[SciPy-Dev] ANN: SciPy 0.9.0 beta 1

Warren Weckesser warren.weckesser@enthought....
Tue Dec 21 22:11:37 CST 2010


On Tue, Dec 14, 2010 at 3:23 PM, Bruce Southey <bsouthey@gmail.com> wrote:

> On Tue, Dec 14, 2010 at 2:15 PM, Bruce Southey <bsouthey@gmail.com> wrote:
> > On 12/14/2010 02:09 PM, Charles R Harris wrote:
> >
> > On Tue, Dec 14, 2010 at 10:52 AM, Bruce Southey <bsouthey@gmail.com>
> wrote:
> >>
> >> On Tue, Dec 14, 2010 at 10:13 AM, Ralf Gommers
> >> <ralf.gommers@googlemail.com> wrote:
> >> >
> >> >
> >> > On Wed, Dec 15, 2010 at 12:01 AM, Benjamin Root <ben.root@ou.edu>
> wrote:
> >> >>
> >> >>
> >> >> On Tue, Dec 14, 2010 at 6:38 AM, Ralf Gommers
> >> >> <ralf.gommers@googlemail.com> wrote:
> >> >>>
> >> >>>
> >> >>> On Tue, Dec 14, 2010 at 12:43 AM, Benjamin Root <ben.root@ou.edu>
> >> >>> wrote:
> >> >>>
> >> >>> Hi Ben,
> >> >>>>
> >> >>>> Just did a clean rebuild (after a clean rebuild of numpy) and had
> two
> >> >>>> errors in the tests:
> >> >>>
> >> >>> What platform are you on?
> >> >>
> >> >> I reran the tests on just this scipy.misc module, here is the output:
> >> >>
> >> >> >>> scipy.misc.test()
> >> >> Running unit tests for scipy.misc
> >> >> NumPy version 2.0.0.dev-799179d
> >> >> NumPy is installed in /home/bvr/Programs/numpy/numpy
> >> >> SciPy version 0.10.0.dev
> >> >> SciPy is installed in /home/bvr/Programs/scipy/scipy
> >> >> Python version 2.6.4 (r264:75706, Jun  4 2010, 18:20:16) [GCC 4.4.4
> >> >> 20100503 (Red Hat 4.4.4-2)]
> >> >> nose version 0.11.3
> >> >> ...........F.....
> >> >>
> ======================================================================
> >> >> FAIL: test_imresize (test_pilutil.TestPILUtil)
> >> >>
> ----------------------------------------------------------------------
> >> >> Traceback (most recent call last):
> >> >>   File "/home/bvr/Programs/numpy/numpy/testing/decorators.py", line
> >> >> 146,
> >> >> in skipper_func
> >> >>     return f(*args, **kwargs)
> >> >>   File "/home/bvr/Programs/scipy/scipy/misc/tests/test_pilutil.py",
> >> >> line
> >> >> 28, in test_imresize
> >> >>     assert_equal(im1.shape,(11,22))
> >> >>   File "/home/bvr/Programs/numpy/numpy/testing/utils.py", line 251,
> in
> >> >> assert_equal
> >> >>     assert_equal(actual[k], desired[k], 'item=%r\n%s' % (k,err_msg),
> >> >> verbose)
> >> >>   File "/home/bvr/Programs/numpy/numpy/testing/utils.py", line 313,
> in
> >> >> assert_equal
> >> >>     raise AssertionError(msg)
> >> >> AssertionError:
> >> >> Items are not equal:
> >> >> item=0
> >> >>
> >> >>  ACTUAL: 10
> >> >>  DESIRED: 11
> >> >>
> >> >>
> ----------------------------------------------------------------------
> >> >> Ran 17 tests in 0.089s
> >> >>
> >> >> FAILED (failures=1)
> >> >> <nose.result.TextTestResult run=17 errors=0 failures=1>
> >> >>
> >> >> Note, that I am still getting this error with the suggested addition
> of
> >> >> "np.random.seed(12345678)" to scipy/misc/tests/test_pilutil.py.  I
> >> >> tried it
> >> >> both at line 20 (before the call to class TestPILUtil) and at line 24
> >> >> (before the call to np.random.random() in test_imresize.  I do not
> see
> >> >> how
> >> >> setting the seed value for these tests would make any difference
> since
> >> >> they
> >> >> are merely testing the resulting shape of the image after a resize,
> not
> >> >> the
> >> >> values of the resized image itself.
> >> >
> >> > The seeding may not matter (I haven't actually looked in detail yet),
> >> > but I
> >> > thought I had seen this error pop up before, but not reproducibly. The
