When I compile with Cython the Python code which uses Python.NET to access .NET assemblies, it can't find those assemblies:
ModuleNotFoundError: No module named 'System'
Without compilation it works ok.
For demo code, I used https://github.com/pythonnet/pythonnet/blob/master/demo/helloform.py
My setup.py file:
from distutils.core import setup
from distutils.extension import Extension
from Cython.Build import cythonize
ext_modules = [
Extension(
'helloform',
sources = ['helloform.py'],
language = 'c++'
)
]
setup(
name = 'helloform',
ext_modules = cythonize(ext_modules),
)
Then I build it with python setup.py build_ext --inplace.
I wanted to load compiled module from Python prompt with import helloform but it failed with
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "helloform.py", line 8, in init helloform
ModuleNotFoundError: No module named 'System'
This answer is untested - I don't think I can easily set up an environment to test so it's a bit of a guess. If it doesn't work I'll remove it.
This probably is a bug, and if you want it fixed in the longer term you should report it. Cython does try to be compatible with Python wherever possible.... A quick investigate suggests that Python.NET overrides the built-in __import__ function. Cython looks to lookup and use this function in Python 2, but not in Python 3. This is no longer the preferred way of customizing import behaviour (but is still supported). I'd guess it would work in Cython + Python 2?
As a workaround you should probably just run the import statements in Python. There's two obvious ways to do it:
Write a small separate module just containing the import statements, then in Cython import from that module:
from import_module import WinForms, Size, Point
Run the import statements in exec; extract the values out of the global dict you pass it:
import_dict = {}
exec("""import clr
# etc...
""", import_dict) # pass a dict in as `globals`
WinForms = import_dict['WinForms']
# etc.
Related
toolsTep.py
def HelloWord():
print('hello word')
testpythran.py
from calaTools.toolsTep import *
#pythran export callOtherPyFiles()
def callOtherPyFiles():
HelloWord()
complie pythran testpythran.py
CRITICAL :
I am in trouble. Your input file does not seem to match Pythran's constraints...
testpythran.py:
None:None error: Module 'calaTools.toolsTep' not found.
when two function in save file and it can find ,in diffrent file it occured those errors
When distributing a Python application with Pythran modules, you can either:
declare the module as a regular Python module. After all, they are 100% Python compatible.
declare them as a PythranExtension and Pythran will compile them:
from distutils.core import setup
These two lines are required to be able to use pythran in the setup.py
import setuptools
setuptools.dist.Distribution(dict(setup_requires='pythran'))
from pythran.dist import PythranExtension, PythranBuildExt
setup(...,
ext_modules=[PythranExtension("mymodule", ["mymodule.py"])],
cmdclass={"build_ext": PythranBuildExt})
PythranBuildExt is optional, but necessary to build extensions with different C++ compilers. It derives from distuil’s build_ext by default, but you can change its base class by using PythranBuildExt[base_cls] instead.
all configuration options supported in .pythranrc can also be passed through the optional config argument, in the form of a list, e.g. config=['compiler.blas=openblas']
from pythran doc.https://pythran.readthedocs.io/en/latest/MANUAL.html
This doesn't make sense to me. How can I use the setup.py to install Cython and then also use the setup.py to compile a library proxy?
import sys, imp, os, glob
from setuptools import setup
from Cython.Build import cythonize # this isn't installed yet
setup(
name='mylib',
version='1.0',
package_dir={'mylib': 'mylib', 'mylib.tests': 'tests'},
packages=['mylib', 'mylib.tests'],
ext_modules = cythonize("mylib_proxy.pyx"), #how can we call cythonize here?
install_requires=['cython'],
test_suite='tests',
)
Later:
python setup.py build
Traceback (most recent call last):
File "setup.py", line 3, in <module>
from Cython.Build import cythonize
ImportError: No module named Cython.Build
It's because cython isn't installed yet.
What's odd is that a great many projects are written this way. A quick github search reveals as much: https://github.com/search?utf8=%E2%9C%93&q=install_requires+cython&type=Code
As I understand it, this is where PEP 518 comes in - also see some clarifications by one of its authors.
The idea is that you add yet another file to your Python project / package: pyproject.toml. It is supposed to contain information on build environment dependencies (among other stuff, long term). pip (or just any other package manager) could look into this file and before running setup.py (or any other build script) install the required build environment. A pyproject.toml could therefore look like this:
[build-system]
requires = ["setuptools", "wheel", "Cython"]
It is a fairly recent development and, as of yet (January 2019), it is not finalized / approved by the Python community, though (limited) support was added to pip in May 2017 / the 10.0 release.
