[SciPy-User] peer review of scientific software

Matthew Brett matthew.brett@gmail....
Thu Jun 6 09:33:17 CDT 2013


On Thu, Jun 6, 2013 at 6:49 AM,  <josef.pktd@gmail.com> wrote:
> On Thu, Jun 6, 2013 at 8:57 AM, Matthew Brett <matthew.brett@gmail.com> wrote:
>> Hi,
>> On Thu, Jun 6, 2013 at 1:19 PM,  <josef.pktd@gmail.com> wrote:
>>> On Thu, Jun 6, 2013 at 7:21 AM, Matthew Brett <matthew.brett@gmail.com> wrote:
>>>> Hi,
>>>> On Thu, Jun 6, 2013 at 6:23 AM, Jerome Kieffer <Jerome.Kieffer@esrf.fr> wrote:
>>>>> On Wed, 5 Jun 2013 23:08:10 +0100
>>>>> Nathaniel Smith <njs@pobox.com> wrote:
>>>>>> But... have you ever sat down and written tests for a piece of widely
>>>>>> used academic software? (Not LAPACK, but some random large package
>>>>>> that's widely used within a field but doesn't have a comprehensive
>>>>>> test suite of its own.) Everyone I've heard of who's done this
>>>>>> discovers bugs all over the place. Would you personally trip over them
>>>>>> if you didn't test the code? Who knows, maybe not. And probably most
>>>>>> of the rest -- off by one errors here and there, maybe an incorrect
>>>>>> normalizing constant, etc., -- end up not mattering too much. Or maybe
>>>>>> they do. How could you even tell?
>>>>> I found bugs in scipy.ndimage.shift and in scipy.stats.linregress.
>>>>> The first took me ages to be spotted as I was assuming the error was on
>>>>> my side as scipy was seen as a "large library widely used".
>>>> Well said.  See also Blake Griffith's current struggles with
>>>> scipy.sparse (last message title "parametric tests, known failures and
>>>> skipped tests").
>>> As far as I understand these are not BUGs.
>>> These are TDD test failures during development while adding support to
>>> additional dtypes.
>> See for example : https://github.com/scipy/scipy/issues/2542
>> In particular that ticket ends with "Existing tests only tested lil
>> with float data."
> you cut off the other part of my statement
> But that doesn't mean scipy.sparse didn't work correctly for the
> initial implementation for float matrices.
> *float*

Sorry - I think I read your message too quickly.

On the other hand that neatly points out the problem that the user
would be unlikely to guess that sparse would only work correctly for



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