Organizing a Cython build with setup.py with more than one C++file

[ashwin .D]

First let me say that I have my cython code that is working as a result of compiling with

cython --cplus point.pyx 

 Now I am trying to get the code organized into a setup.py file so that I can use it a complex project. I am trying to wrap C++ code with Cython so that I 
can call it in a Python script(s).

In my working directory - I have several C++ files that can be compiled with g++. 

My questions are related to the scope of setup.py. Is it possible to compile the C++ files as part of setup.py or must they be compiled separately ? 
Is it a problem that the .pxd and .pyx file be located in the same directory ? The issue with the code below of setup.py file is that the environment of 
setup.py seems to think the flags I have added are meant for the Cython code. That is incorrect. It is actually meant for the C++ code. 

from distutils.core import setup
from distutils.extension import Extension
from Cython.Distutils import build_ext
from Cython.Build import cythonize

import os

# Building
setup(
    cmdclass = {'build_ext': build_ext},
    ext_modules = [
    Extension("p2", 
              sources=["point.pyx", \
                       "./Point.cpp", \
                       "./Distance.cpp", \
                       ],
              language="c++",
              extra_compile_args=["-Wall","-std=c++17","-I/usr/local/include"], 
              extra_link_args=["-lGeographic","-L/usr/local/lib"],
              )
    ]
)                   

I have looked at this SO answer - Project Organization With C++ and Cython but I am still not clear on what exactly needs to be done. I am looking for some
sample setup.py file that wrap several C++ files and then use them in a .pyx/.pxd file. Any suggestions ?

[Hai Nguyen]

Hi, you can see mdtraj project on github.

Hai

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[ashwin .D]

Thanks. I have enclosed the smallest possible code that I believe reproduces my problem and any help will be appreciated.

point.pyx

#distutils : language = c++
#distutils : sources = Point.cpp
from libcpp.memory cimport shared_ptr
from libcpp.vector cimport vector

from point cimport Point

cdef class PyA:

     def __cinit__(self):
        print("hello")

     def buildPoints(self):

        cdef shared_ptr[Point] point
        point = shared_ptr[Point](new SphericalPoint())

and my point.pxd file -

from libcpp.memory cimport shared_ptr
from libcpp.vector cimport vector

cdef extern from "Point.h":
    cdef cppclass Point:
        Point() except +
        double getCoordinate1()
        double getCoordinate2()
        void setCoordinate1(double coordinate1)
        void setCoordinate2(double coordinate2)

    cdef cppclass SphericalPoint(Point):
       SphericalPoint() except +
       double getCoordinate1()
       double getCoordinate2()
       void setCoordinate1(double lat)
       void setCoordinate2(double lon)

and my setup.py file -

from distutils.core import setup
from distutils.extension import Extension
from Cython.Distutils import

build_ext

ext_modules = [Extension("test",
                     ["point.pyx", "Point.cpp"],
                     language='c++',
                     )]

setup(
  name = 'test',

  cmdclass = {'build_ext': build_ext},

  ext_modules = ext_modules
)

gives me these errors -

Error compiling Cython file:
------------------------------------------------------------
...
        print("hello")

     def buildPoints(self):

        cdef shared_ptr[Point] point
        point = shared_ptr[Point](new SphericalPoint())
                                     ^
------------------------------------------------------------

point.pyx:14:38: 'SphericalPoint' is not a type identifier

Error compiling Cython file:
------------------------------------------------------------
...
        print("hello")

     def buildPoints(self):

        cdef shared_ptr[Point] point
        point = shared_ptr[Point](new SphericalPoint())
                                     ^
------------------------------------------------------------

point.pyx:14:38: new operator can only be applied to a C++ class

But the same when compiled with cython --cplus point.pyx gives only a warning and no errors. Where am I going wrong 

/usr/local/lib/python3.6/dist-packages/Cython-0.29.7-py3.6-linux-x86_64.egg/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /home/winash12/test_cython/point.pxd
  tree = Parsing.p_module(s, pxd, full_module_name)

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