Mailman 3 October 2010 - NumPy-Discussion

Running tests that are marked as KNOWNFAIL
by Lutz Maibaum Oct. 25, 2010

Oct. 25, 2010

Is there a way to execute tests even if they are marked as KNOWNFAIL? For example, the module scipy.sparse.linalg has a few tests that are marked as such on my architecture (OS-X 64 bit). Running scipy.sparse.linalg(extra_argv=["--no-knownfail"]) changes the test result to ERROR, but it looks the actual test is still not run. The reason I'm asking is that when I remove the @dec.knownfailureif decorator from these tests by hand, they actually pass on my machine. Thanks, Lutz

1 0

How to limit the numpy.memmap's RAM usage?
by braingateway Oct. 25, 2010

Oct. 25, 2010

Hi everyone, I noticed the numpy.memmap using RAM to buffer data from memmap files. If I get a 100GB array in a memmap file and process it block by block, the RAM usage is going to increasing with the process running until there is no available space in RAM (4GB), even though the block size is only 1MB. for example: #### a = numpy.memmap(‘a.bin’, dtype='float64', mode='r') blocklen=1e5 b=npy.zeros((len(a)/blocklen,)) for i in range(0,len(a)/blocklen): b[i]=npy.mean(a[i*blocklen:(i+1)*blocklen]) #### Is there any way to restrict the memory usage in numpy.memmap? LittleBigBrain

4 9

tests fails when run $nosetests numpy, but not from python prompt
by Vincent Davis Oct. 25, 2010

