[SciPy-Dev] Scipy on Python 3

Christoph Gohlke cgohlke@uci....
Mon Sep 13 23:23:58 CDT 2010



On 9/11/2010 6:10 PM, Pauli Virtanen wrote:
> Hi,
>
> I flushed the Python 3 branch containing work from me and David to SVN
> trunk. Scipy now builds with Python 3, and all tests pass, except for
> scipy.weave which still needs to be ported.
>
> More testing is welcome. I suspect Scipy's test suite does not cover all
> of the code, so there might be some work left to do. You'll probably need
> the latest 1.5.x branch Numpy to build, due to some fixes in Numpy's
> distutils that are not in 1.5.0.
>
> 	Pauli
>


Thank you and David for making this available.

Will numscons eventually be ported to Python 3? So far numscons has been 
the most reliable way to build scipy with Microsoft C and Intel Fortran 
compilers.

Anyway, I succeeded building scipy 0.9 rev 6805 on Python 3.1 for 
Windows (64 bit) using the distutils method after applying some bold 
fixes. Most problems encountered are not Python 3 specific. The attached 
patch gives a hint what needs to be addressed.

I am using this site.cfg with numpy 1.5.0 svn rev 8714:

[mkl]
include_dirs = C:/Program Files (x86)/Intel/Compiler/11.1/067/mkl/include
library_dirs = C:/Program Files 
(x86)/Intel/Compiler/11.1/067/mkl/em64t/lib;C:/Program Files 
(x86)/Intel/Compiler/11.1/067/lib/intel64
mkl_libs = 
mkl_lapack95_lp64,mkl_blas95_lp64,mkl_intel_lp64,mkl_intel_thread,mkl_core,libiomp5md,libifportmd
lapack_libs = 
mkl_lapack95_lp64,mkl_blas95_lp64,mkl_intel_lp64,mkl_intel_thread,mkl_core,libiomp5md,libifportmd

The problem with this configuration is that numpy.distutils expects all 
the libraries to be found in a single directory, which is not the case. 
Hence it claims that MKL is not available. A quick solution is to copy 
libiomp5md.lib and libifportmd.lib from '.../lib/intel64' to 
'.../mkl/em64t/lib'.

In order for numpy.distutils to find the ifort compiler, call 
"ifortvars.bat intel64 vs2008" before "python setup.py build".

The Visual C compiler reproducibly crashes while compiling 
scipy\special\cephes\polevl.c. Running the build command twice works.

Scipy\interpolate\interpnd.c uses the C99 fmax() function, which is 
unknown to msvc9. Using max() instead of fmax().

The atlas_version.c files in scipy/lib/lapack/ and scipy/lib/blas/ are 
not Python 3 compatible. Using the atlas_version.c file from 
scipy/linalg, which has been ported.

Atlas_version.c needs 'NO_ATLAS_INFO' defined when using MKL. Using 
"define_macros = [('NO_ATLAS_INFO', 1)]" when defining the extension in 
setup.py.

Removing 'lsame.c' from the SuperLU source files in 
scipy/sparse/linalg/dsolve/setup.py. lsame is provided by MKL.

Scipy/optimize/lbfgsb/routines.f and 
scipy/sparse/linalg/eigen/arpack/ARPACK/UTIL/second.f use the etime 
function, which can not be resolved even though libifportmd is linked. 
Probably some underscore/case issue. Boldly replacing the function call 
with a constant for now.

Scipy.test() crashes during sparse matrix slicing. See 
<http://projects.scipy.org/scipy/ticket/1210>. Deleting 
scipy\sparse\tests\test_base.py for now.

Below is the the test output. Looks good. The TestODR and TestNdimage 
failures are known. See <http://projects.scipy.org/scipy/ticket/678> and 
<http://projects.scipy.org/scipy/ticket/1238>.

--
Christoph



Running unit tests for scipy
NumPy version 1.5.0
NumPy is installed in X:\Python31\lib\site-packages\numpy
SciPy version 0.9.0.dev6805
SciPy is installed in X:\Python31\lib\site-packages\scipy
Python version 3.1.2 (r312:79149, Mar 20 2010, 22:55:39) [MSC v.1500 64 
bit (AMD64)]
nose version 0.11.0

<snip>

======================================================================
ERROR: test suite for <module 'test_streams' from 
'X:\Python31\lib\site-packages\scipy\io\matlab\tests\test_streams.py'>
----------------------------------------------------------------------
Traceback (most recent call last):
   File "X:\Python31\lib\site-packages\nose\suite.py", line 173, in run
     self.tearDown()
   File "X:\Python31\lib\site-packages\nose\suite.py", line 295, in tearDown
     self.teardownContext(ancestor)
   File "X:\Python31\lib\site-packages\nose\suite.py", line 311, in 
teardownContext
     try_run(context, names)
   File "X:\Python31\lib\site-packages\nose\util.py", line 453, in try_run
     return func()
   File 
"X:\Python31\lib\site-packages\scipy\io\matlab\tests\test_streams.py", 
line 47, in teardown
     os.unlink(fname)
WindowsError: [Error 32] The process cannot access the file because it 
is being
used by another process: 
'c:\\users\\gohlke\\appdata\\local\\temp\\tmppbkhkm'

