Mailman 3 June 2007 - NumPy-Discussion

PyArray_ContiguousFromObject & PyDECREF
by Michiel Jan Laurens de Hoon 17 May '11

17 May '11

Dear pythoneers, In Chapter 12 ("Writing a C extension") in the Numerical Python manual, in the first example PyArray_ContiguousFromObject is used together with PyDECREF, while in the last example PyArray_ContiguousFromObject is used but the arrays are not PyDECREF'ed before the function returns. From Chapter 13 ("C API Reference") it seems that a PyDECREF is needed in both cases. Or am I missing something here? Is PyDECREF not needed for some reason in the last example? Thanks in advance, Michiel de Hoon U Tokyo First example: ============== static PyObject * trace(PyObject *self, PyObject *args) { PyObject *input; PyArrayObject *array; double sum; int i, n; if (!PyArg_ParseTuple(args, "O", &input)) return NULL; array = (PyArrayObject *) PyArray_ContiguousFromObject(input, PyArray_DOUBLE, 2, 2); if (array == NULL) return NULL; n = array->dimensions[0]; if (n > array->dimensions[1]) n = array->dimensions[1]; sum = 0.; for (i = 0; i < n; i++) sum += *(double *)(array->data + i*array->strides[0] + i*array->strides[1]); Py_DECREF(array); return PyFloat_FromDouble(sum); } Last example: ============= static PyObject * matrix_vector(PyObject *self, PyObject *args) { PyObject *input1, *input2; PyArrayObject *matrix, *vector, *result; int dimensions[1]; double factor[1]; double real_zero[1] = {0.}; long int_one[1] = {1}; long dim0[1], dim1[1]; extern dgemv_(char *trans, long *m, long *n, double *alpha, double *a, long *lda, double *x, long *incx, double *beta, double *Y, long *incy); if (!PyArg_ParseTuple(args, "dOO", factor, &input1, &input2)) return NULL; matrix = (PyArrayObject *) PyArray_ContiguousFromObject(input1, PyArray_DOUBLE, 2, 2); if (matrix == NULL) return NULL; vector = (PyArrayObject *) PyArray_ContiguousFromObject(input2, PyArray_DOUBLE, 1, 1); if (vector == NULL) return NULL; if (matrix->dimensions[1] != vector->dimensions[0]) { PyErr_SetString(PyExc_ValueError, "array dimensions are not compatible"); return NULL; } dimensions[0] = matrix->dimensions[0]; result = (PyArrayObject *)PyArray_FromDims(1, dimensions, PyArray_DOUBLE); if (result == NULL) return NULL; dim0[0] = (long)matrix->dimensions[0]; dim1[0] = (long)matrix->dimensions[1]; dgemv_("T", dim1, dim0, factor, (double *)matrix->data, dim1, (double *)vector->data, int_one, real_zero, (double *)result->data, int_one); return PyArray_Return(result); } -- Michiel de Hoon, Assistant Professor University of Tokyo, Institute of Medical Science Human Genome Center 4-6-1 Shirokane-dai, Minato-ku Tokyo 108-8639 Japan http://bonsai.ims.u-tokyo.ac.jp/~mdehoon

3 2

Compact way of performing array math with specified result type?
by Russell E. Owen 08 Feb '10

08 Feb '10

I often find myself doing simple math on sequences of numbers (which might or might not be numpy arrays) where I want the result (and thus the inputs) coerced to a particular data type. I'd like to be able to say: numpy.divide(seq1, seq2, dtype=float) but ufuncs don't allow on to specify a result type. So I do this instead: numpy.array(seq1, dtype=float) / numpy.array(seq2, dtype=float) Is there a more compact solution (without having to create the result array first and supply it as an argument)? -- Russell

4 3

Re: [Numpy-discussion] Floating point exception with numpy and embedded python interpreter
by Andrew Straw 20 Sep '07

20 Sep '07

Arkaitz Bitorika wrote: > > On 19 Apr 2006, at 18:37, Andrew Straw wrote: > >> >>> I've been embedding Python for ages on the same program and other >>> modules work fine, only numpy fails. >> >> >> Most other modules don't use the SSE units, so wouldn't get hit by such >> a bug. > > > Is there a way of not using those units from numpy, to check if > that's what's going on? I think that numpy only accesses the SSE units through ATLAS or other external library. So, build numpy without ATLAS. But I'm not 100% sure anymore if there aren't any optimizations that directly use SSE if it's available. > Or alternatively, how would I check if my program is messing with the > SSE bits? Hmm, I think that's a bit hairy. I'd suggest simply asking the C++ library's mailing list if they alter the error bits on the control registers of the SSE unit. (Out of curiousity, what library is it?) If you want hairy, though, I think you'd have to check from C with the appropriate calls -- I'd start with the source code in that bug report. It looks like they're inlining an assembly statement to query a SSE control register.

5 7

Building numpy 1.0.3-2 on Linux 2.6.8 i686 (Debian 3.1)
by Michael Hoffman 15 Sep '07

