On Jul 24, 2010, at 6:21 PM, David Cournapeau wrote:
> On Sun, Jul 25, 2010 at 7:12 AM, Jonathan Tu <[email protected]> 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
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