[Biopython-dev] biopython-1.51 test log, sage inclusion

[Marshall Hampton]

Yep, I tried again and the test_SeqIO_online was ok, so I guess it was a 
transient failure.

I agree that copying my Tests folder isn't a great solution.  I will try 
to increase my understanding of the biopython test framework - I am used 
to the Sage method of mainly using docstring tests.

-Marshall

On Mon, 17 Aug 2009, Peter wrote:

> On Mon, Aug 17, 2009 at 10:25 PM, Marshall Hampton<mhampton at d.umn.edu> wrote:
>>
>> After copying the Tests folder from the source to my site-packages
>> directory, most of the errors go away,
>
> Well that does suggest some sort of path issue, but moving the
> test directory around that isn't a very good solution.
>
>> except for the one mentioned above and this one:
>
> Assuming the "one mentioned above" was the EMBOSS one, fine.
>
>> ERROR: test_SeqIO_online
>> ----------------------------------------------------------------------
>> Traceback (most recent call last):
>>  File "run_tests.py", line 248, in runTest
>>    suite = unittest.TestLoader().loadTestsFromName(name)
>>  File "/Users/mh/sagestuff/sage-4.1/local/lib/python/unittest.py", line 576,
>> in loadTestsFromName
>>    module = __import__('.'.join(parts_copy))
>>  File "test_SeqIO_online.py", line 62, in <module>
>>    record = SeqIO.read(handle, format) # checks there is exactly one record
>>  File
>> "/Users/mh/sagestuff/sage-4.1/local/lib/python2.6/site-packages/Bio/SeqIO/__init__.py",
>> line 485, in read
>>    raise ValueError("No records found in handle")
>> ValueError: No records found in handle
>>
>> ...not sure what the problem might be with that.
>
> That is an online test using the NCBI's web services. This could
> be a transient failure due to the network.
>
> Peter
>