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cppyy-knn: An example of cppyy-generated bindings for a simple knn implementation

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This is an example project showing how to integrate a C++ kNearestNeighbors implementation with cppyy to enable calling from Python. It's c++ code comes from an alternative example which uses cppyy's bundled cmake sources; this version is based on my own rewrite first demonstrated in cppyy-bbhash. This packaging implementation makes a number of improvements and changes:

  • genreflex and a selection XML are use instead of a direct rootcling invocation. This makes name selection much easier.
  • Python package files are generated using template files. This allows them to be customized for the particular library being wrapped.
  • The python package is more complete: it includes a MANIFEST, LICENSE, and README; it properly recognizes submodules; it includes a tests submodule for bindings tests; it directly copies a python module file and directory structure for its pure python code.
  • The cppyy initializor routine has basic support for packaging cppyy pythonizors. These are stored in the pythonizors/ submodule, in files of the form pythonize_*.py. The pythonizor routines themselves should be named pythonize_<NAMESPACE>_*.py, where <NAMESPACE> refers to the namespace the pythonizor will be added to in the cppyy.py.add_pythonization call. These will be automatically found and added by the initializor.

cppyy-bbhash has a more complicated C++ codebase, with templating and namespaces; however, it's header only and I opted to simply compile it into a static library and bundle it with the bindings' shared library. Here, I've created dynamic library, linked the cppyy bindings library against it, set up things to be relocatable, and set up all the install targets to install both the library headers and SO and the Python wheel.

Repo Structure

  • CMakeLists.txt: The CMake file for bindings generation.
  • selection.xml: The genreflex selection file.
  • interface.hh: The interface header used by genreflex. Should include the headers and template declarations desired in the bindings.
  • cmake/: CMake files for the build. Should not need to be modified.
  • pkg_templates/: Templates for the generated python package. Users can modify the templates to their liking; they will be configured and copied into the build and package directory.
  • py/: Python package structure that will be copied into the generated package. Add any pure python code you'd like include in your bindings package here.
  • py/initializor.py: The cppyy bindings initializor that will be copied in the package. Do not delete!

Example Usage

For this repository with anaconda:

conda create -n cppyy-example python=3 cmake cxx-compiler c-compiler clangdev libcxx libstdcxx-ng libgcc-ng pytest
conda activate cppyy-example 
pip install cppyy clang

git clone https://github.com/camillescott/cppyy-knn
cd cppyy-knn

mkdir build; cd build
cmake ..
make install

And then to test:

py.test -v -s cppyy_simpleknn/tests/test_knn.py

I still generate the knn c++ executable; it gets spit out in the build directory. The test files demonstrates the bindings usage:

from cppyy.gbl import std
from cppyy_simpleknn import NearestNeighbors, Point


def test_point_iter_pythonizor():
    pt = Point(1.0, 2.0)
    test = [p for p in pt]
    assert test == [1.0, 2.0]


def test_point_repr_pythonizor():
    pt = Point(1.0, 2.0)
    assert repr(pt) == '(1.0, 2.0)'


def test_knn_nearest():
    knn = NearestNeighbors()
    points = [Point(2,0), Point(1,0), Point(0,10), Point(5,5), Point(2,5)]
    knn.points = std.vector[Point](points)
    result = [tuple(res) for res in knn.nearest(Point(0.0, 0.0), 3)]
    assert result == [(1.0, 0.0), (2.0, 0.0), (2.0, 5.0)]

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An example repo for packaging cppyy bindings for a simple k-nearest neighbors implementation, based on https://github.com/jclay/cppyy-knearestneighbors-example

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