Hi, I am pleased to announce the availability of the first beta of SciPy 0.9.0. This will be the first SciPy release to include support for Python 3, as well as for Python 2.7. Please try this beta and report any problems on the scipy-dev mailing list. Binaries, sources and release notes can be found athttp://sourceforge.net/projects/scipy/files/scipy/0.9.0b1/<https://sourceforge.net/projects/numpy/files/>. Note that not all binaries (win32-py27, *-macosx10.3) are uploaded yet, they will follow in the next day or two. There are still a few known issues (so no need to report these): 1. Arpack related errors on 64-bit OS X. 2. Correlate complex192 errors on Windows. 3. correlate/conjugate current behavior is deprecated and should be removed before RC1. Enjoy, Ralf
On Mon, Dec 13, 2010 at 10:12 AM, Ralf Gommers <ralf.gommers@googlemail.com>wrote:
Hi,
I am pleased to announce the availability of the first beta of SciPy 0.9.0. This will be the first SciPy release to include support for Python 3, as well as for Python 2.7. Please try this beta and report any problems on the scipy-dev mailing list.
Binaries, sources and release notes can be found athttp://sourceforge.net/projects/scipy/files/scipy/0.9.0b1/<https://sourceforge.net/projects/numpy/files/>. Note that not all binaries (win32-py27, *-macosx10.3) are uploaded yet, they will follow in the next day or two.
There are still a few known issues (so no need to report these): 1. Arpack related errors on 64-bit OS X. 2. Correlate complex192 errors on Windows. 3. correlate/conjugate current behavior is deprecated and should be removed before RC1.
Enjoy, Ralf
Just did a clean rebuild (after a clean rebuild of numpy) and had two errors in the tests: ====================================================================== FAIL: test_imresize (test_pilutil.TestPILUtil) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/bvr/Programs/numpy/numpy/testing/decorators.py", line 146, in skipper_func return f(*args, **kwargs) File "/home/bvr/Programs/scipy/scipy/misc/tests/test_pilutil.py", line 25, in test_imresize assert_equal(im1.shape,(11,22)) File "/home/bvr/Programs/numpy/numpy/testing/utils.py", line 251, in assert_equal assert_equal(actual[k], desired[k], 'item=%r\n%s' % (k,err_msg), verbose) File "/home/bvr/Programs/numpy/numpy/testing/utils.py", line 313, in assert_equal raise AssertionError(msg) AssertionError: Items are not equal: item=0 ACTUAL: 10 DESIRED: 11 ====================================================================== FAIL: test_basic (test_signaltools.TestMedFilt) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/bvr/Programs/scipy/scipy/signal/tests/test_signaltools.py", line 284, in test_basic [ 0, 7, 11, 7, 4, 4, 19, 19, 24, 0]]) File "/home/bvr/Programs/numpy/numpy/testing/utils.py", line 686, in assert_array_equal verbose=verbose, header='Arrays are not equal') File "/home/bvr/Programs/numpy/numpy/testing/utils.py", line 618, in assert_array_compare raise AssertionError(msg) AssertionError: Arrays are not equal (mismatch 8.0%) x: array([[ 0., 50., 50., 50., 42., 15., 15., 18., 27., 0.], [ 0., 50., 50., 50., 50., 42., 19., 21., 29., 0.], [ 50., 50., 50., 50., 50., 47., 34., 34., 46., 35.],... y: array([[ 0, 50, 50, 50, 42, 15, 15, 18, 27, 0], [ 0, 50, 50, 50, 50, 42, 19, 21, 29, 0], [50, 50, 50, 50, 50, 47, 34, 34, 46, 35],... ---------------------------------------------------------------------- Ran 4822 tests in 199.244s FAILED (KNOWNFAIL=12, SKIP=35, failures=2) <nose.result.TextTestResult run=4822 errors=0 failures=2> Don't know about the first one, but the second one looks like a type-casting issue, because all the values are the same, except one is floating point and the other is integer. Ben Root
On Tue, Dec 14, 2010 at 12:43 AM, Benjamin Root <ben.root@ou.edu> wrote:
On Mon, Dec 13, 2010 at 10:12 AM, Ralf Gommers < ralf.gommers@googlemail.com> wrote:
Hi,
I am pleased to announce the availability of the first beta of SciPy 0.9.0. This will be the first SciPy release to include support for Python 3, as well as for Python 2.7. Please try this beta and report any problems on the scipy-dev mailing list.
Binaries, sources and release notes can be found athttp://sourceforge.net/projects/scipy/files/scipy/0.9.0b1/<https://sourceforge.net/projects/numpy/files/>. Note that not all binaries (win32-py27, *-macosx10.3) are uploaded yet, they will follow in the next day or two.
There are still a few known issues (so no need to report these): 1. Arpack related errors on 64-bit OS X. 2. Correlate complex192 errors on Windows. 3. correlate/conjugate current behavior is deprecated and should be removed before RC1.
Enjoy, Ralf
Hi Ben,
Just did a clean rebuild (after a clean rebuild of numpy) and had two errors in the tests:
What platform are you on?
====================================================================== FAIL: test_imresize (test_pilutil.TestPILUtil) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/bvr/Programs/numpy/numpy/testing/decorators.py", line 146, in skipper_func return f(*args, **kwargs) File "/home/bvr/Programs/scipy/scipy/misc/tests/test_pilutil.py", line 25, in test_imresize assert_equal(im1.shape,(11,22)) File "/home/bvr/Programs/numpy/numpy/testing/utils.py", line 251, in assert_equal assert_equal(actual[k], desired[k], 'item=%r\n%s' % (k,err_msg), verbose) File "/home/bvr/Programs/numpy/numpy/testing/utils.py", line 313, in assert_equal raise AssertionError(msg) AssertionError: Items are not equal: item=0
ACTUAL: 10 DESIRED: 11
This test should be changed to use a fixed seed (add as a first line of the test "np.random.seed(12345678)"). Can you provide one that fails?
====================================================================== FAIL: test_basic (test_signaltools.TestMedFilt) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/bvr/Programs/scipy/scipy/signal/tests/test_signaltools.py", line 284, in test_basic [ 0, 7, 11, 7, 4, 4, 19, 19, 24, 0]]) File "/home/bvr/Programs/numpy/numpy/testing/utils.py", line 686, in assert_array_equal verbose=verbose, header='Arrays are not equal') File "/home/bvr/Programs/numpy/numpy/testing/utils.py", line 618, in assert_array_compare raise AssertionError(msg) AssertionError: Arrays are not equal
(mismatch 8.0%) x: array([[ 0., 50., 50., 50., 42., 15., 15., 18., 27., 0.], [ 0., 50., 50., 50., 50., 42., 19., 21., 29., 0.], [ 50., 50., 50., 50., 50., 47., 34., 34., 46., 35.],... y: array([[ 0, 50, 50, 50, 42, 15, 15, 18, 27, 0], [ 0, 50, 50, 50, 50, 42, 19, 21, 29, 0], [50, 50, 50, 50, 50, 47, 34, 34, 46, 35],...
---------------------------------------------------------------------- Ran 4822 tests in 199.244s
FAILED (KNOWNFAIL=12, SKIP=35, failures=2) <nose.result.TextTestResult run=4822 errors=0 failures=2>
Don't know about the first one, but the second one looks like a type-casting issue, because all the values are the same, except one is floating point and the other is integer.
This was also reported by Nils some days ago, he had one value that was different between arrays. Ralf
Ben Root
_______________________________________________ SciPy-Dev mailing list SciPy-Dev@scipy.org http://mail.scipy.org/mailman/listinfo/scipy-dev
On Tue, Dec 14, 2010 at 6:38 AM, Ralf Gommers <ralf.gommers@googlemail.com>wrote:
On Tue, Dec 14, 2010 at 12:43 AM, Benjamin Root <ben.root@ou.edu> wrote:
On Mon, Dec 13, 2010 at 10:12 AM, Ralf Gommers < ralf.gommers@googlemail.com> wrote:
Hi,
I am pleased to announce the availability of the first beta of SciPy 0.9.0. This will be the first SciPy release to include support for Python 3, as well as for Python 2.7. Please try this beta and report any problems on the scipy-dev mailing list.
Binaries, sources and release notes can be found athttp://sourceforge.net/projects/scipy/files/scipy/0.9.0b1/<https://sourceforge.net/projects/numpy/files/>. Note that not all binaries (win32-py27, *-macosx10.3) are uploaded yet, they will follow in the next day or two.
There are still a few known issues (so no need to report these): 1. Arpack related errors on 64-bit OS X. 2. Correlate complex192 errors on Windows. 3. correlate/conjugate current behavior is deprecated and should be removed before RC1.
Enjoy, Ralf
Hi Ben,
Just did a clean rebuild (after a clean rebuild of numpy) and had two errors in the tests:
What platform are you on?
