ANN: Scipy 0.13.0 beta 1 release
Hi all, I'm happy to announce the availability of the first beta release of Scipy 0.13.0. Please try this beta and report any issues on the scipy-dev mailing list. Source tarballs and release notes can be found at https://sourceforge.net/projects/scipy/files/scipy/0.13.0b1/. Windows and OS X installers will follow later (we have a minor infrastructure issue to solve, and I'm at EuroScipy now). Cheers, Ralf
On 8/22/2013 6:12 AM, Ralf Gommers wrote:
Hi all,
I'm happy to announce the availability of the first beta release of Scipy 0.13.0. Please try this beta and report any issues on the scipy-dev mailing list.
Source tarballs and release notes can be found at https://sourceforge.net/projects/scipy/files/scipy/0.13.0b1/. Windows and OS X installers will follow later (we have a minor infrastructure issue to solve, and I'm at EuroScipy now).
Cheers, Ralf
Hi Ralf, I built and tested scipy 0.13.0b1 on Windows 8 with Visual Studio 2008 & 2010, Intel Studio XE 2013 Fortran and MKL, Python 2.7 & 3.3 (32 & 64 bit), and numpy 1.7.1. The `scipy.ndimage._ni_label` extension fails to compile <https://github.com/scipy/scipy/pull/2770>. The win-amd64-py2.7 build passes all tests. On Python 3 there are 12 errors in `test_wavfile.test_write_roundtrip` of the following kind: ``` ====================================================================== ERROR: test_wavfile.test_write_roundtrip(False, 8000, dtype('>i8'), 1) ---------------------------------------------------------------------- Traceback (most recent call last): File "X:\Python33\lib\site-packages\nose\case.py", line 198, in runTest self.test(*self.arg) File "X:\Python33\lib\site-packages\scipy\io\tests\test_wavfile.py", line 73, in _check_roundtrip rate2, data2 = wavfile.read(tmpfile, mmap=mmap) File "X:\Python33\lib\site-packages\scipy\io\wavfile.py", line 166, in read data = _read_data_chunk(fid, comp, noc, bits, mmap=mmap) File "X:\Python33\lib\site-packages\scipy\io\wavfile.py", line 71, in _read_data_chunk data = numpy.fromstring(fid.read(size), dtype=dtype) ValueError: cannot expose native-only dtype 'q' in non-native byte order '>' via buffer interface ``` On 32 bit Python `test_distributions.TestFitMethod.test_fix_fit_beta` fails with an error: ``` ====================================================================== ERROR: test_distributions.TestFitMethod.test_fix_fit_beta ---------------------------------------------------------------------- Traceback (most recent call last): File "X:\Python33-x32\lib\site-packages\nose\case.py", line 198, in runTest self.test(*self.arg) File "X:\Python33-x32\lib\site-packages\scipy\stats\tests\test_distributions.py", line 928, in test_fix_fit_beta assert_raises(ValueError, stats.beta.fit, x, floc=0.5, fscale=1) File "X:\Python33-x32\lib\site-packages\numpy\testing\utils.py", line 1019, in assert_raises return nose.tools.assert_raises(*args,**kwargs) File "X:\Python33-x32\lib\unittest\case.py", line 570, in assertRaises return context.handle('assertRaises', callableObj, args, kwargs) File "X:\Python33-x32\lib\unittest\case.py", line 135, in handle callable_obj(*args, **kwargs) File "X:\Python33-x32\lib\site-packages\scipy\stats\distributions.py", line 2533, in fit raise FitSolverError(mesg=mesg) scipy.stats.distributions.FitSolverError: Solver for the MLE equations failed to converge: The iteration is not making good progress, as measured by the improvement from the last ten iterations. ``` Also on 32 bit Python, `test_windows.test_windowfunc_basics` and `test_decomp.TestEig.test_singular` sometimes fail: ``` ====================================================================== FAIL: test_windows.test_windowfunc_basics ---------------------------------------------------------------------- Traceback (most recent call last): File "X:\Python33-x32\lib\site-packages\nose\case.py", line 198, in runTest self.test(*self.arg) File "X:\Python33-x32\lib\site-packages\scipy\signal\tests\test_windows.py", line 100, in test_windowfunc_basics assert_array_almost_equal(w1, w2) File "X:\Python33-x32\lib\site-packages\numpy\testing\utils.py", line 812, in assert_array_almost_equal header=('Arrays are not almost equal to %d decimals' % decimal)) File "X:\Python33-x32\lib\site-packages\numpy\testing\utils.py", line 645, in assert_array_compare raise AssertionError(msg) AssertionError: Arrays are not almost equal to 6 decimals (mismatch 85.71428571428571%) x: array([ 0.02221406, 1. , 0.32944607, 0.16207939, 0.18485882, 0.36183308, 0.02298899]) y: array([ 0.01910267, 1. , 0.34644519, 0.09150573, 0.09150573, 0.17127567, 0.12123497]) ====================================================================== FAIL: test_decomp.TestEig.test_singular ---------------------------------------------------------------------- Traceback (most recent call last): File "X:\Python33-x32\lib\site-packages\nose\case.py", line 198, in runTest self.test(*self.arg) File "X:\Python33-x32\lib\site-packages\scipy\linalg\tests\test_decomp.py", line 219, in test_singular self._check_gen_eig(A, B) File "X:\Python33-x32\lib\site-packages\scipy\linalg\tests\test_decomp.py", line 206, in _check_gen_eig err_msg=msg) File "X:\Python33-x32\lib\site-packages\numpy\testing\utils.py", line 812, in assert_array_almost_equal header=('Arrays are not almost equal to %d decimals' % decimal)) File "X:\Python33-x32\lib\site-packages\numpy\testing\utils.py", line 645, in assert_array_compare raise AssertionError(msg) AssertionError: Arrays are not almost equal to 6 decimals array([[22, 34, 31, 31, 17], [45, 45, 42, 19, 29], [39, 47, 49, 26, 34], [27, 31, 26, 21, 15], [38, 44, 44, 24, 30]]) array([[13, 26, 25, 17, 24], [31, 46, 40, 26, 37], [26, 40, 19, 25, 25], [16, 25, 27, 14, 23], [24, 35, 18, 21, 22]]) (mismatch 50.0%) x: array([ -5.90370943e-01+0.j, -1.54128768e-07+0.j, 1.54128748e-07+0.j, 2.00000000e+00+0.j]) y: array([ -1.32014829e-08+0.j, 1.32014809e-08+0.j, 1.33224503e+00+0.j, 2.00000000e+00+0.j]) ``` Christoph
On 8/22/13, Christoph Gohlke <cgohlke@uci.edu> wrote:
On 8/22/2013 6:12 AM, Ralf Gommers wrote:
Hi all,
I'm happy to announce the availability of the first beta release of Scipy 0.13.0. Please try this beta and report any issues on the scipy-dev mailing list.
Source tarballs and release notes can be found at https://sourceforge.net/projects/scipy/files/scipy/0.13.0b1/. Windows and OS X installers will follow later (we have a minor infrastructure issue to solve, and I'm at EuroScipy now).
Cheers, Ralf
Hi Ralf,
I built and tested scipy 0.13.0b1 on Windows 8 with Visual Studio 2008 & 2010, Intel Studio XE 2013 Fortran and MKL, Python 2.7 & 3.3 (32 & 64 bit), and numpy 1.7.1.
The `scipy.ndimage._ni_label` extension fails to compile <https://github.com/scipy/scipy/pull/2770>.
The win-amd64-py2.7 build passes all tests.
