Cython Wrapping of a C++ Algorithm

Overview

This project demonstrates how to use Cython to wrap a C++ algorithm, enabling parameter access and modification using Python keyword arguments. This example can be used as a reference for improving parameter accessibility in PyOpenMS.

Features

• Wraps a C++ class using Cython.
• Allows setting and retrieving parameters via Python keyword arguments.
• Provides a simple setup for compiling the C++ code and using it in Python.

Prerequisites

Ensure you have the following installed:

• Python 3.8 or later
• Cython
• A C++ compiler (e.g., MSVC on Windows, g++ on Linux/Mac)

Project Structure

Cython-example/
│── src/
│   │── cpp/
│   │   │── algorithm.h       # C++ header file defining the class
│   │   │── algorithm.cpp     # C++ implementation file
│   │── cython/
│   │   │── algorithm.pxd     # Cython header file
│   │   │── algorithm.pyx     # Cython wrapper file
│   │── setup.py              # Build script for Cython
│   │── test.py               # Python script to test the wrapped C++ class

Installation and Setup

1. Clone the repository:

   git clone https://github.com/yourusername/Cython-example.git
   cd Cython-example/src

2. Install dependencies:

   pip install cython

3. Compile the Cython module:

   python setup.py build_ext --inplace

Usage

Run the test script to see the algorithm in action:

python test.py

Expected output:

Initial parameters: {'param1': 20.0, 'param2': 10, 'param3': True}
Updated parameters: {'param1': 5.0, 'param2': 10, 'param3': False}
Computation result: 15.0
algo2 parameters: {'param1': 210.0, 'param2': 100, 'param3': True}
Computation result: 21000.0
algo3 parameters: {'param1': 210.0, 'param2': 5, 'param3': True}
Computation result: 1050.0

Update test.py to try different examples.

Explanation

• cpp/algorithm.h & cpp/algorithm.cpp: Define the C++ class with multiple parameters.
• cython/algorithm.pxd & cython/algorithm.pyx: The Cython wrapper that exposes the C++ class to Python.
• setup.py: Compiles the C++ and Cython files into a Python module.
• test.py: Runs a simple test to verify functionality.

Troubleshooting

• If you encounter a compilation error, ensure that your compiler is installed and accessible.
• On Windows, use MSVC from Visual Studio Build Tools.
• On Linux/Mac, install g++ via your package manager.
• If ModuleNotFoundError: No module named 'algorithm' occurs, ensure you are running test.py inside the src directory.

Contributing

Feel free to fork and contribute by submitting pull requests!