[SciPy-Dev] scipy test errors

Ralf Gommers ralf.gommers@gmail....
Fri Dec 21 13:51:06 CST 2012


On Fri, Dec 21, 2012 at 4:19 PM, Skipper Seabold <jsseabold@gmail.com>wrote:

> On Fri, Dec 21, 2012 at 4:39 AM, Pauli Virtanen <pav@iki.fi> wrote:
> > Skipper Seabold <jsseabold <at> gmail.com> writes:
> > [clip]
> >> http://projects.scipy.org/scipy/ticket/1796
> >>
> >> But I installed master numpy/scipy yesterday on a new system, and I'm
> >> also experience a large number of errors. Not all the same as listed
> >> on the ticket.
> >>
> >> FAILED (KNOWNFAIL=17, SKIP=37, errors=48)
> >>
> >> Test output attached.
> >
> > I think all these are due to changes made in Numpy master,
> > with an older Numpy version (e.g. 1.6.2) all of them should go away.
> >
>
> That's what I figured. I submitted a PR for the indexing with a float.
> Not sure why the deprecation warnings raised errors though. Don't
> recall seeing this before. Maybe some configuration that I've
> overlooked?
>
> I was curious if the problems coming from as_strided were a numpy
> problem. Similarly, I get these errors with numpy 1.7.0b2
>

These should be fixed with the latest numpy 1.7.x branch. If not, please
open a new numpy issue.

Ralf



>
> ======================================================================
> ERROR: test_interpolate.TestInterp1D.test_bounds
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File
> "/usr/local/lib/python2.7/dist-packages/nose-1.2.1-py2.7.egg/nose/case.py",
> line 197, in runTest
>     self.test(*self.arg)
>   File
> "/usr/local/lib/python2.7/dist-packages/scipy/interpolate/tests/test_interpolate.py",
> line 257, in test_bounds
>     self._bounds_check(kind)
>   File
> "/usr/local/lib/python2.7/dist-packages/scipy/interpolate/tests/test_interpolate.py",
> line 224, in _bounds_check
>     extrap10(11.2),
>   File
> "/usr/local/lib/python2.7/dist-packages/scipy/interpolate/interpolate.py",
> line 419, in __call__
>     y_new = self._call(x_new)
>   File
> "/usr/local/lib/python2.7/dist-packages/scipy/interpolate/interpolate.py",
> line 395, in _call_spline
>     result = spleval(self._spline,x_new.ravel())
>   File
> "/usr/local/lib/python2.7/dist-packages/scipy/interpolate/interpolate.py",
> line 858, in spleval
>     res[sl] = _fitpack._bspleval(xx,xj,cvals[sl],k,deriv)
> IndexError: too many indices
>
> ======================================================================
> ERROR: test_interpolate.TestInterp1D.test_complex
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File
> "/usr/local/lib/python2.7/dist-packages/nose-1.2.1-py2.7.egg/nose/case.py",
> line 197, in runTest
>     self.test(*self.arg)
>   File
> "/usr/local/lib/python2.7/dist-packages/scipy/interpolate/tests/test_interpolate.py",
> line 349, in test_complex
>     self._check_complex(np.complex64, kind)
>   File
> "/usr/local/lib/python2.7/dist-packages/scipy/interpolate/tests/test_interpolate.py",
> line 337, in _check_complex
>     assert_array_almost_equal(y[:-1], c(x)[:-1])
>   File
> "/usr/local/lib/python2.7/dist-packages/scipy/interpolate/interpolate.py",
> line 419, in __call__
>     y_new = self._call(x_new)
>   File
> "/usr/local/lib/python2.7/dist-packages/scipy/interpolate/interpolate.py",
> line 395, in _call_spline
>     result = spleval(self._spline,x_new.ravel())
>   File
> "/usr/local/lib/python2.7/dist-packages/scipy/interpolate/interpolate.py",
> line 855, in spleval
>     res[sl].real = _fitpack._bspleval(xx,xj,cvals.real[sl],k,deriv)
> IndexError: too many indices
>
> ======================================================================
> ERROR: Check the actual implementation of spline interpolation.