On Python 3 there are 12 errors in `test_wavfile.test_write_roundtrip` of the following kind: ``` ====================================================================== ERROR: test_wavfile.test_write_roundtrip(False, 8000, dtype('>i8'), 1) ---------------------------------------------------------------------- Traceback (most recent call last): File "X:\Python33\lib\site-packages\nose\case.py", line 198, in runTest self.test(*self.arg) File "X:\Python33\lib\site-packages\scipy\io\tests\test_wavfile.py", line 73, in _check_roundtrip rate2, data2 = wavfile.read(tmpfile, mmap=mmap) File "X:\Python33\lib\site-packages\scipy\io\wavfile.py", line 166, in read data = _read_data_chunk(fid, comp, noc, bits, mmap=mmap) File "X:\Python33\lib\site-packages\scipy\io\wavfile.py", line 71, in _read_data_chunk data = numpy.fromstring(fid.read(size), dtype=dtype) ValueError: cannot expose native-only dtype 'q' in non-native byte order '>' via buffer interface ```
On 32 bit Python `test_distributions.TestFitMethod.test_fix_fit_beta` fails with an error:
``` ====================================================================== ERROR: test_distributions.TestFitMethod.test_fix_fit_beta ---------------------------------------------------------------------- Traceback (most recent call last): File "X:\Python33-x32\lib\site-packages\nose\case.py", line 198, in runTest self.test(*self.arg) File "X:\Python33-x32\lib\site-packages\scipy\stats\tests\test_distributions.py",
line 928, in test_fix_fit_beta assert_raises(ValueError, stats.beta.fit, x, floc=0.5, fscale=1) File "X:\Python33-x32\lib\site-packages\numpy\testing\utils.py", line 1019, in assert_raises return nose.tools.assert_raises(*args,**kwargs) File "X:\Python33-x32\lib\unittest\case.py", line 570, in assertRaises return context.handle('assertRaises', callableObj, args, kwargs) File "X:\Python33-x32\lib\unittest\case.py", line 135, in handle callable_obj(*args, **kwargs) File "X:\Python33-x32\lib\site-packages\scipy\stats\distributions.py", line 2533, in fit raise FitSolverError(mesg=mesg) scipy.stats.distributions.FitSolverError: Solver for the MLE equations failed to converge: The iteration is not making good progress, as measured by the improvement from the last ten iterations. ```
Thanks, Christoph. I'll look into this one. I created an issue for it here: https://github.com/scipy/scipy/issues/2771 Warren
Also on 32 bit Python, `test_windows.test_windowfunc_basics` and `test_decomp.TestEig.test_singular` sometimes fail: ``` ====================================================================== FAIL: test_windows.test_windowfunc_basics ---------------------------------------------------------------------- Traceback (most recent call last): File "X:\Python33-x32\lib\site-packages\nose\case.py", line 198, in runTest self.test(*self.arg) File "X:\Python33-x32\lib\site-packages\scipy\signal\tests\test_windows.py", line 100, in test_windowfunc_basics assert_array_almost_equal(w1, w2) File "X:\Python33-x32\lib\site-packages\numpy\testing\utils.py", line 812, in assert_array_almost_equal header=('Arrays are not almost equal to %d decimals' % decimal)) File "X:\Python33-x32\lib\site-packages\numpy\testing\utils.py", line 645, in assert_array_compare raise AssertionError(msg) AssertionError: Arrays are not almost equal to 6 decimals
(mismatch 85.71428571428571%) x: array([ 0.02221406, 1. , 0.32944607, 0.16207939, 0.18485882, 0.36183308, 0.02298899]) y: array([ 0.01910267, 1. , 0.34644519, 0.09150573, 0.09150573, 0.17127567, 0.12123497])
====================================================================== FAIL: test_decomp.TestEig.test_singular ---------------------------------------------------------------------- Traceback (most recent call last): File "X:\Python33-x32\lib\site-packages\nose\case.py", line 198, in runTest self.test(*self.arg) File "X:\Python33-x32\lib\site-packages\scipy\linalg\tests\test_decomp.py", line 219, in test_singular self._check_gen_eig(A, B) File "X:\Python33-x32\lib\site-packages\scipy\linalg\tests\test_decomp.py", line 206, in _check_gen_eig err_msg=msg) File "X:\Python33-x32\lib\site-packages\numpy\testing\utils.py", line 812, in assert_array_almost_equal header=('Arrays are not almost equal to %d decimals' % decimal)) File "X:\Python33-x32\lib\site-packages\numpy\testing\utils.py", line 645, in assert_array_compare raise AssertionError(msg) AssertionError: Arrays are not almost equal to 6 decimals
array([[22, 34, 31, 31, 17], [45, 45, 42, 19, 29], [39, 47, 49, 26, 34], [27, 31, 26, 21, 15], [38, 44, 44, 24, 30]]) array([[13, 26, 25, 17, 24], [31, 46, 40, 26, 37], [26, 40, 19, 25, 25], [16, 25, 27, 14, 23], [24, 35, 18, 21, 22]]) (mismatch 50.0%) x: array([ -5.90370943e-01+0.j, -1.54128768e-07+0.j, 1.54128748e-07+0.j, 2.00000000e+00+0.j]) y: array([ -1.32014829e-08+0.j, 1.32014809e-08+0.j, 1.33224503e+00+0.j, 2.00000000e+00+0.j]) ```
Christoph _______________________________________________ SciPy-Dev mailing list SciPy-Dev@scipy.org http://mail.scipy.org/mailman/listinfo/scipy-dev
Christoph, didn't you have any issues with too many files open failures ? I am using windows 7 and not 8, and I always have to restart the build several times to get it finished. David On Fri, Aug 23, 2013 at 12:45 AM, Christoph Gohlke <cgohlke@uci.edu> wrote:
On 8/22/2013 6:12 AM, Ralf Gommers wrote:
Hi all,
I'm happy to announce the availability of the first beta release of Scipy 0.13.0. Please try this beta and report any issues on the scipy-dev mailing list.
Source tarballs and release notes can be found at https://sourceforge.net/projects/scipy/files/scipy/0.13.0b1/. Windows and OS X installers will follow later (we have a minor infrastructure issue to solve, and I'm at EuroScipy now).
Cheers, Ralf
Hi Ralf,
I built and tested scipy 0.13.0b1 on Windows 8 with Visual Studio 2008 & 2010, Intel Studio XE 2013 Fortran and MKL, Python 2.7 & 3.3 (32 & 64 bit), and numpy 1.7.1.
The `scipy.ndimage._ni_label` extension fails to compile <https://github.com/scipy/scipy/pull/2770>.
The win-amd64-py2.7 build passes all tests.
