[SciPy-Dev] Schur decomposition test failure under Python 2.5

Ralf Gommers ralf.gommers@googlemail....
Mon Nov 7 16:52:30 CST 2011


On Mon, Nov 7, 2011 at 10:22 PM, Ralf Gommers
<ralf.gommers@googlemail.com>wrote:

>
>
> On Mon, Nov 7, 2011 at 3:47 AM, Bruce Southey <bsouthey@gmail.com> wrote:
>
>> On Sun, Nov 6, 2011 at 2:22 AM, Ralf Gommers
>> <ralf.gommers@googlemail.com> wrote:
>> >
>> >
>> > On Sun, Nov 6, 2011 at 3:26 AM, Bruce Southey <bsouthey@gmail.com>
>> wrote:
>> >>
>> >> On Sat, Nov 5, 2011 at 1:40 PM, Ralf Gommers
>> >> <ralf.gommers@googlemail.com> wrote:
>> >> > Hi,
>> >> >
>> >> > There's a problem with schur(.., sort='lhp') under Python 2.5 that
>> seems
>> >> > to
>> >> > be related to the Lapack function gees:
>> >> > http://projects.scipy.org/scipy/ticket/1555
>> >> >
>> >> > It would be great if someone could have a look at this for the 0.10.0
>> >> > release, but if not I'll mark it as a knownfailure because it's not a
>> >> > regression.
>> >> >
>> >> > Ralf
>> >> >
>> >> >
>> >> > _______________________________________________
>> >> > SciPy-Dev mailing list
>> >> > SciPy-Dev@scipy.org
>> >> > http://mail.scipy.org/mailman/listinfo/scipy-dev
>> >> >
>> >> >
>> >> I have only tested the RC on my 32-bit Windows install using the
>> >> provided binary.
>> >> I get the test_decomp.TestSchur and syntax error in
>> test_distributions.py.
>> >>
>> >> But buried in the test output (when run within command line Python but
>> >> not under IDLE) is this:
>> >> "capi_return is NULL
>> >> Call-back cb_dselect_in_dgees__user__routines failed."
>> >>
>> > That's the cause of the TestSchur failure.
>> >
>> >>
>> >> This also appears with the current dev version under Linux.
>> >>
>> >> Bruce
>> >>
>> >> $ python2.5 test_decomp.py
>> >>
>> >>
>> ................................................................................................................................................capi_return
>> >> is NULL
>> >> Call-back cb_dselect_in_dgees__user__routines failed.
>> >>
>> >>
>> E.....................................................................................................................................E
>> >> ======================================================================
>> >> ERROR: test_sort (test_decomp.TestSchur)
>> >> ----------------------------------------------------------------------
>> >> Traceback (most recent call last):
>> >>  File
>> >>
>> "/home/bsouthey/python/scipystuff/git/scipy/scipy/linalg/tests/test_decomp.py",
>> >> line 1498, in test_sort
>> >>    s,u,sdim = schur(a,sort='lhp')
>> >>  File
>> >> "/usr/local/lib/python2.5/site-packages/scipy/linalg/decomp_schur.py",
>> >> line 118, in schur
>> >>    sort_t=sort_t)
>> >>  File
>> >> "/usr/local/lib/python2.5/site-packages/scipy/linalg/decomp_schur.py",
>> >> line 106, in <lambda>
>> >>    sfunction = lambda x: (x.real < 0.0)
>> >> AttributeError: 'float' object has no attribute 'real'
>> >>
>> >> ======================================================================
>> >> ERROR: test_decomp.test_lapack_misaligned
>> >> ----------------------------------------------------------------------
>> >> Traceback (most recent call last):
>> >>  File "/usr/local/lib/python2.5/site-packages/nose/case.py", line
>> >> 186, in runTest
>> >>    self.test(*self.arg)
>> >>  File
>> >> "/usr/local/lib/python2.5/site-packages/numpy/testing/decorators.py",
>> >> line 213, in knownfailer
>> >>    raise KnownFailureTest, msg
>> >> KnownFailureTest: Ticket #1152, triggers a segfault in rare cases.
