BPN: BioPerl Nouveau [Was: Re: [Bioperl-l] distant thoughts from a dinosaur...]

[Ewan Birney]

On Mon, 7 Jul 2003, Aaron J Mackey wrote:

> A few of us had discussed (offline) the idea of a new repository,
> "bioperl-experimental" that contained a skeletal base Bio::Root::
> distribution and not much else; furthermore, various ideas/proposals would
> live in their own branches off this repository ("freaky" or not).  I'm
> happy to spearhead this effort.  Note that this is *NOT* BioPerl 2.0 -
> this is a place to play with new core ideas that may or may not be useful
> for BioPerl 1.4, or should be included in a BioPerl 2.0 when such a beast
> begins to exist.  Of course, if wildly successful, bioperl-experimental
> could later become bioperl-2.0-live, but it doesn't necessarily have to
> be.  I hope that point isn't too subtle to appreciate.
>
> But here's how bioperl-experimental might work; it centers around the idea
> of a "Hero" for any new experiment:

I like this idea.

>
> 1) there's bioperl-experimental-l and bioperl-experimental-dev mailing
> lists for discussion and commits, respectively.
>

I think the discussion should happen here, but it should have its own
commit list - we should split the discussion of experimental stuff from
the mainstream - it encourages silly cross-posting and multiple
subscriptions and becomes a pain in teh arse (for those who can remember,
remember we used to have the split between bioperl-l and guts like this,
but that just got silly).


>
> 7) Nobody calls this effort BioPerl 2.0; it's experimental, nouveau
> bioperl, nothing more.  Perhaps it's actually BioPerl 3.14, we won't know
> until we get there.
>

right - bioperl i.0 ;)

> > >     --- We are bound to have a proposal to change the start from
> > > 1 to 0 of sequences. We should have some reasoned discussion and
> > > then vote/or leave to the leader's taste (I prefer the latter...)
>
> Our first experiment!  Heroes to the battlefield!
>
> > >     --- should be actively lead by one or a very small number of
> > > people who have serious bioinformatics experience
>
> the idea of the experimental branches is that we can divide and conquer; a
> small number of people don't have to do everything by themselves.
>
> > >     --- who should **not** be me, as I am clearly going to be happy as a
> > > pig in mud with the Bioperl 1.x series for a long long time ;), I am
> > > a dinosaur compared to some of the young-crazy-boys-and-girls out there
> > > and will probably be coding $seq->trunc($start,$end)->revcom() for
> > > the rest of life...
>
> And you'll be the first to try to get that to work with the new
> experimental feature model, right?
>
> > >         - whoever codes it wins the argument
> > >            aka:
> > >         - working code trumps abstract arguments
>
> But see Aaron's Corollary to Ewan's Rule #1:
>
> * one person's working code should not trump someone else's alternative
>   abstract argument that *could* be shown in code, but has not yet been
>   written because we all have paying day jobs that get in the way and
>   often have only a few minutes to read over the gobs of proposed stuff
>   and respond with a "Hurm, are you sure that's the right thing to do when
>   you might just (A, B, and C) instead?".
>

Certainly, people should listen to criticism and people who get all huffy
about their code being the best thing since sliced bread just because they
wrote it and it works shouldn't get too much respect...


... but, talk is cheap in this world (especially vague sort of "why didn't
you use an inverted decorator pattern as in Gang-of-Four xyz"), and code
is what counts. I think often there are too many people trying to
influence by throw-away comments. It is the code which counts at the end
of the day. If they get really annoyed, they should code it up (and if
there is two working code bases, then the best one should win, and it is
normally obvious which one that is...)