[Numpy-discussion] How to run NumPy's tests with coverage?
josef.pktd at gmail.com
josef.pktd at gmail.com
Sun May 6 23:25:48 EDT 2012
On Sun, May 6, 2012 at 4:39 PM, Ralf Gommers
<ralf.gommers at googlemail.com> wrote:
>
>
> On Sun, May 6, 2012 at 9:08 PM, Chris Ball <ceball at gmail.com> wrote:
>>
>> Hi,
>>
>> I'm trying to figure out how to run NumPy's tests with coverage enabled
>> (i.e.
>> numpy.test(coverage=True) ). I can run the tests successfully like this:
>
>
> This seems to have been broken somewhere along the way. If you remove the
> argument "--cover-inclusive" from line 242 in numpy/testing/nosetester.py,
> that should fix all errors except TestNewBufferProtocol.test_roundtrip. Not
> sure what's going on with that one.
removing "--cover-inclusive" helped me also with statsmodels, with it
it ran all example scripts and got stuck several times,
(permanently stuck in some multiprocessing example?)
Now coverage=True worked for the first time.
Is it possible to make this optional or remove it from numpy?
from a beneficiary of the nice numpy testing support outside of numpy
Thanks for the tip,
Josef
>
> Ralf
>
>
>
>>
>> $ git clone git://github.com/numpy/numpy.git
>> [...]
>> $ cd numpy/
>> $ python setup.py build_ext -i
>> [...]
>> $ cd .. # (avoid running from source directory)
>> $ export PYTHONPATH=numpy/
>> $ python
>> Python 2.6.5 (r265:79063, Apr 16 2010, 13:57:41)
>> [GCC 4.4.3] on linux2
>> Type "help", "copyright", "credits" or "license" for more information.
>> python> import numpy
>> python> numpy.test()
>> Running unit tests for numpy
>> NumPy version 1.7.0.dev-259fff8
>> NumPy is installed in [...]/numpy
>> Python version 2.6.5 (r265:79063, Apr 16 2010, 13:57:41) [GCC 4.4.3]
>> nose version 0.11.1
>> [...]
>> Ran 3710 tests in 27.654s
>>
>> OK (KNOWNFAIL=3, SKIP=6)
>> <nose.result.TextTestResult run=3710 errors=0 failures=0>
>>
>>
>> However, if I try to run the tests with coverage, I get lots of errors
>> (and
>> seven more tests are run than without coverage):
>>
>> python> numpy.test(coverage=True)
>> Running unit tests for numpy
>> NumPy version 1.7.0.dev-259fff8
>> NumPy is installed in [...]/numpy
>> Python version 2.6.5 (r265:79063, Apr 16 2010, 13:57:41) [GCC 4.4.3]
>> nose version 0.11.1
>> Could not locate executable icc
>> Could not locate executable ecc
>> [...]/numpy/numarray/alter_code2.py:12: UserWarning:
>> numpy.numarray.alter_code2
>> is not working yet.
>> warnings.warn("numpy.numarray.alter_code2 is not working yet.")
>> [...]/numpy/oldnumeric/alter_code2.py:26: UserWarning:
>> numpy.oldnumeric.alter_code2 is not working yet.
>> warnings.warn("numpy.oldnumeric.alter_code2 is not working yet.")
>> [...]
