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CONTRIBUTING.md

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Contributing to Catecholamine Research

Thank you for your interest in contributing to this research repository!

Getting Started

  1. Fork the repository
  2. Clone your fork locally
  3. Set up your development environment (see README.md)
  4. Create a new branch for your contribution

Development Setup

# Create virtual environment
python -m venv .venv
source .venv/bin/activate  # On Windows: .venv\Scripts\activate

# Install dependencies
pip install -r requirements.txt

Contributing Data

Adding Raw Data

All raw data must follow the data provenance rules outlined in protocol/PROTOCOL.md:

  1. Place raw data files in data/raw/
  2. Create a companion .meta.yaml file for each data file
  3. Follow the schema defined in schemas/raw_meta.schema.yaml
  4. Run validation: python scripts/validate_raw.py

Data Quality

  • Never edit raw data in place
  • Document extraction methods clearly
  • Include all relevant metadata
  • Mark questionable data with quality flags

Code Contributions

Scripts and Analysis

  • Keep scripts modular and well-documented
  • Follow existing code style
  • Add comments for complex logic
  • Test your scripts before submitting

Paper Contributions

  • Use Quarto for narrative documents (.qmd)
  • Keep code and narrative together
  • Ensure all figures are generated from code
  • Maintain citation integrity in refs/references.bib

Pull Request Process

  1. Ensure your code passes validation scripts
  2. Update documentation as needed
  3. Describe your changes clearly in the PR
  4. Link to any relevant issues

Research Ethics

  • Ensure all data sources are properly cited
  • Follow anti-cherry-picking protocols
  • Document inclusion/exclusion decisions
  • Maintain reproducibility standards

Questions?

Open an issue for questions or discussions about the research protocol or contribution process.