[SciPy-Dev] ANN: SciPy 0.8.0 beta 1

Derek Homeier derek@astro.physik.uni-goettingen...
Fri Jun 11 18:05:52 CDT 2010


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])

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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