[Numpy-discussion] [SciPy-Dev] 1.8.0rc1
Charles R Harris
charlesr.harris at gmail.com
Mon Sep 30 22:27:42 EDT 2013
On Mon, Sep 30, 2013 at 6:37 PM, Charles R Harris <charlesr.harris at gmail.com
> wrote:
>
>
>
> On Mon, Sep 30, 2013 at 6:13 PM, Christoph Gohlke <cgohlke at uci.edu> wrote:
>
>> On 9/30/2013 4:44 PM, Julian Taylor wrote:
>> > On 01.10.2013 01:30, Charles R Harris wrote:
>> >>
>> >>
>> >>
>> >> On Mon, Sep 30, 2013 at 5:12 PM, Christoph Gohlke <cgohlke at uci.edu
>> >> <mailto:cgohlke at 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 at uci.edu
>> >> <mailto:cgohlke at uci.edu>
>> >> > <mailto:cgohlke at uci.edu <mailto:cgohlke at uci.edu>>> wrote:
>> >> >
>> >> >
>> >> >
>> >> > On 9/30/2013 11:02 AM, Nathaniel Smith wrote:> Everyone
>> please do
>> >> > 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
>> >> > > <charlesr.harris at gmail.com
>> >> <mailto:charlesr.harris at gmail.com> <mailto:
>> charlesr.harris at gmail.com
>> >> <mailto:charlesr.harris at 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
>> 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
>> >> >
>> >> > 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/binary.py#L32
>> >>
>> >>
>> >> 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.
>
>
The pandas test passes for current pandas dev, so it looks like a bug on
their end that has been taken care of.
test_nansum_buglet (__main__.TestNanops) ... ok
Chuck
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