On Sat, Jul 24, 2010 at 3:39 PM, Jonathan Tu
On Jul 24, 2010, at 6:21 PM, David Cournapeau wrote:
On Sun, Jul 25, 2010 at 7:12 AM, Jonathan Tu
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)
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.
Yes, you should be worried. To run the numpy tests you need to install nose. That's what your output said: ImportError: Need nose >= 0.10.0 for tests - see http://somethingaboutorange.com/mrl/projects/nose For h5py, you might want to try the h5py list. Did you remove the build directory? Because I don't know much about installation, I remove everything: the installed package, the build directory.