[Biopython-dev] pypaml

[Brandon Invergo]

Since the options are stored in a dict() object keyed by strings, I 
think it would be easiest to have the arguments passed as ("option", 
value) tuples or to have a dict() passed in with "option":value pairs.

Alternatively, the set_option & get_option methods can be dropped 
altogether and we can just let the user have full access to the options 
dict. The write_ctl_file method can be used then to check the validity 
of each option, to prevent erroneous option names from being used. 
Perhaps that's better, despite being slightly more work to implement.

What do you think?

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
>     >>> >
>     >>> _______________________________________________
>     >>> 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
>     >>
>     >>
>     >
>
>