# NeuroStrip
[](https://pypi.org/project/neurostrip/)
[](https://github.com/dyollb/neurostrip/actions/workflows/ci.yml)
[](LICENSE)
[](https://pypi.org/project/neurostrip/)
CNN based skull stripping (brain masking) from MRI
## Installation
For CPU support:
```bash
pip install neurostrip[cpu]
```
For GPU support:
```bash
pip install neurostrip[gpu]
```
## Usage
```bash
neurostrip --image-path input.nii.gz --output-path output.nii.gz
```
## Development
### Setup Development Environment
1. Clone the repository
2. Set up the development environment:
```bash
make setup-dev
```
This will:
- Install the package in editable mode with development dependencies
- Install pre-commit hooks for automatic code quality checks
### Development Tools
The project uses modern Python development tools optimized for Python ≥3.10:
- **Ruff**: Ultra-fast Python linter and formatter (replaces Black, isort, flake8, and more)
- **MyPy**: Static type checking
- **Bandit**: Security vulnerability scanning
- **pytest**: Testing framework
- **pre-commit**: Git hooks for automated code quality
### Available Commands
```bash
make help # Show all available commands
make format # Format code with ruff
make lint # Run ruff linter
make fix # Run ruff linter with auto-fix
make type-check # Run mypy type checker
make security # Run bandit security scanner
make test # Run tests with pytest
make test-cov # Run tests with coverage report
make check # Run all checks (format, lint, type-check, test)
make pre-commit-run # Run pre-commit on all files
make clean # Clean build artifacts
```
### Pre-commit Hooks
Pre-commit hooks run automatically on every commit to ensure code quality:
- **General checks**: trailing whitespace, end-of-file fixing, YAML/TOML validation
- **Ruff linting and formatting**: comprehensive Python code analysis and formatting
- **MyPy type checking**: static type analysis
- **Bandit security scanning**: security vulnerability detection
- **Safety dependency checking**: known security vulnerabilities in dependencies
- **Typos spell checking**: documentation and comment spell checking
### Code Quality Standards
The project enforces strict code quality standards:
#### Ruff Configuration
- **Target**: Python 3.10+
- **Rules**: Comprehensive set including pycodestyle, pyflakes, isort, pyupgrade, simplify, type-checking, and pylint
#### Type Checking
- **MyPy**: Strict type checking enabled
- **Required**: Type annotations for all public functions
- **Configuration**: Comprehensive warnings and strict equality checks
### Running Tests
```bash
# Run all tests
make test
# Run with coverage report
make test-cov
# Run specific test file
python -m pytest tests/test_main.py -v
# Run specific test function
python -m pytest tests/test_main.py::test_predict_basic -v
```
### Development Workflow
1. **Make changes**: Edit code in `src/` directory
2. **Format and check**: Run `make check` to ensure code quality
3. **Test**: Run `make test` to verify functionality
4. **Commit**: Pre-commit hooks will run automatically
5. **Push**: Create pull request
### Adding Dependencies
- **Runtime dependencies**: Add to `dependencies` in `pyproject.toml`
- **Development dependencies**: Add to `dev` optional dependencies
- **GPU support**: Already configured with `gpu` optional dependencies
### Project Structure
```
neurostrip/
├── src/neurostrip/ # Main package source
├── tests/ # Test files
├── pyproject.toml # Project configuration
├── .pre-commit-config.yaml # Pre-commit hook configuration
├── Makefile # Development commands
└── README.md # This file
```
## Contributing
1. Fork the repository
2. Create a feature branch: `git checkout -b feature-name`
3. Set up development environment: `make setup-dev`
4. Make your changes
5. Run quality checks: `make check`
6. Commit changes (pre-commit hooks will run automatically)
7. Push and create a pull request
All contributions must:
- Pass pre-commit hooks
- Maintain or improve test coverage
- Include type annotations
- Follow Google docstring conventions
- Pass all CI checks
## License
MIT License - see LICENSE file for details.
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