<div dir="ltr">>>> from scipy import stats<br>>>> stats.test()<br>Running unit tests for scipy.stats<br>NumPy version 1.9.0.dev-61c699e<br>NumPy is installed in /home/nils/local/lib64/python2.7/site-packages/numpy<br>
SciPy version 0.15.0.dev-87df1db<br>SciPy is installed in /home/nils/local/lib64/python2.7/site-packages/scipy<br>Python version 2.7.3 (default, Apr 14 2012, 08:58:41) [GCC]<br>nose version 1.3.1<br><br>...<br><br>======================================================================<br>
ERROR: test_gmean (test_mstats_basic.TestCompareWithStats)<br>----------------------------------------------------------------------<br>Traceback (most recent call last):<br> File "/home/nils/local/lib64/python2.7/site-packages/scipy/stats/tests/test_mstats_basic.py", line 763, in test_gmean<br>
rm = stats.mstats.gmean(abs(xm))<br> File "/home/nils/local/lib64/python2.7/site-packages/scipy/stats/stats.py", line 516, in gmean<br> log_a = np.log(a)<br> File "/home/nils/local/lib64/python2.7/site-packages/numpy/ma/core.py", line 2837, in __array_wrap__<br>
d = filled(domain(*args), True)<br> File "/home/nils/local/lib64/python2.7/site-packages/numpy/ma/core.py", line 795, in __call__<br> return umath.less_equal(x, self.critical_value)<br>RuntimeWarning: invalid value encountered in less_equal<br>
<br>======================================================================<br>ERROR: test_hmean (test_mstats_basic.TestCompareWithStats)<br>----------------------------------------------------------------------<br>Traceback (most recent call last):<br>
File "/home/nils/local/lib64/python2.7/site-packages/scipy/stats/tests/test_mstats_basic.py", line 775, in test_hmean<br> rm = stats.mstats.hmean(abs(xm))<br> File "/home/nils/local/lib64/python2.7/site-packages/scipy/stats/stats.py", line 562, in hmean<br>
if np.all(a > 0): # Harmonic mean only defined if greater than zero<br>RuntimeWarning: invalid value encountered in greater<br><br>======================================================================<br>ERROR: test_tmax (test_mstats_basic.TestCompareWithStats)<br>
----------------------------------------------------------------------<br>Traceback (most recent call last):<br> File "/home/nils/local/lib64/python2.7/site-packages/scipy/stats/tests/test_mstats_basic.py", line 908, in test_tmax<br>
stats.mstats.tmax(xm,2.), 10)<br> File "/home/nils/local/lib64/python2.7/site-packages/scipy/stats/mstats_basic.py", line 1383, in tmax<br> am = trima(a, (None, upperlimit), (False, inclusive))<br> File "/home/nils/local/lib64/python2.7/site-packages/scipy/stats/mstats_basic.py", line 1018, in trima<br>
condition |= (a > upper_lim)<br>RuntimeWarning: invalid value encountered in greater<br><br>======================================================================<br>ERROR: test_tmin (test_mstats_basic.TestCompareWithStats)<br>
----------------------------------------------------------------------<br>Traceback (most recent call last):<br> File "/home/nils/local/lib64/python2.7/site-packages/scipy/stats/tests/test_mstats_basic.py", line 919, in test_tmin<br>
stats.mstats.tmin(xm,lowerlimit=-1.), 10)<br> File "/home/nils/local/lib64/python2.7/site-packages/scipy/stats/mstats_basic.py", line 1376, in tmin<br> am = trima(a, (lowerlimit, None), (inclusive, False))<br>
File "/home/nils/local/lib64/python2.7/site-packages/scipy/stats/mstats_basic.py", line 1013, in trima<br> condition |= (a < lower_lim)<br>RuntimeWarning: invalid value encountered in less<br><br>======================================================================<br>
ERROR: test_tsem (test_mstats_basic.TestCompareWithStats)<br>----------------------------------------------------------------------<br>Traceback (most recent call last):<br> File "/home/nils/local/lib64/python2.7/site-packages/scipy/stats/tests/test_mstats_basic.py", line 958, in test_tsem<br>
stats.mstats.tsem(xm,limits=(-2.,2.)),<br> File "/home/nils/local/lib64/python2.7/site-packages/scipy/stats/mstats_basic.py", line 1393, in tsem<br> am = trima(a.ravel(), limits, inclusive)<br> File "/home/nils/local/lib64/python2.7/site-packages/scipy/stats/mstats_basic.py", line 1013, in trima<br>
