[Biopython-dev] Code review request for phyloxml branch

[Peter]

On Sat, Jan 9, 2010 at 11:38 PM, Eric Talevich <eric.talevich at gmail.com> wrote:
>
> I'm trying to avoid having to update Phylo/__init__.py each time I add
> or rename a public function in Utils.py or IO. So, how about this:
> I've added "__all__" definitions to Utils.py and IO/__init__.py so
> that only the relevant public functions are loaded when
> Phylo/__init__.py imports * from those two sub-modules. Testing
> manually, this seems to do the right thing.

Previously bits of Biopython have used __all__, and then
abandoned this a long term maintenance load. This was before
my time, so I am not familiar with the full history, but it makes me
wary about using __all__ here.

Personally I don't see a big problem with having just explicit
manual imports within Bio/Phylo/__init__.py if and when you
decide a new function/class/etc in Bio/Phylo/Utils.py or IO.py
should be made available at the top level. In general I would
think relatively few things should be exposed like that.

Peter