On Mon, Sep 30, 2013 at 6:13 PM, Christoph Gohlke <cgoh...@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 <cgoh...@uci.edu > >> <mailto:cgoh...@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 < > cgoh...@uci.edu > >> <mailto:cgoh...@uci.edu> > >> > <mailto:cgoh...@uci.edu <mailto:cgoh...@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.har...@gmail.com > >> <mailto:charlesr.har...@gmail.com> <mailto: > charlesr.har...@gmail.com > >> <mailto:charlesr.har...@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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