[SciPy-Dev] update on 0.11.0 status
Jake Vanderplas
vanderplas at astro.washington.edu
Tue Jul 10 16:52:44 EDT 2012
On 07/10/2012 01:34 PM, Ralf Gommers wrote:
>
>
> On Tue, Jul 10, 2012 at 6:25 PM, Jake Vanderplas
> <vanderplas at astro.washington.edu
> <mailto:vanderplas at 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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