pybind11: how to package c++ and python code into a single package?

Question

I am trying to package together an existing Python code and a new C++ 11 code using CMake and pybind 11. I think I am missing something simple to add into CMake scripts, but can't find it anywhere: pybind11 examples have only C++ code and none of Python, other online resources are rather convoluted and not up-to-date -- so I just can't figure out how to package functions in both languages together and make them available via Python's import my_package down the line... as an example, I have cloned the cmake_example from pybind11 and added a mult function into cmake_example/mult.py

def mult(a, b):
    return a * b

how would I make it visible along with add and subtract to pass the test below?

import cmake_example as m

assert m.__version__ == '0.0.1'
assert m.add(1, 2) == 3
assert m.subtract(1, 2) == -1
assert m.mult(2, 2) == 4

currently, this test fails..

Thanks!

Answer 1

The simplest solution has nothing to do with pybind11 as such. What authors usually do when they want to combine pure Python and C/Cython/other native extensions in the same package, is the following.

You create two modules.

1. mymodule is a public interface, a pure Python module
2. _mymodule is a private implementation, a complied module

Then in mymodule you import necessary symbols from _mymoudle (and fallback to pure Python version if necessary).

Here's example from yarl package:

1. quoting.py

   try:
       from ._quoting import _quote, _unquote
       quote = _quote
       unquote = _unquote
   except ImportError:  # pragma: no cover
       quote = _py_quote
       unquote = _py_unquote
   

2. _quoting.pyx

Update

Here follows the script. For the sake of reproducibility I'm doing it against original cmake_example.

git clone --recursive https://github.com/pybind/cmake_example.git
# at the time of writing https://github.com/pybind/cmake_example/commit/8818f493  
cd cmake_example

Now create pure Python modules (inside cmake_example/cmake_example).

cmake_example/__init__.py

"""Root module of your package"""

cmake_example/math.py

def mul(a, b):
    """Pure Python-only function"""
    return a * b


def add(a, b):
    """Fallback function"""    
    return a + b    

try:
    from ._math import add
except ImportError:
    pass

Now let's modify existing files to turn cmake_example module into cmake_example._math.

src/main.cpp (subtract removed for brevity)

#include <pybind11/pybind11.h>

int add(int i, int j) {
    return i + j;
}

namespace py = pybind11;

PYBIND11_MODULE(_math, m) {
    m.doc() = R"pbdoc(
        Pybind11 example plugin
        -----------------------

        .. currentmodule:: _math

        .. autosummary::
           :toctree: _generate

           add
    )pbdoc";

    m.def("add", &add, R"pbdoc(
        Add two numbers

        Some other explanation about the add function.
    )pbdoc");

#ifdef VERSION_INFO
    m.attr("__version__") = VERSION_INFO;
#else
    m.attr("__version__") = "dev";
#endif
}

CMakeLists.txt

cmake_minimum_required(VERSION 2.8.12)
project(cmake_example)

add_subdirectory(pybind11)
pybind11_add_module(_math src/main.cpp)

setup.py

# the above stays intact

from subprocess import CalledProcessError

kwargs = dict(
    name='cmake_example',
    version='0.0.1',
    author='Dean Moldovan',
    author_email='dean0x7d@gmail.com',
    description='A test project using pybind11 and CMake',
    long_description='',
    ext_modules=[CMakeExtension('cmake_example._math')],
    cmdclass=dict(build_ext=CMakeBuild),
    zip_safe=False,
    packages=['cmake_example']
)

# likely there are more exceptions, take a look at yarl example
try:
    setup(**kwargs)        
except CalledProcessError:
    print('Failed to build extension!')
    del kwargs['ext_modules']
    setup(**kwargs)

Now we can build it.

python setup.py bdist_wheel

In my case it produces dist/cmake_example-0.0.1-cp27-cp27mu-linux_x86_64.whl (if C++ compilation fails it's cmake_example-0.0.1-py2-none-any.whl). Here is what it contents (unzip -l ...):

Archive:  cmake_example-0.0.1-cp27-cp27mu-linux_x86_64.whl
  Length      Date    Time    Name
---------  ---------- -----   ----
        0  2017-12-05 21:42   cmake_example/__init__.py
    81088  2017-12-05 21:43   cmake_example/_math.so
      223  2017-12-05 21:46   cmake_example/math.py
       10  2017-12-05 21:48   cmake_example-0.0.1.dist-info/DESCRIPTION.rst
      343  2017-12-05 21:48   cmake_example-0.0.1.dist-info/metadata.json
       14  2017-12-05 21:48   cmake_example-0.0.1.dist-info/top_level.txt
      105  2017-12-05 21:48   cmake_example-0.0.1.dist-info/WHEEL
      226  2017-12-05 21:48   cmake_example-0.0.1.dist-info/METADATA
      766  2017-12-05 21:48   cmake_example-0.0.1.dist-info/RECORD
---------                     -------
    82775                     9 files

Answer 2

Once you've cloned the repo, cd to top level directory `cmake_example'

Change ./src/main.cpp to include a "mult" function:

#include <pybind11/pybind11.h>

int add(int i, int j) {
    return i + j;
}

int mult(int i, int j) {
   return i * j;
}

namespace py = pybind11;

PYBIND11_MODULE(cmake_example, m) {
    m.doc() = R"pbdoc(
        Pybind11 example plugin
        -----------------------

        .. currentmodule:: cmake_example

        .. autosummary::
           :toctree: _generate

           add
           subtract
           mult

    )pbdoc";

    m.def("add", &add, R"pbdoc(
        Add two numbers

        Some other explanation about the add function.
    )pbdoc");

   m.def("mult", &mult, R"pbdoc(
        Multiply two numbers

        Some other explanation about the mult function.
    )pbdoc");

(the rest of the file is the same)

Now make it:

$ cmake -H. -Bbuild
$ cmake --build build -- -j3

The module for import will be created in the ./build directory. Go to it, then within a python shell your example should work.

For the namespace import, you could do something with pkgutil:

create the directory structure:

./my_mod
    __init__.py
    cmake_example.***.so

and another parallel structure

./extensions
    /my_mod
        __init__.py
        cmake_example_py.py

and place in ./my_mod/__init__.py

import pkgutil
__path__ = pkgutil.extend_path(__path__, __name__)

from .cmake_example import add, subtract
from .cmake_example_py import mult

in ./extensions/my_mod/__init__.py

from cmake_example_py import mult

Then append both ./my_mod and ./extensions/my_mod to your $PYTHONPATH, it just might work (it does in my example)