[Biopython-dev] test_PhyloXML.py error on Python 2.4

[Eric Talevich]

On Thu, Apr 8, 2010 at 6:55 AM, Peter <biopython at maubp.freeserve.co.uk>wrote:

> Hi Eric,
>
> I noticed that test_PhyloXML.py is failing on Python 2.4, it should
> be skipped since I don't have ElementTree installed. Have you got
> access to a Python 2.4 installation to look at this?
>

The traceback says the PhyloXML module is missing, but PhyloXMLIO and the
rest of Bio.Phylo are there. Is that normal? I would expect that PhyloXML
would still be installed with Biopython on Py2.4, but when the test runs it
would trigger a MissingExternalDependency error for ElementTree when
importing PhyloXMLIO, and run_tests.py would then skip it.

I don't have Py2.4 on this machine but I can track down a copy. (Annoyingly,
Ubuntu seems to have dropped Pythons 2.4 and 2.5 from the official repos in
Lucid Lynx.)

-Eric



> ======================================================================
> ERROR: test_PhyloXML
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>  File "run_tests.py", line 267, in runTest
>    suite = unittest.TestLoader().loadTestsFromName(name)
>  File "c:\python24\lib\unittest.py", line 524, in loadTestsFromName
>    module = __import__('.'.join(parts_copy))
>  File "test_PhyloXML.py", line 15, in ?
>    from Bio.Phylo import PhyloXML as PX, PhyloXMLIO
>  File
> "C:\repositories\biopython_official\build\lib.win32-2.4\Bio\Phylo\__init_
> _.py", line 12, in ?
>    from Bio.Phylo._io import parse, read, write, convert
>  File
> "C:\repositories\biopython_official\build\lib.win32-2.4\Bio\Phylo\_io.py"
> , line 15, in ?
>    import PhyloXMLIO
>  File
> "C:\repositories\biopython_official\build\lib.win32-2.4\Bio\Phylo\PhyloXM
> LIO.py", line 23, in ?
>    from Bio.Phylo import PhyloXML as PX
> ImportError: cannot import name PhyloXML
>