[SciPy-Dev] review request - test noise clean up

Wed Jan 12 09:37:51 EST 2011

On Wed, Jan 12, 2011 at 6:25 PM, Ralf Gommers
<ralf.gommers at googlemail.com>wrote:

>
>
> On Wed, Jan 12, 2011 at 6:18 PM, Ralf Gommers <ralf.gommers at googlemail.com
> > wrote:
>
>>
>>
>> On Tue, Jan 11, 2011 at 11:44 PM, Charles R Harris <
>> charlesr.harris at gmail.com> wrote:
>>
>>>
>>>
>>> On Tue, Jan 11, 2011 at 8:32 AM, Ralf Gommers <
>>> ralf.gommers at googlemail.com> wrote:
>>>
>>>> Hi,
>>>>
>>>> I cleaned most of the noise in the test output (only stats module and a
>>>> few random ones left): https://github.com/rgommers/scipy/tree/testnoise
>>>> Can someone please check this and confirm that this can go into trunk as
>>>> well as 0.9.x? Especially for the scipy.special commit.
>>>>
>>>> There are a few warnings that I'll only silence in 0.9.x because they
>>>> indicate actual problems or should be fixed elsewhere (like astype() in
>>>> numpy: http://projects.scipy.org/numpy/ticket/1709).
>>>>
>>>> For the ComplexWarning filter, is it preferable to be really granular
>>>> with linenos like
>>>>
>>>> warnings.filterwarnings('ignore', category=np.ComplexWarning, lineno=98)
>>>> or just filter it out of the whole module?
>>>>
>>>>
>>> Are the complex warnings for things that could be easily fixed?
>>>
>>> After looking again, yes:
>> https://github.com/rgommers/scipy/commit/fdf18166. They were calls to
>> fblas funcs with the wrong dtype, obscured a bit by subclassing the test
>> classes. So the only ones left are for ndarray.astype(), which should be
>> fixed in numpy.
>>
>>
>
Actually, there's one left that may be a bug. It happens in linalg.qr(), the
failing test is TestQR.test_random_complex() (and a similar one in
decomp_schur). But I can't reproduce it standalone, only if I run all linalg
tests. Could you perhaps have a look?

The other ones I'd like your opinion on is the fitpack warnings below. Not
sure what's going on there.

Ralf

Running unit tests for scipy
NumPy version 1.5.1
NumPy is installed in
/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/numpy
SciPy version 0.10.0.dev
SciPy is installed in /Users/rgommers/Code/scipy/scipy
Python version 2.6.4 (r264:75821M, Oct 27 2009, 19:48:32) [GCC 4.0.1 (Apple
Inc. build 5493)]
nose version 0.11.1
....................................................................................................................................................................................................................K.............................................................................../Users/rgommers/Code/scipy/scipy/interpolate/fitpack2.py:673:
UserWarning:
The coefficients of the spline returned have been computed as the
minimal norm least-squares solution of a (numerically) rank deficient
system (deficiency=7). If deficiency is large, the results may be
inaccurate. Deficiency may strongly depend on the value of eps.
  warnings.warn(message)
....../Users/rgommers/Code/scipy/scipy/interpolate/fitpack2.py:604:
UserWarning:
The required storage space exceeds the available storage space: nxest
or nyest too small, or s too small.
The weighted least-squares spline corresponds to the current set of
knots.
  warnings.warn(message)
......................K..K......................................................................................................................................../Users/rgommers/Code/scipy/scipy/io/matlab/mio.py:232:
FutureWarning: Using oned_as default value ('column') This will change to
'row' in future versions
  oned_as=oned_as)
............................................................................................................................................................................................................................................................................./Users/rgommers/Code/scipy/scipy/io/wavfile.py:31:
WavFileWarning: Unfamiliar format bytes
  warnings.warn("Unfamiliar format bytes", WavFileWarning)
/Users/rgommers/Code/scipy/scipy/io/wavfile.py:121: WavFileWarning: chunk
not understood
  warnings.warn("chunk not understood", WavFileWarning)
...............................................................................................................................................................................................................................SSSSSS......SSSSSS......SSSS.................................................................S.................................................../Users/rgommers/Code/scipy/scipy/linalg/decomp_qr.py:91:
ComplexWarning: Casting complex values to real discards the imaginary part
  qr, tau, work, info = geqrf(a1, lwork=lwork, overwrite_a=overwrite_a)
/Users/rgommers/Code/scipy/scipy/linalg/decomp_qr.py:125: ComplexWarning:
Casting complex values to real discards the imaginary part
  Q, work, info = gor_un_gqr(qqr, tau, lwork=lwork, overwrite_a=1)
......................../Users/rgommers/Code/scipy/scipy/linalg/decomp_schur.py:72:
ComplexWarning: Casting complex values to real discards the imaginary part
  result = gees(lambda x: None, a, lwork=result[-2][0],
overwrite_a=overwrite_a)
.....................................................................................................................................K.......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................SSSSSSSSSSS................................................................................................................................................................K...............................................................K...........................................................................................................................................................KK...............................................................................................................................................................................................................................................................................................................................................................................................................................K.K........................................................................................................................................................................................................................................................................................................................................................................................K........K.........SSSSSSS............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................S.......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
----------------------------------------------------------------------
Ran 4815 tests in 83.378s

OK (KNOWNFAIL=12, SKIP=36)
Out[1]: <nose.result.TextTestResult run=4815 errors=0 failures=0>

What's the reason for the almost identical test_fblas.py files in
> lib/blas/tests and linalg/tests by the way?
>
> Ralf
>
>
>
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