[Biopython-dev] Import problems when testing under PyPy 2.2

[Peter Cock]

Hello all,
TravisCI is being updated to target PyPy 2.2 any day now,
http://about.travis-ci.org/blog/2013-11-18-upcoming-build-environment-updates/

Meanwhile in local testing on Mac OS X, Biopython looks fine
under PyPy 2.2.

However, I'm seeing some oddities with imports failing under
PyPy 2.2 via run_tests.py on Windows 32 bit & Linux 64 though -
can anyone reproduce this? e.g.


C:\repositories\biopython\Tests>c:\pypy-2.2\pypy test_Nexus.py
test_NexusTest1 (__main__.NexusTest1)
Test Nexus module ... ok
test_TreeTest1 (__main__.NexusTest1)
Test Tree module. ... ok
test_WriteToFileName (__main__.NexusTest1)
Test writing to a given filename. ... ok
test_internal_node_labels (__main__.NexusTest1)
Handle text labels on internal nodes. ... ok

----------------------------------------------------------------------
Ran 4 tests in 0.125s

OK

i.e. Here test_Nexus.py works fine using the installed Biopython.
However, via run_tests.py which tries to mess with the Python path
to use the local not-yet installed Biopython:

C:\repositories\biopython\Tests>c:\pypy-2.2\pypy run_tests.py test_Nexus.py
Python version: 2.7.3 (2cec7296d7fb, Nov 12 2013, 13:24:40)
[PyPy 2.2.0 with MSC v.1500 32 bit]
Operating system: nt win32
test_Nexus ... ERROR
======================================================================
ERROR: test_Nexus
----------------------------------------------------------------------
Traceback (most recent call last):
  File "run_tests.py", line 407, in runTest
    suite = unittest.TestLoader().loadTestsFromName(name)
  File "c:\pypy-2.2\lib-python\2.7\unittest\loader.py", line 91, in loadTestsFro
mName
    module = __import__('.'.join(parts_copy))
  File "C:\repositories\biopython\Tests\test_Nexus.py", line 13, in <module>
    from Bio._py3k import StringIO
ImportError: cannot import name 'StringIO'
----------------------------------------------------------------------
Ran 1 test in 0.016 seconds

FAILED (failures = 1)


Note:

C:\repositories\biopython\Tests>
C:\repositories\biopython\Tests>c:\pypy-2.2\pypy
Python 2.7.3 (2cec7296d7fb, Nov 12 2013, 13:24:40)
[PyPy 2.2.0 with MSC v.1500 32 bit] on win32
Type "help", "copyright", "credits" or "license" for more information.
And now for something completely different: ``do you know about a toaster with
8KB of RAM and 64KB of ROM?''
>>>> from Bio._py3k import StringIO
>>>> quit()


This seems rather odd...

Thanks,

Peter