stonebig34 | 20 Dec 10:14 2014
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is there a schedule for next cython update (0.21.2) ?

hi,

I see a lot of commits since 0.21.1.

Wouldn't it be time to do an incremental release ?

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Jernej | 19 Dec 12:22 2014
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Wrapping a C++ class involving abstract classses with virtual functions

Dear cython-users,

I am currently playing with the idea of creating a wrapper for a certain C++ library. The main header file looks like this

====================================================
    namespace bliss {
      class AbstractGraph;
    }
     
    class AbstractGraph
    {
      friend class Partition;

    .............lots of stuff.......

    public:
      AbstractGraph();
      virtual ~AbstractGraph();
     
    }
     
    class Graph : public AbstractGraph
    {
    public:
     
      Graph(const unsigned int N = 0);
      ~Graph();
     
      static Graph* read_dimacs(FILE* const fp, FILE* const errstr = stderr);
    .... lots of stuff ...........
    }
====================================================

Working through the guide available at http://docs.cython.org/src/userguide/wrapping_CPlusPlus.html I couldn't find any explanation related to the above scenario. Hence I am wondering:

What would be the best way to create a Cython library enabling one to access the Graph class and make use of the public methods within it? Is this actually possible?

Best,

Jernej

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Marko Grdinic | 18 Dec 22:04 2014
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'new' operator does not work

I've been trying all day to figure out how to create a C++ class in Cython to no avail. Stack allocation works normally, but when I try to do it with new as in the example below it compiles fine, but gives me 'DLL load failed: The specified procedure could not be found' when I try to import the module. It occured to me to test memory allocation with malloc and that worked. I am unsure whether this error is because of my Windows install has quite a few missing .dll in its system directory as reported by Dependancy Walker (it is old and I cannot even reinstall the OS properly for some reason) or whether there is something fundamental I am missing about Cython.

Please have a look.

-testclass.cpp

class TestClass {

public:

int x, y;

TestClass(){}

~TestClass(){}

};


-helloworld2.pyx


# distutils: language = c++


cdef extern from "addtwo.cpp":

cppclass TestClass:

int x,y

TestClass()


cpdef test_the_class():

cdef TestClass *T = new TestClass()   #<---It breaks here.

T.x = 15

print(T.x)

del T


-setup.py

from distutils.core import setup

from Cython.Build import cythonize


setup(ext_modules = cythonize('helloworld2.pyx'))


print('Hello.')

import helloworld2 as h


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Heikki Arponen | 18 Dec 18:50 2014
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Way around Rich Compare?

Hi! Sorry if this is a somewhat trivial question, but I have a loop with an if comparison like this

...
if binnumber < 0 or binnumber > nbins - 1:
   ...

which gives almost max yellow with PyObject_RichComparePyNumber_Subtract and __Pyx_PyObject_IsTrue. Both binnumber and nbins are typed as int32_t. If I just drop the latter comparison, I get about 6x speed boost, so I'd like to get around that slowdown... is it possible?

Here's the complete info from the annotation:

+62: if binnumber < 0 or binnumber > nbins - 1: __pyx_t_21 = ((__pyx_v_binnumber < 0) != 0); if (!__pyx_t_21) { } else { __pyx_t_20 = __pyx_t_21; goto __pyx_L10_bool_binop_done; } __pyx_t_2 = __Pyx_PyInt_From_int32_t(__pyx_v_binnumber); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __pyx_t_3 = PyNumber_Subtract(__pyx_v_nbins, __pyx_int_1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __pyx_t_6 = PyObject_RichCompare(__pyx_t_2, __pyx_t_3, Py_GT); __Pyx_XGOTREF(__pyx_t_6); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __pyx_t_21 = __Pyx_PyObject_IsTrue(__pyx_t_6); if (unlikely(__pyx_t_21 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; __pyx_t_20 = __pyx_t_21; __pyx_L10_bool_binop_done:; if (__pyx_t_20) {

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Francisco Paisana | 16 Dec 20:38 2014
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Picon

Distinguishing std::list from python list

Hey,

I am trying to import some C++ classes to python through cython and I run into problems trying to create a std::list variable in cython. If my variable was a std::vector or std::map it would be easy. Just create a vector[] or map[] and that's it. However, with the std::list case, I don't know how to make cython distinguish it from the python list type. I tried to use the words std::list, std_list but nothing worked. Any ideas?

