[Biopython-dev] pypaml

[Brandon Invergo]

Hi Eric,

Yes, I was feeling that as well while I was doing it. I think it would 
be easy enough to implement, so I'll take care of that today...

Cheers,
Brandon

On 07/01/2011 04:17 AM, Eric Talevich wrote:
> 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 
> <mailto: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 <mailto: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 <mailto: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 <mailto: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 <mailto: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
>     <mailto:Biopython-dev at lists.open-bio.org>
>     >>> > http://lists.open-bio.org/mailman/listinfo/biopython-dev
>     >>> >
>     >>> _______________________________________________
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>     >>> http://lists.open-bio.org/mailman/listinfo/biopython-dev
>     >>
>     >>
>     >
>
>