>> ======================================================================
>> ERROR: Failure: ImportError (No module named waflib.Configure)
>> ----------------------------------------------------------------------
>> Traceback (most recent call last):
>> File "/usr/lib/pymodules/python2.6/nose/loader.py", line 379, in
>> loadTestsFromName
>> addr.filename, addr.module)
>> File "/usr/lib/pymodules/python2.6/nose/importer.py", line 39, in
>> importFromPath
>> return self.importFromDir(dir_path, fqname)
>> File "/usr/lib/pymodules/python2.6/nose/importer.py", line 86, in
>> importFromDir
>> mod = load_module(part_fqname, fh, filename, desc)
>> File "[...]/numpy/build_utils/waf.py", line 4, in <module>
>> import waflib.Configure
>> ImportError: No module named waflib.Configure
>>
>> ======================================================================
>> ERROR: Failure: ImportError (No module named numscons.numdist)
>> ----------------------------------------------------------------------
>> Traceback (most recent call last):
>> File "/usr/lib/pymodules/python2.6/nose/loader.py", line 379, in
>> loadTestsFromName
>> addr.filename, addr.module)
>> File "/usr/lib/pymodules/python2.6/nose/importer.py", line 39, in
>> importFromPath
>> return self.importFromDir(dir_path, fqname)
>> File "/usr/lib/pymodules/python2.6/nose/importer.py", line 86, in
>> importFromDir
>> mod = load_module(part_fqname, fh, filename, desc)
>> File "[...]/numpy/core/scons_support.py", line 21, in <module>
>> from numscons.numdist import process_c_str as process_str
>> ImportError: No module named numscons.numdist
>>
>> ======================================================================
>> ERROR: Failure: ImportError (No module named numscons)
>> ----------------------------------------------------------------------
>> Traceback (most recent call last):
>> File "/usr/lib/pymodules/python2.6/nose/loader.py", line 379, in
>> loadTestsFromName
>> addr.filename, addr.module)
>> File "/usr/lib/pymodules/python2.6/nose/importer.py", line 39, in
>> importFromPath
>> return self.importFromDir(dir_path, fqname)
>> File "/usr/lib/pymodules/python2.6/nose/importer.py", line 86, in
>> importFromDir
>> mod = load_module(part_fqname, fh, filename, desc)
>> File "[...]/numpy/core/setupscons.py", line 8, in <module>
>> from numscons import get_scons_build_dir
>> ImportError: No module named numscons
>>
>> ======================================================================
>> ERROR: test_multiarray.TestNewBufferProtocol.test_roundtrip
>> ----------------------------------------------------------------------
>> Traceback (most recent call last):
>> File "/usr/lib/pymodules/python2.6/nose/case.py", line 183, in runTest
>> self.test(*self.arg)
>> File "[...]/numpy/core/tests/test_multiarray.py", line 2233, in
>> test_roundtrip
>> assert_raises(ValueError, self._check_roundtrip, x)
>> File "[...]/numpy/testing/utils.py", line 1053, in assert_raises
>> return nose.tools.assert_raises(*args,**kwargs)
>> File "/usr/lib/python2.6/unittest.py", line 336, in failUnlessRaises
>> callableObj(*args, **kwargs)
>> File "[...]/numpy/core/tests/test_multiarray.py", line 2167, in
>> _check_roundtrip
>> y = np.asarray(x)
>> File "[...]/numpy/core/tests/test_multiarray.py", line 2167, in
>> _check_roundtrip
>> y = np.asarray(x)
>> File "/usr/lib/python2.6/dist-packages/coverage.py", line 322, in t
>> self.c[(f.f_code.co_filename, f.f_lineno)] = 1
>> RuntimeWarning: tp_compare didn't return -1 or -2 for exception
>>
>> ======================================================================
>> ERROR: Failure: ImportError (No module named np.core.fromnumeric)
>> ----------------------------------------------------------------------
>> Traceback (most recent call last):
>> File "/usr/lib/pymodules/python2.6/nose/loader.py", line 379, in
>> loadTestsFromName
>> addr.filename, addr.module)
>> File "/usr/lib/pymodules/python2.6/nose/importer.py", line 39, in
>> importFromPath
>> return self.importFromDir(dir_path, fqname)
>> File "/usr/lib/pymodules/python2.6/nose/importer.py", line 86, in
>> importFromDir
>> mod = load_module(part_fqname, fh, filename, desc)
>> File "[...]/numpy/ma/timer_comparison.py", line 6, in <module>
>> import np.core.fromnumeric as fromnumeric
>> ImportError: No module named np.core.fromnumeric
>>
>> ======================================================================
>> ERROR: Failure: AttributeError ('module' object has no attribute
>> '__revision__')
>> ----------------------------------------------------------------------
>> Traceback (most recent call last):
>> File "/usr/lib/pymodules/python2.6/nose/loader.py", line 379, in
>> loadTestsFromName
>> addr.filename, addr.module)
>> File "/usr/lib/pymodules/python2.6/nose/importer.py", line 39, in
>> importFromPath
>> return self.importFromDir(dir_path, fqname)
>> File "/usr/lib/pymodules/python2.6/nose/importer.py", line 86, in
>> importFromDir
>> mod = load_module(part_fqname, fh, filename, desc)
>> File "[...]/numpy/ma/version.py", line 9, in <module>
>> revision = [core.__revision__.split(':')[-1][:-1].strip(),
>> AttributeError: 'module' object has no attribute '__revision__'
>>
>> ======================================================================
>> ERROR: Failure: ImportError (The convolve package is not installed.
