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

[Peter Cock]

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<javascript:;>>
> 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<javascript:;>>
> wrote:
> >> On Tue, Apr 22, 2014 at 10:36 PM, Manlio Calvi <manlio.calvi at gmail.com<javascript:;>>
> 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
>