[SciPy-Dev] ANN: SciPy 0.8.0 beta 1

josef.pktd@gmai... josef.pktd@gmai...
Fri Jun 11 18:37:49 CDT 2010


On Fri, Jun 11, 2010 at 7:05 PM, Derek Homeier
<derek@astro.physik.uni-goettingen.de> wrote:
> Hi,
>
> On Jun 8, 2010, at 5:40 PM, Bruce Southey wrote:
>
>> I got 2 errors and 1 failure when I installed the beta using Python 2.6
>> (Linux 64-bit) with numpy '2.0.0.dev8445' .
>>
>> Can we get a fix for ticket 1152 or at least mark it as known?
>> http://projects.scipy.org/scipy/ticket/1152
>>
>> The others are below.
>>
>> There are also a number of overflow warnings that should be checked and
>> avoided. The same warnings also occur in test_continuous_basic for
>> certain distributions.
>> test_iv_cephes_vs_amos (test_basic.TestBessel) ... Warning: overflow
>> encountered in iv
>> Warning: overflow encountered in iv
>> Warning: invalid value encountered in isinf
>>
> FYI, this test fails on MacOS X 10.5  darwin-ppc /w numpy 1.4.1 both in scipy 0.7.2 and 0.8.0b1:
>
> FAIL: test_iv_cephes_vs_amos (test_basic.TestBessel)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>  File "/sw/lib/python2.6/site-packages/scipy/special/tests/test_basic.py", line 1690, in test_iv_cephes_vs_amos
>    self.check_cephes_vs_amos(iv, iv, rtol=1e-12, atol=1e-305)
>  File "/sw/lib/python2.6/site-packages/scipy/special/tests/test_basic.py", line 1671, in check_cephes_vs_amos
>    assert_tol_equal(c1, c2, err_msg=(v, z), rtol=rtol, atol=atol)
>  File "/sw/lib/python2.6/site-packages/scipy/special/tests/test_basic.py", line 38, in assert_tol_equal
>    verbose=verbose, header=header)
>  File "/sw/lib/python2.6/site-packages/numpy/testing/utils.py", line 609, in assert_array_compare
>    raise AssertionError(msg)
> AssertionError:
> Not equal to tolerance rtol=1e-12, atol=1e-305
> (-120, 700.60000000000002)
> (mismatch 100.0%)
>  x: array(9.7596849076267918e+297)
>  y: array((9.7596849444884899e+297+0j))
>
> while the following also fails on darwin-i386:
>
> FAIL: test_iv_cephes_vs_amos_mass_test (test_basic.TestBessel)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>  File "/sw/lib/python2.6/site-packages/scipy/special/tests/test_basic.py", line 1712, in test_iv_cephes_vs_amos_mass_test
>    assert dc[k] < 1e-9, (iv(v[k], x[k]), iv(v[k], x[k]+0j))
> AssertionError: (1.8320048963545875e+306, (inf+0j))
>
> - following Chuck Harris' suggestion, should I try if updating to Numpy revision r8455
> removes the failures as well?
>
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
> This next one fails on 0.8.0b1/darwin-i386 as well, but with twice the mismatch (1.8018...%):
>
>> FAIL: test_random_real (test_basic.TestSingleIFFT)
>> ----------------------------------------------------------------------
