[Numpy-discussion] [SciPy-Dev] 1.8.0rc1
Charles R Harris
charlesr.harris at gmail.com
Mon Sep 30 20:37:25 EDT 2013
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.
Chuck
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