On Python 3 there are 12 errors in `test_wavfile.test_write_roundtrip` of the following kind: ``` ====================================================================== ERROR: test_wavfile.test_write_roundtrip(False, 8000, dtype('>i8'), 1) ---------------------------------------------------------------------- Traceback (most recent call last): File "X:\Python33\lib\site-packages\nose\case.py", line 198, in runTest self.test(*self.arg) File "X:\Python33\lib\site-packages\scipy\io\tests\test_wavfile.py", line 73, in _check_roundtrip rate2, data2 = wavfile.read(tmpfile, mmap=mmap) File "X:\Python33\lib\site-packages\scipy\io\wavfile.py", line 166, in read data = _read_data_chunk(fid, comp, noc, bits, mmap=mmap) File "X:\Python33\lib\site-packages\scipy\io\wavfile.py", line 71, in _read_data_chunk data = numpy.fromstring(fid.read(size), dtype=dtype) ValueError: cannot expose native-only dtype 'q' in non-native byte order '>' via buffer interface ```
On 32 bit Python `test_distributions.TestFitMethod.test_fix_fit_beta` fails with an error:
``` ====================================================================== ERROR: test_distributions.TestFitMethod.test_fix_fit_beta ---------------------------------------------------------------------- Traceback (most recent call last): File "X:\Python33-x32\lib\site-packages\nose\case.py", line 198, in runTest self.test(*self.arg) File
"X:\Python33-x32\lib\site-packages\scipy\stats\tests\test_distributions.py", line 928, in test_fix_fit_beta assert_raises(ValueError, stats.beta.fit, x, floc=0.5, fscale=1) File "X:\Python33-x32\lib\site-packages\numpy\testing\utils.py", line 1019, in assert_raises return nose.tools.assert_raises(*args,**kwargs) File "X:\Python33-x32\lib\unittest\case.py", line 570, in assertRaises return context.handle('assertRaises', callableObj, args, kwargs) File "X:\Python33-x32\lib\unittest\case.py", line 135, in handle callable_obj(*args, **kwargs) File "X:\Python33-x32\lib\site-packages\scipy\stats\distributions.py", line 2533, in fit raise FitSolverError(mesg=mesg) scipy.stats.distributions.FitSolverError: Solver for the MLE equations failed to converge: The iteration is not making good progress, as measured by the improvement from the last ten iterations. ```
Also on 32 bit Python, `test_windows.test_windowfunc_basics` and `test_decomp.TestEig.test_singular` sometimes fail: ``` ====================================================================== FAIL: test_windows.test_windowfunc_basics ---------------------------------------------------------------------- Traceback (most recent call last): File "X:\Python33-x32\lib\site-packages\nose\case.py", line 198, in runTest self.test(*self.arg) File "X:\Python33-x32\lib\site-packages\scipy\signal\tests\test_windows.py", line 100, in test_windowfunc_basics assert_array_almost_equal(w1, w2) File "X:\Python33-x32\lib\site-packages\numpy\testing\utils.py", line 812, in assert_array_almost_equal header=('Arrays are not almost equal to %d decimals' % decimal)) File "X:\Python33-x32\lib\site-packages\numpy\testing\utils.py", line 645, in assert_array_compare raise AssertionError(msg) AssertionError: Arrays are not almost equal to 6 decimals
(mismatch 85.71428571428571%) x: array([ 0.02221406, 1. , 0.32944607, 0.16207939, 0.18485882, 0.36183308, 0.02298899]) y: array([ 0.01910267, 1. , 0.34644519, 0.09150573, 0.09150573, 0.17127567, 0.12123497])
====================================================================== FAIL: test_decomp.TestEig.test_singular ---------------------------------------------------------------------- Traceback (most recent call last): File "X:\Python33-x32\lib\site-packages\nose\case.py", line 198, in runTest self.test(*self.arg) File "X:\Python33-x32\lib\site-packages\scipy\linalg\tests\test_decomp.py", line 219, in test_singular self._check_gen_eig(A, B) File "X:\Python33-x32\lib\site-packages\scipy\linalg\tests\test_decomp.py", line 206, in _check_gen_eig err_msg=msg) File "X:\Python33-x32\lib\site-packages\numpy\testing\utils.py", line 812, in assert_array_almost_equal header=('Arrays are not almost equal to %d decimals' % decimal)) File "X:\Python33-x32\lib\site-packages\numpy\testing\utils.py", line 645, in assert_array_compare raise AssertionError(msg) AssertionError: Arrays are not almost equal to 6 decimals
array([[22, 34, 31, 31, 17], [45, 45, 42, 19, 29], [39, 47, 49, 26, 34], [27, 31, 26, 21, 15], [38, 44, 44, 24, 30]]) array([[13, 26, 25, 17, 24], [31, 46, 40, 26, 37], [26, 40, 19, 25, 25], [16, 25, 27, 14, 23], [24, 35, 18, 21, 22]]) (mismatch 50.0%) x: array([ -5.90370943e-01+0.j, -1.54128768e-07+0.j, 1.54128748e-07+0.j, 2.00000000e+00+0.j]) y: array([ -1.32014829e-08+0.j, 1.32014809e-08+0.j, 1.33224503e+00+0.j, 2.00000000e+00+0.j]) ```
Christoph _______________________________________________ SciPy-Dev mailing list SciPy-Dev@scipy.org http://mail.scipy.org/mailman/listinfo/scipy-dev
Yes, I have to restart the build once because of too many (~2000) open files. Could be that numpy.distutils.exec_command does not close all handles? My build script does `setup.py build` before `setup.py bdist_wininst` so I usually don't notice. Christoph On 8/30/2013 4:21 AM, David Cournapeau wrote:
Christoph, didn't you have any issues with too many files open failures ? I am using windows 7 and not 8, and I always have to restart the build several times to get it finished.
David
On Fri, Aug 23, 2013 at 12:45 AM, Christoph Gohlke <cgohlke@uci.edu <mailto:cgohlke@uci.edu>> wrote:
On 8/22/2013 6:12 AM, Ralf Gommers wrote: > Hi all, > > I'm happy to announce the availability of the first beta release of > Scipy 0.13.0. Please try this beta and report any issues on the > scipy-dev mailing list. > > Source tarballs and release notes can be found at >https://sourceforge.net/projects/scipy/files/scipy/0.13.0b1/. Windows > and OS X installers will follow later (we have a minor infrastructure > issue to solve, and I'm at EuroScipy now). > > Cheers, > Ralf > >
Hi Ralf,
I built and tested scipy 0.13.0b1 on Windows 8 with Visual Studio 2008 & 2010, Intel Studio XE 2013 Fortran and MKL, Python 2.7 & 3.3 (32 & 64 bit), and numpy 1.7.1.
The `scipy.ndimage._ni_label` extension fails to compile <https://github.com/scipy/scipy/pull/2770>.
The win-amd64-py2.7 build passes all tests.
On Python 3 there are 12 errors in `test_wavfile.test_write_roundtrip` of the following kind: ``` ====================================================================== ERROR: test_wavfile.test_write_roundtrip(False, 8000, dtype('>i8'), 1) ---------------------------------------------------------------------- Traceback (most recent call last): File "X:\Python33\lib\site-packages\nose\case.py", line 198, in runTest self.test(*self.arg) File "X:\Python33\lib\site-packages\scipy\io\tests\test_wavfile.py", line 73, in _check_roundtrip rate2, data2 = wavfile.read(tmpfile, mmap=mmap) File "X:\Python33\lib\site-packages\scipy\io\wavfile.py", line 166, in read data = _read_data_chunk(fid, comp, noc, bits, mmap=mmap) File "X:\Python33\lib\site-packages\scipy\io\wavfile.py", line 71, in _read_data_chunk data = numpy.fromstring(fid.read(size), dtype=dtype) ValueError: cannot expose native-only dtype 'q' in non-native byte order '>' via buffer interface ```
On 32 bit Python `test_distributions.TestFitMethod.test_fix_fit_beta` fails with an error:
``` ====================================================================== ERROR: test_distributions.TestFitMethod.test_fix_fit_beta ---------------------------------------------------------------------- Traceback (most recent call last): File "X:\Python33-x32\lib\site-packages\nose\case.py", line 198, in runTest self.test(*self.arg) File "X:\Python33-x32\lib\site-packages\scipy\stats\tests\test_distributions.py", line 928, in test_fix_fit_beta assert_raises(ValueError, stats.beta.fit, x, floc=0.5, fscale=1) File "X:\Python33-x32\lib\site-packages\numpy\testing\utils.py", line 1019, in assert_raises return nose.tools.assert_raises(*args,**kwargs) File "X:\Python33-x32\lib\unittest\case.py", line 570, in assertRaises return context.handle('assertRaises', callableObj, args, kwargs) File "X:\Python33-x32\lib\unittest\case.py", line 135, in handle callable_obj(*args, **kwargs) File "X:\Python33-x32\lib\site-packages\scipy\stats\distributions.py", line 2533, in fit raise FitSolverError(mesg=mesg) scipy.stats.distributions.FitSolverError: Solver for the MLE equations failed to converge: The iteration is not making good progress, as measured by the improvement from the last ten iterations. ```
Also on 32 bit Python, `test_windows.test_windowfunc_basics` and `test_decomp.TestEig.test_singular` sometimes fail: ``` ====================================================================== FAIL: test_windows.test_windowfunc_basics ---------------------------------------------------------------------- Traceback (most recent call last): File "X:\Python33-x32\lib\site-packages\nose\case.py", line 198, in runTest self.test(*self.arg) File "X:\Python33-x32\lib\site-packages\scipy\signal\tests\test_windows.py", line 100, in test_windowfunc_basics assert_array_almost_equal(w1, w2) File "X:\Python33-x32\lib\site-packages\numpy\testing\utils.py", line 812, in assert_array_almost_equal header=('Arrays are not almost equal to %d decimals' % decimal)) File "X:\Python33-x32\lib\site-packages\numpy\testing\utils.py", line 645, in assert_array_compare raise AssertionError(msg) AssertionError: Arrays are not almost equal to 6 decimals
(mismatch 85.71428571428571%) x: array([ 0.02221406, 1. , 0.32944607, 0.16207939, 0.18485882, 0.36183308, 0.02298899]) y: array([ 0.01910267, 1. , 0.34644519, 0.09150573, 0.09150573, 0.17127567, 0.12123497])
====================================================================== FAIL: test_decomp.TestEig.test_singular ---------------------------------------------------------------------- Traceback (most recent call last): File "X:\Python33-x32\lib\site-packages\nose\case.py", line 198, in runTest self.test(*self.arg) File "X:\Python33-x32\lib\site-packages\scipy\linalg\tests\test_decomp.py", line 219, in test_singular self._check_gen_eig(A, B) File "X:\Python33-x32\lib\site-packages\scipy\linalg\tests\test_decomp.py", line 206, in _check_gen_eig err_msg=msg) File "X:\Python33-x32\lib\site-packages\numpy\testing\utils.py", line 812, in assert_array_almost_equal header=('Arrays are not almost equal to %d decimals' % decimal)) File "X:\Python33-x32\lib\site-packages\numpy\testing\utils.py", line 645, in assert_array_compare raise AssertionError(msg) AssertionError: Arrays are not almost equal to 6 decimals
array([[22, 34, 31, 31, 17], [45, 45, 42, 19, 29], [39, 47, 49, 26, 34], [27, 31, 26, 21, 15], [38, 44, 44, 24, 30]]) array([[13, 26, 25, 17, 24], [31, 46, 40, 26, 37], [26, 40, 19, 25, 25], [16, 25, 27, 14, 23], [24, 35, 18, 21, 22]]) (mismatch 50.0%) x: array([ -5.90370943e-01+0.j, -1.54128768e-07+0.j, 1.54128748e-07+0.j, 2.00000000e+00+0.j]) y: array([ -1.32014829e-08+0.j, 1.32014809e-08+0.j, 1.33224503e+00+0.j, 2.00000000e+00+0.j]) ```
Christoph _______________________________________________ SciPy-Dev mailing list SciPy-Dev@scipy.org <mailto:SciPy-Dev@scipy.org> http://mail.scipy.org/mailman/listinfo/scipy-dev
_______________________________________________ SciPy-Dev mailing list SciPy-Dev@scipy.org http://mail.scipy.org/mailman/listinfo/scipy-dev
On Fri, Aug 30, 2013 at 7:56 PM, Christoph Gohlke <cgohlke@uci.edu> wrote:
Yes, I have to restart the build once because of too many (~2000) open files. Could be that numpy.distutils.exec_command does not close all handles? My build script does `setup.py build` before `setup.py bdist_wininst` so I usually don't notice.
