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Contributing to 3DCS

Thank you for considering contributing to 3DCS! This document explains how to set up a development environment and submit changes.

Development Setup

# Clone the repository
git clone https://github.com/ComDec/3DCS.git
cd 3DCS

# Create a virtual environment
python -m venv .venv
source .venv/bin/activate

# Install in editable mode with dev dependencies
pip install -e ".[dev]"

# Install RDKit (required for molecule parsing)
pip install rdkit-pypi

# Install pre-commit hooks
pre-commit install

Running Tests

# Run all tests
pytest

# Run with coverage
pytest --cov=three_dbench

# Skip slow tests (those requiring HF downloads)
pytest -m "not slow"

Code Style

This project uses ruff for linting and formatting.

# Check for issues
ruff check src/ tests/

# Auto-fix issues
ruff check --fix src/ tests/

# Format code
ruff format src/ tests/

Key style rules:

  • Line length: 120 characters
  • Python 3.9+ syntax
  • Imports sorted with isort rules (via ruff)

Adding a New Benchmark

  1. Create a subpackage under src/three_dbench/ (e.g., my_task/)
  2. Add dataset conversion in src/three_dbench/datasets/my_task.py
  3. Add evaluation logic in src/three_dbench/my_task/evaluation.py
  4. Add a benchmark entry point in src/three_dbench/benchmarks/my_task.py
  5. Register the task in src/three_dbench/__main__.py
  6. Add tests under tests/

Submitting Changes

  1. Fork the repository and create a feature branch
  2. Make your changes with tests
  3. Run make lint and make test to verify
  4. Submit a pull request with a clear description

Reporting Issues

Use the GitHub issue tracker to report bugs or request features. Please include:

  • Python version and OS
  • Steps to reproduce the issue
  • Expected vs. actual behavior