I reran the tests on just this scipy.misc module, here is the output:
scipy.misc.test() Running unit tests for scipy.misc NumPy version 2.0.0.dev-799179d NumPy is installed in /home/bvr/Programs/numpy/numpy SciPy version 0.10.0.dev SciPy is installed in /home/bvr/Programs/scipy/scipy Python version 2.6.4 (r264:75706, Jun 4 2010, 18:20:16) [GCC 4.4.4 20100503 (Red Hat 4.4.4-2)] nose version 0.11.3 ...........F..... ====================================================================== FAIL: test_imresize (test_pilutil.TestPILUtil)
Traceback (most recent call last): File "/home/bvr/Programs/numpy/numpy/testing/decorators.py", line 146, in skipper_func return f(*args, **kwargs) File "/home/bvr/Programs/scipy/scipy/misc/tests/test_pilutil.py", line 28, in test_imresize assert_equal(im1.shape,(11,22)) File "/home/bvr/Programs/numpy/numpy/testing/utils.py", line 251, in assert_equal assert_equal(actual[k], desired[k], 'item=%r\n%s' % (k,err_msg), verbose) File "/home/bvr/Programs/numpy/numpy/testing/utils.py", line 313, in assert_equal raise AssertionError(msg) AssertionError: Items are not equal: item=0 ACTUAL: 10 DESIRED: 11 ---------------------------------------------------------------------- Ran 17 tests in 0.089s FAILED (failures=1) <nose.result.TextTestResult run=17 errors=0 failures=1> Note, that I am still getting this error with the suggested addition of "np.random.seed(12345678)" to scipy/misc/tests/test_pilutil.py. I tried it both at line 20 (before the call to class TestPILUtil) and at line 24 (before the call to np.random.random() in test_imresize. I do not see how setting the seed value for these tests would make any difference since they are merely testing the resulting shape of the image after a resize, not the values of the resized image itself.
====================================================================== FAIL: test_imresize (test_pilutil.TestPILUtil) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/bvr/Programs/numpy/numpy/testing/decorators.py", line 146, in skipper_func return f(*args, **kwargs) File "/home/bvr/Programs/scipy/scipy/misc/tests/test_pilutil.py", line 25, in test_imresize assert_equal(im1.shape,(11,22)) File "/home/bvr/Programs/numpy/numpy/testing/utils.py", line 251, in assert_equal assert_equal(actual[k], desired[k], 'item=%r\n%s' % (k,err_msg), verbose) File "/home/bvr/Programs/numpy/numpy/testing/utils.py", line 313, in assert_equal raise AssertionError(msg) AssertionError: Items are not equal: item=0
ACTUAL: 10 DESIRED: 11
This test should be changed to use a fixed seed (add as a first line of the test "np.random.seed(12345678)"). Can you provide one that fails?
Also, I am not sure what you mean by "Can you provide one that fails?".
====================================================================== FAIL: test_basic (test_signaltools.TestMedFilt) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/bvr/Programs/scipy/scipy/signal/tests/test_signaltools.py", line 284, in test_basic [ 0, 7, 11, 7, 4, 4, 19, 19, 24, 0]]) File "/home/bvr/Programs/numpy/numpy/testing/utils.py", line 686, in assert_array_equal verbose=verbose, header='Arrays are not equal') File "/home/bvr/Programs/numpy/numpy/testing/utils.py", line 618, in assert_array_compare raise AssertionError(msg) AssertionError: Arrays are not equal
(mismatch 8.0%) x: array([[ 0., 50., 50., 50., 42., 15., 15., 18., 27., 0.], [ 0., 50., 50., 50., 50., 42., 19., 21., 29., 0.], [ 50., 50., 50., 50., 50., 47., 34., 34., 46., 35.],... y: array([[ 0, 50, 50, 50, 42, 15, 15, 18, 27, 0], [ 0, 50, 50, 50, 50, 42, 19, 21, 29, 0], [50, 50, 50, 50, 50, 47, 34, 34, 46, 35],...
---------------------------------------------------------------------- Ran 4822 tests in 199.244s
FAILED (KNOWNFAIL=12, SKIP=35, failures=2) <nose.result.TextTestResult run=4822 errors=0 failures=2>
Oddly enough, this second error does not always repeat itself (I had one run of the test where it did not happen...). Also, something interesting occurred while trying to get more verbose output from scipy.signal.test. When I ran it for the second time in a python session, a regression error pops up, but this never happens in the first run of the test. ====================================================================== FAIL: Regression test for #651: better handling of badly conditioned ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/bvr/Programs/scipy/scipy/signal/tests/test_filter_design.py", line 32, in test_bad_filter assert_raises(BadCoefficients, tf2zpk, [1e-15], [1.0, 1.0]) File "/home/bvr/Programs/numpy/numpy/testing/utils.py", line 982, in assert_raises return nose.tools.assert_raises(*args,**kwargs) AssertionError: BadCoefficients not raised I hope this is helpful. Let me know what other information I can provide. Ben Root
On Wed, Dec 15, 2010 at 12:01 AM, Benjamin Root <ben.root@ou.edu> wrote:
On Tue, Dec 14, 2010 at 6:38 AM, Ralf Gommers <ralf.gommers@googlemail.com
wrote:
On Tue, Dec 14, 2010 at 12:43 AM, Benjamin Root <ben.root@ou.edu> wrote:
Hi Ben,
Just did a clean rebuild (after a clean rebuild of numpy) and had two errors in the tests:
What platform are you on?
I reran the tests on just this scipy.misc module, here is the output:
scipy.misc.test() Running unit tests for scipy.misc NumPy version 2.0.0.dev-799179d NumPy is installed in /home/bvr/Programs/numpy/numpy SciPy version 0.10.0.dev SciPy is installed in /home/bvr/Programs/scipy/scipy Python version 2.6.4 (r264:75706, Jun 4 2010, 18:20:16) [GCC 4.4.4 20100503 (Red Hat 4.4.4-2)] nose version 0.11.3 ...........F.....
====================================================================== FAIL: test_imresize (test_pilutil.TestPILUtil) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/bvr/Programs/numpy/numpy/testing/decorators.py", line 146, in skipper_func return f(*args, **kwargs) File "/home/bvr/Programs/scipy/scipy/misc/tests/test_pilutil.py", line 28, in test_imresize
assert_equal(im1.shape,(11,22)) File "/home/bvr/Programs/numpy/numpy/testing/utils.py", line 251, in assert_equal assert_equal(actual[k], desired[k], 'item=%r\n%s' % (k,err_msg), verbose) File "/home/bvr/Programs/numpy/numpy/testing/utils.py", line 313, in assert_equal raise AssertionError(msg) AssertionError: Items are not equal: item=0
ACTUAL: 10 DESIRED: 11
---------------------------------------------------------------------- Ran 17 tests in 0.089s
FAILED (failures=1) <nose.result.TextTestResult run=17 errors=0 failures=1>
Note, that I am still getting this error with the suggested addition of "np.random.seed(12345678)" to scipy/misc/tests/test_pilutil.py. I tried it both at line 20 (before the call to class TestPILUtil) and at line 24 (before the call to np.random.random() in test_imresize. I do not see how setting the seed value for these tests would make any difference since they are merely testing the resulting shape of the image after a resize, not the values of the resized image itself.
The seeding may not matter (I haven't actually looked in detail yet), but I thought I had seen this error pop up before, but not reproducibly. The imresize function does some interpolation, so the numerical values could matter. In that case seeding would help.
====================================================================== FAIL: test_imresize (test_pilutil.TestPILUtil) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/bvr/Programs/numpy/numpy/testing/decorators.py", line 146, in skipper_func return f(*args, **kwargs) File "/home/bvr/Programs/scipy/scipy/misc/tests/test_pilutil.py", line 25, in test_imresize assert_equal(im1.shape,(11,22)) File "/home/bvr/Programs/numpy/numpy/testing/utils.py", line 251, in assert_equal assert_equal(actual[k], desired[k], 'item=%r\n%s' % (k,err_msg), verbose) File "/home/bvr/Programs/numpy/numpy/testing/utils.py", line 313, in assert_equal raise AssertionError(msg) AssertionError: Items are not equal: item=0
ACTUAL: 10 DESIRED: 11
This test should be changed to use a fixed seed (add as a first line of the test "np.random.seed(12345678)"). Can you provide one that fails?
Also, I am not sure what you mean by "Can you provide one that fails?".
I meant a seed value that fails. This one does, that's all we need.
====================================================================== FAIL: test_basic (test_signaltools.TestMedFilt) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/bvr/Programs/scipy/scipy/signal/tests/test_signaltools.py", line 284, in test_basic [ 0, 7, 11, 7, 4, 4, 19, 19, 24, 0]]) File "/home/bvr/Programs/numpy/numpy/testing/utils.py", line 686, in assert_array_equal verbose=verbose, header='Arrays are not equal') File "/home/bvr/Programs/numpy/numpy/testing/utils.py", line 618, in assert_array_compare raise AssertionError(msg) AssertionError: Arrays are not equal
(mismatch 8.0%) x: array([[ 0., 50., 50., 50., 42., 15., 15., 18., 27., 0.], [ 0., 50., 50., 50., 50., 42., 19., 21., 29., 0.], [ 50., 50., 50., 50., 50., 47., 34., 34., 46., 35.],... y: array([[ 0, 50, 50, 50, 42, 15, 15, 18, 27, 0], [ 0, 50, 50, 50, 50, 42, 19, 21, 29, 0], [50, 50, 50, 50, 50, 47, 34, 34, 46, 35],...