>> Traceback (most recent call last):
>>   File
>> "/usr/lib64/python2.6/site-packages/scipy/fftpack/tests/test_basic.py",
>> line 205, in test_random_real
>>     assert_array_almost_equal (y1, x)
>>   File "/usr/lib64/python2.6/site-packages/numpy/testing/utils.py",
>> line 774, in assert_array_almost_equal
>>     header='Arrays are not almost equal')
>>   File "/usr/lib64/python2.6/site-packages/numpy/testing/utils.py",
>> line 618, in assert_array_compare
>>     raise AssertionError(msg)
>> AssertionError:
>> Arrays are not almost equal
>>
>> (mismatch 0.900900900901%)
>>  x: array([ 0.41364330 +5.90676663e-09j,  0.80715483 +2.64462052e-08j,
>>         0.05271048 -3.67830459e-08j,  0.72591031 -9.31092980e-09j,
>>         0.35162351 +1.40012923e-09j,  0.17632297 -1.25899486e-08j,...
>>  y: array([ 0.41364321,  0.80715483,  0.05271063,  0.72591019,  0.35162321,
>>         0.17632306,  0.3850981 ,  0.75712842,  0.68898875,  0.52632052,
>>         0.69728118,  0.68721569,  0.69135427,  0.34033701,  0.65788335,...
>>>> raise AssertionError('\nArrays are not almost equal\n\n(mismatch
>> 0.900900900901%)\n x: array([ 0.41364330 +5.90676663e-09j,  0.80715483
>> +2.64462052e-08j,\n        0.05271048 -3.67830459e-08j,  0.72591031
>> -9.31092980e-09j,\n        0.35162351 +1.40012923e-09j,  0.17632297
>> -1.25899486e-08j,...\n y: array([ 0.41364321,  0.80715483,  0.05271063,
>> 0.72591019,  0.35162321,\n        0.17632306,  0.3850981 ,  0.75712842,
>> 0.68898875,  0.52632052,\n        0.69728118,  0.68721569,  0.69135427,
>> 0.34033701,  0.65788335,...')
>
> The Ticket #1124 did not occur on MacOS 10.5,
>
> but a number of other tests failed on various MacOS architectures, the following one
> on darwin-ppc in 0.7.2 and 0.8.0b1
>  (while I don't understand the alleged mismatch...):
>
> FAIL: test_stats.test_kstest
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>  File "/sw/lib/python2.6/site-packages/nose/case.py", line 186, in runTest
>    self.test(*self.arg)
>  File "/sw/lib/python2.6/site-packages/scipy/stats/tests/test_stats.py", line 1078, in test_kstest
>    np.array((0.0072115233216310994, 0.98531158590396228)), 14)
>  File "/sw/lib/python2.6/site-packages/numpy/testing/utils.py", line 441, in assert_almost_equal
>    return assert_array_almost_equal(actual, desired, decimal, err_msg)
>  File "/sw/lib/python2.6/site-packages/numpy/testing/utils.py", line 765, in assert_array_almost_equal
>    header='Arrays are not almost equal')
>  File "/sw/lib/python2.6/site-packages/numpy/testing/utils.py", line 609, in assert_array_compare
>    raise AssertionError(msg)
> AssertionError:
> Arrays are not almost equal
>
> (mismatch 100.0%)
>  x: array([ 0.007,  0.985])
>  y: array([ 0.007,  0.985])

