[SciPy-Dev] update on 0.11.0 status

Jake Vanderplas vanderplas@astro.washington....
Tue Jul 10 15:52:44 CDT 2012


On 07/10/2012 01:34 PM, Ralf Gommers wrote:
>
>
> On Tue, Jul 10, 2012 at 6:25 PM, Jake Vanderplas 
> <vanderplas@astro.washington.edu 
> <mailto:vanderplas@astro.washington.edu>> wrote:
>
>     Hi,
>     The graph_laplacian issue is fixed in PR 266, which I just opened
>     [1].  There is still the related but larger issue of errant fancy
>     indexing in LIL matrix, discussed in ticket 1681 [2].  The LIL
>     issue is more complicated, as it has potential for breaking
>     backward compatibility.
>
> Great. If that is fixed, I'm not sure if the LIL issue is still a blocker.
>
>     I have still been unable to reproduce the csgraph.shortest_path
>     failure.
>
>
> I can reproduce this for about 1 in 10 runs, which is really weird 
> because I can't find any randomness in the test or code. Plus, it once 
> again shows how annoying generator tests are; can't see which method 
> is failing. Failures are also not always the same:
>
> <failure 1>
> x and y nan location mismatch:
>  x: array([[  0.,  nan,   3.,   2.,   4.],
>        [ nan,  nan,  nan,  nan,  nan],
>        [  1.,  nan,   0.,   3.,   5.],
>        [  1.,  nan,   4.,   0.,   3.]])
>  y: array([[ 0.,  3.,  3.,  1.,  2.],
>        [ 3.,  0.,  6.,  2.,  4.],
>        [ 3.,  6.,  0.,  4.,  5.],
>        [ 1.,  2.,  4.,  0.,  2.]])
>
>
> <failure 2>
> (mismatch 30.0%)
>  x: array([[ 0.,  3.,  3.,  2.,  4.],
>        [ 3.,  0.,  6.,  2.,  4.],
>        [ 3.,  6.,  0.,  5.,  7.],
>        [ 1.,  1.,  4.,  0.,  3.]])
>  y: array([[ 0.,  3.,  3.,  1.,  2.],
>        [ 3.,  0.,  6.,  2.,  4.],
>        [ 3.,  6.,  0.,  4.,  5.],
>        [ 1.,  2.,  4.,  0.,  2.]])
>
>
> Any idea where to look?

I just ran the test_shortest_path.py code a few dozen times, and didn't 
have any failures.  Both these cases above seem to be from the 
`test_shortest_path_indices()` function, for indshape=(4,).  Is that the 
only test you get errors from?  Is the y array the same in each failure?

The fact that it's not happening every time for you makes it sound like 
a memory issue.  If that's the case, I suspect some variable is 
uninitialized in the Fibonacci heap code, as that's the only part of the 
code that uses raw pointers.

I'll try running valgrind to see if I can find the culprit.
    Jake

>
> Ralf
>
>
>        Jake
>
>     [1] https://github.com/scipy/scipy/pull/266
>     [2] http://projects.scipy.org/scipy/ticket/1681
>
>
>     On 07/10/2012 07:13 AM, Ralf Gommers wrote:
>>     Hi all,
>>
>>     Here's a short update on the status of the 0.11.0 release. Some
>>     of the reported issues for the beta release have been fixed or
>>     PRs for them are waiting to be merged. There is one failure not
>>     yet fixed (sparse.csgrapg.shortest_path failure) and one blocker
>>     also in the sparse.csgraph module:
>>     http://projects.scipy.org/scipy/ticket/1681. Once the csgraph
>>     issues are fixed we're ready to release the first RC.
>>
>>     To be merged and backported:
>>     Umfpack failure: https://github.com/scipy/scipy/pull/257
>>     Interpolate failure under Python 3.x:
>>     https://github.com/scipy/scipy/pull/258
>>
>>     To not fix: weave error when running the tests under Python 3.x.
>>     It's not easy to avoid the printed error, because importing the
>>     whole module fails. And in the end the result is the same, weave
>>     doesn't work at all for 3.x.
>>
>>     Cheers,
>>     Ralf
>>
>>
>>
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>
>
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