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File
> "/usr/local/lib/python2.7/dist-packages/nose-1.2.1-py2.7.egg/nose/case.py",
> line 197, in runTest
>     self.test(*self.arg)
>   File
> "/usr/local/lib/python2.7/dist-packages/scipy/interpolate/tests/test_interpolate.py",
> line 177, in test_cubic
>     interp10(self.x10),
>   File
> "/usr/local/lib/python2.7/dist-packages/scipy/interpolate/interpolate.py",
> line 419, in __call__
>     y_new = self._call(x_new)
>   File
> "/usr/local/lib/python2.7/dist-packages/scipy/interpolate/interpolate.py",
> line 395, in _call_spline
>     result = spleval(self._spline,x_new.ravel())
>   File
> "/usr/local/lib/python2.7/dist-packages/scipy/interpolate/interpolate.py",
> line 858, in spleval
>     res[sl] = _fitpack._bspleval(xx,xj,cvals[sl],k,deriv)
> IndexError: too many indices
>
> ======================================================================
> ERROR: test_interpolate.TestInterp1D.test_nd
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File
> "/usr/local/lib/python2.7/dist-packages/nose-1.2.1-py2.7.egg/nose/case.py",
> line 197, in runTest
>     self.test(*self.arg)
>   File
> "/usr/local/lib/python2.7/dist-packages/scipy/interpolate/tests/test_interpolate.py",
> line 327, in test_nd
>     self._nd_check_interp(kind)
>   File
> "/usr/local/lib/python2.7/dist-packages/scipy/interpolate/tests/test_interpolate.py",
> line 267, in _nd_check_interp
>     interp10(np.array([[3., 5.], [2., 7.]])),
>   File
> "/usr/local/lib/python2.7/dist-packages/scipy/interpolate/interpolate.py",
> line 419, in __call__
>     y_new = self._call(x_new)
>   File
> "/usr/local/lib/python2.7/dist-packages/scipy/interpolate/interpolate.py",
> line 395, in _call_spline
>     result = spleval(self._spline,x_new.ravel())
>   File
> "/usr/local/lib/python2.7/dist-packages/scipy/interpolate/interpolate.py",
> line 858, in spleval
>     res[sl] = _fitpack._bspleval(xx,xj,cvals[sl],k,deriv)
> IndexError: too many indices
>
> ======================================================================
> ERROR: test_ndgriddata.TestGriddata.test_1d
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File
> "/usr/local/lib/python2.7/dist-packages/nose-1.2.1-py2.7.egg/nose/case.py",
> line 197, in runTest
>     self.test(*self.arg)
>   File
> "/usr/local/lib/python2.7/dist-packages/scipy/interpolate/tests/test_ndgriddata.py",
> line 73, in test_1d
>     assert_allclose(griddata(x, y, x, method=method), y,
>   File
> "/usr/local/lib/python2.7/dist-packages/scipy/interpolate/ndgriddata.py",
> line 178, in griddata
>     return ip(xi)
>   File
> "/usr/local/lib/python2.7/dist-packages/scipy/interpolate/interpolate.py",
> line 419, in __call__
>     y_new = self._call(x_new)
>   File
> "/usr/local/lib/python2.7/dist-packages/scipy/interpolate/interpolate.py",
> line 395, in _call_spline
>     result = spleval(self._spline,x_new.ravel())
>   File
> "/usr/local/lib/python2.7/dist-packages/scipy/interpolate/interpolate.py",
> line 858, in spleval
>     res[sl] = _fitpack._bspleval(xx,xj,cvals[sl],k,deriv)
> IndexError: too many indices
>
> ======================================================================
> ERROR: test_ndgriddata.TestGriddata.test_1d_unsorted
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File
> "/usr/local/lib/python2.7/dist-packages/nose-1.2.1-py2.7.egg/nose/case.py",
> line 197, in runTest
>     self.test(*self.arg)
>   File
> "/usr/local/lib/python2.7/dist-packages/scipy/interpolate/tests/test_ndgriddata.py",