I did even finer-grained separation between build_clib and build_ext, to no avail. I have to restart the build 2/3 times. Regarding exec_command, the code uses old os.system and co, but the code is so messy that I would not dare touch it at this point. David
Christoph
On 8/30/2013 4:21 AM, David Cournapeau wrote:
Christoph, didn't you have any issues with too many files open failures ? I am using windows 7 and not 8, and I always have to restart the build several times to get it finished.
David
On Fri, Aug 23, 2013 at 12:45 AM, Christoph Gohlke <cgohlke@uci.edu <mailto:cgohlke@uci.edu>> wrote:
On 8/22/2013 6:12 AM, Ralf Gommers wrote: > Hi all, > > I'm happy to announce the availability of the first beta release of > Scipy 0.13.0. Please try this beta and report any issues on the > scipy-dev mailing list. > > Source tarballs and release notes can be found at >https://sourceforge.net/projects/scipy/files/scipy/0.13.0b1/. Windows > and OS X installers will follow later (we have a minor infrastructure > issue to solve, and I'm at EuroScipy now). > > Cheers, > Ralf > >
Hi Ralf,
I built and tested scipy 0.13.0b1 on Windows 8 with Visual Studio 2008 & 2010, Intel Studio XE 2013 Fortran and MKL, Python 2.7 & 3.3 (32 & 64 bit), and numpy 1.7.1.
The `scipy.ndimage._ni_label` extension fails to compile <https://github.com/scipy/scipy/pull/2770>.
The win-amd64-py2.7 build passes all tests.
On Python 3 there are 12 errors in `test_wavfile.test_write_roundtrip` of the following kind: ```
======================================================================
ERROR: test_wavfile.test_write_roundtrip(False, 8000, dtype('>i8'),
1)
----------------------------------------------------------------------
Traceback (most recent call last): File "X:\Python33\lib\site-packages\nose\case.py", line 198, in runTest self.test(*self.arg) File
"X:\Python33\lib\site-packages\scipy\io\tests\test_wavfile.py",
line 73, in _check_roundtrip rate2, data2 = wavfile.read(tmpfile, mmap=mmap) File "X:\Python33\lib\site-packages\scipy\io\wavfile.py", line
166,
in read data = _read_data_chunk(fid, comp, noc, bits, mmap=mmap) File "X:\Python33\lib\site-packages\scipy\io\wavfile.py", line 71, in _read_data_chunk data = numpy.fromstring(fid.read(size), dtype=dtype) ValueError: cannot expose native-only dtype 'q' in non-native byte
order
'>' via buffer interface ```
On 32 bit Python `test_distributions.TestFitMethod.test_fix_fit_beta` fails with an error:
```
======================================================================
ERROR: test_distributions.TestFitMethod.test_fix_fit_beta
----------------------------------------------------------------------
Traceback (most recent call last): File "X:\Python33-x32\lib\site-packages\nose\case.py", line 198,
in
runTest self.test(*self.arg) File
"X:\Python33-x32\lib\site-packages\scipy\stats\tests\test_distributions.py",
line 928, in test_fix_fit_beta assert_raises(ValueError, stats.beta.fit, x, floc=0.5,
fscale=1)
File "X:\Python33-x32\lib\site-packages\numpy\testing\utils.py", line 1019, in assert_raises return nose.tools.assert_raises(*args,**kwargs) File "X:\Python33-x32\lib\unittest\case.py", line 570, in assertRaises return context.handle('assertRaises', callableObj, args,
kwargs)
File "X:\Python33-x32\lib\unittest\case.py", line 135, in handle callable_obj(*args, **kwargs) File "X:\Python33-x32\lib\site-packages\scipy\stats\distributions.py",
line
2533, in fit raise FitSolverError(mesg=mesg) scipy.stats.distributions.FitSolverError: Solver for the MLE
equations
failed to converge: The iteration is not making good progress, as measured by the improvement from the last ten iterations. ```
Also on 32 bit Python, `test_windows.test_windowfunc_basics` and `test_decomp.TestEig.test_singular` sometimes fail: ```
======================================================================
FAIL: test_windows.test_windowfunc_basics
----------------------------------------------------------------------
Traceback (most recent call last): File "X:\Python33-x32\lib\site-packages\nose\case.py", line 198,
in
runTest self.test(*self.arg) File
"X:\Python33-x32\lib\site-packages\scipy\signal\tests\test_windows.py",
line 100, in test_windowfunc_basics assert_array_almost_equal(w1, w2) File "X:\Python33-x32\lib\site-packages\numpy\testing\utils.py", line 812, in assert_array_almost_equal header=('Arrays are not almost equal to %d decimals' %
decimal))
File "X:\Python33-x32\lib\site-packages\numpy\testing\utils.py", line 645, in assert_array_compare raise AssertionError(msg) AssertionError: Arrays are not almost equal to 6 decimals
(mismatch 85.71428571428571%) x: array([ 0.02221406, 1. , 0.32944607, 0.16207939, 0.18485882, 0.36183308, 0.02298899]) y: array([ 0.01910267, 1. , 0.34644519, 0.09150573, 0.09150573, 0.17127567, 0.12123497])
======================================================================
FAIL: test_decomp.TestEig.test_singular
----------------------------------------------------------------------
Traceback (most recent call last): File "X:\Python33-x32\lib\site-packages\nose\case.py", line 198,
in
runTest self.test(*self.arg) File
"X:\Python33-x32\lib\site-packages\scipy\linalg\tests\test_decomp.py",
line 219, in test_singular self._check_gen_eig(A, B) File
"X:\Python33-x32\lib\site-packages\scipy\linalg\tests\test_decomp.py",
line 206, in _check_gen_eig err_msg=msg) File "X:\Python33-x32\lib\site-packages\numpy\testing\utils.py", line 812, in assert_array_almost_equal header=('Arrays are not almost equal to %d decimals' %
decimal))
File "X:\Python33-x32\lib\site-packages\numpy\testing\utils.py", line 645, in assert_array_compare raise AssertionError(msg) AssertionError: Arrays are not almost equal to 6 decimals
array([[22, 34, 31, 31, 17], [45, 45, 42, 19, 29], [39, 47, 49, 26, 34], [27, 31, 26, 21, 15], [38, 44, 44, 24, 30]]) array([[13, 26, 25, 17, 24], [31, 46, 40, 26, 37], [26, 40, 19, 25, 25], [16, 25, 27, 14, 23], [24, 35, 18, 21, 22]]) (mismatch 50.0%) x: array([ -5.90370943e-01+0.j, -1.54128768e-07+0.j, 1.54128748e-07+0.j, 2.00000000e+00+0.j]) y: array([ -1.32014829e-08+0.j, 1.32014809e-08+0.j, 1.33224503e+00+0.j, 2.00000000e+00+0.j]) ```
Christoph _______________________________________________ SciPy-Dev mailing list SciPy-Dev@scipy.org <mailto:SciPy-Dev@scipy.org> http://mail.scipy.org/mailman/listinfo/scipy-dev
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On Sat, Aug 31, 2013 at 10:47 AM, David Cournapeau <cournape@gmail.com>wrote:
On Fri, Aug 30, 2013 at 7:56 PM, Christoph Gohlke <cgohlke@uci.edu> wrote:
Yes, I have to restart the build once because of too many (~2000) open files. Could be that numpy.distutils.exec_command does not close all handles? My build script does `setup.py build` before `setup.py bdist_wininst` so I usually don't notice.
