[Biopython-dev] Making biopython release

Iddo Friedberg idoerg at burnham.org
Thu Nov 21 12:47:08 EST 2002


I updated the test_FSSP 3 weeks ago, should be clean & fast. (Well, 
faster). Can you email me the errors you are getting?

Good move on the release.


Jeffrey Chang wrote:
> Hello everybody,
> Biopython's *way* overdue for a release -- most of our bug fixes seem
> to be of the get-files-from-CVS variety.  Let's try to get things
> stabilized so we can ship out another version.  Here's what we need to
> do.  Please let me know, with a well-reasoned argument, if you
> disagree.
> Bug fixes
> ---------
> We have a bugzilla database at bugzilla.bioperl.org.  Here are the
> bugs I think should be fixed before we release.  I've made a best
> guess at who should be working on them.
> 4   jchang  GenBank search should support "limits"
> 10  dalke   BerkeleyDB.py Problem?
> 11  cayte   Tests/MetaTool/Meta9.out conflicts with meta9.out
> 12  cayte   potential conflict between Bio/Rebase/Rebase.py and Bio/Rebase/__init__.py
> 16  idoerg  test_FSSP takes a long time to run
> 17  gec     Bio/SCOP/tests should be integrated with rest of regression tests
> 22  jchang  Some NCBI scripts will be obsolete Dec 2002
> XX  jchang  make the seqdb load _ini files on access
> Please take ownership of your bug in the database.
> All the regression tests must pass (on a properly configured system)
> before we can make a release.  I ran the tests today (BioSQL stuff was
> skipped) and found 7 tests to be failing.  Please check your code and
> make sure the tests pass!
>   test_locuslink
>   test_FSSP
>   test_ais
>   test_align
>   test_easy
>   test_format_registry
>   test_locus_http
> Thomas, I've gotten some reports that people are having trouble
> compiling the C++ KDTree module.  Do you know what the issues are in
> compiling C++ software, and where problems might be?  Sorry to be so
> vague about it.  I don't have a reproducible.  I'll try and hunt down
> the reports.  If people have problems compiling it, we will have to
> back it out.
> Michael, do you mind moving easy.py and GenericTools.py somewhere
> else, e.g. into GFF?  I'm not sure I like them directly in the Bio
> namespace.
> Misc Tasks
> ----------
> Other things to do are:
> 1.  Update the README file, making sure requirements, etc are still up
> to date.
> 2.  Make sure the tutorial is still current.  Modules have moved
> around.
> 3.  Make sure example scripts are still work.  Either fix or remove
> them.
> 4.  Update the NEWS file.  Figure out all new features, etc.
> Let me know if you can take charge of any of these tasks.
> Addendum
> --------
> In an earlier email, Brad had wanted to shoot for a next Wednesday
> release.  That means that all the above must be done by Tuesday, so
> that I will have a change to make the final tarball.  Let me know your
> status, and whether you think this is realistic, given holidays, etc.
> Nevertheless, let's keep communicating through the dev mailing list on
> progress, updates, concerns, etc.  Anybody with code in the repository
> should let me know when your code is ready to go.
> Thanks, Brad, for getting the ball rolling!  This is going to be a
> beefy release.
> Jeff
> _______________________________________________
> Biopython-dev mailing list
> Biopython-dev at biopython.org
> http://biopython.org/mailman/listinfo/biopython-dev

Iddo Friedberg
The Burnham Institute
10901 N. Torrey Pines Rd.
La Jolla, CA 92037
Tel: +1 (858) 646 3100 x3516
Fax: +1 (858) 646 3171

More information about the Biopython-dev mailing list