[Biopython-dev] Versions of numpy/Numeric

[Bruce Southey]

Hi,
I just built and installed Python 2.6 with gcc version 4.3.2. I then 
installed numpy 1.2 with it (so no Numeric).

I did a cvs update on biopython and installed with Python 2.5.2 and 
Python 2.6.  In both cases I noticed many gcc warnings 'differ in 
signedness'  (should I file a bug report?) in Bio/cstringfnsmodule.c and 
Bio/trie.c and also Bio/triemodule.c has a couple of other warnings.

In both cases 'python setup.py test' opened graphical window - it did 
not do that before when I tested. What should the default be?

All expected tests (ie I do not have biosql setup) passed with Python 2.5.2.

With Python 2.6, running tests gave two warnings (should I file a bug 
report?):
biopython/build/lib.linux-x86_64-2.6/Bio/Data/CodonTable.py:580: 
DeprecationWarning: the sets module is deprecated
  from sets import Set
biopython/build/lib.linux-x86_64-2.6/Bio/Crystal/__init__.py:42: 
DeprecationWarning: BaseException.message has been deprecated as of 
Python 2.6
  self.message = message

Also I got three errors with Python 2.6 (without the -3 flag as that 
provides warnings for Python 3) so I filed bug reports:
test_CAPS
test_PDB
test_Restriction

The failure for test_CAPS and and test_Restriction is due to the same 
line "Bio/Restriction/Restriction.py" (line 217).

Apart from these everything else passed.

Bruce