I did even finer-grained separation between build_clib and build_ext, to no avail. I have to restart the build 2/3 times.
Regarding exec_command, the code uses old os.system and co, but the code is so messy that I would not dare touch it at this point.
It looks like even if we'd revert https://github.com/scipy/scipy/pull/2761, if scipy grows any more we can't build it with distutils. So if this is due to exec_command, it needs to be fixed. Unless we want to take a leap and go Bento-only.... Note also that this is not a new issue, here's some build instructions from 2010 with a remark on this: https://code.google.com/p/iocbio/wiki/BuildWindowsInstallersOnLinux Ralf
David
Christoph
On 8/30/2013 4:21 AM, David Cournapeau wrote:
Christoph, didn't you have any issues with too many files open failures ? I am using windows 7 and not 8, and I always have to restart the build several times to get it finished.
David
On Fri, Aug 23, 2013 at 12:45 AM, Christoph Gohlke <cgohlke@uci.edu <mailto:cgohlke@uci.edu>> wrote:
On 8/22/2013 6:12 AM, Ralf Gommers wrote: > Hi all, > > I'm happy to announce the availability of the first beta release of > Scipy 0.13.0. Please try this beta and report any issues on the > scipy-dev mailing list. > > Source tarballs and release notes can be found at >https://sourceforge.net/projects/scipy/files/scipy/0.13.0b1/. Windows > and OS X installers will follow later (we have a minor infrastructure > issue to solve, and I'm at EuroScipy now). > > Cheers, > Ralf > >
Hi Ralf,
I built and tested scipy 0.13.0b1 on Windows 8 with Visual Studio 2008 & 2010, Intel Studio XE 2013 Fortran and MKL, Python 2.7 & 3.3 (32 & 64 bit), and numpy 1.7.1.
The `scipy.ndimage._ni_label` extension fails to compile <https://github.com/scipy/scipy/pull/2770>.
The win-amd64-py2.7 build passes all tests.
On Python 3 there are 12 errors in `test_wavfile.test_write_roundtrip` of the following kind: ```
======================================================================
ERROR: test_wavfile.test_write_roundtrip(False, 8000, dtype('>i8'),
1)
----------------------------------------------------------------------
Traceback (most recent call last): File "X:\Python33\lib\site-packages\nose\case.py", line 198, in runTest self.test(*self.arg) File
"X:\Python33\lib\site-packages\scipy\io\tests\test_wavfile.py",
line 73, in _check_roundtrip rate2, data2 = wavfile.read(tmpfile, mmap=mmap) File "X:\Python33\lib\site-packages\scipy\io\wavfile.py", line
166,
in read data = _read_data_chunk(fid, comp, noc, bits, mmap=mmap) File "X:\Python33\lib\site-packages\scipy\io\wavfile.py", line 71, in _read_data_chunk data = numpy.fromstring(fid.read(size), dtype=dtype) ValueError: cannot expose native-only dtype 'q' in non-native byte
order
'>' via buffer interface ```
On 32 bit Python
`test_distributions.TestFitMethod.test_fix_fit_beta`
fails with an error:
```
======================================================================
ERROR: test_distributions.TestFitMethod.test_fix_fit_beta
----------------------------------------------------------------------
Traceback (most recent call last): File "X:\Python33-x32\lib\site-packages\nose\case.py", line
198, in
runTest self.test(*self.arg) File
"X:\Python33-x32\lib\site-packages\scipy\stats\tests\test_distributions.py",
line 928, in test_fix_fit_beta assert_raises(ValueError, stats.beta.fit, x, floc=0.5,
fscale=1)
File "X:\Python33-x32\lib\site-packages\numpy\testing\utils.py", line 1019, in assert_raises return nose.tools.assert_raises(*args,**kwargs) File "X:\Python33-x32\lib\unittest\case.py", line 570, in assertRaises return context.handle('assertRaises', callableObj, args,
kwargs)
File "X:\Python33-x32\lib\unittest\case.py", line 135, in handle callable_obj(*args, **kwargs) File "X:\Python33-x32\lib\site-packages\scipy\stats\distributions.py",
line
2533, in fit raise FitSolverError(mesg=mesg) scipy.stats.distributions.FitSolverError: Solver for the MLE
equations
failed to converge: The iteration is not making good progress, as measured by the improvement from the last ten iterations. ```
Also on 32 bit Python, `test_windows.test_windowfunc_basics` and `test_decomp.TestEig.test_singular` sometimes fail: ```
======================================================================
FAIL: test_windows.test_windowfunc_basics
----------------------------------------------------------------------
Traceback (most recent call last): File "X:\Python33-x32\lib\site-packages\nose\case.py", line
198, in
runTest self.test(*self.arg) File
"X:\Python33-x32\lib\site-packages\scipy\signal\tests\test_windows.py",
line 100, in test_windowfunc_basics assert_array_almost_equal(w1, w2) File "X:\Python33-x32\lib\site-packages\numpy\testing\utils.py", line 812, in assert_array_almost_equal header=('Arrays are not almost equal to %d decimals' %
decimal))
File "X:\Python33-x32\lib\site-packages\numpy\testing\utils.py", line 645, in assert_array_compare raise AssertionError(msg) AssertionError: Arrays are not almost equal to 6 decimals
(mismatch 85.71428571428571%) x: array([ 0.02221406, 1. , 0.32944607, 0.16207939, 0.18485882, 0.36183308, 0.02298899]) y: array([ 0.01910267, 1. , 0.34644519, 0.09150573, 0.09150573, 0.17127567, 0.12123497])
======================================================================
FAIL: test_decomp.TestEig.test_singular
----------------------------------------------------------------------
Traceback (most recent call last): File "X:\Python33-x32\lib\site-packages\nose\case.py", line
198, in
runTest self.test(*self.arg) File
"X:\Python33-x32\lib\site-packages\scipy\linalg\tests\test_decomp.py",
line 219, in test_singular self._check_gen_eig(A, B) File
"X:\Python33-x32\lib\site-packages\scipy\linalg\tests\test_decomp.py",
line 206, in _check_gen_eig err_msg=msg) File "X:\Python33-x32\lib\site-packages\numpy\testing\utils.py", line 812, in assert_array_almost_equal header=('Arrays are not almost equal to %d decimals' %
decimal))
File "X:\Python33-x32\lib\site-packages\numpy\testing\utils.py", line 645, in assert_array_compare raise AssertionError(msg) AssertionError: Arrays are not almost equal to 6 decimals
array([[22, 34, 31, 31, 17], [45, 45, 42, 19, 29], [39, 47, 49, 26, 34], [27, 31, 26, 21, 15], [38, 44, 44, 24, 30]]) array([[13, 26, 25, 17, 24], [31, 46, 40, 26, 37], [26, 40, 19, 25, 25], [16, 25, 27, 14, 23], [24, 35, 18, 21, 22]]) (mismatch 50.0%) x: array([ -5.90370943e-01+0.j, -1.54128768e-07+0.j, 1.54128748e-07+0.j, 2.00000000e+00+0.j]) y: array([ -1.32014829e-08+0.j, 1.32014809e-08+0.j, 1.33224503e+00+0.j, 2.00000000e+00+0.j]) ```
Christoph _______________________________________________ SciPy-Dev mailing list SciPy-Dev@scipy.org <mailto:SciPy-Dev@scipy.org> http://mail.scipy.org/mailman/listinfo/scipy-dev
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On Sat, Aug 31, 2013 at 12:13 PM, Ralf Gommers <ralf.gommers@gmail.com>wrote:
On Sat, Aug 31, 2013 at 10:47 AM, David Cournapeau <cournape@gmail.com>wrote:
On Fri, Aug 30, 2013 at 7:56 PM, Christoph Gohlke <cgohlke@uci.edu>wrote:
Yes, I have to restart the build once because of too many (~2000) open files. Could be that numpy.distutils.exec_command does not close all handles? My build script does `setup.py build` before `setup.py bdist_wininst` so I usually don't notice.