Oct. 25, 2010

python2.7 10.5, osx 10.6, numpy 1.5.1rc1 Test pass when run from python prompt (see bottom) but fail when run from $nosetests numpy. 105osxpython:~ Vincent$ nosetests numpy .........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................E........................................................................................................................................................................................................................................E......................Warning: overflow encountered in ldexp .......................................................................E......................E...........................................................................................EEEEEE...................................................................................................................................................................................................................................................................................................................................................................................EEEEEEEEEE.EE..........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................S............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................. ====================================================================== ERROR: test_array_from_sequence_scalar_array2 (test_regression.TestRegression) Ticket #1081: weird array with strange input... ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/testing/decorators.py", line 213, in knownfailer raise KnownFailureTest, msg KnownFailureTest: Fix this for 1.5.0. ====================================================================== ERROR: test_umath.TestComplexFunctions.test_branch_cuts_failing ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nose-0.11.3-py2.7.egg/nose/case.py", line 186, in runTest self.test(*self.arg) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/testing/decorators.py", line 213, in knownfailer raise KnownFailureTest, msg KnownFailureTest: These branch cuts are known to fail ====================================================================== ERROR: test_umath_complex.TestCarg.test_zero ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nose-0.11.3-py2.7.egg/nose/case.py", line 186, in runTest self.test(*self.arg) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/testing/decorators.py", line 213, in knownfailer raise KnownFailureTest, msg KnownFailureTest: Complex arithmetic with signed zero is buggy on most implementation ====================================================================== ERROR: test_umath_complex.TestCexp.test_special_values2 ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nose-0.11.3-py2.7.egg/nose/case.py", line 186, in runTest self.test(*self.arg) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/testing/decorators.py", line 213, in knownfailer raise KnownFailureTest, msg KnownFailureTest: cexp(nan + 0I) is wrong on most implementations ====================================================================== ERROR: Failure: ImportError (cannot import name fib2) ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nose-0.11.3-py2.7.egg/nose/loader.py", line 382, in loadTestsFromName addr.filename, addr.module) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nose-0.11.3-py2.7.egg/nose/importer.py", line 39, in importFromPath return self.importFromDir(dir_path, fqname) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nose-0.11.3-py2.7.egg/nose/importer.py", line 86, in importFromDir mod = load_module(part_fqname, fh, filename, desc) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/distutils/tests/f2py_ext/tests/test_fib2.py", line 3, in <module> from f2py_ext import fib2 ImportError: cannot import name fib2 ====================================================================== ERROR: Failure: ImportError (cannot import name foo) ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nose-0.11.3-py2.7.egg/nose/loader.py", line 382, in loadTestsFromName addr.filename, addr.module) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nose-0.11.3-py2.7.egg/nose/importer.py", line 39, in importFromPath return self.importFromDir(dir_path, fqname) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nose-0.11.3-py2.7.egg/nose/importer.py", line 86, in importFromDir mod = load_module(part_fqname, fh, filename, desc) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/distutils/tests/f2py_f90_ext/tests/test_foo.py", line 3, in <module> from f2py_f90_ext import foo ImportError: cannot import name foo ====================================================================== ERROR: Failure: ImportError (cannot import name fib3) ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nose-0.11.3-py2.7.egg/nose/loader.py", line 382, in loadTestsFromName addr.filename, addr.module) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nose-0.11.3-py2.7.egg/nose/importer.py", line 39, in importFromPath return self.importFromDir(dir_path, fqname) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nose-0.11.3-py2.7.egg/nose/importer.py", line 86, in importFromDir mod = load_module(part_fqname, fh, filename, desc) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/distutils/tests/gen_ext/tests/test_fib3.py", line 3, in <module> from gen_ext import fib3 ImportError: cannot import name fib3 ====================================================================== ERROR: Failure: ImportError (No module named primes) ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nose-0.11.3-py2.7.egg/nose/loader.py", line 382, in loadTestsFromName addr.filename, addr.module) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nose-0.11.3-py2.7.egg/nose/importer.py", line 39, in importFromPath return self.importFromDir(dir_path, fqname) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nose-0.11.3-py2.7.egg/nose/importer.py", line 86, in importFromDir mod = load_module(part_fqname, fh, filename, desc) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/distutils/tests/pyrex_ext/tests/test_primes.py", line 3, in <module> from pyrex_ext.primes import primes ImportError: No module named primes ====================================================================== ERROR: Failure: ImportError (cannot import name example) ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nose-0.11.3-py2.7.egg/nose/loader.py", line 382, in loadTestsFromName addr.filename, addr.module) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nose-0.11.3-py2.7.egg/nose/importer.py", line 39, in importFromPath return self.importFromDir(dir_path, fqname) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nose-0.11.3-py2.7.egg/nose/importer.py", line 86, in importFromDir mod = load_module(part_fqname, fh, filename, desc) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/distutils/tests/swig_ext/tests/test_example.py", line 3, in <module> from swig_ext import example ImportError: cannot import name example ====================================================================== ERROR: Failure: ImportError (cannot import name example2) ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nose-0.11.3-py2.7.egg/nose/loader.py", line 382, in loadTestsFromName addr.filename, addr.module) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nose-0.11.3-py2.7.egg/nose/importer.py", line 39, in importFromPath return self.importFromDir(dir_path, fqname) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nose-0.11.3-py2.7.egg/nose/importer.py", line 86, in importFromDir mod = load_module(part_fqname, fh, filename, desc) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/distutils/tests/swig_ext/tests/test_example2.py", line 3, in <module> from swig_ext import example2 ImportError: cannot import name example2 ====================================================================== ERROR: test_callback.TestF77Callback.test_all ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nose-0.11.3-py2.7.egg/nose/case.py", line 367, in setUp try_run(self.inst, ('setup', 'setUp')) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nose-0.11.3-py2.7.egg/nose/util.py", line 491, in try_run return func() File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/f2py/tests/util.py", line 341, in setUp module_name=self.module_name) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/f2py/tests/util.py", line 73, in wrapper memo[key] = func(*a, **kw) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/f2py/tests/util.py", line 156, in build_code module_name=module_name) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/f2py/tests/util.py", line 73, in wrapper memo[key] = func(*a, **kw) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/f2py/tests/util.py", line 137, in build_module __import__(module_name) ImportError: dlopen(/tmp/tmpOjoP4S/_test_ext_module_5403.so, 2): no suitable image found. Did find: /tmp/tmpOjoP4S/_test_ext_module_5403.so: mach-o, but wrong architecture ====================================================================== ERROR: test_mixed.TestMixed.test_all ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nose-0.11.3-py2.7.egg/nose/case.py", line 367, in setUp try_run(self.inst, ('setup', 'setUp')) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nose-0.11.3-py2.7.egg/nose/util.py", line 491, in try_run return func() File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/f2py/tests/util.py", line 346, in setUp module_name=self.module_name) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/f2py/tests/util.py", line 73, in wrapper memo[key] = func(*a, **kw) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/f2py/tests/util.py", line 137, in build_module __import__(module_name) ImportError: dlopen(/tmp/tmpOjoP4S/_test_ext_module_5403.so, 2): no suitable image found. Did find: /tmp/tmpOjoP4S/_test_ext_module_5403.so: mach-o, but wrong architecture ====================================================================== ERROR: test_return_character.TestF77ReturnCharacter.test_all ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nose-0.11.3-py2.7.egg/nose/case.py", line 367, in setUp try_run(self.inst, ('setup', 'setUp')) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nose-0.11.3-py2.7.egg/nose/util.py", line 491, in try_run return func() File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/f2py/tests/util.py", line 341, in setUp module_name=self.module_name) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/f2py/tests/util.py", line 73, in wrapper memo[key] = func(*a, **kw) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/f2py/tests/util.py", line 156, in build_code module_name=module_name) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/f2py/tests/util.py", line 73, in wrapper memo[key] = func(*a, **kw) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/f2py/tests/util.py", line 137, in build_module __import__(module_name) ImportError: dlopen(/tmp/tmpOjoP4S/_test_ext_module_5403.so, 2): no suitable image found. Did find: /tmp/tmpOjoP4S/_test_ext_module_5403.so: mach-o, but wrong architecture ====================================================================== ERROR: test_return_character.TestF90ReturnCharacter.test_all ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nose-0.11.3-py2.7.egg/nose/case.py", line 367, in setUp try_run(self.inst, ('setup', 'setUp')) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nose-0.11.3-py2.7.egg/nose/util.py", line 491, in try_run return func() File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/f2py/tests/util.py", line 341, in setUp module_name=self.module_name) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/f2py/tests/util.py", line 73, in wrapper memo[key] = func(*a, **kw) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/f2py/tests/util.py", line 156, in build_code module_name=module_name) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/f2py/tests/util.py", line 73, in wrapper memo[key] = func(*a, **kw) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/f2py/tests/util.py", line 137, in build_module __import__(module_name) ImportError: dlopen(/tmp/tmpOjoP4S/_test_ext_module_5403.so, 2): no suitable image found. Did find: /tmp/tmpOjoP4S/_test_ext_module_5403.so: mach-o, but wrong architecture ====================================================================== ERROR: test_return_complex.TestF77ReturnComplex.test_all ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nose-0.11.3-py2.7.egg/nose/case.py", line 367, in setUp try_run(self.inst, ('setup', 'setUp')) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nose-0.11.3-py2.7.egg/nose/util.py", line 491, in try_run return func() File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/f2py/tests/util.py", line 341, in setUp module_name=self.module_name) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/f2py/tests/util.py", line 73, in wrapper memo[key] = func(*a, **kw) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/f2py/tests/util.py", line 156, in build_code module_name=module_name) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/f2py/tests/util.py", line 73, in wrapper memo[key] = func(*a, **kw) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/f2py/tests/util.py", line 137, in build_module __import__(module_name) ImportError: dlopen(/tmp/tmpOjoP4S/_test_ext_module_5403.so, 2): no suitable image found. Did find: /tmp/tmpOjoP4S/_test_ext_module_5403.so: mach-o, but wrong architecture ====================================================================== ERROR: test_return_complex.TestF90ReturnComplex.test_all ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nose-0.11.3-py2.7.egg/nose/case.py", line 367, in setUp try_run(self.inst, ('setup', 'setUp')) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nose-0.11.3-py2.7.egg/nose/util.py", line 491, in try_run return func() File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/f2py/tests/util.py", line 341, in setUp module_name=self.module_name) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/f2py/tests/util.py", line 73, in wrapper memo[key] = func(*a, **kw) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/f2py/tests/util.py", line 156, in build_code module_name=module_name) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/f2py/tests/util.py", line 73, in wrapper memo[key] = func(*a, **kw) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/f2py/tests/util.py", line 137, in build_module __import__(module_name) ImportError: dlopen(/tmp/tmpOjoP4S/_test_ext_module_5403.so, 2): no suitable image found. Did find: /tmp/tmpOjoP4S/_test_ext_module_5403.so: mach-o, but wrong architecture ====================================================================== ERROR: test_return_integer.TestF77ReturnInteger.test_all ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nose-0.11.3-py2.7.egg/nose/case.py", line 367, in setUp try_run(self.inst, ('setup', 'setUp')) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nose-0.11.3-py2.7.egg/nose/util.py", line 491, in try_run return func() File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/f2py/tests/util.py", line 341, in setUp module_name=self.module_name) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/f2py/tests/util.py", line 