程序包的Cython C级接口：* .pxd文件未找到 [英] Cython C-level interface of package: *.pxd files are not found

问题描述

简而言之

我尝试编译一个名为 extension2 的cython扩展从自己创建的包中导入文件扩展名。构建 extension2 时，出现错误：虽然此文件正好位于分隔路径中，但未找到 extension.pxd 。

详细信息

我正在构建两个涉及cython的软件包，一个软件包 A 和依赖于 A 的软件包 B 。 A 是命名空间包 nsp 的子包。也就是说，文件夹结构如下所示：

 ├──nsp 
│└──A 
 | ├──extension.pxd 
 | ├──extension.pyx 
│└──__init__.py 
└──setup.py 
  

在这里， setup.py 的内容如下：

 从setuptools导入setup 
从setuptools.extension import扩展
 
＃工厂功能
 def my_build_ext（pars）：
＃导入延迟：
从setuptools.command.build_ext将build_ext导入为_build_ext 
 
＃include_dirs已调整：
 class build_ext（_build_ext）：
 def finalize_options（self）：
 _build_ext.finalize_options（self） ）
＃防止numpy认为它仍在设置过程中：
 __builtins __.__ NUMPY_SETUP__ = False 
 import numpy 
 self.include_dirs.append（numpy.get_include（））
 
＃返回对象：
 return build_ext（pars）
 
 extensions = [Extension（nsp.A.extension，['nsp / A / extension.cpp'] ）] 
 
设置（
 cmdclass = {'build_ext' ：my_build_ext}，
 setup_requires = ['numpy']，
 install_requires = ['numpy']，
个包= ['nsp.A']，
 ext_modules =扩展
 package_data = {
'nsp / A'：['* .pxd'，'* .pyx'] 
}，
）
  

设置文件的灵感来自>添加numpy-get-include-argument-to-setuptools-没有预安装的numpy 和 distributing-cython-modules 。 cython文件已使用另一个脚本成功转换为 .cpp 文件。

我使用

<$ p安装软件包 A $ p> pip install。 setup.py 目录中的


。一切正常，我可以在 ... \Anaconda3\Lib\site-packages\nsp\A 下找到该包的所有文件，包括 *。pxd 文件。

现在，我尝试为扩展名2 *。cpp 文件c $ c>，以便稍后将其打包在第二个包 B 中。文件 extension2.pxd 从nsp.A.extension cimport读取

  mymethod 
  

用于创建 *。cpp 文件读取

 从distutils.core导入设置，扩展名
从Cython。构建导入cythonize 
导入numpy as np 
 import sys 
 print（sys.executable）
 
 NAME ='extension2'
 extensions = [Extension（NAME，[NAME +'。pyx'] ，
 include_dirs = [np.get_include（）] 
）
] 
 
设置（名称= NAME，
 ext_modules = cythonize（扩展名，语言=  c ++，
 Compiler_directives = compiler_directives），
 include_dirs = [np.get_include（）] 
）
  

当我使用 python myscript build_ext --inplace 运行此脚本时，出现错误，指出 pxd 文件丢失：

  f rom nsp.A.extension cimport mymethod 
 ^ 
 --------------------------------- --------------------------- 
 
 .\extension2.pxd：11：0：'nsp\找不到A\extension.pxd'
  

但是，此文件完全存在。 （ sys.executable 是包含已安装软件包的 Anaconda3 文件夹）如何解决此问题？

其他信息

我正在Windows x64上使用python 3.7

解决方案

Cython不支持隐式命名空间包。也就是说，cython仅搜索包含文件 init。* 的子目录，因此 * 可以是 py ， pyc ， pyx 和 pxd 。

我已经创建了 bugtracker报告，此问题，以防您想了解是否已在较新版本中解决此问题（我与Cython 0.29.14一起工作过。）。

在此之前，解决方法是在文件夹 nsp 中创建一个空文件 __ init __。pxd 。该文件应由python忽略，因为它不是 *。py 文件，并且可以让cython在子目录中搜索包。然后，文件结构如下：

 ├──nsp 
│├──__init __。pxd 
│└──A 
 | ├──extension.pxd 
 | ├──extension.pyx 
│└──__init__.py 
└──setup.py 
  

要在名称空间包中安装其他文件 __ init __。pxd ，请更改 packages 参数 setup（...）到 packages = ['nsp'，'nsp.A'] 和<$ package_data = {''的c $ c> package_data 参数：['* .pxd'，'* .pyx']} 。

编辑：

该错误已为cython开发人员所知，并将得到修复在版本3中。请参见从PEP420名称空间修复cimport 。

In a nutshell

I try to compile a cython extension called extension2 that cimports a file extension from a self-created package. When building extension2, I get the error that extension.pxd is not found though this file is exactly at the sepcified path.

