[SciPy-Dev] ANN: Scipy 0.13.0 beta 1 release

David Cournapeau cournape@gmail....
Sat Aug 31 10:00:19 CDT 2013


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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