Hi, I am pleased to announce the availability of the first beta of NumPy 1.6.0. Due to the extensive changes in the Numpy core for this release, the beta testing phase will last at least one month. Please test this beta and report any problems on the Numpy mailing list. Sources and binaries can be found at: http://sourceforge.net/projects/numpy/files/NumPy/1.6.0b1/ For (preliminary) release notes see below. Enjoy, Ralf ========================= NumPy 1.6.0 Release Notes ========================= This release includes several new features as well as numerous bug fixes and improved documentation. It is backward compatible with the 1.5.0 release, and supports Python 2.4 - 2.7 and 3.1 - 3.2. Highlights ========== * Re-introduction of datetime dtype support to deal with dates in arrays. * A new 16-bit floating point type. * A new iterator, which improves performance of many functions. New features ============ New 16-bit floating point type ------------------------------ This release adds support for the IEEE 754-2008 binary16 format, available as the data type ``numpy.half``. Within Python, the type behaves similarly to `float` or `double`, and C extensions can add support for it with the exposed half-float API. New iterator ------------ A new iterator has been added, replacing the functionality of the existing iterator and multi-iterator with a single object and API. This iterator works well with general memory layouts different from C or Fortran contiguous, and handles both standard NumPy and customized broadcasting. The buffering, automatic data type conversion, and optional output parameters, offered by ufuncs but difficult to replicate elsewhere, are now exposed by this iterator. Legendre, Laguerre, Hermite, HermiteE polynomials in ``numpy.polynomial`` ------------------------------------------------------------------------- Extend the number of polynomials available in the polynomial package. In addition, a new ``window`` attribute has been added to the classes in order to specify the range the ``domain`` maps to. This is mostly useful for the Laguerre, Hermite, and HermiteE polynomials whose natural domains are infinite and provides a more intuitive way to get the correct mapping of values without playing unnatural tricks with the domain. Fortran assumed shape array and size function support in ``numpy.f2py`` ----------------------------------------------------------------------- F2py now supports wrapping Fortran 90 routines that use assumed shape arrays. Before such routines could be called from Python but the corresponding Fortran routines received assumed shape arrays as zero length arrays which caused unpredicted results. Thanks to Lorenz Hüdepohl for pointing out the correct way to interface routines with assumed shape arrays. In addition, f2py interprets Fortran expression ``size(array, dim)`` as ``shape(array, dim-1)`` which makes it possible to automatically wrap Fortran routines that use two argument ``size`` function in dimension specifications. Before users were forced to apply this mapping manually. Other new functions ------------------- ``numpy.ravel_multi_index`` : Converts a multi-index tuple into an array of flat indices, applying boundary modes to the indices. ``numpy.einsum`` : Evaluate the Einstein summation convention. Using the Einstein summation convention, many common multi-dimensional array operations can be represented in a simple fashion. This function provides a way compute such summations. ``numpy.count_nonzero`` : Counts the number of non-zero elements in an array. ``numpy.result_type`` and ``numpy.min_scalar_type`` : These functions expose the underlying type promotion used by the ufuncs and other operations to determine the types of outputs. These improve upon the ``numpy.common_type`` and ``numpy.mintypecode`` which provide similar functionality but do not match the ufunc implementation. Changes ======= Changes and improvements in the numpy core ------------------------------------------ ``numpy.distutils`` ------------------- Several new compilers are supported for building Numpy: the Portland Group Fortran compiler on OS X, the PathScale compiler suite and the 64-bit Intel C compiler on Linux. ``numpy.testing`` ----------------- The testing framework gained ``numpy.testing.assert_allclose``, which provides a more convenient way to compare floating point arrays than `assert_almost_equal`, `assert_approx_equal` and `assert_array_almost_equal`. ``C API`` --------- In addition to the APIs for the new iterator and half data type, a number of other additions have been made to the C API. The type promotion mechanism used by ufuncs is exposed via ``PyArray_PromoteTypes``, ``PyArray_ResultType``, and ``PyArray_MinScalarType``. A new enumeration ``NPY_CASTING`` has been added which controls what types of casts are permitted. This is used by the new functions ``PyArray_CanCastArrayTo`` and ``PyArray_CanCastTypeTo``. A more flexible way to handle conversion of arbitrary python objects into arrays is exposed by ``PyArray_GetArrayParamsFromObject``. Removed features ================ ``numpy.fft`` ------------- The functions `refft`, `refft2`, `refftn`, `irefft`, `irefft2`, `irefftn`, which were aliases for the same functions without the 'e' in the name, were removed. ``numpy.memmap`` ---------------- The `sync()` and `close()` methods of memmap were removed. Use `flush()` and "del memmap" instead. ``numpy.lib`` ------------- The deprecated functions ``numpy.unique1d``, ``numpy.setmember1d``, ``numpy.intersect1d_nu`` and ``numpy.lib.ufunclike.log2`` were removed. ``numpy.ma`` ------------ Several deprecated items were removed from the ``numpy.ma`` module:: * ``numpy.ma.MaskedArray`` "raw_data" method * ``numpy.ma.MaskedArray`` constructor "flag" keyword * ``numpy.ma.make_mask`` "flag" keyword * ``numpy.ma.allclose`` "fill_value" keyword ``numpy.distutils`` ------------------- The ``numpy.get_numpy_include`` function was removed, use ``numpy.get_include`` instead. Checksums ========= 89f52ae0f0ea84cfcb457298190bee14 release/installers/numpy-1.6.0b1-py2.7-python.org.dmg 8dee06b362540b2c8c033399951e5386 release/installers/numpy-1.6.0b1-win32-superpack-python2.5.exe c1b11bf48037ac8fe025bfd297969840 release/installers/numpy-1.6.0b1-win32-superpack-python2.6.exe 2b005cb359d8123bd5ee3063d9eae3ac release/installers/numpy-1.6.0b1-win32-superpack-python2.7.exe 45627e8f63fe34011817df66722c39a5 release/installers/numpy-1.6.0b1-win32-superpack-python3.1.exe 1d8b214752b19b51ee747a6436ca1d38 release/installers/numpy-1.6.0b1-win32-superpack-python3.2.exe aeab5881974aac595b87a848c0c6344a release/installers/numpy-1.6.0b1.tar.gz 3ffc6e308f9e0614531fa3babcb75544 release/installers/numpy-1.6.0b1.zip
On 03/23/2011 11:07 AM, Ralf Gommers wrote:
Hi,
I am pleased to announce the availability of the first beta of NumPy 1.6.0. Due to the extensive changes in the Numpy core for this release, the beta testing phase will last at least one month. Please test this beta and report any problems on the Numpy mailing list.
Sources and binaries can be found at: http://sourceforge.net/projects/numpy/files/NumPy/1.6.0b1/ For (preliminary) release notes see below.
