On Jul 24, 2010, at 6:21 PM, David Cournapeau wrote:
On Sun, Jul 25, 2010 at 7:12 AM, Jonathan Tu jhtu@princeton.edu wrote:
What does that part do? It turns out that by fixing my library path, numpy now imports. I assume that my installation of h5py doesn't need to be redone just because I reinstalled Numpy?
Actually, you may have to if you installed h5py against the numpy built from the trunk. I don't think the trunk ABI is forward compatible with 1.4.1,
David
Ok, so I reinstalled numpy as we've discussed, and now I've reinstalled h5py too. When I test numpy, I get the following
import numpy numpy.test() Running unit tests for numpy Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/home/jhtu/local/lib/python2.6/site-packages/numpy/testing/nosetester.py", line 326, in test self._show_system_info() File "/home/jhtu/local/lib/python2.6/site-packages/numpy/testing/nosetester.py", line 187, in _show_system_info nose = import_nose() File "/home/jhtu/local/lib/python2.6/site-packages/numpy/testing/nosetester.py", line 69, in import_nose raise ImportError(msg) ImportError: Need nose >= 0.10.0 for tests - see http://somethingaboutorange.com/mrl/projects/nose
Note that when I try test(level=1) it tells me this is an unexpected keyword argument. (The level=1 was suggested by the scipy website.) Though this test seems to fail, the simple math tests I've tried seem to work ok.
Then I tried to test h5py: import h5py import h5py.tests h5py.tests.runtests()
====================================================================== ERROR: test_data (h5py.tests.test_filters.TestFilters) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/jhtu/local/lib/python2.6/site-packages/h5py/tests/test_filters.py", line 124, in test_data test_dset(s, t, compression=c, shuffle=False) File "/home/jhtu/local/lib/python2.6/site-packages/h5py/tests/test_filters.py", line 117, in test_dset dset[...] = arr File "/home/jhtu/local/lib/python2.6/site-packages/h5py/highlevel.py", line 1288, in __setitem__ self.id.write(mspace, fspace, val, mtype) File "h5d.pyx", line 231, in h5py.h5d.DatasetID.write (h5py/h5d.c:2336) File "_proxy.pyx", line 115, in h5py._proxy.dset_rw (h5py/_proxy.c:1143) TypeError: Not a dataset (Invalid arguments to routine: Inappropriate type)
====================================================================== FAIL: (File) Backing store for core driver ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/jhtu/local/lib/python2.6/site-packages/h5py/tests/high/test_file.py", line 135, in test_backing self.assert_('g' in self.f) AssertionError
====================================================================== FAIL: (File) Append ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/jhtu/local/lib/python2.6/site-packages/h5py/tests/high/test_file.py", line 52, in test_a self.assert_('g' in self.f) AssertionError
====================================================================== FAIL: (File) Readwrite ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/jhtu/local/lib/python2.6/site-packages/h5py/tests/high/test_file.py", line 72, in test_rp self.assert_('g' in self.f) AssertionError
====================================================================== FAIL: test_open_close (h5py.tests.test_h5g.TestH5G) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/jhtu/local/lib/python2.6/site-packages/h5py/tests/test_h5g.py", line 39, in test_open_close self.assert_(self.is_grp(grp)) AssertionError
---------------------------------------------------------------------- Ran 247 tests in 1.307s
FAILED (failures=4, errors=1) <unittest._TextTestResult run=247 errors=1 failures=4>
But again, I seem to be able to open hdf5 files and look into them ok, though sometimes the files randomly close, i.e.
f = h5py.File( '/path/to/file.h5','r') ... f <Closed hdf5 file> (or something like this)
Should I be worried about these errors, or are things working ok? Someone had once mentioned to me that the numpy tests are prone to failure.
Jonathan Tu