[SciPy-Dev] ANN: Scipy 0.13.0 beta 1 release
David Cournapeau
cournape at gmail.com
Sat Aug 31 11:00:19 EDT 2013
On Sat, Aug 31, 2013 at 12:13 PM, Ralf Gommers <ralf.gommers at gmail.com>wrote:
>
>
>
> On Sat, Aug 31, 2013 at 10:47 AM, David Cournapeau <cournape at gmail.com>wrote:
>
>>
>>
>>
>> On Fri, Aug 30, 2013 at 7:56 PM, Christoph Gohlke <cgohlke at 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 at uci.edu
>>> > <mailto:cgohlke at 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
>>> > _______________________________________________
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>>> >
>>> >
>>> >
>>> >
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