[Numpy-discussion] NumPy 1.8.0rc2 release
Charles R Harris
charlesr.harris at gmail.com
Tue Oct 15 15:06:12 EDT 2013
Hi David,
On Tue, Oct 15, 2013 at 12:46 PM, David Cournapeau <cournape at gmail.com>wrote:
> It looks better than rc1, thanks for the great work. I have only tested on
> rh5 for now, but building the following against numpy 1.7.1 and running
> against 1.8.0 rc2 only give a few failures for the full list of packages
> supported by Enthought. Bottleneck / larry are caused by numpy, the sklearn
> may be a bug in numpy or scikit learn or scipy (eigh issue).
>
> List of packages:
>
> GDAL-1.10.0
> MDP-3.3
> Pycluster-1.50
> ScientificPython-2.9.0
> SimPy-2.2
> astropy-0.2.4
> basemap-1.0.6
> biopython-1.59
> chaco-4.3.0
> enable-4.3.0
> fastnumpy-1.0
> fwrap-0.1.1
> h5py-2.2.0
> llvmmath-0.1.1
> matplotlib-1.3.0
> mayavi-4.3.0
> netCDF4-1.0.5
> networkx-1.8.1
> nltk-2.0.1
> numba-0.10.2
> opencv-2.4.5
> pandas-0.12.0
> pyfits-3.0.6
> pygarrayimage-0.0.7
> pygrib-1.9.2
> pyhdf-0.8.3
> pysparse-1.2.dev213
> pytables-2.4.0
> scikits.image-0.8.2
> scikits.rsformats-0.1
> scikits.timeseries-0.91.3
> scimath-4.1.2
> scipy-0.12.0
> traits-4.3.0
>
> As for the bottleneck/larry failures (for reference):
>
> ======================================================================
> FAIL: Test nanargmin.
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File
> "/home/vagrant/src/master-env/lib/python2.7/site-packages/nose/case.py",
> line 197, in runTest
> self.test(*self.arg)
> File
> "/home/vagrant/src/master-env/lib/python2.7/site-packages/bottleneck/tests/func_test.py",
> line 78, in unit_maker
> assert_array_equal(actual, desired, err_msg)
> File
> "/home/vagrant/src/master-env/lib/python2.7/site-packages/numpy/testing/utils.py",
> line 718, in assert_array_equal
> verbose=verbose, header='Arrays are not equal')
> File
> "/home/vagrant/src/master-env/lib/python2.7/site-packages/numpy/testing/utils.py",
> line 644, in assert_array_compare
> raise AssertionError(msg)
> AssertionError:
> Arrays are not equal
>
> func nanargmin | input a44 (float32) | shape (4,) | axis -1
>
> Input array:
> [ nan nan nan nan]
>
> (mismatch 100.0%)
> x: array(nan)
> y: array('Crashed',
> dtype='|S7')
>
> ======================================================================
> FAIL: Test nanargmax.
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File
> "/home/vagrant/src/master-env/lib/python2.7/site-packages/nose/case.py",
> line 197, in runTest
> self.test(*self.arg)
> File
> "/home/vagrant/src/master-env/lib/python2.7/site-packages/bottleneck/tests/func_test.py",
> line 78, in unit_maker
> assert_array_equal(actual, desired, err_msg)
> File
> "/home/vagrant/src/master-env/lib/python2.7/site-packages/numpy/testing/utils.py",
> line 718, in assert_array_equal
> verbose=verbose, header='Arrays are not equal')
> File
> "/home/vagrant/src/master-env/lib/python2.7/site-packages/numpy/testing/utils.py",
> line 644, in assert_array_compare
> raise AssertionError(msg)
> AssertionError:
> Arrays are not equal
>
> func nanargmax | input a44 (float32) | shape (4,) | axis -1
>
> Input array:
> [ nan nan nan nan]
>
> (mismatch 100.0%)
> x: array(nan)
> y: array('Crashed',
> dtype='|S7')
>
> ----------------------------------------------------------------------
> Ran 124 tests in 85.714s
>
> FAILED (failures=2)
> FAIL
>
>
Not going to fix these, nanarg{max, min} now raises an exception for this
case.
> and larry:
>
> ======================================================================
> ERROR: Failure: IndexError (too many indices)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File
> "/home/vagrant/src/master-env/lib/python2.7/site-packages/nose/loader.py",
> line 253, in generate
> for test in g():
> File
> "/home/vagrant/src/master-env/lib/python2.7/site-packages/la/tests/all_nan_test.py",
> line 31, in test_all_nan
> actual = getattr(lar(), method)(*parameters)
> File
> "/home/vagrant/src/master-env/lib/python2.7/site-packages/la/deflarry.py",
> line 3066, in quantile
> x = quantile(self.x, q, axis=axis)
> File
> "/home/vagrant/src/master-env/lib/python2.7/site-packages/la/farray/normalize.py",
> line 289, in quantile
> y = np.apply_along_axis(_quantileraw1d, axis, x, q)
> File
> "/home/vagrant/src/master-env/lib/python2.7/site-packages/numpy/lib/shape_base.py",
> line 79, in apply_along_axis
> res = func1d(arr[tuple(i.tolist())],*args)
> File
> "/home/vagrant/src/master-env/lib/python2.7/site-packages/la/farray/normalize.py",
> line 228, in _quantileraw1d
> xi = xi[idx,:]
> IndexError: too many indices
>
> ======================================================================
> ERROR: larry.quantile_1
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File
> "/home/vagrant/src/master-env/lib/python2.7/site-packages/la/tests/deflarry_test.py",
> line 3401, in test_quantile_1
> actual = self.l1.quantile(2)
> File
> "/home/vagrant/src/master-env/lib/python2.7/site-packages/la/deflarry.py",
> line 3066, in quantile
> x = quantile(self.x, q, axis=axis)
> File
> "/home/vagrant/src/master-env/lib/python2.7/site-packages/la/farray/normalize.py",
> line 289, in quantile
> y = np.apply_along_axis(_quantileraw1d, axis, x, q)
> File
> "/home/vagrant/src/master-env/lib/python2.7/site-packages/numpy/lib/shape_base.py",
> line 79, in apply_along_axis
> res = func1d(arr[tuple(i.tolist())],*args)
> File
> "/home/vagrant/src/master-env/lib/python2.7/site-packages/la/farray/normalize.py",
> line 228, in _quantileraw1d
> xi = xi[idx,:]
> IndexError: too many indices
>
> (more similar)
>
Iarry problem, the proper form here is xi[x,...]
Chuck
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