[Numpy-discussion] ANN: Numpy 1.6.1 release candidate 1

Bruce Southey bsouthey@gmail....
Tue Jun 21 09:38:15 CDT 2011


On 06/21/2011 01:01 AM, Ralf Gommers wrote:
>
>
> On Tue, Jun 21, 2011 at 3:55 AM, Bruce Southey <bsouthey@gmail.com 
> <mailto:bsouthey@gmail.com>> wrote:
>
>     On Mon, Jun 20, 2011 at 2:43 PM, Ralf Gommers
>     <ralf.gommers@googlemail.com <mailto:ralf.gommers@googlemail.com>>
>     wrote:
>     >
>     >
>     > On Mon, Jun 20, 2011 at 8:50 PM, Bruce Southey
>     <bsouthey@gmail.com <mailto:bsouthey@gmail.com>> wrote:
>     >>
>     >> I copied the files but that just moves the problem. So that
>     patch is
>     >> incorrect.
>     >>
>     >> I get the same errors on Fedora 15 supplied Python3.2 for numpy
>     1.6.0 and
>     >> using git from 'https://github.com/rgommers/numpy.git'.  Numpy
>     is getting
>     >> Fedora supplied Atlas (1.5.1 does not).
>     >>
>     >> It appears that there is a misunderstanding of the PEP because
>     'SO' and
>     >> 'SOABI' do exactly what the PEP says on my systems:
>     >
>     > It doesn't on OS X. But that's not even the issue. As I
>     explained before,
>     > the issue is that get_config_var('SO') is used to determine the
>     extension of
>     > system libraries (such as liblapack.so) and python-related ones
>     (such as
>     > multiarray.cpython-32m.so <http://multiarray.cpython-32m.so>). 
>     And the current functions don't do mindreading.
>     >>
>     >> >>> from distutils import sysconfig sysconfig.get_config_var('SO')
>     >> '.cpython-32m.so'
>     >> >>> sysconfig.get_config_var('SOABI')
>     >> 'cpython-32m'
>     >>
>     >> Consequently, the name, 'multiarray.pyd', created within numpy
>     is invalid.
>     >
>     > I removed the line in ctypeslib that was trying this, so I think
>     you are not
>     > testing my patch.
>     >
>     > Ralf
>     >
>     >>
>     >> Looking the code, I see this line which makes no sense given
>     that the
>     >> second part is true under Linux:
>     >>
>     >> if (not is_python_ext) and 'SOABI' in
>     >> distutils.sysconfig.get_config_vars():
>     >>
>     >> So I think the 'get_shared_lib_extension' function is wrong and
>     probably
>     >> unneeded.
>     >>
>     >>
>     >> Bruce
>     >>
>
>     Just to show that this is the new version, I added two print
>     statements in the 'get_shared_lib_extension' function:
>     >>> from numpy.distutils.misc_util import get_shared_lib_extension
>     >>> get_shared_lib_extension(True)
>     first so_ext .cpython-32mu.so
>     returned so_ext .cpython-32mu.so
>     '.cpython-32mu.so'
>     >>> get_shared_lib_extension(False)
>     first so_ext .cpython-32mu.so
>     returned so_ext .so
>     '.so'
>
>
> This all looks correct. Before you were saying you were still getting 
> 'multiarray.pyd', now your error says 'multiarray.so'. So now you are 
> testing the right thing. Test test_basic2() in test_ctypeslib was 
> fixed, but I forgot to fix it in two other places. I updated both my 
> branches on github, please try again.
>
>
>     The reason for the same location is obvious because all the patch does
>     is move  the code to get the extension into that function. So the
>     'get_shared_lib_extension' function returns the extension '.so' to the
>     load_library function. However that name is wrong under Linux as it
>     has to be 'multiarray.cpython-32mu.so
>     <http://multiarray.cpython-32mu.so>' and hence the error in the same
>     location. I did come across this thread
>     'http://bugs.python.org/issue10262' which indicates why Linux is
>     different by default.
>
>     So what is the actual name of the multiarray shared library with
>     the Mac?
>     If it is ' 'multiarray.so' then the correct name is "libname +
>     sysconfig.get_config_var('SO')" as I previously indicated.
>
> It is, and yes that's correct. Orthogonal to the actual issue though.
>
> Ralf
>
>
>

While the test now pass, you have now changed an API for load_library. 
This is not something that is meant to occur in a bug-fix release as 
well as the new argument is undocumented. But I do not understand the 
need for this extra complexity when "libname + 
sysconfig.get_config_var('SO')" works on Linux, Windows and Mac.

