[BioPython] Feedback from Biopython 1.50 beta?

[Peter]

On Wed, Apr 15, 2009 at 3:08 PM, Martin MOKREJŠ
<mmokrejs at ribosome.natur.cuni.cz> wrote:
> Peter wrote:
>> Dear Biopythoneers,
>>
>> There is a saying "no news is good news", but as per the title - can
>> we have some feedback from the Biopython 1.50 beta release please?
>
> The tests gave me:
>
> test_DocSQL ... /usr/lib/python2.6/site-packages/MySQLdb/__init__.py:34: DeprecationWarning: the sets module is deprecated
>  from sets import ImmutableSet

That is a harmless bug in MySQLdb (it wasn't quite ready for Python
2.6), which I think has been fixed on their trunk, although I'm not
sure if it is in their latest release or not.

> test_NCBIStandalone ... ERROR
>
> ======================================================================
> ERROR: test_NCBIStandalone
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>  File "run_tests.py", line 247, in runTest
>    suite = unittest.TestLoader().loadTestsFromName(name)
>  File "/usr/lib/python2.6/unittest.py", line 576, in loadTestsFromName
>    module = __import__('.'.join(parts_copy))
>  File "test_NCBIStandalone.py", line 9, in <module>
>    from Bio.Blast import NCBIStandalone
>  File "/home/mmokrejs/proj/biopython/build/lib.linux-i686-2.6/Bio/Blast/NCBIStandalone.py", line 1673
>    <<<<<<< NCBIStandalone.py
>     ^
> SyntaxError: invalid syntax
> ----------------------------------------------------------------------

That "<<<<<<<" text looks like a CVS merge failed, inserting a diff
marker into the file.  How did you install the Biopython 1.50 beta?
I've just download and checked the Bio/Blast/NCBIStandalone.py file
looks OK in both the archives:
http://biopython.org/DIST/biopython-1.50b.tar.gz
http://biopython.org/DIST/biopython-1.50b.zip

Peter