[sinab]

Interesting article on the history of Perl for bioinformatics.

As someone who is currently a bioinformatics PhD student, Perl has become the vinyl of programming languages. While some older folks script with Perl, most packages I’ve seen published recently use either R, python, c++, and more recently, rust.

[acomjean]

I’ve been working with biology data. A lot of our older scripts are Perl. It’s really good at this stuff. The great thing is the language is super stable so we don’t have to rewrite them usually.

Our new stuff tends to be in R or python though.

[throwaway984393]

The Perl scripts I wrote 20 years ago are still running on modern systems today. It's almost scary how stable the language and interpreter have been.

Turns out it's not an accident, though! There were a lot of good decisions that kept the language stable, and test frameworks and code coverage have been a critical part of Perl and its modules since the 1980's. In fact, pretty much all of CPAN gets tested on a matrix of Perl versions and operating systems (ex: http://www.cpantesters.org/distro/N/Net-Amazon-EC2.html)

[cutler]

In many ways Perl's testing culture was the forerunner of TDD. CPAN Testers earned a lot of respect for making the Perl ecosystem stable.

[a-dub]

this.

i remember silly java consultants rabbiting on about TDD and agile while dismissing oss.

meanwhile, the curation of both testing and documentation as well as overall code quality on CPAN was light years beyond the best corporate code i've ever seen.

i'd argue that perl (with CPAN) was the first internet native programming environment.

[otherme123]

Yes, I also was there in those years. Perl snippets were shared by everyone, but almost nobody knew how they work, much less how to tweak them to adapt to new scenarios or how to contribute to a library. I remember a snippet that read a FASTA file and counted the GC%, but it had an error somewhere that made it fail when it reached the 1001 sequence. Nobody was able to find the error, they just splitted the FASTAs in smaller files. Until someone wrote a less esoteric Python script, and the Perl snippet died.

[throwaway984393]

Might be unrelated, but Perl does have a hard limit on recursion within the same function; after 100 recursions it'll die with an error and you have to unroll your loops.

[bmn__]

False.

    $ perl -Mwarnings -E'sub f { $c++; say $c if 0 == $c % 1_000_000; f() } f'
    Deep recursion on subroutine "main::f" at -e line 1.
    1000000
    2000000
    3000000
    4000000
    5000000
    6000000
    7000000
    8000000
    9000000
    10000000
    11000000
    12000000
    13000000
    14000000
    15000000
    16000000
    17000000
    18000000
    19000000
    20000000
    Terminated

You get a warning after 100 calls which almost always indicates a bug. In case it's a genuine deep recursion, the warning can be easily suppressed with `no warnings "recursion"`.

On my computer, the program continues to run for about 10 seconds, consuming 9 GB virt./res. after which it is killed off by `earlyoom`.

[throwaway984393]

It might have behaved slightly differently 20 years ago when I ran into it :) or maybe I misremember!