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

[Manlio Calvi]

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