Enjoy, Ralf
[snip] Python 3.1 failed to build it due to import error of _inspect module and Python2.4 failed 'test_iterator.test_iter_broadcasting_errors'. Yet all tests passed on Python versions 2.5, 2.6 and 2.7. Bruce PS I do want to go through the bugs I indicated but I have not found sufficient time. Python3.1 error: Traceback (most recent call last): File "setup.py", line 201, in <module> setup_package() File "setup.py", line 178, in setup_package from numpy.distutils.core import setup File "/home/bsouthey/python/numpystuff/numpy-1.6.0b1/numpy/distutils/__init__.py", line 22, in <module> import numpy.distutils.ccompiler File "/home/bsouthey/python/numpystuff/numpy-1.6.0b1/numpy/distutils/ccompiler.py", line 15, in <module> from numpy.distutils.exec_command import exec_command File "/home/bsouthey/python/numpystuff/numpy-1.6.0b1/numpy/distutils/exec_command.py", line 58, in <module> from numpy.compat import open_latin1 File "/home/bsouthey/python/numpystuff/numpy-1.6.0b1/numpy/compat/__init__.py", line 11, in <module> import _inspect ImportError: No module named _inspect Python 2.4 failed test: $ python2.4 -c "import numpy; numpy.test()" Running unit tests for numpy NumPy version 1.6.0b1 NumPy is installed in /usr/local/lib/python2.4/site-packages/numpy Python version 2.4.6 (#1, Sep 13 2010, 15:54:12) [GCC 4.4.4 20100630 (Red Hat 4.4.4-10)] nose version 0.11.2 .............................................................................................................................................................................F...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................K.................................................................................................K......................K....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................S................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................SS............ ====================================================================== FAIL: test_iterator.test_iter_broadcasting_errors ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/local/lib/python2.4/site-packages/nose/case.py", line 186, in runTest self.test(*self.arg) File "/usr/local/lib/python2.4/site-packages/numpy/core/tests/test_iterator.py", line 639, in test_iter_broadcasting_errors 'Message "%s" doesn\'t contain operand shape (2,3)' % msg) File "/usr/local/lib/python2.4/site-packages/numpy/testing/utils.py", line 34, in assert_ raise AssertionError(msg) AssertionError: Message "non-broadcastable output operand with shape (%zd,%zd) doesn't match the broadcast shape (%zd,%zd,%zd)" doesn't contain operand shape (2,3) ---------------------------------------------------------------------- Ran 3382 tests in 19.454s FAILED (KNOWNFAIL=3, SKIP=3, failures=1)
On Wed, Mar 23, 2011 at 5:29 PM, Bruce Southey <bsouthey@gmail.com> wrote:
On 03/23/2011 11:07 AM, Ralf Gommers wrote:
Hi,
I am pleased to announce the availability of the first beta of NumPy 1.6.0. Due to the extensive changes in the Numpy core for this release, the beta testing phase will last at least one month. Please test this beta and report any problems on the Numpy mailing list.
Sources and binaries can be found at: http://sourceforge.net/projects/numpy/files/NumPy/1.6.0b1/ For (preliminary) release notes see below.
Enjoy, Ralf
[snip] Python 3.1 failed to build it due to import error of _inspect module and Python2.4 failed 'test_iterator.test_iter_broadcasting_errors'. Yet all tests passed on Python versions 2.5, 2.6 and 2.7.
Bruce PS I do want to go through the bugs I indicated but I have not found sufficient time.
Python3.1 error:
Traceback (most recent call last): File "setup.py", line 201, in <module> setup_package() File "setup.py", line 178, in setup_package from numpy.distutils.core import setup File "/home/bsouthey/python/numpystuff/numpy-1.6.0b1/numpy/distutils/__init__.py", line 22, in <module> import numpy.distutils.ccompiler File "/home/bsouthey/python/numpystuff/numpy-1.6.0b1/numpy/distutils/ccompiler.py", line 15, in <module> from numpy.distutils.exec_command import exec_command File "/home/bsouthey/python/numpystuff/numpy-1.6.0b1/numpy/distutils/exec_command.py", line 58, in <module> from numpy.compat import open_latin1 File "/home/bsouthey/python/numpystuff/numpy-1.6.0b1/numpy/compat/__init__.py", line 11, in <module> import _inspect ImportError: No module named _inspect
This is strange. I checked that numpy/compat/_inspect.py is present in the tarball. What build command did you use, and can you give the complete output of that command? Ralf
On 03/23/2011 11:38 AM, Ralf Gommers wrote:
On 03/23/2011 11:07 AM, Ralf Gommers wrote:
Hi,
I am pleased to announce the availability of the first beta of NumPy 1.6.0. Due to the extensive changes in the Numpy core for this release, the beta testing phase will last at least one month. Please test this beta and report any problems on the Numpy mailing list.
Sources and binaries can be found at: http://sourceforge.net/projects/numpy/files/NumPy/1.6.0b1/ For (preliminary) release notes see below.
Enjoy, Ralf
[snip] Python 3.1 failed to build it due to import error of _inspect module and Python2.4 failed 'test_iterator.test_iter_broadcasting_errors'. Yet all tests passed on Python versions 2.5, 2.6 and 2.7.
Bruce PS I do want to go through the bugs I indicated but I have not found sufficient time.
Python3.1 error:
Traceback (most recent call last): File "setup.py", line 201, in<module> setup_package() File "setup.py", line 178, in setup_package from numpy.distutils.core import setup File "/home/bsouthey/python/numpystuff/numpy-1.6.0b1/numpy/distutils/__init__.py", line 22, in<module> import numpy.distutils.ccompiler File "/home/bsouthey/python/numpystuff/numpy-1.6.0b1/numpy/distutils/ccompiler.py", line 15, in<module> from numpy.distutils.exec_command import exec_command File "/home/bsouthey/python/numpystuff/numpy-1.6.0b1/numpy/distutils/exec_command.py", line 58, in<module> from numpy.compat import open_latin1 File "/home/bsouthey/python/numpystuff/numpy-1.6.0b1/numpy/compat/__init__.py", line 11, in<module> import _inspect ImportError: No module named _inspect This is strange. I checked that numpy/compat/_inspect.py is present in
On Wed, Mar 23, 2011 at 5:29 PM, Bruce Southey<bsouthey@gmail.com> wrote: the tarball. What build command did you use, and can you give the complete output of that command?
Ralf _______________________________________________ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion Yes, I know that it is there and not sure what is missing! The typical way: $python3.1 setup.py build
Also I know that it builds with Python3.1 and Python 3.2 with the latest git pull! But I have update nose before I can test it. Bruce
On Wed, Mar 23, 2011 at 6:00 PM, Bruce Southey <bsouthey@gmail.com> wrote:
On 03/23/2011 11:38 AM, Ralf Gommers wrote:
On Wed, Mar 23, 2011 at 5:29 PM, Bruce Southey<bsouthey@gmail.com> wrote:
On 03/23/2011 11:07 AM, Ralf Gommers wrote:
Hi,
I am pleased to announce the availability of the first beta of NumPy 1.6.0. Due to the extensive changes in the Numpy core for this release, the beta testing phase will last at least one month. Please test this beta and report any problems on the Numpy mailing list.
