On Mon, Sep 30, 2013 at 6:37 PM, Charles R Harris <[email protected] > wrote:
> > > > On Mon, Sep 30, 2013 at 6:13 PM, Christoph Gohlke <[email protected]> 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 <[email protected] >> >> <mailto:[email protected]>> wrote: >> >> >> >> On 9/30/2013 3:45 PM, Charles R Harris wrote: >> >> > >> >> > >> >> > >> >> > On Mon, Sep 30, 2013 at 3:51 PM, Christoph Gohlke < >> [email protected] >> >> <mailto:[email protected]> >> >> > <mailto:[email protected] <mailto:[email protected]>>> 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 >> >> > > <[email protected] >> >> <mailto:[email protected]> <mailto: >> [email protected] >> >> <mailto:[email protected]>>> 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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