maybe the precision (decimal 14) is too high for this test across platforms

Could you check how large the difference is ?

np.random.seed(987654321)
x = stats.norm.rvs(loc=0.2, size=100)
np.array(stats.kstest(x,'norm', alternative = 'greater')) -
                np.array((0.0072115233216310994, 0.98531158590396228))

(my line numbers differ, but this should be the right test given your numbers)

Thanks,

Josef

>
> while the next three are new in 0.8.0b1 / darwin-ppc:
>
> FAIL: test_data.test_boost(<Data for gamma: test_gamma_data_ipp-near_m55>,)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>  File "/sw/lib/python2.6/site-packages/nose/case.py", line 186, in runTest
>    self.test(*self.arg)
>  File "/sw/lib/python2.6/site-packages/scipy/special/tests/test_data.py", line 205, in _test_factory
>    test.check(dtype=dtype)
>  File "/sw/lib/python2.6/site-packages/scipy/special/tests/testutils.py", line 187, in check
>    assert False, "\n".join(msg)
> AssertionError:
> Max |adiff|: 5.56451e-80
> Max |rdiff|: 6.01399e-12
> Bad results for the following points (in output 0):
>                        -55.25 =>          1.281342652143248e-73 !=         1.2813426521356121e-73  (rdiff         5.9592794108831318e-12)
>                      -55.0625 =>         9.8673260749254454e-73 !=         9.8673260748719804e-73  (rdiff         5.4183854671083142e-12)
>                    -55.015625 =>          4.736069454765531e-72 !=         4.7360694547400013e-72  (rdiff         5.3904770710359471e-12)
>                 -55.001953125 =>         4.0011527026054843e-71 !=         4.0011527025839184e-71  (rdiff         5.3899101047365405e-12)
>                -55.0009765625 =>         8.0337165791763099e-71 !=         8.0337165791330061e-71  (rdiff          5.390260882973932e-12)
>            -55.00006103515625 =>         1.2901278999535244e-69 !=         1.2901278999465708e-69  (rdiff         5.3898362867905277e-12)
>           -55.000015258789062 =>         5.1614604487935911e-69 !=         5.1614604487657727e-69  (rdiff         5.3896432998251817e-12)
>           -55.000007629394531 =>         1.0323237221382923e-68 !=         1.0323237221327282e-68  (rdiff         5.3898770611534905e-12)
>           -54.999992370605469 =>        -1.0323869903952338e-68 !=        -1.0323869903896693e-68  (rdiff         5.3899456366789772e-12)
>           -54.999969482421875 =>        -2.5812047538146166e-69 !=        -2.5812047538007038e-69  (rdiff         5.3900484385549852e-12)
>              -54.999755859375 =>         -3.229275765714629e-70 !=        -3.2292757656972238e-70  (rdiff         5.3898088494869903e-12)
>               -54.99951171875 =>        -1.6162223904478387e-70 !=        -1.6162223904391274e-70  (rdiff         5.3898993756420872e-12)
>                 -54.998046875 =>        -4.0644220032500644e-71 !=        -4.0644220032281559e-71  (rdiff         5.3903083062977191e-12)
>                   -54.9921875 =>        -1.0403990765960148e-71 !=         -1.040399076590406e-71  (rdiff          5.391034204122906e-12)
>                    -54.984375 =>        -5.3694203178537616e-72 !=        -5.3694203178248015e-72  (rdiff         5.3935130122571759e-12)
>                      -54.9375 =>        -1.6301847489550233e-72 !=        -1.6301847489461702e-72  (rdiff         5.4307621029371105e-12)
>                       -54.875 =>        -1.0680846658730133e-72 !=        -1.0680846658670925e-72  (rdiff         5.5434016349406124e-12)
>                       -54.875 =>        -1.0680846658730133e-72 !=        -1.0680846658670925e-72  (rdiff         5.5434016349406124e-12)
>                        -54.75 =>        -9.5458361856825864e-73 !=        -9.5458361856251778e-73  (rdiff          6.013992626968188e-12)
>                       -54.625 =>        -1.2061864756549609e-72 !=        -1.2061864756493961e-72  (rdiff         4.6135414163673135e-12)
>
> ======================================================================
> FAIL: test_data.test_boost(<Data for gammaincinv: gamma_inv_big_data_ipp-gamma_inv_big_data>,)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>  File "/sw/lib/python2.6/site-packages/nose/case.py", line 186, in runTest
>    self.test(*self.arg)
>  File "/sw/lib/python2.6/site-packages/scipy/special/tests/test_data.py", line 205, in _test_factory
>    test.check(dtype=dtype)
>  File "/sw/lib/python2.6/site-packages/scipy/special/tests/testutils.py", line 187, in check
>    assert False, "\n".join(msg)
> AssertionError:
> Max |adiff|: 39782.8
> Max |rdiff|: 1
> Bad results for the following points (in output 0):
>                   40010.84375             0.12698681652545929 =>                            0.0 !=             39782.764004009827  (rdiff                            1.0)
>
> ERROR: test_wavfile.test_read_1
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>  File "/sw/lib/python2.6/site-packages/nose/case.py", line 186, in runTest
