TravisCI now supports Python 3.4
Close these handles
Comment regarding rU mode and Python 3
Avoid open(filename, 'rU') on Python 3

Perhaps some of these examples can be just mode 'r' on Python 2?
We would need more testing under Windows to be sure through...
newline characters are a pain.
Skip tests for 'bwa aln' when 'aln' is unrecognized

'bwa aln' is failing for bwa[0.7.6a-r433], see:
http://lists.open-bio.org/pipermail/biopython-dev/2014-April/011342.html
update the NEWS (Bio.CodonAlign)
add experimental warning to Bio.CodonAlign
return a generic_nucleotide alphabet when slice a CodonAlignment
typo bug fixing
We don't checkin compiled documentation files
Correctly detect EMBOSS 6.5

Noticed by Andreas Tille during Debian packaging.
Tweak PIL/Image detection, should work with Pillow now.

Noticed by Andreas Tille during Debian packaging.
Make test_CodonAlign.py less noisy if SciPy missing
Fix handle leaks in Tutorial doctests

Problems identified with:

$ python3.4 -W all test_Tutorial.py
Remove deprecated Bio.Motif section from Tutorial.

Bio.Motif was formally deprecated in Biopython 1.62 (August 2013),
and will be removed after August 2014.
Close handle in Bio.SeqIO.PhdIO doctest

Tested with:

$ python3.3 -W all Bio/SeqIO/PhdIO.py
Fix context manager error in self-test.

Still a problem through:

$ python2.7 -W all SffIO.py
...
omega
Traceback (most recent call last):
  File SffIO.py, line 1385, in <module>
    for record in SffIterator(handle):
  File SffIO.py, line 852, in SffIterator
    assert 0 == handle.tell()
AssertionError
Fix handle leaks in SFF self-test

Still a problem here:

$ python3.4 -W all SffIO.py
...
omega
Traceback (most recent call last):
  File SffIO.py, line 1399, in <module>
    for record in SffIterator(handle):
  File SffIO.py, line 852, in SffIterator
    assert 0 == handle.tell()
AssertionError
Clearer SFF error message
Avoid deprecated unittest assertAlmostEquals method