Re: [Numpy-discussion] [SciPy-Dev] 1.8.0rc1

30 Sep 2013


      On Mon, Sep 30, 2013 at 6:13 PM, Christoph Gohlke  wrote:
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On 01.10.2013 01:30, Charles R Harris wrote:
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On Mon, Sep 30, 2013 at 5:12 PM, Christoph Gohlke mailto:cgohlke@uci.edu> wrote:
On 9/30/2013 3:45 PM, Charles R Harris wrote:
     >
     >
     >
     > On Mon, Sep 30, 2013 at 3:51 PM, Christoph Gohlke <
cgohlke@uci.edu
...
mailto:cgohlke@uci.edu
     > mailto:cgohlke@uci.edu>> wrote:
     >
     >
     >
     >     On 9/30/2013 11:02 AM, Nathaniel Smith wrote:> Everyone
...
...
>     actually test this! It is really in your best
     >     > interest, and I think people don't always realize this.
     >     >
     >     > Here's how it works:
     >     > - If you test it *now*, and it breaks your code that worked
     with 1.7,
     >     > and you *tell* us this now, then it's *our* problem and we
     hold up the
     >     > release to fix the bug.
     >     > - If you test it *after* we release, and it breaks your
     code, then we
     >     > are sad but you have to work around it (because we can't
     magically
     >     > make that release not have happened, your users will be
using it
...
>     > anyway), and we put it on the stack with all the other
bugs.
...
All of
     >     > which we care about but it's a large enough stack that it's
     not going
     >     > to get any special priority, because, see above about how
at
...
this
     >     > point you'll have had to work around it anyway.
     >     >
     >     > -n
     >     >
     >     > On Mon, Sep 30, 2013 at 4:17 PM, Charles R Harris
     >     > mailto:charlesr.harris@gmail.com 
charlesr.harris@gmail.com
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mailto:charlesr.harris@gmail.com>> wrote:
     >     >> Hi All,
     >     >>
     >     >> NumPy 1.8.0rc1 is up now on sourceforge .The binary builds
     are included
     >     >> except for Python 3.3 on windows, which will arrive later.
     Many thanks to
     >     >> Ralf for the binaries, and to those who found and fixed
On 9/30/2013 4:44 PM, Julian Taylor wrote:
please do
the
...
...
bugs in the last
     >     >> beta. Any remaining bugs are all my fault ;) I hope this
     will be the last
     >     >> release before final, so please test it thoroughly.
     >     >>
     >     >> Chuck
     >
     >
     >     Hello,
     >
     >     NumPy 1.8.0rc1 looks good. All tests pass on Windows and most
     3rd party
     >     packages test OK now. Thank you.
     >
     >     A few tests still fail in the following packages when run
with
...
>     numpy-MKL-1.8.0rc1-win-amd64-py3.3 compared to
     >     numpy-MKL-1.7.1-win-amd64-py3.3:
     >
     >     1) Pandas 0.12.0
     >
     >     ```
     >
======================================================================
...
>     FAIL: test_nansum_buglet
(pandas.tests.test_series.TestNanops)
...
>

...
...
>     Traceback (most recent call last):
     >         File
     "X:\Python33\lib\site-packages\pandas\tests\test_series.py",
     >     line 254, in test_nansum_buglet
     >           assert_almost_equal(result, 1)
     >         File
     "X:\Python33\lib\site-packages\pandas\util\testing.py", line
     >     134, in assert_almost_equal
     >           np.testing.assert_(isiterable(b))
     >         File
     "D:\Dev\Compile\Test\numpy-build\numpy\testing\utils.py", line
     >     44, in assert_
     >           raise AssertionError(msg)
     >     AssertionError
     >     ```
     >
     >     Possibly related:
     >
     >     ```
     >     >>> import numpy as np
     >     >>> from pandas import Series
     >     >>> s = Series([0.0])
     >     >>> result = np.nansum(s)
     >     >>> print(result)
     >     Traceback (most recent call last):
     >         File "<stdin>", line 1, in <module>
     >         File
"X:\Python33\lib\site-packages\pandas\core\base.py", line
...
>     19, in
     >     __str__
     >           return self.__unicode__()
     >         File
     "X:\Python33\lib\site-packages\pandas\core\series.py", line
     >     1115, in __unicode__
     >           length=len(self) > 50,
     >     TypeError: len() of unsized object
     >     ```
     >
     >     2) Bottleneck 0.7.0
     >
     >
https://github.com/kwgoodman/bottleneck/issues/71#issuecomment-25331701
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>
     >     3) skimage 0.8.2
     >
     >     These tests passed with numpy 1.8.0b2:
     >
     >     ```
     >
======================================================================
...
>     FAIL: test_grey.test_non_square_image
     >

...
...
>     Traceback (most recent call last):
     >         File "X:\Python33\lib\site-packages\nose\case.py", line
     198, in
     >     runTest
     >           self.test(*self.arg)
     >         File
     >
"X:\Python33\lib\site-packages\skimage\morphology\tests\test_grey.py",
...
>     line 162, in test_non_square_image
     >           testing.assert_array_equal(binary_res, grey_res)
     >         File
     "X:\Python33\lib\site-packages\numpy\testing\utils.py", line
     >     718, in assert_array_equal
     >           verbose=verbose, header='Arrays are not equal')
     >         File
     "X:\Python33\lib\site-packages\numpy\testing\utils.py", line
     >     644, in assert_array_compare
     >           raise AssertionError(msg)
     >     AssertionError:
     >     Arrays are not equal
     >
     >     (mismatch 50.6328125%)
     >        x: array([[False, False, False, ..., False, False, False],
     >              [False, False, False, ..., False, False, False],
     >              [False, False, False, ..., False, False, False],...
     >        y: array([[ True,  True,  True, ...,  True, False, False],
     >              [ True,  True,  True, ..., False, False, False],
     >              [ True,  True,  True, ..., False, False, False],...
     >
     >
======================================================================
...
>     FAIL: test_grey.test_binary_erosion
     >

