[Numpy-discussion] NumPy 1.8.0rc2 release

Charles R Harris charlesr.harris at gmail.com
Wed Oct 16 12:55:23 EDT 2013


On Tue, Oct 15, 2013 at 1:06 PM, Charles R Harris <charlesr.harris at gmail.com
> wrote:

> 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,...]
>

It has been fixed in larry master

Chuck

>
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