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| 1 | +# Contributing to Neurevo |
| 2 | + |
| 3 | +Thank you for your interest in contributing to Neurevo. This document outlines the process for contributing to the project. |
| 4 | + |
| 5 | +## Getting Started |
| 6 | + |
| 7 | +1. Fork the repository and clone your fork: |
| 8 | + |
| 9 | +```bash |
| 10 | +git clone https://github.com/<your-username>/creatures.git |
| 11 | +cd creatures |
| 12 | +``` |
| 13 | + |
| 14 | +2. Set up the development environment: |
| 15 | + |
| 16 | +```bash |
| 17 | +make setup |
| 18 | +``` |
| 19 | + |
| 20 | +3. Run the test suite to verify everything works: |
| 21 | + |
| 22 | +```bash |
| 23 | +make test |
| 24 | +``` |
| 25 | + |
| 26 | +## Development Workflow |
| 27 | + |
| 28 | +1. Create a feature branch from `main`: |
| 29 | + |
| 30 | +```bash |
| 31 | +git checkout -b feature/your-feature-name |
| 32 | +``` |
| 33 | + |
| 34 | +2. Make your changes, following the coding standards below. |
| 35 | + |
| 36 | +3. Run tests and ensure they pass: |
| 37 | + |
| 38 | +```bash |
| 39 | +# Python tests |
| 40 | +make test |
| 41 | + |
| 42 | +# Frontend tests (if you modified creatures-web) |
| 43 | +cd creatures-web && npm test |
| 44 | +``` |
| 45 | + |
| 46 | +4. Commit your changes with a clear message: |
| 47 | + |
| 48 | +```bash |
| 49 | +git commit -m "Add description of what changed and why" |
| 50 | +``` |
| 51 | + |
| 52 | +5. Push to your fork and open a pull request against `main`. |
| 53 | + |
| 54 | +## Coding Standards |
| 55 | + |
| 56 | +### Python (creatures-core, creatures-api) |
| 57 | + |
| 58 | +- Python 3.13+ |
| 59 | +- Follow PEP 8 style guidelines |
| 60 | +- Use type hints for function signatures |
| 61 | +- Write docstrings for public functions and classes |
| 62 | +- Keep functions focused -- one function, one responsibility |
| 63 | +- Add unit tests for new functionality in `creatures-core/tests/` |
| 64 | + |
| 65 | +### TypeScript (creatures-web) |
| 66 | + |
| 67 | +- TypeScript strict mode |
| 68 | +- Use functional components with hooks |
| 69 | +- Keep components small and composable |
| 70 | +- Use Zustand for shared state, not prop drilling |
| 71 | + |
| 72 | +### General |
| 73 | + |
| 74 | +- No committed secrets, API keys, or credentials |
| 75 | +- Keep dependencies minimal -- justify new additions |
| 76 | +- Write clear commit messages that explain *why*, not just *what* |
| 77 | + |
| 78 | +## Project Structure |
| 79 | + |
| 80 | +| Directory | Language | Purpose | |
| 81 | +|-----------|----------|---------| |
| 82 | +| `creatures-core/` | Python | Core library: connectome, neural simulation, evolution, pharmacology | |
| 83 | +| `creatures-api/` | Python | FastAPI server with REST and WebSocket endpoints | |
| 84 | +| `creatures-web/` | TypeScript | React + Three.js frontend | |
| 85 | +| `scripts/` | Python | CLI tools for evolution, validation, and reporting | |
| 86 | +| `notebooks/` | Jupyter | Interactive demos and exploration | |
| 87 | + |
| 88 | +## Where to Contribute |
| 89 | + |
| 90 | +### High-Impact Areas |
| 91 | + |
| 92 | +- **New organisms**: Add connectome loaders and body models for zebrafish, mouse, or other species |
| 93 | +- **Neuron models**: Implement Hodgkin-Huxley or multi-compartment models alongside the existing LIF engine |
| 94 | +- **Fitness functions**: Design new behavioral assays for evolution (foraging efficiency, learning tasks, social behavior) |
| 95 | +- **Performance**: Optimize Brian2 simulation speed, parallelize evolution runs, GPU acceleration |
| 96 | +- **Pharmacology**: Add new drug models with receptor-level specificity |
| 97 | +- **Visualization**: Improve 3D rendering, add connectome graph views, evolution dashboards |
| 98 | + |
| 99 | +### Good First Issues |
| 100 | + |
| 101 | +Look for issues labeled `good first issue` on GitHub. These are scoped tasks suitable for new contributors. |
| 102 | + |
| 103 | +## Testing |
| 104 | + |
| 105 | +All contributions should include tests where applicable. |
| 106 | + |
| 107 | +```bash |
| 108 | +# Run Python tests with verbose output |
| 109 | +python -m pytest creatures-core/tests/ -v |
| 110 | + |
| 111 | +# Run a specific test file |
| 112 | +python -m pytest creatures-core/tests/test_connectome.py -v |
| 113 | + |
| 114 | +# Run with coverage |
| 115 | +python -m pytest creatures-core/tests/ --cov=creatures --cov-report=term-missing |
| 116 | +``` |
| 117 | + |
| 118 | +## Pull Request Guidelines |
| 119 | + |
| 120 | +- Keep PRs focused on a single change |
| 121 | +- Include a clear description of what changed and why |
| 122 | +- Reference any related issues |
| 123 | +- Ensure CI passes before requesting review |
| 124 | +- Add tests for new functionality |
| 125 | +- Update documentation if the public API changes |
| 126 | + |
| 127 | +## Reporting Bugs |
| 128 | + |
| 129 | +Open a GitHub issue with: |
| 130 | + |
| 131 | +1. A clear title describing the bug |
| 132 | +2. Steps to reproduce |
| 133 | +3. Expected behavior vs. actual behavior |
| 134 | +4. Your environment (OS, Python version, relevant package versions) |
| 135 | + |
| 136 | +## Requesting Features |
| 137 | + |
| 138 | +Open a GitHub issue with the `enhancement` label. Include: |
| 139 | + |
| 140 | +1. The problem you are trying to solve |
| 141 | +2. Your proposed solution |
| 142 | +3. Any alternatives you considered |
| 143 | + |
| 144 | +## Code of Conduct |
| 145 | + |
| 146 | +Be respectful and constructive. We are building tools to advance neuroscience and reduce animal testing. Treat fellow contributors with the same care we bring to the science. |
| 147 | + |
| 148 | +## License |
| 149 | + |
| 150 | +By contributing, you agree that your contributions will be licensed under the MIT License. |
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