73, in wrapper memo[key] = func(*a, **kw) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/f2py/tests/util.py", line 156, in build_code module_name=module_name) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/f2py/tests/util.py", line 73, in wrapper memo[key] = func(*a, **kw) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/f2py/tests/util.py", line 137, in build_module __import__(module_name) ImportError: dlopen(/tmp/tmpOjoP4S/_test_ext_module_5403.so, 2): no suitable image found. Did find: /tmp/tmpOjoP4S/_test_ext_module_5403.so: mach-o, but wrong architecture ====================================================================== ERROR: test_return_integer.TestF90ReturnInteger.test_all ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nose-0.11.3-py2.7.egg/nose/case.py", line 367, in setUp try_run(self.inst, ('setup', 'setUp')) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nose-0.11.3-py2.7.egg/nose/util.py", line 491, in try_run return func() File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/f2py/tests/util.py", line 341, in setUp module_name=self.module_name) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/f2py/tests/util.py", line 73, in wrapper memo[key] = func(*a, **kw) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/f2py/tests/util.py", line 156, in build_code module_name=module_name) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/f2py/tests/util.py", line 73, in wrapper memo[key] = func(*a, **kw) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/f2py/tests/util.py", line 137, in build_module __import__(module_name) ImportError: dlopen(/tmp/tmpOjoP4S/_test_ext_module_5403.so, 2): no suitable image found. Did find: /tmp/tmpOjoP4S/_test_ext_module_5403.so: mach-o, but wrong architecture ====================================================================== ERROR: test_return_logical.TestF77ReturnLogical.test_all ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nose-0.11.3-py2.7.egg/nose/case.py", line 367, in setUp try_run(self.inst, ('setup', 'setUp')) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nose-0.11.3-py2.7.egg/nose/util.py", line 491, in try_run return func() File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/f2py/tests/util.py", line 341, in setUp module_name=self.module_name) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/f2py/tests/util.py", line 73, in wrapper memo[key] = func(*a, **kw) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/f2py/tests/util.py", line 156, in build_code module_name=module_name) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/f2py/tests/util.py", line 73, in wrapper memo[key] = func(*a, **kw) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/f2py/tests/util.py", line 137, in build_module __import__(module_name) ImportError: dlopen(/tmp/tmpOjoP4S/_test_ext_module_5403.so, 2): no suitable image found. Did find: /tmp/tmpOjoP4S/_test_ext_module_5403.so: mach-o, but wrong architecture ====================================================================== ERROR: test_return_logical.TestF90ReturnLogical.test_all ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nose-0.11.3-py2.7.egg/nose/case.py", line 367, in setUp try_run(self.inst, ('setup', 'setUp')) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nose-0.11.3-py2.7.egg/nose/util.py", line 491, in try_run return func() File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/f2py/tests/util.py", line 341, in setUp module_name=self.module_name) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/f2py/tests/util.py", line 73, in wrapper memo[key] = func(*a, **kw) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/f2py/tests/util.py", line 156, in build_code module_name=module_name) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/f2py/tests/util.py", line 73, in wrapper memo[key] = func(*a, **kw) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/f2py/tests/util.py", line 137, in build_module __import__(module_name) ImportError: dlopen(/tmp/tmpOjoP4S/_test_ext_module_5403.so, 2): no suitable image found. Did find: /tmp/tmpOjoP4S/_test_ext_module_5403.so: mach-o, but wrong architecture ====================================================================== ERROR: test_return_real.TestF77ReturnReal.test_all ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nose-0.11.3-py2.7.egg/nose/case.py", line 367, in setUp try_run(self.inst, ('setup', 'setUp')) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nose-0.11.3-py2.7.egg/nose/util.py", line 491, in try_run return func() File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/f2py/tests/util.py", line 341, in setUp module_name=self.module_name) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/f2py/tests/util.py", line 73, in wrapper memo[key] = func(*a, **kw) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/f2py/tests/util.py", line 156, in build_code module_name=module_name) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/f2py/tests/util.py", line 73, in wrapper memo[key] = func(*a, **kw) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/f2py/tests/util.py", line 137, in build_module __import__(module_name) ImportError: dlopen(/tmp/tmpOjoP4S/_test_ext_module_5403.so, 2): no suitable image found. Did find: /tmp/tmpOjoP4S/_test_ext_module_5403.so: mach-o, but wrong architecture ====================================================================== ERROR: test_return_real.TestF90ReturnReal.test_all ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nose-0.11.3-py2.7.egg/nose/case.py", line 367, in setUp try_run(self.inst, ('setup', 'setUp')) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nose-0.11.3-py2.7.egg/nose/util.py", line 491, in try_run return func() File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/f2py/tests/util.py", line 341, in setUp module_name=self.module_name) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/f2py/tests/util.py", line 73, in wrapper memo[key] = func(*a, **kw) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/f2py/tests/util.py", line 156, in build_code module_name=module_name) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/f2py/tests/util.py", line 73, in wrapper memo[key] = func(*a, **kw) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/f2py/tests/util.py", line 137, in build_module __import__(module_name) ImportError: dlopen(/tmp/tmpOjoP4S/_test_ext_module_5403.so, 2): no suitable image found. Did find: /tmp/tmpOjoP4S/_test_ext_module_5403.so: mach-o, but wrong architecture ---------------------------------------------------------------------- Ran 3025 tests in 30.682s FAILED (SKIP=1, errors=22) python2.7 >>> numpy.test() Running unit tests for numpy NumPy version 1.5.1rc1 NumPy is installed in /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy Python version 2.7 (r27:82508, Jul 3 2010, 21:12:11) [GCC 4.0.1 (Apple Inc. build 5493)] nose version 0.11.3 <snip> ---------------------------------------------------------------------- Ran 3006 tests in 14.112s OK (KNOWNFAIL=4, SKIP=1) <nose.result.TextTestResult run=3006 errors=0 failures=0> python2.7-32 >>> numpy.test() Running unit tests for numpy NumPy version 1.5.1rc1 NumPy is installed in /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy Python version 2.7 (r27:82508, Jul 3 2010, 21:12:11) [GCC 4.0.1 (Apple Inc. build 5493)] nose version 0.11.3 ---------------------------------------------------------------------- Ran 3006 tests in 14.060s OK (KNOWNFAIL=4, SKIP=1) <nose.result.TextTestResult run=3006 errors=0 failures=0 -- Thanks Vincent Davis 720-301-3003

