[BioPython] Feedback from Biopython 1.50 beta?

[Martin MOKREJŠ]

Peter wrote:
> 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_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

Yes, sorry, I forgot to delete my old changes to it. Dropped the file and read-in
current version from cvs now. ;)

Anyway, I think "python setup.py clean" should zap .pyc files
find Bio -name \*.pyc | xargs rm -f
find BioSQL -name \*.pyc | xargs rm -f
rm -f Tests/Quality/temp.fastq
rm -f Tests/Quality/temp.qual

The built-in tests ran fine for me.
M.