[Biopython-dev] Python 3 status (ignoring our C code and most dependencies)

[Peter]

Hi Bartek, Eric, et al,

I've rerun the test suite on the trunk code, and we have the
following issues, most of which I'd already noted in this thread:
http://lists.open-bio.org/pipermail/biopython-dev/2010-July/008079.html

Bartek - I was seeing a couple of issues with Bio.Motif which came
down to relative import issues, this seems to have fixed things.
Could you confirm this change looks OK to you?
http://github.com/biopython/biopython/commit/4700d1be7afffe5e06b41df6ee8cc19e68a9a6c1

Eric - Can you reproduce this test_Phylo.py failure on your machine?
And is there any chance you'll be able to look at the Bio.PDB issue
with DisorderedResidue?

Thanks,

Peter

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test_LocationParser ... Syntax error at or near `467' token

Something in the spark parser isn't handled by 2to3, not urgent as I want
to deprecate Bio.GenBank.LocationParser which is the only thing using spark.
http://lists.open-bio.org/pipermail/biopython/2010-September/006734.html

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test_PDB ... FAIL

TypeError: 'DisorderedResidue' object is not subscriptable

See:
http://lists.open-bio.org/pipermail/biopython-dev/2010-August/008159.html

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test_Phylo ... FAIL

Traceback (most recent call last):
  File "test_Phylo.py", line 47, in test_convert
    Phylo.convert(self.mem_file, 'nexus', mem_file_2, 'phyloxml')
  File "/home/xxx/repositories/biopython/Bio/Phylo/_io.py", line 102, in convert
    return write(trees, out_file, out_format, **kwargs)
  File "/home/xxx/repositories/biopython/Bio/Phylo/_io.py", line 92, in write
    n = getattr(supported_formats[format], 'write')(trees, file, **kwargs)
  File "/home/xxx/repositories/biopython/Bio/Phylo/PhyloXMLIO.py",
line 148, in write
    return Writer(obj).write(file, encoding=encoding, indent=indent)
  File "/home/xxx/repositories/biopython/Bio/Phylo/PhyloXMLIO.py",
line 684, in write
    self._tree.write(file, encoding)
  File "/home/xxx/lib/python3.1/xml/etree/ElementTree.py", line 659, in write
    self._write(file, self._root, encoding, {})
  File "/home/xxx/lib/python3.1/xml/etree/ElementTree.py", line 677, in _write
    file.write(_encode("<" + tag, encoding))
TypeError: string argument expected, got 'bytes'

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test_SeqIO_online ... FAIL

May need to turn all online byte handles into unicode handles,
http://lists.open-bio.org/pipermail/biopython-dev/2010-July/008076.html

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test_property_manager ... FAIL

Looks like a formatting change of some kind, but I want to deprecate this:
http://lists.open-bio.org/pipermail/biopython-dev/2010-September/008231.html

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Peter