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

Ralf Gommers ralf.gommers@gmail....
Sat Aug 31 06:13:43 CDT 2013


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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