---------------------------------------------------------------------- Ran 4822 tests in 199.244s
FAILED (KNOWNFAIL=12, SKIP=35, failures=2) <nose.result.TextTestResult run=4822 errors=0 failures=2>
Oddly enough, this second error does not always repeat itself (I had one run of the test where it did not happen...). Also, something interesting occurred while trying to get more verbose output from scipy.signal.test. When I ran it for the second time in a python session, a regression error pops up, but this never happens in the first run of the test.
That's just because warnings like that are only raised once from the same module. So the second time the check fails. Nothing to worry about. Cheers, Ralf
====================================================================== FAIL: Regression test for #651: better handling of badly conditioned
---------------------------------------------------------------------- Traceback (most recent call last): File "/home/bvr/Programs/scipy/scipy/signal/tests/test_filter_design.py", line 32, in test_bad_filter assert_raises(BadCoefficients, tf2zpk, [1e-15], [1.0, 1.0]) File "/home/bvr/Programs/numpy/numpy/testing/utils.py", line 982, in assert_raises return nose.tools.assert_raises(*args,**kwargs) AssertionError: BadCoefficients not raised
I hope this is helpful. Let me know what other information I can provide.
Ben Root
_______________________________________________ SciPy-Dev mailing list SciPy-Dev@scipy.org http://mail.scipy.org/mailman/listinfo/scipy-dev
On Tue, Dec 14, 2010 at 10:13 AM, Ralf Gommers <ralf.gommers@googlemail.com> wrote:
On Wed, Dec 15, 2010 at 12:01 AM, Benjamin Root <ben.root@ou.edu> wrote:
On Tue, Dec 14, 2010 at 6:38 AM, Ralf Gommers <ralf.gommers@googlemail.com> wrote:
On Tue, Dec 14, 2010 at 12:43 AM, Benjamin Root <ben.root@ou.edu> wrote:
Hi Ben,
Just did a clean rebuild (after a clean rebuild of numpy) and had two errors in the tests:
What platform are you on?
I reran the tests on just this scipy.misc module, here is the output:
scipy.misc.test() Running unit tests for scipy.misc NumPy version 2.0.0.dev-799179d NumPy is installed in /home/bvr/Programs/numpy/numpy SciPy version 0.10.0.dev SciPy is installed in /home/bvr/Programs/scipy/scipy Python version 2.6.4 (r264:75706, Jun 4 2010, 18:20:16) [GCC 4.4.4 20100503 (Red Hat 4.4.4-2)] nose version 0.11.3 ...........F..... ====================================================================== FAIL: test_imresize (test_pilutil.TestPILUtil)
Traceback (most recent call last): File "/home/bvr/Programs/numpy/numpy/testing/decorators.py", line 146, in skipper_func return f(*args, **kwargs) File "/home/bvr/Programs/scipy/scipy/misc/tests/test_pilutil.py", line 28, in test_imresize assert_equal(im1.shape,(11,22)) File "/home/bvr/Programs/numpy/numpy/testing/utils.py", line 251, in assert_equal assert_equal(actual[k], desired[k], 'item=%r\n%s' % (k,err_msg), verbose) File "/home/bvr/Programs/numpy/numpy/testing/utils.py", line 313, in assert_equal raise AssertionError(msg) AssertionError: Items are not equal: item=0
ACTUAL: 10 DESIRED: 11
---------------------------------------------------------------------- Ran 17 tests in 0.089s
FAILED (failures=1) <nose.result.TextTestResult run=17 errors=0 failures=1>
Note, that I am still getting this error with the suggested addition of "np.random.seed(12345678)" to scipy/misc/tests/test_pilutil.py. I tried it both at line 20 (before the call to class TestPILUtil) and at line 24 (before the call to np.random.random() in test_imresize. I do not see how setting the seed value for these tests would make any difference since they are merely testing the resulting shape of the image after a resize, not the values of the resized image itself.
The seeding may not matter (I haven't actually looked in detail yet), but I thought I had seen this error pop up before, but not reproducibly. The imresize function does some interpolation, so the numerical values could matter. In that case seeding would help.
====================================================================== FAIL: test_imresize (test_pilutil.TestPILUtil) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/bvr/Programs/numpy/numpy/testing/decorators.py", line 146, in skipper_func return f(*args, **kwargs) File "/home/bvr/Programs/scipy/scipy/misc/tests/test_pilutil.py", line 25, in test_imresize assert_equal(im1.shape,(11,22)) File "/home/bvr/Programs/numpy/numpy/testing/utils.py", line 251, in assert_equal assert_equal(actual[k], desired[k], 'item=%r\n%s' % (k,err_msg), verbose) File "/home/bvr/Programs/numpy/numpy/testing/utils.py", line 313, in assert_equal raise AssertionError(msg) AssertionError: Items are not equal: item=0
ACTUAL: 10 DESIRED: 11
This test should be changed to use a fixed seed (add as a first line of the test "np.random.seed(12345678)"). Can you provide one that fails?
Also, I am not sure what you mean by "Can you provide one that fails?".
I meant a seed value that fails. This one does, that's all we need.
On my 64-bit linux system with Python 2.7, the error appears comes from float16 dtype rather than the actual seed
np.random.seed(12345678) for T in np.sctypes['float'] + [float]: ... im1 = pilutil.imresize(im,T(1.1)) ... print T, im.shape, im1.shape ... <type 'numpy.float16'> (10, 20) (10, 21) <type 'numpy.float32'> (10, 20) (11, 22) <type 'numpy.float64'> (10, 20) (11, 22) <type 'numpy.float128'> (10, 20) (11, 22) <type 'float'> (10, 20) (11, 22)
Here only the float16 has different shape from the rest. Two other items: There is a print statement in the function test_cg for 'conjugate gradient optimization routine' that needs to be commented out: See line 70 of scipy-0.9.0b1/scipy/optimize/tests/test_optimize.py: 'print self.funccalls, self.gradcalls' There is a PendingDeprecationWarning with Python2.7 which I can add a ticket for if this is non-trivial. Relevant line from verbose=10: binary dilation 29 ... /usr/lib64/python2.7/site-packages/scipy/ndimage/morphology.py:254: PendingDeprecationWarning: The CObject type is marked Pending Deprecation in Python 2.7. Please use capsule objects instead. structure, mask, output, border_value, origin, invert, cit, 1) ok Is it possible to silence the 'ComplexWarning: Casting complex values to real discards the imaginary part' message and perhaps the 'Warning: divide by zero encountered in log' message while running the tests? My reasoning is that these tend to hide real problems. Bruce
On Tue, Dec 14, 2010 at 10:52 AM, Bruce Southey <bsouthey@gmail.com> wrote:
On Tue, Dec 14, 2010 at 10:13 AM, Ralf Gommers <ralf.gommers@googlemail.com> wrote:
On Wed, Dec 15, 2010 at 12:01 AM, Benjamin Root <ben.root@ou.edu> wrote:
On Tue, Dec 14, 2010 at 6:38 AM, Ralf Gommers <ralf.gommers@googlemail.com> wrote:
On Tue, Dec 14, 2010 at 12:43 AM, Benjamin Root <ben.root@ou.edu>
Hi Ben,
Just did a clean rebuild (after a clean rebuild of numpy) and had two errors in the tests:
What platform are you on?
I reran the tests on just this scipy.misc module, here is the output:
scipy.misc.test() Running unit tests for scipy.misc NumPy version 2.0.0.dev-799179d NumPy is installed in /home/bvr/Programs/numpy/numpy SciPy version 0.10.0.dev SciPy is installed in /home/bvr/Programs/scipy/scipy Python version 2.6.4 (r264:75706, Jun 4 2010, 18:20:16) [GCC 4.4.4 20100503 (Red Hat 4.4.4-2)] nose version 0.11.3 ...........F..... ====================================================================== FAIL: test_imresize (test_pilutil.TestPILUtil)
Traceback (most recent call last): File "/home/bvr/Programs/numpy/numpy/testing/decorators.py", line 146, in skipper_func return f(*args, **kwargs) File "/home/bvr/Programs/scipy/scipy/misc/tests/test_pilutil.py", line 28, in test_imresize assert_equal(im1.shape,(11,22)) File "/home/bvr/Programs/numpy/numpy/testing/utils.py", line 251, in assert_equal assert_equal(actual[k], desired[k], 'item=%r\n%s' % (k,err_msg), verbose) File "/home/bvr/Programs/numpy/numpy/testing/utils.py", line 313, in assert_equal raise AssertionError(msg) AssertionError: Items are not equal: item=0
ACTUAL: 10 DESIRED: 11
---------------------------------------------------------------------- Ran 17 tests in 0.089s
FAILED (failures=1) <nose.result.TextTestResult run=17 errors=0 failures=1>
Note, that I am still getting this error with the suggested addition of "np.random.seed(12345678)" to scipy/misc/tests/test_pilutil.py. I tried it both at line 20 (before the call to class TestPILUtil) and at line 24 (before the call to np.random.random() in test_imresize. I do not see how setting the seed value for these tests would make any difference since
are merely testing the resulting shape of the image after a resize, not
values of the resized image itself.
The seeding may not matter (I haven't actually looked in detail yet), but I thought I had seen this error pop up before, but not reproducibly. The imresize function does some interpolation, so the numerical values could matter. In that case seeding would help.