Sources and binaries can be found at: http://sourceforge.net/projects/numpy/files/NumPy/1.6.0b1/ For (preliminary) release notes see below.
Enjoy, Ralf
[snip] Python 3.1 failed to build it due to import error of _inspect module and Python2.4 failed 'test_iterator.test_iter_broadcasting_errors'. Yet all tests passed on Python versions 2.5, 2.6 and 2.7.
Bruce PS I do want to go through the bugs I indicated but I have not found sufficient time.
Python3.1 error:
Traceback (most recent call last): File "setup.py", line 201, in<module> setup_package() File "setup.py", line 178, in setup_package from numpy.distutils.core import setup File
"/home/bsouthey/python/numpystuff/numpy-1.6.0b1/numpy/distutils/__init__.py", line 22, in<module> import numpy.distutils.ccompiler File
"/home/bsouthey/python/numpystuff/numpy-1.6.0b1/numpy/distutils/ccompiler.py", line 15, in<module> from numpy.distutils.exec_command import exec_command File
"/home/bsouthey/python/numpystuff/numpy-1.6.0b1/numpy/distutils/exec_command.py", line 58, in<module> from numpy.compat import open_latin1 File
"/home/bsouthey/python/numpystuff/numpy-1.6.0b1/numpy/compat/__init__.py", line 11, in<module> import _inspect ImportError: No module named _inspect
This is strange. I checked that numpy/compat/_inspect.py is present in the tarball. What build command did you use, and can you give the complete output of that command?
Ralf _______________________________________________ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
Yes, I know that it is there and not sure what is missing! The typical way: $python3.1 setup.py build
It runs 2to3, but then for some reason decides not to use the output of that on your system. Is that failing each time? If so, can you look just above where it is failing, and see what's going on before/after switching the path. Relevant code is: old_path = os.getcwd() os.chdir(src_path) sys.path.insert(0, src_path) Just inserting some print statements to look at os.getcwd() before and after and at sys.path may tell you what's going on. Ralf
Also I know that it builds with Python3.1 and Python 3.2 with the latest git pull! But I have update nose before I can test it.
On 03/23/2011 12:25 PM, Ralf Gommers wrote:
On Wed, Mar 23, 2011 at 6:00 PM, Bruce Southey<bsouthey@gmail.com> wrote:
On 03/23/2011 11:38 AM, Ralf Gommers wrote:
On 03/23/2011 11:07 AM, Ralf Gommers wrote:
Hi,
I am pleased to announce the availability of the first beta of NumPy 1.6.0. Due to the extensive changes in the Numpy core for this release, the beta testing phase will last at least one month. Please test this beta and report any problems on the Numpy mailing list.
Sources and binaries can be found at: http://sourceforge.net/projects/numpy/files/NumPy/1.6.0b1/ For (preliminary) release notes see below.
Enjoy, Ralf
[snip] Python 3.1 failed to build it due to import error of _inspect module and Python2.4 failed 'test_iterator.test_iter_broadcasting_errors'. Yet all tests passed on Python versions 2.5, 2.6 and 2.7.
Bruce PS I do want to go through the bugs I indicated but I have not found sufficient time.
Python3.1 error:
Traceback (most recent call last): File "setup.py", line 201, in<module> setup_package() File "setup.py", line 178, in setup_package from numpy.distutils.core import setup File
"/home/bsouthey/python/numpystuff/numpy-1.6.0b1/numpy/distutils/__init__.py", line 22, in<module> import numpy.distutils.ccompiler File
"/home/bsouthey/python/numpystuff/numpy-1.6.0b1/numpy/distutils/ccompiler.py", line 15, in<module> from numpy.distutils.exec_command import exec_command File
"/home/bsouthey/python/numpystuff/numpy-1.6.0b1/numpy/distutils/exec_command.py", line 58, in<module> from numpy.compat import open_latin1 File
"/home/bsouthey/python/numpystuff/numpy-1.6.0b1/numpy/compat/__init__.py", line 11, in<module> import _inspect ImportError: No module named _inspect This is strange. I checked that numpy/compat/_inspect.py is present in
On Wed, Mar 23, 2011 at 5:29 PM, Bruce Southey<bsouthey@gmail.com> wrote: the tarball. What build command did you use, and can you give the complete output of that command?
Ralf _______________________________________________ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion Yes, I know that it is there and not sure what is missing! The typical way: $python3.1 setup.py build It runs 2to3, but then for some reason decides not to use the output of that on your system. Is that failing each time? If so, can you look just above where it is failing, and see what's going on before/after switching the path. Relevant code is:
old_path = os.getcwd() os.chdir(src_path) sys.path.insert(0, src_path)
Just inserting some print statements to look at os.getcwd() before and after and at sys.path may tell you what's going on.
Ralf
Also I know that it builds with Python3.1 and Python 3.2 with the latest git pull! But I have update nose before I can test it.
NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion I can not figure out what is different between git and this version :-(
All the paths appear to be the same. Further it continues onwards when I do: $python3.1 -m pdb setup.py build I added these lines to the start of "numpy/compat/__init__.py" import os print(os.getcwd()) /home/bsouthey/python/numpystuff/tmp6/numpy-1.6.0b1/build/py3k This is equivalent to the git version. Unless someone else finds it, I will consider it just my problem and ignore it. Bruce
On Wed, 23 Mar 2011 14:17:20 -0500, Bruce Southey wrote:
I can not figure out what is different between git and this version :-(
All the paths appear to be the same. Further it continues onwards when I do: $python3.1 -m pdb setup.py build
I added these lines to the start of "numpy/compat/__init__.py" import os print(os.getcwd())
/home/bsouthey/python/numpystuff/tmp6/numpy-1.6.0b1/build/py3k This is equivalent to the git version.
Unless someone else finds it, I will consider it just my problem and ignore it.
There's some magic in setup.py for generating numpy/version.py, which behaves differently depending whether `.git` is present or not. It might do some stuff that goes wrong --- I fixed it once already, but maybe it's broken again. Pauli
On 03/23/2011 02:32 PM, Pauli Virtanen wrote:
On Wed, 23 Mar 2011 14:17:20 -0500, Bruce Southey wrote:
I can not figure out what is different between git and this version :-(
All the paths appear to be the same. Further it continues onwards when I do: $python3.1 -m pdb setup.py build
I added these lines to the start of "numpy/compat/__init__.py" import os print(os.getcwd())
/home/bsouthey/python/numpystuff/tmp6/numpy-1.6.0b1/build/py3k This is equivalent to the git version.
Unless someone else finds it, I will consider it just my problem and ignore it. There's some magic in setup.py for generating numpy/version.py, which behaves differently depending whether `.git` is present or not. It might do some stuff that goes wrong --- I fixed it once already, but maybe it's broken again.
