[Biopython-dev] Test failures on Jython 2.5.1

[Peter]

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>".

ERROR: Round-trip parsing and serialization of bcl_2.xml.
ExpatError: The element type "phy:branch_length" must be terminated by
the matching end-tag "</phy:branch_length>".

ERROR: Round-trip parsing and serialization of o_tol_332_d_dollo.xml.
ExpatError: XML document structures must start and end within the same entity.

ERROR: Round-trip parsing and serialization of made_up.xml.
ExpatError: Premature end of file.

ERROR: Round-trip parsing and serialization of phyloxml_examples.xml.
ExpatError: XML document structures must start and end within the same entity.

It would probably be instructive to look at the serialisation output in
an XML validator - if there is a problem it may be the Jython parser
is stricter than the C Python XML parser.

There are also a couple of SeqIO related problems with large files:

ERROR: test_SeqIO
OutOfMemoryError: java.lang.OutOfMemoryError: Java heap space
ERROR: Write and read back Human_contigs.embl
OutOfMemoryError: java.lang.OutOfMemoryError: Java heap space

Example Tests/EMBL/Human_contigs.embl is causing the problem.
This is a sequence of length 958952, but the file doesn't actually
hold the sequence so we use an UnknownSeq object. The two
out of heap space error are both from trying to create a string of
958952 "N" characters. I'll have a look at this - we can probably
avoid it in the test.

Peter