On Mon, Sep 30, 2013 at 10:21 AM, Julian Taylor < jtaylor.debian@googlemail.com> wrote:

On 30.09.2013 17:17, Charles R Harris wrote:

...

Hi All,

NumPy 1.8.0rc1 is up now on sourceforge <http://sourceforge.net/projects/numpy/files/NumPy/1.8.0rc1/> .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.

Can we also do a rc for 1.7.2? The number of fixes that went in is not small and they should be tested by some users before release.

I was planning on that right after 1.8 is done. I still need to backport your little cpp fixes, the changes since 1.7 make that a bit tricky. Then there is checking for other missing backports... Chuck

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@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],... ``` Christoph

On Mon, Sep 30, 2013 at 4:45 PM, Charles R Harris <charlesr.harris@gmail.com

wrote:

On Mon, Sep 30, 2013 at 3:51 PM, Christoph Gohlke <cgohlke@uci.edu> wrote:

...

...

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@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

On 9/30/2013 11:02 AM, Nathaniel Smith wrote:> Everyone please do actually test this! It is really in your best 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...

Reverting that commit fixes those skimage failures. However, there are a number of python2.7 failures that look pretty strange. Chuck

On Mon, Sep 30, 2013 at 5:12 PM, Christoph Gohlke <cgohlke@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@uci.edu <mailto:cgohlke@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@gmail.com <mailto:charlesr.harris@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/...

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. Chuck

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@uci.edu <mailto:cgohlke@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@uci.edu <mailto:cgohlke@uci.edu> > <mailto:cgohlke@uci.edu <mailto:cgohlke@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@gmail.com <mailto:charlesr.harris@gmail.com> <mailto:charlesr.harris@gmail.com <mailto:charlesr.harris@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/...

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> Christoph

On Mon, Sep 30, 2013 at 6:37 PM, Charles R Harris <charlesr.harris@gmail.com

wrote:

On Mon, Sep 30, 2013 at 6:13 PM, Christoph Gohlke <cgohlke@uci.edu> wrote:

...

...

On 01.10.2013 01:30, Charles R Harris wrote:

...

On Mon, Sep 30, 2013 at 5:12 PM, Christoph Gohlke <cgohlke@uci.edu <mailto:cgohlke@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@uci.edu

...

<mailto:cgohlke@uci.edu> > <mailto:cgohlke@uci.edu <mailto:cgohlke@uci.edu>>> wrote: > > > > On 9/30/2013 11:02 AM, Nathaniel Smith wrote:> Everyone

...

...

> 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@gmail.com <mailto:charlesr.harris@gmail.com> <mailto:

charlesr.harris@gmail.com

...

<mailto:charlesr.harris@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

On 9/30/2013 4:44 PM, Julian Taylor wrote: please do 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/...

...

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

On 30 September 2013 17:17, Charles R Harris <charlesr.harris@gmail.com>wrote:

NumPy 1.8.0rc1 is up now on sourceforge<http://sourceforge.net/projects/numpy/files/NumPy/1.8.0rc1/>.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.

...

...

import numpy as np Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/usr/lib64/python2.7/site-packages/numpy/__init__.py", line 137, in <module> import add_newdocs File "/usr/lib64/python2.7/site-packages/numpy/add_newdocs.py", line 13, in <module> from numpy.lib import add_newdoc File "/usr/lib64/python2.7/site-packages/numpy/lib/__init__.py", line 4, in <module> from type_check import * File "/usr/lib64/python2.7/site-packages/numpy/lib/type_check.py", line 8, in <module> import numpy.core.numeric as _nx File "/usr/lib64/python2.7/site-packages/numpy/core/__init__.py", line 45, in <module> from numpy.testing import Tester File "/usr/lib64/python2.7/site-packages/numpy/testing/__init__.py", line 10, in <module> import decorators as dec File "/usr/lib64/python2.7/site-packages/numpy/testing/decorators.py",

