[Bioperl-l] Priorities for a bioperl-1.6 release

Nathan S Haigh n.haigh at sheffield.ac.uk
Wed Feb 13 03:46:02 EST 2008

Hash: SHA1

Chris Fields wrote:
> On Feb 12, 2008, at 12:10 PM, Sendu Bala wrote:
>> Chris Fields wrote:
>>> * perl 5.10 compliance (appears to mostly work now)
>>> * outstanding bugs (core only)
>>> * POD and test coverage
>> I'm fine with everything you said, but I'll just say that, at a
>> minimum, the above is what needs to be done.
> I think we should also try to get bioperl-db up to speed for the BioSQL
> 1.0 release (at least Bio::Species-related issues).
>> Someone needs to step up and organise that 3rd point, since it will
>> require a lot of work. As I've already done work on the test suite, if
>> no one else expresses an interest I might look into it myself.
> Jason and I discussed it off list (along with Nathan Haigh).  We also
> brought up the idea of smoke tests, which should pinpoint how stable
> bioperl-live distributions are.  Having those set up would pinpoint
> modules we think need to stay in core or should go into a separate
> 'dev/extras' distribution.  We could test smoke/coverage/POD on those as
> well.

I've moved away from Perl coding over the past 6-12 months but try to keep an eye on the BioPerl mailing list and chip in when I can. The last time
the Devel::Cover module came up, it was lacking the ability to sort the coverage report table by each of the coverage metrics - which was a problem
for us as we have so many modules and it was time consuming to find those with poor coverage. However, this feature were implemented in Devel::Cover
0.62, so it makes things slightly easier/neater. I'm not sure if the problem of failing tests still mess up the completion of the coverage report or not.

>>> Now that SVN migration is complete
>> Speaking of which, is there a way a file (like, oh, I don't know,
>> bioperl-live/trunk/t/lib/BioperlTest.pm) can exist just once in SVN
>> but be seen in other locations (like
>> bioperl-run/trunk/t/lib/BioperlTest.pm)? Such that a commit to the
>> version in bioperl-run also affects the version in bioperl-live? Or is
>> there some appropriate other way to organise where cross-repository
>> files are kept and dealt with?

See the subversion FAQs:

> Maybe using external definitions, though I haven't messed with it
> personally.
> http://svnbook.red-bean.com/en/1.4/svn.advanced.externals.html
> One of the outstanding issues on SVN migration is the use of aliases for
> a checkout ('bioperl-all'); that would probably require setting
> svn:externals in some way.
> chris

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