[Biopython-dev] [Bug 2733] New: Unit tests incorrectly assume that Biopthyon was built from source

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Thu Jan 15 14:37:57 UTC 2009


           Summary: Unit tests incorrectly assume that Biopthyon was built
                    from source
           Product: Biopython
           Version: Not Applicable
          Platform: PC
        OS/Version: All
            Status: NEW
          Severity: minor
          Priority: P4
         Component: Unit Tests
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: bsouthey at gmail.com

If Biopython is not built from source and the tests are run from a different
place than the installation, the test that use C objects fail because these are
not found (an example is below).

Currently the test environment uses the Biopython in the build directory. It
would be nice to be able to optionally specify some other Biopython such as the
installed version using say a command line argument.

Example of a failure:

ERROR: test_KDTree                                                    
Traceback (most recent call last):                                    
  File "run_tests.py.orig", line 125, in runTest                      
  File "run_tests.py.orig", line 138, in runSafeTest                  
    cur_test = __import__(self.test_name)                             
  File "test_KDTree.py", line 10, in <module>                         
    from Bio.KDTree.KDTree import _neighbor_test, _test               
  File "/home/bsouthey/python/biopython_cvs/biopython/Bio/KDTree/__init__.py",
line 10, in <module>
    from KDTree import KDTree                                                   
  File "/home/bsouthey/python/biopython_cvs/biopython/Bio/KDTree/KDTree.py",
line 20, in <module>  
    from Bio.KDTree import _CKDTree                                             
ImportError: cannot import name _CKDTree  

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