[SciPy-user] [Numpy-discussion] scipy 0.7.1 rc3

Fri Jun 12 20:14:41 EDT 2009

On Fri, Jun 12, 2009 at 7:09 PM, <josef.pktd at gmail.com> wrote:
> On Fri, Jun 12, 2009 at 6:26 PM, George Nurser<gnurser at googlemail.com> wrote:
>> Hi,
>> I have just two failures on svn r 5835, which I believe is the same as
>> 0.7.1.rc3.
>
> Are you sure you are using the tag version and not the trunk version?
> I think the test failure with ksone was created when I corrected and
> tightened the test in revision 5831 in the trunk,
>
> the precision in 0.7.1 is set low enough that it should not report
> this as a failure.
>
> I didn't catch the error in the changes to the trunk because I skipped
> the slow tests. This also means there is a bug or imprecision in ksone
> or special.smirnov
>
> Josef
>
>
>> OS x 10.5.7,python.org 2.5.2, numpy svn 7044, gfortran 4.3.2, apple gcc 4.0.1.
>> scipy built with
>> python setup.py build_src build_clib config_fc --fcompiler=gnu95
>> --f77flags=" -O3 -march=core2" build_ext config_fc --fcompiler=gnu95
>> --f77flags=" -O3 -march=core2" build > & inst.log &
>>
>> scipy.test('10')
>> [snip]
>> =====================================================================
>> FAIL: test_random_real (test_basic.TestSingleIFFT)
>> ----------------------------------------------------------------------
>> Traceback (most recent call last):
>>  File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/fftpack/tests/test_basic.py",
>> line 205, in test_random_real
>>    assert_array_almost_equal (y1, x)
>>  File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/numpy/testing/utils.py",
>> line 537, in assert_array_almost_equal
>>    header='Arrays are not almost equal')
>>  File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/numpy/testing/utils.py",
>> line 395, in assert_array_compare
>>    raise AssertionError(msg)
>> AssertionError:
>> Arrays are not almost equal
>>
>> (mismatch 0.900900900901%)
>>  x: array([ 0.56936401 -1.61093638e-09j,  0.42778808 -9.66561764e-09j,
>>        0.52186930 -1.07395759e-09j,  0.09524378 -1.19960097e-12j,
>>        0.37034556 -1.55349547e-08j,  0.87382299 +7.88580223e-09j,...
>>  y: array([ 0.56936431,  0.42778817,  0.52186954,  0.09524398,  0.37034538,
>>        0.87382281,  0.11707421,  0.78889829,  0.92179215,  0.82394433,
>>        0.23986711,  0.61445147,  0.64488971,  0.77991045,  0.91312933,...
>>
>> ======================================================================
>> FAIL: test_continuous_basic.test_cont_basic_slow(<scipy.stats.distributions.ksone_gen
>> object at 0x15d6f2d0>, (22,), 'ksone')
>> ----------------------------------------------------------------------
>> Traceback (most recent call last):
>>  File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/nose-0.10.3-py2.5.egg/nose/case.py",
>> line 182, in runTest
>>    self.test(*self.arg)
>>  File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/stats/tests/test_continuous_basic.py",
>> line 290, in check_cdf_ppf
>>    ' - cdf-ppf roundtrip')
>>  File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/numpy/testing/utils.py",
>> line 262, in assert_almost_equal
>>    return assert_array_almost_equal(actual, desired, decimal, err_msg)
>>  File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/numpy/testing/utils.py",
>> line 537, in assert_array_almost_equal
>>    header='Arrays are not almost equal')
>>  File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/numpy/testing/utils.py",
>> line 395, in assert_array_compare
>>    raise AssertionError(msg)
>> AssertionError:
>> Arrays are not almost equal
>> ksone - cdf-ppf roundtrip
>> (mismatch 33.3333333333%)
>>  x: array([ 0.   ,  0.5  ,  0.999])
>>  y: array([ 0.001,  0.5  ,  0.999])
>>
>> ----------------------------------------------------------------------
>> Ran 4273 tests in 588.327s
>>
>> --George.
>>
>>
>>
>> 2009/6/12 David Cournapeau <david at ar.media.kyoto-u.ac.jp>:
>>> Hi,
>>>
>>>    I have uploaded the binaries and source tarballs for 0.7.1rc3. The
>>> rc3 fixes some issues in scipy.special, which caused wrong
