docs: Fix README and CONTRIBUTING inconsistencies with implementation (#56)

* docs: Fix README and CONTRIBUTING inconsistencies with implementation

- Update README.md API Reference to match actual implementation
  - Add detailed parameter descriptions for all methods
  - Include missing getter methods for precision control
  - Fix insert() signature to show optional parameters
  - Add len() and n property documentation
  - Remove "(2D only)" from varargs query (works for 3D/4D too)
  - Add return type annotations for clarity

- Update CONTRIBUTING.md project structure
  - Update file paths to reflect current project layout
  - Change cpp/ to include/prtree/core/ and src/cpp/bindings/
  - Update Python wrapper path from __init__.py to core.py
  - Add pyproject.toml to project structure
  - Update test directory structure (unit/integration/e2e)

All examples verified to work correctly with current implementation.

* docs: Comprehensive documentation update with detailed docstrings

Major improvements:
1. **README.md**:
   - Clarified Thread Safety section with detailed explanations
   - Distinguished between read and write operations
   - Added concrete examples of thread-safe usage patterns
   - Explained when external synchronization is needed

2. **src/python_prtree/core.py**:
   - Added comprehensive docstrings to all classes and methods
   - Included detailed Args, Returns, Raises, Examples sections
   - Added performance complexity analysis
   - Documented thread safety for each method
   - Added See Also cross-references
   - Explained precision selection behavior
   - Provided extensive usage examples for each method

3. **docs/README.md** (new):
   - Created documentation directory guide
   - Explained purpose of each subdirectory
   - Added navigation guide for users and developers

Documentation now follows NumPy/Google docstring style with:
- Complete parameter descriptions with types
- Return value specifications
- Exception documentation
- Performance characteristics
- Thread safety notes
- Practical examples for all methods
- Cross-references between related methods

All README examples verified to work correctly with implementation.

* docs: Fix documentation inconsistencies across all files

Thoroughly verified all documentation against actual implementation
and fixed the following inconsistencies:

**README.md:**
- Removed precision control methods (set/get_adaptive_epsilon, etc.)
  that are not exposed in the Python API. These methods exist in C++
  bindings but are not accessible to users through the Python wrapper.

**docs/DEVELOPMENT.md:**
- Removed reference to non-existent benchmarks/python/ directory
- Removed tests/legacy/ from test organization section (internal only)
- Fixed cross-reference paths to use ../ prefix (CONTRIBUTING.md,
  README.md, CHANGES.md) since DEVELOPMENT.md is in docs/ subdirectory

**docs/ARCHITECTURE.md:**
- Removed benchmarks/python/README.md from directory structure
- Added tests/legacy/ directory to test suite structure

**Makefile:**
- Fixed CPP_DIR variable from 'cpp' to 'src/cpp' to match actual
  directory structure

All changes verified with tests - README examples still pass.

---------

Co-authored-by: Claude <[email protected]>

Author: atksh

CONTRIBUTING.md

@@ -103,9 +103,10 @@ make quick       # Quick test (clean + build + test)
    ```
 
 3. **Make changes**
-   - C++ code: `cpp/prtree.h`, `cpp/main.cc`
-   - Python wrapper: `src/python_prtree/__init__.py`
-   - Tests: `tests/test_PRTree.py`
+   - C++ core: `include/prtree/core/prtree.h`
+   - Python bindings: `src/cpp/bindings/python_bindings.cc`
+   - Python wrapper: `src/python_prtree/core.py`
+   - Tests: `tests/unit/`, `tests/integration/`, `tests/e2e/`
 
 4. **Build and test**
    ```bash
@@ -144,7 +145,7 @@ make quick       # Quick test (clean + build + test)
 
 3. **Implement feature**
    ```cpp
-   // cpp/prtree.h
+   // include/prtree/core/prtree.h
    // Add implementation
    ```
 