>>
>> It can be downloaded by checking out the latest source from
>> http://svn.scipy.org/svn/scipy/trunk/Lib/stsci or by downloading and
>> installing all of SciPy from http://www.scipy.org.
>> )
>> ----------------------------------------------------------------------
>> Traceback (most recent call last):
>> File "/usr/lib/pymodules/python2.6/nose/loader.py", line 379, in
>> loadTestsFromName
>> addr.filename, addr.module)
>> File "/usr/lib/pymodules/python2.6/nose/importer.py", line 39, in
>> importFromPath
>> return self.importFromDir(dir_path, fqname)
>> File "/usr/lib/pymodules/python2.6/nose/importer.py", line 86, in
>> importFromDir
>> mod = load_module(part_fqname, fh, filename, desc)
>> File "[...]/numpy/numarray/convolve.py", line 14, in <module>
>> raise ImportError(msg)
>> ImportError: The convolve package is not installed.
>>
>> It can be downloaded by checking out the latest source from
>> http://svn.scipy.org/svn/scipy/trunk/Lib/stsci or by downloading and
>> installing all of SciPy from http://www.scipy.org.
>>
>>
>> ======================================================================
>> ERROR: Failure: ImportError (The image package is not installed
>>
>> It can be downloaded by checking out the latest source from
>> http://svn.scipy.org/svn/scipy/trunk/Lib/stsci or by downloading and
>> installing all of SciPy from http://www.scipy.org.
>> )
>> ----------------------------------------------------------------------
>> Traceback (most recent call last):
>> File "/usr/lib/pymodules/python2.6/nose/loader.py", line 379, in
>> loadTestsFromName
>> addr.filename, addr.module)
>> File "/usr/lib/pymodules/python2.6/nose/importer.py", line 39, in
>> importFromPath
>> return self.importFromDir(dir_path, fqname)
>> File "/usr/lib/pymodules/python2.6/nose/importer.py", line 86, in
>> importFromDir
>> mod = load_module(part_fqname, fh, filename, desc)
>> File "[...]/numpy/numarray/image.py", line 14, in <module>
>> raise ImportError(msg)
>> ImportError: The image package is not installed
>>
>> It can be downloaded by checking out the latest source from
>> http://svn.scipy.org/svn/scipy/trunk/Lib/stsci or by downloading and
>> installing all of SciPy from http://www.scipy.org.
>>
>>
>> ======================================================================
>> FAIL: test_blasdot.test_dot_3args
>> ----------------------------------------------------------------------
>> Traceback (most recent call last):
>> File "/usr/lib/pymodules/python2.6/nose/case.py", line 183, in runTest
>> self.test(*self.arg)
>> File "[...]/numpy/core/tests/test_blasdot.py", line 52, in test_dot_3args
>> assert_equal(sys.getrefcount(r), 2)
>> File "[...]/numpy/testing/utils.py", line 313, in assert_equal
>> raise AssertionError(msg)
>> AssertionError:
>> Items are not equal:
>> ACTUAL: 3
>> DESIRED: 2
>>
>> ======================================================================
>> FAIL: test_dot_3args (test_multiarray.TestDot)
>> ----------------------------------------------------------------------
>> Traceback (most recent call last):
>> File "[...]/numpy/core/tests/test_multiarray.py", line 1698, in
>> test_dot_3args
>> assert_equal(sys.getrefcount(r), 2)
>> File "[...]/numpy/testing/utils.py", line 313, in assert_equal
>> raise AssertionError(msg)
>> AssertionError:
>> Items are not equal:
>> ACTUAL: 3
>> DESIRED: 2
>>
>> [...]
>>
>> Ran 3717 tests in 31.447s
>>
>> FAILED (KNOWNFAIL=3, SKIP=6, errors=8, failures=2)
>> <nose.result.TextTestResult run=3717 errors=8 failures=2>
>>
>>
>> Anyone know what I'm doing wrong?
>>
>> I'm using Ubuntu 10.04 LTS in case that matters.
>>
>> Thanks,
>> Chris
>>
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>
>
>
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