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clearing after build; Some directories missing in .gitignore?
by Friedrich Romstedt Oct. 25, 2010

Oct. 25, 2010

I was tearing my hear out yesterday evening with trying to find out and to understand how this directories occur in the build process and what role they play: build_doc/ doc/source/reference/generated/ The build process of the docs is rather opaque to me, so I don't know what to do with them. The question is: Do I really have to clean my working directory before doing a new build. I have problems with this because it seems that the cleaning is neither complete nor is .gitignore (see above). In pavement.py I read: @needs('clean', 'clean_bootstrap') def nuke(options): """Remove everything: build dir, installers, bootstrap dirs, etc...""" for d in [options.superpack.builddir, options.installers.releasedir]: if os.path.exists(d): shutil.rmtree(d) So :func:`nuke`, as opposed to what I was told before, also removes the installers. :func:`clean` removes build/, dist/, numpy.egg-info/, and doc/build/. :func:`clean_bootstrap` is a noop for us. None of them treats the directories listed above. I don't know if the generated docs in doc/source/reference/generated are included automatically, so that garbage from previous builds could make it into later doc builds? Further, I don't know what may dangle around what I simply don't see because it's hidden by .gitignore. E.g. what's about doc/cdoc/build? doc/numpy.scipy.org/_build? I don't have this dirs, though. I will, for now, just remove the directories listed above and hope that :func:`clean` does the rest to the extent needed, but I really have the impressions that the binary build system is rather "organic" and needs a general overhaul. A bit lost, Friedrich

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compile fortran from python
by Ioan Ferencik Oct. 25, 2010

Oct. 25, 2010

Hello list, on compiling some F95 code into a library I got following message: Warning: Nonconforming tab character at (1) i figured out it is because setup uses default compiler flags. this is my set-up command python setup.py config_fc --fcompiler=gnu95 install --home=./tbuild I tried to pass -ffree-form flag to the setup using build_info parameter config.add_library('hm1d', sources = ['src/hm1d.f95'], build_info = {'extra_compiler_args':'-ffree-form'}) but is still get the warnings. the setup does not seem to receive these flags or it is ignoring them. Any hints? Cheers Ioan Ferencik PhD student Aalto University School of Science and Technology Faculty Of Civil and Env. Engineering Lahti Center Tel: +358505122707