15 Sep '07

Hi. I have been trying to build NumPy on a 32-bit Linux box using python setup.py build. I received the following errors: """ creating build/temp.linux-i686-2.5/numpy/linalg compile options: '-DATLAS_WITHOUT_LAPACK -DATLAS_INFO="\"3.6.0\"" -I/usr/include -Inumpy/core/include -Ibuild/src.linux-i686-2.5/numpy/core -I/nfs/acari/mh5/include/python2.5 -I/nfs/acari/mh5/include -I/software/python-2.5/include/python2.5 -Inumpy/core/src -Inumpy/core/include -c' gcc: numpy/linalg/lapack_litemodule.c g77 build/temp.linux-i686-2.5/numpy/linalg/lapack_litemodule.o -L/usr/lib/sse2 -L/usr/lib -lf77blas -lcblas -latlas -llapack -lg2c-pic -o build/lib.linux-i686-2.5/numpy/linalg/lapack_lite.so build/temp.linux-i686-2.5/numpy/linalg/lapack_litemodule.o(.text+0x44): In function `initlapack_lite': numpy/linalg/lapack_litemodule.c:827: undefined reference to `Py_InitModule4' build/temp.linux-i686-2.5/numpy/linalg/lapack_litemodule.o(.text+0x57):numpy/linalg/lapack_litemodule.c:831: undefined reference to `PyModule_GetDict' build/temp.linux-i686-2.5/numpy/linalg/lapack_litemodule.o(.text+0x73):numpy/linalg/lapack_litemodule.c:832: undefined reference to `PyErr_NewException' build/temp.linux-i686-2.5/numpy/linalg/lapack_litemodule.o(.text+0x8f):numpy/linalg/lapack_litemodule.c:833: undefined reference to `PyDict_SetItemString' build/temp.linux-i686-2.5/numpy/linalg/lapack_litemodule.o(.text+0xa1):numpy/linalg/lapack_litemodule.c:836: undefined reference to `PyErr_Print' build/temp.linux-i686-2.5/numpy/linalg/lapack_litemodule.o(.text+0xa7):numpy/linalg/lapack_litemodule.c:836: undefined reference to `PyExc_ImportError' build/temp.linux-i686-2.5/numpy/linalg/lapack_litemodule.o(.text+0xbb):numpy/linalg/lapack_litemodule.c:836: undefined reference to `PyErr_SetString' [...] /usr/lib/libfrtbegin.a(frtbegin.o)(.text+0x32): In function `main': : undefined reference to `MAIN__' collect2: ld returned 1 exit status error: Command "g77 build/temp.linux-i686-2.5/numpy/linalg/lapack_litemodule.o -L/usr/lib/sse2 -L/usr/lib -lf77blas -lcblas -latlas -llapack -lg2c-pic -o build/lib.linux-i686-2.5/numpy/linalg/lapack_lite.so" failed with exit status 1 """ After some Googling, I found a recommendation to unset CFLAGS and LDFLAGS, but they are not set in the transcript above. Any suggestions? -- Michael Hoffman

2 5

.transpose() of memmap array fails to close()
by Glen W. Mabey 17 Aug '07

17 Aug '07

Hello, When assigning a variable that is the transpose() of a memmap array, the ._mmap member doesn't get copied, I guess: In [1]:import numpy In [2]:amemmap = numpy.memmap( '/tmp/afile', dtype=numpy.float32, shape=(4,5), mode='w+' ) In [3]:bmemmap = amemmap.transpose() In [4]:bmemmap.close() --------------------------------------------------------------------------- <type 'exceptions.AttributeError'> Traceback (most recent call last) /home/gmabey/src/R9619_dev_acqlibweb/Projects/R9619_NChannelDetection/NED/<ipython console> in <module>() /usr/local/stow/numpy-20070605_svn-py2.5/lib/python2.5/site-packages/numpy/core/memmap.py in close(self) 86 87 def close(self): ---> 88 self._mmap.close() 89 90 def __del__(self): <type 'exceptions.AttributeError'>: 'NoneType' object has no attribute 'close' > /usr/local/stow/numpy-20070605_svn-py2.5/lib/python2.5/site-packages/numpy/core/memmap.py(88)close() 87 def close(self): ---> 88 self._mmap.close() 89 This is an issue when the data is accessed in an order that is different from how it is stored on disk, as: bmemmap = numpy.memmap( '/tmp/afile', dtype=numpy.float32, shape=(4,5), mode='w+' ).transpose() So the object that was originally produced not accessible. I imagine there is some better way to indicate order of dimensions, but regardless, doing In [4]:bmemmap._mmap = amemmap._mmap is a hack workaround. Best regards, Glen Mabey

4 11

rant against from numpy import * / from pylab import *
by Sebastian Haase 09 Aug '07

09 Aug '07

Hi! I use the wxPython PyShell. I like especially the feature that when typing a module and then the dot "." I get a popup list of all available functions (names) inside that module. Secondly, I think it really makes code clearer when one can see where a function comes from. I have a default import numpy as N executed before my shell even starts. In fact I have a bunch of my "standard" modules imported as <some single capital letter>. This - I think - is a good compromise to the commonly used "extra typing" and "unreadable" argument. a = sin(b) * arange(10,50, .1) * cos(d) vs. a = N.sin(b) * N.arange(10,50, .1) * N.cos(d) I would like to hear some comments by others. On a different note: I just started using pylab, so I did added an automatic "from matplotlib import pylab as P" -- but now P contains everything that I already have in N. It makes it really hard to *find* (as in *see* n the popup-list) the pylab-only functions. -- what can I do about this ? Thanks, Sebastian

2 3

Intel MKL 9.1 on Windows (was: Re: VMWare Virtual Appliance...)
by Albert Strasheim 28 Jul '07

