[Bioperl-l] BioPerl long-term, was Re: dependencies on perl version

[Fields, Christopher J]

On Feb 7, 2013, at 3:36 PM, George Hartzell <hartzell at alerce.com> wrote:

> Fields, Christopher J writes:
>> George,
>> 
>> Should put your post on a pedestal :)
>> 
>> tl;dr version: I completely agree, but we need help in order to do this.
>> [...]
> 
> And therein lies the [a] problem.  Don't look at me....
> 
> I'm not coding on bioinformatics problems these days (though I'm
> available...) so _maybe_ I shouldn't have gotten up on the soapbox.
> 
> But I'm so sick of getting into arguments (or walking away from
> them...) with Ruby and Python [and lisp and *PHP*] fans; Perl is dead,
> you can't write good code in Perl, look - Ruby has GEMS!, etc…

Right, but that's a perception not just in the Bio* world.  It's larger and more pervasive than that.  

> Perl of the olden days was an easy language in which to write really
> shitty code.  Even the Perl of the BioPerl heyday wasn't really much
> help; role your own OO, role your own distro-building, mountains of
> monkey-work to provide consistent POD, versioning, etc...
> 
> But that's not the Perl that I use.  I have Moose and Moo.  TAP and
> the things built on it.  Dist::Zilla.  PerlTidy.  PerlCritic.  cpanm.
> MetaCPAN.  Pinto.  GitHub.  Perlbrew.  Wow.

Yes, and that is the direction we need to go in.

> It isn't any harder to write good code, for measures that I care
> about, using Perl than it is *any* of the other similar languages.
> 
> And it's just as easy, and happens just as frequently, for people to
> write shitty (undocumented, untested, poorly managed, poorly packaged,
> ...) stuff in the other languages.

Oh, I know.  I'm working on some very nice looking but terribly implemented Python code now.

> GET OFF MY LAWN, KID! (Yeah, I know...)
> 
> But BioPerl *is* dying.  You might be standing on the shoulders of
> giants when you use it to solve a problem, but you *definitely* have
> those same giants (and their extended families) on your shoulders
> every time I see you try move the project forward.  All of that
> history has become the tail that's wagging the dog.

Yep.

> If all y'all are going to keep the thing alive, moving forward and
> contributing to new great works then make Apple your hero.  Deprecate
> the stuff that's holding you back, give folks a path forward and move
> on.

That's fine.

> Have fun.  Use sharp tools.  Do cool science.  Build cool things.
> Advance your careers (forgot that one last time).  Be reasonable and
> professional.
> 
> Supporting last year's projects is someone else's business
> opportunity.
> 
> g.

Right, but this isn't just my show.  I can't do this alone; it's simply too much code and I don't have even 1/4 the time I used to have.

> ps.  Are all y'all following this thread?
> 
>     http://news.ycombinator.com/item?id=5123022
> 
> Maybe someone should search down for this bit: "Where to start? Any
> list of this [sic] projects?" and insert a plug for the various
> open-bio projects.  (But "someone" doesn't work here, he said…).

Read the original guy's post.  He's completely delusional (okay, maybe not *completely*, but he comes across as quite bitter and unrealistic).  

Frankly I don't feel so bad if he wants to leave.  He doesn't like messy things.  Biology is messy, if one doesn't understand that then computational biology is not for them.

chris