PEP8 cleanup before real changes
Genepop execution in an isolated, temporary directory (to allow parallel execution)
PEP8 cleanup
Switch import testing order for Bio.Cluster test
Clean up test files after running BWA & samtools tests
Put return code at start of Bio.Application error message.

This is in case the ApplicationError exception message
gets truncated and this information is lost (e.g. due to
a very long command line from several long file names).
Just use relative paths in this test
Update due to changed Bio.Application error message
Match case; I should install this dependency locally...
More side effects from changing exception...

Also show actual error if assert fails.
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