====================================================================== FAIL: test_imresize (test_pilutil.TestPILUtil) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/bvr/Programs/numpy/numpy/testing/decorators.py", line
146,
in skipper_func return f(*args, **kwargs) File "/home/bvr/Programs/scipy/scipy/misc/tests/test_pilutil.py",
wrote: they the line
25, in test_imresize assert_equal(im1.shape,(11,22)) File "/home/bvr/Programs/numpy/numpy/testing/utils.py", line 251, in assert_equal assert_equal(actual[k], desired[k], 'item=%r\n%s' % (k,err_msg), verbose) File "/home/bvr/Programs/numpy/numpy/testing/utils.py", line 313, in assert_equal raise AssertionError(msg) AssertionError: Items are not equal: item=0
ACTUAL: 10 DESIRED: 11
This test should be changed to use a fixed seed (add as a first line of the test "np.random.seed(12345678)"). Can you provide one that fails?
Also, I am not sure what you mean by "Can you provide one that fails?".
I meant a seed value that fails. This one does, that's all we need.
On my 64-bit linux system with Python 2.7, the error appears comes from float16 dtype rather than the actual seed
np.random.seed(12345678) for T in np.sctypes['float'] + [float]: ... im1 = pilutil.imresize(im,T(1.1)) ... print T, im.shape, im1.shape ... <type 'numpy.float16'> (10, 20) (10, 21) <type 'numpy.float32'> (10, 20) (11, 22) <type 'numpy.float64'> (10, 20) (11, 22) <type 'numpy.float128'> (10, 20) (11, 22) <type 'float'> (10, 20) (11, 22)
Here only the float16 has different shape from the rest.
Ah, you compiled against numpy master instead of numpy 1.5.1, float16 is only in the development branch. I think the test should be fixed to use an explicit list of types supported by pilutil. Chuck
On 12/14/2010 02:09 PM, Charles R Harris wrote:
On Tue, Dec 14, 2010 at 10:52 AM, Bruce Southey <bsouthey@gmail.com <mailto:bsouthey@gmail.com>> wrote:
On Tue, Dec 14, 2010 at 10:13 AM, Ralf Gommers <ralf.gommers@googlemail.com <mailto:ralf.gommers@googlemail.com>> wrote: > > > On Wed, Dec 15, 2010 at 12:01 AM, Benjamin Root <ben.root@ou.edu <mailto:ben.root@ou.edu>> wrote: >> >> >> On Tue, Dec 14, 2010 at 6:38 AM, Ralf Gommers >> <ralf.gommers@googlemail.com <mailto:ralf.gommers@googlemail.com>> wrote: >>> >>> >>> On Tue, Dec 14, 2010 at 12:43 AM, Benjamin Root <ben.root@ou.edu <mailto:ben.root@ou.edu>> wrote: >>> >>> Hi Ben, >>>> >>>> Just did a clean rebuild (after a clean rebuild of numpy) and had two >>>> errors in the tests: >>> >>> What platform are you on? >> >> I reran the tests on just this scipy.misc module, here is the output: >> >> >>> scipy.misc.test() >> Running unit tests for scipy.misc >> NumPy version 2.0.0.dev-799179d >> NumPy is installed in /home/bvr/Programs/numpy/numpy >> SciPy version 0.10.0.dev >> SciPy is installed in /home/bvr/Programs/scipy/scipy >> Python version 2.6.4 (r264:75706, Jun 4 2010, 18:20:16) [GCC 4.4.4 >> 20100503 (Red Hat 4.4.4-2)] >> nose version 0.11.3 >> ...........F..... >> ====================================================================== >> FAIL: test_imresize (test_pilutil.TestPILUtil) >> ---------------------------------------------------------------------- >> Traceback (most recent call last): >> File "/home/bvr/Programs/numpy/numpy/testing/decorators.py", line 146, >> in skipper_func >> return f(*args, **kwargs) >> File "/home/bvr/Programs/scipy/scipy/misc/tests/test_pilutil.py", line >> 28, in test_imresize >> assert_equal(im1.shape,(11,22)) >> File "/home/bvr/Programs/numpy/numpy/testing/utils.py", line 251, in >> assert_equal >> assert_equal(actual[k], desired[k], 'item=%r\n%s' % (k,err_msg), >> verbose) >> File "/home/bvr/Programs/numpy/numpy/testing/utils.py", line 313, in >> assert_equal >> raise AssertionError(msg) >> AssertionError: >> Items are not equal: >> item=0 >> >> ACTUAL: 10 >> DESIRED: 11 >> >> ---------------------------------------------------------------------- >> Ran 17 tests in 0.089s >> >> FAILED (failures=1) >> <nose.result.TextTestResult run=17 errors=0 failures=1> >> >> Note, that I am still getting this error with the suggested addition of >> "np.random.seed(12345678)" to scipy/misc/tests/test_pilutil.py. I tried it >> both at line 20 (before the call to class TestPILUtil) and at line 24 >> (before the call to np.random.random() in test_imresize. I do not see how >> setting the seed value for these tests would make any difference since they >> are merely testing the resulting shape of the image after a resize, not the >> values of the resized image itself. > > The seeding may not matter (I haven't actually looked in detail yet), but I > thought I had seen this error pop up before, but not reproducibly. The > imresize function does some interpolation, so the numerical values could > matter. In that case seeding would help. >> >> >>>> >>>> ====================================================================== >>>> FAIL: test_imresize (test_pilutil.TestPILUtil) >>>> ---------------------------------------------------------------------- >>>> Traceback (most recent call last): >>>> File "/home/bvr/Programs/numpy/numpy/testing/decorators.py", line 146, >>>> in skipper_func >>>> return f(*args, **kwargs) >>>> File "/home/bvr/Programs/scipy/scipy/misc/tests/test_pilutil.py", line >>>> 25, in test_imresize >>>> assert_equal(im1.shape,(11,22)) >>>> File "/home/bvr/Programs/numpy/numpy/testing/utils.py", line 251, in >>>> assert_equal >>>> assert_equal(actual[k], desired[k], 'item=%r\n%s' % (k,err_msg), >>>> verbose) >>>> File "/home/bvr/Programs/numpy/numpy/testing/utils.py", line 313, in >>>> assert_equal >>>> raise AssertionError(msg) >>>> AssertionError: >>>> Items are not equal: >>>> item=0 >>>> >>>> ACTUAL: 10 >>>> DESIRED: 11 >>> >>> This test should be changed to use a fixed seed (add as a first line of >>> the test "np.random.seed(12345678)"). Can you provide one that fails? >>> >> >> Also, I am not sure what you mean by "Can you provide one that fails?". > > I meant a seed value that fails. This one does, that's all we need.
On my 64-bit linux system with Python 2.7, the error appears comes from float16 dtype rather than the actual seed >>> np.random.seed(12345678) >>> for T in np.sctypes['float'] + [float]: ... im1 = pilutil.imresize(im,T(1.1)) ... print T, im.shape, im1.shape ... <type 'numpy.float16'> (10, 20) (10, 21) <type 'numpy.float32'> (10, 20) (11, 22) <type 'numpy.float64'> (10, 20) (11, 22) <type 'numpy.float128'> (10, 20) (11, 22) <type 'float'> (10, 20) (11, 22)
Here only the float16 has different shape from the rest.
Ah, you compiled against numpy master instead of numpy 1.5.1, float16 is only in the development branch. I think the test should be fixed to use an explicit list of types supported by pilutil.
Chuck
Sorry, I forgot to add the numpy version '2.0.0.dev-799179d' because 1.5.1 is just too old and I am too lazy to go back and downgrade :-) Bruce
On Tue, Dec 14, 2010 at 2:15 PM, Bruce Southey <bsouthey@gmail.com> wrote:
On 12/14/2010 02:09 PM, Charles R Harris wrote:
On Tue, Dec 14, 2010 at 10:52 AM, Bruce Southey <bsouthey@gmail.com> wrote:
On Tue, Dec 14, 2010 at 10:13 AM, Ralf Gommers <ralf.gommers@googlemail.com> wrote:
On Wed, Dec 15, 2010 at 12:01 AM, Benjamin Root <ben.root@ou.edu> wrote:
On Tue, Dec 14, 2010 at 6:38 AM, Ralf Gommers <ralf.gommers@googlemail.com> wrote:
On Tue, Dec 14, 2010 at 12:43 AM, Benjamin Root <ben.root@ou.edu> wrote:
Hi Ben,
Just did a clean rebuild (after a clean rebuild of numpy) and had two errors in the tests:
What platform are you on?
I reran the tests on just this scipy.misc module, here is the output:
> scipy.misc.test() Running unit tests for scipy.misc NumPy version 2.0.0.dev-799179d NumPy is installed in /home/bvr/Programs/numpy/numpy SciPy version 0.10.0.dev SciPy is installed in /home/bvr/Programs/scipy/scipy Python version 2.6.4 (r264:75706, Jun 4 2010, 18:20:16) [GCC 4.4.4 20100503 (Red Hat 4.4.4-2)] nose version 0.11.3 ...........F..... ====================================================================== FAIL: test_imresize (test_pilutil.TestPILUtil)
Traceback (most recent call last): File "/home/bvr/Programs/numpy/numpy/testing/decorators.py", line 146, in skipper_func return f(*args, **kwargs) File "/home/bvr/Programs/scipy/scipy/misc/tests/test_pilutil.py", line 28, in test_imresize assert_equal(im1.shape,(11,22)) File "/home/bvr/Programs/numpy/numpy/testing/utils.py", line 251, in assert_equal assert_equal(actual[k], desired[k], 'item=%r\n%s' % (k,err_msg), verbose) File "/home/bvr/Programs/numpy/numpy/testing/utils.py", line 313, in assert_equal raise AssertionError(msg) AssertionError: Items are not equal: item=0
ACTUAL: 10 DESIRED: 11
---------------------------------------------------------------------- Ran 17 tests in 0.089s
FAILED (failures=1) <nose.result.TextTestResult run=17 errors=0 failures=1>
Note, that I am still getting this error with the suggested addition of "np.random.seed(12345678)" to scipy/misc/tests/test_pilutil.py. I tried it both at line 20 (before the call to class TestPILUtil) and at line 24 (before the call to np.random.random() in test_imresize. I do not see how setting the seed value for these tests would make any difference since they are merely testing the resulting shape of the image after a resize, not the values of the resized image itself.
