[Biopython-dev] Testings on Win 7 x64

[Manlio Calvi]

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