[Bioperl-l] release march: get your changes in

[Jason Stajich]

If you've got outstanding changes you have planned to make or fix in
bioperl before 1.0 is released now is the time to get them in.  If you
have any major things to check in, please send a note out so I know what
to expect.  This means you.

No new modules will be accepted as part of the 1.0 release without special
arrangement.  These new modules won't get dropped from the main-trunk, but
will be pruned from the 1.0 branch when that is made.  So bug fixes only
and I would prefer that you report any bugs to the bugtracking first
before checking in changes unless it is a trivial doc fix or silly code
fix.  I realize we kind of broke this policy whilst at the hackathon, but
I think we're still going to have a mostly bug free release.

I will put the release candidate together this weekend and release
1.0alpha2-rc by Monday at the latest.  1.0 should then be ready in about 2
weeks if all the below is done (YOU can help it go along faster by testing
the release candidate and reporting [and fixing] bugs).

Big issues remaining:

* Do we want to try and fix Seq::trunc per our discussion about making
  features which are cut in the middle now fuzzy features.  Ewan did you
  tackle this at the hackathon?

* Code reviews - Me thinks this concept didn't work so well.
  All we're hoping here for is a fresh pair of eyeballs to look over
  every module and insure that things seem kosher.  Make sure there is a
  test for each module you're reviewing.

* SearchIO can't parse bl2seq right now (cause it is a crappy format), but
  will try and add that in if I can, otherwise will have to point people
  to BPbl2seq.

Outstanding bugs which we could surely use voluteers on:

1098 - Jim Diggans were you able to fix this yourself and commit the
       changes?  (SeqIO infinite loop condition)

1100,1096 Bundle updates

1101 srs.pm is part of the LiveSeq pkg and maintained by Josep Insana
     so we'll leave the dependacy in there but probably need to include a
     msg in a README in that directory.   Heikki can you see if Josep will
     write that.

1091 new genbank LOCUS parsing - this should be simple fix as bug
     reporter gives a code fix, but needs to be tested on real sequence
     file and probably have that be included as part of the test system.

1090 Not clear if this is a real bug, need to find test case that breaks
     Has to do with swissprot writing.

1069 Handle one-of descriptors in feature table for FTHelper.

1068 Make sure we output dates in GenBank LOCUS line

1052 Handle Win32 issues with filenames that are not 8.3 compliant
     - fix needs to be more subtle as we are not going to ever put a
	'use Win32' statement in bioperl.  Runtime detection of OS and
       outputting appropriate filename length is more likely.

1048 Heikki Pretty sure you fixed this, can you just confirm and we'll
     clear it. (expanding AA 'Z')


That's all on my list, but feel free to pipe up if you think there are
other issues not on the list.



-- 
Jason Stajich
Duke University
jason@cgt.mc.duke.edu