test_get_raw_tables_view fails on Python 2.7.2

[ctb]

  File "/Users/t/dev/khmer/tests/test_counting_hash.py", line 117, in test_get_raw_tables_view
    memv = memoryview(tab)
TypeError: cannot make memory view because object does not have the buffer interface

c.f. #671

[kdm9]

Oh balls. Will investigate.

I think the issue may be old/new style buffers in CPython???

I was examining how to efficiently pass these to Cython as memory views and hit upon a similar issue (to do with read only buffers).

[kdm9]

Although that's rather intriguing, as type(tab) is buffer. And you'd hope that a buffer exposed the buffer interface 😀.

NB:

$ python --version
Python 2.7.8

[luizirber]

This also breaks Python 2.6, but I guess we're not aiming for 2.6 anymore.

Traceback (most recent call last):
  File "khmer/.tox/py26/lib/python2.6/site-packages/nose/case.py", line 197, in runTest
    self.test(*self.arg)
  File "khmer/tests/test_counting_hash.py", line 117, in test_get_raw_tables_view
    memv = memoryview(tab)
NameError: global name 'memoryview' is not defined

[kdm9]

Mmmh, not good. I'll add a fix for @luizirber's observation.

[kdm9]

I haven't been able to find any python bugs/changes that indicate this is a python problem, but that may be my poor google skills.

[kdm9]

@luizirber any chance you could post your tox.ini? or even check it in, if that's ok.

[luizirber]

I didn't make a PR because it needs more polishing, for now I'm using something that works but is also wrong (the ideal would be moving parts from the Makefile here, and then calling tox on the Makefile)

[tox]
envlist=py26,py27

[testenv]
commands=
    make install-dependencies
    make clean
    make test

[ctb]

Note, further investigation suggests that it is a problem in Python 2.7.2 but not Python 2.7.6.

[kdm9]

Interesingly, while testing on another machine (supercomputer using ICC), I got this:

khmer/_khmermodule.cc: In function 'PyObject* hash_get_raw_tables(khmer_KCountingHash_Object*, PyObject*)':
khmer/_khmermodule.cc:691: error: reference to 'Byte' is ambiguous
third-party/zlib/zconf.h:368: error: candidates are: typedef unsigned char Byte
lib/khmer.hh:83: error:                 typedef unsigned char khmer::Byte
khmer/_khmermodule.cc:691: error: reference to 'Byte' is ambiguous
third-party/zlib/zconf.h:368: error: candidates are: typedef unsigned char Byte
lib/khmer.hh:83: error:                 typedef unsigned char khmer::Byte
khmer/_khmermodule.cc:691: error: 'table_ptrs' was not declared in this scope
error: command 'gcc' failed with exit status 1

I.e, zlib.h has a similar typedef for Byte.

Using khmer::Byte in khmer/_khmermodule.cc fixed that, so I'll add that to #869.

[kdm9]

#869 fixed this, AFAICT