[Biopython-dev] Python 2.6

[Peter]

Peter wrote:
> One of the python 2.6 issues Bruce flagged up was the deprecation of
> the Sets module.  Based on a quick grep, this affects several modules:
> ...
> On balance I think it would make sense to convert all these to use the
> new built in "set(...)" instead of "Set(...)", with a fall back for python 2.3

Seq.py - fixed in CVS

Align/AlignInfo.py - complicated by the lack of a union_update method
for the built in set class, but fixed in CVS.

AlignIO/__init__.py - removed unused import in CVS

AlignIO/PhylipIO.py - fixed in CVS

Data/CodonTable.py - fixed in CVS

Nexus/Nexus.py and Nexus/Trees.py - with my suggested fix, the unit
test output will currently say Set or set depending on the version of
python.  A further minor change to test_Nexus.py would be needed to
cope with this.

Restriction/Restriction.py - this subclasses the Set object, so needs
a little more checking.

SeqIO/__init__.py - fixed in CVS

SeqIO/PhylipIO.py - was deprecated, now removed

Peter