<div dir="ltr"><br><div class="gmail_extra"><br><br><div class="gmail_quote">On Mon, Sep 30, 2013 at 6:37 PM, Charles R Harris <span dir="ltr"><<a href="mailto:charlesr.harris@gmail.com" target="_blank">charlesr.harris@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><br><div class="gmail_extra"><br><br><div class="gmail_quote"><div><div class="h5">On Mon, Sep 30, 2013 at 6:13 PM, Christoph Gohlke <span dir="ltr"><<a href="mailto:cgohlke@uci.edu" target="_blank">cgohlke@uci.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div><div>On 9/30/2013 4:44 PM, Julian Taylor wrote:<br>
> On 01.10.2013 01:30, Charles R Harris wrote:<br>
>><br>
>><br>
>><br>
>> On Mon, Sep 30, 2013 at 5:12 PM, Christoph Gohlke <<a href="mailto:cgohlke@uci.edu" target="_blank">cgohlke@uci.edu</a><br>
>> <mailto:<a href="mailto:cgohlke@uci.edu" target="_blank">cgohlke@uci.edu</a>>> wrote:<br>
>><br>
>> On 9/30/2013 3:45 PM, Charles R Harris wrote:<br>
>> ><br>
>> ><br>
>> ><br>
>> > On Mon, Sep 30, 2013 at 3:51 PM, Christoph Gohlke <<a href="mailto:cgohlke@uci.edu" target="_blank">cgohlke@uci.edu</a><br>
>> <mailto:<a href="mailto:cgohlke@uci.edu" target="_blank">cgohlke@uci.edu</a>><br>
>> > <mailto:<a href="mailto:cgohlke@uci.edu" target="_blank">cgohlke@uci.edu</a> <mailto:<a href="mailto:cgohlke@uci.edu" target="_blank">cgohlke@uci.edu</a>>>> wrote:<br>
>> ><br>
>> ><br>
>> ><br>
>> > On 9/30/2013 11:02 AM, Nathaniel Smith wrote:> Everyone please do<br>
>> > actually test this! It is really in your best<br>
>> > > interest, and I think people don't always realize this.<br>
>> > ><br>
>> > > Here's how it works:<br>
>> > > - If you test it *now*, and it breaks your code that worked<br>
>> with 1.7,<br>
>> > > and you *tell* us this now, then it's *our* problem and we<br>
>> hold up the<br>
>> > > release to fix the bug.<br>
>> > > - If you test it *after* we release, and it breaks your<br>
>> code, then we<br>
>> > > are sad but you have to work around it (because we can't<br>
>> magically<br>
>> > > make that release not have happened, your users will be using it<br>
>> > > anyway), and we put it on the stack with all the other bugs.<br>
>> All of<br>
>> > > which we care about but it's a large enough stack that it's<br>
>> not going<br>
>> > > to get any special priority, because, see above about how at<br>
>> this<br>
>> > > point you'll have had to work around it anyway.<br>
>> > ><br>
>> > > -n<br>
>> > ><br>
>> > > On Mon, Sep 30, 2013 at 4:17 PM, Charles R Harris<br>
>> > > <<a href="mailto:charlesr.harris@gmail.com" target="_blank">charlesr.harris@gmail.com</a><br>
>> <mailto:<a href="mailto:charlesr.harris@gmail.com" target="_blank">charlesr.harris@gmail.com</a>> <mailto:<a href="mailto:charlesr.harris@gmail.com" target="_blank">charlesr.harris@gmail.com</a><br>
>> <mailto:<a href="mailto:charlesr.harris@gmail.com" target="_blank">charlesr.harris@gmail.com</a>>>> wrote:<br>
>> > >> Hi All,<br>
>> > >><br>
>> > >> NumPy 1.8.0rc1 is up now on sourceforge .The binary builds<br>
>> are included<br>
>> > >> except for Python 3.3 on windows, which will arrive later.<br>
>> Many thanks to<br>
>> > >> Ralf for the binaries, and to those who found and fixed the<br>
>> bugs in the last<br>
>> > >> beta. Any remaining bugs are all my fault ;) I hope this<br>
>> will be the last<br>
>> > >> release before final, so please test it thoroughly.<br>
>> > >><br>
>> > >> Chuck<br>
>> ><br>
>> ><br>
>> > Hello,<br>
>> ><br>
>> > NumPy 1.8.0rc1 looks good. All tests pass on Windows and most<br>
>> 3rd party<br>
>> > packages test OK now. Thank you.<br>
>> ><br>
>> > A few tests still fail in the following packages when run with<br>
>> > numpy-MKL-1.8.0rc1-win-amd64-py3.3 compared to<br>
>> > numpy-MKL-1.7.1-win-amd64-py3.3:<br>
>> ><br>
>> > 1) Pandas 0.12.0<br>
>> ><br>
>> > ```<br>
>> ><br>
>> ======================================================================<br>
>> > FAIL: test_nansum_buglet (pandas.tests.test_series.TestNanops)<br>
>> ><br>
>> ----------------------------------------------------------------------<br>
>> > Traceback (most recent call last):<br>
>> > File<br>
>> "X:\Python33\lib\site-packages\pandas\tests\test_series.py",<br>
>> > line 254, in test_nansum_buglet<br>
>> > assert_almost_equal(result, 1)<br>
>> > File<br>