28 Jul '07

Cancel that. It seems the problems with these two tests are being caused by Intel MKL 9.1 on Windows. However, 9.0 works fine. You basically you have 2 options when linking against MKL on Windows as far as the mkl_libs go. [mkl] include_dirs = C:\Program Files\Intel\MKL\9.1\include library_dirs = C:\Program Files\Intel\MKL\9.1\ia32\lib mkl_libs = mkl_c, libguide40 lapack_libs = mkl_lapack or mkl_libs = mkl_c, libguide I think libguide is the library that contains various thread and OpenMP related bits and pieces. If you link against libguide, you get the following error when running the NumPy tests: OMP abort: Initializing libguide.lib, but found libguide.lib already initialized. This may cause performance degradation and correctness issues. Set environment variable KMP_DUPLICATE_LIB_OK=TRUE to ignore this problem and force the program to continue anyway. Please note that the use of KMP_DUPLICATE_LIB_OK is unsupported and using it may cause undefined behavior. For more information, please contact Intel(R) Premier Support. I think this happens because multiple submodules inside NumPy are linked against this libguide library, but this caused some initialization code to be executed multiple times inside the same process, which shouldn't happen. If one sets KMP_DUPLICATE_LIB_OK=TRUE, the tests actually work with Intel MKL 9.0, but no matter what you do with Intel MKL 9.1, i.e., - link against libguide40 or - link against libguide and don't set KMP_... or - link against libguide and set KMP_... the following tests always segfault: numpy.core.tests.test_defmatrix.test_casting.check_basic numpy.core.tests.test_numeric.test_dot.check_matmat Cheers, Albert On Tue, 12 Jun 2007, Albert Strasheim wrote: > I've set up a 32-bit Windows XP guest inside VMWare Server 1.0.3 on a 64-bit > Linux machine and two of the NumPy tests are segfaulting for some strange > reason. They are: > > numpy.core.tests.test_defmatrix.test_casting.check_basic > numpy.core.tests.test_numeric.test_dot.check_matmat > > Do these pass for you? I'm inclined to blame VMWare at this point...

1 1

segfault caused by incorrect Py_DECREF in ufunc
by Tom Denniston 23 Jul '07

23 Jul '07

Below is the code around line 900 for ufuncobject.c (http://svn.scipy.org/svn/numpy/trunk/numpy/core/src/ufuncobject.c) There is a decref labeled with ">>>" below that is incorrect. As per the python documentation (http://docs.python.org/api/dictObjects.html): #PyObject* PyDict_GetItem( PyObject *p, PyObject *key) # #Return value: Borrowed reference. #Return the object from dictionary p which has a key key. Return NULL if the key #key is not present, but without setting an exception. PyDict_GetItem returns a borrowed reference. Therefore this code does not own the contents to which the obj pointer points and should not decref on it. Simply removing the Py_DECREF(obj) line gets rid of the segfault. I was wondering if someone could confirm that my interpretation is correct and remove the line. I don't have access to the svn or know how to change it. Most people do not see this problem because it only affects user defined types. --Tom if (userdef > 0) { PyObject *key, *obj; int ret; obj = NULL; key = PyInt_FromLong((long) userdef); if (key == NULL) return -1; obj = PyDict_GetItem(self->userloops, key); Py_DECREF(key); if (obj == NULL) { PyErr_SetString(PyExc_TypeError, "user-defined type used in ufunc" \ " with no registered loops"); return -1; } /* extract the correct function data and argtypes */ ret = _find_matching_userloop(obj, arg_types, scalars, function, data, self->nargs, self->nin); >>> Py_DECREF(obj); return ret; }