One solution to this is to not make Cython a build requirement, and instead distribute the Cython generated C files with your package. I'm sure there is a simpler example somewhere, but this is what pandas does - it conditionally imports Cython, and if not present can be built from the c files.
https://github.com/pandas-dev/pandas/blob/3ff845b4e81d4dde403c29908f5a9bbfe4a87788/setup.py#L433
Edit: The doc link from #danny has an easier to follow example.
http://docs.cython.org/en/latest/src/reference/compilation.html#distributing-cython-modules
When you use setuptool, you should add cython to setup_requires (and also to install_requires if cython is used by installation), i.e.
# don't import cython, it isn't yet there
from setuptools import setup, Extension
# use Extension, rather than cythonize (it is not yet available)
cy_extension = Extension(name="mylib_proxy", sources=["mylib_proxy.pyx"])
setup(
name='mylib',
...
ext_modules = [cy_extension],
setup_requires=["cython"],
...
)
Cython isn't imported (it is not yet available when setup.pystarts), but setuptools.Extension is used instead of cythonize to add cython-extension to the setup.
It should work now. The reason: setuptools will try to import cython, after setup_requires are fulfilled:
...
try:
# Attempt to use Cython for building extensions, if available
from Cython.Distutils.build_ext import build_ext as _build_ext
# Additionally, assert that the compiler module will load
# also. Ref #1229.
__import__('Cython.Compiler.Main')
except ImportError:
_build_ext = _du_build_ext
...
It becomes more complicated, if your Cython-extension uses numpy, but also this is possible - see this SO post.
It doesn't make sense in general. It is, as you suspect, an attempt to use something that (possibly) has yet to be installed. If tested on a system that already has the dependency installed, you might not notice this defect. But run it on a system where your dependency is absent, and you will certainly notice.
There is another setup() keyword argument, setup_requires, that can appear to be parallel in form and use to install_requires, but this is an illusion. Whereas install_requires triggers a lovely ballet of automatic installation in environments that lack the dependencies it names, setup_requires is more documentation than automation. It won't auto-install, and certainly not magically jump back in time to auto-install modules that have already been called for in import statements.
There's more on this at the setuptools docs, but the quick answer is that you're right to be confused by a module that is trying to auto-install its own setup pre-requisites.
For a practical workaround, try installing cython separately, and then run this setup. While it won't fix the metaphysical illusions of this setup script, it will resolve the requirements and let you move on.
I am trying to link to my own C library from Cython, following the directions I've found on the web, including this answer:
Using Cython To Link Python To A Shared Library
I am running IPython through Spyder.
My setup.py looks like this:
from distutils.core import setup
from distutils.extension import Extension
from Cython.Build import cythonize
import numpy as np
setup(
ext_modules = cythonize(
[Extension("*",["*.pyx"],
libraries =["MyLib"],
extra_compile_args = ["-fopenmp","-O3"],
extra_link_args=["-L/path/to/lib"])
]),
include_dirs = [np.get_include()],
)
The file libMyLib.so is in /path/to/lib and it compiles fine.
I have a Python script in my IPython profile startup folder that does this
try:
os.environ["LD_LIBRARY_PATH"] += ":/path/to/lib"
except KeyError:
os.environ["LD_LIBRARY_PATH"] = "/path/to/lib"
I can confirm that this is running, because if I type os.environ["LD_LIBRARY_PATH"] into the IPython interpreter, it returns /path/to/lib
But when I try to load the Cython module (i.e. import mycythonmodule) I get:
ImportError: libMyLib.so: cannot open shared object file: No such file or directory
I've also tried putting libMyLib.so in other places to see if cython would find it:
In the directory where Python is running
On the Python path
In the same folder as the cython module
But it still doesn't find the shared library. The only way I can get it to find the library is by dropping it in /usr/lib, but I don't want it there, I want to be able to set the library path.
Am I missing something?
I'm self-answering, in case anyone else runs into the same problem. Looks like the answers are here:
Set LD_LIBRARY_PATH before importing in python
Changing LD_LIBRARY_PATH at runtime for ctypes
According to these answers (and my experience), the linker reads LD_LIBRARY_PATH when python is launched, so changing it from within python doesn't have any useful effect, at least not the effect I was hoping for. The only solution is to either wrap python in a shell script that sets LD_LIBRARY_PATH, or else drop the shared object somewhere on the linker search path.