Thanks for the attention.

Regards,
Francisco

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Eric Moore | 16 Dec 14:43 2014
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Support real and imag attributes on double/float

Similarly to how float and double (possibly all numeric types?) support a conjugate() method, it would be nice to support 'real' and 'imag' attributes.  For types that do not represent a complex number, real would be a no op (similar to how conjugate() works), and imag could become a literal zero.

Presently the following code generates a not very helpful "Coercion from Python not allowed without the GIL" error message.

ctypedef double complex double_complex
ctypedef fused number_t:
    double
    double_complex

cdef int works(number_t b) nogil:
    cdef number_t a
    a = b.conjugate()
    return 0

 cdef int fails(number_t b) nogil:
     cdef double a
     a =  b.real
     return 0

Thoughts?

Eric

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Richard Dybowski | 15 Dec 11:00 2014
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C from Cython to be called by a C++ program

Hi,

Using Cython, is it possible to convert Python code (foo.py) to C (foo.c) in such a way that the resulting C code can be called by another program (bar.cpp) written in C++?

Richard

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Michael Barz | 11 Dec 13:34 2014

Wrapping videoInput library with cython results in linker errors

I'm trying to build a python wrapper for the library videoInput by ofTheo with Cython. I'm using Python 2.7 on Windows 8.1 x64 and Cython with the Visual Studio 2008 compiler (2012 is also installed). The first problem I faced was that the pre-built videoInput.lib is available for x86 only. For that I found a solution in a fork by liquidzym providing an x64 version. Unfortunately I got stuck with another problem. I get a linker error, LNK1120: 8 unresolved externals.

The extension in setup.py is defined as follows:

extensions = [Extension(  name="pyVideoInput",
                sources
=['pyVideoInput.pyx'],
                language
="c++",
                extra_objects
= ['videoInput.lib'],
                include_dirs
= ['videoInput/videoInputSrcAndDemos/libs/'],
                library_dirs
= ['vi_x64/'])
   
]

When building with setup.py build_ext --inplace I get a console output like:

E:\Entwicklung\Python\pyvideoinput>setup.py build_ext --inplace
running build_ext
building
'pyVideoInput' extension
C
:\Program Files (x86)\Microsoft Visual Studio 9.0\VC\BIN\amd64\cl.exe /c /nologo /Ox /MD /W3 /GS- /DNDEBUG -IvideoInput/videoInputSrcAndDemos/libs/ -IC:\Python27\include -IC:\Python27\PC /TppyVideoInput.cpp /Fobuild\temp.win-amd64-2.7\Release\pyVideoInput.obj
pyVideoInput
.cpp
C
:\Program Files (x86)\Microsoft Visual Studio 9.0\VC\INCLUDE\xlocale(342) : warning C4530: C++ exception handler used, but unwind semantics are not enabled. Specify /EHsc
C
:\Program Files (x86)\Microsoft Visual Studio 9.0\VC\BIN\amd64\link.exe /DLL /nologo /INCREMENTAL:NO /LIBPATH:vi_x64/ /LIBPATH:C:\Python27\libs /LIBPATH:C:\Python27\PCbuild\amd64 /EXPORT:initpyVideoInput build\temp.win-amd64-2.7\Release\pyVideoInput.obj videoInput.lib /OUT:E:\Entwicklung\Python\pyvideoinput\pyVideoInput.pyd /IMPLIB:build\temp.win-amd64-2.7\Release\pyVideoInput.lib /MANIFESTFILE:build\temp.win-amd64-2.7\Release\pyVideoInput.pyd.manifest
videoInput
.lib(videoInput.obj) : warning LNK4229: invalid directive '/FAILIFMISMATCH:_MSC_VER=1700' encountered; ignored
videoInput
.lib(videoInput.obj) : warning LNK4229: invalid directive '/FAILIFMISMATCH:_ITERATOR_DEBUG_LEVEL=0' encountered; ignored
videoInput
.lib(videoInput.obj) : warning LNK4229: invalid directive '/FAILIFMISMATCH:RuntimeLibrary=MT_StaticRelease' encountered; ignored
pyVideoInput
.obj : warning LNK4197: export 'initpyVideoInput' specified multiple times; using first specification
Creating library build\temp.win-amd64-2.7\Release\pyVideoInput.lib and object build\temp.win-amd64-2.7\Release\pyVideoInput.exp
LINK
: warning LNK4098: defaultlib 'LIBCMT' conflicts with use of other libs; use /NODEFAULTLIB:library
videoInput
.lib(videoInput.obj) : error LNK2019: unresolved external symbol "void __cdecl std::_Xbad_alloc(void)" (?_Xbad_alloc <at> std <at> <at> YAXXZ) referenced in function "char * __cdecl std::_Allocate<char>(unsigned __int64,char *)" (??$_Allocate <at> D <at> std <at> <at> YAPEAD_KPEAD <at> Z)
videoInput
.lib(videoInput.obj) : error LNK2019: unresolved external symbol "void __cdecl std::_Xlength_error(char const *)" (?_Xlength_error <at> std <at> <at> YAXPEBD <at> Z) referenced in function "public: bool __cdecl std::basic_string<char,struct std::char_traits<char>,class std::allocator<char> >::_Grow(unsigned__int64,bool)" (?_Grow <at> ?$basic_string <at> DU?$char_traits <at> D <at> std <at> <at> V?$allocator <at> D <at> 2 <at> <at> std <at> <at> QEAA_N_K_N <at> Z)
videoInput
.lib(videoInput.obj) : error LNK2019: unresolved external symbol "void __cdecl std::_Xout_of_range(char const *)" (?_Xout_of_range <at> std <at> <at> YAXPEBD <at> Z) referenced in function "public: void __cdecl std::basic_string<char,struct std::char_traits<char>,class std::allocator<char> >::_Xran(void)const " (?_Xran <at> ?$basic_string <at> DU?$char_traits <at> D <at> std <at> <at> V?$allocator <at> D <at> 2 <at> <at> std <at> <at> QEBAXXZ)
videoInput
.lib(videoInput.obj) : error LNK2019: unresolved external symbol "char const * __cdecl std::_Syserror_map(int)" (?_Syserror_map <at> std <at> <at> YAPEBDH <at> Z) referenced in function "public: virtual class
std::error_condition __cdecl std::_System_error_category::default_error_condition(int)const "
(?default_error_condition <at> _System_error_category <at> std <at> <at> UEBA?AVerror_condition <at> 2 <at> H <at> Z)
videoInput
.lib(videoInput.obj) : error LNK2019: unresolved external symbol "char const * __cdecl std::_Winerror_map(int)" (?_Winerror_map <at> std <at> <at> YAPEBDH <at> Z) referenced in function "public: virtual class
std::basic_string<char,struct std::char_traits<char>,class std::allocator<char> > __cdecl std::_System_error_category::message(int)const "
(?message <at> _System_error_category <at> std <at> <at> UEBA?AV?$basic_string <at> DU?$char_traits <at> D <at> std <at> <at> V?$allocator <at> D <at> 2 <at> <at> 2 <at> H <at> Z)
videoInput
.lib(videoInput.obj) : error LNK2019: unresolved external symbol __imp_VariantInit referenced in function "private: long __cdecl videoInput::getDevice(struct IBaseFilter * *,int,wchar_t *,char *)" (?getDevice <at> videoInput <at> <at> AEAAJPEAPEAUIBaseFilter <at> <at> HPEA_WPEAD <at> Z)
videoInput
.lib(videoInput.obj) : error LNK2019: unresolved external symbol __imp_VariantClear referenced in function "private: long __cdecl videoInput::getDevice(struct IBaseFilter * *,int,wchar_t *,char *)" (?getDevice <at> videoInput <at> <at> AEAAJPEAPEAUIBaseFilter <at> <at> HPEA_WPEAD <at> Z)
videoInput
.lib(videoInput.obj) : error LNK2019: unresolved external symbol __imp_OleCreatePropertyFrame referenced in function "private: static long __cdecl videoInput::ShowFilterPropertyPages(structIBaseFilter *)" (?ShowFilterPropertyPages <at> videoInput <at> <at> CAJPEAUIBaseFilter <at> <at> <at> Z)
E
:\Entwicklung\Python\pyvideoinput\pyVideoInput.pyd : fatal error LNK1120: 8 unresolved externals
error
: command '"C:\Program Files (x86)\Microsoft Visual Studio 9.0\VC\BIN\amd64\link.exe"' failed with exit status 1120