>> "X:\Python33\lib\site-packages\pandas\util\testing.py", line<br>
>> > 134, in assert_almost_equal<br>
>> > np.testing.assert_(isiterable(b))<br>
>> > File<br>
>> "D:\Dev\Compile\Test\numpy-build\numpy\testing\utils.py", line<br>
>> > 44, in assert_<br>
>> > raise AssertionError(msg)<br>
>> > AssertionError<br>
>> > ```<br>
>> ><br>
>> > Possibly related:<br>
>> ><br>
>> > ```<br>
>> > >>> import numpy as np<br>
>> > >>> from pandas import Series<br>
>> > >>> s = Series([0.0])<br>
>> > >>> result = np.nansum(s)<br>
>> > >>> print(result)<br>
>> > Traceback (most recent call last):<br>
>> > File "<stdin>", line 1, in <module><br>
>> > File "X:\Python33\lib\site-packages\pandas\core\base.py", line<br>
>> > 19, in<br>
>> > __str__<br>
>> > return self.__unicode__()<br>
>> > File<br>
>> "X:\Python33\lib\site-packages\pandas\core\series.py", line<br>
>> > 1115, in __unicode__<br>
>> > length=len(self) > 50,<br>
>> > TypeError: len() of unsized object<br>
>> > ```<br>
>> ><br>
>> > 2) Bottleneck 0.7.0<br>
>> ><br>
>> ><br>
>> <a href="https://github.com/kwgoodman/bottleneck/issues/71#issuecomment-25331701" target="_blank">https://github.com/kwgoodman/bottleneck/issues/71#issuecomment-25331701</a><br>
>> ><br>
>> > 3) skimage 0.8.2<br>
>> ><br>
>> > These tests passed with numpy 1.8.0b2:<br>
>> ><br>
>> > ```<br>
>> ><br>
>> ======================================================================<br>
>> > FAIL: test_grey.test_non_square_image<br>
>> ><br>
>> ----------------------------------------------------------------------<br>
>> > Traceback (most recent call last):<br>
>> > File "X:\Python33\lib\site-packages\nose\case.py", line<br>
>> 198, in<br>
>> > runTest<br>
>> > self.test(*self.arg)<br>
>> > File<br>
>> ><br>
>> "X:\Python33\lib\site-packages\skimage\morphology\tests\test_grey.py",<br>
>> > line 162, in test_non_square_image<br>
>> > testing.assert_array_equal(binary_res, grey_res)<br>
>> > File<br>
>> "X:\Python33\lib\site-packages\numpy\testing\utils.py", line<br>
>> > 718, in assert_array_equal<br>
>> > verbose=verbose, header='Arrays are not equal')<br>
>> > File<br>
>> "X:\Python33\lib\site-packages\numpy\testing\utils.py", line<br>
>> > 644, in assert_array_compare<br>
>> > raise AssertionError(msg)<br>
>> > AssertionError:<br>
>> > Arrays are not equal<br>
>> ><br>
>> > (mismatch 50.6328125%)<br>
>> > x: array([[False, False, False, ..., False, False, False],<br>
>> > [False, False, False, ..., False, False, False],<br>
>> > [False, False, False, ..., False, False, False],...<br>
>> > y: array([[ True, True, True, ..., True, False, False],<br>
>> > [ True, True, True, ..., False, False, False],<br>
>> > [ True, True, True, ..., False, False, False],...<br>
>> ><br>
>> ><br>
>> ======================================================================<br>
>> > FAIL: test_grey.test_binary_erosion<br>
>> ><br>
>> ----------------------------------------------------------------------<br>
>> > Traceback (most recent call last):<br>
>> > File "X:\Python33\lib\site-packages\nose\case.py", line<br>
>> 198, in<br>
>> > runTest<br>
>> > self.test(*self.arg)<br>
>> > File<br>
>> ><br>
>> "X:\Python33\lib\site-packages\skimage\morphology\tests\test_grey.py",<br>
>> > line 169, in test_binary_erosion<br>
>> > testing.assert_array_equal(binary_res, grey_res)<br>
>> > File<br>
>> "X:\Python33\lib\site-packages\numpy\testing\utils.py", line<br>
>> > 718, in assert_array_equal<br>
>> > verbose=verbose, header='Arrays are not equal')<br>
>> > File<br>
>> "X:\Python33\lib\site-packages\numpy\testing\utils.py", line<br>
>> > 644, in assert_array_compare<br>
>> > raise AssertionError(msg)<br>
>> > AssertionError:<br>
>> > Arrays are not equal<br>
>> ><br>
>> > (mismatch 48.260498046875%)<br>
>> > x: array([[False, False, False, ..., False, False, False],<br>
>> > [False, False, False, ..., False, False, False],<br>
>> > [False, False, False, ..., False, False, False],...<br>
>> > y: array([[ True, True, True, ..., True, False, False],<br>
>> > [ True, True, True, ..., False, False, False],<br>
>> > [ True, True, True, ..., False, False, False],...<br>
>> ><br>
>> ><br>
>> ======================================================================<br>
>> > FAIL: test_grey.test_binary_closing<br>
>> ><br>
>> ----------------------------------------------------------------------<br>