I installed it with # python setup.py install But something is wrong there: line 19, in <module> from numpy.testing.utils import \ File "/usr/lib64/python2.7/site-packages/numpy/testing/utils.py", line 12, in <module> from .nosetester import import_nose File "/usr/lib64/python2.7/site-packages/numpy/testing/nosetester.py", line 12, in <module> from numpy.compat import basestring ImportError: cannot import name basestring I am using Python27 on Fedora 19. $ gcc --version gcc (GCC) 4.8.1 20130603 (Red Hat 4.8.1-1)

On Tue, Oct 1, 2013 at 11:00 AM, Jens Jørgen Mortensen <jensj@fysik.dtu.dk> wrote:

I seems that solve() doesn't like arrays like zeros((3, 0)). I get this with 1.8.0rc1 on Ubuntu 13.04 and Python 2.7.4:

Yep, looks like a simple bug in the new gufunc stuff, thanks for catching it. Filed here: https://github.com/numpy/numpy/issues/3847 -n

On Tue, Oct 1, 2013 at 3:27 AM, Charles R Harris <charlesr.harris@gmail.com> wrote:

...

...

...

...

On Mon, Sep 30, 2013 at 5:12 PM, Christoph Gohlke <cgohlke@uci.edu <mailto:cgohlke@uci.edu>> wrote: > 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 > ``` [...]

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

I'm concerned about this. 0.12.0 is currently the latest pandas release, so even if it is a bug on their side, we're going to be converting it from a latent bug to a real bug when we release... CC'ing pydata, do you guys have any insight into what changed here? The code is: s = pandas.Series([1.0, np.nan]) result = np.nansum(s) With numpy 1.7.1, 'result' comes out as a np.float64. With numpy maintenance/1.8.x, 'result' comes out as a 0-d Series object. Series is a subclass of ndarray, but it's supposed to always be 1-d, so all kinds of stuff blows up as soon as you have a 0-d Series object. I'm not sure what changed in numpy's nansum; if I try this same test with a simple no-op ndarray subclass: class MyArray(np.ndarray): pass np.nansum(np.array([1.0, np.nan]).view(MyArray)) then 1.7.1 and maintenance/1.8.x both act the same, and both return a 0-d MyArray, so it's not just a question of whether we remembered to handle subclasses at all. -n

On Tue, Oct 1, 2013 at 4:43 AM, Nathaniel Smith <njs@pobox.com> wrote:

On Mon, Sep 30, 2013 at 10:51 PM, Christoph Gohlke <cgohlke@uci.edu> wrote:

...

2) Bottleneck 0.7.0

https://github.com/kwgoodman/bottleneck/issues/71#issuecomment-25331701

I can't tell if these are real bugs in numpy, or tests checking that bottleneck is bug-for-bug compatible with old numpy and we just fixed some bugs, or what. It's clearly something to do with the nanarg{max,min} rewrite -- @charris, do you know what's going on here?

Yes ;) The previous behaviour of nanarg for all-nan axis was to cast nan to intp when the result was an array, and return nan when a scalar. The current behaviour is to return the most negative value of intp as an error marker in both cases and raise a warning. It is a change in behavior, but I think one that needs to be made. Chuck

On Tue, Oct 1, 2013 at 7:25 AM, Nathaniel Smith <njs@pobox.com> wrote:

On Tue, Oct 1, 2013 at 1:56 PM, Charles R Harris <charlesr.harris@gmail.com> wrote:

...

On Tue, Oct 1, 2013 at 4:43 AM, Nathaniel Smith <njs@pobox.com> wrote:

...

On Mon, Sep 30, 2013 at 10:51 PM, Christoph Gohlke <cgohlke@uci.edu> wrote:

...

2) Bottleneck 0.7.0

https://github.com/kwgoodman/bottleneck/issues/71#issuecomment-25331701

...