>> >>
>> >> ----------------------------------------------------------------------
>> >
>> > This one is new. Is this python 2.5 on Linux? Is the error
>> reproduceable?
>> >
>> > Ralf
>> >
>> Sorry as it is a known failure just that running the test file does
>> not pickup the declaration.
>>
>
> Odd. @dec.knownfailureif(True, "...") doesn't work. Code looks fine to me,
> can't reproduce it.
>
>
>> I am presuming others will test Python2.6, Python2.7 and Python3.1.
>>
>> This Python3.2 error:
>> =====================================================================
>> ERROR: Failure: AttributeError ('module' object has no attribute
>> 'FileType')
>> ----------------------------------------------------------------------
>> Traceback (most recent call last):
>>   File
>> "/usr/lib/python3.2/site-packages/nose-1.0.0-py3.2.egg/nose/failure.py",
>> line 37, in runTest
>>    raise self.exc_class(self.exc_val).with_traceback(self.tb)
>>  File
>> "/usr/lib/python3.2/site-packages/nose-1.0.0-py3.2.egg/nose/loader.py",
>> line 390, in loadTestsFromName
>>    addr.filename, addr.module)
>>   File
>> "/usr/lib/python3.2/site-packages/nose-1.0.0-py3.2.egg/nose/importer.py",
>> line 39, in importFromPath
>>    return self.importFromDir(dir_path, fqname)
>>   File
>> "/usr/lib/python3.2/site-packages/nose-1.0.0-py3.2.egg/nose/importer.py",
>> line 86, in importFromDir
>>    mod = load_module(part_fqname, fh, filename, desc)
>>   File "/usr/lib64/python3.2/site-packages/scipy/weave/__init__.py",
>> line 22, in <module>
>>    from .blitz_tools import blitz
>>  File "/usr/lib64/python3.2/site-packages/scipy/weave/blitz_tools.py",
>> line 6, in <module>
>>    from . import converters
>>  File "/usr/lib64/python3.2/site-packages/scipy/weave/converters.py",
>> line 19, in <module>
>>    c_spec.file_converter(),
>>  File "/usr/lib64/python3.2/site-packages/scipy/weave/c_spec.py",
>> line 74, in __init__
>>    self.init_info()
>>  File "/usr/lib64/python3.2/site-packages/scipy/weave/c_spec.py",
>> line 264, in init_info
>>    self.matching_types = [types.FileType]
>> AttributeError: 'module' object has no attribute 'FileType'
>>
>> ----------------------------------------------------------------------
>>
>> Due to weave not being py3k compatible. Perhaps we should raise a clearer
> error here.
>
>
>>
>> Is Python2.4 still being supported as there are 8 errors (see below)?
>>
>> It is. Just kind of hard to support it in practice with no one using it
> and no buildbot. Thanks for finding these errors.
>
>>
>> Bruce
>>
>> $ python2.4 -c "import scipy; scipy.test()"
>> Running unit tests for scipy
>> NumPy version 2.0.0.dev-93236a2
>> NumPy is installed in /usr/local/lib/python2.4/site-packages/numpy
>> SciPy version 0.10.0rc1
>> SciPy is installed in /usr/local/lib/python2.4/site-packages/scipy
>> Python version 2.4.6 (#1, Sep 13 2010, 15:54:12) [GCC 4.4.4 20100630
>> (Red Hat 4.4.4-10)]
>> nose version 0.11.2
>> /usr/local/lib/python2.4/site-packages/scipy/maxentropy/__init__.py:19:
>> DeprecationWarning:
>> The scipy.maxentropy module is deprecated in scipy 0.10, and scheduled to
>> be
>> removed in 0.11.
>>
>> If you are using some of the functionality in this module and are of the
>> opinion that it should be kept or moved somewhere - or you are even
>> interested
>> to maintain/improve this whole module - please ask on the scipy-dev
>> mailing
>> list.