The seeding may not matter (I haven't actually looked in detail yet), but I thought I had seen this error pop up before, but not reproducibly. The imresize function does some interpolation, so the numerical values could matter. In that case seeding would help.
====================================================================== FAIL: test_imresize (test_pilutil.TestPILUtil)
---------------------------------------------------------------------- Traceback (most recent call last): File "/home/bvr/Programs/numpy/numpy/testing/decorators.py", line 146, in skipper_func return f(*args, **kwargs) File "/home/bvr/Programs/scipy/scipy/misc/tests/test_pilutil.py", line 25, in test_imresize assert_equal(im1.shape,(11,22)) File "/home/bvr/Programs/numpy/numpy/testing/utils.py", line 251, in assert_equal assert_equal(actual[k], desired[k], 'item=%r\n%s' % (k,err_msg), verbose) File "/home/bvr/Programs/numpy/numpy/testing/utils.py", line 313, in assert_equal raise AssertionError(msg) AssertionError: Items are not equal: item=0
ACTUAL: 10 DESIRED: 11
This test should be changed to use a fixed seed (add as a first line of the test "np.random.seed(12345678)"). Can you provide one that fails?
Also, I am not sure what you mean by "Can you provide one that fails?".
I meant a seed value that fails. This one does, that's all we need.
On my 64-bit linux system with Python 2.7, the error appears comes from float16 dtype rather than the actual seed
np.random.seed(12345678) for T in np.sctypes['float'] + [float]: ... im1 = pilutil.imresize(im,T(1.1)) ... print T, im.shape, im1.shape ... <type 'numpy.float16'> (10, 20) (10, 21) <type 'numpy.float32'> (10, 20) (11, 22) <type 'numpy.float64'> (10, 20) (11, 22) <type 'numpy.float128'> (10, 20) (11, 22) <type 'float'> (10, 20) (11, 22)
Here only the float16 has different shape from the rest.
Ah, you compiled against numpy master instead of numpy 1.5.1, float16 is only in the development branch. I think the test should be fixed to use an explicit list of types supported by pilutil.
Chuck
Sorry, I forgot to add the numpy version '2.0.0.dev-799179d' because 1.5.1 is just too old and I am too lazy to go back and downgrade :-)
Bruce
Okay, No issues with numpy 1.5.1 under Python 2.7 - given below. I get this error under Python 3.1:' FAIL: test_highpass (test_fir_filter_design.TestFirWinMore)'. This appears to be integer division as the test passes when line 126 of 'scipy/signal/tests/test_fir_filter_design.py' is changed to: assert_array_almost_equal(taps[:ntaps//2], taps[ntaps:ntaps-ntaps//2-1:-1]) Bruce $ python -c "import scipy; scipy.test()" Running unit tests for scipy NumPy version 1.5.1 NumPy is installed in /usr/lib64/python2.7/site-packages/numpy SciPy version 0.9.0b1 SciPy is installed in /usr/lib64/python2.7/site-packages/scipy Python version 2.7 (r27:82500, Sep 16 2010, 18:02:00) [GCC 4.5.1 20100907 (Red Hat 4.5.1-3)] nose version 0.11.2 [snip] ......................................................................... ---------------------------------------------------------------------- Ran 4794 tests in 41.009s OK (KNOWNFAIL=12, SKIP=35) $ python3 -c "import scipy; scipy.test()" Running unit tests for scipy NumPy version 1.5.1 NumPy is installed in /usr/lib64/python3.1/site-packages/numpy SciPy version 0.9.0b1 SciPy is installed in /usr/lib64/python3.1/site-packages/scipy Python version 3.1.2 (r312:79147, Sep 8 2010, 23:02:57) [GCC 4.5.1 20100812 (Red Hat 4.5.1-1)] nose version 3.0.0 [snip] ..............................................................................................................................E ====================================================================== ERROR: Failure: ImportError (No module named c_spec) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python3.1/site-packages/nose/failure.py", line 37, in runTest reraise(self.exc_class, self.exc_val, self.tb) File "/usr/lib/python3.1/site-packages/nose/_3.py", line 7, in reraise raise exc_class(exc_val).with_traceback(tb) File "/usr/lib/python3.1/site-packages/nose/loader.py", line 389, in loadTestsFromName addr.filename, addr.module) File "/usr/lib/python3.1/site-packages/nose/importer.py", line 39, in importFromPath return self.importFromDir(dir_path, fqname) File "/usr/lib/python3.1/site-packages/nose/importer.py", line 86, in importFromDir mod = load_module(part_fqname, fh, filename, desc) File "/usr/lib64/python3.1/site-packages/scipy/weave/__init__.py", line 13, in <module> from .inline_tools import inline File "/usr/lib64/python3.1/site-packages/scipy/weave/inline_tools.py", line 5, in <module> from . import ext_tools File "/usr/lib64/python3.1/site-packages/scipy/weave/ext_tools.py", line 7, in <module> from . import converters File "/usr/lib64/python3.1/site-packages/scipy/weave/converters.py", line 5, in <module> from . import c_spec File "/usr/lib64/python3.1/site-packages/scipy/weave/c_spec.py", line 380, in <module> import os, c_spec # yes, I import myself to find out my __file__ location. ImportError: No module named c_spec ====================================================================== FAIL: test_highpass (test_fir_filter_design.TestFirWinMore) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib64/python3.1/site-packages/scipy/signal/tests/test_fir_filter_design.py", line 126, in test_highpass assert_array_almost_equal(taps[:ntaps/2], taps[ntaps:ntaps-ntaps/2-1:-1]) File "/usr/lib64/python3.1/site-packages/numpy/testing/utils.py", line 774, in assert_array_almost_equal header='Arrays are not almost equal') File "/usr/lib64/python3.1/site-packages/numpy/testing/utils.py", line 579, in assert_array_compare raise AssertionError(msg) AssertionError: Arrays are not almost equal (shapes (196,), (197,) mismatch) x: array([ -2.21482814e-21, 9.49475306e-08, -8.72925108e-21, -1.69672728e-07, -2.55604897e-21, 2.73170159e-07, -9.89221963e-22, -4.12424017e-07, 4.88221354e-21,... y: array([ -2.21482814e-21, 9.49475306e-08, -8.72925108e-21, -1.69672728e-07, -2.55604897e-21, 2.73170159e-07, -9.89221963e-22, -4.12424017e-07, 4.88221354e-21,... ---------------------------------------------------------------------- Ran 4657 tests in 42.204s FAILED (KNOWNFAIL=12, SKIP=41, errors=1, failures=1)
On Tue, Dec 14, 2010 at 3:23 PM, Bruce Southey <bsouthey@gmail.com> wrote:
On Tue, Dec 14, 2010 at 2:15 PM, Bruce Southey <bsouthey@gmail.com> wrote:
On 12/14/2010 02:09 PM, Charles R Harris wrote:
On Tue, Dec 14, 2010 at 10:52 AM, Bruce Southey <bsouthey@gmail.com> wrote:
On Tue, Dec 14, 2010 at 10:13 AM, Ralf Gommers <ralf.gommers@googlemail.com> wrote:
On Wed, Dec 15, 2010 at 12:01 AM, Benjamin Root <ben.root@ou.edu>
wrote:
On Tue, Dec 14, 2010 at 6:38 AM, Ralf Gommers <ralf.gommers@googlemail.com> wrote:
On Tue, Dec 14, 2010 at 12:43 AM, Benjamin Root <ben.root@ou.edu> wrote:
Hi Ben, > > Just did a clean rebuild (after a clean rebuild of numpy) and had
two
> errors in the tests:
What platform are you on?
I reran the tests on just this scipy.misc module, here is the output:
>> scipy.misc.test() Running unit tests for scipy.misc NumPy version 2.0.0.dev-799179d NumPy is installed in /home/bvr/Programs/numpy/numpy SciPy version 0.10.0.dev SciPy is installed in /home/bvr/Programs/scipy/scipy Python version 2.6.4 (r264:75706, Jun 4 2010, 18:20:16) [GCC 4.4.4 20100503 (Red Hat 4.4.4-2)] nose version 0.11.3 ...........F.....