11 42

scipy.test() warnings, errors and failures
by mpjohnson＠gmail.com 09 Jul '07

09 Jul '07

Hi, I just installed numpy (1.0.3) and scipy (0.5.2) on a Windows machine running Python 2.5.1. They both complete installation, and numpy.test() reports no errors. scipy.test() produces a huge stream (see below) of warnings, errors (19), and failures (2), however. Also, there's a deprecation warning when I import scipy. Is this behavior normal? These appear to be the latest versions of everything. Thanks, Matt Python 2.5.1 (r251:54863, Apr 18 2007, 08:51:08) [MSC v.1310 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 1.2.1 >>> import numpy >>> import scipy Warning (from warnings module): File "C:\Python25\lib\site-packages\scipy\misc\__init__.py", line 25 test = ScipyTest().test DeprecationWarning: ScipyTest is now called NumpyTest; please update your code >>> scipy.test() Warning (from warnings module): File "C:\Python25\lib\site-packages\scipy\ndimage\__init__.py", line 40 test = ScipyTest().test DeprecationWarning: ScipyTest is now called NumpyTest; please update your code Warning (from warnings module): File "C:\Python25\lib\site-packages\scipy\sparse\__init__.py", line 9 test = ScipyTest().test DeprecationWarning: ScipyTest is now called NumpyTest; please update your code Warning (from warnings module): File "C:\Python25\lib\site-packages\scipy\io\__init__.py", line 20 test = ScipyTest().test DeprecationWarning: ScipyTest is now called NumpyTest; please update your code Warning (from warnings module): File "C:\Python25\lib\site-packages\scipy\lib\__init__.py", line 5 test = ScipyTest().test DeprecationWarning: ScipyTest is now called NumpyTest; please update your code Warning (from warnings module): File "C:\Python25\lib\site-packages\scipy\linsolve\umfpack \__init__.py", line 7 test = ScipyTest().test DeprecationWarning: ScipyTest is now called NumpyTest; please update your code Warning (from warnings module): File "C:\Python25\lib\site-packages\scipy\linsolve\__init__.py", line 13 test = ScipyTest().test DeprecationWarning: ScipyTest is now called NumpyTest; please update your code Warning (from warnings module): File "C:\Python25\lib\site-packages\scipy\interpolate\__init__.py", line 15 test = ScipyTest().test DeprecationWarning: ScipyTest is now called NumpyTest; please update your code Warning (from warnings module): File "C:\Python25\lib\site-packages\scipy\optimize\__init__.py", line 17 test = ScipyTest().test DeprecationWarning: ScipyTest is now called NumpyTest; please update your code Warning (from warnings module): File "C:\Python25\lib\site-packages\scipy\linalg\__init__.py", line 32 test = ScipyTest().test DeprecationWarning: ScipyTest is now called NumpyTest; please update your code Warning (from warnings module): File "C:\Python25\lib\site-packages\scipy\special\__init__.py", line 22 test = ScipyTest().test DeprecationWarning: ScipyTest is now called NumpyTest; please update your code Warning (from warnings module): File "C:\Python25\lib\site-packages\scipy\stats\__init__.py", line 15 test = ScipyTest().test DeprecationWarning: ScipyTest is now called NumpyTest; please update your code Warning (from warnings module): File "C:\Python25\lib\site-packages\scipy\fftpack\__init__.py", line 21 test = ScipyTest().test DeprecationWarning: ScipyTest is now called NumpyTest; please update your code Warning (from warnings module): File "C:\Python25\lib\site-packages\scipy\integrate\__init__.py", line 16 test = ScipyTest().test DeprecationWarning: ScipyTest is now called NumpyTest; please update your code Warning (from warnings module): File "C:\Python25\lib\site-packages\scipy\lib\lapack\__init__.py", line 93 test = ScipyTest().test DeprecationWarning: ScipyTest is now called NumpyTest; please update your code Warning (from warnings module): File "C:\Python25\lib\site-packages\scipy\signal\__init__.py", line 17 test = ScipyTest().test DeprecationWarning: ScipyTest is now called NumpyTest; please update your code Warning (from warnings module): File "C:\Python25\lib\site-packages\scipy\lib\blas\__init__.py", line 61 test = ScipyTest().test DeprecationWarning: ScipyTest is now called NumpyTest; please update your code Warning (from warnings module): File "C:\Python25\lib\site-packages\scipy\maxentropy\__init__.py", line 12 test = ScipyTest().test DeprecationWarning: ScipyTest is now called NumpyTest; please update your code Warning (from warnings module): File "C:\Python25\lib\site-packages\scipy\__init__.py", line 77 return ScipyTest(scipy).test(level, verbosity) DeprecationWarning: ScipyTest is now called NumpyTest; please update your code Found 1 tests for scipy.cluster.vq Warning (from warnings module): File "C:\Python25\lib\site-packages\scipy\fftpack\__init__.py", line 21 test = ScipyTest().test DeprecationWarning: ScipyTest is now called NumpyTest; please update your code Warning (from warnings module): File "C:\Python25\lib\site-packages\numpy\testing\numpytest.py", line 408 suite = obj(mthname) DeprecationWarning: ScipyTestCase is now called NumpyTestCase; please update your code Found 18 tests for scipy.fftpack.basic Found 4 tests for scipy.fftpack.helper Found 20 tests for scipy.fftpack.pseudo_diffs Found 1 tests for scipy.integrate Found 10 tests for scipy.integrate.quadpack Found 3 tests for scipy.integrate.quadrature Warning (from warnings module): File "C:\Python25\lib\site-packages\scipy\interpolate\__init__.py", line 15 test = ScipyTest().test DeprecationWarning: ScipyTest is now called NumpyTest; please update your code Found 6 tests for scipy.interpolate Found 6 tests for scipy.interpolate.fitpack Warning (from warnings module): File "C:\Python25\lib\site-packages\scipy\io\__init__.py", line 20 test = ScipyTest().test DeprecationWarning: ScipyTest is now called NumpyTest; please update your code Found 4 tests for scipy.io.array_import Warning (from warnings module): File "C:\Python25\lib\site-packages\scipy\io\tests\test_mio.py", line 28 super(test_mio_array, self).__init__(*args, **kwargs) DeprecationWarning: ScipyTestCase is now called NumpyTestCase; please update your code Found 28 tests for scipy.io.mio Found 12 tests for scipy.io.mmio Found 4 tests for scipy.io.recaster Warning (from warnings module): File "C:\Python25\lib\site-packages\scipy\lib\blas\__init__.py", line 61 test = ScipyTest().test DeprecationWarning: ScipyTest is now called NumpyTest; please update your code Found 16 tests for scipy.lib.blas Found 128 tests for scipy.lib.blas.fblas Warning (from warnings module): File "C:\Python25\lib\site-packages\scipy\lib\lapack\__init__.py", line 93 test = ScipyTest().test DeprecationWarning: ScipyTest is now called NumpyTest; please update your code Found 42 tests for scipy.lib.lapack Warning (from warnings module): File "C:\Python25\lib\site-packages\scipy\linalg\__init__.py", line 32 test = ScipyTest().test DeprecationWarning: ScipyTest is now called NumpyTest; please update your code Found 41 tests for scipy.linalg.basic Found 14 tests for scipy.linalg.blas Warning (from warnings module): File "C:\Python25\lib\site-packages\scipy\linalg\tests \test_decomp.py", line 117 ScipyTestCase.__init__(self, *args) DeprecationWarning: ScipyTestCase is now called NumpyTestCase; please update your code Found 53 tests for scipy.linalg.decomp Found 128 tests for scipy.linalg.fblas Found 4 tests for scipy.linalg.lapack Found 7 tests for scipy.linalg.matfuncs Warning: FAILURE importing tests for <module 'scipy.linsolve.umfpack' from '...