Kind of a pain, but it is what it is.
I have fixed it by change setup.py.
I have a C++ dynamic shared library called "libtmsmdreader.so". and a header file named "TmsMdReader.hpp"
I wrapper C++ shared library to cython library called "tmsmdreader-pythonxxxxxx.so"
from setuptools import setup
from distutils.extension import Extension
from Cython.Build import cythonize
setup(
name="tmsmdreader",
ext_modules=cythonize([
Extension(
name="tmsmdreader",
language="c++",
sources=["TmsMdReaderApi.pyx"],
libraries=["tmsmdreader"],
library_dirs=["."],
include_dirs=["."],
extra_compile_args=["-std=c++14"],
compiler_directives={'language_level': 3},
runtime_library_dirs=["."])
]))
library_dirs=["."] and runtime_library_dirs=["."] can fixed LD_LIBRARY_PATH if libtmsmdreader.so in python scripy directory
I would like to create a setup.py script for a python package with several submodules that depend on both cython and f2py. I have attempted to use setuptools and numpy.distutils, but have so far failed:
Using setuptools
I am able to compile my cython extensions (and create an installation for the rest of the package) using setuptools. I have, however, been unable to figure out how to use setuptools to generate the f2py extension. After extensive searching, I only found rather old messages like this one that state that f2py modules must be compiled using numpy.distutils.
Using numpy.distutils
I am able to compile my f2py extensions (and create an installation for the rest of the package) using numpy.distutils. I have, however, been unable to figure out how to get numpy.distutils to compile my cython extensions as it always attempts to use pyrex to compile it (and I am using extensions specific to cython) recent. I have done a search to figure out how to get numpy.distutils for cython files and - at least as of a year ago - they recommend applying a monkey patch to numpy.distutils. It seems applying such a monkey patch also restricts the options that can be passed to Cython.
My question is: what is the recommended way to write a setup.py script for packages that depend on both f2py and cython? Is applying a patch to numpy.distutils really the way to go still?
You can just call each separately in your setup.py as in
http://answerpot.com/showthread.php?601643-cython%20and%20f2py
# Cython extension
from distutils.core import setup
from distutils.extension import Extension
from Cython.Distutils import build_ext
setup(
ext_modules = [Extension( 'cext', ['cext.pyx'] )],
cmdclass = {'build_ext': build_ext},
script_args = ['build_ext', '--inplace'],
)
# Fortran extension
from numpy.distutils.core import setup, Extension
setup(
ext_modules = [Extension( 'fext', ['fext.f90'] )],
)
Your calling context (I think they call this namespace, not sure)
has to change as to what the current object Extension and function
setup() is.
The first setup() call, it's the distutils.extension.Extension
and distutils.core.setup()
The second setup() call, it's the numpy.distutils.core.Extension
and numpy.distutils.core.setup()
Turns out this is no longer true. With both setuptools and distutils (at least the numpy version) it is possible to have extensions with C, Cython and f2py. The only caveat is that to compile f2py modules one must always use numpy.distutils for both the setup and Extension functions. But setuptools can still be used for the installation (for example, allowing the installation of a developer version with python setup.py develop).
To use distutils exclusively you use the following:
from numpy.distutils.core import setup
from numpy.distutils.extension import Extension
To use setuptools, you need to import it before the distutils imports:
import setuptools
And then the rest of the code is identical:
from numpy import get_include
from Cython.Build import cythonize
NAME = 'my_package'
NUMPY_INC = get_include()
extensions = [
Extension(name=NAME + ".my_cython_ext",
include_dirs=[NUMPY_INC, "my_c_dir"]
sources=["my_cython_ext.pyx", "my_c_dir/my_ext_c_file.c"]),
Extension(name=NAME + ".my_f2py_ext",
sources=["my_f2py_ext.f"]),
]
extensions = cythonize(extensions)
setup(..., ext_modules=extensions)
Obviously you need to put all your other stuff in the setup() call. In the above I assume that you'll use numpy with Cython, along with an external C file (my_ext_c_file.c) that will be at my_c_dir/, and that the f2py module is only one Fortran file. Adjust as needed.
