[Biopython-dev] pypaml

[Eric Talevich]

Hey Brandon,

I cherry-picked those commits, finally:
https://github.com/biopython/biopython/commit/e2bb900212bd5113385a239b4ed42b570f06e146
https://github.com/biopython/biopython/commit/ab62ac508f02b3df1d2475f599fcd92eda6c078b
https://github.com/biopython/biopython/commit/de671e1baf3faa0ed8c10835397e308b1cf1b59d

Cheers,
Eric

On Fri, Jul 1, 2011 at 12:28 PM, Brandon Invergo <b.invergo at gmail.com>wrote:

> Hi Eric,
>
> I lied. I took a moment to at least implement the kwargs change:
> https://github.com/**brandoninvergo/biopython/**commit/**
> 533b06476899b631ec28a6e4cc97a2**e669a45ea0<https://github.com/brandoninvergo/biopython/commit/533b06476899b631ec28a6e4cc97a2e669a45ea0>
>
> It seems to work swimmingly but I haven't tested it extensively yet. There
> was already exception-handling in place.
>
> Ok, *now* I'm off for the weekend!
> Cheers,
> Brandon
>
>
>
> On Fri 01 Jul 2011 06:20:30 PM CEST, Brandon Invergo wrote:
>
>> 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<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<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/**
>>> 190a85c5bde9c079fa5cee4ab9f8ee**3362538cb8<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
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>>> >
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>>> >>> >
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>>> >>
>>> >>
>>> >
>>>
>>
>
>