[SciPy-Dev] Errors with numpy-devel
Ralf Gommers
ralf.gommers at gmail.com
Mon Apr 21 15:11:57 EDT 2014
On Tue, Apr 15, 2014 at 9:19 PM, Nils Wagner <nils106 at googlemail.com> wrote:
> >>> from scipy import stats
> >>> stats.test()
> Running unit tests for scipy.stats
> NumPy version 1.9.0.dev-61c699e
> NumPy is installed in /home/nils/local/lib64/python2.7/site-packages/numpy
> SciPy version 0.15.0.dev-87df1db
> SciPy is installed in /home/nils/local/lib64/python2.7/site-packages/scipy
> Python version 2.7.3 (default, Apr 14 2012, 08:58:41) [GCC]
> nose version 1.3.1
>
> ...
>
> ======================================================================
> ERROR: test_gmean (test_mstats_basic.TestCompareWithStats)
>
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File
> "/home/nils/local/lib64/python2.7/site-packages/scipy/stats/tests/test_mstats_basic.py",
> line 763, in test_gmean
> rm = stats.mstats.gmean(abs(xm))
> File
> "/home/nils/local/lib64/python2.7/site-packages/scipy/stats/stats.py", line
> 516, in gmean
> log_a = np.log(a)
> File "/home/nils/local/lib64/python2.7/site-packages/numpy/ma/core.py",
> line 2837, in __array_wrap__
> d = filled(domain(*args), True)
> File "/home/nils/local/lib64/python2.7/site-packages/numpy/ma/core.py",
> line 795, in __call__
> return umath.less_equal(x, self.critical_value)
> RuntimeWarning: invalid value encountered in less_equal
>
> ======================================================================
> ERROR: test_hmean (test_mstats_basic.TestCompareWithStats)
>
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File
> "/home/nils/local/lib64/python2.7/site-packages/scipy/stats/tests/test_mstats_basic.py",
> line 775, in test_hmean
> rm = stats.mstats.hmean(abs(xm))
> File
> "/home/nils/local/lib64/python2.7/site-packages/scipy/stats/stats.py", line
> 562, in hmean
> if np.all(a > 0): # Harmonic mean only defined if greater than zero
> RuntimeWarning: invalid value encountered in greater
>
> ======================================================================
> ERROR: test_tmax (test_mstats_basic.TestCompareWithStats)
>
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File
> "/home/nils/local/lib64/python2.7/site-packages/scipy/stats/tests/test_mstats_basic.py",
> line 908, in test_tmax
> stats.mstats.tmax(xm,2.), 10)
> File
> "/home/nils/local/lib64/python2.7/site-packages/scipy/stats/mstats_basic.py",
> line 1383, in tmax
> am = trima(a, (None, upperlimit), (False, inclusive))
> File
> "/home/nils/local/lib64/python2.7/site-packages/scipy/stats/mstats_basic.py",
> line 1018, in trima
> condition |= (a > upper_lim)
> RuntimeWarning: invalid value encountered in greater
>
> ======================================================================
> ERROR: test_tmin (test_mstats_basic.TestCompareWithStats)
>
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File
> "/home/nils/local/lib64/python2.7/site-packages/scipy/stats/tests/test_mstats_basic.py",
> line 919, in test_tmin
> stats.mstats.tmin(xm,lowerlimit=-1.), 10)
> File
> "/home/nils/local/lib64/python2.7/site-packages/scipy/stats/mstats_basic.py",
> line 1376, in tmin
> am = trima(a, (lowerlimit, None), (inclusive, False))
> File
> "/home/nils/local/lib64/python2.7/site-packages/scipy/stats/mstats_basic.py",
> line 1013, in trima
> condition |= (a < lower_lim)
> RuntimeWarning: invalid value encountered in less
>
> ======================================================================
> ERROR: test_tsem (test_mstats_basic.TestCompareWithStats)
>
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File
> "/home/nils/local/lib64/python2.7/site-packages/scipy/stats/tests/test_mstats_basic.py",
> line 958, in test_tsem
> stats.mstats.tsem(xm,limits=(-2.,2.)),
> File
> "/home/nils/local/lib64/python2.7/site-packages/scipy/stats/mstats_basic.py",
> line 1393, in tsem
> am = trima(a.ravel(), limits, inclusive)
> File
> "/home/nils/local/lib64/python2.7/site-packages/scipy/stats/mstats_basic.py",
> line 1013, in trima
> condition |= (a < lower_lim)
> RuntimeWarning: invalid value encountered in less
>
> ======================================================================
