[SciPy-User] How to run individual failed scipy.test() tests?

josef.pktd@gmai... josef.pktd@gmai...
Mon Apr 16 10:10:22 CDT 2012


On Sun, Apr 15, 2012 at 4:12 PM, sergio <sergio_r@mail.com> wrote:
> Hello all,
>
>  I just manually installed python 2.7 with numpy 1.6.1, scipy0.10.1
> and nose version 1.1.2 under ubuntu 10.04.
>
> I would like to know how to run failed tests of numpy.test('full') and
> scipy.test('full') individually,
> and to read a description of what exactly the test does.

I usually run individual testfiles
http://readthedocs.org/docs/nose/en/latest/usage.html#selecting-tests
or use --pdb option to get into a test error

Josef

>
> Thanks in advance for your help,
>
> Sergio
>
> PS. In what follows I am including the summary
> from each test command:
>
>>>> numpy.test('full')
> Running unit tests for numpy
> NumPy version 1.6.1
> NumPy is installed in /home/myProg/Python272/Linux32b/lib/python2.7/
> site-
> packages/numpy
> Python version 2.7.2 (default, Apr 14 2012, 20:45:06) [GCC 4.4.3]
> nose version 1.1.2
>
> ======================================================================
> FAIL: test_kind.TestKind.test_all
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>  File "/home/srojas/myProg/Python272/Linux32b/lib/python2.7/site-
> packages/nose/
> case.py", line 197, in runTest
>    self.test(*self.arg)
>  File "/home/srojas/myProg/Python272/Linux32b/lib/python2.7/site-
> packages/numpy
> /f2py/tests/test_kind.py", line 30, in test_all
>    'selectedrealkind(%s): expected %r but got %r' %  (i,
> selected_real_kind(i),
>  selectedrealkind(i)))
>  File "/home/srojas/myProg/Python272/Linux32b/lib/python2.7/site-
> packages/numpy
> /testing/utils.py", line 34, in assert_
>    raise AssertionError(msg)
> AssertionError: selectedrealkind(16): expected 10 but got 16
>
> ----------------------------------------------------------------------
> Ran 3560 tests in 259.496s
>
> FAILED (KNOWNFAIL=3, SKIP=4, failures=1)
>
>
>>>> scipy.test('full')
> ......................
> ======================================================================
> ERROR: test_iv_cephes_vs_amos_mass_test (test_basic.TestBessel)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>  File "/home/srojas/myProg/Python272/Linux32b/lib/python2.7/site-
> packages/scipy
> /special/tests/test_basic.py", line 1642, in
> test_iv_cephes_vs_amos_mass_test
>    c1 = special.iv(v, x)
> RuntimeWarning: divide by zero encountered in iv
>
> ======================================================================
> ERROR: test_fdtri (test_basic.TestCephes)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>  File "/home/srojas/myProg/Python272/Linux32b/lib/python2.7/site-
> packages/scipy
> /special/tests/test_basic.py", line 153, in test_fdtri
>    cephes.fdtri(1,1,0.5)
> RuntimeWarning: invalid value encountered in fdtri
>
> ======================================================================
> ERROR:
> test_continuous_extra.test_cont_extra(<scipy.stats.distributions.loggamma
> _gen object at 0xa560c2c>, (0.4141193182605212,), 'loggamma loc, scale
> test')
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>  File "/home/srojas/myProg/Python272/Linux32b/lib/python2.7/site-
> packages/nose/
> case.py", line 197, in runTest
>    self.test(*self.arg)
>  File "/home/srojas/myProg/Python272/Linux32b/lib/python2.7/site-
> packages/scipy
> /stats/tests/test_continuous_extra.py", line 78, in check_loc_scale
>    m,v = distfn.stats(*arg)
>  File "/home/srojas/myProg/Python272/Linux32b/lib/python2.7/site-
> packages/scipy
> /stats/distributions.py", line 1631, in stats
>    mu = self._munp(1.0,*goodargs)
>  File "/home/srojas/myProg/Python272/Linux32b/lib/python2.7/site-
> packages/scipy
> /stats/distributions.py", line 4119, in _munp
>    return self._mom0_sc(n,*args)
>  File "/home/srojas/myProg/Python272/Linux32b/lib/python2.7/site-
> packages/scipy
> /stats/distributions.py", line 1165, in _mom0_sc
>    self.b, args=(m,)+args)[0]
>  File "/home/srojas/myProg/Python272/Linux32b/lib/python2.7/site-
> packages/scipy
> /integrate/quadpack.py", line 247, in quad
>    retval =
> _quad(func,a,b,args,full_output,epsabs,epsrel,limit,points)
>  File "/home/srojas/myProg/Python272/Linux32b/lib/python2.7/site-
> packages/scipy
> /integrate/quadpack.py", line 314, in _quad
>    return
> _quadpack._qagie(func,bound,infbounds,args,full_output,epsabs,epsrel,
