[SciPy-Dev] request for testing: SciPy 0.7.2 RC1 + NumPy 1.4.1 RC1

Bruce Southey bsouthey@gmail....
Mon Apr 5 21:19:26 CDT 2010


On Mon, Apr 5, 2010 at 12:47 PM, Ralf Gommers
<ralf.gommers@googlemail.com> wrote:
> Hi everyone,
>
> The first release candidate of both Scipy 0.7.2 and NumPy 1.4.1 is ready,
> and I want to ask for some help with testing. I'm interested to hear about
> both installs where everything is OK and where there is a problem. SciPy
> 0.7.2 should work with both NumPy 1.3.0 and 1.4.1. Also, reports on whether
> these binaries work with matplotlib/pygame/<your favorite package here> will
> be very useful.
>
> For scipy 0.7.2 there are no new features compared to 0.7.1, the one change
> is that all cython sources have been regenerated with cython 0.12 so the
> resulting binary works with numpy 1.4.1. Numpy 1.4.1 has important bug fixes
> that should have solved the incompatibilities with scipy and other packages
> that were introduced with numpy 1.4.0.
>
> Windows binaries:
> http://www.filefactory.com/file/b0ghb9e/n/numpy-1.4.1rc1-win32-superpack-python2.6.exe
> http://filefactory.com/file/b0ghce6/n/scipy-0.7.2rc1-win32-superpack-python2.6.exe
>
> OS X binaries:
> http://www.filefactory.com/file/b0gh5h1/n/numpy-1.4.1rc1-py2.6-python.org.dmg
> http://www.filefactory.com/file/b0gh638/n/scipy-0.7.2rc1-py2.6-python.org.dmg
>
> I have not yet received the keys to the sourceforge site, so the above
> temporary hosting will have to do for rc1 (apologies for the flashy ads and
> download delay). Bandwidth is 150MB/hr so if the download is slow or not
> working please try again a bit later.
>
> Known issues:
> - there are failing datetime tests in numpy, they should probably be marked
> as knownfail or removed from the 1.4.x branch.
> - the numpy OS X installer still needs artwork.
>
> Cheers,
> Ralf
>
>
> _______________________________________________
> SciPy-Dev mailing list
> SciPy-Dev@scipy.org
> http://mail.scipy.org/mailman/listinfo/scipy-dev
>
>
HI,
Scipy installed okay on Win7 pro 32 bit Python 2.6 but the tests were
interesting.  Several times during the scipy.test() windows came and
went. There are also warnings indicating some incompatibility.

Why is the histogram warning here? It does say removal in Numpy 1.4 so
should be gone. Also, shouldn't some of the other stats functions also
be removed?

While not your fault, we should not have these "FutureWarning" coming
from the tests such as:
Warning (from warnings module):
  File "E:\Python26\lib\site-packages\scipy\io\matlab\mio.py", line 165
    oned_as=oned_as)
FutureWarning: Using oned_as default value ('column') This will change
to 'row' in future versions


Bruce

Python 2.6.3 (r263rc1:75186, Oct  2 2009, 20:40:30) [MSC v.1500 32 bit
(Intel)] on win32
Type "copyright", "credits" or "license()" for more information.

    ****************************************************************
    Personal firewall software may warn about the connection IDLE
    makes to its subprocess using this computer's internal loopback
    interface.  This connection is not visible on any external
    interface and no data is sent to or received from the Internet.
    ****************************************************************

IDLE 2.6.3
>>> import scipy
>>> scipy.__version__
'0.7.2rc1'
>>> scipy.test()
Running unit tests for scipy
NumPy version 1.4.1rc1
NumPy is installed in E:\Python26\lib\site-packages\numpy
SciPy version 0.7.2rc1
SciPy is installed in E:\Python26\lib\site-packages\scipy
Python version 2.6.3 (r263rc1:75186, Oct  2 2009, 20:40:30) [MSC
v.1500 32 bit (Intel)]
nose version 0.11.1

Warning (from warnings module):
  File "E:\Python26\lib\site-packages\scipy\spatial\__init__.py", line 7
    from ckdtree import *
RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility

Warning (from warnings module):
  File "E:\Python26\lib\site-packages\scipy\spatial\__init__.py", line 7
    from ckdtree import *
RuntimeWarning: numpy.flatiter size changed, may indicate binary incompatibility

Warning (from warnings module):
  File "E:\Python26\lib\site-packages\scipy\linsolve\__init__.py", line 4
    warn('scipy.linsolve has moved to scipy.sparse.linalg.dsolve',
DeprecationWarning)
DeprecationWarning: scipy.linsolve has moved to scipy.sparse.linalg.dsolve

Warning (from warnings module):
  File "E:\Python26\lib\site-packages\scipy\stats\distributions.py", line 27
    import vonmises_cython
RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility

Warning (from warnings module):
  File "E:\Python26\lib\site-packages\scipy\stats\distributions.py", line 27
    import vonmises_cython
RuntimeWarning: numpy.flatiter size changed, may indicate binary incompatibility
......................................................................................................................................................
Warning (from warnings module):
  File "E:\Python26\lib\site-packages\scipy\cluster\vq.py", line 570
    warnings.warn("One of the clusters is empty. "
UserWarning: One of the clusters is empty. Re-run kmean with a
different initialization.
.......................................................................
Warning (from warnings module):
  File "E:\Python26\lib\site-packages\scipy\interpolate\fitpack2.py", line 498
    warnings.warn(message)
UserWarning:
The coefficients of the spline returned have been computed as the
minimal norm least-squares solution of a (numerically) rank deficient
system (deficiency=7). If deficiency is large, the results may be
inaccurate. Deficiency may strongly depend on the value of eps.
.....
Warning (from warnings module):
  File "E:\Python26\lib\site-packages\scipy\interpolate\fitpack2.py", line 439
    warnings.warn(message)
UserWarning:
The required storage space exceeds the available storage space: nxest
or nyest too small, or s too small.
The weighted least-squares spline corresponds to the current set of
knots.
...........................................K..K.................................................................................................
Warning (from warnings module):
  File "E:\Python26\lib\site-packages\scipy\io\matlab\mio.py", line 111
    matfile_dict = MR.get_variables()
Warning: Unreadable variable "testfunc", because "Cannot read matlab functions"
..........
Warning (from warnings module):
  File "E:\Python26\lib\site-packages\scipy\io\matlab\mio.py", line 165
    oned_as=oned_as)
FutureWarning: Using oned_as default value ('column') This will change
to 'row' in future versions
.........................
Warning (from warnings module):
  File "E:\Python26\lib\site-packages\scipy\io\matlab\tests\test_mio.py",
line 438
    mfw = MatFile5Writer(StringIO())
FutureWarning: Using oned_as default value ('column') This will change
to 'row' in future versions
........
Warning (from warnings module):
  File "E:\Python26\lib\site-packages\scipy\io\matlab\mio.py", line 84
    return MatFile5Reader(byte_stream, **kwargs)
FutureWarning: Using struct_as_record default value (False) This will
change to True in future versions
................................
Warning (from warnings module):
  File "E:\Python26\lib\site-packages\numpy\lib\utils.py", line 140
    warnings.warn(depdoc, DeprecationWarning)
DeprecationWarning: `write_array` is deprecated!


This function is replaced by numpy.savetxt which allows the same functionality
through a different syntax.


Warning (from warnings module):
  File "E:\Python26\lib\site-packages\numpy\lib\utils.py", line 140
    warnings.warn(depdoc, DeprecationWarning)
DeprecationWarning: `read_array` is deprecated!

The functionality of read_array is in numpy.loadtxt which allows the same
functionality using different syntax.

.......................
Warning (from warnings module):
  File "E:\Python26\lib\site-packages\numpy\lib\utils.py", line 140
    warnings.warn(depdoc, DeprecationWarning)
DeprecationWarning: `npfile` is deprecated!

You can achieve the same effect as using npfile, using ndarray.tofile
and numpy.fromfile.

Even better you can use memory-mapped arrays and data-types to map out a
file format for direct manipulation in NumPy.