> >> > imresize function does some interpolation, so the numerical values
> could
> >> > matter. In that case seeding would help.
> >> >>
> >> >>
> >> >>>>
> >> >>>>
> >> >>>>
> ======================================================================
> >> >>>> FAIL: test_imresize (test_pilutil.TestPILUtil)
> >> >>>>
> >> >>>>
> ----------------------------------------------------------------------
> >> >>>> Traceback (most recent call last):
> >> >>>>   File "/home/bvr/Programs/numpy/numpy/testing/decorators.py", line
> >> >>>> 146,
> >> >>>> in skipper_func
> >> >>>>     return f(*args, **kwargs)
> >> >>>>   File "/home/bvr/Programs/scipy/scipy/misc/tests/test_pilutil.py",
> >> >>>> line
> >> >>>> 25, in test_imresize
> >> >>>>     assert_equal(im1.shape,(11,22))
> >> >>>>   File "/home/bvr/Programs/numpy/numpy/testing/utils.py", line 251,
> >> >>>> in
> >> >>>> assert_equal
> >> >>>>     assert_equal(actual[k], desired[k], 'item=%r\n%s' %
> (k,err_msg),
> >> >>>> verbose)
> >> >>>>   File "/home/bvr/Programs/numpy/numpy/testing/utils.py", line 313,
> >> >>>> in
> >> >>>> assert_equal
> >> >>>>     raise AssertionError(msg)
> >> >>>> AssertionError:
> >> >>>> Items are not equal:
> >> >>>> item=0
> >> >>>>
> >> >>>>  ACTUAL: 10
> >> >>>>  DESIRED: 11
> >> >>>
> >> >>> This test should be changed to use a fixed seed (add as a first line
> >> >>> of
> >> >>> the test "np.random.seed(12345678)"). Can you provide one that
> fails?
> >> >>>
> >> >>
> >> >> Also, I am not sure what you mean by "Can you provide one that
> fails?".
> >> >
> >> > I meant a seed value that fails. This one does, that's all we need.
> >>
> >> On my 64-bit linux system with Python 2.7, the error appears comes
> >> from float16 dtype rather than the actual seed
> >> >>> np.random.seed(12345678)
> >> >>> for T in np.sctypes['float'] + [float]:
> >> ...     im1 = pilutil.imresize(im,T(1.1))
> >> ...     print T, im.shape, im1.shape
> >> ...
> >> <type 'numpy.float16'> (10, 20) (10, 21)
> >> <type 'numpy.float32'> (10, 20) (11, 22)
> >> <type 'numpy.float64'> (10, 20) (11, 22)
> >> <type 'numpy.float128'> (10, 20) (11, 22)
> >> <type 'float'> (10, 20) (11, 22)
> >>
> >> Here only the float16 has different shape from the rest.
> >>
> >
> > Ah, you compiled against numpy master instead of numpy 1.5.1, float16 is
> > only in the development branch. I think the test should be fixed to use
> an
> > explicit list of types supported by pilutil.
> >
> > Chuck
> >
> >
> > Sorry,
> > I forgot to add the numpy version '2.0.0.dev-799179d' because 1.5.1 is
> just
> > too old and I am too lazy to go back and downgrade :-)
> >
> >
> > Bruce
> >
>
> Okay,
> No issues with numpy 1.5.1 under Python 2.7 - given below.
>
> I get this error under Python 3.1:' FAIL: test_highpass
> (test_fir_filter_design.TestFirWinMore)'.
> This appears to be integer division as the test passes when line 126
> of  'scipy/signal/tests/test_fir_filter_design.py' is changed to:
> assert_array_almost_equal(taps[:ntaps//2], taps[ntaps:ntaps-ntaps//2-1:-1])
>
> Bruce
>
> $ python -c "import scipy; scipy.test()"
> Running unit tests for scipy
> NumPy version 1.5.1
> NumPy is installed in /usr/lib64/python2.7/site-packages/numpy
> SciPy version 0.9.0b1
> SciPy is installed in /usr/lib64/python2.7/site-packages/scipy
> Python version 2.7 (r27:82500, Sep 16 2010, 18:02:00) [GCC 4.5.1
> 20100907 (Red Hat 4.5.1-3)]
> nose version 0.11.2
> [snip]
> .........................................................................
> ----------------------------------------------------------------------
> Ran 4794 tests in 41.009s
>