Pauli
_______________________________________________ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion That's it! I commented out the setup.py line 'from numpy.version import git_revision as GIT_REVISION' and defined GIT_VERSION.
(I reverted to an older nose version for nose) Python3.1 passes all tests but Python3.2 has a failure but I have to cleanup my messes in case it is me. Bruce $ python3.2 -c "import numpy; numpy.test()" Running unit tests for numpy NumPy version 1.6.0b1 NumPy is installed in /usr/local/lib/python3.2/site-packages/numpy Python version 3.2 (r32:88445, Mar 23 2011, 11:36:08) [GCC 4.5.1 20100924 (Red Hat 4.5.1-4)] nose version 3.0.0 ..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................K.....................................................................Warning: invalid value encountered in true_divide Warning: invalid value encountered in true_divide Warning: invalid value encountered in true_divide .................................................................................................................K.................................................................................................K......................K..........................................................................................................STart of distr core ......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................./usr/local/lib/python3.2/site-packages/numpy/lib/format.py:575: ResourceWarning: unclosed file <_io.BufferedReader name='/tmp/tmpathakb'> mode=mode, offset=offset) ....................................................................................................................................................................................................................................................................................................................................................................................................................................................................../usr/local/lib/python3.2/subprocess.py:460: ResourceWarning: unclosed file <_io.BufferedReader name=3> return Popen(*popenargs, **kwargs).wait() /usr/local/lib/python3.2/subprocess.py:460: ResourceWarning: unclosed file <_io.BufferedReader name=8> return Popen(*popenargs, **kwargs).wait() ..............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................E........ ====================================================================== ERROR: Failure: OSError (/usr/local/lib/python3.2/site-packages/numpy/core/multiarray.pyd: cannot open shared object file: No such file or directory) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/local/lib/python3.2/site-packages/nose-3.0.0.dev-py3.2.egg/nose/failure.py", line 37, in runTest reraise(self.exc_class, self.exc_val, self.tb) File "/usr/local/lib/python3.2/site-packages/nose-3.0.0.dev-py3.2.egg/nose/_3.py", line 7, in reraise raise exc_class(exc_val).with_traceback(tb) File "/usr/local/lib/python3.2/site-packages/nose-3.0.0.dev-py3.2.egg/nose/loader.py", line 389, in loadTestsFromName addr.filename, addr.module) File "/usr/local/lib/python3.2/site-packages/nose-3.0.0.dev-py3.2.egg/nose/importer.py", line 39, in importFromPath return self.importFromDir(dir_path, fqname) File "/usr/local/lib/python3.2/site-packages/nose-3.0.0.dev-py3.2.egg/nose/importer.py", line 86, in importFromDir mod = load_module(part_fqname, fh, filename, desc) File "/usr/local/lib/python3.2/site-packages/numpy/tests/test_ctypeslib.py", line 8, in <module> cdll = load_library('multiarray', np.core.multiarray.__file__) File "/usr/local/lib/python3.2/site-packages/numpy/ctypeslib.py", line 122, in load_library raise exc File "/usr/local/lib/python3.2/site-packages/numpy/ctypeslib.py", line 119, in load_library return ctypes.cdll[libpath] File "/usr/local/lib/python3.2/ctypes/__init__.py", line 415, in __getitem__ return getattr(self, name) File "/usr/local/lib/python3.2/ctypes/__init__.py", line 410, in __getattr__ dll = self._dlltype(name) File "/usr/local/lib/python3.2/ctypes/__init__.py", line 340, in __init__ self._handle = _dlopen(self._name, mode) OSError: /usr/local/lib/python3.2/site-packages/numpy/core/multiarray.pyd: cannot open shared object file: No such file or directory
On Wed, Mar 23, 2011 at 8:32 PM, Pauli Virtanen <pav@iki.fi> wrote:
On Wed, 23 Mar 2011 14:17:20 -0500, Bruce Southey wrote:
I can not figure out what is different between git and this version :-(
All the paths appear to be the same. Further it continues onwards when I do: $python3.1 -m pdb setup.py build
I added these lines to the start of "numpy/compat/__init__.py" import os print(os.getcwd())
/home/bsouthey/python/numpystuff/tmp6/numpy-1.6.0b1/build/py3k This is equivalent to the git version.
Unless someone else finds it, I will consider it just my problem and ignore it.
There's some magic in setup.py for generating numpy/version.py, which behaves differently depending whether `.git` is present or not. It might do some stuff that goes wrong --- I fixed it once already, but maybe it's broken again.
I un-fixed your fix by accident, since I missed why you did that and your fix broke the paver script. Leaving the FULLVERSION line outside write_version_py() but putting the import inside should fix it, only the commit part will be missing when building packages for an unreleased version. Ralf
On Wed, Mar 23, 2011 at 9:29 PM, Ralf Gommers <ralf.gommers@googlemail.com> wrote:
On Wed, Mar 23, 2011 at 8:32 PM, Pauli Virtanen <pav@iki.fi> wrote:
On Wed, 23 Mar 2011 14:17:20 -0500, Bruce Southey wrote:
I can not figure out what is different between git and this version :-(
All the paths appear to be the same. Further it continues onwards when I do: $python3.1 -m pdb setup.py build
I added these lines to the start of "numpy/compat/__init__.py" import os print(os.getcwd())
/home/bsouthey/python/numpystuff/tmp6/numpy-1.6.0b1/build/py3k This is equivalent to the git version.
Unless someone else finds it, I will consider it just my problem and ignore it.
There's some magic in setup.py for generating numpy/version.py, which behaves differently depending whether `.git` is present or not. It might do some stuff that goes wrong --- I fixed it once already, but maybe it's broken again.
I un-fixed your fix by accident, since I missed why you did that and your fix broke the paver script. Leaving the FULLVERSION line outside write_version_py() but putting the import inside should fix it, only the commit part will be missing when building packages for an unreleased version.
It's a little ugly, but this seems to work for all use cases: https://github.com/rgommers/numpy/commit/a9fb1be2 Can someone please review that? Ralf
Hi again, On 23 Mar 2011, at 17:07, Ralf Gommers wrote:
I am pleased to announce the availability of the first beta of NumPy 1.6.0. Due to the extensive changes in the Numpy core for this release, the beta testing phase will last at least one month. Please test this beta and report any problems on the Numpy mailing list.
tests with the fink-installed pythons on MacOS X mostly succeeded, with one failure in python2.4 and a couple of issues seemingly related to PPC floating point accuracy, as below: OSX/Python 2.4 2.5 2.6 2.7 3.1 3.2 10.5/i386 FAIL[1] pass pass pass pass pass 10.5/ppc FAIL[1,2] FAIL[2] FAIL[2] FAIL[2] FAIL[2] FAIL[2] 10.6/x86_64 n/a pass pass pass pass pass Failures: [1] Python 2.4.4 (#1, Jan 5 2011, 03:05:41) [GCC 4.0.1 (Apple Inc. build 5493)] on darwin Type "help", "copyright", "credits" or "license" for more information.