>    self.test(*self.arg)
>  File "/sw/lib/python2.6/site-packages/scipy/io/tests/test_wavfile.py", line 12, in test_read_1
>    rate, data = wavfile.read(datafile('test-44100-le-1ch-4bytes.wav'))
>  File "/sw/lib/python2.6/site-packages/scipy/io/wavfile.py", line 124, in read
>    return rate, data
> UnboundLocalError: local variable 'data' referenced before assignment
>
> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
> Finally on MacOS 10.6 / darwin-x86_64 these additional failures occur since 0.7.2:
>
> ERROR: test_complex_nonsymmetric_modes (test_arpack.TestEigenComplexNonSymmetric)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>  File "/sw/lib/python2.6/site-packages/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py", line 267, in test_complex_nonsymmetric_modes
>    self.eval_evec(m,typ,k,which)
>  File "/sw/lib/python2.6/site-packages/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py", line 248, in eval_evec
>    eval,evec=eigen(a,k,which=which)
>  File "/sw/lib/python2.6/site-packages/scipy/sparse/linalg/eigen/arpack/arpack.py", line 397, in eigen
>    params.iterate()
>  File "/sw/lib/python2.6/site-packages/scipy/sparse/linalg/eigen/arpack/arpack.py", line 222, in iterate
>    raise RuntimeError("Error info=%d in arpack" % self.info)
> RuntimeError: Error info=-8 in arpack
>
> ======================================================================
> ERROR: test_nonsymmetric_modes (test_arpack.TestEigenNonSymmetric)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>  File "/sw/lib/python2.6/site-packages/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py", line 204, in test_nonsymmetric_modes
>    self.eval_evec(m,typ,k,which)
>  File "/sw/lib/python2.6/site-packages/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py", line 186, in eval_evec
>    eval,evec=eigen(a,k,which=which,**kwds)
>  File "/sw/lib/python2.6/site-packages/scipy/sparse/linalg/eigen/arpack/arpack.py", line 397, in eigen
>    params.iterate()
>  File "/sw/lib/python2.6/site-packages/scipy/sparse/linalg/eigen/arpack/arpack.py", line 222, in iterate
>    raise RuntimeError("Error info=%d in arpack" % self.info)
> RuntimeError: Error info=-8 in arpack
>
> ======================================================================
> ERROR: test_starting_vector (test_arpack.TestEigenNonSymmetric)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>  File "/sw/lib/python2.6/site-packages/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py", line 214, in test_starting_vector
>    self.eval_evec(self.symmetric[0],typ,k,which='LM',v0=v0)
>  File "/sw/lib/python2.6/site-packages/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py", line 186, in eval_evec
>    eval,evec=eigen(a,k,which=which,**kwds)
>  File "/sw/lib/python2.6/site-packages/scipy/sparse/linalg/eigen/arpack/arpack.py", line 397, in eigen
>    params.iterate()
>  File "/sw/lib/python2.6/site-packages/scipy/sparse/linalg/eigen/arpack/arpack.py", line 222, in iterate
>    raise RuntimeError("Error info=%d in arpack" % self.info)
> RuntimeError: Error info=-8 in arpack
>
> ======================================================================
> FAIL: test_complex_symmetric_modes (test_arpack.TestEigenComplexSymmetric)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>  File "/sw/lib/python2.6/site-packages/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py", line 156, in test_complex_symmetric_modes
>    self.eval_evec(self.symmetric[0],typ,k,which)
>  File "/sw/lib/python2.6/site-packages/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py", line 145, in eval_evec
>    assert_array_almost_equal(eval,exact_eval,decimal=_ndigits[typ])
>  File "/sw/lib/python2.6/site-packages/numpy/testing/utils.py", line 765, in assert_array_almost_equal
>    header='Arrays are not almost equal')
>  File "/sw/lib/python2.6/site-packages/numpy/testing/utils.py", line 609, in assert_array_compare
>    raise AssertionError(msg)
> AssertionError:
> Arrays are not almost equal
>
> (mismatch 100.0%)
>  x: array([ 1.07188725 +6.23436023e-08j,  4.91291142 -3.25412906e-08j], dtype=complex64)
>  y: array([ 5.+0.j,  6.+0.j], dtype=complex64)
>
> plus this last one, new in 0.8.0b1:
>
> ======================================================================
> FAIL: test_definition (test_basic.TestIfftnDouble)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>  File "/sw/lib/python2.6/site-packages/scipy/fftpack/tests/test_basic.py", line 498, in test_definition
>    assert_array_almost_equal_nulp(ifftn(x),direct_idftn(x),self.maxnlp)
>  File "/sw/lib/python2.6/site-packages/numpy/testing/utils.py", line 1116, in assert_array_almost_equal_nulp
>    raise AssertionError(msg)
> AssertionError: X and Y are not equal to 2000 ULP
>
>
> HTH,
>                                                        Derek
>
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