Test Failure: AttributeError: incompatible shape for a non-contiguous array

Greetings,

I’ve banged my head against this problem for 2 days and have given up on figuring it out on my own…

After updating numpy and matplotlib to the latest versions from github Saturday morning, I keep getting “AttributeError: incompatible shape for a non-contiguous array” errors all over the place when plotting. When I run tests on numpy, everything passes. When I run tests on matplotlib, I get 51 errors, with a vast majority of them (possibly all) being the non-contiguous array errors. (Sample below)

Any suggestions here? I’m totally stumped.

PTM

···

Traceback (most recent call last):

File “/home/Patrick.Marsh/.local/lib/python2.7/site-packages/nose-1.2.1-py2.7.egg/nose/case.py”, line 197, in runTest

self.test(*self.arg)

File “/home/Patrick.Marsh/.local/lib/python2.7/site-packages/matplotlib/testing/decorators.py”, line 39, in failer

result = f(*args, **kwargs)

File “/home/Patrick.Marsh/.local/lib/python2.7/site-packages/matplotlib/testing/decorators.py”, line 145, in do_test

figure.savefig(actual_fname)

File “/home/Patrick.Marsh/.local/lib/python2.7/site-packages/matplotlib/figure.py”, line 1363, in savefig

self.canvas.print_figure(*args, **kwargs)

File “/home/Patrick.Marsh/.local/lib/python2.7/site-packages/matplotlib/backend_bases.py”, line 2118, in print_figure

**kwargs)

File “/home/Patrick.Marsh/.local/lib/python2.7/site-packages/matplotlib/backend_bases.py”, line 1894, in print_svg

return svg.print_svg(*args, **kwargs)

File “/home/Patrick.Marsh/.local/lib/python2.7/site-packages/matplotlib/backends/backend_svg.py”, line 1103, in print_svg

return self._print_svg(filename, svgwriter, fh_to_close, **kwargs)

File “/home/Patrick.Marsh/.local/lib/python2.7/site-packages/matplotlib/backends/backend_svg.py”, line 1139, in _print_svg

self.figure.draw(renderer)

File “/home/Patrick.Marsh/.local/lib/python2.7/site-packages/matplotlib/artist.py”, line 54, in draw_wrapper

draw(artist, renderer, *args, **kwargs)

File “/home/Patrick.Marsh/.local/lib/python2.7/site-packages/matplotlib/figure.py”, line 999, in draw

func(*args)

File “/home/Patrick.Marsh/.local/lib/python2.7/site-packages/matplotlib/artist.py”, line 54, in draw_wrapper

draw(artist, renderer, *args, **kwargs)

File “/home/Patrick.Marsh/.local/lib/python2.7/site-packages/matplotlib/axes.py”, line 2086, in draw

a.draw(renderer)

File “/home/Patrick.Marsh/.local/lib/python2.7/site-packages/matplotlib/artist.py”, line 54, in draw_wrapper

draw(artist, renderer, *args, **kwargs)

File “/home/Patrick.Marsh/.local/lib/python2.7/site-packages/matplotlib/collections.py”, line 699, in draw

return Collection.draw(self, renderer)

File “/home/Patrick.Marsh/.local/lib/python2.7/site-packages/matplotlib/artist.py”, line 54, in draw_wrapper

draw(artist, renderer, *args, **kwargs)

File “/home/Patrick.Marsh/.local/lib/python2.7/site-packages/matplotlib/collections.py”, line 248, in draw

transform, transOffset, offsets, paths = self._prepare_points()

File “/home/Patrick.Marsh/.local/lib/python2.7/site-packages/matplotlib/collections.py”, line 222, in _prepare_points

offsets.shape = (-1, 2) # Make it Nx2

AttributeError: incompatible shape for a non-contiguous array


Ran 1123 tests in 401.586s

FAILED (KNOWNFAIL=282, SKIP=3, errors=51)


Patrick Marsh
Ph.D. Candidate / Liaison to the HWT
School of Meteorology / University of Oklahoma

Cooperative Institute for Mesoscale Meteorological Studies
National Severe Storms Laboratory
http://www.patricktmarsh.com

I am guessing this is a problem introduced with NumPy. I just tried the tests with an older NumPy branch, and all seemed fine. Now testing with the most recent branch.