condition |= (a < lower_lim)<br>RuntimeWarning: invalid value encountered in less<br><br>======================================================================<br>ERROR: test_zmap (test_mstats_basic.TestCompareWithStats)<br>
----------------------------------------------------------------------<br>Traceback (most recent call last):<br> File "/home/nils/local/lib64/python2.7/site-packages/scipy/stats/tests/test_mstats_basic.py", line 927, in test_zmap<br>
zm = stats.mstats.zmap(xm,ym)<br> File "/home/nils/local/lib64/python2.7/site-packages/scipy/stats/stats.py", line 2063, in zmap<br> return (scores - mns) / sstd<br> File "/home/nils/local/lib64/python2.7/site-packages/numpy/ma/core.py", line 3735, in __truediv__<br>
return true_divide(self, other)<br> File "/home/nils/local/lib64/python2.7/site-packages/numpy/ma/core.py", line 1089, in __call__<br> m |= filled(domain(da, db), True)<br> File "/home/nils/local/lib64/python2.7/site-packages/numpy/ma/core.py", line 783, in __call__<br>
return umath.absolute(a) * self.tolerance >= umath.absolute(b)<br>RuntimeWarning: invalid value encountered in greater_equal<br><br>======================================================================<br>FAIL: test_example1a (test_morestats.TestAndersonKSamp)<br>
----------------------------------------------------------------------<br>Traceback (most recent call last):<br> File "/home/nils/local/lib64/python2.7/site-packages/scipy/stats/tests/test_morestats.py", line 97, in test_example1a<br>
midrank=False)<br> File "/home/nils/local/lib64/python2.7/site-packages/numpy/testing/utils.py", line 1593, in assert_warns<br> % func.__name__)<br>AssertionError: No warning raised when calling anderson_ksamp<br>
<br>======================================================================<br>FAIL: test_tmean (test_mstats_basic.TestCompareWithStats)<br>----------------------------------------------------------------------<br>Traceback (most recent call last):<br>
File "/home/nils/local/lib64/python2.7/site-packages/scipy/stats/tests/test_mstats_basic.py", line 901, in test_tmean<br> assert_equal(stats.tmean(x),stats.mstats.tmean(xm))<br> File "/home/nils/local/lib64/python2.7/site-packages/numpy/ma/testutils.py", line 100, in assert_equal<br>
raise AssertionError(msg)<br>AssertionError: <br>Items are not equal:<br> ACTUAL: 0.040175456835823721<br> DESIRED: 0.040175456835823714<br><br>======================================================================<br>
FAIL: test_trim (test_mstats_basic.TestTrimming)<br>----------------------------------------------------------------------<br>Traceback (most recent call last):<br> File "/home/nils/local/lib64/python2.7/site-packages/scipy/stats/tests/test_mstats_basic.py", line 274, in test_trim<br>
assert_equal(trimx._mask.ravel(),[1]*20+[0]*70+[1]*20)<br> File "/home/nils/local/lib64/python2.7/site-packages/numpy/ma/testutils.py", line 123, in assert_equal<br> return assert_array_equal(actual, desired, err_msg)<br>
File "/home/nils/local/lib64/python2.7/site-packages/numpy/ma/testutils.py", line 196, in assert_array_equal<br> header='Arrays are not equal')<br> File "/home/nils/local/lib64/python2.7/site-packages/numpy/ma/testutils.py", line 189, in assert_array_compare<br>
verbose=verbose, header=header)<br> File "/home/nils/local/lib64/python2.7/site-packages/numpy/testing/utils.py", line 660, in assert_array_compare<br> raise AssertionError(msg)<br>AssertionError: <br>Arrays are not equal<br>
<br>(mismatch 9.09090909091%)<br> x: array([ True, True, True, True, True, True, True, True, True,<br> True, True, True, True, True, True, True, True, True,<br> True, True, False, False, False, False, False, False, False,...<br>
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,<br> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,<br> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,...<br>
<br>----------------------------------------------------------------------<br>Ran 1957 tests in 50.047s<br><br>FAILED (KNOWNFAIL=4, SKIP=3, errors=6, failures=3)<br><nose.result.TextTestResult run=1957 errors=6 failures=3><br>