@@ -205,20 +206,30 @@ make test-coverage
 
 ```
 python_prtree/
-├── cpp/                    # C++ implementation
-│   ├── prtree.h           # PRTree core implementation
-│   ├── main.cc            # Python bindings
-│   ├── parallel.h         # Parallel processing utilities
-│   └── small_vector.h     # Optimized vector
-├── src/python_prtree/     # Python wrapper
-│   └── __init__.py
+├── include/               # C++ public headers
+│   └── prtree/
+│       ├── core/          # Core algorithm headers
+│       │   └── prtree.h   # PRTree core implementation
+│       └── utils/         # Utility headers
+│           ├── parallel.h # Parallel processing utilities
+│           └── small_vector.h # Optimized vector
+├── src/
+│   ├── cpp/               # C++ implementation
+│   │   └── bindings/      # Python bindings
+│   │       └── python_bindings.cc
+│   └── python_prtree/     # Python wrapper
+│       ├── __init__.py    # Package entry point
+│       └── core.py        # Main user-facing classes
 ├── tests/                 # Test suite
-│   └── test_PRTree.py
+│   ├── unit/              # Unit tests
+│   ├── integration/       # Integration tests
+│   └── e2e/               # End-to-end tests
 ├── third/                 # Third-party libraries (submodules)
 │   ├── pybind11/
 │   └── snappy/
 ├── CMakeLists.txt         # CMake configuration
-├── setup.py               # Packaging configuration
+├── pyproject.toml         # Project metadata and dependencies
+├── setup.py               # Build configuration
 ├── Makefile              # Development workflow
 └── README.md             # User documentation
 ```

Makefile

@@ -17,7 +17,7 @@ PIP := $(PYTHON) -m pip
 
 # Project directories
 SRC_DIR := src/python_prtree
-CPP_DIR := cpp
+CPP_DIR := src/cpp
 TEST_DIR := tests
 BUILD_DIR := build
 DIST_DIR := dist

README.md

@@ -67,7 +67,7 @@ tree4d = PRTree4D(indices, boxes_4d)  # 4D boxes
 ```python
 # Query with point coordinates
 result = tree.query([0.5, 0.5])        # Returns indices
-result = tree.query(0.5, 0.5)          # Varargs also supported (2D only)
+result = tree.query(0.5, 0.5)          # Varargs also supported
 ```
 
 ### Dynamic Updates
@@ -178,24 +178,38 @@ The library supports native float32 and float64 precision with automatic selecti
 - **Auto-detection**: Precision automatically selected based on numpy array dtype
 - **Save/Load**: Precision automatically detected when loading from file
 
-Advanced precision control available:
-```python
-# Configure precision parameters for challenging cases
-tree = PRTree2D(indices, boxes)
-tree.set_adaptive_epsilon(True)  # Adaptive epsilon based on box sizes
-tree.set_relative_epsilon(1e-6)   # Relative epsilon for intersection tests
-tree.set_absolute_epsilon(1e-12)  # Absolute epsilon for near-zero cases
-tree.set_subnormal_detection(True) # Handle subnormal numbers correctly
-```
-
 The new architecture eliminates the previous float32 tree + refinement approach,
 providing true native precision at each level for better performance and accuracy.
 
 ### Thread Safety
 
-- Query operations are thread-safe
-- Insert/erase operations are NOT thread-safe
-- Use external synchronization for concurrent updates
+**Read Operations (Thread-Safe):**
+- `query()` and `batch_query()` are thread-safe when used concurrently from multiple threads
+- Multiple threads can safely perform read operations simultaneously
+- No external synchronization needed for concurrent queries
+
+**Write Operations (Require Synchronization):**
+- `insert()`, `erase()`, and `rebuild()` modify the tree structure
+- These operations use internal mutex locks for atomicity
+- **Important**: Do NOT perform write operations concurrently with read operations
+- Use external synchronization (locks) to prevent concurrent reads and writes
+
+**Recommended Pattern:**
+```python
+import threading
+
+tree = PRTree2D([1, 2], [[0, 0, 1, 1], [2, 2, 3, 3]])
+lock = threading.Lock()
+
+# Multiple threads can query safely without locks
+def query_worker():
+    result = tree.query([0.5, 0.5, 1.5, 1.5])  # Safe without lock
+
+# Write operations need external synchronization
+def insert_worker(idx, box):
+    with lock:  # Protect against concurrent reads/writes
+        tree.insert(idx, box)
+```
 
 ## Installation from Source
 
@@ -216,22 +230,68 @@ For detailed development setup, see [DEVELOPMENT.md](docs/DEVELOPMENT.md).
 
