[Biopython-dev] Making biopython release

Jeffrey Chang jchang at smi.stanford.edu
Wed Nov 20 23:32:45 EST 2002

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

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!

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

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

3.  Make sure example scripts are still work.  Either fix or remove

4.  Update the NEWS file.  Figure out all new features, etc.

Let me know if you can take charge of any of these tasks.


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.


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