...
...
>     Traceback (most recent call last):
     >         File "X:\Python33\lib\site-packages\nose\case.py", line
     198, in
     >     runTest
     >           self.test(*self.arg)
     >         File
     >
"X:\Python33\lib\site-packages\skimage\morphology\tests\test_grey.py",
...
>     line 169, in test_binary_erosion
     >           testing.assert_array_equal(binary_res, grey_res)
     >         File
     "X:\Python33\lib\site-packages\numpy\testing\utils.py", line
     >     718, in assert_array_equal
     >           verbose=verbose, header='Arrays are not equal')
     >         File
     "X:\Python33\lib\site-packages\numpy\testing\utils.py", line
     >     644, in assert_array_compare
     >           raise AssertionError(msg)
     >     AssertionError:
     >     Arrays are not equal
     >
     >     (mismatch 48.260498046875%)
     >        x: array([[False, False, False, ..., False, False, False],
     >              [False, False, False, ..., False, False, False],
     >              [False, False, False, ..., False, False, False],...
     >        y: array([[ True,  True,  True, ...,  True, False, False],
     >              [ True,  True,  True, ..., False, False, False],
     >              [ True,  True,  True, ..., False, False, False],...
     >
     >
======================================================================
...
>     FAIL: test_grey.test_binary_closing
     >

...
...
>     Traceback (most recent call last):
     >         File "X:\Python33\lib\site-packages\nose\case.py", line
     198, in
     >     runTest
     >           self.test(*self.arg)
     >         File
     >
"X:\Python33\lib\site-packages\skimage\morphology\tests\test_grey.py",
...
>     line 183, in test_binary_closing
     >           testing.assert_array_equal(binary_res, grey_res)
     >         File
     "X:\Python33\lib\site-packages\numpy\testing\utils.py", line
     >     718, in assert_array_equal
     >           verbose=verbose, header='Arrays are not equal')
     >         File
     "X:\Python33\lib\site-packages\numpy\testing\utils.py", line
     >     644, in assert_array_compare
     >           raise AssertionError(msg)
     >     AssertionError:
     >     Arrays are not equal
     >
     >     (mismatch 66.302490234375%)
     >        x: array([[False, False, False, ..., False, False, False],
     >              [False, False, False, ..., False, False, False],
     >              [False, False, False, ..., False, False, False],...
     >        y: array([[ True,  True,  True, ...,  True,  True,  True],
     >              [ True,  True,  True, ...,  True,  True,  True],
     >              [ True,  True,  True, ..., False, False, False],...
     >
     >
======================================================================
...
>     FAIL: test_grey.test_binary_opening
     >

...
...
>     Traceback (most recent call last):
     >         File "X:\Python33\lib\site-packages\nose\case.py", line
     198, in
     >     runTest
     >           self.test(*self.arg)
     >         File
     >
"X:\Python33\lib\site-packages\skimage\morphology\tests\test_grey.py",
...
>     line 190, in test_binary_opening
     >           testing.assert_array_equal(binary_res, grey_res)
     >         File
     "X:\Python33\lib\site-packages\numpy\testing\utils.py", line
     >     718, in assert_array_equal
     >           verbose=verbose, header='Arrays are not equal')
     >         File
     "X:\Python33\lib\site-packages\numpy\testing\utils.py", line
     >     644, in assert_array_compare
     >           raise AssertionError(msg)
     >     AssertionError:
     >     Arrays are not equal
     >
     >     (mismatch 58.465576171875%)
     >        x: array([[False, False, False, ..., False, False, False],
     >              [False, False, False, ..., False, False, False],
     >              [False, False, False, ..., False, False, False],...
     >        y: array([[ True,  True,  True, ...,  True,  True, False],
     >              [ True,  True,  True, ...,  True,  True, False],
     >              [ True,  True,  True, ..., False, False, False],...
     >     ```
     >
     > I'll bet the skimage problems come from
     > https://github.com/numpy/numpy/pull/3811. They may be doing
something
...
> naughty...
     >
     > Chuck
     >
A bool image is convolved with a uint8 kernel and the result
compared
...
for equality with an uint32 scalar...
https://github.com/scikit-image/scikit-image/blob/master/skimage/morphology/...
...
Looks like the result of the convolution is probably output as a bool,
which now means 0,1, which does not work when checking equality with the
number of pixels in the kernel. I'd call expressing the result of a
convolution as a boolean very naughty.
using a view should fix it:
conv = ndimage.convolve((image > 0).view(np.uint8), selem, output=out,
                             mode='constant', cval=1)
but it needs check for sum(selem) < 255 too.
I opened an issue at
https://github.com/scikit-image/scikit-image/issues/745
The errors in skimage for Python 2.7 are also present for numpy 1.7.1.
Maybe I'm missing some dependencies? A bunch of tests are skipped for
Python 3.3 and I suspect the failing tests are among them.

Chuck