I did even finer-grained separation between build_clib and build_ext, to no avail. I have to restart the build 2/3 times.
Regarding exec_command, the code uses old os.system and co, but the code is so messy that I would not dare touch it at this point.
It looks like even if we'd revert https://github.com/scipy/scipy/pull/2761, if scipy grows any more we can't build it with distutils.
I saw those issues before (for 0.10 even), but not consistantly, so I agree reverting is not really a fix. I am not sure it is even due to distutils, TBH. I have noticed those issues in other (non python) packages, it may be a hard limitation of the DOS subsystem, in which case we're clearly in trouble :) I will try to make some experiments next week with dumy project having thousand of files to reproduce the issue easily. David
So if this is due to exec_command, it needs to be fixed. Unless we want to take a leap and go Bento-only....
Note also that this is not a new issue, here's some build instructions from 2010 with a remark on this: https://code.google.com/p/iocbio/wiki/BuildWindowsInstallersOnLinux
Ralf
David
Christoph
On 8/30/2013 4:21 AM, David Cournapeau wrote:
Christoph, didn't you have any issues with too many files open failures ? I am using windows 7 and not 8, and I always have to restart the build several times to get it finished.
David
On Fri, Aug 23, 2013 at 12:45 AM, Christoph Gohlke <cgohlke@uci.edu <mailto:cgohlke@uci.edu>> wrote:
On 8/22/2013 6:12 AM, Ralf Gommers wrote: > Hi all, > > I'm happy to announce the availability of the first beta release of > Scipy 0.13.0. Please try this beta and report any issues on the > scipy-dev mailing list. > > Source tarballs and release notes can be found at >https://sourceforge.net/projects/scipy/files/scipy/0.13.0b1/. Windows > and OS X installers will follow later (we have a minor infrastructure > issue to solve, and I'm at EuroScipy now). > > Cheers, > Ralf > >
Hi Ralf,
I built and tested scipy 0.13.0b1 on Windows 8 with Visual Studio 2008 & 2010, Intel Studio XE 2013 Fortran and MKL, Python 2.7 & 3.3 (32 & 64 bit), and numpy 1.7.1.
The `scipy.ndimage._ni_label` extension fails to compile <https://github.com/scipy/scipy/pull/2770>.
The win-amd64-py2.7 build passes all tests.
On Python 3 there are 12 errors in `test_wavfile.test_write_roundtrip` of the following kind: ```
======================================================================
ERROR: test_wavfile.test_write_roundtrip(False, 8000,
dtype('>i8'), 1)
----------------------------------------------------------------------
Traceback (most recent call last): File "X:\Python33\lib\site-packages\nose\case.py", line 198, in runTest self.test(*self.arg) File
"X:\Python33\lib\site-packages\scipy\io\tests\test_wavfile.py",
line 73, in _check_roundtrip rate2, data2 = wavfile.read(tmpfile, mmap=mmap) File "X:\Python33\lib\site-packages\scipy\io\wavfile.py", line
166,
in read data = _read_data_chunk(fid, comp, noc, bits, mmap=mmap) File "X:\Python33\lib\site-packages\scipy\io\wavfile.py", line 71, in _read_data_chunk data = numpy.fromstring(fid.read(size), dtype=dtype) ValueError: cannot expose native-only dtype 'q' in non-native byte
order
'>' via buffer interface ```
On 32 bit Python
`test_distributions.TestFitMethod.test_fix_fit_beta`
fails with an error:
```
======================================================================
ERROR: test_distributions.TestFitMethod.test_fix_fit_beta
----------------------------------------------------------------------
Traceback (most recent call last): File "X:\Python33-x32\lib\site-packages\nose\case.py", line
198, in
runTest self.test(*self.arg) File
"X:\Python33-x32\lib\site-packages\scipy\stats\tests\test_distributions.py",
line 928, in test_fix_fit_beta assert_raises(ValueError, stats.beta.fit, x, floc=0.5,
fscale=1)
File
"X:\Python33-x32\lib\site-packages\numpy\testing\utils.py",
line 1019, in assert_raises return nose.tools.assert_raises(*args,**kwargs) File "X:\Python33-x32\lib\unittest\case.py", line 570, in assertRaises return context.handle('assertRaises', callableObj, args,
kwargs)
File "X:\Python33-x32\lib\unittest\case.py", line 135, in
handle
callable_obj(*args, **kwargs) File "X:\Python33-x32\lib\site-packages\scipy\stats\distributions.py",
line
2533, in fit raise FitSolverError(mesg=mesg) scipy.stats.distributions.FitSolverError: Solver for the MLE
equations
failed to converge: The iteration is not making good progress, as measured by the improvement from the last ten iterations. ```
Also on 32 bit Python, `test_windows.test_windowfunc_basics` and `test_decomp.TestEig.test_singular` sometimes fail: ```
======================================================================
FAIL: test_windows.test_windowfunc_basics
----------------------------------------------------------------------
Traceback (most recent call last): File "X:\Python33-x32\lib\site-packages\nose\case.py", line
198, in
runTest self.test(*self.arg) File
"X:\Python33-x32\lib\site-packages\scipy\signal\tests\test_windows.py",
line 100, in test_windowfunc_basics assert_array_almost_equal(w1, w2) File
"X:\Python33-x32\lib\site-packages\numpy\testing\utils.py",
line 812, in assert_array_almost_equal header=('Arrays are not almost equal to %d decimals' %
decimal))
File
"X:\Python33-x32\lib\site-packages\numpy\testing\utils.py",
line 645, in assert_array_compare raise AssertionError(msg) AssertionError: Arrays are not almost equal to 6 decimals
(mismatch 85.71428571428571%) x: array([ 0.02221406, 1. , 0.32944607, 0.16207939, 0.18485882, 0.36183308, 0.02298899]) y: array([ 0.01910267, 1. , 0.34644519, 0.09150573, 0.09150573, 0.17127567, 0.12123497])
======================================================================
FAIL: test_decomp.TestEig.test_singular
----------------------------------------------------------------------
Traceback (most recent call last): File "X:\Python33-x32\lib\site-packages\nose\case.py", line
198, in
runTest self.test(*self.arg) File
"X:\Python33-x32\lib\site-packages\scipy\linalg\tests\test_decomp.py",
line 219, in test_singular self._check_gen_eig(A, B) File
"X:\Python33-x32\lib\site-packages\scipy\linalg\tests\test_decomp.py",
line 206, in _check_gen_eig err_msg=msg) File
"X:\Python33-x32\lib\site-packages\numpy\testing\utils.py",
line 812, in assert_array_almost_equal header=('Arrays are not almost equal to %d decimals' %
decimal))
File
"X:\Python33-x32\lib\site-packages\numpy\testing\utils.py",
line 645, in assert_array_compare raise AssertionError(msg) AssertionError: Arrays are not almost equal to 6 decimals
array([[22, 34, 31, 31, 17], [45, 45, 42, 19, 29], [39, 47, 49, 26, 34], [27, 31, 26, 21, 15], [38, 44, 44, 24, 30]]) array([[13, 26, 25, 17, 24], [31, 46, 40, 26, 37], [26, 40, 19, 25, 25], [16, 25, 27, 14, 23], [24, 35, 18, 21, 22]]) (mismatch 50.0%) x: array([ -5.90370943e-01+0.j, -1.54128768e-07+0.j, 1.54128748e-07+0.j, 2.00000000e+00+0.j]) y: array([ -1.32014829e-08+0.j, 1.32014809e-08+0.j, 1.33224503e+00+0.j, 2.00000000e+00+0.j]) ```
Christoph _______________________________________________ SciPy-Dev mailing list SciPy-Dev@scipy.org <mailto:SciPy-Dev@scipy.org> http://mail.scipy.org/mailman/listinfo/scipy-dev
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On Thu, Aug 22, 2013 at 03:12:21PM +0200, Ralf Gommers wrote:
Hi all,
I'm happy to announce the availability of the first beta release of Scipy 0.13.0. Please try this beta and report any issues on the scipy-dev mailing list.
