[Biopython-dev] pypaml

[Brandon Invergo]

Hi Eric,
You're right, I had the functionality of kwargs mixed up in my head 
(I've rarely used it) and I forgot that it's passed in as a dict. In 
that case, it's relatively straight-forward to do. Something like this:

def set_options(self, **kwargs):
    for option, value in kwargs.items():
        if option in self._options:
            self._options[option] = value
        # else:
        #    Raise exception

Not sure if raising an exception would really be necessary here. (ps - 
I haven't tested that code, I just typed it up quickly now)

Regarding the splitting of functionality, to an extent it makes sense 
but I wonder if it's worth it, since the PAML commandline programs only 
take a single argument, the path to the control file. However, if the 
main advantages lie in code readability and standardization with the 
rest of the applications framework, then I think it's ok.

Unfortunately I'll be unavailable all weekend (starting in about 3 
minutes) but I should be free on Monday to work on it.

Cheers, 
Brandon

On Fri 01 Jul 2011 04:17:26 AM CEST, 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
>      >>> >
>      >>> _______________________________________________
>      >>> Biopython-dev mailing list
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>      >>> http://lists.open-bio.org/mailman/listinfo/biopython-dev
>      >>
>      >>
>      >