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Contributing to DNA Sequence Analysis Tool

Thank you for your interest in contributing to the DNA Sequence Analysis Tool! We welcome contributions from the community to help improve this project.

Table of Contents

Code of Conduct

This project adheres to the Contributor Covenant code of conduct. By participating, you are expected to uphold this code.

Getting Started

  1. Fork the repository on GitHub
  2. Clone your fork locally
  3. Set up the development environment (see below)
  4. Create a new branch for your changes
  5. Make your changes
  6. Run tests
  7. Submit a pull request

Development Setup

Prerequisites

Installation

  1. Clone the repository:

    git clone https://github.com/yourusername/DNASequenceAnalysisTool.git
cd DNASequenceAnalysisTool

  2. Install dependencies:

    poetry install

  3. Set up pre-commit hooks:

    pre-commit install

Making Changes

  1. Create a new branch for your feature or bugfix:

    git checkout -b feature/your-feature-name
# or
git checkout -b fix/issue-number-description

  2. Make your changes following the code style guidelines

  3. Run tests to ensure everything works:

    poetry run pytest

  4. Commit your changes with a descriptive message:

    git commit -m "Add feature: your feature description"

Code Style

We use several tools to maintain code quality and style:

  • Black for code formatting
  • isort for import sorting
  • Flake8 for linting
  • Mypy for type checking

These are automatically checked by pre-commit hooks. To run them manually:

poetry run black .
poetry run isort .
poetry run flake8
poetry run mypy .

Testing

We use pytest for testing. To run the test suite:

poetry run pytest

For test coverage:

poetry run pytest --cov=dna_sequence_analysis_tool tests/

Documentation

We use Sphinx for documentation. To build the docs locally:

cd docs
poetry run make html

Documentation will be available in docs/_build/html/index.html.

Submitting a Pull Request

  1. Push your changes to your fork:

    git push origin your-branch-name

  2. Open a pull request against the main branch

  3. Fill in the PR template with all relevant information

  4. Ensure all CI checks pass

  5. Address any review comments

Reporting Issues

When reporting an issue, please include:

  • A clear description of the issue
  • Steps to reproduce
  • Expected vs actual behavior
  • Environment information (Python version, OS, etc.)
  • Any relevant error messages or logs

Feature Requests

We welcome feature requests! Please open an issue and use the "Feature Request" template to describe:

  • The feature you'd like to see
  • Why it would be useful
  • Any implementation ideas you have

Thank you for contributing to the DNA Sequence Analysis Tool!