I found some hints related to name mangling and differences in MSVC compiler versions. But nothing could help me...

It would be great if someone can help me with that.



Thanks in advance!

Best, Michael

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Christoph Deil | 12 Dec 16:04 2014

Cython compiler error output in color?

Hi,

the clang compiler shows warnings and errors in color ... this is very nice when browsing build logs to quickly find e.g. errors.
See examples here: http://clang.llvm.org/diagnostics.html 

Would it be possible to implement the same for Cython?
(or does it already exist and I just can't find the right option?)

If this is not worth implementing OK ... I'll try to write fewer errors ...

Cheers,
Christoph




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Jonathan Hanke | 12 Dec 04:53 2014
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Trouble enabling the cython debugger

Hi,

I was interested in enabling the cython debugger, and after reading the debugging page added the gdb_enable=True argument to the cythonize command in setup.py.  

from distutils.core import setup
from Cython.Build import cythonize

setup(
    name = "QFLIBapp",
    ext_modules = cythonize('*.pyx', gdb_debug=True),
)

However this gives an error related to some path settings:

python setup.py build_ext --inplace
Compiling matrix_mpz.pyx because it changed.
Cythonizing matrix_mpz.pyx
Traceback (most recent call last):
  File "setup.py", line 6, in <module>
    ext_modules = cythonize('*.pyx', gdb_debug=True),
  File "/Users/jonhanke/Library/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/Cython/Build/Dependencies.py", line 840, in cythonize
    cythonize_one(*args[1:])
  File "/Users/jonhanke/Library/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/Cython/Build/Dependencies.py", line 942, in cythonize_one
    result = compile([pyx_file], options)
  File "/Users/jonhanke/Library/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/Cython/Compiler/Main.py", line 629, in compile
    return compile_multiple(source, options)
  File "/Users/jonhanke/Library/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/Cython/Compiler/Main.py", line 607, in compile_multiple
    result = run_pipeline(source, options, context=context)
  File "/Users/jonhanke/Library/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/Cython/Compiler/Main.py", line 438, in run_pipeline
    pipeline = Pipeline.create_pyx_pipeline(context, options, result)
  File "/Users/jonhanke/Library/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/Cython/Compiler/Pipeline.py", line 231, in create_pyx_pipeline
    options.output_dir)
  File "/Users/jonhanke/Library/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/Cython/Debugger/DebugWriter.py", line 45, in __init__
    self.output_dir = os.path.join(output_dir, 'cython_debug')
  File "/Applications/Canopy.app/appdata/canopy-1.4.1.1975.macosx-x86_64/Canopy.app/Contents/lib/python2.7/posixpath.py", line 77, in join
    elif path == '' or path.endswith('/'):
AttributeError: 'NoneType' object has no attribute 'endswith'
make: *** [build] Error 1

Will I need to change setup.py to use the Extensions command for this to work, or is it supposed to be ok to add the debugging flag when distutils takes its arguments from the .pyx file? 

