[Biopython-dev] Win7 x64 - python 3.4 - Phylo and searchIO

[Wibowo Arindrarto]

Thanks, Peter. The change is here:
https://github.com/biopython/biopython/commit/82c23cb6afe48864f3dcdb3099cac2116842e9b2.
All test pass on my box (except for the trie bug). We can't see the
results in Travis yet
 (Python 3.4 support is coming soon they say[1]), but
hopefully it will say the same thing then :).

Cheers,
Bow

[1] https://github.com/travis-ci/travis-ci/issues/1989

On Thu, Apr 24, 2014 at 12:02 AM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> Good work Bow - that sounds like a better plan :)
>
> Peter
>
> On Wednesday, April 23, 2014, Wibowo Arindrarto <bow at bow.web.id> wrote:
>>
>> Hi Peter, Manlio,
>>
>> Thanks for looking deeper into the tests :). For the SearchIO issue,
>> I'm not too fond of relaxing the filter, as that could mean the test
>> passes even though warnings for this particular case is never raised.
>>
>> After checking more, I actually found that this isn't due to the
>> global warning filter settings. Apparently, the 'U' file read mode is
>> deprecated in Python 3.4[1] and SearchIO is using the 'rU' mode to
>> open its files. So the number of warnings in Python 3.4 is indeed 2:
>> the rU DeprecationWarning and the BiopythonParserWarning we are
>> checking.
>>
>> Since it looks like we can't remove 'rU' altogether from our codebase,
>> the more appropriate fix for this case would be to check for len(w) == 2
>> when
>> Python version is >= 3.4.
>>
>> Best,
>> Bow
>>
>> [1] https://docs.python.org/3.5/whatsnew/3.4.html#deprecated-3-4
>>
>> On Wed, Apr 23, 2014 at 6:51 AM, Manlio Calvi <manlio.calvi at gmail.com>
>> wrote:
>> > Ops a bit of overzealousness here, yesterday night was a bit tired and
>> > I preferred to be sure than skip an issue.
>> > However the second one I raised on the first round of my tests  but
>> > don't get addressed
>> >
>> > Manlio
>> >
>> > On Tue, Apr 22, 2014 at 11:58 PM, Peter Cock <p.j.a.cock at googlemail.com>
>> > wrote:
>> >> On Tue, Apr 22, 2014 at 10:36 PM, Manlio Calvi <manlio.calvi at gmail.com>
>> >> wrote:
>> >>> I got those two new errors:
>> >>>
>> >>> ======================================================================
>> >>> ERROR: test_unicode_exception (test_Phylo.IOTests)
>> >>> ----------------------------------------------------------------------
>> >>> Traceback (most recent call last):
>> >>>   File "C:\Users\Public\BioPython3\biopython\Tests\test_Phylo.py",
>> >>> line 57, in test_unicode_exception
>> >>>     tree = Phylo.read(EX_NEWICK_BOM, 'newick')
>> >>>   File
>> >>> "C:\Users\Public\BioPython3\biopython\build\lib.win-amd64-3.4\Bio\Phylo\_io.py",
>> >>> line 65, in read
>> >>>     tree = next(tree_gen)
>> >>>   File
>> >>> "C:\Users\Public\BioPython3\biopython\build\lib.win-amd64-3.4\Bio\Phylo\_io.py",
>> >>> line 53, in parse
>> >>>     for tree in getattr(supported_formats[format], 'parse')(fp,
>> >>> **kwargs):
>> >>>   File
>> >>> "C:\Users\Public\BioPython3\biopython\build\lib.win-amd64-3.4\Bio\Phylo\NewickIO.py",
>> >>> line 107, in parse
>> >>>     for line in self.handle:
>> >>>   File "C:\Python34\lib\encodings\cp1252.py", line 23, in decode
>> >>>     return codecs.charmap_decode(input,self.errors,decoding_table)[0]
>> >>> UnicodeDecodeError: 'charmap' codec can't decode byte 0x9d in position
>> >>> 15: character maps to <undefined>
>> >>>
>> >>
>> >> Yep, see https://github.com/biopython/biopython/issues/311
>> >>
>> >>> ======================================================================
>> >>> FAIL: test_xml_2226_blastn_006
>> >>> (test_SearchIO_blast_xml.BlastXmlSpecialCases)
>> >>> ----------------------------------------------------------------------
>> >>> Traceback (most recent call last):
>> >>>   File
>> >>> "C:\Users\Public\BioPython3\biopython\Tests\test_SearchIO_blast_xml.py",
>> >>> line 3127, in test_xml_2226_blastn_006
>> >>>     "Expected one BiopythonParserWarning, got %r" % w)
>> >>> AssertionError: 2 != 1 : Expected one BiopythonParserWarning, got
>> >>> [<warnings.WarningMessage object at 0x000000000BD0FE10>,
>> >>> <warnings.WarningMessage object at 0x000000000C0219B0>]
>> >>>
>> >>
>> >> I suspect I have seen that before... must double check that.
>> >>
>> >> @Bow, I think this check needs to be relaxed slightly (e.g. at
>> >> least one warning?) as it can potentially interact with global
>> >> warning settings (even though the test framework tries to
>> >> restore the filters to a known state before each test). Could
>> >> you take a look?
>> >>
>> >> Thanks,
>> >>
>> >> Peter