[Bioperl-l] "progress": useful changes vs. "shiny new thingie"

Brian Osborne bosborne11 at verizon.net
Wed Nov 15 15:19:13 EST 2006


I just looked at the most recent bioperl-db and bioperl-run, I don't see any
Build.pl there. Are you suggesting that the Bioperl core build should be
mediated by Build.pl yet all other packages are built by some Makefile.PL?

Brian O.

On 11/15/06 2:33 PM, "Sendu Bala" <bix at sendu.me.uk> wrote:

> Aaron J Mackey/PharmRD/GSK wrote on 11/15/2006 01:29:30 PM:
>> What actual needs prompted the change from ExtUtils::MakeMaker to
>> Module::Build?
> For the old Makefile.PL:
> At the time I started, script installation was broken. Documentation
> installation hasn't worked in a very long time. Handling of true
> requirements and optional pre-requisites is completely inadequate. It
> can't generate a suitable META.yml, and leaves the package non-ideal for
> distribution on CPAN.
> It was also a nightmare keeping the Makefile.PL scripts in each cvs
> module (live, run, db, network) in sync with each other. Now they can
> have simple module-specific Build.PL scripts, with all the advanced
> functionality in a rarely-updated and unchanged-between-modules
> ModuleBuildBioperl.pm.
>> It seems that the switch was made without a complete understanding of
>> all the bits and bobs in the existing Makefile.PL
> I hope that's not the case; I tried to understand everything. Please let
> me know if I've missed something. (To tidy up a question I asked about
> the symlink script, I've resolved that and the symlink should also work
> given the proviso outlined in the POD for maintenance/symlink_script.pl)
>> For one, the Bio::DB::GFF Makefile.PL is independent (yet triggered
>> by the main Makefile.PL) such that users can choose whether to test
>> the install vs. a live database or not.
> The Makefile.PL in Bio/DB? As far as I can tell, it achieves no such
> functionality. Letting the user choose to do live database tests was a
> function of the main Makefile.PL, which I have carried over to the new
> Build.PL. (And made it better in the process.)
>> This is an example of encapsulation: the specializied testing/install
>> process for a module is kept with the module, and not in the
>> monolithic main script.
>  From a maintenance point of view, it seems to me to be much easier if
> all install-related things are in one place rather than scattered where
> you might miss things.
>> For two, it seems that the ability to install bp_*.pl scripts was
>> "lost" in the transition.
> What makes you say that? It certainly shouldn't be. What should happen
> is you get asked what scripts you'd like to install (the same question
> as before), but again its done in a much nicer way.
> (The major difference, I suppose, is that scripts_temp is no longer
> generated; prior to "./Build install" you'll find the scripts in
> blib/script/)
>> For three, there's certainly a lot more that I can't remember right
>> now.
> Please try and remember. I spent a lot of time trying to make sure that
> Build.PL does everything Makefile.PL did, but much much better.
> Thank you,
> Sendu.
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