> line 85, in test_1d_unsorted
>     assert_allclose(griddata(x, y, x, method=method), y,
>   File
> "/usr/local/lib/python2.7/dist-packages/scipy/interpolate/ndgriddata.py",
> line 178, in griddata
>     return ip(xi)
>   File
> "/usr/local/lib/python2.7/dist-packages/scipy/interpolate/interpolate.py",
> line 419, in __call__
>     y_new = self._call(x_new)
>   File
> "/usr/local/lib/python2.7/dist-packages/scipy/interpolate/interpolate.py",
> line 395, in _call_spline
>     result = spleval(self._spline,x_new.ravel())
>   File
> "/usr/local/lib/python2.7/dist-packages/scipy/interpolate/interpolate.py",
> line 858, in spleval
>     res[sl] = _fitpack._bspleval(xx,xj,cvals[sl],k,deriv)
> IndexError: too many indices
>
> ======================================================================
> ERROR: test_kdtree.test_vectorization.test_vectorized_query
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File
> "/usr/local/lib/python2.7/dist-packages/nose-1.2.1-py2.7.egg/nose/case.py",
> line 197, in runTest
>     self.test(*self.arg)
>   File
> "/usr/local/lib/python2.7/dist-packages/scipy/spatial/tests/test_kdtree.py",
> line 159, in test_vectorized_query
>     d, i = self.kdtree.query(np.zeros((2,4,3)))
>   File "/usr/local/lib/python2.7/dist-packages/scipy/spatial/kdtree.py",
> line 434, in query
>     for c in np.ndindex(retshape):
>   File "/usr/local/lib/python2.7/dist-packages/numpy/lib/index_tricks.py",
> line 536, in __init__
>     x = as_strided(_nx.zeros(1), shape=shape,
> strides=_nx.zeros_like(shape))
>   File "/usr/local/lib/python2.7/dist-packages/numpy/lib/stride_tricks.py",
> line 28, in as_strided
>     return np.asarray(DummyArray(interface, base=x))
>   File "/usr/local/lib/python2.7/dist-packages/numpy/core/numeric.py",
> line 320, in asarray
>     return array(a, dtype, copy=False, order=order)
> ValueError: negative dimensions are not allowed
>
> ======================================================================
> ERROR: test_kdtree.test_vectorization.test_vectorized_query_all_neighbors
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File
> "/usr/local/lib/python2.7/dist-packages/nose-1.2.1-py2.7.egg/nose/case.py",
> line 197, in runTest
>     self.test(*self.arg)
>   File
> "/usr/local/lib/python2.7/dist-packages/scipy/spatial/tests/test_kdtree.py",
> line 187, in test_vectorized_query_all_neighbors
>     d, i =
> self.kdtree.query(np.zeros((2,4,3)),k=None,distance_upper_bound=1.1)
>   File "/usr/local/lib/python2.7/dist-packages/scipy/spatial/kdtree.py",
> line 434, in query
>     for c in np.ndindex(retshape):
>   File "/usr/local/lib/python2.7/dist-packages/numpy/lib/index_tricks.py",
> line 536, in __init__
>     x = as_strided(_nx.zeros(1), shape=shape,
> strides=_nx.zeros_like(shape))
>   File "/usr/local/lib/python2.7/dist-packages/numpy/lib/stride_tricks.py",
> line 28, in as_strided
>     return np.asarray(DummyArray(interface, base=x))
>   File "/usr/local/lib/python2.7/dist-packages/numpy/core/numeric.py",
> line 320, in asarray
>     return array(a, dtype, copy=False, order=order)
> ValueError: negative dimensions are not allowed
>
> ======================================================================
> ERROR:
> test_kdtree.test_vectorization.test_vectorized_query_multiple_neighbors
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File
> "/usr/local/lib/python2.7/dist-packages/nose-1.2.1-py2.7.egg/nose/case.py",
> line 197, in runTest
>     self.test(*self.arg)
>   File
