[SciPy-Dev] ANN: SciPy 0.8.0 beta 1
josef.pktd at gmail.com
josef.pktd at gmail.com
Fri Jun 11 19:37:49 EDT 2010
On Fri, Jun 11, 2010 at 7:05 PM, Derek Homeier
<derek at 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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