Modernize project structure for better OSS contribution experience

This commit restructures the project to follow modern Python packaging
best practices and makes it easier for contributors to get started.

Major changes:
- Add pyproject.toml for unified project configuration (PEP 621)
- Simplify setup.py to only handle C++ extension building
- Consolidate requirements.txt files into pyproject.toml
- Reorganize development scripts into tools/ directory
- Add comprehensive DEVELOPMENT.md guide for contributors
- Update Makefile with modern development workflows
- Update CI/CD workflows to use new structure
- Clean up root directory for better organization

Benefits:
- Single source of truth for dependencies and metadata
- Easier setup for new contributors (pip install -e ".[dev]")
- Modern tooling integration (black, ruff, mypy)
- Clear development documentation
- Cleaner, more maintainable project structure

Files removed:
- init_develop.sh, run_test.sh (replaced by Makefile targets)
- requirements.txt, requirements-dev.txt (moved to pyproject.toml)

Files added:
- pyproject.toml (project configuration)
- DEVELOPMENT.md (contributor guide)
- tools/ directory (development utilities)

Files updated:
- setup.py (simplified, metadata moved to pyproject.toml)
- Makefile (new targets for modern workflow)
- README.md (updated installation instructions)
- CI/CD workflows (updated for new structure)
- MANIFEST.in (updated for new file structure)

Author: claude

.github/workflows/cibuildwheel.yml

@@ -45,12 +45,11 @@ jobs:
           python-version: ${{ matrix.python }}
       - name: Install dependencies
         run: |
-          python -m pip install --upgrade pip wheel setuptools
-          python -m pip install numpy pytest
+          python -m pip install --upgrade pip build
       - name: Build and install
-        run: python -m pip install -e .
+        run: python -m pip install -e ".[dev]"
       - name: Run tests
-        run: pytest tests -vv
+        run: python -m pytest tests -vv
 
   build_wheels:
     # Skip wheel builds on PRs - only build on main branch and tags