I can't tell if these are real bugs in numpy, or tests checking that bottleneck is bug-for-bug compatible with old numpy and we just fixed some bugs, or what. It's clearly something to do with the nanarg{max,min} rewrite -- @charris, do you know what's going on here?

Yes ;) The previous behaviour of nanarg for all-nan axis was to cast nan to intp when the result was an array, and return nan when a scalar. The current behaviour is to return the most negative value of intp as an error marker in both cases and raise a warning. It is a change in behavior, but I think one that needs to be made.

Ah, okay! I kind of lost track of the nanfunc changes by the end there.

So for the bottleneck issue, it sounds like the problem is just that bottleneck is still emulating the old numpy behaviour in this corner case, which isn't really a problem. So we don't really need to worry about that, both behaviours are correct, just maybe out of sync.

I'm a little dubious about this "make up some weird value that will *probably* blow up if people try to use it without checking, and also raise a warning" thing, wouldn't it make more sense to just raise an error? That's what exceptions are for? I guess I should have said something earlier though...

I figure the blowup is safe, as we can't allocate arrays big enough that the minimum intp value would be a valid index. I considered raising an error, and if there is a consensus the behavior could be changed. Or we could add a keyword to determine the behavior. Chuck

This is a complicated issue to describe but i think the bottom line is that the test is just wonky here. the behaviour it's checking for is: wrong in old numpy, but we do it anyway (bug) wrong in current numpy without RELAXED_STRIDES, and we get it right (I.e. don't do it, fixed bug) correct in current numpy with RELAXED_STRIDES (and I think the test will pass if you build 1.8 this way?) (fixed bug again, since the definition of "correct" flipped) correct in future numpys (@seberg, does that look right?) I guess maybe we could go back and make sure it stays broken in 1.8, but it's probably not worth the trouble because this is such a corner case. Nothing real is going to break because of this AFAICT. -n On 2 Oct 2013 08:31, "Christoph Gohlke" <cgohlke@uci.edu> wrote:

On 9/30/2013 8:17 AM, Charles R Harris wrote:

...

Hi All,

NumPy 1.8.0rc1 is up now on sourceforge <http://sourceforge.net/**projects/numpy/files/NumPy/1.**8.0rc1/<http://sourceforge.net/projects/numpy/files/NumPy/1.8.0rc1/>> .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

One more: Cython-0.19.1 fails relaxed_strides.test_one_sized with "ValueError: ndarray is not C-contiguous". Tested on numpy-MKL-1.8.0rc1-win-amd64-**py2.7 and msvc9.

https://github.com/cython/**cython/blob/0.19.x/tests/** memoryview/relaxed_strides.**pyx#L29<https://github.com/cython/cython/blob/0.19.x/tests/memoryview/relaxed_strides.pyx#L29>

The relevant test output is attached.

Christoph

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On Wed, 2013-10-02 at 12:54 +0200, Sebastian Berg wrote:

On Wed, 2013-10-02 at 10:04 +0100, Nathaniel Smith wrote:

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This is a complicated issue to describe but i think the bottom line is that the test is just wonky here. the behaviour it's checking for is: wrong in old numpy, but we do it anyway (bug) wrong in current numpy without RELAXED_STRIDES, and we get it right (I.e. don't do it, fixed bug) correct in current numpy with RELAXED_STRIDES (and I think the test will pass if you build 1.8 this way?) (fixed bug again, since the definition of "correct" flipped) correct in future numpys

OK, I had a look. And it is the 1-dimensional size-1 special case that was always "relaxed", but is not anymore. If anyone thinks this is a problem, we could re-add the special case (rethinking it, it is almost impossible to hurt, since the array has only one element). Otherwise, I think the test should check if numpy was compiled with relaxed strides, for more extensive tests this is necessary anyway. - Sebastian

Sounds about right, but I did not yet look at the test exactly. The old numpy had some corner cases where the *not* relaxed strides were not enforced. I could imagine that the test was written to accommodate the relaxed strides, but runs through fine with the old behaviour, too.

