[Biopython-dev] Testings on Win 7 x64

[Manlio Calvi]

Hi Zheng,

A failed manual import of scipy make me control what happened to my
distro, the scipy was there (infact for some other math computation
script it works) but for some reason wasn't used by biopython, however
I reinstalled the last version available, rebuilt and retest and the
problem disappeared.

Peter, the C modules instead I have no idea to how make them works,
they're compiled and installed in place but seems that my snake's nest
don't want to load it, I don't know why. Apparently they don't looks
like an importable python module.

Manlio

On Thu, Apr 24, 2014 at 6:53 PM, Zheng Ruan <zruan1991 at gmail.com> wrote:
> Hi Manlio,
>
> As for the test_CodonAlign warning, what's the scipy version you installed?
> Are
> you able to manually import `scipy.linalg.expm` and
> `scipy.optimize.minimize`
> manually? scipy.optimize.minimize is added to scipy since v0.11
> (http://docs.scipy.org/doc/scipy-0.11.0/reference/tutorial/optimize.html).
> I'm not sure why `scipy.linalg.expm` is not able to be import, since it's
> available
> in the earliest version of scipy
> (http://docs.scipy.org/doc/scipy-0.7.x/reference/linalg.html).
>
> Thank you!
> Zheng
>
>
> On Thu, Apr 24, 2014 at 12:34 PM, Manlio Calvi <manlio.calvi at gmail.com>
> wrote:
>>
>> OK I launched the tests on all my serpent's nest :)
>>
>> As some changes are made on .git folders and files and seeing how
>> badly git on windows manage those I erased the biopython folders and
>> started from scratch, that's the results:
>>
>> Python 3.4 x64 NO error (yay!):
>> The only note here is the fact that bio.trieand KDtree get skipped
>> because the C module refuse to compile.
>>
>> Python 3.3 (WinPython 3.3.3.3 x64 2 errors (one may be temporary):
>> CDAO test fail with (an issue we already seen):
>>
>> ======================================================================
>> ERROR: test_write_0 (test_Phylo_CDAO.WriterTests)
>> Write and re-parse the phylogenies in test.cdao.
>> ----------------------------------------------------------------------
>> Traceback (most recent call last):
>>   File ".\test_Phylo_CDAO.py", line 62, in test_write
>>     CDAOIO.write([t1], outfile)
>>   File "C:\Users\xxx\3.3 - Biopython
>>
>> test\WinPython-64bit-3.3.3.3\python-3.3.3.amd64\biopython\build\lib.win-amd64-3.3\Bio\Phylo\CDAOIO.py",
>> line 74, in write
>>     return Writer(trees).write(handle, plain=plain, **kwargs)
>>   File "C:\Users\xxx\3.3 - Biopython
>>
>> test\WinPython-64bit-3.3.3.3\python-3.3.3.amd64\biopython\build\lib.win-amd64-3.3\Bio\Phylo\CDAOIO.py",
>> line 268, in write
>>     handle.write('@prefix %s: <%s> .\n' % (k, v))
>> TypeError: 'str' does not support the buffer interface
>> ---------------------------------------
>>
>> Also during the test this line popped over and over
>>
>> file://C:\Users\xxx\3.3 - Biopython
>>
>> test\WinPython-64bit-3.3.3.3\python-3.3.3.amd64\biopython\Tests\CDAO\test.cdao/tree0000001#edge_annotation0000071
>> does not look like a valid URI, trying to serialize this will break.
>>
>> --------------------------------ù
>>
>> The other isssue is related with NCBI qblast but being NCBI probably
>> was I hit a server down.
>>
>> ######################################
>>
>> Python 2.7 x64 NO issues!
>>
>>
>> Adding to that I hit a "strangeness" I don't understand because the
>> mentioned scipy module IS installed, the test pass but not with
>> "flying colours":
>> test_CodonAlign ... test_CodonAlign.py:156: UserWarning: Importing
>> scipy.linalg.expm failed. Skip testing ML method for dN/dS estimation
>>   warnings.warn('Importing scipy.linalg.expm failed. Skip testing ML
>> method for dN/dS estimation')
>> test_CodonAlign.py:164: UserWarning: Importing scipy.optimize.minimize
>> failed. Skip testing ML method for dN/dS estimation
>>   warnings.warn('Importing scipy.optimize.minimize failed. Skip
>> testing ML method for dN/dS estimation')
>> ok
>>
>> Second a more general signalation, I've seen some test depends on PIL
>> but PIL library get discontinued and substituted by one called Pillow
>> that is said compatible with it predecessor (but I'm not sure how much
>> it is). This is a more general issue because require an scan of the
>> entire codebase. Looking around seems to me the NLTK package is in a
>> situation like this, too.
>>
>> Manlio
>>
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>
>