.........................................................................................................................................................SSSSSS......SSSSSS......SSSS.............................................................S.....................................................
Warning (from warnings module):
  File "E:\Python26\lib\site-packages\scipy\linalg\decomp.py", line 1177
    "the mode='economic' argument.", DeprecationWarning)
DeprecationWarning: qr econ argument will be removed after scipy 0.7.
The economy transform will then be available through the
mode='economic' argument.
.............................................................................................................................................................................................................................................................................................Result
may be inaccurate, approximate err = 5.76591035582e-08
...Result may be inaccurate, approximate err = 1.00314019744e-10
.....SSS..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................SSSSSSSSSSS...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................K.K...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
Warning (from warnings module):
  File "E:\Python26\lib\site-packages\numpy\lib\function_base.py", line 185
    """, Warning)
Warning:
            The new semantics of histogram is now the default and the `new`
            keyword will be removed in NumPy 1.4.

....................................................................................S..................................................................................
Warning (from warnings module):
  File "E:\Python26\lib\site-packages\scipy\stats\stats.py", line 420
    axis=0, ddof=1).""", DeprecationWarning)
DeprecationWarning: scipy.stats.mean is deprecated; please update your
code to use numpy.mean.
Please note that:
    - numpy.mean axis argument defaults to None, not 0
    - numpy.mean has a ddof argument to replace bias in a more general manner.
      scipy.stats.mean(a, bias=True) can be replaced by numpy.mean(x,
axis=0, ddof=1).
.
Warning (from warnings module):
  File "E:\Python26\lib\site-packages\scipy\stats\stats.py", line 1329
    ddof=1).""", DeprecationWarning)
DeprecationWarning: scipy.stats.std is deprecated; please update your
code to use numpy.std.
Please note that:
    - numpy.std axis argument defaults to None, not 0
    - numpy.std has a ddof argument to replace bias in a more general manner.
      scipy.stats.std(a, bias=True) can be replaced by numpy.std(x,
      axis=0, ddof=0), scipy.stats.std(a, bias=False) by numpy.std(x, axis=0,
      ddof=1).

Warning (from warnings module):
  File "E:\Python26\lib\site-packages\scipy\stats\stats.py", line 1305
    ddof=1).""", DeprecationWarning)
DeprecationWarning: scipy.stats.var is deprecated; please update your
code to use numpy.var.
Please note that:
    - numpy.var axis argument defaults to None, not 0
    - numpy.var has a ddof argument to replace bias in a more general manner.
      scipy.stats.var(a, bias=True) can be replaced by numpy.var(x,
      axis=0, ddof=0), scipy.stats.var(a, bias=False) by var(x, axis=0,
      ddof=1).
.
Warning (from warnings module):
  File "E:\Python26\lib\site-packages\scipy\stats\morestats.py", line 603
    warnings.warn("Ties preclude use of exact statistic.")
UserWarning: Ties preclude use of exact statistic.
......
Warning (from warnings module):
  File "E:\Python26\lib\site-packages\scipy\stats\stats.py", line 498
    axis=0, ddof=1).""", DeprecationWarning)
DeprecationWarning: scipy.stats.median is deprecated; please update
your code to use numpy.median.
Please note that:
    - numpy.median axis argument defaults to None, not 0
    - numpy.median has a ddof argument to replace bias in a more general manner.
      scipy.stats.median(a, bias=True) can be replaced by numpy.median(x,
axis=0, ddof=1).
....................................................................................................................................................................................................Warning:
friedmanchisquare test using Chisquared aproximation
...............warning: specified build_dir '_bad_path_' does not
exist or is not writable. Trying default locations
.....warning: specified build_dir '_bad_path_' does not exist or is
not writable. Trying default locations
.............................error removing
e:\users\me\appdata\local\temp\tmpumnxuucat_test:
e:\users\me\appdata\local\temp\tmpumnxuucat_test: The directory is not
empty
..building extensions here:
e:\users\me\appdata\local\temp\Me\python26_compiled\m0
................................................................................................
----------------------------------------------------------------------
Ran 3488 tests in 65.938s

OK (KNOWNFAIL=4, SKIP=32)
<nose.result.TextTestResult run=3488 errors=0 failures=0>
>>>


More information about the SciPy-Dev mailing list