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Recent Commits to biopython:master Adding Frank to the NEWS file for the next release (small Bio.Nexus updates) PhyloXMLIO: cElementTree is fixed in the next patch release of Py3.1 (supposedly) assertAlmostEqual requires places to be a keyword argument on Python 3 (and 2to3 doesn't fix this automatically) Skip unit tests requiring Bio.KDTree._CKDTree when it is not compiled handle.readline() rather than handle.next() for 2to3 Slicing in Bio.Crystal via __getitem__ etc rather than using obsolete __getslice__ etc Should fix Bio.Restriction on Python 3 (need explicit __hash__ and list comprehensions don't leak variable) Use just absolute imports in Bio/Seq.py instead of a mix with some local Skip Bio.Seq doctest under Python 3.1 due to problem with exceptions, see http://bugs.python.org/issue7490 Revert "Give full exception name in Bio.Seq doctest, ..." Mention the Seq object's alphabet in the docstring more explicitly (query from Peng Yu on mailing list) Try to clarify Nexus error message (the line variable is often empty, showing the sequence is more informative I think). See also Bug 3119 minor updates in CharBuffer to handle different types of quotes Support for large genepop files Avoid printing without newline which made test_pairwise2.py fail on Python 3 Skip test_prosite_patterns.py on Python 3 (it fails due to missing sgmllib and Bio.Prosite is deprecated anyway) Opening the pickled file in binary more should fix test_SubsMat.py on Python 3 Give full exception name in Bio.Seq doctest, seems to be required on Python 3 but optional on Python 2 Python 3 bytes/unicode fix for error handling in Bio.Entrez._open() function Explictly convert from bytes to strings on Python 3 to fix QBLAST