[Biopython-dev] pypaml

[Brad Chapman]

Brandon;

[pass and return parameters]
> Done!
> Funnily enough, it was originally that way but then I remembered that
> Python passes arguments by reference, so I changed it to not return
> the dict every time. I thought I was being clever and Pythonic but I
> agree that this way is more readable/maintainable.

That looks fabulous; thanks much. We can invoke the 'Explicit is
better than implicit' clause of the Zen of Python for this one.

> Ok, the pure Python version is back in. Once PAML is officially part
> of Biopython, I can write some documentation for the wiki and provide
> a warning about the high df values...

Great, thanks for this as well. From my point of view, the only
thing you need is some documentation to finish it off. It would
definitely be worthwhile to send it to the main list to see if
others have feedback. I'm happy to work on merging it in if everyone
else is agreed.

Thanks again,
Brad