Source tarballs and release notes can be found at https://sourceforge.net/projects/scipy/files/scipy/0.13.0b1/. Windows and OS X installers will follow later (we have a minor infrastructure issue to solve, and I'm at EuroScipy now).
Cheers, Ralf
Ralf, FYI, if the proposed elimination of support for the Accelerate framework on darwin was implemented in scipy 0.13, you will definietely want to consider reverting that change. It appears that the issues in the Accelerate framework (at least as tested with scipy 0.12.0) are resolved in the next darwin release... Ran 6134 tests in 88.016s OK (KNOWNFAIL=15, SKIP=36) compared to darwin12... Ran 6134 tests in 96.886s FAILED (KNOWNFAIL=15, SKIP=36, failures=63) and darwin11... Ran 6134 tests in 118.346s FAILED (KNOWNFAIL=15, SKIP=36, failures=65) Jack ps I have looked at the proposed replacement of using openblas and it is rather suboptimal. Please don't inflict that on us.
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On Sat, Aug 24, 2013 at 1:58 AM, Jack Howarth <howarth@bromo.med.uc.edu>wrote:
On Thu, Aug 22, 2013 at 03:12:21PM +0200, Ralf Gommers wrote:
Hi all,
I'm happy to announce the availability of the first beta release of Scipy 0.13.0. Please try this beta and report any issues on the scipy-dev mailing list.
Source tarballs and release notes can be found at https://sourceforge.net/projects/scipy/files/scipy/0.13.0b1/. Windows and OS X installers will follow later (we have a minor infrastructure issue to solve, and I'm at EuroScipy now).
Cheers, Ralf
Ralf, FYI, if the proposed elimination of support for the Accelerate framework on darwin was implemented in scipy 0.13, you will definietely want to consider reverting that change. It appears that the issues in the Accelerate framework (at least as tested with scipy 0.12.0) are resolved in the next darwin release...
Hi Jack, the issues appear to have been resolved completely (thanks to Michael Wimmer and Pauli), so we didn't drop support or used OpenBLAS for the binaries. Ralf
Ran 6134 tests in 88.016s
OK (KNOWNFAIL=15, SKIP=36)
compared to darwin12...
Ran 6134 tests in 96.886s
FAILED (KNOWNFAIL=15, SKIP=36, failures=63)
and darwin11...
Ran 6134 tests in 118.346s
FAILED (KNOWNFAIL=15, SKIP=36, failures=65)
Jack ps I have looked at the proposed replacement of using openblas and it is rather suboptimal. Please don't inflict that on us.
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_______________________________________________ SciPy-Dev mailing list SciPy-Dev@scipy.org http://mail.scipy.org/mailman/listinfo/scipy-dev
On Sat, Aug 24, 2013 at 11:11:36AM +0200, Ralf Gommers wrote:
On Sat, Aug 24, 2013 at 1:58 AM, Jack Howarth <howarth@bromo.med.uc.edu>wrote:
On Thu, Aug 22, 2013 at 03:12:21PM +0200, Ralf Gommers wrote:
Hi all,
I'm happy to announce the availability of the first beta release of Scipy 0.13.0. Please try this beta and report any issues on the scipy-dev mailing list.
Source tarballs and release notes can be found at https://sourceforge.net/projects/scipy/files/scipy/0.13.0b1/. Windows and OS X installers will follow later (we have a minor infrastructure issue to solve, and I'm at EuroScipy now).
Cheers, Ralf
Ralf, FYI, if the proposed elimination of support for the Accelerate framework on darwin was implemented in scipy 0.13, you will definietely want to consider reverting that change. It appears that the issues in the Accelerate framework (at least as tested with scipy 0.12.0) are resolved in the next darwin release...
Hi Jack, the issues appear to have been resolved completely (thanks to Michael Wimmer and Pauli), so we didn't drop support or used OpenBLAS for the binaries.
Ralf
Ralf, Unfortunately, I am seeing a linkage failure in 0.13.0 beta1 on darwin13 using the same build recipe that we use in fink for 0.12.0... /sw/bin/gfortran -Wall -L/sw/lib build/temp.macosx-10.9-x86_64-2.7/build/src.macosx-10.9-x86_64-2.7/scipy/linalg/_interpolativemodule.o build/temp.macosx-10.9-x86_64-2.7/build/src.macosx-10.9-x86_64-2.7/fortranobject.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/dfft_subr_0.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/dfft_subr_1.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/dfft_subr_2.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/dfft_subr_3.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/dfft_subr_4.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/dfft_subr_5.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/dfft_subr_6.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/dfft_subr_7.o 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build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idz_house_subr_2.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idz_id_subr_0.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idz_id_subr_1.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idz_id_subr_2.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idz_id_subr_3.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idz_id_subr_4.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idz_id_subr_5.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idz_id_subr_6.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idz_id_subr_7.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idz_id2svd_subr_0.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idz_id2svd_subr_1.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idz_id2svd_subr_2.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idz_id2svd_subr_3.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idz_id2svd_subr_4.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idz_id2svd_subr_5.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idz_qrpiv_subr_0.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idz_qrpiv_subr_1.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idz_qrpiv_subr_2.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idz_qrpiv_subr_3.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idz_qrpiv_subr_4.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idz_qrpiv_subr_5.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idz_sfft_subr_0.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idz_sfft_subr_1.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idz_sfft_subr_2.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idz_snorm_subr_0.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idz_snorm_subr_1.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idz_snorm_subr_2.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idz_snorm_subr_3.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idz_svd_subr_0.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idz_svd_subr_1.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idz_svd_subr_2.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idz_svd_subr_3.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idz_svd_subr_4.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idz_svd_subr_5.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idzp_aid_subr_0.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idzp_aid_subr_1.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idzp_aid_subr_2.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idzp_aid_subr_3.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idzp_aid_subr_4.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idzp_aid_subr_5.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idzp_asvd_subr_0.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idzp_asvd_subr_1.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idzp_asvd_subr_2.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idzp_rid_subr_0.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idzp_rid_subr_1.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idzp_rid_subr_2.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idzp_rid_subr_3.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idzp_rid_subr_4.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idzp_rsvd_subr_0.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idzp_rsvd_subr_1.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idzp_rsvd_subr_2.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idzr_aid_subr_0.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idzr_aid_subr_1.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idzr_aid_subr_2.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idzr_aid_subr_3.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idzr_asvd_subr_0.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idzr_asvd_subr_1.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idzr_rid_subr_0.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idzr_rid_subr_1.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idzr_rsvd_subr_0.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idzr_rsvd_subr_1.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/prini_subr_0.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/prini_subr_1.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/prini_subr_2.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/prini_subr_3.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/prini_subr_4.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/prini_subr_5.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/prini_subr_6.o -L/sw/lib/gcc4.8/lib/gcc/x86_64-apple-darwin13.0.0/4.8.1 -Lbuild/temp.macosx-10.9-x86_64-2.7 -lgfortran -o build/lib.macosx-10.9-x86_64-2.7/scipy/linalg/_interpolative.so -Wl,-framework -Wl,Accelerate Undefined symbols for architecture x86_64: "_PyArg_ParseTupleAndKeywords", referenced from: _f2py_rout__interpolative_id_srand in _interpolativemodule.o _f2py_rout__interpolative_id_srandi in _interpolativemodule.o _f2py_rout__interpolative_id_srando in _interpolativemodule.o _f2py_rout__interpolative_idd_frm in _interpolativemodule.o _f2py_rout__interpolative_idd_sfrm in _interpolativemodule.o _f2py_rout__interpolative_idd_frmi in _interpolativemodule.o _f2py_rout__interpolative_idd_sfrmi in _interpolativemodule.o ... etc. This is using... a site.cfg with... [amd] library_dirs = /sw/lib include_dirs = /sw/include/suitesparse amd_libs = amd [umfpack] library_dirs = /sw/lib include_dirs = /sw/include/suitesparse umfpack_libs = umfpack and export CC=clang export CXX=clang++ export FFLAGS=-ff2c export FC=/sw/bin/gfortran unset LDFLAGS /sw/bin/python2.7 setup.py build --fcompiler gnu95 with a build against suitesparse 4.0.2 and numpy 1.7.1. Jack
Ran 6134 tests in 88.016s
OK (KNOWNFAIL=15, SKIP=36)
compared to darwin12...