import numpy numpy.test('full') Running unit tests for numpy NumPy version 1.6.0b1 NumPy is installed in /sw/lib/python2.4/site-packages/numpy Python version 2.4.4 (#1, Jan 5 2011, 03:05:41) [GCC 4.0.1 (Apple Inc. build 5493)] nose version 1.0.0 ........ FAIL: test_iterator.test_iter_broadcasting_errors
Traceback (most recent call last): File "/sw/lib/python2.4/site-packages/nose/case.py", line 187, in runTest self.test(*self.arg) File "/sw/lib/python2.4/site-packages/numpy/core/tests/ test_iterator.py", line 639, in test_iter_broadcasting_errors 'Message "%s" doesn\'t contain operand shape (2,3)' % msg) File "/sw/lib/python2.4/site-packages/numpy/testing/utils.py", line 34, in assert_ raise AssertionError(msg) AssertionError: Message "non-broadcastable output operand with shape (%zd,%zd) doesn't match the broadcast shape (%zd,%zd,%zd)" doesn't contain operand shape (2,3) [2] identical in Python 2.5.5 (r255:77872, Jan 4 2011, 03:26:36) Python 2.6.6 (r266:84292, Jan 4 2011, 03:36:52) Python 2.7.1 (r271:86832, Dec 17 2010, 19:39:40) Python 3.1.3 (r313:86834, Dec 17 2010, 19:49:56) Python 3.2 (r32:88445, Mar 1 2011, 18:28:16) [GCC 4.0.1 (Apple Inc. build 5493)] on darwin Type "help", "copyright", "credits" or "license" for more information.
import numpy numpy.test() Running unit tests for numpy NumPy version 1.6.0b1 NumPy is installed in /sw/lib/python3.2/site-packages/numpy Python version 3.2 (r32:88445, Mar 1 2011, 18:28:16) [GCC 4.0.1 (Apple Inc. build 5493)] nose version 1.0.0 ..............................................................................................................................................Warning : overflow encountered in add Warning: invalid value encountered in subtract Warning: invalid value encountered in subtract Warning: overflow encountered in add Warning: invalid value encountered in subtract Warning: invalid value encountered in subtract ..................................................................................................................................................................................................................................................................................................................FF ................................................................................................................................................................................................................................K .....................................................................Warning : invalid value encountered in true_divide Warning: invalid value encountered in true_divide Warning: invalid value encountered in true_divide .................................................................................................................K ...K ...........................................................F ..F.....Warning: invalid value encountered in exp .........................K ...SK .S .......S ........................................................................ ............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................./sw /lib/python3.2/site-packages/numpy/lib/format.py:575: ResourceWarning: unclosed file <_io.BufferedReader name='/scratch/derek/tmp/tmpuqv5id'> mode=mode, offset=offset) ........................................................................ ........................................................................ ........................................................................ ........................................................................ ........................................................................ ........................................................................ ......................S........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... ====================================================================== FAIL: Test basic arithmetic function errors
Traceback (most recent call last): File "/sw/lib/python3.2/site-packages/numpy/core/tests/ test_numeric.py", line 308, in test_floating_exceptions lambda a,b:a/b, ft_tiny, ft_max) File "/sw/lib/python3.2/site-packages/numpy/core/tests/ test_numeric.py", line 261, in assert_raises_fpe "Type %s did not raise fpe error '%s'." % (ftype, fpeerr)) File "/sw/lib/python3.2/site-packages/numpy/testing/utils.py", line 34, in assert_ raise AssertionError(msg) AssertionError: Type <class 'numpy.float128'> did not raise fpe error 'underflow'. ====================================================================== FAIL: Test basic arithmetic function errors ---------------------------------------------------------------------- Traceback (most recent call last): File "/sw/lib/python3.2/site-packages/numpy/testing/decorators.py", line 216, in knownfailer return f(*args, **kwargs) File "/sw/lib/python3.2/site-packages/numpy/core/tests/ test_numeric.py", line 352, in test_floating_exceptions_power np.power, ftype(2), ftype(2**fi.nexp)) File "/sw/lib/python3.2/site-packages/numpy/core/tests/ test_numeric.py", line 261, in assert_raises_fpe "Type %s did not raise fpe error '%s'." % (ftype, fpeerr)) File "/sw/lib/python3.2/site-packages/numpy/testing/utils.py", line 34, in assert_ raise AssertionError(msg) AssertionError: Type <class 'numpy.float128'> did not raise fpe error 'overflow'. ====================================================================== FAIL: test_umath.test_nextafterl ---------------------------------------------------------------------- Traceback (most recent call last): File "/sw/lib/python3.2/site-packages/nose/case.py", line 188, in runTest self.test(*self.arg) File "/sw/lib/python3.2/site-packages/numpy/testing/decorators.py", line 216, in knownfailer return f(*args, **kwargs) File "/sw/lib/python3.2/site-packages/numpy/core/tests/ test_umath.py", line 1085, in test_nextafterl return _test_nextafter(np.longdouble) File "/sw/lib/python3.2/site-packages/numpy/core/tests/ test_umath.py", line 1071, in _test_nextafter assert np.nextafter(one, two) - one == eps AssertionError ====================================================================== FAIL: test_umath.test_spacingl ---------------------------------------------------------------------- Traceback (most recent call last): File "/sw/lib/python3.2/site-packages/nose/case.py", line 188, in runTest self.test(*self.arg) File "/sw/lib/python3.2/site-packages/numpy/testing/decorators.py", line 216, in knownfailer return f(*args, **kwargs) File "/sw/lib/python3.2/site-packages/numpy/core/tests/ test_umath.py", line 1110, in test_spacingl return _test_spacing(np.longdouble) File "/sw/lib/python3.2/site-packages/numpy/core/tests/ test_umath.py", line 1094, in _test_spacing assert np.spacing(one) == eps AssertionError ---------------------------------------------------------------------- Ran 3362 tests in 64.845s FAILED (KNOWNFAIL=5, SKIP=4, failures=4)
On 24 Mar 2011, at 00:34, Derek Homeier wrote:
tests with the fink-installed pythons on MacOS X mostly succeeded, with one failure in python2.4 and a couple of issues seemingly related to PPC floating point accuracy, as below:
Probably last update for tonight: with the 'full' test suite, there's one additional failure and error, respectively under 10.5/ppc and 10.6/x86_64 (in all Python versions): PowerPC: FAIL: test_kind.TestKind.test_all ---------------------------------------------------------------------- Traceback (most recent call last): File "/sw/lib/python2.5/site-packages/nose/case.py", line 187, in runTest self.test(*self.arg) File "/sw/lib/python2.5/site-packages/numpy/f2py/tests/test_kind.py", line 30, in test_all 'selectedrealkind(%s): expected %r but got %r' % (i, selected_real_kind(i), selectedrealkind(i))) File "/sw/lib/python2.5/site-packages/numpy/testing/utils.py", line 34, in assert_ raise AssertionError(msg) AssertionError: selectedrealkind(16): expected 10 but got 16 Intel-64bit: ERROR: test_assumed_shape.TestAssumedShapeSumExample.test_all ---------------------------------------------------------------------- Traceback (most recent call last): File "/sw/lib/python3.2/site-packages/nose/case.py", line 372, in setUp try_run(self.inst, ('setup', 'setUp')) File "/sw/lib/python3.2/site-packages/nose/util.py", line 478, in try_run return func() File "/sw/lib/python3.2/site-packages/numpy/f2py/tests/util.py", line 352, in setUp module_name=self.module_name) File "/sw/lib/python3.2/site-packages/numpy/f2py/tests/util.py", line 73, in wrapper memo[key] = func(*a, **kw) File "/sw/lib/python3.2/site-packages/numpy/f2py/tests/util.py", line 134, in build_module % (cmd[4:], asstr(out))) RuntimeError: Running f2py failed: ['-m', '_test_ext_module_5403', '/var/folders/DC/DC7g9UNr2RWkb++8ZSn1J+++0Dk/-Tmp-/tmpfiy1jn/foo_free.f90', '/var/folders/DC/DC7g9UNr2RWkb++8ZSn1J+++0Dk/-Tmp-/tmpfiy1jn/foo_use.f90', '/var/folders/DC/DC7g9UNr2RWkb++8ZSn1J+++0Dk/-Tmp-/tmpfiy1jn/precision.f90'] Reading .f2py_f2cmap ... Mapping "real(kind=rk)" to "double" Succesfully applied user defined changes from .f2py_f2cmap running build running config_cc unifing config_cc, config, build_clib, build_ext, build commands --compiler options running config_fc unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options running build_src build_src building extension "_test_ext_module_5403" sources f2py options: [] f2py:> /var/folders/DC/DC7g9UNr2RWkb++8ZSn1J+++0Dk/-Tmp-/tmpv567as/src.macosx-10.6-x86_64-3.2/_test_ext_module_5403module.c creating /var/folders/DC/DC7g9UNr2RWkb++8ZSn1J+++0Dk/-Tmp-/tmpv567as creating /var/folders/DC/DC7g9UNr2RWkb++8ZSn1J+++0Dk/-Tmp-/tmpv567as/src.macosx-10.6-x86_64-3.2 Reading fortran codes... Reading file '/var/folders/DC/DC7g9UNr2RWkb++8ZSn1J+++0Dk/-Tmp-/tmpfiy1jn/foo_free.f90' (format:free) Reading file '/var/folders/DC/DC7g9UNr2RWkb++8ZSn1J+++0Dk/-Tmp-/tmpfiy1jn/foo_use.f90' (format:free) Reading file '/var/folders/DC/DC7g9UNr2RWkb++8ZSn1J+++0Dk/-Tmp-/tmpfiy1jn/precision.f90' (format:free) Post-processing... Block: _test_ext_module_5403 Block: sum Block: fsum Block: sum_with_use Block: precision Post-processing (stage 2)... Block: _test_ext_module_5403 Block: unknown_interface Block: sum Block: fsum Block: sum_with_use Block: precision Building modules... Building module "_test_ext_module_5403"... Creating wrapper for Fortran subroutine "sum"("sum")... Constructing wrapper function "sum"... res = sum(x) Creating wrapper for Fortran function "fsum"("fsum")... Constructing wrapper function "fsum"... res = fsum(x) Creating wrapper for Fortran subroutine "sum_with_use"("sum_with_use")... Constructing wrapper function "sum_with_use"... res = sum_with_use(x) Constructing F90 module support for "precision"... Variables: ik rk Wrote C/API module "_test_ext_module_5403" to file "/var/folders/DC/DC7g9UNr2RWkb++8ZSn1J+++0Dk/- [skipping additional compiler output] compiling Fortran sources Fortran f77 compiler: /sw/bin/gfortran -Wall -ffixed-form -fno-second-underscore -fPIC -O3 -funroll-loops Fortran f90 compiler: /sw/bin/gfortran -Wall -fno-second-underscore -fPIC -O3 -funroll-loops Fortran fix compiler: /sw/bin/gfortran -Wall -ffixed-form -fno-second-underscore -Wall -fno-second-underscore -fPIC -O3 -funroll-loops compile options: '-I/var/folders/DC/DC7g9UNr2RWkb++8ZSn1J+++0Dk/-Tmp-/tmpv567as/src.macosx-10.6-x86_64-3.2 -I/sw/lib/python3.2/site-packages/numpy/core/include -I/sw/include/python3.2m -c' extra options: '-J/var/folders/DC/DC7g9UNr2RWkb++8ZSn1J+++0Dk/-Tmp-/tmpv567as/ -I/var/folders/DC/DC7g9UNr2RWkb++8ZSn1J+++0Dk/-Tmp-/tmpv567as/' gfortran:f90: /var/folders/DC/DC7g9UNr2RWkb++8ZSn1J+++0Dk/-Tmp-/tmpfiy1jn/foo_free.f90 gfortran:f90: /var/folders/DC/DC7g9UNr2RWkb++8ZSn1J+++0Dk/-Tmp-/tmpfiy1jn/foo_use.f90 