> OK (KNOWNFAIL=12, SKIP=35)
>
>
> $ python3 -c "import scipy; scipy.test()"
> Running unit tests for scipy
> NumPy version 1.5.1
> NumPy is installed in /usr/lib64/python3.1/site-packages/numpy
> SciPy version 0.9.0b1
> SciPy is installed in /usr/lib64/python3.1/site-packages/scipy
> Python version 3.1.2 (r312:79147, Sep  8 2010, 23:02:57) [GCC 4.5.1
> 20100812 (Red Hat 4.5.1-1)]
> nose version 3.0.0
> [snip]
>
>
> ..............................................................................................................................E
> ======================================================================
> ERROR: Failure: ImportError (No module named c_spec)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File "/usr/lib/python3.1/site-packages/nose/failure.py", line 37, in
> runTest
>    reraise(self.exc_class, self.exc_val, self.tb)
>  File "/usr/lib/python3.1/site-packages/nose/_3.py", line 7, in reraise
>    raise exc_class(exc_val).with_traceback(tb)
>  File "/usr/lib/python3.1/site-packages/nose/loader.py", line 389, in
> loadTestsFromName
>    addr.filename, addr.module)
>  File "/usr/lib/python3.1/site-packages/nose/importer.py", line 39,
> in importFromPath
>    return self.importFromDir(dir_path, fqname)
>  File "/usr/lib/python3.1/site-packages/nose/importer.py", line 86,
> in importFromDir
>    mod = load_module(part_fqname, fh, filename, desc)
>  File "/usr/lib64/python3.1/site-packages/scipy/weave/__init__.py",
> line 13, in <module>
>    from .inline_tools import inline
>  File "/usr/lib64/python3.1/site-packages/scipy/weave/inline_tools.py",
> line 5, in <module>
>    from . import ext_tools
>  File "/usr/lib64/python3.1/site-packages/scipy/weave/ext_tools.py",
> line 7, in <module>
>    from . import converters
>  File "/usr/lib64/python3.1/site-packages/scipy/weave/converters.py",
> line 5, in <module>
>    from . import c_spec
>  File "/usr/lib64/python3.1/site-packages/scipy/weave/c_spec.py",
> line 380, in <module>
>    import os, c_spec # yes, I import myself to find out my __file__
> location.
> ImportError: No module named c_spec
>
> ======================================================================
> FAIL: test_highpass (test_fir_filter_design.TestFirWinMore)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File
> "/usr/lib64/python3.1/site-packages/scipy/signal/tests/test_fir_filter_design.py",
> line 126, in test_highpass
>    assert_array_almost_equal(taps[:ntaps/2],
> taps[ntaps:ntaps-ntaps/2-1:-1])
>  File "/usr/lib64/python3.1/site-packages/numpy/testing/utils.py",
> line 774, in assert_array_almost_equal
>    header='Arrays are not almost equal')
>  File "/usr/lib64/python3.1/site-packages/numpy/testing/utils.py",
> line 579, in assert_array_compare
>    raise AssertionError(msg)
> AssertionError:
> Arrays are not almost equal
>
> (shapes (196,), (197,) mismatch)
>  x: array([ -2.21482814e-21,   9.49475306e-08,  -8.72925108e-21,
>        -1.69672728e-07,  -2.55604897e-21,   2.73170159e-07,
>        -9.89221963e-22,  -4.12424017e-07,   4.88221354e-21,...
>  y: array([ -2.21482814e-21,   9.49475306e-08,  -8.72925108e-21,
>        -1.69672728e-07,  -2.55604897e-21,   2.73170159e-07,
>        -9.89221963e-22,  -4.12424017e-07,   4.88221354e-21,...
>
> ----------------------------------------------------------------------
> Ran 4657 tests in 42.204s
>
> FAILED (KNOWNFAIL=12, SKIP=41, errors=1, failures=1)
>


In r7019, I updated test_fir_filter_design.py in trunk to use explicit
integer division where appropriate.

Warren
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