\\linsolve\\umfpack\\__init__.pyc'> C:\Python25\Lib\site-packages\scipy\linsolve\umfpack\tests \test_umfpack.py:17: AttributeError: 'module' object has no attribute 'umfpack' (in <module>) Warning: FAILURE importing tests for <module 'scipy.linsolve.umfpack.umfpack' from '...y\\linsolve\\umfpack\ \umfpack.pyc'> C:\Python25\Lib\site-packages\scipy\linsolve\umfpack\tests \test_umfpack.py:17: AttributeError: 'module' object has no attribute 'umfpack' (in <module>) Found 2 tests for scipy.maxentropy Found 397 tests for scipy.ndimage Found 6 tests for scipy.optimize Warning (from warnings module): File "C:\Python25\lib\site-packages\scipy\optimize\__init__.py", line 17 test = ScipyTest().test DeprecationWarning: ScipyTest is now called NumpyTest; please update your code Found 1 tests for scipy.optimize.cobyla Found 4 tests for scipy.optimize.zeros Found 4 tests for scipy.signal.signaltools Found 96 tests for scipy.sparse Warning (from warnings module): File "C:\Python25\lib\site-packages\scipy\special\__init__.py", line 22 test = ScipyTest().test DeprecationWarning: ScipyTest is now called NumpyTest; please update your code Found 358 tests for scipy.special.basic Warning (from warnings module): File "C:\Python25\lib\site-packages\scipy\stats\__init__.py", line 15 test = ScipyTest().test DeprecationWarning: ScipyTest is now called NumpyTest; please update your code Found 98 tests for scipy.stats Found 70 tests for scipy.stats.distributions Found 10 tests for scipy.stats.morestats Found 0 tests for __main__ ...........................................Residual: 1.05006987327e-007 ...........Took 13 points. ......... Warning (from warnings module): File "C:\Python25\lib\site-packages\scipy\interpolate\fitpack2.py", line 457 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. ...... Don't worry about a warning regarding the number of bytes read. ....EEEE.E.EE.E.E.EE.E.E.E.EEEEE....................................................F......................................................................................................................................................................................................................................................................................................................................................................................................Result may be inaccurate, approximate err = 1.82697723188e-008 ...Result may be inaccurate, approximate err = 1.50259560743e-010 ..........................................................................................................................................................................................................................................................................................................................................................................................................................................Resizing... 16 17 24 Resizing... 20 7 35 Resizing... 23 7 47 Resizing... 24 25 58 Resizing... 28 7 68 Resizing... 28 27 73 ................................................Resizing... 16 17 24 Resizing... 20 7 35 Resizing... 23 7 47 Resizing... 24 25 58 Resizing... 28 7 68 Resizing... 28 27 73 ......................Resizing... 16 17 24 Resizing... 20 7 35 Resizing... 23 7 47 Resizing... 24 25 58 Resizing... 28 7 68 Resizing... 28 27 73 ...............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................F.Ties preclude use of exact statistic. ..Ties preclude use of exact statistic. ...... ====================================================================== ERROR: check loadmat case 3dmatrix ---------------------------------------------------------------------- Traceback (most recent call last): File "C:\Python25\Lib\site-packages\scipy\io\tests\test_mio.py", line 85, in cc self._check_case(name, files, expected) File "C:\Python25\Lib\site-packages\scipy\io\tests\test_mio.py", line 75, in _check_case matdict = loadmat(file_name) File "C:\Python25\Lib\site-packages\scipy\io\mio.py", line 96, in loadmat matfile_dict = MR.get_variables() File "C:\Python25\Lib\site-packages\scipy\io\miobase.py", line 269, in get_variables mdict = self.file_header() File "C:\Python25\Lib\site-packages\scipy\io\mio5.py", line 510, in file_header hdict['__header__'] = hdr['description'].strip(' \t\n\000') AttributeError: 'numpy.ndarray' object has no attribute 'strip' ====================================================================== ERROR: check loadmat case cell ---------------------------------------------------------------------- Traceback (most recent call last): File "C:\Python25\Lib\site-packages\scipy\io\tests\test_mio.py", line 85, in cc self._check_case(name, files, expected) File "C:\Python25\Lib\site-packages\scipy\io\tests\test_mio.py", line 75, in _check_case matdict = loadmat(file_name) File "C:\Python25\Lib\site-packages\scipy\io\mio.py", line 96, in loadmat matfile_dict = MR.get_variables() File "C:\Python25\Lib\site-packages\scipy\io\miobase.py", line 269, in get_variables mdict = self.file_header() File "C:\Python25\Lib\site-packages\scipy\io\mio5.py", line 510, in file_header hdict['__header__'] = hdr['description'].strip(' \t\n\000') AttributeError: 'numpy.ndarray' object has no attribute 'strip' ====================================================================== ERROR: check loadmat case cellnest ---------------------------------------------------------------------- Traceback (most recent call last): File "C:\Python25\Lib\site-packages\scipy\io\tests\test_mio.py", line 85, in cc self._check_case(name, files, expected) File "C:\Python25\Lib\site-packages\scipy\io\tests\test_mio.py", line 75, in _check_case matdict = loadmat(file_name) File "C:\Python25\Lib\site-packages\scipy\io\mio.py", line 96, in loadmat matfile_dict = MR.get_variables() File "C:\Python25\Lib\site-packages\scipy\io\miobase.py", line 269, in get_variables mdict = self.file_header() File "C:\Python25\Lib\site-packages\scipy\io\mio5.py", line 510, in file_header hdict['__header__'] = hdr['description'].strip(' \t\n\000') AttributeError: 'numpy.ndarray' object has no attribute 'strip' ====================================================================== ERROR: check loadmat case complex ---------------------------------------------------------------------- Traceback (most recent call last): File "C:\Python25\Lib\site-packages\scipy\io\tests\test_mio.py", line 85, in cc self._check_case(name, files, expected) File "C:\Python25\Lib\site-packages\scipy\io\tests\test_mio.py", line 75, in _check_case matdict = loadmat(file_name) File "C:\Python25\Lib\site-packages\scipy\io\mio.py", line 96, in loadmat matfile_dict = MR.get_variables() File "C:\Python25\Lib\site-packages\scipy\io\miobase.py", line 269, in get_variables mdict = self.file_header() File "C:\Python25\Lib\site-packages\scipy\io\mio5.py", line 510, in file_header hdict['__header__'] = hdr['description'].strip(' \t\n\000') AttributeError: 'numpy.ndarray' object has no attribute 'strip' ====================================================================== ERROR: check loadmat case double ---------------------------------------------------------------------- Traceback (most recent call last): File "C:\Python25\Lib\site-packages\scipy\io\tests\test_mio.py", line 85, in cc self._check_case(name, files, expected) File "C:\Python25\Lib\site-packages\scipy\io\tests\test_mio.py", line 75, in _check_case matdict = loadmat(file_name) File "C:\Python25\Lib\site-packages\scipy\io\mio.py", line 96, in loadmat matfile_dict = MR.get_variables() File "C:\Python25\Lib\site-packages\scipy\io\miobase.py", line 269, in get_variables mdict = self.file_header() File "C:\Python25\Lib\site-packages\scipy\io\mio5.py", line 510, in file_header hdict['__header__'] = hdr['description'].strip(' \t\n\000') AttributeError: 'numpy.ndarray' object has no attribute 'strip' ====================================================================== ERROR: check loadmat case emptycell ---------------------------------------------------------------------- Traceback (most recent call last): File "C:\Python25\Lib\site-packages\scipy\io\tests\test_mio.py", line 85, in cc self._check_case(name, files, expected) File "C:\Python25\Lib\site-packages\scipy\io\tests\test_mio.py", line 75, in _check_case matdict = loadmat(file_name) File "C:\Python25\Lib\site-packages\scipy\io\mio.py", line 96, in loadmat matfile_dict = MR.get_variables() File "C:\Python25\Lib\site-packages\scipy\io\miobase.py", line 269, in get_variables mdict = self.file_header() File "C:\Python25\Lib\site-packages\scipy\io\mio5.py", line 510, in file_header hdict['__header__'] = hdr['description'].strip(' \t\n\000') AttributeError: 'numpy.ndarray' object has no attribute 'strip' ====================================================================== ERROR: check loadmat case matrix ---------------------------------------------------------------------- Traceback (most recent call last): File "C:\Python25\Lib\site-packages\scipy\io\tests\test_mio.py", line 85, in cc self._check_case(name, files, expected) File "C:\Python25\Lib\site-packages\scipy\io\tests\test_mio.py", line 75, in _check_case matdict = loadmat(file_name) File "C:\Python25\Lib\site-packages\scipy\io\mio.py", line 96, in loadmat matfile_dict = MR.get_variables() File "C:\Python25\Lib\site-packages\scipy\io\miobase.py", line 269, in get_variables mdict = self.file_header() File "C:\Python25\Lib\site-packages\scipy\io\mio5.py", line 510, in file_header hdict['__header__'] = hdr['description'].strip(' \t\n\000') AttributeError: 'numpy.ndarray' object has no attribute 'strip' ====================================================================== ERROR: check loadmat case minus ---------------------------------------------------------------------- Traceback (most recent call last): File "C:\Python25\Lib\site-packages\scipy\io\tests\test_mio.py", line 85, in cc self._check_case(name, files, expected) File "C:\Python25\Lib\site-packages\scipy\io\tests\test_mio.py", line 75, in _check_case matdict = loadmat(file_name) File "C:\Python25\Lib\site-packages\scipy\io\mio.py", line 96, in loadmat matfile_dict = MR.get_variables() File "C:\Python25\Lib\site-packages\scipy\io\miobase.py", line 269, in get_variables mdict = self.file_header() File "C:\Python25\Lib\site-packages\scipy\io\mio5.py", line 510, in file_header hdict['__header__'] = hdr['description'].strip(' \t\n\000') AttributeError: 'numpy.ndarray' object has no attribute 'strip' ====================================================================== ERROR: check loadmat case multi ---------------------------------------------------------------------- Traceback (most recent call last): File "C:\Python25\Lib\site-packages\scipy\io\tests\test_mio.py", line 85, in cc self._check_case(name, files, expected) File "C:\Python25\Lib\site-packages\scipy\io\tests\test_mio.py", line 75, in _check_case matdict = loadmat(file_name) File "C:\Python25\Lib\site-packages\scipy\io\mio.py", line 96, in loadmat matfile_dict = MR.get_variables() File "C:\Python25\Lib\site-packages\scipy\io\miobase.py", line 269, in get_variables mdict = self.file_header() File "C:\Python25\Lib\site-packages\scipy\io\mio5.py", line 510, in file_header hdict['__header__'] = hdr['description'].strip(' \t\n\000') AttributeError: 'numpy.ndarray' object has no attribute 'strip' ====================================================================== ERROR: check loadmat case object ---------------------------------------------------------------------- Traceback (most recent call last): File "C:\Python25\Lib\site-packages\scipy\io\tests\test_mio.py", line 85, in cc self._check_case(name, files, expected) File "C:\Python25\Lib\site-packages\scipy\io\tests\test_mio.py", line 75, in _check_case matdict = loadmat(file_name) File "C:\Python25\Lib\site-packages\scipy\io\mio.py", line 96, in loadmat matfile_dict = MR.get_variables() File "C:\Python25\Lib\site-packages\scipy\io\miobase.py", line 269, in get_variables mdict = self.file_header() File "C:\Python25\Lib\site-packages\scipy\io\mio5.py", line 510, in file_header hdict['__header__'] = hdr['description'].strip(' \t\n\000') AttributeError: 'numpy.ndarray' object has no attribute 'strip' ====================================================================== ERROR: check loadmat case onechar ---------------------------------------------------------------------- Traceback (most recent call last): File "C:\Python25\Lib\site-packages\scipy\io\tests\test_mio.py", line 85, in cc self._check_case(name, files, expected) File "C:\Python25\Lib\site-packages\scipy\io\tests\test_mio.py", line 75, in _check_case matdict = loadmat(file_name) File "C:\Python25\Lib\site-packages\scipy\io\mio.py", line 96, in loadmat matfile_dict = MR.get_variables() File "C:\Python25\Lib\site-packages\scipy\io\miobase.py", line 269, in get_variables mdict = self.file_header() File "C:\Python25\Lib\site-packages\scipy\io\mio5.py", line 510, in file_header hdict['__header__'] = hdr['description'].strip(' \t\n\000') AttributeError: 'numpy.ndarray' object has no attribute 'strip' ====================================================================== ERROR: check loadmat case sparse ---------------------------------------------------------------------- Traceback (most recent call last): File "C:\Python25\Lib\site-packages\scipy\io\tests\test_mio.py", line 85, in cc self._check_case(name, files, expected) File "C:\Python25\Lib\site-packages\scipy\io\tests\test_mio.py", line 75, in _check_case matdict = loadmat(file_name) File "C:\Python25\Lib\site-packages\scipy\io\mio.py", line 96, in loadmat matfile_dict = MR.get_variables() File "C:\Python25\Lib\site-packages\scipy\io\miobase.py", line 269, in get_variables mdict = self.file_header() File "C:\Python25\Lib\site-packages\scipy\io\mio5.py", line 510, in file_header hdict['__header__'] = hdr['description'].strip(' \t\n\000') AttributeError: 'numpy.ndarray' object has no attribute 'strip' ====================================================================== ERROR: check loadmat case sparsecomplex ---------------------------------------------------------------------- Traceback (most recent call last): File "C:\Python25\Lib\site-packages\scipy\io\tests\test_mio.py", line 85, in cc self._check_case(name, files, expected) File "C:\Python25\Lib\site-packages\scipy\io\tests\test_mio.py", line 75, in _check_case matdict = loadmat(file_name) File "C:\Python25\Lib\site-packages\scipy\io\mio.py", line 96, in loadmat matfile_dict = MR.get_variables() File "C:\Python25\Lib\site-packages\scipy\io\miobase.py", line 269, in