Hi Ghislain, On Fri, Dec 23, 2016 at 10:02:33AM +0000, Ghislain Vaillant wrote: > On Fri, 2016-12-23 at 10:43 +0100, Andreas Tille wrote: > > Hi, > > > > I have cloned bug #848758 where I suggested to revert the python-numpy > > transition which other posters agreed upon. Besides breaking > > python-skbio I spotted another package python-skimage which fails with: > > > > > > ====================================================================== > > ERROR: skimage.filters.rank.tests.test_rank.test_all > > ---------------------------------------------------------------------- > > Traceback (most recent call last): > > File "/usr/lib/python2.7/dist-packages/nose/case.py", line 197, in runTest > > self.test(*self.arg) > > File > > "/build/skimage-0.12.3/debian/tmp/usr/lib/python2.7/dist-packages/skimage/filters/rank/tests/test_rank.py", > > line 16, in test_all > > check_all() > > File > > "/build/skimage-0.12.3/debian/tmp/usr/lib/python2.7/dist-packages/skimage/_shared/testing.py", > > line 232, in inner > > result = func(*args, **kwargs) > > File > > "/build/skimage-0.12.3/debian/tmp/usr/lib/python2.7/dist-packages/skimage/filters/rank/tests/test_rank.py", > > line 89, in check_all > > rank.windowed_histogram(image, selem)) > > File > > "/build/skimage-0.12.3/debian/tmp/usr/lib/python2.7/dist-packages/skimage/filters/rank/generic.py", > > line 986, in windowed_histogram > > pixel_size=n_bins) > > File > > "/build/skimage-0.12.3/debian/tmp/usr/lib/python2.7/dist-packages/skimage/filters/rank/generic.py", > > line 90, in _apply_vector_per_pixel > > pixel_size=pixel_size) > > File > > "/build/skimage-0.12.3/debian/tmp/usr/lib/python2.7/dist-packages/skimage/filters/rank/generic.py", > > line 53, in _handle_input > > out = np.empty(image.shape+(pixel_size,), dtype=out_dtype) > > TypeError: 'numpy.float64' object cannot be interpreted as an index > > > > ---------------------------------------------------------------------- > > Ran 1383 tests in 181.697s > > Sounds like the kind of bug upstream would be interested in getting > fixed. This implementation must be relying on an implicit integer type > for the overall shape of the filter. My initial guess would be that > pixel_size ends-up being a float rather than an int here?
Yes, sure. Any volunteer to submit the issue upstream? Sorry, I will not manage it in a sensible time frame. > Not sure whether it is worth reverting numpy for this. From a quick > search, it looks like skimage has had issues like this in the past. I'm also not sure and people who know better than me should feel free to close bug #849177. I'd be really happy if there are better solutions to fix python-skimage in the next 36 hours. My reading of the arguments in #849177 is that there are other reasons to revert the upgrade even without the additional problem - thus I was opening the bug report independently from other packages like python-skimage and python-skbio. Kind regards Andreas. -- http://fam-tille.de