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Build Process and Version Control
by Friedrich Romstedt Oct. 25, 2010

Oct. 25, 2010

Hi, here is a summary of what we got so far with the Mac OS X build process: - We found it useful to put /Library/Frameworks/Python.framework/Versions/2.x under version control with git. This lets us get rid of the paver bootstrap thingy, since we just switch to a branch via ``git checkout numpy``. We can have a full-blown polluted Python and a minimial numpy Python in parallel, and we can revert to the built numpy libraries when we find some issue later. We will note the sha of the numpy system commit in the commits in the numpy build git repo. - We also modified the Pythons via a print statement in sitecustomize.py to tell what numpy is running on startup, this goes to the logfiles etc., it also tells the branch family of the system git repo (hardcoded). - We established a numpy git "build repo". It'll contain all the dmgs and so on, along with the log files of the build process. I will push soon. Its location is http://github.com/friedrichromstedt/numpy. We tried hard to make good design choices about the branches, but this is discussable, and might be easy to revert in this early stage where noone has fetched so far. - We also set up the "numpy build site", it's here: http://vincentdavis.info/, or for the hard-core people here :-) http://vincentdavis.info/numpy-build-doc. It's not that hard-core at all. Just a Sphinx site where we document what we're doing to our build system. Atm I'm not *that* satisfied with it, because I tend to document *too much* when new to some subject. I believe it will turn out as a well-readable detailed instruction for ourselves, usable to others too, and then we just crossref that instruction instead of writing down all the stuff again and again. Currently the numpy-build-docs are in another repo, http://github.com/friedrichromstedt/numpy-build-doc, I'm not sure if it is useful to merge this into my numpy repo. Pro: Users of the numpy repo will get all the stuff with little overhead. Con: Users of the numpy-build-doc repo will have *lots* of overhead. But I guess the latter are rather rare. Please comment. The process is open for others to chime in. The Sphinx site is ready to host also build logs of other systems. The sources are included in the git repo (numpy-build-docs), together with a current html build. Please use the Sphinx site online (http://vincentdavis.info/numpy-build-doc) and not the git repo, but I'll push soon. Documentation goes via Python functional programming, but this are details. In fact, Sphinx just documents Python functions. We are working towards an automatisation of build process steps using this Python functions. Yet another build system. But this is future. Please refrain from fetching anything until I did the authoritative push, so that you'll have a working system, which is at least beta and not rather alpha like the current things I put on github. Friedrich

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RailGun: ctypes utilities for faster and easier simulation programming in C and Python - announcement
by Takafumi Arakaki Oct. 25, 2010

Oct. 25, 2010

I hope this mailing list is right place to post. Please read full document here: http://tkf.bitbucket.org/railgun-doc/index.html RailGun: Accelerate your simulation programing with "C on Rails" ================================================================ Overview -------- RailGun is ctypes utilities for faster and easier simulation programming in C and Python. It requires constraint to C library loaded from Python and gives you automatically generated Python class which calls C functions safely. Installation ------------ :: easy_install railgun # using setuptools pip install railgun # using pip Usage ----- Please read `document <http://tkf.bitbucket.org/railgun-doc/index.html>`_ and `samples <https://bitbucket.org/tkf/railgun/src/tip/samples/>`_. Requirement ----------- - Numpy - (matplotlib for sample code) Sincerely, Takafumi Arakaki --- Master course student Department of Modern Mechanical Engineering Waseda University Laboratory of Neurophysics and Physiology Universite Paris Descartes

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[numpy-discussion] Transform 3d data
by Thomas Königstein Oct. 25, 2010

