[Biopython-dev] major refactoring

[Jeffrey Chang]

Hello everybody,

I just finished a major refactoring of many of the modules.
Specifically, I moved all the instances of X/X to X/__init__.  For
example, code from Bio/Fasta/Fasta.py was moved to Bio/Fasta/__init__.py.
Because of this, import code now looks a bit cleaner, i.e.
    from Bio import Fasta
instead of
    from Bio.Fasta import Fasta


Unfortunately, this breaks existing code that imports these modules.
I've fixed all the occurrences of this in Biopython that I could find.
However, please be on the lookout in case I missed something!

Jeff