Details

I am building two packages involving cython, a package A and a package B that depends on A. A is a subpacke of a namespace package nsp. That is, the folder structure looks as follows:

├── nsp
│   └── A
|       ├── extension.pxd
|       ├── extension.pyx
│       └── __init__.py
└── setup.py

Here, setup.py reads as follows:

from setuptools import setup
from setuptools.extension import Extension

# factory function
def my_build_ext(pars):
    # import delayed:
    from setuptools.command.build_ext import build_ext as _build_ext

    # include_dirs adjusted: 
    class build_ext(_build_ext):
        def finalize_options(self):
            _build_ext.finalize_options(self)
            # Prevent numpy from thinking it is still in its setup process:
            __builtins__.__NUMPY_SETUP__ = False
            import numpy
            self.include_dirs.append(numpy.get_include())

    #object returned:
    return build_ext(pars)

extensions = [Extension(nsp.A.extension, ['nsp/A/extension.cpp'])]

setup(
    cmdclass={'build_ext' : my_build_ext},
    setup_requires=['numpy'],
    install_requires=['numpy'], 
    packages=['nsp.A'],
    ext_modules=extensions
    package_data={
        'nsp/A': ['*.pxd', '*.pyx']
    },
)

The setup file is inspired by add-numpy-get-include-argument-to-setuptools-without-preinstalled-numpy and distributing-cython-modules. The cython files were already successfully transformed to .cpp files with another script.

I install the the package A with

pip install .

in the directory of the setup.py. Everything works as desired, and I can find all files of the package under ...\Anaconda3\Lib\site-packages\nsp\A, including the *.pxd files.

Now I seek to create a *.cpp file for an extension2 in order to package it later in the second package B. The file extension2.pxd reads

from nsp.A.extension cimport mymethod

The script to create the *.cpp file reads

from distutils.core import setup, Extension
from Cython.Build import cythonize
import numpy as np
import sys
print(sys.executable)

NAME = 'extension2'
extensions = [Extension(NAME, [NAME+'.pyx'],
                        include_dirs=[np.get_include()]
                        )
              ]

setup(name=NAME,
      ext_modules = cythonize(extensions, language="c++", 
                              compiler_directives=compiler_directives),
      include_dirs=[np.get_include()]
      ) 

When I run this script with python myscript build_ext --inplace, I get an error indicating the pxd file is missing:

from nsp.A.extension cimport mymethod
^
------------------------------------------------------------

.\extension2.pxd:11:0: 'nsp\A\extension.pxd' not found

However, this file exists exactly there. (sys.executable is the Anaconda3 folder that contains the installed package) How can I resolve the issue?

Additional info

I am using python 3.7 on Windows x64

解决方案

Cython does not support implicit namespace packages as of yet. That is, cython searches only subdirectories that contain a file init.*, whereby * can be anything from py, pyc, pyx, and pxd.

I have created a bugtracker report for this issue, in case you want to follow up on whether the issue has been fixed in a newer version yet (I worked with Cython 0.29.14).

Until then, a workaround is to create an empty file __init__.pxd in the folder nsp. This file should be ignored by python, as it is not a *.py file, and lets cython search the subdirectories for packages. The file structure then reads as follows:

├── nsp
│   ├── __init__.pxd
│   └── A
|       ├── extension.pxd
|       ├── extension.pyx
│       └── __init__.py
└── setup.py

To install the additional file __init__.pxd in the namespace package, change the packages argument of setup(...) to packages=['nsp', 'nsp.A'] and the package_data argument to package_data={'': ['*.pxd', '*.pyx']}.

Edit:

The bug has been known to the cython developers and will be fixed in version 3. See Fix for cimport from PEP420 namespace.

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