Add tests for Entrez online access
Hack to make Entrez work with its XML parser and other Bio parsers

Previously, Entrez's _open can either work with Entrez.read / Entrez.parse or
the other parsers (SeqIO, Medline), but not both. This was because Entrez's XML
parser expects binary data while the other parsers expect strings.
Merge pull request #134 from bow/patch_entrez-bin

Patch for Entrez parsing. Let's revisit this once Python3 has been fixed.
Updating the documentation on position-weight matrices
Merge branch 'master' of github.com:biopython/biopython
Update Seq.startswith and Seq.endswith for Python2.5+

A loop was used previously for checking against multiple strings due to
incompatibilities with Python <2.4. Since 2.4 is now not supported, we
can replace the loop with a cleaner fall back on str.startswith or
str.endswith.
Use a generator expression rather than a list expression (shorter)
Fix variable name in Windows Python 2.5 fix
Fix another float('-inf') Windows Python 2.5 issue.

Note this doesn't seem to be covered in the unit tests...
Remove unused imports and rearrange import order in Bio.SeqUtils
In seq1(), compare the uppercase versions of the three letter codes.

Otherwise this function is hard to use, as users have to bring their
sequences into the Xxx spelling format.
Travis should be providing NumPy on Python 3.2 now (or soon)
TravisCI should support Python 3.3 now.

They're also dropping Python 3.1 but that wasn't officiall
supported and we were not using it anyway.
Generalise TravisCI Python 3 support
Even float('inf') fails on Windows Python 2.5
Refactor utility functions in Bio.SearchIO

Some general-usage functions are now in Bio._utils
Refactor Bio.Phylo._sugar into Bio._utils
Refactor doctests in various submodules to use Bio._utils.run_doctest
Fix mass spectrometry method parsing.
Fix typos.