProBioPred, you can open an issue or contact the maintainers.