<br></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Sun, Apr 13, 2014 at 10:58 PM, Ralf Gommers <span dir="ltr"><<a href="mailto:ralf.gommers@gmail.com" target="_blank">ralf.gommers@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><br><div class="gmail_extra"><br><br><div class="gmail_quote"><div class="">On Sun, Apr 13, 2014 at 7:42 AM, Charles R Harris <span dir="ltr"><<a href="mailto:charlesr.harris@gmail.com" target="_blank">charlesr.harris@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div><div><div>Hi All,<br><br></div>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.<br>
<br></div><div>The main question I have is what is the best way to deal with the deprecations?<br></div></div></div></blockquote><div><br></div></div><div>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.<br>
<br></div><div>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.<br></div><div><br>Ralf<br><br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div><div class="h5">
<div dir="ltr"><div><div></div><div><br><br></div>FAIL: test_lsmr.TestLSMR.testBidiagonalA<br>----------------------------------------------------------------------<br>
Traceback (most recent call last):<br> File "/usr/lib/python2.7/site-packages/nose/case.py", line 197, in runTest<br> self.test(*self.arg)<br> File "/home/charris/.local/lib/python2.7/site-packages/scipy/sparse/linalg/isolve/tests/test_lsmr.py", line 60, in testBidiagonalA<br>
self.assertCompatibleSystem(A,xtrue)<br> File "/home/charris/.local/lib/python2.7/site-packages/scipy/sparse/linalg/isolve/tests/test_lsmr.py", line 40, in assertCompatibleSystem<br> assert_almost_equal(norm(x - xtrue), 0, 6)<br>
File "/home/charris/.local/lib/python2.7/site-packages/numpy/testing/utils.py", line 486, in assert_almost_equal<br> raise AssertionError(_build_err_msg())<br>AssertionError: <br>Arrays are not almost equal to 6 decimals<br>
ACTUAL: 6.048630163037888e-07<br> DESIRED: 0<br><br>======================================================================<br>FAIL: test_qhull.TestUtilities.test_degenerate_barycentric_transforms<br>----------------------------------------------------------------------<br>
Traceback (most recent call last):<br> File "/usr/lib/python2.7/site-packages/nose/case.py", line 197, in runTest<br> self.test(*self.arg)<br> File "/home/charris/.local/lib/python2.7/site-packages/numpy/testing/decorators.py", line 146, in skipper_func<br>
return f(*args, **kwargs)<br> File "/home/charris/.local/lib/python2.7/site-packages/scipy/spatial/tests/test_qhull.py", line 296, in test_degenerate_barycentric_transforms<br> assert_(bad_count < 20, bad_count)<br>
File "/home/charris/.local/lib/python2.7/site-packages/numpy/testing/utils.py", line 50, in assert_<br> raise AssertionError(smsg)<br>AssertionError: 20<br><br>======================================================================<br>
FAIL: test_trim (test_mstats_basic.TestTrimming)<br>----------------------------------------------------------------------<br>Traceback (most recent call last):<br> File "/home/charris/.local/lib/python2.7/site-packages/scipy/stats/tests/test_mstats_basic.py", line 270, in test_trim<br>
assert_equal(trimx._mask.ravel(),[1]*20+[0]*70+[1]*20)<br> File "/home/charris/.local/lib/python2.7/site-packages/numpy/ma/testutils.py", line 123, in assert_equal<br> return assert_array_equal(actual, desired, err_msg)<br>
File "/home/charris/.local/lib/python2.7/site-packages/numpy/ma/testutils.py", line 196, in assert_array_equal<br> header='Arrays are not equal')<br> File "/home/charris/.local/lib/python2.7/site-packages/numpy/ma/testutils.py", line 189, in assert_array_compare<br>
verbose=verbose, header=header)<br> File "/home/charris/.local/lib/python2.7/site-packages/numpy/testing/utils.py", line 660, in assert_array_compare<br> raise AssertionError(msg)<br>AssertionError: <br>
Arrays are not equal<br><br>(mismatch 9.09090909091%)<br> x: array([ True, True, True, True, True, True, True, True, True,<br> True, True, True, True, True, True, True, True, True,<br> True, True, False, False, False, False, False, False, False,...<br>
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,<br> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,<br> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,...<br>
<br></div>Chuck<br><div><div><br><br></div></div></div>
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