[Biopython-dev] Python 3.2 testing

[Peter]

Hi all,

Today I've been running the Biopython test suite under
Python 3.2 beta 2, which identified a few issues.

There is a new ResourceWarning when file handles are
not closed, something I'd already addressed in Bio.SeqIO
and AlignIO from problems found on Jython on Windows
where you can't delete a file when a handle to it is still
open. I've resolved the vast majority of cases in the test
suite, but there is room for improvement still.

I found test_Phylo.py is failing on Python 3.2 beta 2 due
to a bug in Python, http://bugs.python.org/issue10777

The Bio.Seq doctest was failing due to exception formatting
changes - I thought this was being fixed but perhaps not
so I have for now disabled this test for all Python 3.x in
run_tests.py - see http://bugs.python.org/issue7490 and:

https://github.com/biopython/biopython/commit/3d88c6b1d6d82ee6b6448d9fde23d774481b4a26

There is a single remaining failure from test_TreeTest1
in test_Nexus.py which I have not yet investigated.

Peter