gfortran:f77: /var/folders/DC/DC7g9UNr2RWkb++8ZSn1J+++0Dk/-Tmp-/tmpv567as/src.macosx-10.6-x86_64-3.2/_test_ext_module_5403-f2pywrappers.f /var/folders/DC/DC7g9UNr2RWkb++8ZSn1J+++0Dk/-Tmp-/tmpv567as/src.macosx-10.6-x86_64-3.2/_test_ext_module_5403-f2pywrappers.f:26.21: real :: res 1 Error: Symbol 'res' at (1) already has basic type of REAL /var/folders/DC/DC7g9UNr2RWkb++8ZSn1J+++0Dk/-Tmp-/tmpv567as/src.macosx-10.6-x86_64-3.2/_test_ext_module_5403-f2pywrappers.f:26.21: real :: res 1 Error: Symbol 'res' at (1) already has basic type of REAL error: Command "/sw/bin/gfortran -Wall -ffixed-form -fno-second-underscore -fPIC -O3 -funroll-loops -I/var/folders/DC/DC7g9UNr2RWkb++8ZSn1J+++0Dk/-Tmp-/tmpv567as/src.macosx-10.6-x86_64-3.2 -I/sw/lib/python3.2/site-packages/numpy/core/include -I/sw/include/python3.2m -c -c /var/folders/DC/DC7g9UNr2RWkb++8ZSn1J+++0Dk/-Tmp-/tmpv567as/src.macosx-10.6-x86_64-3.2/_test_ext_module_5403-f2pywrappers.f -o /var/folders/DC/DC7g9UNr2RWkb++8ZSn1J+++0Dk/-Tmp-/tmpv567as/var/folders/DC/DC7g9UNr2RWkb++8ZSn1J+++0Dk/-Tmp-/tmpv567as/src.macosx-10.6-x86_64-3.2/_test_ext_module_5403-f2pywrappers.o -J/var/folders/DC/DC7g9UNr2RWkb++8ZSn1J+++0Dk/-Tmp-/tmpv567as/ -I/var/folders/DC/DC7g9UNr2RWkb++8ZSn1J+++0Dk/-Tmp-/tmpv567as/" failed with exit status 1 ---------------------------------------------------------------------- Ran 3415 tests in 75.507s FAILED (KNOWNFAIL=4, SKIP=1, errors=1)
On Thu, Mar 24, 2011 at 2:04 AM, Derek Homeier < derek@astro.physik.uni-goettingen.de> wrote:
On 24 Mar 2011, at 00:34, Derek Homeier wrote:
tests with the fink-installed pythons on MacOS X mostly succeeded, with one failure in python2.4 and a couple of issues seemingly related to PPC floating point accuracy, as below:
Probably last update for tonight: with the 'full' test suite, there's one additional failure and error, respectively under 10.5/ppc and 10.6/x86_64 (in all Python versions):
PowerPC:
FAIL: test_kind.TestKind.test_all ---------------------------------------------------------------------- Traceback (most recent call last): File "/sw/lib/python2.5/site-packages/nose/case.py", line 187, in runTest self.test(*self.arg) File "/sw/lib/python2.5/site-packages/numpy/f2py/tests/test_kind.py", line 30, in test_all 'selectedrealkind(%s): expected %r but got %r' % (i, selected_real_kind(i), selectedrealkind(i))) File "/sw/lib/python2.5/site-packages/numpy/testing/utils.py", line 34, in assert_ raise AssertionError(msg) AssertionError: selectedrealkind(16): expected 10 but got 16
Regarding this test failure, could you hack the numpy/f2py/tests/test_kind.py script by adding the following code for i in range(20): print '%s -> %s, %s' % (i, selected_real_kind(i), selectedrealkind(i)) and send me the output? Also, what Fortran compiler version has been used to build the test modules?
Intel-64bit: ERROR: test_assumed_shape.TestAssumedShapeSumExample.test_all ---------------------------------------------------------------------- Traceback (most recent call last): File "/sw/lib/python3.2/site-packages/nose/case.py", line 372, in setUp try_run(self.inst, ('setup', 'setUp')) File "/sw/lib/python3.2/site-packages/nose/util.py", line 478, in try_run return func() File "/sw/lib/python3.2/site-packages/numpy/f2py/tests/util.py", line 352, in setUp module_name=self.module_name) File "/sw/lib/python3.2/site-packages/numpy/f2py/tests/util.py", line 73, in wrapper memo[key] = func(*a, **kw) File "/sw/lib/python3.2/site-packages/numpy/f2py/tests/util.py", line 134, in build_module % (cmd[4:], asstr(out))) RuntimeError: Running f2py failed: ['-m', '_test_ext_module_5403', '/var/folders/DC/DC7g9UNr2RWkb++8ZSn1J+++0Dk/-Tmp-/tmpfiy1jn/foo_free.f90', '/var/folders/DC/DC7g9UNr2RWkb++8ZSn1J+++0Dk/-Tmp-/tmpfiy1jn/foo_use.f90', '/var/folders/DC/DC7g9UNr2RWkb++8ZSn1J+++0Dk/-Tmp-/tmpfiy1jn/precision.f90']
Reading .f2py_f2cmap ... Mapping "real(kind=rk)" to "double" Hmm, this should not happen as real(kind=rk) should be mapped to "float". It seems that you have .f2py_f2cmap file lying around. Could you remove it and try again. Pearu
On Thu, Mar 24, 2011 at 10:11 AM, Pearu Peterson <pearu.peterson@gmail.com>wrote:
Regarding this test failure, could you hack the numpy/f2py/tests/test_kind.py script by adding the following code
for i in range(20): print '%s -> %s, %s' % (i, selected_real_kind(i), selectedrealkind(i))
and send me the output? Also, what Fortran compiler version has been used to build the test modules?
Even better, you can report the result to http://projects.scipy.org/numpy/ticket/1767 Pearu
On 24.03.2011, at 9:11AM, Pearu Peterson wrote:
Intel-64bit: ERROR: test_assumed_shape.TestAssumedShapeSumExample.test_all ---------------------------------------------------------------------- Traceback (most recent call last): File "/sw/lib/python3.2/site-packages/nose/case.py", line 372, in setUp try_run(self.inst, ('setup', 'setUp')) File "/sw/lib/python3.2/site-packages/nose/util.py", line 478, in try_run return func() File "/sw/lib/python3.2/site-packages/numpy/f2py/tests/util.py", line 352, in setUp module_name=self.module_name) File "/sw/lib/python3.2/site-packages/numpy/f2py/tests/util.py", line 73, in wrapper memo[key] = func(*a, **kw) File "/sw/lib/python3.2/site-packages/numpy/f2py/tests/util.py", line 134, in build_module % (cmd[4:], asstr(out))) RuntimeError: Running f2py failed: ['-m', '_test_ext_module_5403', '/var/folders/DC/DC7g9UNr2RWkb++8ZSn1J+++0Dk/-Tmp-/tmpfiy1jn/foo_free.f90', '/var/folders/DC/DC7g9UNr2RWkb++8ZSn1J+++0Dk/-Tmp-/tmpfiy1jn/foo_use.f90', '/var/folders/DC/DC7g9UNr2RWkb++8ZSn1J+++0Dk/-Tmp-/tmpfiy1jn/precision.f90'] Reading .f2py_f2cmap ... Mapping "real(kind=rk)" to "double"
Hmm, this should not happen as real(kind=rk) should be mapped to "float". It seems that you have .f2py_f2cmap file lying around. Could you remove it and try again.