get_variables mdict = self.file_header() File "C:\Python25\Lib\site-packages\scipy\io\mio5.py", line 510, in file_header hdict['__header__'] = hdr['description'].strip(' \t\n\000') AttributeError: 'numpy.ndarray' object has no attribute 'strip' ====================================================================== ERROR: check loadmat case string ---------------------------------------------------------------------- Traceback (most recent call last): File "C:\Python25\Lib\site-packages\scipy\io\tests\test_mio.py", line 85, in cc self._check_case(name, files, expected) File "C:\Python25\Lib\site-packages\scipy\io\tests\test_mio.py", line 75, in _check_case matdict = loadmat(file_name) File "C:\Python25\Lib\site-packages\scipy\io\mio.py", line 96, in loadmat matfile_dict = MR.get_variables() File "C:\Python25\Lib\site-packages\scipy\io\miobase.py", line 269, in get_variables mdict = self.file_header() File "C:\Python25\Lib\site-packages\scipy\io\mio5.py", line 510, in file_header hdict['__header__'] = hdr['description'].strip(' \t\n\000') AttributeError: 'numpy.ndarray' object has no attribute 'strip' ====================================================================== ERROR: check loadmat case stringarray ---------------------------------------------------------------------- Traceback (most recent call last): File "C:\Python25\Lib\site-packages\scipy\io\tests\test_mio.py", line 85, in cc self._check_case(name, files, expected) File "C:\Python25\Lib\site-packages\scipy\io\tests\test_mio.py", line 75, in _check_case matdict = loadmat(file_name) File "C:\Python25\Lib\site-packages\scipy\io\mio.py", line 96, in loadmat matfile_dict = MR.get_variables() File "C:\Python25\Lib\site-packages\scipy\io\miobase.py", line 269, in get_variables mdict = self.file_header() File "C:\Python25\Lib\site-packages\scipy\io\mio5.py", line 510, in file_header hdict['__header__'] = hdr['description'].strip(' \t\n\000') AttributeError: 'numpy.ndarray' object has no attribute 'strip' ====================================================================== ERROR: check loadmat case struct ---------------------------------------------------------------------- Traceback (most recent call last): File "C:\Python25\Lib\site-packages\scipy\io\tests\test_mio.py", line 85, in cc self._check_case(name, files, expected) File "C:\Python25\Lib\site-packages\scipy\io\tests\test_mio.py", line 75, in _check_case matdict = loadmat(file_name) File "C:\Python25\Lib\site-packages\scipy\io\mio.py", line 96, in loadmat matfile_dict = MR.get_variables() File "C:\Python25\Lib\site-packages\scipy\io\miobase.py", line 269, in get_variables mdict = self.file_header() File "C:\Python25\Lib\site-packages\scipy\io\mio5.py", line 510, in file_header hdict['__header__'] = hdr['description'].strip(' \t\n\000') AttributeError: 'numpy.ndarray' object has no attribute 'strip' ====================================================================== ERROR: check loadmat case structarr ---------------------------------------------------------------------- Traceback (most recent call last): File "C:\Python25\Lib\site-packages\scipy\io\tests\test_mio.py", line 85, in cc self._check_case(name, files, expected) File "C:\Python25\Lib\site-packages\scipy\io\tests\test_mio.py", line 75, in _check_case matdict = loadmat(file_name) File "C:\Python25\Lib\site-packages\scipy\io\mio.py", line 96, in loadmat matfile_dict = MR.get_variables() File "C:\Python25\Lib\site-packages\scipy\io\miobase.py", line 269, in get_variables mdict = self.file_header() File "C:\Python25\Lib\site-packages\scipy\io\mio5.py", line 510, in file_header hdict['__header__'] = hdr['description'].strip(' \t\n\000') AttributeError: 'numpy.ndarray' object has no attribute 'strip' ====================================================================== ERROR: check loadmat case structnest ---------------------------------------------------------------------- Traceback (most recent call last): File "C:\Python25\Lib\site-packages\scipy\io\tests\test_mio.py", line 85, in cc self._check_case(name, files, expected) File "C:\Python25\Lib\site-packages\scipy\io\tests\test_mio.py", line 75, in _check_case matdict = loadmat(file_name) File "C:\Python25\Lib\site-packages\scipy\io\mio.py", line 96, in loadmat matfile_dict = MR.get_variables() File "C:\Python25\Lib\site-packages\scipy\io\miobase.py", line 269, in get_variables mdict = self.file_header() File "C:\Python25\Lib\site-packages\scipy\io\mio5.py", line 510, in file_header hdict['__header__'] = hdr['description'].strip(' \t\n\000') AttributeError: 'numpy.ndarray' object has no attribute 'strip' ====================================================================== ERROR: check loadmat case unicode ---------------------------------------------------------------------- Traceback (most recent call last): File "C:\Python25\Lib\site-packages\scipy\io\tests\test_mio.py", line 85, in cc self._check_case(name, files, expected) File "C:\Python25\Lib\site-packages\scipy\io\tests\test_mio.py", line 75, in _check_case matdict = loadmat(file_name) File "C:\Python25\Lib\site-packages\scipy\io\mio.py", line 96, in loadmat matfile_dict = MR.get_variables() File "C:\Python25\Lib\site-packages\scipy\io\miobase.py", line 269, in get_variables mdict = self.file_header() File "C:\Python25\Lib\site-packages\scipy\io\mio5.py", line 510, in file_header hdict['__header__'] = hdr['description'].strip(' \t\n\000') AttributeError: 'numpy.ndarray' object has no attribute 'strip' ====================================================================== FAIL: check_y_stride (scipy.lib.blas.tests.test_fblas.test_cgemv) ---------------------------------------------------------------------- Traceback (most recent call last): File "C:\Python25\Lib\site-packages\scipy\lib\blas\tests \test_fblas.py", line 367, in check_y_stride assert_array_almost_equal(desired_y,y) File "C:\Python25\Lib\site-packages\numpy\testing\utils.py", line 230, in assert_array_almost_equal header='Arrays are not almost equal') File "C:\Python25\Lib\site-packages\numpy\testing\utils.py", line 215, in assert_array_compare assert cond, msg AssertionError: Arrays are not almost equal (mismatch 16.6666666667%) x: array([-5.39065742 +5.39065742j, 1. +1.j , 3.86268878 +0.13731122j, 3. +3.j , -9.09618664+17.09618759j, 5. +5.j ], dtype=complex64) y: array([-5.39065742 +5.39065742j, 1. +1.j , 3.86268878 +0.13731124j, 3. +3.j , -9.09618664+17.09618568j, 5. +5.j ], dtype=complex64) ====================================================================== FAIL: check_expon (scipy.stats.tests.test_morestats.test_anderson) ---------------------------------------------------------------------- Traceback (most recent call last): File "C:\Python25\Lib\site-packages\scipy\stats\tests \test_morestats.py", line 57, in check_expon assert_array_less(A, crit[-2:]) File "C:\Python25\Lib\site-packages\numpy\testing\utils.py", line 235, in assert_array_less header='Arrays are not less-ordered') File "C:\Python25\Lib\site-packages\numpy\testing\utils.py", line 215, in assert_array_compare assert cond, msg AssertionError: Arrays are not less-ordered (mismatch 100.0%) x: array(1.9482886531944246) y: array([ 1.587, 1.934]) ---------------------------------------------------------------------- Ran 1596 tests in 20.720s FAILED (failures=2, errors=19) <unittest.TextTestRunner object at 0x022F6B90>

