[Biopython-dev] pypaml
Brandon Invergo
b.invergo at gmail.com
Thu Jul 14 04:49:07 EDT 2011
Hi Eric,
I'm really sorry about that!!! I was on holiday for some days and now
I'm up to my neck in grant applications, so it totally slipped my mind.
Is there anything left to do?
I see Peter's email about the unit tests so I'll look into that...
Apologies,
-brandon
On Thu 14 Jul 2011 05:23:15 AM CEST, Eric Talevich wrote:
> 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
> <mailto: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>
> <mailto: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>
> <mailto: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>
> <mailto: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/__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>
> <mailto: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>
> <mailto: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>
> <mailto:Biopython-dev at lists.__open-bio.org
> <mailto:Biopython-dev at lists.open-bio.org>>
> >>> >
> http://lists.open-bio.org/__mailman/listinfo/biopython-dev
> <http://lists.open-bio.org/mailman/listinfo/biopython-dev>
> >>> >
> >>> _________________________________________________
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> >>>
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> >>
> >>
> >
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