[Biopython-dev] Python 2.7 failure from test_Tutorial.py, was: Compiling Biopython on 64 bit Windows

[Manlio Calvi]

OK tested, all good on my machine, the only failed test is the TogoWS
that don't depend on us.

Manlio

On Tue, Apr 22, 2014 at 2:57 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> On Tue, Apr 22, 2014 at 9:32 AM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
>> On Tue, Apr 22, 2014 at 6:51 AM, Manlio Calvi <manlio.calvi at gmail.com> wrote:
>>> Hi Peter,
>>> I just run this one from the Tests folder (the tests are there and
>>> don'tget moved in the installation)
>>
>> Sorry, yes - I should have said that.
>>
>>> I got this:
>>>
>>> Running Tutorial doctests...
>>> **********************************************************************
>>> File "Tests/test_Tutorial.py", line 153, in
>>> __main__.TutorialDocTestHolder.doctest_test_from_line_04424
>>> Failed example:
>>>     align_array.shape
>>> Expected:
>>>     (7, 52)
>>> Got:
>>>     (7L, 52L)
>>> **********************************************************************
>>> 1 items had failures:
>>>    1 of   7 in __main__.TutorialDocTestHolder.doctest_test_from_line_04424
>>> ***Test Failed*** 1 failures.
>>> C:\python27\lib\site-packages\Bio\Motif\__init__.py:26:
>>> BiopythonDeprecationWarning: The module Bio.Motif has been deprecated
>>> and will be removed in a future release of Biopython. Instead please
>>> use the new module Bio.motifs instead. Please be aware that though the
>>> functionality of Bio.Motif is retained (and extended) in Bio.motifs,
>>> usage may be different.
>>>   BiopythonDeprecationWarning)
>>> Traceback (most recent call last):
>>>   File "Tests/test_Tutorial.py", line 185, in <module>
>>> RuntimeError: 1/806 tests failed
>>>
>>>
>>> Another Python2/3 compatibility problem...
>>
>> Well yes, but also a 32 bit versus 64 bit Windows issue.
>> Python 3 hides the C level differences between ints and longs,
>> while Python 2 can sometimes expose this - odd that this test
>> didn't give longs on the other platforms, just 64 bit windows.
>>
>> I suggest we switch from:
>>
>> %This example fails under PyPy 2.0, https://bugs.pypy.org/issue1546
>> %doctest examples lib:numpy
>> \begin{verbatim}
>>>>> import numpy as np
>>>>> from Bio import AlignIO
>>>>> alignment = AlignIO.read("PF05371_seed.
>> sth", "stockholm")
>>>>> align_array = np.array([list(rec) for rec in alignment], np.character)
>>>>> align_array.shape
>> (7, 52)
>> \end{verbatim}
>>
>> To:
>>
>> %This example fails under PyPy 2.0, https://bugs.pypy.org/issue1546
>> %doctest examples lib:numpy
>> \begin{verbatim}
>>>>> import numpy as np
>>>>> from Bio import AlignIO
>>>>> alignment = AlignIO.read("PF05371_seed.sth", "stockholm")
>>>>> align_array = np.array([list(rec) for rec in alignment], np.character)
>>>>> print("Array shape %i by %i" % align_array.shape)
>> Array shape 7 by 52
>> \end{verbatim}
>>
>> That should be safe :)
>>
>> Peter
>
> Change applied to git,
> https://github.com/biopython/biopython/commit/0e26dfb40ab1ce78319eaf6893e35abda43c8738
>
> Peter