>>
>> The logsumexp function has already been moved to scipy.misc.
>>  DeprecationWarning)
>>
>> ............................................................................................................................................................................................................................K............................................................................................................/usr/local/lib/python2.4/site-packages/scipy/interpolate/fitpack2.py:674:
>> 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)
>>
>> ....../usr/local/lib/python2.4/site-packages/scipy/interpolate/fitpack2.py:605:
>> 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................................................................................................................................................................................................................................................................................................................................................................................................................................................../usr/local/lib/python2.4/site-packages/scipy/io/wavfile.py:31:
>> WavFileWarning: Unfamiliar format bytes
>>  warnings.warn("Unfamiliar format bytes", WavFileWarning)
>> /usr/local/lib/python2.4/site-packages/scipy/io/wavfile.py:121:
>> WavFileWarning: chunk not understood
>>  warnings.warn("chunk not understood", WavFileWarning)
>>
>> ...............................................................................................................................................................................................................................SSSSSS......SSSSSS......SSSS......................................................................................................................................................................................................capi_return
>> is NULL
>> Call-back cb_dselect_in_dgees__user__routines failed.
>>
>> E.....................................................................................................................................K......................................................................................................................................................................................................SSSSS............S............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................E...........................................K...............................................SSSSSSSSSSS.......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................K...............................................................K...........................................................................................E....................E.......E.....E.......E....................KK.............................................................................................................................................................................................................................................................................................................................................................................................................................................K.K.............................................................................................................................................................................................................................................................................................................................................................................................K........K..............SSSSSSS....................................................................................................................................................../usr/local/lib/python2.4/site-packages/scipy/stats/distributions.py:1258:
>> DeprecationWarning: putmask has been deprecated. Use copyto with
>> 'where' as the mask instead
>>  putmask(output,(1-cond0)*array(cond1,bool),self.badvalue)
>>
>> ....SE.....................................................................................................................................................................................................................................................................................................................................................................................................................
>> ======================================================================
>> ERROR: test_sort (test_decomp.TestSchur)
>> ----------------------------------------------------------------------
>> Traceback (most recent call last):
>>   File
>> "/usr/local/lib/python2.4/site-packages/scipy/linalg/tests/test_decomp.py",
>> line 1230, in test_sort
>>     s,u,sdim = schur(a,sort='lhp')
>>   File
>> "/usr/local/lib/python2.4/site-packages/scipy/linalg/decomp_schur.py",
>> line 118, in schur
>>    sort_t=sort_t)
>>   File
>> "/usr/local/lib/python2.4/site-packages/scipy/linalg/decomp_schur.py",
>> line 106, in <lambda>
>>    sfunction = lambda x: (x.real < 0.0)
>> AttributeError: 'float' object has no attribute 'real'
>>
>
> http://projects.scipy.org/scipy/ticket/1555
>
>>
>> ======================================================================
>> ERROR: test_signaltools.TestHilbert2.test_bad_args
>> ----------------------------------------------------------------------
>> Traceback (most recent call last):
>>   File "/usr/local/lib/python2.4/site-packages/nose/case.py", line
>> 186, in runTest
>>    self.test(*self.arg)
>>  File
>> "/usr/local/lib/python2.4/site-packages/scipy/signal/tests/test_signaltools.py",
>> line 708, in test_bad_args
>>    assert_raises(ValueError, hilbert2, x, N=(2,0))
>>  File "/usr/local/lib/python2.4/site-packages/numpy/testing/utils.py",
>> line 1053, in assert_raises
>>    return nose.tools.assert_raises(*args,**kwargs)
>>  File "/usr/local/lib/python2.4/unittest.py", line 320, in
>> failUnlessRaises
>>    callableObj(*args, **kwargs)
>>  File
>> "/usr/local/lib/python2.4/site-packages/scipy/signal/signaltools.py",
>> line 746, in hilbert2
>>    elif len(N) != 2 or any(n <= 0 for n in N):
>> NameError: name 'any' is not defined
>>
>
> Will push a fix for that in a minute.
