[Bioperl-l] versioning

[Aaron J. Mackey]

To be fair, the problem Juguang is pointing out is that the method in 
which ExtUtils (and therefore CPAN) uses to determine the version of an 
already-installed module is not handled (nor can it be) by 
Bio::Root::Version.  Therefore, if someone else's package "Foo" has a 
Makefile.PL that specifies a requirement for Bio::Perl version 1.4, 
when CPAN tries to install the "Foo" module it may complain that the 
right version isn't present (I believe, however, that when a requisite 
version cannot be determined by parsing, it doesn't prompt for 
(re)installation; furthermore, the "correct" answer is to require 
Bio::Root::Version 1.4).

But since 1.4 is out in the wild now, we can only sit back and see what 
happens.

-Aaron

On Dec 23, 2003, at 10:54 AM, Heikki Lehvaslaiho wrote:

> Juguang,
>
> We've had quite a lot of trouble with $VERSION. Pre-1.4 we did not 
> have any
> consistent system.  I was planning a script based system probably quite
> similar to yours when Aaron came up with Bio::Root::Version.
>
> Now all modules get their version from Bio::Root::Version (via
> Bio::Root::RootI). This system has its limitations: most importantly, 
> you can
> not query the verson from multiple modules.  However, getting a 
> consistent
> answer from any module using, e.g.
>
> 	perl -MBio::Perl -le 'print Bio::Perl->VERSION;'
>
> is quite an advancement in my opinion.
>
> The problem I can see in your implementation is that perl 5.005 that 
> we are
> still supporting, does not know 'our'. (like pointed out  by Hilmar
> yesterday)
>
> So again, I'd like to err to the conservative side rather than change 
> for its
> own sake. Let's give the current version implementation a chance, but 
> keep
> your script in mind for the future.  If the current system does not 
> work in
> practise,we could change it for the next release.
>
> It would be nice to modernize bioperl a bit. I guess we should poll 
> our users
> if we could drop supporting versions pre 5.6.
>
> Have a good holidays,
>
> 	-Heikki
>
> On Tuesday 23 Dec 2003 9:33 am, Juguang Xiao wrote:
>> Hi list,
>>
>> I think this is more meaningful suggestion than what I had previously.
>> Most of Bioperl modules does not have $VERSION, which is encouraged by
>> CPAN community. Should we make it in release 1.4? I am aware that 
>> there
>> are an array of emails in this list about this versioning, but they do
>> not pass the simple condition,
>>
>> perl -MExtUtils::MakeMaker -le  'print MM->parse_version(shift)' 
>> 'file'
>>
>> in http://www.cpan.org/modules/04pause.html#conventions
>>
>> I have written a quite short script, maintenance/version.pl, in CVS
>> now. It append
>>
>> our $VERSION="1.4";
>>
>> after the package declaration line. It changes almost all bioperl
>> modules, except
>>
>> 1.4
>> /home/juguang/src/bioperl-live//Bio/Root/Version.pm
>> 0.50
>> /home/juguang/src/bioperl-live//Bio/Tools/dpAlign.pm
>> 1.15
>> /home/juguang/src/bioperl-live//t/Test.pm
>>
>> After the changes, all my tests pass, except t/RestrictionIO, it never
>> passes on my MacOS 10.2.8, Perl 5.6.
>>
>> I do not think other way except writing 'our $VERSION="1.4";' line
>> explicitly in each file. Since we should do this before compile time.
>> Also I don't think it is good to let Makefile to do it for us, since 
>> it
>> should be done before distribution.
>>
>> Let me know if you like this idea and script. Core guys, you can run 
>> it
>> on your machine and commit 700 modules!, or I can do it, if you do not
>> say no.
>>
>> Juguang
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at portal.open-bio.org
>> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>
> -- 
> ______ _/      _/_____________________________________________________
>       _/      _/                      http://www.ebi.ac.uk/mutations/
>      _/  _/  _/  Heikki Lehvaslaiho    heikki_at_ebi ac uk
>     _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
>    _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
>   _/  _/  _/  Cambs. CB10 1SD, United Kingdom
>      _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
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