[Cython] Cython code producing different, incorrect results under Python 2.7 (not 3.x) under Cython 0.19

[Nikita Nemkin]

On Wed, 24 Apr 2013 12:19:36 +0600, Stefan Behnel <stefan_ml at behnel.de>  
wrote:

The bug is here (at least one of them):
https://github.com/scikit-image/scikit-image/blob/master/skimage/graph/_mcp.pyx#L179
"shape[:-1]" returns incorrect result: input (8, 8), expected output (8,),
actual output ().

I guess that means something is wrong with __Pyx_PyObject_GetSlice utility,
although I wasn't able to create a simple repro yet.


Best regards,
Nikita Nemkin


> Hi,
>
> Josh Warner, 24.04.2013 08:06:
>> Over in scikit-image we have traced an odd problem with a particular  
>> Cython
>> file to the 0.19 update of Cython. From at least Cython 0.15.1 (probably
>> earlier) through 0.18, `_mcp.pyx` in `skimage.graph` compiled and  
>> executed
>> correctly, passing all package tests on both Python 2.7 and Python 3.
>>
>> After 0.19 was released and the Travis builds began using it, we began
>> getting 100% repeatable errors from the previously clean master branch
>> (example of an otherwise clean Python
>> 2.7<https://travis-ci.org/scikit-image/scikit-image/jobs/6545505>Travis
>> build; the
>> Python 3 build  
>> passed<https://travis-ci.org/scikit-image/scikit-image/builds/6545504>all
>> tests). All of these errors/failures trace back to this Cython file.
>> Oddly, the errors only happen on Python 2.7; our Python 3 Travis build
>> passes.
>>
>> We are discussing this issue in scikit-image Github Issue
>> #534<https://github.com/scikit-image/scikit-image/issues/534>;
>> feel free to join the discussion there.
>>
>> The .pyx Cython file is located
>> here<https://github.com/scikit-image/scikit-image/blob/master/skimage/graph/_mcp.pyx>and
>> it has
>> an associated .pxd file
>> here<https://github.com/scikit-image/scikit-image/blob/master/skimage/graph/_mcp.pxd>.
>> It should be noted the file compiles and executes without errors, but  
>> its
>> output is now incorrect in Python 2.x.
>>
>> In case the compiled results might be relevant, for your diffing  
>> pleasure here
>> is the compiled .c file from Cython
>> 0.18<https://gist.github.com/JDWarner/af4f8ea85dce356ce95c>which
>> passes all tests on both Python 2.7 and Python 3.x, while here
>> is the compiled .c file from Cython
>> 0.19<https://gist.github.com/JDWarner/56d15b7a7527b8d4314e>which
>> produces different, incorrect results in Python 2.7.
>>
>> In the short term we are temporarily forcing Travis to use the 0.18  
>> release
>> of Cython, but that isn't a viable long term solution.
>>
>> It's possible the error is on our end, but seeing as it worked with  
>> prior
>> Cython releases we'd appreciate you taking a look.
>
> Thanks for bringing this up. You could make it a little easier for us by
> pointing us at the code that produces the incorrect results you are
> experiencing. The set of failing tests seems to be quite small, but  
> before
> we start digging through your code, I'm sure you can provide pointers to
> the relevant code snippets for a couple of these tests (i.e. the test  
> code
> itself and the major code parts that produce the results) much more  
> quickly.
>
> Stefan
>
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