> "/usr/local/lib/python2.7/dist-packages/scipy/spatial/tests/test_kdtree.py",
> line 175, in test_vectorized_query_multiple_neighbors
>     d, i = self.kdtree.query(np.zeros((2,4,3)),k=kk)
>   File "/usr/local/lib/python2.7/dist-packages/scipy/spatial/kdtree.py",
> line 434, in query
>     for c in np.ndindex(retshape):
>   File "/usr/local/lib/python2.7/dist-packages/numpy/lib/index_tricks.py",
> line 536, in __init__
>     x = as_strided(_nx.zeros(1), shape=shape,
> strides=_nx.zeros_like(shape))
>   File "/usr/local/lib/python2.7/dist-packages/numpy/lib/stride_tricks.py",
> line 28, in as_strided
>     return np.asarray(DummyArray(interface, base=x))
>   File "/usr/local/lib/python2.7/dist-packages/numpy/core/numeric.py",
> line 320, in asarray
>     return array(a, dtype, copy=False, order=order)
> ValueError: negative dimensions are not allowed
>
> ======================================================================
> ERROR: test_kdtree.test_random_ball_vectorized
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File
> "/usr/local/lib/python2.7/dist-packages/nose-1.2.1-py2.7.egg/nose/case.py",
> line 197, in runTest
>     self.test(*self.arg)
>   File
> "/usr/local/lib/python2.7/dist-packages/scipy/spatial/tests/test_kdtree.py",
> line 332, in test_random_ball_vectorized
>     r = T.query_ball_point(np.random.randn(2,3,m),1)
>   File "/usr/local/lib/python2.7/dist-packages/scipy/spatial/kdtree.py",
> line 544, in query_ball_point
>     for c in np.ndindex(retshape):
>   File "/usr/local/lib/python2.7/dist-packages/numpy/lib/index_tricks.py",
> line 536, in __init__
>     x = as_strided(_nx.zeros(1), shape=shape,
> strides=_nx.zeros_like(shape))
>   File "/usr/local/lib/python2.7/dist-packages/numpy/lib/stride_tricks.py",
> line 28, in as_strided
>     return np.asarray(DummyArray(interface, base=x))
>   File "/usr/local/lib/python2.7/dist-packages/numpy/core/numeric.py",
> line 320, in asarray
>     return array(a, dtype, copy=False, order=order)
> ValueError: negative dimensions are not allowed
>
> ======================================================================
> ERROR: test_kdtree.test_random_ball_vectorized_compiled
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File
> "/usr/local/lib/python2.7/dist-packages/nose-1.2.1-py2.7.egg/nose/case.py",
> line 197, in runTest
>     self.test(*self.arg)
>   File
> "/usr/local/lib/python2.7/dist-packages/scipy/spatial/tests/test_kdtree.py",
> line 342, in test_random_ball_vectorized_compiled
>     r = T.query_ball_point(np.random.randn(2,3,m),1)
>   File "ckdtree.pyx", line 1399, in
> scipy.spatial.ckdtree.cKDTree.query_ball_point
> (scipy/spatial/ckdtree.c:11875)
>   File "/usr/local/lib/python2.7/dist-packages/numpy/lib/index_tricks.py",
> line 536, in __init__
>     x = as_strided(_nx.zeros(1), shape=shape,
> strides=_nx.zeros_like(shape))
>   File "/usr/local/lib/python2.7/dist-packages/numpy/lib/stride_tricks.py",
> line 28, in as_strided
>     return np.asarray(DummyArray(interface, base=x))
>   File "/usr/local/lib/python2.7/dist-packages/numpy/core/numeric.py",
> line 320, in asarray
>     return array(a, dtype, copy=False, order=order)
> ValueError: negative dimensions are not allowed
>
> ----------------------------------------------------------------------
> Ran 5744 tests in 59.973s
>
> FAILED (KNOWNFAIL=15, SKIP=36, errors=11)
> [2]: <nose.result.TextTestResult run=5744 errors=11 failures=0>
> _______________________________________________
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