Bug#849177: Python-numpy transition breaks at least two packages
Hi all, On 23.12.2016 11:19, Andreas Tille wrote: > 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. While the original FTBFS for skimage is solved now, I found another problem with numpy 1.12 RC (and skimage) which I reported upstream: https://github.com/numpy/numpy/issues/8413 Currently, this keeps up to get a version of skimage into Debian that has a chance to migrate. This is really very disappointing to run into those problems just a few hours before the window for the stretch migration closes. Sandro, could you please *immediately* rollback the numpy RC or at least upload a version that otherwise solves all the regressions that are still open? Please put a stable, working version of numpy that we all can rely on. Time matters here. Best regards Ole (quite angry in the moment, sorry.)
Bug#849177: Python-numpy transition breaks at least two packages
Hi Ghislain, On Fri, Dec 23, 2016 at 10:02:33AM +, 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
Bug#849177: Python-numpy transition breaks at least two packages
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? 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. Ghis
Bug#849177: Python-numpy transition breaks at least two packages
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 I'll leave it to the reader to consider lowering the severity of this bug and risking that python-skimage (and possibly other packages) will not reach the next stable release. While python-skbio is a package of minor importance python-skimage has several reverse depends and should be saved. Kind regards Andreas. -- http://fam-tille.de