Thanks,

-Jon

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Michael Barz | 11 Dec 13:18 2014

Unresolved external symbols when wrapping a C++ library

Hello together,

I'm trying to build a python wrapper for the library videoInput by ofTheo with Cython. I'm using Python 2.7 on Windows 8.1 x64 and Cython with the Visual Studio 2008 compiler (2012 is also installed). The first problem I faced was that the pre-built videoInput.lib is available for x86 only. For that I found a solution in a fork by liquidzym providing an x64 version. Unfortunately I got stuck with another problem. I get a linker error, LNK1120: 8 unresolved externals.

The extension in setup.py is defined as follows:

extensions = [Extension(  name="pyVideoInput",
                sources
=['pyVideoInput.pyx'],
                language
="c++",
                extra_objects
= ['videoInput.lib'],
                include_dirs
= ['videoInput/videoInputSrcAndDemos/libs/'],
                library_dirs
= ['vi_x64/'])
   
]

When building with setup.py build_ext --inplace I get a console output like:

E:\Entwicklung\Python\pyvideoinput>setup.py build_ext --inplace
running build_ext
building
'pyVideoInput' extension
C
:\Program Files (x86)\Microsoft Visual Studio 9.0\VC\BIN\amd64\cl.exe /c /nologo /Ox /MD /W3 /GS- /DNDEBUG -IvideoInput/videoInputSrcAndDemos/libs/ -IC:\Python27\include -IC:\Python27\PC /TppyVideoInput.cpp /Fobuild\temp.win-amd64-2.7\Release\pyVideoInput.obj
pyVideoInput
.cpp
C
:\Program Files (x86)\Microsoft Visual Studio 9.0\VC\INCLUDE\xlocale(342) : warning C4530: C++ exception handler used, but unwind semantics are not enabled. Specify /EHsc
C
:\Program Files (x86)\Microsoft Visual Studio 9.0\VC\BIN\amd64\link.exe /DLL /nologo /INCREMENTAL:NO /LIBPATH:vi_x64/ /LIBPATH:C:\Python27\libs /LIBPATH:C:\Python27\PCbuild\amd64 /EXPORT:initpyVideoInput build\temp.win-amd64-2.7\Release\pyVideoInput.obj videoInput.lib /OUT:E:\Entwicklung\Python\pyvideoinput\pyVideoInput.pyd /IMPLIB:build\temp.win-amd64-2.7\Release\pyVideoInput.lib /MANIFESTFILE:build\temp.win-amd64-2.7\Release\pyVideoInput.pyd.manifest
videoInput
.lib(videoInput.obj) : warning LNK4229: invalid directive '/FAILIFMISMATCH:_MSC_VER=1700' encountered; ignored
videoInput
.lib(videoInput.obj) : warning LNK4229: invalid directive '/FAILIFMISMATCH:_ITERATOR_DEBUG_LEVEL=0' encountered; ignored
videoInput
.lib(videoInput.obj) : warning LNK4229: invalid directive '/FAILIFMISMATCH:RuntimeLibrary=MT_StaticRelease' encountered; ignored
pyVideoInput
.obj : warning LNK4197: export 'initpyVideoInput' specified multiple times; using first specification
Creating library build\temp.win-amd64-2.7\Release\pyVideoInput.lib and object build\temp.win-amd64-2.7\Release\pyVideoInput.exp
LINK
: warning LNK4098: defaultlib 'LIBCMT' conflicts with use of other libs; use /NODEFAULTLIB:library
videoInput
.lib(videoInput.obj) : error LNK2019: unresolved external symbol "void __cdecl std::_Xbad_alloc(void)" (?_Xbad_alloc <at> std <at> <at> YAXXZ) referenced in function "char * __cdecl std::_Allocate<char>(unsigned __int64,char *)" (??$_Allocate <at> D <at> std <at> <at> YAPEAD_KPEAD <at> Z)
videoInput
