[Bioperl-l] Size of BioPerl distribution

[Chris Fields]

Maybe attempt trimming them down a bit first, if that's possible.  If  
not, no worries (breaking up the distribution will help as Robert  
said).  Archive::Tar and IO::Zlib were added in core after 5.8  
(5.009003 to be exact), so I would rather not have to worry about any  
test-specific dependencies.

Anyway, we've got a little more time.  I'm getting a META.yml popping  
up (though everything appears to pass here).  Will look into it; may  
be related to a previously reported bug, but I would like to see some  
CPANPLUS tests coming in first.  That's what an alpha is for!

chris

On Sep 17, 2009, at 9:13 PM, Mark A. Jensen wrote:

> t/data compresses from 21M to 9M. We could ship with
> $ tar -czf data.tar.gz data
> $ rm -rf data
>
> and do the following in Bio::Root::Test, if we're willing to expect  
> Archive::Tar and IO::Zlib :
>
> use vars qw( $ARCHIVE );
> $ARCHIVE = "data.tar.gz";
> ...
>
> sub test_input_file {
>   # if it's there, fine
>   my $fn =  File::Spec->catfile('t', 'data', @_);
>   return $fn if -e $fn;
>   # if it's not, expand the archive
>   my $arch = File::Spec->catfile('t', $ARCHIVE);
>   Bio::Root::Root->throw("Test data archive not present") unless (-e  
> $arch);
>   my $tar = Archive::Tar->new($arch);
>   Bio::Root::Root->throw ("Can't extract test data archive") unless  
> $tar;
>   $tar->extract;
>   return $fn if -e $fn;
>   return;
> }
>
>
> ----- Original Message ----- From: "Chris Fields" <cjfields at illinois.edu 
> >
> To: "BioPerl List" <bioperl-l at lists.open-bio.org>
> Sent: Thursday, September 17, 2009 5:38 PM
> Subject: [Bioperl-l] Size of BioPerl distribution
>
>
>> After uploading the latest bioperl alpha to CPAN I noticed the size  
>> of  the distribution archive has jumped up from ~7 MB to just over  
>> 10 MB.   It looks like a majority of this is attributable to three  
>> data files  for testing in t/data added after the 1.6.0 release:
>> gmap_f9-multiple_results.txt  (3 MB)
>> withrefm.906                  (2.5 MB)
>> 1ZZ19XR301R-Alignment.tblastn (2 MB)
>> I'm not sure there is an easy way around the problem.  We could   
>> attempt to reduce the file size down, but I'm not convinced that's  
>> a  long-term solution (the test data will only get larger as more  
>> test  cases come up).
>> Any ideas?  Should we try to have a common biodata repo again?
>> chris
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