> limit)
>  File "/home/srojas/myProg/Python272/Linux32b/lib/python2.7/site-
> packages/scipy
> /stats/distributions.py", line 1162, in _mom_integ0
>    return x**m * self.pdf(x,*args)
>  File "/home/srojas/myProg/Python272/Linux32b/lib/python2.7/site-
> packages/scipy
> /stats/distributions.py", line 1262, in pdf
>    place(output,cond,self._pdf(*goodargs) / scale)
>  File "/home/srojas/myProg/Python272/Linux32b/lib/python2.7/site-
> packages/scipy
> /stats/distributions.py", line 4112, in _pdf
>    return exp(c*x-exp(x)-gamln(c))
> RuntimeWarning: overflow encountered in exp
>
> ======================================================================
> ERROR:
> test_continuous_extra.test_cont_extra(<scipy.stats.distributions.lomax_ge
> n object at 0xa56758c>, (1.8771398388773268,), 'lomax loc, scale
> test')
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>  File "/home/srojas/myProg/Python272/Linux32b/lib/python2.7/site-
> packages/nose/
> case.py", line 197, in runTest
>    self.test(*self.arg)
>  File "/home/srojas/myProg/Python272/Linux32b/lib/python2.7/site-
> packages/scipy
> /stats/tests/test_continuous_extra.py", line 78, in check_loc_scale
>    m,v = distfn.stats(*arg)
>  File "/home/srojas/myProg/Python272/Linux32b/lib/python2.7/site-
> packages/scipy
> /stats/distributions.py", line 1617, in stats
>    mu, mu2, g1, g2 = self._stats(*args)
>  File "/home/srojas/myProg/Python272/Linux32b/lib/python2.7/site-
> packages/scipy
> /stats/distributions.py", line 4643, in _stats
>    mu, mu2, g1, g2 = pareto.stats(c, loc=-1.0, moments='mvsk')
>  File "/home/srojas/myProg/Python272/Linux32b/lib/python2.7/site-
> packages/scipy
> /stats/distributions.py", line 1615, in stats
>    mu, mu2, g1, g2 = self._stats(*args,**{'moments':moments})
>  File "/home/srojas/myProg/Python272/Linux32b/lib/python2.7/site-
> packages/scipy
> /stats/distributions.py", line 4594, in _stats
>    vals = 2*(bt+1.0)*sqrt(b-2.0)/((b-3.0)*sqrt(b))
> RuntimeWarning: invalid value encountered in sqrt
>
> ======================================================================
> ERROR:
> test_discrete_basic.test_discrete_extra(<scipy.stats.distributions.hyperg
> eom_gen object at 0xa56d7ec>, (30, 12, 6), 'hypergeom entropy nan
> test')
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>  File "/home/srojas/myProg/Python272/Linux32b/lib/python2.7/site-
> packages/nose/
> case.py", line 197, in runTest
>    self.test(*self.arg)
>  File "/home/srojas/myProg/Python272/Linux32b/lib/python2.7/site-
> packages/scipy
> /stats/tests/test_discrete_basic.py", line 199, in check_entropy
>    ent = distfn.entropy(*arg)
>  File "/home/srojas/myProg/Python272/Linux32b/lib/python2.7/site-
> packages/scipy
> /stats/distributions.py", line 6314, in entropy
>    place(output,cond0,self.vecentropy(*goodargs))
>  File "/home/srojas/myProg/Python272/Linux32b/lib/python2.7/site-
> packages/numpy
> /lib/function_base.py", line 1862, in __call__
>    theout = self.thefunc(*newargs)
>  File "/home/srojas/myProg/Python272/Linux32b/lib/python2.7/site-
> packages/scipy
> /stats/distributions.py", line 6668, in _entropy
>    lvals = where(vals==0.0,0.0,log(vals))
> RuntimeWarning: divide by zero encountered in log
>
> ======================================================================
> ERROR:
> test_discrete_basic.test_discrete_extra(<scipy.stats.distributions.hyperg
> eom_gen object at 0xa56d7ec>, (21, 3, 12), 'hypergeom entropy nan
> test')
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>  File "/home/srojas/myProg/Python272/Linux32b/lib/python2.7/site-
> packages/nose/
> case.py", line 197, in runTest
>    self.test(*self.arg)
>  File "/home/srojas/myProg/Python272/Linux32b/lib/python2.7/site-
> packages/scipy
> /stats/tests/test_discrete_basic.py", line 199, in check_entropy
>    ent = distfn.entropy(*arg)
>  File "/home/srojas/myProg/Python272/Linux32b/lib/python2.7/site-
> packages/scipy
> /stats/distributions.py", line 6314, in entropy
>    place(output,cond0,self.vecentropy(*goodargs))
>  File "/home/srojas/myProg/Python272/Linux32b/lib/python2.7/site-
> packages/numpy
> /lib/function_base.py", line 1862, in __call__
>    theout = self.thefunc(*newargs)
>  File "/home/srojas/myProg/Python272/Linux32b/lib/python2.7/site-
> packages/scipy
> /stats/distributions.py", line 6668, in _entropy
>    lvals = where(vals==0.0,0.0,log(vals))