Bruce

$ git clone git://github.com/rgommers/numpy.git numpy
$ cd numpy
$ git checkout sharedlib-ext
Switched to branch 'sharedlib-ext'
$ git branch -a
   master
* sharedlib-ext
   remotes/origin/1.5.x
   remotes/origin/HEAD -> origin/master
   remotes/origin/compilation-issues-doc
   remotes/origin/doc-noinstall
   remotes/origin/maintenance/1.4.x
   remotes/origin/maintenance/1.5.x
   remotes/origin/maintenance/1.6.x
   remotes/origin/master
   remotes/origin/sharedlib-ext
   remotes/origin/sharedlib-ext-1.6.x
   remotes/origin/swigopts
   remotes/origin/ticket-1218-array2string
   remotes/origin/ticket-1689-fromstring
   remotes/origin/ticket-99
   remotes/origin/warn-noclean-build

[built and installed numpy]

$ python3
Python 3.2 (r32:88445, Feb 21 2011, 21:11:06)
[GCC 4.6.0 20110212 (Red Hat 4.6.0-0.7)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
 >>> import numpy as np
 >>> np.__version__
'2.0.0.dev-Unknown'
 >>> np.test()
Running unit tests for numpy
NumPy version 2.0.0.dev-Unknown
NumPy is installed in /usr/lib64/python3.2/site-packages/numpy
Python version 3.2 (r32:88445, Feb 21 2011, 21:11:06) [GCC 4.6.0 
20110212 (Red Hat 4.6.0-0.7)]
nose version 1.0.0
...F..............F.....E..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................K............................................................................................................................................................................................K..................................................................................................K......................K..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................../usr/lib64/python3.2/site-packages/numpy/lib/format.py:575: 
ResourceWarning: unclosed file <_io.BufferedReader name='/tmp/tmphws7d4'>
   mode=mode, offset=offset)
.........................................................................................................................................................................................................................................................................................................................................................................................................................................................................../usr/lib64/python3.2/subprocess.py:460: 
ResourceWarning: unclosed file <_io.BufferedReader name=3>
   return Popen(*popenargs, **kwargs).wait()
/usr/lib64/python3.2/subprocess.py:460: ResourceWarning: unclosed file 
<_io.BufferedReader name=8>
   return Popen(*popenargs, **kwargs).wait()
........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
======================================================================
ERROR: test_datetime_divide (test_datetime.TestDateTime)
----------------------------------------------------------------------
Traceback (most recent call last):
   File 
"/usr/lib64/python3.2/site-packages/numpy/core/tests/test_datetime.py", 
line 762, in test_datetime_divide
     assert_equal(tda / tdb, 6.0 / 9.0)
TypeError: internal error: could not find appropriate datetime inner 
loop in true_divide ufunc

======================================================================
FAIL: Test custom format function for each element in array.
----------------------------------------------------------------------
Traceback (most recent call last):
   File 
"/usr/lib64/python3.2/site-packages/numpy/core/tests/test_arrayprint.py", line 
86, in test_format_function
     "[0x0L 0x1L 0x2L]")
   File "/usr/lib64/python3.2/site-packages/numpy/testing/utils.py", 
line 313, in assert_equal
     raise AssertionError(msg)
AssertionError:
Items are not equal:
  ACTUAL: '[0x0 0x1 0x2]'
  DESIRED: '[0x0L 0x1L 0x2L]'

======================================================================
FAIL: test_datetime_as_string (test_datetime.TestDateTime)
----------------------------------------------------------------------
Traceback (most recent call last):
   File 
"/usr/lib64/python3.2/site-packages/numpy/core/tests/test_datetime.py", 
line 1001, in test_datetime_as_string
     '1959')
   File "/usr/lib64/python3.2/site-packages/numpy/testing/utils.py", 
line 313, in assert_equal
     raise AssertionError(msg)
AssertionError:
Items are not equal:
  ACTUAL: b'1959'
  DESIRED: '1959'

----------------------------------------------------------------------
Ran 3578 tests in 36.278s

FAILED (KNOWNFAIL=4, errors=1, failures=2)
<nose.result.TextTestResult run=3578 errors=1 failures=2>
 >>>
 >>> from numpy.distutils.misc_util import get_shared_lib_extension
 >>> get_shared_lib_extension(True)
'.cpython-32mu.so'
 >>> get_shared_lib_extension(False)
'.so'
 >>> load_library('multiarray', 
'/usr/lib64/python3.2/site-packages/numpy/core/', True)
<CDLL 
'/usr/lib64/python3.2/site-packages/numpy/core/multiarray.cpython-32mu.so', 
handle a5a070 at 17dd9d0>
 >>> load_library('multiarray', 
'/usr/lib64/python3.2/site-packages/numpy/core/')
Traceback (most recent call last):
   File "<stdin>", line 1, in <module>
   File "/usr/lib64/python3.2/site-packages/numpy/ctypeslib.py", line 
124, in load_library
     raise exc
   File "/usr/lib64/python3.2/site-packages/numpy/ctypeslib.py", line 
121, in load_library
     return ctypes.cdll[libpath]
   File "/usr/lib64/python3.2/ctypes/__init__.py", line 415, in __getitem__
     return getattr(self, name)
   File "/usr/lib64/python3.2/ctypes/__init__.py", line 410, in __getattr__
     dll = self._dlltype(name)
   File "/usr/lib64/python3.2/ctypes/__init__.py", line 340, in __init__
     self._handle = _dlopen(self._name, mode)
OSError: /usr/lib64/python3.2/site-packages/numpy/core/multiarray.so: 
cannot open shared object file: No such file or directory








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