> ERROR: test_zmap (test_mstats_basic.TestCompareWithStats)
>
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File
> "/home/nils/local/lib64/python2.7/site-packages/scipy/stats/tests/test_mstats_basic.py",
> line 927, in test_zmap
> zm = stats.mstats.zmap(xm,ym)
> File
> "/home/nils/local/lib64/python2.7/site-packages/scipy/stats/stats.py", line
> 2063, in zmap
> return (scores - mns) / sstd
> File "/home/nils/local/lib64/python2.7/site-packages/numpy/ma/core.py",
> line 3735, in __truediv__
> return true_divide(self, other)
> File "/home/nils/local/lib64/python2.7/site-packages/numpy/ma/core.py",
> line 1089, in __call__
> m |= filled(domain(da, db), True)
> File "/home/nils/local/lib64/python2.7/site-packages/numpy/ma/core.py",
> line 783, in __call__
> return umath.absolute(a) * self.tolerance >= umath.absolute(b)
> RuntimeWarning: invalid value encountered in greater_equal
>
> ======================================================================
> FAIL: test_example1a (test_morestats.TestAndersonKSamp)
>
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File
> "/home/nils/local/lib64/python2.7/site-packages/scipy/stats/tests/test_morestats.py",
> line 97, in test_example1a
> midrank=False)
> File
> "/home/nils/local/lib64/python2.7/site-packages/numpy/testing/utils.py",
> line 1593, in assert_warns
> % func.__name__)
> AssertionError: No warning raised when calling anderson_ksamp
>
> ======================================================================
> FAIL: test_tmean (test_mstats_basic.TestCompareWithStats)
>
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File
> "/home/nils/local/lib64/python2.7/site-packages/scipy/stats/tests/test_mstats_basic.py",
> line 901, in test_tmean
> assert_equal(stats.tmean(x),stats.mstats.tmean(xm))
> File
> "/home/nils/local/lib64/python2.7/site-packages/numpy/ma/testutils.py",
> line 100, in assert_equal
> raise AssertionError(msg)
> AssertionError:
> Items are not equal:
> ACTUAL: 0.040175456835823721
> DESIRED: 0.040175456835823714
>
>
> ======================================================================
> FAIL: test_trim (test_mstats_basic.TestTrimming)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File
> "/home/nils/local/lib64/python2.7/site-packages/scipy/stats/tests/test_mstats_basic.py",
> line 274, in test_trim
>
> assert_equal(trimx._mask.ravel(),[1]*20+[0]*70+[1]*20)
> File
> "/home/nils/local/lib64/python2.7/site-packages/numpy/ma/testutils.py",
> line 123, in assert_equal
> return assert_array_equal(actual, desired, err_msg)
> File
> "/home/nils/local/lib64/python2.7/site-packages/numpy/ma/testutils.py",
> line 196, in assert_array_equal
>
> header='Arrays are not equal')
> File
> "/home/nils/local/lib64/python2.7/site-packages/numpy/ma/testutils.py",
> line 189, in assert_array_compare
> verbose=verbose, header=header)
> File
> "/home/nils/local/lib64/python2.7/site-packages/numpy/testing/utils.py",
> line 660, in assert_array_compare
>
> raise AssertionError(msg)
> AssertionError:
> Arrays are not equal
>
> (mismatch 9.09090909091%)
> x: array([ True, True, True, True, True, True, True, True, True,
> True, True, True, True, True, True, True, True, True,
> True, True, False, False, False, False, False, False, False,...
> y: array([1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0,
> 0, 0,
> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
> 0,...
>
> ----------------------------------------------------------------------
> Ran 1957 tests in 50.047s
>
> FAILED (KNOWNFAIL=4, SKIP=3, errors=6, failures=3)
> <nose.result.TextTestResult run=1957 errors=6 failures=3>
>
>
>
> On Sun, Apr 13, 2014 at 10:58 PM, Ralf Gommers <ralf.gommers at gmail.com>wrote:
>
>>
>>
>>
>> On Sun, Apr 13, 2014 at 7:42 AM, Charles R Harris <
>> charlesr.harris at gmail.com> wrote:
>>
>>> Hi All,
>>>
>>> I get 75 errors and 3 failures when testing against current numpy on my
>>> machine. Most of the errors are due to either the deprecation of the binary
>>> '-' operator for booleans or to the deprecation of double ellipsis for
>>> indexing, i.e., '(..., ...)' . The remainder look like two numerical
>>> precision problems and one I can't immediately identify.