I'd like to make a Python package containing some Cython code. I've got the the Cython code working nicely. However, now I want to know how best to package it.
For most people who just want to install the package, I'd like to include the .c file that Cython creates, and arrange for setup.py to compile that to produce the module. Then the user doesn't need Cython installed in order to install the package.
But for people who may want to modify the package, I'd also like to provide the Cython .pyx files, and somehow also allow for setup.py to build them using Cython (so those users would need Cython installed).
How should I structure the files in the package to cater for both these scenarios?
The Cython documentation gives a little guidance. But it doesn't say how to make a single setup.py that handles both the with/without Cython cases.
I've done this myself now, in a Python package simplerandom (BitBucket repo - EDIT: now github) (I don't expect this to be a popular package, but it was a good chance to learn Cython).
This method relies on the fact that building a .pyx file with Cython.Distutils.build_ext (at least with Cython version 0.14) always seems to create a .c file in the same directory as the source .pyx file.
Here is a cut-down version of setup.py which I hope shows the essentials:
from distutils.core import setup
from distutils.extension import Extension
try:
from Cython.Distutils import build_ext
except ImportError:
use_cython = False
else:
use_cython = True
cmdclass = {}
ext_modules = []
if use_cython:
ext_modules += [
Extension("mypackage.mycythonmodule", ["cython/mycythonmodule.pyx"]),
]
cmdclass.update({'build_ext': build_ext})
else:
ext_modules += [
Extension("mypackage.mycythonmodule", ["cython/mycythonmodule.c"]),
]
setup(
name='mypackage',
...
cmdclass=cmdclass,
ext_modules=ext_modules,
...
)
I also edited MANIFEST.in to ensure that mycythonmodule.c is included in a source distribution (a source distribution that is created with python setup.py sdist):
...
recursive-include cython *
...
I don't commit mycythonmodule.c to version control 'trunk' (or 'default' for Mercurial). When I make a release, I need to remember to do a python setup.py build_ext first, to ensure that mycythonmodule.c is present and up-to-date for the source code distribution. I also make a release branch, and commit the C file into the branch. That way I have a historical record of the C file that was distributed with that release.
Adding to Craig McQueen's answer: see below for how to override the sdist command to have Cython automatically compile your source files before creating a source distribution.
That way your run no risk of accidentally distributing outdated C sources. It also helps in the case where you have limited control over the distribution process e.g. when automatically creating distributions from continuous integration etc.
from distutils.command.sdist import sdist as _sdist
...
class sdist(_sdist):
def run(self):
# Make sure the compiled Cython files in the distribution are up-to-date
from Cython.Build import cythonize
cythonize(['cython/mycythonmodule.pyx'])
_sdist.run(self)
cmdclass['sdist'] = sdist
http://docs.cython.org/en/latest/src/userguide/source_files_and_compilation.html#distributing-cython-modules
It is strongly recommended that you distribute the generated .c files as well as your Cython sources, so that users can install your module without needing to have Cython available.
It is also recommended that Cython compilation not be enabled by default in the version you distribute. Even if the user has Cython installed, he probably doesn’t want to use it just to install your module. Also, the version he has may not be the same one you used, and may not compile your sources correctly.
This simply means that the setup.py file that you ship with will just be a normal distutils file on the generated .c files, for the basic example we would have instead:
from distutils.core import setup
from distutils.extension import Extension
setup(
ext_modules = [Extension("example", ["example.c"])]
)
The easiest is to include both but just use the c-file? Including the .pyx file is nice, but it's not needed once you have the .c file anyway. People who want to recompile the .pyx can install Pyrex and do it manually.
Otherwise you need to have a custom build_ext command for distutils that builds the C file first. Cython already includes one. http://docs.cython.org/src/userguide/source_files_and_compilation.html
What that documentation doesn't do is say how to make this conditional, but
try:
from Cython.distutils import build_ext
except ImportError:
from distutils.command import build_ext
Should handle it.
Including (Cython) generated .c files are pretty weird. Especially when we include that in git. I'd prefer to use setuptools_cython. When Cython is not available, it will build an egg which has built-in Cython environment, and then build your code using the egg.
A possible example: https://github.com/douban/greenify/blob/master/setup.py
Update(2017-01-05):
Since setuptools 18.0, there's no need to use setuptools_cython. Here is an example to build Cython project from scratch without setuptools_cython.
