[Biopython-dev] Testings on Win 7 x64

[Zheng Ruan]

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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