[Numpy-discussion] Questions about fixes for 1.9.0rc2

[Nathaniel Smith]

On Fri, Jul 4, 2014 at 9:48 PM, Charles R Harris
<charlesr.harris at gmail.com> wrote:
>
> On Fri, Jul 4, 2014 at 2:41 PM, Nathaniel Smith <njs at pobox.com> wrote:
>>
>> On Fri, Jul 4, 2014 at 9:33 PM, Charles R Harris
>> <charlesr.harris at gmail.com> wrote:
>> >
>> > On Fri, Jul 4, 2014 at 2:09 PM, Nathaniel Smith <njs at pobox.com> wrote:
>> >>
>> >> On Fri, Jul 4, 2014 at 9:02 PM, Ralf Gommers <ralf.gommers at gmail.com>
>> >> wrote:
>> >> >
>> >> > On Fri, Jul 4, 2014 at 10:00 PM, Charles R Harris
>> >> > <charlesr.harris at gmail.com> wrote:
>> >> >>
>> >> >> On Fri, Jul 4, 2014 at 1:42 PM, Charles R Harris
>> >> >> <charlesr.harris at gmail.com> wrote:
>> >> >>>
>> >> >>> Sebastian Seberg has fixed one class of test failures due to the
>> >> >>> indexing
>> >> >>> changes in numpy 1.9.0b1.  There are some remaining errors, and in
>> >> >>> the
>> >> >>> case
>> >> >>> of the Matplotlib failures, they look to me to be Matplotlib bugs.
>> >> >>> The
>> >> >>> 2-d
>> >> >>> arrays that cause the error are returned by the overloaded
>> >> >>> _interpolate_single_key function in CubicTriInterpolator that is
>> >> >>> documented
>> >> >>> in the base class to return a 1-d array, whereas the actual
>> >> >>> dimensions
>> >> >>> are
>> >> >>> of the form (n, 1). The question is, what is the best work around
>> >> >>> here
>> >> >>> for
>> >> >>> these sorts errors? Can we afford to break Matplotlib and other
>> >> >>> packages on
>> >> >>> account of a bug that was previously accepted by Numpy?
>> >> >
>> >> >
>> >> > It depends how bad the break is, but in principle I'd say that
>> >> > breaking
>> >> > Matplotlib is not OK.
>> >>
>> >> I agree. If it's easy to hack around it and issue a warning for now,
>> >> and doesn't have other negative consequences, then IMO we should give
>> >> matplotlib a release or so worth of grace period to fix things.
>> >
>> >
>> > Here is another example, from skimage.
>> >
>> > ======================================================================
>> > ERROR: test_join.test_relabel_sequential_offset1
>> > ----------------------------------------------------------------------
>> > Traceback (most recent call last):
>> >   File "X:\Python27-x64\lib\site-packages\nose\case.py", line 197, in
>> > runTest
>> >     self.test(*self.arg)
>> >   File
>> >
>> > "X:\Python27-x64\lib\site-packages\skimage\segmentation\tests\test_join.py",
>> > line 30, in test_relabel_sequential_offset1
>> >     ar_relab, fw, inv = relabel_sequential(ar)
>> >   File
>> > "X:\Python27-x64\lib\site-packages\skimage\segmentation\_join.py",
>> > line 127, in relabel_sequential
>> >     forward_map[labels0] = np.arange(offset, offset + len(labels0) + 1)
>> > ValueError: shape mismatch: value array of shape (6,) could not be
>> > broadcast
>> > to indexing result of shape (5,)
>> >
>> > Which is pretty clearly a coding error. Unfortunately, the error is in
>> > the
>> > package rather than the test.
>> >
>> > The only easy way to fix all of these sorts of things is to revert the
>> > indexing changes, and I'm loathe to do that. Grrr...
>>
>> Ugh, that's pretty bad :-/. Do you really think we can't use a
>> band-aid over the new indexing code, though?
>
>
> Yeah, we can. But Sebastian doesn't have time and I'm unfamiliar with the
> code, so it may take a while...

Fair enough!

I guess that if what are (arguably) bugs in matplotlib and
scikit-image are holding up the numpy release, then it's worth CC'ing
their mailing lists in case someone feels like volunteering to fix
it... ;-).

-n

-- 
Nathaniel J. Smith
Postdoctoral researcher - Informatics - University of Edinburgh
http://vorpus.org