[Biopython-dev] [Biopython (old issues only) - Bug #2733] (Closed) Runing unit tests where Biopthyon wasn't built from source

[redmine at redmine.open-bio.org]

Issue #2733 has been updated by Peter Cock.

Description updated
Status changed from New to Closed
% Done changed from 0 to 100

Looking at this afresh, I think the test suite should fail in this situation.

----------------------------------------
Bug #2733: Runing unit tests where Biopthyon wasn't built from source
https://redmine.open-bio.org/issues/2733#change-15401

* Author: Bruce Southey
* Status: Closed
* Priority: Low
* Assignee: Biopython Dev Mailing List
* Category: Unit Tests
* Target version: Not Applicable
* URL: 
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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                      
    self.runSafeTest()                                                
  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  
======================================================================

---Files--------------------------------
run_test.patch (659 Bytes)
bug2733.patch (813 Bytes)


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