[SciPy-Dev] update on 0.11.0 status

Josh Lawrence josh.k.lawrence@gmail....
Mon Jul 16 19:43:13 CDT 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@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@googlemail.com> wrote:
>>>> 
>>>> 
>>>> On Tue, Jul 10, 2012 at 11:33 PM, Jake Vanderplas <vanderplas@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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