======================================================================
FAIL: test_imresize (test_pilutil.TestPILUtil)
Traceback (most recent call last): File "/home/bvr/Programs/numpy/numpy/testing/decorators.py", line 146, in skipper_func return f(*args, **kwargs) File "/home/bvr/Programs/scipy/scipy/misc/tests/test_pilutil.py", line 28, in test_imresize assert_equal(im1.shape,(11,22)) File "/home/bvr/Programs/numpy/numpy/testing/utils.py", line 251, in assert_equal assert_equal(actual[k], desired[k], 'item=%r\n%s' % (k,err_msg), verbose) File "/home/bvr/Programs/numpy/numpy/testing/utils.py", line 313, in assert_equal raise AssertionError(msg) AssertionError: Items are not equal: item=0
ACTUAL: 10 DESIRED: 11
Ran 17 tests in 0.089s
FAILED (failures=1) <nose.result.TextTestResult run=17 errors=0 failures=1>
Note, that I am still getting this error with the suggested addition of "np.random.seed(12345678)" to scipy/misc/tests/test_pilutil.py. I tried it both at line 20 (before the call to class TestPILUtil) and at line 24 (before the call to np.random.random() in test_imresize. I do not see how setting the seed value for these tests would make any difference since they are merely testing the resulting shape of the image after a resize, not the values of the resized image itself.
The seeding may not matter (I haven't actually looked in detail yet), but I thought I had seen this error pop up before, but not reproducibly. The imresize function does some interpolation, so the numerical values could matter. In that case seeding would help.
> > >
======================================================================
> FAIL: test_imresize (test_pilutil.TestPILUtil) > >
> Traceback (most recent call last): > File "/home/bvr/Programs/numpy/numpy/testing/decorators.py", line > 146, > in skipper_func > return f(*args, **kwargs) > File "/home/bvr/Programs/scipy/scipy/misc/tests/test_pilutil.py", > line > 25, in test_imresize > assert_equal(im1.shape,(11,22)) > File "/home/bvr/Programs/numpy/numpy/testing/utils.py", line 251, > in > assert_equal > assert_equal(actual[k], desired[k], 'item=%r\n%s' % (k,err_msg), > verbose) > File "/home/bvr/Programs/numpy/numpy/testing/utils.py", line 313, > in > assert_equal > raise AssertionError(msg) > AssertionError: > Items are not equal: > item=0 > > ACTUAL: 10 > DESIRED: 11
This test should be changed to use a fixed seed (add as a first line of the test "np.random.seed(12345678)"). Can you provide one that fails?
Also, I am not sure what you mean by "Can you provide one that fails?".
I meant a seed value that fails. This one does, that's all we need.
On my 64-bit linux system with Python 2.7, the error appears comes from float16 dtype rather than the actual seed
np.random.seed(12345678) for T in np.sctypes['float'] + [float]: ... im1 = pilutil.imresize(im,T(1.1)) ... print T, im.shape, im1.shape ... <type 'numpy.float16'> (10, 20) (10, 21) <type 'numpy.float32'> (10, 20) (11, 22) <type 'numpy.float64'> (10, 20) (11, 22) <type 'numpy.float128'> (10, 20) (11, 22) <type 'float'> (10, 20) (11, 22)
Here only the float16 has different shape from the rest.
Ah, you compiled against numpy master instead of numpy 1.5.1, float16 is only in the development branch. I think the test should be fixed to use an explicit list of types supported by pilutil.
Chuck
Sorry, I forgot to add the numpy version '2.0.0.dev-799179d' because 1.5.1 is just too old and I am too lazy to go back and downgrade :-)
Bruce
Okay, No issues with numpy 1.5.1 under Python 2.7 - given below.
I get this error under Python 3.1:' FAIL: test_highpass (test_fir_filter_design.TestFirWinMore)'. This appears to be integer division as the test passes when line 126 of 'scipy/signal/tests/test_fir_filter_design.py' is changed to: assert_array_almost_equal(taps[:ntaps//2], taps[ntaps:ntaps-ntaps//2-1:-1])
Bruce
$ python -c "import scipy; scipy.test()" Running unit tests for scipy NumPy version 1.5.1 NumPy is installed in /usr/lib64/python2.7/site-packages/numpy SciPy version 0.9.0b1 SciPy is installed in /usr/lib64/python2.7/site-packages/scipy Python version 2.7 (r27:82500, Sep 16 2010, 18:02:00) [GCC 4.5.1 20100907 (Red Hat 4.5.1-3)] nose version 0.11.2 [snip] ......................................................................... ---------------------------------------------------------------------- Ran 4794 tests in 41.009s
OK (KNOWNFAIL=12, SKIP=35)
$ python3 -c "import scipy; scipy.test()" Running unit tests for scipy NumPy version 1.5.1 NumPy is installed in /usr/lib64/python3.1/site-packages/numpy SciPy version 0.9.0b1 SciPy is installed in /usr/lib64/python3.1/site-packages/scipy Python version 3.1.2 (r312:79147, Sep 8 2010, 23:02:57) [GCC 4.5.1 20100812 (Red Hat 4.5.1-1)] nose version 3.0.0 [snip]
..............................................................................................................................E ====================================================================== ERROR: Failure: ImportError (No module named c_spec) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python3.1/site-packages/nose/failure.py", line 37, in runTest reraise(self.exc_class, self.exc_val, self.tb) File "/usr/lib/python3.1/site-packages/nose/_3.py", line 7, in reraise raise exc_class(exc_val).with_traceback(tb) File "/usr/lib/python3.1/site-packages/nose/loader.py", line 389, in loadTestsFromName addr.filename, addr.module) File "/usr/lib/python3.1/site-packages/nose/importer.py", line 39, in importFromPath return self.importFromDir(dir_path, fqname) File "/usr/lib/python3.1/site-packages/nose/importer.py", line 86, in importFromDir mod = load_module(part_fqname, fh, filename, desc) File "/usr/lib64/python3.1/site-packages/scipy/weave/__init__.py", line 13, in <module> from .inline_tools import inline File "/usr/lib64/python3.1/site-packages/scipy/weave/inline_tools.py", line 5, in <module> from . import ext_tools File "/usr/lib64/python3.1/site-packages/scipy/weave/ext_tools.py", line 7, in <module> from . import converters File "/usr/lib64/python3.1/site-packages/scipy/weave/converters.py", line 5, in <module> from . import c_spec File "/usr/lib64/python3.1/site-packages/scipy/weave/c_spec.py", line 380, in <module> import os, c_spec # yes, I import myself to find out my __file__ location. ImportError: No module named c_spec
====================================================================== FAIL: test_highpass (test_fir_filter_design.TestFirWinMore) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib64/python3.1/site-packages/scipy/signal/tests/test_fir_filter_design.py", line 126, in test_highpass assert_array_almost_equal(taps[:ntaps/2], taps[ntaps:ntaps-ntaps/2-1:-1]) File "/usr/lib64/python3.1/site-packages/numpy/testing/utils.py", line 774, in assert_array_almost_equal header='Arrays are not almost equal') File "/usr/lib64/python3.1/site-packages/numpy/testing/utils.py", line 579, in assert_array_compare raise AssertionError(msg) AssertionError: Arrays are not almost equal
(shapes (196,), (197,) mismatch) x: array([ -2.21482814e-21, 9.49475306e-08, -8.72925108e-21, -1.69672728e-07, -2.55604897e-21, 2.73170159e-07, -9.89221963e-22, -4.12424017e-07, 4.88221354e-21,... y: array([ -2.21482814e-21, 9.49475306e-08, -8.72925108e-21, -1.69672728e-07, -2.55604897e-21, 2.73170159e-07, -9.89221963e-22, -4.12424017e-07, 4.88221354e-21,...
---------------------------------------------------------------------- Ran 4657 tests in 42.204s
FAILED (KNOWNFAIL=12, SKIP=41, errors=1, failures=1)
In r7019, I updated test_fir_filter_design.py in trunk to use explicit integer division where appropriate. Warren
On Tue, Dec 14, 2010 at 2:09 PM, Charles R Harris <charlesr.harris@gmail.com
wrote:
On Tue, Dec 14, 2010 at 10:52 AM, Bruce Southey <bsouthey@gmail.com>wrote:
On Tue, Dec 14, 2010 at 10:13 AM, Ralf Gommers <ralf.gommers@googlemail.com> wrote:
On Wed, Dec 15, 2010 at 12:01 AM, Benjamin Root <ben.root@ou.edu>
On Tue, Dec 14, 2010 at 6:38 AM, Ralf Gommers <ralf.gommers@googlemail.com> wrote:
On Tue, Dec 14, 2010 at 12:43 AM, Benjamin Root <ben.root@ou.edu>
wrote:
Hi Ben,
Just did a clean rebuild (after a clean rebuild of numpy) and had two errors in the tests:
What platform are you on?