>
>>
>> ======================================================================
>> ERROR: adding a dense matrix to a sparse matrix
>> ----------------------------------------------------------------------
>> Traceback (most recent call last):
>>   File
>> "/usr/local/lib/python2.4/site-packages/scipy/sparse/tests/test_base.py",
>> line 519, in test_add_dense
>>    sum1 = self.dat + self.datsp
>>  File "/usr/local/lib/python2.4/site-packages/scipy/sparse/dok.py",
>> line 133, in __getitem__
>>    raise TypeError('index must be a pair of integers or slices')
>> TypeError: index must be a pair of integers or slices
>>
>> ======================================================================
>> ERROR: test_matmat_sparse (test_base.TestDOK)
>> ----------------------------------------------------------------------
>> Traceback (most recent call last):
>>   File
>> "/usr/local/lib/python2.4/site-packages/scipy/sparse/tests/test_base.py",
>> line 417, in test_matmat_sparse
>>    assert_array_almost_equal( a2*bsp, a*b)
>>  File "/usr/local/lib/python2.4/site-packages/scipy/sparse/dok.py",
>> line 133, in __getitem__
>>    raise TypeError('index must be a pair of integers or slices')
>> TypeError: index must be a pair of integers or slices
>>
>> ======================================================================
>> ERROR: test_radd (test_base.TestDOK)
>> ----------------------------------------------------------------------
>> Traceback (most recent call last):
>>   File
>> "/usr/local/lib/python2.4/site-packages/scipy/sparse/tests/test_base.py",
>> line 279, in test_radd
>>    c = a + b
>>  File "/usr/local/lib/python2.4/site-packages/scipy/sparse/dok.py",
>> line 133, in __getitem__
>>    raise TypeError('index must be a pair of integers or slices')
>> TypeError: index must be a pair of integers or slices
>>
>> ======================================================================
>> ERROR: test_rsub (test_base.TestDOK)
>> ----------------------------------------------------------------------
>> Traceback (most recent call last):
>>   File
>> "/usr/local/lib/python2.4/site-packages/scipy/sparse/tests/test_base.py",
>> line 290, in test_rsub
>>    assert_array_equal((self.dat -
>> self.datsp),[[0,0,0,0],[0,0,0,0],[0,0,0,0]])
>>  File "/usr/local/lib/python2.4/site-packages/scipy/sparse/dok.py",
>> line 133, in __getitem__
>>    raise TypeError('index must be a pair of integers or slices')
>> TypeError: index must be a pair of integers or slices
>>
>> ======================================================================
>> ERROR: subtracting a dense matrix to/from a sparse matrix
>> ----------------------------------------------------------------------
>> Traceback (most recent call last):
>>   File
>> "/usr/local/lib/python2.4/site-packages/scipy/sparse/tests/test_base.py",
>> line 527, in test_sub_dense
>>    sum1 = 3*self.dat - self.datsp
>>  File "/usr/local/lib/python2.4/site-packages/scipy/sparse/dok.py",
>> line 133, in __getitem__
>>    raise TypeError('index must be a pair of integers or slices')
>> TypeError: index must be a pair of integers or slices
>>
>> These are odd. A dok_matrix can't be indexed with a single integer, which
> causes errors when we do ``obj + dokmatrix`` when obj is an ndarray or
> matrix. It looks to me like indexing with single integers should trigger a
> conversion to a dense array or something like that.
>

dok_matrix.__radd__ (which has the todense() call) is called for Python >=
2.5, but not for 2.4. I can't find anything related to this in the "what's
new in python 2.5" doc.

Ralf


Also I don't understand why it doesn't fail for other Python versions. Are
> numpy arrays somehow aware of sparse matrix details?
>
> If anyone with more knowledge of how this sparse matrix arithmetic is
> supposed to work can explain or have a look, that would be great.
>
> Ralf
>
>
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