>>> behavior/crashes on some platforms. Hopefully, this will be the 0.7.1
>>> release,
>>>
>>> cheers,
>>>
>>> David
>>>
>>> =========================
>>> SciPy 0.7.1 Release Notes
>>> =========================
>>>
>>> .. contents::
>>>
>>> SciPy 0.7.1 is a bug-fix release with no new features compared to 0.7.0.
>>>
>>> scipy.io
>>> ========
>>>
>>> Bugs fixed:
>>>
>>> - Several fixes in Matlab file IO
>>>
>>> scipy.odr
>>> =========
>>>
>>> Bugs fixed:
>>>
>>> - Work around a failure with Python 2.6
>>>
>>> scipy.signal
>>> ============
>>>
>>> Memory leak in lfilter have been fixed, as well as support for array object
>>>
>>> Bugs fixed:
>>>
>>> - #880, #925: lfilter fixes
>>> - #871: bicgstab fails on Win32
>>>
>>>
>>> scipy.sparse
>>> ============
>>>
>>> Bugs fixed:
>>>
>>> - #883: scipy.io.mmread with scipy.sparse.lil_matrix broken
>>> - lil_matrix and csc_matrix reject now unexpected sequences,
>>>  cf. http://thread.gmane.org/gmane.comp.python.scientific.user/19996
>>>
>>> scipy.special
>>> =============
>>>
>>> Several bugs of varying severity were fixed in the special functions:
>>>
>>> - #503, #640: iv: problems at large arguments fixed by new implementation
>>> - #623: jv: fix errors at large arguments
>>> - #679: struve: fix wrong output for v < 0
>>> - #803: pbdv produces invalid output
>>> - #804: lqmn: fix crashes on some input
>>> - #823: betainc: fix documentation
>>> - #834: exp1 strange behavior near negative integer values
>>> - #852: jn_zeros: more accurate results for large s, also in
>>> jnp/yn/ynp_zeros
>>> - #853: jv, yv, iv: invalid results for non-integer v < 0, complex x
>>> - #854: jv, yv, iv, kv: return nan more consistently when out-of-domain
>>> - #927: ellipj: fix segfault on Windows
>>> - #946: ellpj: fix segfault on Mac OS X/python 2.6 combination.
>>> - ive, jve, yve, kv, kve: with real-valued input, return nan for
>>> out-of-domain
>>>  instead of returning only the real part of the result.
>>>
>>> Also, when ``scipy.special.errprint(1)`` has been enabled, warning
>>> messages are now issued as Python warnings instead of printing them to
>>> stderr.
>>>
>>>
>>> scipy.stats
>>> ===========
>>>
>>> - linregress, mannwhitneyu, describe: errors fixed
>>> - kstwobign, norm, expon, exponweib, exponpow, frechet, genexpon, rdist,
>>>  truncexpon, planck: improvements to numerical accuracy in distributions
>>>
>>> Windows binaries for python 2.6
>>> ===============================
>>>
>>> python 2.6 binaries for windows are now included. The binary for python 2.5
>>> requires numpy 1.2.0 or above, and and the one for python 2.6 requires numpy
>>> 1.3.0 or above.
>>>
>>> Universal build for scipy
>>> =========================
>>>
>>> Mac OS X binary installer is now a proper universal build, and does not
>>> depend
>>> on gfortran anymore (libgfortran is statically linked). The python 2.5
>>> version
>>> of scipy requires numpy 1.2.0 or above, the python 2.6 version requires
>>> numpy
>>> 1.3.0 or above.
>>>
>>> Checksums
>>> =========
>>>
>>> 9dd5af43cc26ae6d38a13b373ba430fa
>>> release/installers/scipy-0.7.1rc3-py2.6-python.org.dmg
>>> 290c2e056fda1f86dfa9f3a76d207a8c
>>> release/installers/scipy-0.7.1rc3-win32-superpack-python2.6.exe
>>> d582dff7535d2b64a097fb4bfbc75d09
>>> release/installers/scipy-0.7.1rc3-win32-superpack-python2.5.exe
>>> a19400ccfd65d1a0a5030848af6f78ea  release/installers/scipy-0.7.1rc3.tar.gz
>>> d4ebf322c62b09c4ebaad7b67f92d032  release/installers/scipy-0.7.1rc3.zip
>>> a0ea0366b178a7827f10a480f97c3c47
>>> release/installers/scipy-0.7.1rc3-py2.5-python.org.dmg
>>>

Why are there now 310 known fail, it was only a few before, what I remember?
now errors or failures.

Josef

Ran 4168 tests in 383.109s
OK (KNOWNFAIL=310, SKIP=29)

Winxp, sse2, 32bit

>python -c "import scipy;scipy.test('full')
Running unit tests for scipy
NumPy version 1.3.0
NumPy is installed in c:\programs\python25\lib\site-packages\numpy
SciPy version 0.7.1rc3
SciPy is installed in c:\programs\python25\lib\site-packages\scipy
Python version 2.5.2 (r252:60911, Feb 21 2008, 13:11:45) [MSC v.1310 32 bit (Int
el)]
nose version 0.11.1