Leon Timmermans | 8 Feb 12:18 2013

Re: BioPerl long-term, was Re: dependencies on perl version

On Thu, Feb 7, 2013 at 10:36 PM, George Hartzell <hartzell <at> alerce.com> wrote:
> 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...
> 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.

I share that experience.

> 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.

I share your sentiment. Most of BioPerl is architected so badly I
can't stomach it most days, and I've worked on hairy codebases
included perl itself. There's just too much sick and wrong. It's like
hundreds of dot-com-era cgi scripts.

The problem (which is common in scientific computing) is that once
code works it's effectively abandoned. BioPerl is essentially a
gathering of more than a thousand such modules.

> 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 would be lovely, but who is going to do that? We're suffering
from the tragedy of the commons.

> Have fun.  Use sharp tools.  Do cool science.  Build cool things.
> Advance your careers (forgot that one last time).  Be reasonable and
> professional.

Sounds like good advice to me :-)

> Supporting last year's projects is someone else's business
> opportunity.


> 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...).

Interesting discussion, though the original post is too cynical even
for my taste.