Merge main into move-no-prediction

Resolved conflicts in classifier.py by combining:
- frame_indexes parameter support from move-no-prediction branch
- CatBoost classifier support from main branch
Both features are now integrated in predict() and predict_proba() methods.

Author: gbeane

.github/workflows/_run-tests-action.yml

@@ -32,4 +32,4 @@ jobs:
         run: uv sync
 
       - name: Test with pytest
-        run: uv run pytest --ignore=tests/test_search_bar_widget.py tests
+        run: uv run pytest tests

CONTRIBUTING.md

@@ -0,0 +1,121 @@
+# Contributing to JABS
+
+Thank you for your interest in contributing to JABS (JAX Animal Behavior System)! This document provides guidelines for contributing to the project.
+
+## Copyright and License
+
+**Important:** By contributing source code to JABS, you agree that your contributions will have their copyright assigned to The Jackson Laboratory.
+
+All code contributions become part of the JABS project and are subject to the project's license terms (see the LICENSE file in the repository root). JABS is licensed under a non-commercial use license. Contact [email protected] for information about commercial licensing.
+
+## Quick Start for Contributors
+
+```bash
+# 1. Fork and clone the repository
+git clone https://github.com/YOUR_USERNAME/JABS-behavior-classifier.git
+cd JABS-behavior-classifier
+
+# 2. Install uv (Python package manager)
+curl -LsSf https://astral.sh/uv/install.sh | sh   # macOS/Linux
+# OR: powershell -c "irm https://astral.sh/uv/install.ps1 | iex"  # Windows
+
+# 3. Set up development environment
+uv sync
+source .venv/bin/activate  # macOS/Linux (or .venv\Scripts\activate on Windows)
+pre-commit install
+
+# 4. Create a feature branch
+git checkout -b feature/my-feature
+
+# 5. Make your changes and commit
+git add .
+git commit -m "Description of changes"
+
+# 6. Run tests
+pytest
+
+# 7. Push and create a pull request
+git push origin feature/my-feature
+```
+
+## Contribution Guidelines
+
+Before submitting a contribution:
+
+1. **Follow the code style guidelines** - JABS uses Ruff for linting and formatting
+2. **Add tests** for new functionality
+3. **Update documentation** as needed (docstrings, user guide, developer guide)
+4. **Run the test suite** to ensure nothing is broken: `pytest`
+5. **Ensure pre-commit hooks pass** - They will run automatically when you commit
+6. **Submit a pull request** with a clear description of your changes
+
+### Code Style
+
+JABS uses [Ruff](https://docs.astral.sh/ruff/) for linting and formatting:
+
+```bash
+# Check for issues
+ruff check .
+
+# Auto-fix issues
+ruff check --fix .
+
+# Format code
+ruff format .
+```
+
+Pre-commit hooks will automatically run these checks before each commit. If your commit is blocked:
+
+1. Fix issues: `ruff check --fix . && ruff format .`
+2. Stage fixes: `git add -u`
+3. Try committing again
+
+### Running Tests
+
+```bash
+pytest              # Run all tests
+pytest -v           # Verbose output
+pytest tests/path/  # Run specific tests
+```
+
+## Types of Contributions Welcome
+
+We welcome various types of contributions:
+
+- **Bug fixes**: Help identify and fix issues
+- **New features**: Add new behavioral features, classifiers, or GUI improvements
+- **Documentation**: Improve user guides, developer documentation, or code comments
+- **Testing**: Add test coverage or improve existing tests
+- **Performance improvements**: Optimize code for better performance
+
+## Developer Documentation
+
+For detailed information about JABS architecture, development setup, and implementation guides, see:
+
+- **[Development Guide](docs/DEVELOPMENT.md)** - Comprehensive guide to JABS architecture, feature extraction system, building, and deployment
+- **[User Guide](docs/user-guide.md)** - End-user documentation
+
+## Pull Request Process
+
+1. **Create a feature branch** from `main`
+2. **Make your changes** with clear, focused commits
+3. **Update tests** and documentation
+4. **Ensure all tests pass** locally
+5. **Create a pull request** against the `main` branch
+6. **Wait for review** - Maintainers will review and may request changes
+7. **CI/CD checks must pass** - Automated checks will run on your PR
+
+## Questions?
+
+- **General questions**: Open an issue on GitHub
+- **Security issues**: Email [email protected] (do not open public issues)
+- **Development questions**: See [DEVELOPMENT.md](docs/DEVELOPMENT.md) or contact [email protected]
+
+## Code of Conduct
+
+Be respectful and professional in all interactions. We aim to foster an inclusive and welcoming community.
+
+---
+
+**Thank you for contributing to JABS!**
+