 #### Constructor
 ```python
-PRTree2D(indices=None, boxes=None)
-PRTree2D(filename)  # Load from file
+PRTree2D()                             # Empty tree
+PRTree2D(indices, boxes)               # With data
+PRTree2D(filename)                     # Load from file
 ```
 
+**Parameters:**
+- `indices` (optional): Array of integer indices for each bounding box
+- `boxes` (optional): Array of bounding boxes (shape: [n, 2*D] where D is dimension)
+- `filename` (optional): Path to saved tree file
+
 #### Methods
-- `query(box, return_obj=False)` - Find overlapping boxes
-- `batch_query(boxes)` - Parallel batch queries
-- `query_intersections()` - Find all intersecting pairs
-- `insert(idx, bb, obj=None)` - Add box
-- `erase(idx)` - Remove box
-- `rebuild()` - Rebuild tree for optimal performance
-- `save(filename)` - Save to binary file
-- `load(filename)` - Load from binary file
-- `size()` - Get number of boxes
-- `get_obj(idx)` - Get stored object
-- `set_obj(idx, obj)` - Update stored object
+
+**Query Methods:**
+- `query(*args, return_obj=False)` → `List[int]` or `List[Any]`
+  - Find all bounding boxes that overlap with the query box or point
+  - Accepts box coordinates as list/array or varargs (e.g., `query(x, y)` for 2D points)
+  - Set `return_obj=True` to return associated objects instead of indices
+
+- `batch_query(boxes)` → `List[List[int]]`
+  - Parallel batch queries for multiple query boxes
+  - Returns a list of result lists, one per query
+
+- `query_intersections()` → `np.ndarray`
+  - Find all pairs of intersecting bounding boxes
+  - Returns array of shape (n_pairs, 2) containing index pairs
+
+**Modification Methods:**
+- `insert(idx=None, bb=None, obj=None)` → `None`
+  - Add a new bounding box to the tree
+  - `idx`: Index for the box (auto-assigned if None)
+  - `bb`: Bounding box coordinates (required)
+  - `obj`: Optional Python object to associate with the box
+
+- `erase(idx)` → `None`
+  - Remove a bounding box by index
+
+- `rebuild()` → `None`
+  - Rebuild tree for optimal performance after many updates
+
+**Persistence Methods:**
+- `save(filename)` → `None`
+  - Save tree to binary file
+
+- `load(filename)` → `None`
+  - Load tree from binary file
+
+**Object Storage Methods:**
+- `get_obj(idx)` → `Any`
+  - Retrieve the Python object associated with a bounding box
+
+- `set_obj(idx, obj)` → `None`
+  - Update the Python object associated with a bounding box
+
+**Size and Properties:**
+- `size()` → `int`
+  - Get the number of bounding boxes in the tree
+
+- `len(tree)` → `int`
+  - Same as `size()`, allows using `len(tree)`
+
+- `n` → `int` (property)
+  - Get the number of bounding boxes (same as `size()`)
 