That said, if this is the case, this must be something like a size 1 array corner case, so I would agree with Nathaniel, that probably the test should just see whether relaxed strides is active or not and change behaviour accordingly.

If this has to do with the Buffer protocol change we have to have a closer look if it might be breaking code out there. (even if the buffer protocol change is correct and this should be fixed on cythons end in that case)

- Sebastian

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(@seberg, does that look right?)

I guess maybe we could go back and make sure it stays broken in 1.8, but it's probably not worth the trouble because this is such a corner case. Nothing real is going to break because of this AFAICT.

-n

On 2 Oct 2013 08:31, "Christoph Gohlke" <cgohlke@uci.edu> wrote: On 9/30/2013 8:17 AM, Charles R Harris wrote: Hi All,

NumPy 1.8.0rc1 is up now on sourceforge <http://sourceforge.net/projects/numpy/files/NumPy/1.8.0rc1/> .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

One more: Cython-0.19.1 fails relaxed_strides.test_one_sized with "ValueError: ndarray is not C-contiguous". Tested on numpy-MKL-1.8.0rc1-win-amd64-py2.7 and msvc9.

https://github.com/cython/cython/blob/0.19.x/tests/memoryview/relaxed_stride...

The relevant test output is attached.

Christoph

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Hi Stefan, On Wed, Oct 2, 2013 at 9:29 AM, Stéfan van der Walt <stefan@sun.ac.za>wrote:

Hi Chuck

On Tue, Oct 1, 2013 at 1:07 AM, Charles R Harris <charlesr.harris@gmail.com> wrote:

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I'll bet the skimage problems come from https://github.com/numpy/numpy/pull/3811. They may be doing something naughty...

Reverting that commit fixes those skimage failures. However, there are a number of python2.7 failures that look pretty strange.

What is the exact change in behavior with that PR? I'm trying to figure out what skimage does wrong in this case.

The current master, and reverted for the 1.8 release only, is stricter about np.bool only taking values 0 or 1. Apparently the convolve returns boolean (I haven't checked) for boolean input, and consequently the check if the return value matches the number of 1 elements in the convolution kernel will fail when that number is greater than one. That is why the proposed fix is to view the boolean as uint8 instead. Note that out=(boolean) will still cause problems. Chuck

On Wed, Oct 2, 2013 at 10:12 AM, Benjamin Root <ben.root@ou.edu> wrote:

On Wed, Oct 2, 2013 at 11:43 AM, Charles R Harris < charlesr.harris@gmail.com> wrote:

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Hi Stefan,

On Wed, Oct 2, 2013 at 9:29 AM, Stéfan van der Walt <stefan@sun.ac.za>wrote:

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Hi Chuck

On Tue, Oct 1, 2013 at 1:07 AM, Charles R Harris <charlesr.harris@gmail.com> wrote:

...

...

I'll bet the skimage problems come from https://github.com/numpy/numpy/pull/3811. They may be doing something naughty...

Reverting that commit fixes those skimage failures. However, there are a number of python2.7 failures that look pretty strange.

What is the exact change in behavior with that PR? I'm trying to figure out what skimage does wrong in this case.

The current master, and reverted for the 1.8 release only, is stricter about np.bool only taking values 0 or 1. Apparently the convolve returns boolean (I haven't checked) for boolean input, and consequently the check if the return value matches the number of 1 elements in the convolution kernel will fail when that number is greater than one. That is why the proposed fix is to view the boolean as uint8 instead. Note that out=(boolean) will still cause problems.

Chuck

So, just to be clear... what would happen if I had an array of floats between 0 and 1 inclusive and I cast that as a boolean using astype()?

You get zeros and ones. I don't think that has changed. Of course, you can still mess things up using views ;) Chuck