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

[Peter Cock]

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