 ## Version History
 

docs/ARCHITECTURE.md

@@ -47,16 +47,15 @@ python_prtree/
 │   ├── e2e/                    # End-to-end tests
 │   │   ├── test_readme_examples.py
 │   │   └── test_user_workflows.py
+│   ├── legacy/                 # Legacy test suite
 │   └── conftest.py             # Shared test fixtures
 │
 ├── benchmarks/                 # Performance Benchmarks
-│   ├── cpp/                    # C++ benchmarks
-│   │   ├── benchmark_construction.cpp
-│   │   ├── benchmark_query.cpp
-│   │   ├── benchmark_parallel.cpp
-│   │   └── stress_test_concurrent.cpp
-│   └── python/                 # Python benchmarks (future)
-│       └── README.md
+│   └── cpp/                    # C++ benchmarks
+│       ├── benchmark_construction.cpp
+│       ├── benchmark_query.cpp
+│       ├── benchmark_parallel.cpp
+│       └── stress_test_concurrent.cpp
 │
 ├── docs/                       # Documentation
 │   ├── examples/               # Example notebooks and scripts

docs/DEVELOPMENT.md

@@ -19,8 +19,7 @@ python_prtree/
 │   ├── integration/       # Integration tests
 │   └── e2e/               # End-to-end tests
 ├── benchmarks/             # Performance benchmarks
-│   ├── cpp/               # C++ benchmarks
-│   └── python/            # Python benchmarks
+│   └── cpp/               # C++ benchmarks
 ├── docs/                   # Documentation
 │   ├── examples/          # Example code
 │   ├── images/            # Images
@@ -198,7 +197,6 @@ All project metadata and dependencies are defined in `pyproject.toml`:
 - `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
 
@@ -343,9 +341,9 @@ pip install -e .
 
 ## Additional Resources
 
-- [CONTRIBUTING.md](CONTRIBUTING.md) - Contribution guidelines
-- [README.md](README.md) - Project overview
-- [CHANGES.md](CHANGES.md) - Version history
+- [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?
@@ -354,6 +352,6 @@ 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
+3. See [CONTRIBUTING.md](../CONTRIBUTING.md) for more details
 
 Happy coding! 🎉

docs/README.md

@@ -0,0 +1,64 @@
+# Documentation Directory
+
+This directory contains comprehensive documentation for python_prtree developers and contributors.
+
+## Contents
+
+### Core Documentation
+
+- **[ARCHITECTURE.md](ARCHITECTURE.md)** - Project architecture and design decisions
+  - Directory structure and separation of concerns
+  - Data flow diagrams
+  - Build system overview
+  - Native precision support architecture
+
+- **[DEVELOPMENT.md](DEVELOPMENT.md)** - Development environment setup
+  - Prerequisites and installation
+  - Build instructions
+  - Testing and code quality tools
+  - Troubleshooting guide
+
+- **[MIGRATION.md](MIGRATION.md)** - Migration guides between versions
+  - v0.7.0 project restructuring guide
+  - Breaking changes and migration steps
+  - Planned future migrations
+
+### Supplementary Resources
+
+- **baseline/** - Performance baseline measurements
+  - System information
+  - Benchmark results and analysis
+  - Used for regression testing and performance comparison
+
+- **examples/** - Example notebooks and scripts
+  - Experimental notebooks for exploring the API
+  - Usage demonstrations
+  - Prototyping and development examples
+
+- **images/** - Documentation images
+  - Benchmark graphs used in README
+  - Performance comparison charts
+  - Referenced by main documentation
+
+## For Users
+
+If you're a user looking for usage documentation, see:
+- [README.md](../README.md) - Main user documentation with examples
+- [CONTRIBUTING.md](../CONTRIBUTING.md) - How to contribute to the project
+- [CHANGES.md](../CHANGES.md) - Version history and changelog
+
+## For Developers
+
+Start with these files in order:
+1. [README.md](../README.md) - Understand what the library does
+2. [DEVELOPMENT.md](DEVELOPMENT.md) - Set up your development environment
+3. [ARCHITECTURE.md](ARCHITECTURE.md) - Understand the codebase structure
+4. [CONTRIBUTING.md](../CONTRIBUTING.md) - Learn the contribution workflow
+
+## Keeping Documentation Updated
+
+When making changes:
+- Update ARCHITECTURE.md if you change the project structure
+- Update DEVELOPMENT.md if you change build/test processes
+- Update MIGRATION.md when introducing breaking changes
+- Regenerate benchmarks if performance characteristics change