Oct. 25, 2010

Hello everyone, I have the following problem: I acquire a (evenly spaced) 3d field of 3d vectors from a HDF5 data file: >>> import tables >>> field=tables.openFile("test.h5").root.YeeMagField.read() now, the data is organized in "nested arrays"... so, when I have, say, 300 data points on the x-axis, 200 data points on the y-axis and 100 data points on the z-axis, I get an array with the shape >>> field.shape >>> (300, 200, 100, 3) When I now want to see a 3D arrow-plot of this field, I use: >>> from enthought.mayavi import mlab as m >>> x,y,z=field.transpose() >>> m.quiver3d(x,y,z) and this works just fine. Here, the arrays (x and y and z) *each* contain one field component (i,e. into one spatial direction) at 300x200x100 points in a 3D array. Now, I would like to have this data in another format, so I can for example save it to a textfile with pylab.savetxt. What I would like are six arrays, each 1d, three for the coordinates and three for the field components. Since I didn't know any better, I wrote the following procedure: def transform_3d_data_(field,lowerBounds,upperBounds): #field is the same as above, lowerBounds and upperBounds each contain three values for x,y,z min/max import pylab as p xx,yy,zz,ex,ey,ez=list(),list(),list(),list(),list(),list() #xx,yy,zz will become the spatial coordinates, ex,ey,ez will become the field components for xi in range(field.shape[0]): #for each x coordinate... for yi in range(field.shape[1]): #for each y coordinate... for zi in range(field.shape[2]): #for each z coordinate... xx.append(lowerBounds[0]+xi*(upperBounds[0]-lowerBounds[0])/float(field.shape[0])) #append this yy.append(lowerBounds[1]+yi*(upperBounds[1]-lowerBounds[1])/float(field.shape[1])) #x, y, z coordinate zz.append(lowerBounds[2]+zi*(upperBounds[2]-lowerBounds[2])/float(field.shape[2])) #to xx, yy, zz .... ex.append(field[xi][yi][zi][0]) #and also ey.append(field[xi][yi][zi][1]) #add this field composition ez.append(field[xi][yi][zi][2]) #to ex, ey, ez. xx,yy,zz,ex,ey,ez=[p.array(_) for _ in [xx,yy,zz,ex,ey,ez]] return xx,yy,zz,ex,ey,ez , so I get the desired six 1D-arrays xx,yy,zz for the coordinates and ex,ey,ez for the field components. It works. Now my question: there has to be a better way to get this re-organization, right? This one here is much too slow, obviously. Is there maybe a single command for pylab that does this? Thanks in advance, cheers Thomas PS. I'm new to this messaging board, and I was wondering if there is a "normal" forum as well? I can't even search through the archives at http://mail.scipy.org/pipermail/numpy-discussion/ :( have there ever been discussions/initiatives about porting the mailing list archives for example to a phpBB based forum?

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[ANN]: FEMTEC 2011: track on Open-source projects and Python in scientific computing.
by Gael Varoquaux Oct. 24, 2010

Oct. 24, 2010

The 3rd International Conference on Finite Element Methods in Engineering and Science (FEMTEC 2011, http://hpfem.org/events/femtec-2011/) will have a track on Open-source projects and Python in scientific computing. FEMTEC 2011 is co-organized by the University of Nevada (Reno), Desert Reseach Institute (Reno), Idaho National Laboratory (Idaho Falls, Idaho), and U.S. Army Engineer Research and Development Center (Vicksburg, Mississippi). The objective of the meeting is to strengthen the interaction between researchers who develop new computational methods, and scientists and engineers from various fields who employ numerical methods in their research. Specific focus areas of FEMTEC 2011 include, but are not limited to, the following: * Computational methods in hydrology, atmospheric modeling, and other earth sciences. * Computational methods in nuclear, mechanical, civil, electrical, and other engineering fields. * Mesh generation and scientific visualization. * Open-source projects and Python in scientific computing. Part of the conference will be a software afternoon featuring open source projects of participants. Proceedings Proceedings of FEMTEC 2011 will appear as a special issue of Journal of Computational and Applied Mathematics (2008 SCI impact factor 1.292), and additional high-impact international journals as needed. ____________ On a personnal note, I was at ESCO 2010 this year, the European version organized by the same community, and it was really a refreshing and friendly conference during which I learned a lot.

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np.dtype(int) 64bit
by Peter Butterworth Oct. 24, 2010

Oct. 24, 2010

Hi, I'm getting some strange behaviour from 64bit numpy on windows. I'm using the win64 mkl builds of numpy from : http://www.lfd.uci.edu/~gohlke/pythonlibs/ Win64: np 1.5.1rc1 >>> np.dtype(int) dtype('int32') >>> type(argmin([2, 4, 5])) <type 'numpy.int64'> I believe the expected result on 64 bit numpy is what I get on Ubuntu with np 2.0.0 dev : >>> np.dtype(int) dtype('int64') Could someone please confirm this ? -- thanks, peter butterworth

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