>>>
>>> The main question I have is what is the best way to deal with the
>>> deprecations?
>>>
>>
>> Fix them? It's not that much work; I'd like to still get that into 0.14.0
>> if possible. Will have a look.
>>
>> The QHull test I've seen fail randomly on various platforms, it has a
>> real issue. The other two look like the tests need adapting.
>>
>> Ralf
>>
>>
>>>
>>> FAIL: test_lsmr.TestLSMR.testBidiagonalA
>>> ----------------------------------------------------------------------
>>> Traceback (most recent call last):
>>> File "/usr/lib/python2.7/site-packages/nose/case.py", line 197, in
>>> runTest
>>> self.test(*self.arg)
>>> File
>>> "/home/charris/.local/lib/python2.7/site-packages/scipy/sparse/linalg/isolve/tests/test_lsmr.py",
>>> line 60, in testBidiagonalA
>>> self.assertCompatibleSystem(A,xtrue)
>>> File
>>> "/home/charris/.local/lib/python2.7/site-packages/scipy/sparse/linalg/isolve/tests/test_lsmr.py",
>>> line 40, in assertCompatibleSystem
>>> assert_almost_equal(norm(x - xtrue), 0, 6)
>>> File
>>> "/home/charris/.local/lib/python2.7/site-packages/numpy/testing/utils.py",
>>> line 486, in assert_almost_equal
>>> raise AssertionError(_build_err_msg())
>>> AssertionError:
>>> Arrays are not almost equal to 6 decimals
>>> ACTUAL: 6.048630163037888e-07
>>> DESIRED: 0
>>>
>>> ======================================================================
>>> FAIL: test_qhull.TestUtilities.test_degenerate_barycentric_transforms
>>> ----------------------------------------------------------------------
>>> Traceback (most recent call last):
>>> File "/usr/lib/python2.7/site-packages/nose/case.py", line 197, in
>>> runTest
>>> self.test(*self.arg)
>>> File
>>> "/home/charris/.local/lib/python2.7/site-packages/numpy/testing/decorators.py",
>>> line 146, in skipper_func
>>> return f(*args, **kwargs)
>>> File
>>> "/home/charris/.local/lib/python2.7/site-packages/scipy/spatial/tests/test_qhull.py",
>>> line 296, in test_degenerate_barycentric_transforms
>>> assert_(bad_count < 20, bad_count)
>>> File
>>> "/home/charris/.local/lib/python2.7/site-packages/numpy/testing/utils.py",
>>> line 50, in assert_
>>> raise AssertionError(smsg)
>>> AssertionError: 20
>>>
>>> ======================================================================
>>> FAIL: test_trim (test_mstats_basic.TestTrimming)
>>> ----------------------------------------------------------------------
>>> Traceback (most recent call last):
>>> File
>>> "/home/charris/.local/lib/python2.7/site-packages/scipy/stats/tests/test_mstats_basic.py",
>>> line 270, in test_trim
>>> assert_equal(trimx._mask.ravel(),[1]*20+[0]*70+[1]*20)
>>> File
>>> "/home/charris/.local/lib/python2.7/site-packages/numpy/ma/testutils.py",
>>> line 123, in assert_equal
>>> return assert_array_equal(actual, desired, err_msg)
>>> File
>>> "/home/charris/.local/lib/python2.7/site-packages/numpy/ma/testutils.py",
>>> line 196, in assert_array_equal
>>> header='Arrays are not equal')
>>> File
>>> "/home/charris/.local/lib/python2.7/site-packages/numpy/ma/testutils.py",
>>> line 189, in assert_array_compare
>>> verbose=verbose, header=header)
>>> File
>>> "/home/charris/.local/lib/python2.7/site-packages/numpy/testing/utils.py",
>>> line 660, in assert_array_compare
>>> raise AssertionError(msg)
>>> AssertionError:
>>> Arrays are not equal
>>>
>>> (mismatch 9.09090909091%)
>>> x: array([ True, True, True, True, True, True, True, True, True,
>>> True, True, True, True, True, True, True, True, True,
>>> True, True, False, False, False, False, False, False, False,...
>>> y: array([1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
>>> 0, 0, 0,
>>> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
>>> 0,
>>> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
>>> 0,...
>>>
>>>
>>>
Except for the Qhull one, all of these should be fixed by
https://github.com/scipy/scipy/pull/3564.
Ralf
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