[Biopython-dev] pypaml

[Eric Talevich]

Hi Brandon,

Looks good, thanks! It's just enough to get the point across, and the wiki
is a fine place for extended examples.

Reading this, I notice that the cml.set_option(key, value) gets kind of
tedious when a lot of options need to be set. It would be nice to be able to
set them all in one go, as keyword arguments:

cml.set_options(
        seqtype=1,
        verbose=0,
        noisy=0,
        RateAncestor=0,
        model=0,
        NSsites=[0, 1, 2],
        CodonFreq=2,
        cleandata=1,
        fix_alpha=1,
        kappa=4.54006,
        )

What do you think? Worth implementing?

Cheers,
Eric


On Wed, Jun 29, 2011 at 11:27 AM, Brandon Invergo <b.invergo at gmail.com>wrote:

> Well, it's not much, but how's this?
> https://github.com/brandoninvergo/biopython/tree/doc-branch
> Do you want me to go more into detail about the options available like
> in the wikior is this sufficient as a tutorial? Just let me know...
>
> Cheers,
> Brandon
>
> On Mon, Jun 27, 2011 at 5:26 PM, Brandon Invergo <b.invergo at gmail.com>
> wrote:
> > Hi Eric,
> > No problem, I'll start writing something up now.
> > Cheers,
> > -brandon
> >
> > On Sun, Jun 26, 2011 at 7:32 PM, Eric Talevich <eric.talevich at gmail.com>
> wrote:
> >> Hi Brandon,
> >>
> >> I just added a stub for Bio.Phylo.PAML to the main Tutorial:
> >>
> https://github.com/biopython/biopython/commit/190a85c5bde9c079fa5cee4ab9f8ee3362538cb8
> >>
> >> Do you think you could add some more to that section, maybe pulling a
> chunk
> >> of content from the wiki page you just wrote? If you're not comfortable
> with
> >> LaTeX you can just point me to some text and I'll add it.
> >>
> >> Thanks,
> >> Eric
> >>
> >> On Thu, Jun 16, 2011 at 11:34 AM, Brandon Invergo <b.invergo at gmail.com>
> >> wrote:
> >>>
> >>> Ok, the documentation is finished:
> >>> http://biopython.org/wiki/PAML
> >>>
> >>> Cheers,
> >>> Brandon
> >>>
> >>> On Wed, Jun 15, 2011 at 1:54 PM, Brad Chapman <chapmanb at 50mail.com>
> wrote:
> >>> > Brandon;
> >>> >
> >>> >> Ok I've just sent the email to the main list.
> >>> >
> >>> > Awesome, thanks for this. Hope this convinces some other folks to
> >>> > take a look.
> >>> >
> >>> >> I can write up some documentation this week. What is the official
> >>> >> procedure for adding documentation to the wiki, if any? Or can I
> just
> >>> >> create an account and start writing?
> >>> >
> >>> > Create an account and start writing. Nothing official except that
> >>> > documentation is good.
> >>> >
> >>> >> Also, just to double-check, are my docstrings all sufficient or
> should
> >>> >> I expand those?
> >>> >
> >>> > Your code comments looked great to me. The end user documentation
> >>> > seems to be the main thing at this point: describing how someone can
> >>> > pick up and get started with the code.
> >>> >
> >>> > Thanks again for all the work,
> >>> > Brad
> >>> > _______________________________________________
> >>> > Biopython-dev mailing list
> >>> > Biopython-dev at lists.open-bio.org
> >>> > http://lists.open-bio.org/mailman/listinfo/biopython-dev
> >>> >
> >>> _______________________________________________
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> >>
> >>
> >
>