Ben Root

···

On Mon, Oct 29, 2012 at 1:51 AM, Patrick Marsh <patrickmarshwx@…149…> wrote:

Greetings,

I’ve banged my head against this problem for 2 days and have given up on figuring it out on my own…

After updating numpy and matplotlib to the latest versions from github Saturday morning, I keep getting “AttributeError: incompatible shape for a non-contiguous array” errors all over the place when plotting. When I run tests on numpy, everything passes. When I run tests on matplotlib, I get 51 errors, with a vast majority of them (possibly all) being the non-contiguous array errors. (Sample below)

Any suggestions here? I’m totally stumped.

PTM

Confirming the bug (and it appears to be happening at a spot that I updated a couple years ago to catch exactly these sort of situations where reshaping would result in a copy when we didn’t want a copy).

I am presuming that it is a NumPy bug and will report it as such to the numpy list.

Cheers!
Ben Root

···

On Mon, Oct 29, 2012 at 9:16 AM, Benjamin Root <ben.root@…553…> wrote:

On Mon, Oct 29, 2012 at 1:51 AM, Patrick Marsh <patrickmarshwx@…149…> wrote:

Greetings,

I’ve banged my head against this problem for 2 days and have given up on figuring it out on my own…

After updating numpy and matplotlib to the latest versions from github Saturday morning, I keep getting “AttributeError: incompatible shape for a non-contiguous array” errors all over the place when plotting. When I run tests on numpy, everything passes. When I run tests on matplotlib, I get 51 errors, with a vast majority of them (possibly all) being the non-contiguous array errors. (Sample below)

Any suggestions here? I’m totally stumped.

PTM

I am guessing this is a problem introduced with NumPy. I just tried the tests with an older NumPy branch, and all seemed fine. Now testing with the most recent branch.

Ben Root

Just a follow up for historical sake:

This is a bug in numpy and was introduced in this commit: https://github.com/numpy/numpy/commit/c48156dfdc408f0a1e59ef54ac490cccbd6b8d73

I’ve filed a ticket with Numpy and those interested can follow up here: https://github.com/numpy/numpy/issues/2700

PTM

···

Patrick Marsh
Ph.D. Candidate / Liaison to the HWT
School of Meteorology / University of Oklahoma
Cooperative Institute for Mesoscale Meteorological Studies

National Severe Storms Laboratory
http://www.patricktmarsh.com

On Mon, Oct 29, 2012 at 8:46 AM, Benjamin Root <ben.root@…553…> wrote:

On Mon, Oct 29, 2012 at 9:16 AM, Benjamin Root <ben.root@…553…> wrote:

On Mon, Oct 29, 2012 at 1:51 AM, Patrick Marsh <patrickmarshwx@…149…> wrote:

Greetings,

I’ve banged my head against this problem for 2 days and have given up on figuring it out on my own…

After updating numpy and matplotlib to the latest versions from github Saturday morning, I keep getting “AttributeError: incompatible shape for a non-contiguous array” errors all over the place when plotting. When I run tests on numpy, everything passes. When I run tests on matplotlib, I get 51 errors, with a vast majority of them (possibly all) being the non-contiguous array errors. (Sample below)

Any suggestions here? I’m totally stumped.

PTM

I am guessing this is a problem introduced with NumPy. I just tried the tests with an older NumPy branch, and all seemed fine. Now testing with the most recent branch.

Ben Root

Confirming the bug (and it appears to be happening at a spot that I updated a couple years ago to catch exactly these sort of situations where reshaping would result in a copy when we didn’t want a copy).

I am presuming that it is a NumPy bug and will report it as such to the numpy list.

Cheers!
Ben Root