Ran 6134 tests in 96.886s
FAILED (KNOWNFAIL=15, SKIP=36, failures=63)
and darwin11...
Ran 6134 tests in 118.346s
FAILED (KNOWNFAIL=15, SKIP=36, failures=65)
Jack ps I have looked at the proposed replacement of using openblas and it is rather suboptimal. Please don't inflict that on us.
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On Fri, Aug 30, 2013 at 2:27 PM, Jack Howarth <howarth@bromo.med.uc.edu>wrote:
On Sat, Aug 24, 2013 at 11:11:36AM +0200, Ralf Gommers wrote:
On Sat, Aug 24, 2013 at 1:58 AM, Jack Howarth <howarth@bromo.med.uc.edu wrote:
On Thu, Aug 22, 2013 at 03:12:21PM +0200, Ralf Gommers wrote:
Hi all,
I'm happy to announce the availability of the first beta release of Scipy 0.13.0. Please try this beta and report any issues on the scipy-dev mailing list.
Source tarballs and release notes can be found at https://sourceforge.net/projects/scipy/files/scipy/0.13.0b1/. Windows and OS X installers will follow later (we have a minor infrastructure issue to solve, and I'm at EuroScipy now).
Cheers, Ralf
Ralf, FYI, if the proposed elimination of support for the Accelerate framework on darwin was implemented in scipy 0.13, you will definietely want to consider reverting that change. It appears that the issues in the Accelerate framework (at least as tested with scipy 0.12.0) are resolved in the next darwin release...
Hi Jack, the issues appear to have been resolved completely (thanks to Michael Wimmer and Pauli), so we didn't drop support or used OpenBLAS for the binaries.
Ralf
Ralf, Unfortunately, I am seeing a linkage failure in 0.13.0 beta1 on darwin13 using the same build recipe that we use in fink for 0.12.0...
Hi Jack, does the same recipe work on OS X 10.8 with 0.13.0b1? And could you try building 050ac31c6e5? That's before some build changes to split all the Fortran files, so it will help to figure out if those build changes introduced the issue. Thanks, Ralf <note to self: darwin13 is the not yet released OS X 10.9>
...<snip>..... p.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/prini_subr_2.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/prini_subr_3.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/prini_subr_4.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/pri ni_subr_5.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/prini_subr_6.o -L/sw/lib/gcc4.8/lib/gcc/x86_64-apple-darwin13.0.0/4.8.1 -Lbuild/temp.macosx-10.9-x86_64-2.7 -lgfortran -o build/lib.macosx-10.9-x86_64-2.7/scipy/linalg/_interpolative.so -Wl,-framework -Wl,Accelerate Undefined symbols for architecture x86_64: "_PyArg_ParseTupleAndKeywords", referenced from: _f2py_rout__interpolative_id_srand in _interpolativemodule.o _f2py_rout__interpolative_id_srandi in _interpolativemodule.o _f2py_rout__interpolative_id_srando in _interpolativemodule.o _f2py_rout__interpolative_idd_frm in _interpolativemodule.o _f2py_rout__interpolative_idd_sfrm in _interpolativemodule.o _f2py_rout__interpolative_idd_frmi in _interpolativemodule.o _f2py_rout__interpolative_idd_sfrmi in _interpolativemodule.o ...
etc. This is using...
a site.cfg with...
[amd] library_dirs = /sw/lib include_dirs = /sw/include/suitesparse amd_libs = amd
[umfpack] library_dirs = /sw/lib include_dirs = /sw/include/suitesparse umfpack_libs = umfpack
and
export CC=clang export CXX=clang++ export FFLAGS=-ff2c export FC=/sw/bin/gfortran
unset LDFLAGS /sw/bin/python2.7 setup.py build --fcompiler gnu95
with a build against suitesparse 4.0.2 and numpy 1.7.1. Jack
Ran 6134 tests in 88.016s
OK (KNOWNFAIL=15, SKIP=36)
compared to darwin12...
Ran 6134 tests in 96.886s
FAILED (KNOWNFAIL=15, SKIP=36, failures=63)
and darwin11...
Ran 6134 tests in 118.346s
FAILED (KNOWNFAIL=15, SKIP=36, failures=65)
Jack ps I have looked at the proposed replacement of using openblas and it
is
rather suboptimal. Please don't inflict that on us.
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_______________________________________________ SciPy-Dev mailing list SciPy-Dev@scipy.org http://mail.scipy.org/mailman/listinfo/scipy-dev
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On 08/22/2013 07:12 AM, Ralf Gommers wrote:
Hi all,
I'm happy to announce the availability of the first beta release of Scipy 0.13.0. Please try this beta and report any issues on the scipy-dev mailing list.
With Fedora Rawhide (but not Fedora 19) I'm seeing: ERROR: test_fitpack.TestSplder.test_kink ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python2.7/site-packages/nose/case.py", line 197, in runTest self.test(*self.arg) File "/builddir/build/BUILDROOT/scipy-0.13.0-0.1.b1.fc21.x86_64/usr/lib64/python2.7/site-packages/scipy/interpolate/tests/test_fitpack.py", line 326, in test_kink splder(spl2, 2) # Should work File "/builddir/build/BUILDROOT/scipy-0.13.0-0.1.b1.fc21.x86_64/usr/lib64/python2.7/site-packages/scipy/interpolate/fitpack.py", line 1186, in splder "and is not differentiable %d times") % n) ValueError: The spline has internal repeated knots and is not differentiable 2 times and the same with python3. -- Orion Poplawski Technical Manager 303-415-9701 x222 NWRA, Boulder/CoRA Office FAX: 303-415-9702 3380 Mitchell Lane orion@nwra.com Boulder, CO 80301 http://www.nwra.com
It looks like it broke the build with MKL as well (in, surprised, ARPACK). I will investigate this further this WE On Thu, Aug 22, 2013 at 2:12 PM, Ralf Gommers <ralf.gommers@gmail.com>wrote:
Hi all,
I'm happy to announce the availability of the first beta release of Scipy 0.13.0. Please try this beta and report any issues on the scipy-dev mailing list.
Source tarballs and release notes can be found at https://sourceforge.net/projects/scipy/files/scipy/0.13.0b1/. Windows and OS X installers will follow later (we have a minor infrastructure issue to solve, and I'm at EuroScipy now).
Cheers, Ralf
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On Fri, Aug 30, 2013 at 7:16 PM, David Cournapeau <cournape@gmail.com>wrote:
It looks like it broke the build with MKL as well (in, surprised, ARPACK). I will investigate this further this WE
Ok, I think the commit 5935030f8cced33e433804a21bdb15572d1d38e8 is quite wrong. It conflates the issue of dealing with Accelerate brokenness and using g77 ABI. I would suggest reverting it for 0.13.0 (and re-disable single precision), as fixing this correctly may require quite some time/testing. David
On Thu, Aug 22, 2013 at 2:12 PM, Ralf Gommers <ralf.gommers@gmail.com>wrote:
Hi all,
I'm happy to announce the availability of the first beta release of Scipy 0.13.0. Please try this beta and report any issues on the scipy-dev mailing list.
Source tarballs and release notes can be found at https://sourceforge.net/projects/scipy/files/scipy/0.13.0b1/. Windows and OS X installers will follow later (we have a minor infrastructure issue to solve, and I'm at EuroScipy now).
Cheers, Ralf
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participants (6)
-
Christoph Gohlke -
David Cournapeau -
Jack Howarth -
Orion Poplawski -
Ralf Gommers -
Warren Weckesser