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Contributing to ComProScanner

Thank you for your interest in contributing to ComProScanner! We welcome contributions from the community and appreciate your effort to improve this project.

Table of Contents

Code of Conduct

By participating in this project, you agree to maintain a respectful and inclusive environment. We expect all contributors to:

  • Use welcoming and inclusive language
  • Respect differing viewpoints and experiences
  • Accept constructive criticism gracefully
  • Focus on what is best for the community
  • Show empathy towards other community members

How Can I Contribute?

There are several ways to contribute to ComProScanner:

  • Report bugs - Help us identify issues in the codebase
  • Suggest features - Propose new features or improvements
  • Fix bugs - Submit fixes for identified issues
  • Add features - Implement new functionality
  • Improve documentation - Enhance existing documentation or add new guides
  • Write tests - Increase test coverage
  • Review pull requests - Help review contributions from other developers

Getting Started

Prerequisites

  • Python 3.12 or 3.13
  • Git
  • Basic understanding of materials science (helpful but not required)

Setting Up Development Environment

  1. Fork the repository on GitHub

  2. Clone your fork locally:

    git clone https://github.com/slimeslab/ComProScanner.git
cd comproscanner

  3. Create a virtual environment:

    python -m venv venv
source venv/bin/activate  # On Windows: venv\Scripts\activate

  4. Install dependencies:

    pip install -e ".[dev]"

  5. Create a .env file based on .env.example:

    cp .env.example .env

  6. Add your API keys to the .env file

Development Workflow

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

    git checkout -b feature/your-feature-name
# or
git checkout -b fix/your-bugfix-name

  2. Make your changes

  3. Test your changes thoroughly

  4. Commit your changes following the commit guidelines

  5. Push to your fork:

    git push origin feature/your-feature-name

  6. Submit a pull request

Commit Guidelines

Commit Message Format

Follow the Conventional Commits specification:

<type>(<scope>): <subject>

<body>

<footer>

Types

  • feat: New feature
  • fix: Bug fix
  • docs: Documentation changes
  • style: Code style changes (formatting, missing semicolons, etc.)
  • refactor: Code refactoring
  • test: Adding or updating tests
  • chore: Maintenance tasks
  • perf: Performance improvements

Examples

feat(extraction): add support for ACS publications

Implement article processing for American Chemical Society journals
using their TDM API.

Closes #123

fix(metadata): handle missing author information

Prevent crashes when author field is absent in article metadata
by providing default values.

Fixes #456

Pull Request Process

  1. Before submitting, ensure:

    • All tests pass
    • Code is formatted and linted
    • Documentation is updated
    • No merge conflicts with main branch

  2. PR Description should include:

    • Clear description of changes
    • Related issue numbers (e.g., "Closes #123")
    • Screenshots (if applicable)
    • Breaking changes (if any)

  3. Review Process:

    • At least one maintainer review is required
    • Address all review comments
    • Keep discussions focused and respectful

  4. After Approval:

    • Maintainers will merge your PR
    • Your contribution will be credited

Reporting Bugs

Before Submitting a Bug Report

  • Check existing issues to avoid duplicates
  • Collect relevant information about the bug
  • Try to reproduce the issue with the latest version

How to Submit a Bug Report

Create an issue with the following information:

  • Clear title - Summarize the problem
  • Description - Detailed description of the issue
  • Steps to reproduce - List exact steps to recreate the bug
  • Expected behavior - What you expected to happen
  • Actual behavior - What actually happened
  • Environment - OS, Python version, package version
  • Error messages - Full error traceback
  • Screenshots - If applicable

Suggesting Enhancements

We welcome feature suggestions! When proposing enhancements:

  • Use a clear title - Summarize the enhancement
  • Provide detailed description - Explain the feature and its benefits
  • Explain use cases - Describe scenarios where this would be useful
  • Consider alternatives - Mention other solutions you've considered
  • Mockups/examples - Provide examples or mockups if applicable

Documentation

Building Documentation Locally

pip install mkdocs mkdocs-material
mkdocs serve

Visit http://127.0.0.1:8000 to view the documentation.

Documentation Guidelines

  • Keep explanations clear and concise
  • Provide code examples
  • Update documentation when changing functionality
  • Follow the existing documentation structure
  • Use proper markdown formatting

Testing

Running Tests

pytest tests/

Writing Tests

  • Write unit tests for new features
  • Maintain or improve code coverage
  • Use descriptive test names
  • Include edge cases and error conditions

Example:

def test_extract_composition_valid_doi():
    """Test composition extraction with valid DOI."""
    result = extract_composition_data('10.1016/j.example.2024.1', 'd33')
    assert isinstance(result, dict)
    assert 'compositions' in result

def test_extract_composition_invalid_doi():
    """Test composition extraction with invalid DOI."""
    with pytest.raises(ValueError):
        extract_composition_data('invalid-doi', 'd33')

License

By contributing to ComProScanner, you agree that your contributions will be licensed under the MIT License.

Questions?

If you have questions about contributing, feel free to:

Thank you for contributing to ComProScanner!