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Buildbot for numpy
by Stefan van der Walt 09 Jul '07

09 Jul '07

Hi all, Short version ============= We now have a numpy buildbot running at http://buildbot.scipy.org Long version ============ Albert Strasheim and I set up a buildbot for numpy this week. For those of you unfamiliar with The Buildbot, it is """ ...a system to automate the compile/test cycle required by most software projects to validate code changes. By automatically rebuilding and testing the tree each time something has changed, build problems are pinpointed quickly, before other developers are inconvenienced by the failure. The guilty developer can be identified and harassed without human intervention. By running the builds on a variety of platforms, developers who do not have the facilities to test their changes everywhere before checkin will at least know shortly afterwards whether they have broken the build or not. Warning counts, lint checks, image size, compile time, and other build parameters can be tracked over time, are more visible, and are therefore easier to improve. The overall goal is to reduce tree breakage and provide a platform to run tests or code-quality checks that are too annoying or pedantic for any human to waste their time with. Developers get immediate (and potentially public) feedback about their changes, encouraging them to be more careful about testing before checkin. """ While we are still working on automatic e-mail notifications, the system already provides valuable feedback -- take a look at the waterfall display: http://buildbot.scipy.org If your platform is not currently on the list, please consider volunteering a machine as a build slave. This machine will be required to run the buildbot client, and to build a new version of numpy whenever changes are made to the repository. (The machine does not have to be dedicated to this task, and can be your own workstation.) We'd like to thank Robert Kern, Jeff Strunk and Gert-Jan van Rooyen who helped us to get the ball rolling, as well as Neilen Marais for offering his workstation as a build slave. Regards Stéfan

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