[Biopython-dev] Test failures on Jython 2.5.1

[Peter]

On Wed, May 19, 2010 at 12:26 AM, Eric Talevich wrote:
> On Mon, May 17, 2010 at 12:37 AM, Peter wrote:
>
>> Hi all (especially Eric),
>>
>> I've just run the test suite with Jython 2.5.1 and this found some new
>> problems. Most of these are XML related from Bio.Phylo
>>
>> ERROR: Round-trip parsing and serialization of apaf.xml.
>> ExpatError: The element type "phy:clade" must be terminated by the
>> matching end-tag "</phy:clade>".
>>
>> ...
>>
>
> Fixed in GitHub:
> http://github.com/biopython/biopython/commit/ad1a618def838d98432e9623367cffb595eadecd
>
> I couldn't replicate this crash doing anything remotely normal in the Jython
> interpreter, but the rewriting scheme in the PhyloXML unit test suite
> crashed with various confusing tracebacks. The rewritten files were valid,
> though, and could be read by Jython outside the test suite.
>
> I know Jython doesn't clean up file handles as diligently as CPython does,
> so my best guess is that some file handles remained open or were
> reused/resurrected while parsing the rewritten files -- i.e. during the
> second parse, Jython's XML parser either started somplace other than the
> start of the file, or terminated early/late, expecting the rewritten file to
> have the same size as the original (which it doesn't because of collapsed
> whitespace). My patch reworks the file rewriting scheme and manages file
> handles obsessively; the PhyloXML parser itself stays the same.
>
> -Eric

Good work :)

Peter