DEVELOPMENT.md

@@ -0,0 +1,347 @@
+# Development Guide
+
+Welcome to the python_prtree development guide! This document will help you get started with contributing to the project.
+
+## Project Structure
+
+```
+python_prtree/
+├── src/                    # Python source code
+│   └── python_prtree/     # Main package
+├── cpp/                    # C++ implementation
+├── tests/                  # Test suite
+│   ├── unit/              # Unit tests
+│   ├── integration/       # Integration tests
+│   └── e2e/               # End-to-end tests
+├── tools/                  # Development tools and scripts
+├── benchmarks/             # Performance benchmarks
+├── docs/                   # Documentation
+├── .github/workflows/      # CI/CD configuration
+└── third/                  # Third-party dependencies (git submodules)
+```
+
+## Prerequisites
+
+- Python 3.8 or higher
+- CMake 3.22 or higher
+- C++17 compatible compiler
+- Git (for submodules)
+
+### Platform-Specific Requirements
+
+**macOS:**
+```bash
+brew install cmake
+```
+
+**Ubuntu/Debian:**
+```bash
+sudo apt-get install cmake build-essential
+```
+
+**Windows:**
+- Visual Studio 2019 or later with C++ development tools
+- CMake (can be installed via Visual Studio installer or from cmake.org)
+
+## Getting Started
+
+### 1. Clone the Repository
+
+```bash
+git clone https://github.com/atksh/python_prtree.git
+cd python_prtree
+```
+
+### 2. Initialize Submodules
+
+The project uses git submodules for third-party dependencies:
+
+```bash
+git submodule update --init --recursive
+```
+
+Or use the Makefile:
+
+```bash
+make init
+```
+
+### 3. Set Up Development Environment
+
+#### Using pip (recommended)
+
+```bash
+# Install in development mode with all dependencies
+pip install -e ".[dev,docs,benchmark]"
+```
+
+#### Using make
+
+```bash
+# Initialize submodules and install dependencies
+make dev
+```
+
+This will:
+- Initialize git submodules
+- Install the package in editable mode
+- Install all development dependencies
+
+### 4. Build the C++ Extension
+
+```bash
+# Build in debug mode (default)
+make build
+
+# Or build in release mode
+make build-release
+```
+
+## Development Workflow
+
+### Running Tests
+
+```bash
+# Run all tests
+make test
+
+# Run tests in parallel (faster)
+make test-fast
+
+# Run tests with coverage report
+make test-coverage
+
+# Run specific test
+make test-one TEST=test_insert
+```
+
+Or use pytest directly:
+
+```bash
+pytest tests -v
+pytest tests/unit/test_insert.py -v
+pytest tests -k "test_insert" -v
+```
+
+### Code Quality
+
+#### Format Code
+
+```bash
+# Format both Python and C++ code
+make format
+
+# Format only Python (uses black)
+python -m black src/ tests/
+
+# Format only C++ (uses clang-format)
+clang-format -i cpp/*.cc cpp/*.h
+```
+
+#### Lint Code
+
+```bash
+# Lint all code
+make lint
+
+# Lint only Python (uses ruff)
+make lint-python
+
+# Lint only C++ (uses clang-tidy)
+make lint-cpp
+
+# Type check Python code (uses mypy)
+make type-check
+```
+
+### Building Documentation
+
+```bash
+make docs
+```
+
+### Cleaning Build Artifacts
+
+```bash
+# Remove build artifacts
+make clean
+
+# Clean everything including submodules
+make clean-all
+```
+
+## Project Configuration
+
+All project metadata and dependencies are defined in `pyproject.toml`:
+
+- **Project metadata**: name, version, description, authors
+- **Dependencies**: runtime and development dependencies
+- **Build system**: setuptools with CMake integration
+- **Tool configurations**: pytest, black, ruff, mypy, coverage
+
+## Testing Guidelines
+
+### Test Organization
+
+- `tests/unit/`: Unit tests for individual components
+- `tests/integration/`: Tests for component interactions
+- `tests/e2e/`: End-to-end workflow tests
+- `tests/legacy/`: Legacy test suite
+
+### Writing Tests
+
+```python
+import pytest
+from python_prtree import PRTree
+
+def test_basic_insertion():
+    """Test basic rectangle insertion."""
+    tree = PRTree()
+    tree.insert([0, 0, 10, 10], "rect1")
+    assert tree.size() == 1
+
+def test_query():
+    """Test rectangle query."""
+    tree = PRTree()
+    tree.insert([0, 0, 10, 10], "rect1")
+    results = tree.query([5, 5, 15, 15])
+    assert len(results) > 0
+```
+
+### Running Specific Test Categories
+
+```bash
+# Run only unit tests
+pytest tests/unit -v
+
+# Run only integration tests
+pytest tests/integration -v
+
+# Run only e2e tests
+pytest tests/e2e -v
+```
+
+## C++ Development
+
+### Building with Debug Symbols
+
+```bash
+make debug-build
+```
+
+### Profiling
+
+```bash
+# Run profiling scripts
+./tools/profile.sh
+python tools/profile.py
+```
+
+### Benchmarks
+
+```bash
+# Run benchmarks (if available)
+make benchmark
+```
+
+## Continuous Integration
+
+The project uses GitHub Actions for CI/CD:
+
+- **Pull Requests**: Runs unit tests on multiple platforms (Linux, macOS, Windows) and Python versions (3.8-3.14)
+- **Main Branch**: Builds wheels for all platforms and Python versions
+- **Version Tags**: Publishes packages to PyPI
+
+## Making Changes
+
+### Workflow
+
+1. Create a new branch:
+   ```bash
+   git checkout -b feature/my-feature
+   ```
+
+2. Make your changes and write tests
+
+3. Run tests and linting:
+   ```bash
+   make test
+   make lint
+   ```
+
+4. Commit your changes:
+   ```bash
+   git add .
+   git commit -m "Add feature: description"
+   ```
+
+5. Push and create a pull request:
+   ```bash
+   git push origin feature/my-feature
+   ```
+
+### Code Style
+
+- **Python**: Follow PEP 8, use black for formatting (100 char line length)
+- **C++**: Follow Google C++ Style Guide, use clang-format
+- **Commits**: Use conventional commit messages
+  - `feat:` for new features
+  - `fix:` for bug fixes
+  - `docs:` for documentation
+  - `test:` for test changes
+  - `refactor:` for refactoring
+  - `chore:` for maintenance tasks
+
+## Troubleshooting
+
+### Submodules Not Initialized
+
+```bash
+git submodule update --init --recursive
+```
+
+### Build Fails
+
+1. Ensure CMake is installed and up to date
+2. Check that all submodules are initialized
+3. Try cleaning and rebuilding:
+   ```bash
+   make clean
+   make build
+   ```
+
+### Tests Fail
+
+1. Ensure the extension is built:
+   ```bash
+   make build
+   ```
+
+2. Check that all dependencies are installed:
+   ```bash
+   pip install -e ".[dev]"
+   ```
+
+### Import Errors
+
+Ensure you've installed the package in development mode:
+```bash
+pip install -e .
+```
+
+## Additional Resources
+
+- [CONTRIBUTING.md](CONTRIBUTING.md) - Contribution guidelines
+- [README.md](README.md) - Project overview
+- [CHANGES.md](CHANGES.md) - Version history
+- [GitHub Issues](https://github.com/atksh/python_prtree/issues) - Bug reports and feature requests
+
+## Questions?
+
+If you have questions or need help, please:
+
+1. Check existing [GitHub Issues](https://github.com/atksh/python_prtree/issues)
+2. Open a new issue with your question
+3. See [CONTRIBUTING.md](CONTRIBUTING.md) for more details
+
+Happy coding! 🎉

MANIFEST.in

@@ -1,6 +1,8 @@
-include README.md LICENSE
-include requirements.txt
+include README.md LICENSE CHANGES.md CONTRIBUTING.md DEVELOPMENT.md
+include pyproject.toml setup.py
 global-include CMakeLists.txt *.cmake
-recursive-include cpp *
-recursive-include src *
-recursive-include third *
+recursive-include cpp *.h *.cc
+recursive-include src *.py
+recursive-include third *
+exclude third/.git*
+prune third/**/.git