I reran the tests on just this scipy.misc module, here is the output:
> scipy.misc.test() Running unit tests for scipy.misc NumPy version 2.0.0.dev-799179d NumPy is installed in /home/bvr/Programs/numpy/numpy SciPy version 0.10.0.dev SciPy is installed in /home/bvr/Programs/scipy/scipy Python version 2.6.4 (r264:75706, Jun 4 2010, 18:20:16) [GCC 4.4.4 20100503 (Red Hat 4.4.4-2)] nose version 0.11.3 ...........F..... ====================================================================== FAIL: test_imresize (test_pilutil.TestPILUtil)
Traceback (most recent call last): File "/home/bvr/Programs/numpy/numpy/testing/decorators.py", line 146, in skipper_func return f(*args, **kwargs) File "/home/bvr/Programs/scipy/scipy/misc/tests/test_pilutil.py",
28, in test_imresize assert_equal(im1.shape,(11,22)) File "/home/bvr/Programs/numpy/numpy/testing/utils.py", line 251, in assert_equal assert_equal(actual[k], desired[k], 'item=%r\n%s' % (k,err_msg), verbose) File "/home/bvr/Programs/numpy/numpy/testing/utils.py", line 313, in assert_equal raise AssertionError(msg) AssertionError: Items are not equal: item=0
ACTUAL: 10 DESIRED: 11
---------------------------------------------------------------------- Ran 17 tests in 0.089s
FAILED (failures=1) <nose.result.TextTestResult run=17 errors=0 failures=1>
Note, that I am still getting this error with the suggested addition of "np.random.seed(12345678)" to scipy/misc/tests/test_pilutil.py. I
both at line 20 (before the call to class TestPILUtil) and at line 24 (before the call to np.random.random() in test_imresize. I do not see how setting the seed value for these tests would make any difference since
are merely testing the resulting shape of the image after a resize, not
wrote: line tried it they the
values of the resized image itself.
The seeding may not matter (I haven't actually looked in detail yet), but I thought I had seen this error pop up before, but not reproducibly. The imresize function does some interpolation, so the numerical values could matter. In that case seeding would help.
======================================================================
FAIL: test_imresize (test_pilutil.TestPILUtil)
Traceback (most recent call last): File "/home/bvr/Programs/numpy/numpy/testing/decorators.py", line 146, in skipper_func return f(*args, **kwargs) File "/home/bvr/Programs/scipy/scipy/misc/tests/test_pilutil.py", line 25, in test_imresize assert_equal(im1.shape,(11,22)) File "/home/bvr/Programs/numpy/numpy/testing/utils.py", line 251, in assert_equal assert_equal(actual[k], desired[k], 'item=%r\n%s' % (k,err_msg), verbose) File "/home/bvr/Programs/numpy/numpy/testing/utils.py", line 313, in assert_equal raise AssertionError(msg) AssertionError: Items are not equal: item=0
ACTUAL: 10 DESIRED: 11
This test should be changed to use a fixed seed (add as a first line of the test "np.random.seed(12345678)"). Can you provide one that fails?
Also, I am not sure what you mean by "Can you provide one that fails?".
I meant a seed value that fails. This one does, that's all we need.
On my 64-bit linux system with Python 2.7, the error appears comes from float16 dtype rather than the actual seed
np.random.seed(12345678) for T in np.sctypes['float'] + [float]: ... im1 = pilutil.imresize(im,T(1.1)) ... print T, im.shape, im1.shape ... <type 'numpy.float16'> (10, 20) (10, 21) <type 'numpy.float32'> (10, 20) (11, 22) <type 'numpy.float64'> (10, 20) (11, 22) <type 'numpy.float128'> (10, 20) (11, 22) <type 'float'> (10, 20) (11, 22)
Here only the float16 has different shape from the rest.
Ah, you compiled against numpy master instead of numpy 1.5.1, float16 is only in the development branch. I think the test should be fixed to use an explicit list of types supported by pilutil.
Chuck
Good eye, Chuck! That is also the case for me. I will give the 1.5.1 build a spin to see if the other error was also dependent on the numpy versions. Ben Root
Tue, 14 Dec 2010 00:12:32 +0800, Ralf Gommers wrote:
I am pleased to announce the availability of the first beta of SciPy 0.9.0. This will be the first SciPy release to include support for Python 3, as well as for Python 2.7.
Note: scipy.weave does not work on Python 3 yet; the other parts of Scipy do. -- Pauli Virtanen
On Tue, Dec 14, 2010 at 12:46 AM, Pauli Virtanen <pav@iki.fi> wrote:
Tue, 14 Dec 2010 00:12:32 +0800, Ralf Gommers wrote:
I am pleased to announce the availability of the first beta of SciPy 0.9.0. This will be the first SciPy release to include support for Python 3, as well as for Python 2.7.
Note: scipy.weave does not work on Python 3 yet; the other parts of Scipy do.
Do you (or anyone else) plan to work on this before the final release? If not I'll update the release notes.
Ralf
Tue, 14 Dec 2010 20:14:57 +0800, Ralf Gommers wrote: [clip]
Do you (or anyone else) plan to work on this before the final release? If not I'll update the release notes.
If I find time for it before the RC. If someone else wants to take a shot at it, be welcome. In any case it's best to update the release notes to reflect the current situation. Pauli
On 12/13/2010 8:12 AM, Ralf Gommers wrote:
Hi,
I am pleased to announce the availability of the first beta of SciPy 0.9.0. This will be the first SciPy release to include support for Python 3, as well as for Python 2.7. Please try this beta and report any problems on the scipy-dev mailing list.
Binaries, sources and release notes can be found athttp://sourceforge.net/projects/scipy/files/scipy/0.9.0b1/ <https://sourceforge.net/projects/numpy/files/>. Note that not all binaries (win32-py27, *-macosx10.3) are uploaded yet, they will follow in the next day or two.
There are still a few known issues (so no need to report these): 1. Arpack related errors on 64-bit OS X. 2. Correlate complex192 errors on Windows. 3. correlate/conjugate current behavior is deprecated and should be removed before RC1.
Enjoy, Ralf
Thank you! I ran into the following issues with scipy 0.9.0b1 on Windows when building with msvc 9 and intel 11.1 compilers. Numpy is version 1.5.1, linked against MKL. 1) after patching some source files and setup scripts (see msvc9.diff attachment), "python setup.py bdist_winist" succeeds on 32- and 64-bit Python 2.6, 2.7, and 3.1. The Visual C compiler reproducibly crashes while compiling scipy\special\cephes\ndtr.c. Running the build command again (without cleaning the build directory) seems to work. 2) the build process fails on Python 3.2b1 with the following errors: scipy\sparse\sparsetools\csr_wrap.cxx(2451) : error C3861: 'PyCObject_Import': identifier not found scipy\sparse\sparsetools\csr_wrap.cxx(2521) : error C3861: 'PyCObject_FromVoidPtr': identifier not found scipy\sparse\sparsetools\csr_wrap.cxx(2544) : error C3861: 'PyCObject_AsVoidPtr': identifier not found 3) 32-bit Python 2.6 is the only platform where scipy.test() finishes; albeit with 32 failures. Besides the Correlate complex192 and TestODR errors (http://projects.scipy.org/scipy/ticket/678) I get FAIL: Real-valued Bessel domains ---------------------------------------------------------------------- Traceback (most recent call last): File "X:\Python26\lib\site-packages\scipy\special\tests\test_basic.py", line 1704, in test_ticket_854 assert_(not isnan(special.airye(-1)[2:4]).any(), special.airye(-1)) File "X:\Python26\lib\site-packages\numpy\testing\utils.py", line 34, in assert_ raise AssertionError(msg) AssertionError: (nan, nan, nan, nan) 4) scipy.test() on Python 2.7 and 3.1 crashes as reported in ticket #1210 <http://projects.scipy.org/scipy/ticket/1210> 5) On 64 bit platforms, scipy.test() quits at the following test test_interpnd.TestCloughTocher2DInterpolator.test_dense ... QH6084 qhull internal error (qh_meminit): sizeof(void*) 8 > sizeof(ptr_intT) 4. Change ptr_intT in mem.h to 'long long' -- Christoph
On Mon, 13 Dec 2010 10:18:13 -0800, Christoph Gohlke wrote: [clip]
I ran into the following issues with scipy 0.9.0b1 on Windows when building with msvc 9 and intel 11.1 compilers. Numpy is version 1.5.1, linked against MKL.
1) after patching some source files and setup scripts (see msvc9.diff attachment), "python setup.py bdist_winist" succeeds on 32- and 64-bit Python 2.6, 2.7, and 3.1. The Visual C compiler reproducibly crashes while compiling scipy\special\cephes\ndtr.c. Running the build command again (without cleaning the build directory) seems to work.
Some of that patch should end up in the tree? I'm not sure which parts, though. [clip]
2) the build process fails on Python 3.2b1 with the following errors:
scipy\sparse\sparsetools\csr_wrap.cxx(2451) : error C3861: 'PyCObject_Import': identifier not found scipy\sparse\sparsetools\csr_wrap.cxx(2521) : error C3861: 'PyCObject_FromVoidPtr': identifier not found scipy\sparse\sparsetools\csr_wrap.cxx(2544) : error C3861: 'PyCObject_AsVoidPtr': identifier not found
It seems that the version of SWIG used there is not compatible with Python 3.2.
3) 32-bit Python 2.6 is the only platform where scipy.test() finishes; albeit with 32 failures. Besides the Correlate complex192 and TestODR errors (http://projects.scipy.org/scipy/ticket/678) I get [clip] FAIL: Real-valued Bessel domains [clip] AssertionError: (nan, nan, nan, nan)
This indicates some issue with AMOS and ifort. What do you get from import warnings, scipy.special as sc warnings.simplefilter('always', sc.SpecialFunctionWarning) sc.errprint(1) sc.airye(-1) It's possible that the test is too strict.
