On Tue, Oct 15, 2013 at 1:06 PM, Charles R Harris <charlesr.har...@gmail.com > wrote:
> Hi David, > > > On Tue, Oct 15, 2013 at 12:46 PM, David Cournapeau <courn...@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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