[SciPy-Dev] update on 0.11.0 status

Ralf Gommers ralf.gommers@googlemail....
Tue Jul 10 16:00:12 CDT 2012


On Tue, Jul 10, 2012 at 10:52 PM, Jake Vanderplas <
vanderplas@astro.washington.edu> wrote:

>  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> 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?
>

Seems to be the same each time.

Ralf


>
> 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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