[SciPy-Dev] update on 0.11.0 status
Josh Lawrence
josh.k.lawrence at gmail.com
Mon Jul 16 20:43:13 EDT 2012
I'll follow on your suggestion of keeping rtol instead of atol. Let me rerun the tests to make sure 1e-14 is not too small for rtol. As far as git goes, should I rebase or should I just leave the rtol commit as is?
--Josh
On Jul 16, 2012, at 8:34 PM, Sturla Molden wrote:
> I believe changing the order of arguments is correct. Currently the rtol test in the call to allclose fails since it is relative to 0.
>
> I think rtol should be kept and/or atol should probably be much smaller than 1E-14.
>
> Sturla
>
>
>
> Den 17.07.2012 01:30, skrev Josh Lawrence:
>>
>> This one needs to be reviewed as well:
>>
>> https://github.com/scipy/scipy/pull/259
>>
>>
>> --Josh
>>
>> On Jul 16, 2012, at 2:34 PM, Ralf Gommers wrote:
>>
>>>
>>>
>>> On Mon, Jul 16, 2012 at 1:49 AM, Jake Vanderplas <vanderplas at astro.washington.edu> wrote:
>>> Good catch, Ralf!
>>> Initializing all values of dist_array to zero is the correct thing to do here. I don't know how I missed that...
>>>
>>> Great, thanks for confirming.
>>>
>>> Now that all issues have fixes available, I plan to merge all open PRs by tomorrow and prepare a release candidate asap. Some PRs haven't been reviewed yet but they're very straightforward - please have a look at them or let me know you intend to do so if you want me to wait.
>>>
>>> https://github.com/scipy/scipy/pull/267
>>> https://github.com/scipy/scipy/pull/268
>>> https://github.com/scipy/scipy/pull/258
>>> https://github.com/scipy/scipy/pull/257
>>> https://github.com/scipy/scipy/pull/266
>>>
>>> Ralf
>>>
>>>
>>>
>>> On 07/15/2012 07:57 AM, Ralf Gommers wrote:
>>>
>>>>
>>>>
>>>> On Wed, Jul 11, 2012 at 11:45 PM, Ralf Gommers <ralf.gommers at googlemail.com> wrote:
>>>>
>>>>
>>>> On Tue, Jul 10, 2012 at 11:33 PM, Jake Vanderplas <vanderplas at astro.washington.edu> wrote:
>>>> Ralf,
>>>> I tried running valgrind on the offending code. I don't see anything out of the ordinary come up on my system (for reference, the scikit-learn developer documentation has some tips on using valgrind for cython code [1]). This makes me suspect that the error you're seeing may be a system-specific issue (i.e. 32 bit/64 bit mismatch), or perhaps something related to the numpy version (I'm using the current numpy 1.8.0-dev).
>>>>
>>>> Could you run valgrind on your system with test_shortest_path.py and see if anything obvious comes up?
>>>>
>>>> It's clean, some noise related to Python itself but nothing related to csgraph.
>>>>
>>>> This was 32-bit python 2.6, numpy 1.8-dev by the way. I haven't yet checked if I get the same when running in 64-bit mode on the same machine yet.
>>>>
>>>> Found the issue (use of an array created with np.empty), see http://projects.scipy.org/scipy/ticket/1701.
>>>>
>>>> Ralf
>>>>
>>>>
>>>>
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>>>
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