[Numpy-discussion] [ANN] numpy 1.4.0 rc2

Charles R Harris charlesr.harris@gmail....
Mon Dec 28 15:36:44 CST 2009


On Mon, Dec 28, 2009 at 2:30 PM, Gökhan Sever <gokhansever@gmail.com> wrote:

>
>
> On Mon, Dec 28, 2009 at 12:15 PM, Gökhan Sever <gokhansever@gmail.com>wrote:
>
>>
>>
>> On Mon, Dec 28, 2009 at 11:16 AM, Gökhan Sever <gokhansever@gmail.com>wrote:
>>
>>>
>>>
>>> On Mon, Dec 28, 2009 at 11:07 AM, Robert Kern <robert.kern@gmail.com>wrote:
>>>
>>>> On Mon, Dec 28, 2009 at 11:00, Gökhan Sever <gokhansever@gmail.com>
>>>> wrote:
>>>>
>>>> > One interesting thing I have noticed while installing the numpy from
>>>> the
>>>> > source is that numpy dependent libraries must be re-installed and this
>>>> must
>>>> > be a clean re-install. For instance I can't import some matplotlib and
>>>> scipy
>>>> > modules without making a fresh installation for these packages. My
>>>> attempts
>>>> > result with a runtime error.
>>>>
>>>> Please, please, always copy-and-paste the traceback when reporting an
>>>> error. I know you aren't formally reporting a bug here, but it always
>>>> helps.
>>>>
>>>> > Could someone clarify this point? Is this due
>>>> > to API change in the numpy core?
>>>>
>>>> Cython/Pyrex code does a runtime check on the struct sizes of types.
>>>> We have carefully added a member to the PyArrayDescr struct; i.e. it
>>>> shouldn't cause any actual problems, but Cython does the check
>>>> anyways. This affects a few modules in scipy, but shouldn't have
>>>> affected anything in matplotlib. The traceback may help us identify
>>>> the issue you are seeing.
>>>>
>>>>
>>> It is too late for the tracebacks. I have already removed the problematic
>>> packages and did clean installs. However, next time I will be more careful
>>> while reporting such issues. If it helps, in both matplotlib (via ipython
>>> -pylab) and scipy.stats import cases the runtime errors was raised due to
>>> numpy.core.multiarray module import.
>>>
>>>
>>>
>>>> --
>>>>
>>>> Robert Kern
>>>>
>>>> "I have come to believe that the whole world is an enigma, a harmless
>>>> enigma that is made terrible by our own mad attempt to interpret it as
>>>> though it had an underlying truth."
>>>>  -- Umberto Eco
>>>> _______________________________________________
>>>> NumPy-Discussion mailing list
>>>> NumPy-Discussion@scipy.org
>>>> http://mail.scipy.org/mailman/listinfo/numpy-discussion
>>>>
>>>
>>>
>>>
>>> --
>>> Gökhan
>>>
>>
>> Here is another interesting point to consider. To reproduce the runtime
>> error I mentioned previously I downgraded numpy (from the latest check-out
>> installation) following these steps:
>>
>> svn co http://svn.scipy.org/svn/numpy/branches/1.3.x/ numpy
>> cd numpy
>> python setup.py install
>> Writing
>> /usr/lib/python2.6/site-packages/numpy-1.3.1.dev8031-py2.6.egg-info
>>
>> I[2]: import matplotlib.pyplot as plt
>> Segmentation fault
>>
>> I[3]: from scipy import stats
>> Segmentation fault
>>
>> I have installed matplotlib and scipy using the latest numpy dev version.
>> A little later I will downgrade matplotlib and scipy to their previous
>> stable versions, and compile them using numpy 1.3.x. Afterwards I will
>> update numpy and test to see if I can re-produce the runtime error to
>> provide the tracebacks. First let me know if any tracebacks needed for these
>> segfaults or are these known failures?
>>
>>
>> ================================================================================
>> Platform     :
>> Linux-2.6.29.6-217.2.3.fc11.i686.PAE-i686-with-fedora-11-Leonidas
>> Python       : ('CPython', 'tags/r26', '66714')
>>
>> ================================================================================
>>
>>
>> --
>> Gökhan
>>
>
>
> Since no one has replied, I tried to reproduce the runtime error but ended
> up with different errors. Read more for the details:
>
> svn co http://svn.scipy.org/svn/scipy/tags/0.7.1/ scipy
> python setup.py install
> Writing /usr/lib/python2.6/site-packages/scipy-0.7.1-py2.6.egg-info
>
> svn co
> https://matplotlib.svn.sourceforge.net/svnroot/matplotlib/tags/v0_99_0/matplotlib
> python setup.py install
> Writing /usr/lib/python2.6/site-packages/matplotlib-0.99.0-py2.6.egg-info
>
> install them using
>
> >>> import numpy
> >>> numpy.__version__
> '1.3.1.dev8031'
>
> scipy import is fine but matplotlib fails with a different import error. I
> wonder if the buildbots test the source and releases for against different
> numpy versions or it is just might system acting weird.
>
> >>> from scipy import stats
>
>
> >>> import matplotlib.pyplot as plt
> Traceback (most recent call last):
>   File "<stdin>", line 1, in <module>
>   File
> "/home/gsever/Desktop/python-repo/matplotlib/lib/matplotlib/pyplot.py", line
> 6, in <module>
>     from matplotlib.figure import Figure, figaspect
>   File
> "/home/gsever/Desktop/python-repo/matplotlib/lib/matplotlib/figure.py", line
> 17, in <module>
>     import artist
>   File
> "/home/gsever/Desktop/python-repo/matplotlib/lib/matplotlib/artist.py", line
> 5, in <module>
>     from transforms import Bbox, IdentityTransform, TransformedBbox,
> TransformedPath
>   File
> "/home/gsever/Desktop/python-repo/matplotlib/lib/matplotlib/transforms.py",
> line 34, in <module>
>     from matplotlib._path import affine_transform
> ImportError: No module named _path
>
> Anyways, back to the main point. First remove the numpy 1.3.x:
>
> [root@ccn site-packages]# rm -rf numpy
> [root@ccn site-packages]# rm -rf numpy-1.3.1.dev8031-py2.6.egg-info
>
> and install from the latest trunk:
>
> svn co http://svn.scipy.org/svn/numpy/trunk numpy
> python setup.py install
> Writing /usr/lib/python2.6/site-packages/numpy-1.5.0.dev8032-py2.6.egg-info
>
> This time scipy asserts:
>
> >>> from scipy import stats
>
> Traceback (most recent call last):
>   File "<stdin>", line 1, in <module>
>   File "/usr/lib/python2.6/site-packages/scipy/stats/__init__.py", line 7,
> in <module>
>     from stats import *
>   File "/usr/lib/python2.6/site-packages/scipy/stats/stats.py", line 203,
> in <module>
>     from morestats import find_repeats #is only reference to scipy.stats
>   File "/usr/lib/python2.6/site-packages/scipy/stats/morestats.py", line 7,
> in <module>
>     import distributions
>   File "/usr/lib/python2.6/site-packages/scipy/stats/distributions.py",
> line 27, in <module>
>     import vonmises_cython
>   File "numpy.pxd", line 30, in scipy.stats.vonmises_cython
> (scipy/stats/vonmises_cython.c:2939)
> ValueError: numpy.dtype does not appear to be the correct type object
>
>
That is the cython problem. I think they fixed it, but I don't know if that
is in the recent release.

Chuck
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