George Hartzell | 7 Feb 22:36 2013

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

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...

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.

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.

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.

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

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

Supporting last year's projects is someone else's business


ps.  Are all y'all following this thread?

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...).