[Bioperl-l] [ANNOUNCEMENT] Alpha 1.6 releases of BioPerl-run, BioPerl-db, BioPerl-network

Mark A. Jensen maj at fortinbras.us
Sun Feb 8 19:17:22 EST 2009

All your points sound reasonable; certainly without a hard look it would
be most expedient just to zap the module. I would say that 1) it would be
pretty useful to have all the BioPerl config data in one place, and
2) M:B's solution is a way to do this that seems pretty convenient
for the installation of a single module, or a single distribution, but
 might not scale well to BioPerl's multi-distribution
complexity, at least not without some help. If there are any Module::Build
hackers listening, hope they'll chime in.

If BP built its own config
module, we could divide the "static" and "dynamic" config information
explicitly according to whatever is decided, and provide that infomation
programmatically; I think I can imagine scenarios (say a failover) that
one might want to check what the current db settings are in a nice standardized
way and then decide what to next. Being vague here intentionally, as I'm
just getting to understand the machinery and techniques of configs
and distributions.

(Could the issue benefit from a wiki page?)

----- Original Message ----- 
From: "Chris Fields" <cjfields at illinois.edu>
To: "Mark A. Jensen" <maj at fortinbras.us>
Cc: "Alex Lancaster" <alexl at users.sourceforge.net>; 
<bioperl-l at lists.open-bio.org>
Sent: Sunday, February 08, 2009 5:41 PM
Subject: Re: [Bioperl-l] [ANNOUNCEMENT] Alpha 1.6 releases of BioPerl-run, 
BioPerl-db, BioPerl-network

> Mark,
> Yes, saw that.  It is a 'feature' of Module::Build that snuck by us,  at least 
> by me.  We can take advantage of that at some future point,  but at this time 
> I think we should attempt turning off installing  Bio::ConfigData completely, 
> at least until we do the following:
> (1) determine whether we want to call it 'Bio::ConfigData'
> (I vote 'no'; I don't like anything installed by default to our core 
> namespace when it should probably be in Bio::Root, such as 
> Bio::Root::ConfigData)
> (2) determine whether we want bioperl core and the subdistributions to  use 
> the same or different ConfigData modules
> (I vote 'same', no need to get overly complicated at this point)
> (3) describe exactly what does and does not belong in any permanent  BioPerl 
> config file
> (I think they should only be relevant to the local build/test/ installation 
> and shouldn't include possibly volatile DB configuration  settings)
> Right now it just houses the feature-related settings used within all  the 
> Build.PL.  Based on their current naming ('BioDBSeqFeature_mysql', 
> 'BioDBSeqFeature_BDB') I don't trust those to always contain the same 
> key/value pairing, so we need to probably standardize these for the  next 
> bioperl minor release (they're potentially too volatile and could  be 
> consolidated in a meaningful way).
> Anyway, until then I wouldn't rely on ConfigData's existence or the  specific 
> namespace Bio::ConfigData; I'll probably add it to  MANIFEST.SKIP.
> chris
> On Feb 8, 2009, at 1:12 PM, Mark A. Jensen wrote:
>> As I understand it, Foo::Bar::ConfigData is generated by M:B to  provide 
>> persistent access to
>> the configuration parameters after (perhaps long after)  installation, via a 
>> script
>> config_data that comes with M:B. Is there a collision between 
>> Bio::ConfigData created by
>> the main distribution and Bio::ConfigData created by bioperl-run?
>> See the docs at
>> http://search.cpan.org/~ewilhelm/Module-Build-0.31012/lib/Module/Build/Authoring.pod#SAVING_CONFIGURATION_INFORMATION
>> ----- Original Message ----- From: "Chris Fields" <cjfields at illinois.edu
>> >
>> To: "Alex Lancaster" <alexl at users.sourceforge.net>
>> Cc: <bioperl-l at lists.open-bio.org>
>> Sent: Sunday, February 08, 2009 1:13 PM
>> Subject: Re: [Bioperl-l] [ANNOUNCEMENT] Alpha 1.6 releases of 
>> BioPerl-run,BioPerl-db, BioPerl-network
>>> Alex,
>>> Odd.  From what I'm reading that file shouldn't be added to the 
>>> distribution or installed.  It's generated on the fly by  Module::Build  for 
>>> build and configuration only (triggered when  using the 'features'  option). 
>>> Makes me wonder if this is an issue  with Module::Build or  our derived 
>>> Bio::Root::Build,  It does  appear this is also popping up  as a possible 
>>> issue with  Module::Build itself (included along with  perl 5.10.0):
>>> http://www.nntp.perl.org/group/perl.module.build/2009/01/msg1809.html
>>> The obvious fix is to have it ignored upon installation.  I'll try  to  get 
>>> a fix up for the next alphas of BioPerl-run/db/network and  the  next point 
>>> release of BioPerl.
>>> chris
>>> On Feb 8, 2009, at 10:41 AM, Alex Lancaster wrote:
>>>>>>>>> "CF" == Chris Fields  writes:
>>>> CF> Alex,
>>>> CF> I don't see Bio::ConfigData with the last BioPerl core  release  on 
>>>> CPAN
>>>> CF> (1.6.0) or any of the BioPerl-*.  Could you send me the  actual  file 
>>>> in
>>>> CF> question?
>>>> You are right that it doesn't appear to be contained in the source,
>>>> but looking at the build log it appears to be dynamically  generated in
>>>> both packages.
>>>> 1) In the case of bioperl:
>>>> Writing config notes to blib/lib/Bio/ConfigData.pm
>>>> and later:
>>>> Manifying blib/lib/Bio/ConfigData.pm ->blib/libdoc/Bio::ConfigData. 3pm
>>>> later still:
>>>> Installing /builddir/build/BUILDROOT/perl- 
>>>> bioperl-1.6.0-1.fc11.noarch/usr/lib/perl5/vendor_perl/5.10.0/Bio/ 
>>>> ConfigData.pm
>>>> See full log here:
>>>> http://kojipkgs.fedoraproject.org/packages/perl-bioperl/1.6.0/1.fc11/data/logs/noarch/build.log
>>>> 2) Similar generation of the ConfigData is done in bioperl-run:
>>>> http://kojipkgs.fedoraproject.org/packages/perl-bioperl-run/1.5.9/0.1.1.fc11/data/logs/noarch/build.log
>>>> Alex
>>>> _______________________________________________
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