>> > Traceback (most recent call last):<br>
>> > File "X:\Python33\lib\site-packages\nose\case.py", line<br>
>> 198, in<br>
>> > runTest<br>
>> > self.test(*self.arg)<br>
>> > File<br>
>> ><br>
>> "X:\Python33\lib\site-packages\skimage\morphology\tests\test_grey.py",<br>
>> > line 183, in test_binary_closing<br>
>> > testing.assert_array_equal(binary_res, grey_res)<br>
>> > File<br>
>> "X:\Python33\lib\site-packages\numpy\testing\utils.py", line<br>
>> > 718, in assert_array_equal<br>
>> > verbose=verbose, header='Arrays are not equal')<br>
>> > File<br>
>> "X:\Python33\lib\site-packages\numpy\testing\utils.py", line<br>
>> > 644, in assert_array_compare<br>
>> > raise AssertionError(msg)<br>
>> > AssertionError:<br>
>> > Arrays are not equal<br>
>> ><br>
>> > (mismatch 66.302490234375%)<br>
>> > x: array([[False, False, False, ..., False, False, False],<br>
>> > [False, False, False, ..., False, False, False],<br>
>> > [False, False, False, ..., False, False, False],...<br>
>> > y: array([[ True, True, True, ..., True, True, True],<br>
>> > [ True, True, True, ..., True, True, True],<br>
>> > [ True, True, True, ..., False, False, False],...<br>
>> ><br>
>> ><br>
>> ======================================================================<br>
>> > FAIL: test_grey.test_binary_opening<br>
>> ><br>
>> ----------------------------------------------------------------------<br>
>> > Traceback (most recent call last):<br>
>> > File "X:\Python33\lib\site-packages\nose\case.py", line<br>
>> 198, in<br>
>> > runTest<br>
>> > self.test(*self.arg)<br>
>> > File<br>
>> ><br>
>> "X:\Python33\lib\site-packages\skimage\morphology\tests\test_grey.py",<br>
>> > line 190, in test_binary_opening<br>
>> > testing.assert_array_equal(binary_res, grey_res)<br>
>> > File<br>
>> "X:\Python33\lib\site-packages\numpy\testing\utils.py", line<br>
>> > 718, in assert_array_equal<br>
>> > verbose=verbose, header='Arrays are not equal')<br>
>> > File<br>
>> "X:\Python33\lib\site-packages\numpy\testing\utils.py", line<br>
>> > 644, in assert_array_compare<br>
>> > raise AssertionError(msg)<br>
>> > AssertionError:<br>
>> > Arrays are not equal<br>
>> ><br>
>> > (mismatch 58.465576171875%)<br>
>> > x: array([[False, False, False, ..., False, False, False],<br>
>> > [False, False, False, ..., False, False, False],<br>
>> > [False, False, False, ..., False, False, False],...<br>
>> > y: array([[ True, True, True, ..., True, True, False],<br>
>> > [ True, True, True, ..., True, True, False],<br>
>> > [ True, True, True, ..., False, False, False],...<br>
>> > ```<br>
>> ><br>
>> > I'll bet the skimage problems come from<br>
>> > <a href="https://github.com/numpy/numpy/pull/3811" target="_blank">https://github.com/numpy/numpy/pull/3811</a>. They may be doing something<br>
>> > naughty...<br>
>> ><br>
>> > Chuck<br>
>> ><br>
>><br>
>> A bool image is convolved with a uint8 kernel and the result compared<br>
>> for equality with an uint32 scalar...<br>
>><br>
>> <a href="https://github.com/scikit-image/scikit-image/blob/master/skimage/morphology/binary.py#L32" target="_blank">https://github.com/scikit-image/scikit-image/blob/master/skimage/morphology/binary.py#L32</a><br>
>><br>
>><br>
>> Looks like the result of the convolution is probably output as a bool,<br>
>> which now means 0,1, which does not work when checking equality with the<br>
>> number of pixels in the kernel. I'd call expressing the result of a<br>
>> convolution as a boolean very naughty.<br>
><br>
> using a view should fix it:<br>
> conv = ndimage.convolve((image > 0).view(np.uint8), selem, output=out,<br>
> mode='constant', cval=1)<br>
> but it needs check for sum(selem) < 255 too.<br>
<br>
</div></div>I opened an issue at<br>
<<a href="https://github.com/scikit-image/scikit-image/issues/745" target="_blank">https://github.com/scikit-image/scikit-image/issues/745</a>><br>
<span><font color="#888888"><br></font></span></blockquote><div><br></div></div></div><div>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.<br>
<br></div></div></div></div></blockquote><div><br></div><div>The pandas test passes for current pandas dev, so it looks like a bug on their end that has been taken care of.<br><br>test_nansum_buglet (__main__.TestNanops) ... ok<br>
<br></div><div>Chuck <br></div></div></div></div>