4) scipy.test() on Python 2.7 and 3.1 crashes as reported in ticket #1210 <http://projects.scipy.org/scipy/ticket/1210>
This smells like something triggering a DeprecationWarning when GIL is released. If so, it should be compiler independent and reproducible on wine+mingw. Or, some PyCObject/PyCapsule issue.
5) On 64 bit platforms, scipy.test() quits at the following test
test_interpnd.TestCloughTocher2DInterpolator.test_dense ... QH6084 qhull internal error (qh_meminit): sizeof(void*) 8 > sizeof(ptr_intT) 4. Change ptr_intT in mem.h to 'long long'
Should be fixed in r7013 -- Pauli Virtanen
On 12/13/2010 1:43 PM, Pauli Virtanen wrote:
On Mon, 13 Dec 2010 10:18:13 -0800, Christoph Gohlke wrote: [clip]
I ran into the following issues with scipy 0.9.0b1 on Windows when building with msvc 9 and intel 11.1 compilers. Numpy is version 1.5.1, linked against MKL.
1) after patching some source files and setup scripts (see msvc9.diff attachment), "python setup.py bdist_winist" succeeds on 32- and 64-bit Python 2.6, 2.7, and 3.1. The Visual C compiler reproducibly crashes while compiling scipy\special\cephes\ndtr.c. Running the build command again (without cleaning the build directory) seems to work.
Some of that patch should end up in the tree? I'm not sure which parts, though.
The patch can not be applied as is. It is a quick hack to get scipy compiling with msvc9/ifort again and likely breaks things in other build environments. I can open tickets later.
[clip]
2) the build process fails on Python 3.2b1 with the following errors:
scipy\sparse\sparsetools\csr_wrap.cxx(2451) : error C3861: 'PyCObject_Import': identifier not found scipy\sparse\sparsetools\csr_wrap.cxx(2521) : error C3861: 'PyCObject_FromVoidPtr': identifier not found scipy\sparse\sparsetools\csr_wrap.cxx(2544) : error C3861: 'PyCObject_AsVoidPtr': identifier not found
It seems that the version of SWIG used there is not compatible with Python 3.2.
Yes, see SWIG bug #3057804 "[Python] wrapper does not compile with python 3.2" <http://sourceforge.net/tracker/?func=detail&aid=3057804&group_id=1645&atid=101645>
3) 32-bit Python 2.6 is the only platform where scipy.test() finishes; albeit with 32 failures. Besides the Correlate complex192 and TestODR errors (http://projects.scipy.org/scipy/ticket/678) I get [clip] FAIL: Real-valued Bessel domains [clip] AssertionError: (nan, nan, nan, nan)
This indicates some issue with AMOS and ifort. What do you get from
import warnings, scipy.special as sc warnings.simplefilter('always', sc.SpecialFunctionWarning) sc.errprint(1)
0
sc.airye(-1)
__main__:1: SpecialFunctionWarning: airye:: unknown error __main__:1: SpecialFunctionWarning: airye:: unknown error (nan, nan, 0.10399738949694459, 0.59237562642279229)
It's possible that the test is too strict.
4) scipy.test() on Python 2.7 and 3.1 crashes as reported in ticket #1210<http://projects.scipy.org/scipy/ticket/1210>
This smells like something triggering a DeprecationWarning when GIL is released. If so, it should be compiler independent and reproducible on wine+mingw. Or, some PyCObject/PyCapsule issue.
5) On 64 bit platforms, scipy.test() quits at the following test
test_interpnd.TestCloughTocher2DInterpolator.test_dense ... QH6084 qhull internal error (qh_meminit): sizeof(void*) 8> sizeof(ptr_intT) 4. Change ptr_intT in mem.h to 'long long'
Should be fixed in r7013
Thanks.
On Mon, 13 Dec 2010 14:21:13 -0800, Christoph Gohlke wrote: [clip]
Yes, see SWIG bug #3057804 "[Python] wrapper does not compile with python 3.2" <http://sourceforge.net/tracker/? func=detail&aid=3057804&group_id=1645&atid=101645>
Possibly addressed by this: https://github.com/pv/scipy-work/tree/bug/sparsetools-reswig If it fixes it, then it's probably the correct solution. It's also possible that the issue (4) is related to this on Python 2.7/3.1, since I can't think of much else than the PyCObject/PyCapsule issue that would have changed in between.
3) 32-bit Python 2.6 is the only platform where scipy.test() finishes; [clip] sc.airye(-1)
__main__:1: SpecialFunctionWarning: airye:: unknown error __main__:1: SpecialFunctionWarning: airye:: unknown error (nan, nan, 0.10399738949694459, 0.59237562642279229)
Then I don't understand why in the test the function gives (nan, nan, nan, nan) OTOH, there are some other bugs, where when linked with MKL, some non-local effects (indicating memory corruption / fp state stuff) on function return values appear. -- Pauli Virtanen
On Tue, Dec 14, 2010 at 5:43 AM, Pauli Virtanen <pav@iki.fi> wrote:
On Mon, 13 Dec 2010 10:18:13 -0800, Christoph Gohlke wrote: [clip]
I ran into the following issues with scipy 0.9.0b1 on Windows when building with msvc 9 and intel 11.1 compilers. Numpy is version 1.5.1, linked against MKL.
1) after patching some source files and setup scripts (see msvc9.diff attachment), "python setup.py bdist_winist" succeeds on 32- and 64-bit Python 2.6, 2.7, and 3.1. The Visual C compiler reproducibly crashes while compiling scipy\special\cephes\ndtr.c. Running the build command again (without cleaning the build directory) seems to work.
Some of that patch should end up in the tree? I'm not sure which parts, though.
[clip]
2) the build process fails on Python 3.2b1 with the following errors:
scipy\sparse\sparsetools\csr_wrap.cxx(2451) : error C3861: 'PyCObject_Import': identifier not found scipy\sparse\sparsetools\csr_wrap.cxx(2521) : error C3861: 'PyCObject_FromVoidPtr': identifier not found scipy\sparse\sparsetools\csr_wrap.cxx(2544) : error C3861: 'PyCObject_AsVoidPtr': identifier not found
It seems that the version of SWIG used there is not compatible with Python 3.2.
3) 32-bit Python 2.6 is the only platform where scipy.test() finishes; albeit with 32 failures. Besides the Correlate complex192 and TestODR errors (http://projects.scipy.org/scipy/ticket/678) I get [clip] FAIL: Real-valued Bessel domains [clip] AssertionError: (nan, nan, nan, nan)
This indicates some issue with AMOS and ifort. What do you get from
import warnings, scipy.special as sc warnings.simplefilter('always', sc.SpecialFunctionWarning) sc.errprint(1) sc.airye(-1)
It's possible that the test is too strict.
4) scipy.test() on Python 2.7 and 3.1 crashes as reported in ticket #1210 <http://projects.scipy.org/scipy/ticket/1210>
This smells like something triggering a DeprecationWarning when GIL is released. If so, it should be compiler independent and reproducible on wine+mingw. Or, some PyCObject/PyCapsule issue.
On wine+mingw there are no crashes. With 3.1 there are no DeprecationWarning's, with 2.7 there is one:
Z:\Users\rgommers\.wine\drive_c\Python27\lib\site-packages\scipy\ndimage\morphology.py:254: PendingDeprecationWarning: The CObject type is marked Pending Deprecation in Python 2.7. Please use capsule objects instead. structure, mask, output, border_value, origin, invert, cit, 1) Other than that there is one other (unrelated) failure that I don't think has been reported before, see below. Full test logs are attached. Cheers, Ralf ====================================================================== FAIL: test_linesearch.TestLineSearch.test_line_search_wolfe1 ---------------------------------------------------------------------- Traceback (most recent call last): File "Z:\Users\rgommers\.wine\drive_c\Python27\lib\site-packages\nose-0.11.4-py2.7.egg\nose\case.py", line 186, in runTest self.test(*self.arg) File "Z:\Users\rgommers\.wine\drive_c\Python27\lib\site-packages\scipy\optimize\tests\test_linesearch.py", line 165, in test_line_search_wolfe1 assert_equal(gv, fprime(x + s*p)) File "Z:\Users\rgommers\.wine\drive_c\Python27\lib\site-packages\numpy\testing\utils.py", line 256, in assert_equal return assert_array_equal(actual, desired, err_msg, verbose) File "Z:\Users\rgommers\.wine\drive_c\Python27\lib\site-packages\numpy\testing\utils.py", line 686, in assert_array_equal verbose=verbose, header='Arrays are not equal') File "Z:\Users\rgommers\.wine\drive_c\Python27\lib\site-packages\numpy\testing\utils.py", line 618, in assert_array_compare raise AssertionError(msg) AssertionError: Arrays are not equal (mismatch 35.0%) x: array([ 0.59815369, 16.47021747, 3.04622715, 15.93277506, 10.10616782, -10.90475125, -10.885384 , 1.20593902, 9.66558674, -8.59479687, 2.08976118, 15.85496522,... y: array([ 0.59815369, 16.47021747, 3.04622715, 15.93277506, 10.10616782, -10.90475125, -10.885384 , 1.20593902, 9.66558674, -8.59479687, 2.08976118, 15.85496522,...
participants (7)
-
Benjamin Root -
Bruce Southey -
Charles R Harris -
Christoph Gohlke -
Pauli Virtanen -
Ralf Gommers -
Warren Weckesser