.lib(videoInput.obj) : error LNK2019: unresolved external symbol "void __cdecl std::_Xlength_error(char const *)" (?_Xlength_error <at> std <at> <at> YAXPEBD <at> Z) referenced in function "public: bool __cdecl std::basic_string<char,struct std::char_traits<char>,class std::allocator<char> >::_Grow(unsigned__int64,bool)" (?_Grow <at> ?$basic_string <at> DU?$char_traits <at> D <at> std <at> <at> V?$allocator <at> D <at> 2 <at> <at> std <at> <at> QEAA_N_K_N <at> Z)
videoInput
.lib(videoInput.obj) : error LNK2019: unresolved external symbol "void __cdecl std::_Xout_of_range(char const *)" (?_Xout_of_range <at> std <at> <at> YAXPEBD <at> Z) referenced in function "public: void __cdecl std::basic_string<char,struct std::char_traits<char>,class std::allocator<char> >::_Xran(void)const " (?_Xran <at> ?$basic_string <at> DU?$char_traits <at> D <at> std <at> <at> V?$allocator <at> D <at> 2 <at> <at> std <at> <at> QEBAXXZ)
videoInput
.lib(videoInput.obj) : error LNK2019: unresolved external symbol "char const * __cdecl std::_Syserror_map(int)" (?_Syserror_map <at> std <at> <at> YAPEBDH <at> Z) referenced in function "public: virtual class
std::error_condition __cdecl std::_System_error_category::default_error_condition(int)const "
(?default_error_condition <at> _System_error_category <at> std <at> <at> UEBA?AVerror_condition <at> 2 <at> H <at> Z)
videoInput
.lib(videoInput.obj) : error LNK2019: unresolved external symbol "char const * __cdecl std::_Winerror_map(int)" (?_Winerror_map <at> std <at> <at> YAPEBDH <at> Z) referenced in function "public: virtual class
std::basic_string<char,struct std::char_traits<char>,class std::allocator<char> > __cdecl std::_System_error_category::message(int)const "
(?message <at> _System_error_category <at> std <at> <at> UEBA?AV?$basic_string <at> DU?$char_traits <at> D <at> std <at> <at> V?$allocator <at> D <at> 2 <at> <at> 2 <at> H <at> Z)
videoInput
.lib(videoInput.obj) : error LNK2019: unresolved external symbol __imp_VariantInit referenced in function "private: long __cdecl videoInput::getDevice(struct IBaseFilter * *,int,wchar_t *,char *)" (?getDevice <at> videoInput <at> <at> AEAAJPEAPEAUIBaseFilter <at> <at> HPEA_WPEAD <at> Z)
videoInput
.lib(videoInput.obj) : error LNK2019: unresolved external symbol __imp_VariantClear referenced in function "private: long __cdecl videoInput::getDevice(struct IBaseFilter * *,int,wchar_t *,char *)" (?getDevice <at> videoInput <at> <at> AEAAJPEAPEAUIBaseFilter <at> <at> HPEA_WPEAD <at> Z)
videoInput
.lib(videoInput.obj) : error LNK2019: unresolved external symbol __imp_OleCreatePropertyFrame referenced in function "private: static long __cdecl videoInput::ShowFilterPropertyPages(structIBaseFilter *)" (?ShowFilterPropertyPages <at> videoInput <at> <at> CAJPEAUIBaseFilter <at> <at> <at> Z)
E
:\Entwicklung\Python\pyvideoinput\pyVideoInput.pyd : fatal error LNK1120: 8 unresolved externals
error
: command '"C:\Program Files (x86)\Microsoft Visual Studio 9.0\VC\BIN\amd64\link.exe"' failed with exit status 1120

I found some hints, one related to name mangling, another related to different MSVC compiler versions, but none of them was really helpful.

It would be great if someone has an idea on how to solve this issue.


Thanks in advance!

Best, Michael

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Gmane