[Biopython-dev] making new release

[Brad Chapman]

Hey Jeff;

> It feels like time to make a new release.  There's been a bunch of new 
> code and fixes, and the BLAST parser is sufficiently out of date.  :)  
> Plus, Michiel is anxious to get his new clustering software available!  
> Hmmm...  I just noticed that Andrew just checked in EUtils as well.

Definitely agree with making a release. I think a few more people 
other then me should hit on EUtils to make sure I fixed everything 
after Andrew checked it in. Just so I'm not soley responsible :-).

> So, everybody working on the code in the CVS repository, please let me 
> know where you are.  Specifically, I need to know whether the code is 
> not ready to be released yet, and when it will be.

The only thing I have (besides double checking EUtils) is the
speed-up stuff in GenBank. I hope that should be finished by the end
of the weekend. I also want to update (at least) the install
documentation so links and things point to the new website. That
should also be done by the end of the weekend.

> All the tests should pass.  On my system now, test_FSSP is failing.  It 
> looks minor -- Iddo?

KDTree and LocusLink are commented out in setup.py (which gives
import warnings in the test). Is there are a reason for this or
should we try to get those working as well?

test_GFF is also failing for me:

12:05pm Tests> python run_tests.py test_GFF.py
test_GFF ... FAIL

======================================================================
FAIL: test_GFF
----------------------------------------------------------------------
Traceback (most recent call last):
  File "run_tests.py", line 131, in runTest
    self.runSafeTest()
  File "run_tests.py", line 168, in runSafeTest
    expected_handle)
  File "run_tests.py", line 268, in compare_output
    assert expected_line == output_line, \
AssertionError: 
Output  :
'*****************************************************************\n'
Expected: 'Bio.GFF doctests complete.\n'
----------------------------------------------------------------------
Ran 1 tests in 0.451s

FAILED (failures=1)

Aaaah, releases,
Brad