> RuntimeWarning: divide by zero encountered in log
>
> ======================================================================
> ERROR: test_fit (test_distributions.TestFitMethod)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>  File "/home/srojas/myProg/Python272/Linux32b/lib/python2.7/site-
> packages/scipy
> /stats/tests/test_distributions.py", line 439, in test_fit
>    vals2 = distfunc.fit(res, optimizer='powell')
>  File "/home/srojas/myProg/Python272/Linux32b/lib/python2.7/site-
> packages/scipy
> /stats/distributions.py", line 1874, in fit
>    vals = optimizer(func,x0,args=(ravel(data),),disp=0)
>  File "/home/srojas/myProg/Python272/Linux32b/lib/python2.7/site-
> packages/scipy
> /optimize/optimize.py", line 1621, in fmin_powell
>    fval, x, direc1 = _linesearch_powell(func, x, direc1,
> tol=xtol*100)
>  File "/home/srojas/myProg/Python272/Linux32b/lib/python2.7/site-
> packages/scipy
> /optimize/optimize.py", line 1491, in _linesearch_powell
>    alpha_min, fret, iter, num = brent(myfunc, full_output=1, tol=tol)
>  File "/home/srojas/myProg/Python272/Linux32b/lib/python2.7/site-
> packages/scipy
> /optimize/optimize.py", line 1312, in brent
>    brent.optimize()
>  File "/home/srojas/myProg/Python272/Linux32b/lib/python2.7/site-
> packages/scipy
> /optimize/optimize.py", line 1213, in optimize
>    tmp2 = (x-v)*(fx-fw)
> RuntimeWarning: invalid value encountered in double_scalars
>
> ======================================================================
> ERROR: test_fix_fit (test_distributions.TestFitMethod)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>  File "/home/srojas/myProg/Python272/Linux32b/lib/python2.7/site-
> packages/scipy
> /stats/tests/test_distributions.py", line 460, in test_fix_fit
>    vals2 = distfunc.fit(res,fscale=1)
>  File "/home/srojas/myProg/Python272/Linux32b/lib/python2.7/site-
> packages/scipy
> /stats/distributions.py", line 1874, in fit
>    vals = optimizer(func,x0,args=(ravel(data),),disp=0)
>  File "/home/srojas/myProg/Python272/Linux32b/lib/python2.7/site-
> packages/scipy
> /optimize/optimize.py", line 301, in fmin
>    and max(abs(fsim[0]-fsim[1:])) <= ftol):
> RuntimeWarning: invalid value encountered in subtract
>
> ======================================================================
> FAIL: test_mio.test_mat4_3d
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>  File "/home/srojas/myProg/Python272/Linux32b/lib/python2.7/site-
> packages/nose/
> case.py", line 197, in runTest
>    self.test(*self.arg)
>  File "/home/srojas/myProg/Python272/Linux32b/lib/python2.7/site-
> packages/scipy
> /io/matlab/tests/test_mio.py", line 740, in test_mat4_3d
>    stream, {'a': arr}, True, '4')
>  File "/home/srojas/myProg/Python272/Linux32b/lib/python2.7/site-
> packages/numpy
> /testing/utils.py", line 1008, in assert_raises
>    return nose.tools.assert_raises(*args,**kwargs)
> AssertionError: DeprecationWarning not raised
>
> ======================================================================
> FAIL: test_datatypes.test_uint64_max
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>  File "/home/srojas/myProg/Python272/Linux32b/lib/python2.7/site-
> packages/nose/
> case.py", line 197, in runTest
>    self.test(*self.arg)
>  File "/home/srojas/myProg/Python272/Linux32b/lib/python2.7/site-
> packages/scipy
> /ndimage/tests/test_datatypes.py", line 57, in test_uint64_max
>    assert_true(x[1] > (2**63))
> AssertionError: False is not true
>
> ======================================================================
> FAIL: Regression test for #651: better handling of badly conditioned
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>  File "/home/srojas/myProg/Python272/Linux32b/lib/python2.7/site-
> packages/scipy
> /signal/tests/test_filter_design.py", line 34, in test_bad_filter
>    assert_raises(BadCoefficients, tf2zpk, [1e-15], [1.0, 1.0])
>  File "/home/srojas/myProg/Python272/Linux32b/lib/python2.7/site-
> packages/numpy
> /testing/utils.py", line 1008, in assert_raises
>    return nose.tools.assert_raises(*args,**kwargs)
> AssertionError: BadCoefficients not raised
>
> ----------------------------------------------------------------------
> Ran 5836 tests in 2718.233s
>
> FAILED (KNOWNFAIL=14, SKIP=42, errors=8, failures=3)
> <nose.result.TextTestResult run=5836 errors=8 failures=3>
>
>
>
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