获取SystemError：父模块''未加载，尝试在Cython扩展中导入numpy时无法执行相对导入

Question

I have a cython extension inside a package which is structured like so:

packagename
├── MANIFEST.in
├── packagename
│   ├── __init__.py
│   ├── packagename.py
│   ├── subpackage1
│   │   ├── __init__.py
│   │   ├── subpackage1.py
│   │   └── cythonExt1.pyx
│   ├── subpackage2
│   │   ├── __init__.py
│   │   ├── subpackage2.py
│   │   └── cythonExt2.pyx
│   └── VERSION
├── requirements.txt
└── setup.py

When I try to add a line in cythonExt2.pyx which imports numpy I get the following error:

-------------------------------------------------------------
SystemError                 Traceback (most recent call last)
<ipython-input-5-5c4ef4d8efd3> in <module>()
      1 # Calling Functions of Interest
----> 2 import pacakge.subpackage2 as thingy
      3 import numpy as np
      4 import matplotlib.pyplot as plt

/home/user/anaconda2/envs/python3/lib/python3.5/site-packages/pacakage-0.0.3-py3.5-linux-x86_64.egg/package/__init__.py in <module>()
     18 
     19 # the following line imports all the functions from package.py
---> 20 from .package import *
     21 import package.subpackage1
     22 import package.subpackage2

/home/user/anaconda2/envs/python3/lib/python3.5/site-packages/package-0.0.3-py3.5-linux-x86_64.egg/package/package.py in <module>()
      1 from package.subpackage1 import thingy1
----> 2 from package.subpackage2 import thingy2
      3 import numpy as _np
      4 from multiprocessing import Pool as _Pool

/home/user/anaconda2/envs/python3/lib/python3.5/site-packages/package-0.0.3-py3.5-linux-x86_64.egg/package/subpackage2/subpackage2.py in <module>()
      3 import os
----> 4 from cythonExt2 import solve as solve_cython
      5 from frange import frange
      6 
/home/user/anaconda2/envs/python3/lib/python3.5/site-packages/package-0.0.3-py3.5-linux-x86_64.egg/package/subpackage2/cythonExt2.pyx in init package.subpackge2.cythonExt2 (package/subpackage2/cythonExt2.c:6158)()
      1 cimport numpy
----> 2 import numpy
      3 cimport cython
      4 
      5 def get_z_n(n, z):

SystemError: Parent module '' not loaded, cannot perform relative import

If I just cimport numpy this works and I have access to the numpy C API but I cannot import the numpy python functions which I need to solve a particular problem.

Why is this and how might I fix it?

I'm wondering if there is an issue with my setup file that is causing this to not work. The cython parts of my setup.py file are like so:

from setuptools import setup                                                                      
from setuptools.extension import Extension
from Cython.Build import cythonize                                                            
from Cython.Build import build_ext
extensions = [Extension(                                                                          
    name="cythonExt1",                                                                               
    sources=["package/subpackage1/cythonExt1.pyx"],                                                   
    include_dirs=[numpy.get_include()],                                                           
    ),                                                                                            
    Extension(                                                                                    
    name="cythonExt2",                                                                           
    sources=["package/subpackage2/cythonExt2.pyx"],                                           
    include_dirs=[numpy.get_include()],                                                           
    )                                                                                             
] 

setup(name='package',                                                                             
      ...  
      include_package_data=True,                                                                  
      packages=['package',                                                                        
                'package.subpackage1',                                                             
                'package.subpackage2',                                                         
      ],                                                                                          
      ext_modules = cythonize(extensions),                                                        
      install_requires=requirements,                                                              
)

Answer 1

The issue was that numpy was not being included properly with this setup.py file and workflow. I fixed this by changing it to be such that the cython extension is cythonized in it's own directory with it's own setup.py file into a .c file and that file is then added as a C extension in the package's setup.py file. This also has the benefit that people installing your module don't need cython as you can distribute the generated .c file with the package.

I have created this complete, but simple, example on my github here .