[Biopython-dev] Failed tests.

[Jeffrey Chang]

I've fixed the GenBank bug (was printing out the keys to a 
dictionary) and one I found in Fasta (name of string type changed in 
Python 2.2).

Jeff


At 11:09 AM -0800 11/6/01, Gavin E. Crooks wrote:
>I have just installed biopython using the latest code in CVS. A whole bunch of
>tests fail. Are these my problem's, or biopython's?
>
>
>Gavin Crooks
>gec at compbio.berkeley.edu
>http://threeplusone.com
>
>=====================================================================
>ERROR: test_KEGG
>----------------------------------------------------------------------
>Traceback (most recent call last):
>   File "./run_tests.py", line 136, in runTest
>     __import__(self.test_name)
>   File "./test_KEGG.py", line 8, in ?
>     from Bio.KEGG import Map
>ImportError: cannot import name Map
>======================================================================
>ERROR: test_Pathway
>----------------------------------------------------------------------
>Traceback (most recent call last):
>   File "./run_tests.py", line 136, in runTest
>     __import__(self.test_name)
>   File "./test_Pathway.py", line 10, in ?
>     from Bio.Pathway import *
>ImportError: No module named Pathway
>======================================================================
>ERROR: test_intelligenetics
>----------------------------------------------------------------------
>Traceback (most recent call last):
>   File "./run_tests.py", line 136, in runTest
>     __import__(self.test_name)
>   File "./test_intelligenetics.py", line 29, in ?
>     src_handle = open( datafile )
>IOError: [Errno 2] No such file or directory: 
>'IntelliGenetics/TAT_mase_nuc.txt'======================================================================
>ERROR: test_metatool
>----------------------------------------------------------------------
>Traceback (most recent call last):
>   File "./run_tests.py", line 136, in runTest
>     __import__(self.test_name)
>   File "./test_metatool.py", line 29, in ?
>     src_handle = open( datafile )
>IOError: [Errno 2] No such file or directory: 'MetaTool/meta.out'
>======================================================================
>FAIL: test_GenBank
>----------------------------------------------------------------------
>Traceback (most recent call last):
>   File "./run_tests.py", line 153, in runTest
>     expected_handle)
>   File "./run_tests.py", line 247, in compare_output
>     assert expected_line == output_line, \
>AssertionError:
>Output  : "keys: ['L31939', 'AJ237582', 'X62281', 'AF297471', 
>'M81224', 'X55053']\n"
>Expected: "keys: ['X55053', 'M81224', 'AF297471', 'X62281', 
>'L31939', 'AJ237582']\n"
>======================================================================
>FAIL: test_SubsMat
>----------------------------------------------------------------------
>Traceback (most recent call last):
>   File "./run_tests.py", line 153, in runTest
>     expected_handle)
>   File "./run_tests.py", line 247, in compare_output
>     assert expected_line == output_line, \
>AssertionError:
>Output  : 'M -0.0 0.4 0.7 0.8 1.0\n'
>Expected: 'M 0.0 0.4 0.7 0.8 1.0\n'
>----------------------------------------------------------------------
>Ran 31 tests in 71.317s                                                
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