======================================================================
ERROR: Failure: ImportError (No module named c_spec)
----------------------------------------------------------------------
Traceback (most recent call last):
   File "X:\Python31\lib\site-packages\nose\failure.py", line 27, in runTest
     reraise(self.exc_class, self.exc_val, self.tb)
   File "X:\Python31\lib\site-packages\nose\_3.py", line 7, in reraise
     raise exc_class(exc_val).with_traceback(tb)
   File "X:\Python31\lib\site-packages\nose\loader.py", line 372, in 
loadTestsFromName
     addr.filename, addr.module)
   File "X:\Python31\lib\site-packages\nose\importer.py", line 39, in 
importFromPath
     return self.importFromDir(dir_path, fqname)
   File "X:\Python31\lib\site-packages\nose\importer.py", line 84, in 
importFromDir
     mod = load_module(part_fqname, fh, filename, desc)
   File "X:\Python31\lib\site-packages\scipy\weave\__init__.py", line 
13, in <module>
     from .inline_tools import inline
   File "X:\Python31\lib\site-packages\scipy\weave\inline_tools.py", 
line 5, in <module>
     from . import ext_tools
   File "X:\Python31\lib\site-packages\scipy\weave\ext_tools.py", line 
7, in <module>
     from . import converters
   File "X:\Python31\lib\site-packages\scipy\weave\converters.py", line 
5, in <module>
     from . import c_spec
   File "X:\Python31\lib\site-packages\scipy\weave\c_spec.py", line 380, 
in <module>
     import os, c_spec # yes, I import myself to find out my __file__ 
location.
ImportError: No module named c_spec

======================================================================
FAIL: test_extrema03 (test_ndimage.TestNdimage)
extrema 3
----------------------------------------------------------------------
Traceback (most recent call last):
   File 
"X:\Python31\lib\site-packages\scipy\ndimage\tests\test_ndimage.py", 
line 3153, in test_extrema03
     self.assertTrue(numpy.all(output1[2]  == output4))
AssertionError: False is not True

======================================================================
FAIL: test_lorentz (test_odr.TestODR)
----------------------------------------------------------------------
Traceback (most recent call last):
   File "X:\Python31\lib\site-packages\scipy\odr\tests\test_odr.py", 
line 292, in test_lorentz
     3.7798193600109009e+00]),
   File "X:\Python31\lib\site-packages\numpy\testing\utils.py", line 
774, in assert_array_almost_equal
     header='Arrays are not almost equal')
   File "X:\Python31\lib\site-packages\numpy\testing\utils.py", line 
618, in assert_array_compare
     raise AssertionError(msg)
AssertionError:
Arrays are not almost equal

(mismatch 100.0%)
  x: array([  1.00000000e+03,   1.00000000e-01,   3.80000000e+00])
  y: array([  1.43067808e+03,   1.33905090e-01,   3.77981936e+00])

======================================================================
FAIL: test_multi (test_odr.TestODR)
----------------------------------------------------------------------
Traceback (most recent call last):
   File "X:\Python31\lib\site-packages\scipy\odr\tests\test_odr.py", 
line 188, in test_multi
     0.5101147161764654,  0.5173902330489161]),
   File "X:\Python31\lib\site-packages\numpy\testing\utils.py", line 
774, in assert_array_almost_equal
     header='Arrays are not almost equal')
   File "X:\Python31\lib\site-packages\numpy\testing\utils.py", line 
618, in assert_array_compare
     raise AssertionError(msg)
AssertionError:
Arrays are not almost equal

(mismatch 100.0%)
  x: array([ 4. ,  2. ,  7. ,  0.4,  0.5])
  y: array([ 4.37998803,  2.43330576,  8.00288459,  0.51011472, 0.51739023])

======================================================================
FAIL: test_pearson (test_odr.TestODR)
----------------------------------------------------------------------
Traceback (most recent call last):
   File "X:\Python31\lib\site-packages\scipy\odr\tests\test_odr.py", 
line 235, in test_pearson
     np.array([ 5.4767400299231674, -0.4796082367610305]),
   File "X:\Python31\lib\site-packages\numpy\testing\utils.py", line 
774, in assert_array_almost_equal
     header='Arrays are not almost equal')
   File "X:\Python31\lib\site-packages\numpy\testing\utils.py", line 
618, in assert_array_compare
     raise AssertionError(msg)
AssertionError:
Arrays are not almost equal

(mismatch 100.0%)
  x: array([ 1.,  1.])
  y: array([ 5.47674003, -0.47960824])

======================================================================
FAIL: test_pdist_minkowski_3_2_iris_float32 (test_distance.TestPdist)
Tests pdist(X, 'minkowski') on iris data. (float32)
----------------------------------------------------------------------
Traceback (most recent call last):
   File 
"X:\Python31\lib\site-packages\scipy\spatial\tests\test_distance.py", 
line 837, in test_pdist_minkowski_3_2_iris_float32
     self.assertTrue(within_tol(Y_test1, Y_right, eps))
AssertionError: False is not True

----------------------------------------------------------------------
Ran 4203 tests in 39.045s

FAILED (KNOWNFAIL=8, SKIP=41, errors=2, failures=5)


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