All other answers either rely on
distutils
importing from Cython.Build, which creates a chicken-and-egg problem between requiring cython via setup_requires and importing it.
A modern solution is to use setuptools instead, see this answer (automatic handling of Cython extensions requires setuptools 18.0, i.e., it's available for many years already). A modern standard setup.py with requirements handling, an entry point, and a cython module could look like this:
from setuptools import setup, Extension
with open('requirements.txt') as f:
requirements = f.read().splitlines()
setup(
name='MyPackage',
install_requires=requirements,
setup_requires=[
'setuptools>=18.0', # automatically handles Cython extensions
'cython>=0.28.4',
],
entry_points={
'console_scripts': [
'mymain = mypackage.main:main',
],
},
ext_modules=[
Extension(
'mypackage.my_cython_module',
sources=['mypackage/my_cython_module.pyx'],
),
],
)
The simple hack I came up with:
from distutils.core import setup
try:
from Cython.Build import cythonize
except ImportError:
from pip import pip
pip.main(['install', 'cython'])
from Cython.Build import cythonize
setup(…)
Just install Cython if it could not be imported. One should probably not share this code, but for my own dependencies it's good enough.
This is a setup script I wrote which makes it easier to include nested directories inside the build. One needs to run it from folder within a package.
Givig structure like this:
__init__.py
setup.py
test.py
subdir/
__init__.py
anothertest.py
setup.py
from setuptools import setup, Extension
from Cython.Distutils import build_ext
# from os import path
ext_names = (
'test',
'subdir.anothertest',
)
cmdclass = {'build_ext': build_ext}
# for modules in main dir
ext_modules = [
Extension(
ext,
[ext + ".py"],
)
for ext in ext_names if ext.find('.') < 0]
# for modules in subdir ONLY ONE LEVEL DOWN!!
# modify it if you need more !!!
ext_modules += [
Extension(
ext,
["/".join(ext.split('.')) + ".py"],
)
for ext in ext_names if ext.find('.') > 0]
setup(
name='name',
ext_modules=ext_modules,
cmdclass=cmdclass,
packages=["base", "base.subdir"],
)
# Build --------------------------
# python setup.py build_ext --inplace
Happy compiling ;)
The easiest way I found using only setuptools instead of the feature limited distutils is
from setuptools import setup
from setuptools.extension import Extension
try:
from Cython.Build import cythonize
except ImportError:
use_cython = False
else:
use_cython = True
ext_modules = []
if use_cython:
ext_modules += cythonize('package/cython_module.pyx')
else:
ext_modules += [Extension('package.cython_module',
['package/cython_modules.c'])]
setup(name='package_name', ext_modules=ext_modules)
I think I found a pretty good way of doing this by providing a custom build_ext command. The idea is the following:
I add the numpy headers by overriding finalize_options() and doing import numpy in the body of the function, which nicely avoids the problem of numpy not being available before setup() installs it.
If cython is available on the system, it hooks into the command's check_extensions_list() method and by cythonizes all out-of-date cython modules, replacing them with C extensions that can later handled by the build_extension() method. We just provide the latter part of the functionality in our module too: this means that if cython is not available but we have a C extension present, it still works, which allows you to do source distributions.
Here's the code:
import re, sys, os.path
from distutils import dep_util, log
from setuptools.command.build_ext import build_ext
try:
import Cython.Build
HAVE_CYTHON = True
except ImportError:
HAVE_CYTHON = False
class BuildExtWithNumpy(build_ext):
def check_cython(self, ext):
c_sources = []
for fname in ext.sources:
cname, matches = re.subn(r"(?i)\.pyx$", ".c", fname, 1)
c_sources.append(cname)
if matches and dep_util.newer(fname, cname):
if HAVE_CYTHON:
return ext
raise RuntimeError("Cython and C module unavailable")
ext.sources = c_sources
return ext
def check_extensions_list(self, extensions):
extensions = [self.check_cython(ext) for ext in extensions]
return build_ext.check_extensions_list(self, extensions)
def finalize_options(self):
import numpy as np
build_ext.finalize_options(self)
self.include_dirs.append(np.get_include())
This allows one to just write the setup() arguments without worrying about imports and whether one has cython available:
setup(
# ...
ext_modules=[Extension("_my_fast_thing", ["src/_my_fast_thing.pyx"])],
setup_requires=['numpy'],
cmdclass={'build_ext': BuildExtWithNumpy}
)