Yes, it's in the tarball and was installed together with the f2py tests! tar tzvf /sw/src/numpy-1.6.0b1.tar.gz | grep f2py_f2 -rw-r--r-- zouzoujing/staff 29 2011-03-15 06:22 numpy-1.6.0b1/numpy/f2py/tests/src/assumed_shape/.f2py_f2cmap cat /sw/lib/python3.2/site-packages/numpy/f2py/tests/src/assumed_shape/.f2py_f2cmap dict(real=dict(rk="double")) But still after removing all installed instances of the file and even removing it from the tarball prior to rebuilding numpy, the test apparently keeps re-creating it in its own tmpdir: building extension "_test_ext_module_5403" sources f2py options: [] f2py:> /var/folders/DC/DC7g9UNr2RWkb++8ZSn1J+++0Dk/-Tmp-/tmpS4KGum/src.macosx-10.6-x86_64-2.7/_test_ext_module_5403module.c creating /var/folders/DC/DC7g9UNr2RWkb++8ZSn1J+++0Dk/-Tmp-/tmpS4KGum creating /var/folders/DC/DC7g9UNr2RWkb++8ZSn1J+++0Dk/-Tmp-/tmpS4KGum/src.macosx-10.6-x86_64-2.7 getctype: "real(kind=rk)" is mapped to C "float" (to override define dict(real = dict(rk="<C typespec>")) in /private/var/folders/DC/DC7g9UNr2RWkb++8ZSn1J+++0Dk/-Tmp-/tmpPo744G/.f2py_f2cmap file). ... gfortran:f77: /var/folders/DC/DC7g9UNr2RWkb++8ZSn1J+++0Dk/-Tmp-/tmpS4KGum/src.macosx-10.6-x86_64-2.7/_test_ext_module_5403-f2pywrappers.f /var/folders/DC/DC7g9UNr2RWkb++8ZSn1J+++0Dk/-Tmp-/tmpS4KGum/src.macosx-10.6-x86_64-2.7/_test_ext_module_5403-f2pywrappers.f:26.21: real :: res 1 Error: Symbol 'res' at (1) already has basic type of REAL /var/folders/DC/DC7g9UNr2RWkb++8ZSn1J+++0Dk/-Tmp-/tmpS4KGum/src.macosx-10.6-x86_64-2.7/_test_ext_module_5403-f2pywrappers.f:26.21: real :: res 1 Error: Symbol 'res' at (1) already has basic type of REAL ... f2py is the one installed with this numpy version, gfortran is COLLECT_GCC=/sw/bin/gfortran COLLECT_LTO_WRAPPER=/sw/lib/gcc4.5/libexec/gcc/x86_64-apple-darwin10.6.0/4.5.2/lto-wrapper Ziel: x86_64-apple-darwin10.6.0 Konfiguriert mit: ../gcc-4.5.2/configure --prefix=/sw --prefix=/sw/lib/gcc4.5 --mandir=/sw/share/man --infodir=/sw/lib/gcc4.5/info --enable-languages=c,c++,fortran,objc,obj-c++,java --with-gmp=/sw --with-libiconv-prefix=/sw --with-ppl=/sw --with-cloog=/sw --with-mpc=/sw --with-system-zlib --x-includes=/usr/X11R6/include --x-libraries=/usr/X11R6/lib --program-suffix=-fsf-4.5 --enable-lto Thread-Modell: posix gcc-Version 4.5.2 (GCC) Any more ideas? Thanks, Derek
On Fri, Mar 25, 2011 at 1:44 AM, Derek Homeier < derek@astro.physik.uni-goettingen.de> wrote:
On 24.03.2011, at 9:11AM, Pearu Peterson wrote:
Intel-64bit: ERROR: test_assumed_shape.TestAssumedShapeSumExample.test_all ---------------------------------------------------------------------- Traceback (most recent call last): File "/sw/lib/python3.2/site-packages/nose/case.py", line 372, in setUp try_run(self.inst, ('setup', 'setUp')) File "/sw/lib/python3.2/site-packages/nose/util.py", line 478, in
try_run
return func() File "/sw/lib/python3.2/site-packages/numpy/f2py/tests/util.py", line 352, in setUp module_name=self.module_name) File "/sw/lib/python3.2/site-packages/numpy/f2py/tests/util.py", line 73, in wrapper memo[key] = func(*a, **kw) File "/sw/lib/python3.2/site-packages/numpy/f2py/tests/util.py", line 134, in build_module % (cmd[4:], asstr(out))) RuntimeError: Running f2py failed: ['-m', '_test_ext_module_5403', '/var/folders/DC/DC7g9UNr2RWkb++8ZSn1J+++0Dk/-Tmp-/tmpfiy1jn/foo_free.f90', '/var/folders/DC/DC7g9UNr2RWkb++8ZSn1J+++0Dk/-Tmp-/tmpfiy1jn/foo_use.f90', '/var/folders/DC/DC7g9UNr2RWkb++8ZSn1J+++0Dk/-Tmp-/tmpfiy1jn/precision.f90'] Reading .f2py_f2cmap ... Mapping "real(kind=rk)" to "double"
Hmm, this should not happen as real(kind=rk) should be mapped to "float". It seems that you have .f2py_f2cmap file lying around. Could you remove it and try again.
Yes, it's in the tarball and was installed together with the f2py tests!
Indeed, f2py tests suite contains the .f2py_f2cmap file. Its effect should be local to the corresponding test but it seems not. I'll look into it..
building extension "_test_ext_module_5403" sources f2py options: [] f2py:> /var/folders/DC/DC7g9UNr2RWkb++8ZSn1J+++0Dk/-Tmp-/tmpS4KGum/src.macosx-10.6-x86_64-2.7/_test_ext_module_5403module.c creating /var/folders/DC/DC7g9UNr2RWkb++8ZSn1J+++0Dk/-Tmp-/tmpS4KGum creating /var/folders/DC/DC7g9UNr2RWkb++8ZSn1J+++0Dk/-Tmp-/tmpS4KGum/src.macosx-10.6-x86_64-2.7 getctype: "real(kind=rk)" is mapped to C "float" (to override define dict(real = dict(rk="<C typespec>")) in /private/var/folders/DC/DC7g9UNr2RWkb++8ZSn1J+++0Dk/-Tmp-/tmpPo744G/.f2py_f2cmap file). ... gfortran:f77: /var/folders/DC/DC7g9UNr2RWkb++8ZSn1J+++0Dk/-Tmp-/tmpS4KGum/src.macosx-10.6-x86_64-2.7/_test_ext_module_5403-f2pywrappers.f
/var/folders/DC/DC7g9UNr2RWkb++8ZSn1J+++0Dk/-Tmp-/tmpS4KGum/src.macosx-10.6-x86_64-2.7/_test_ext_module_5403-f2pywrappers.f:26.21:
real :: res 1 Error: Symbol 'res' at (1) already has basic type of REAL
/var/folders/DC/DC7g9UNr2RWkb++8ZSn1J+++0Dk/-Tmp-/tmpS4KGum/src.macosx-10.6-x86_64-2.7/_test_ext_module_5403-f2pywrappers.f:26.21:
real :: res 1 Error: Symbol 'res' at (1) already has basic type of REAL ...
f2py is the one installed with this numpy version, gfortran is COLLECT_GCC=/sw/bin/gfortran
COLLECT_LTO_WRAPPER=/sw/lib/gcc4.5/libexec/gcc/x86_64-apple-darwin10.6.0/4.5.2/lto-wrapper Ziel: x86_64-apple-darwin10.6.0 Konfiguriert mit: ../gcc-4.5.2/configure --prefix=/sw --prefix=/sw/lib/gcc4.5 --mandir=/sw/share/man --infodir=/sw/lib/gcc4.5/info --enable-languages=c,c++,fortran,objc,obj-c++,java --with-gmp=/sw --with-libiconv-prefix=/sw --with-ppl=/sw --with-cloog=/sw --with-mpc=/sw --with-system-zlib --x-includes=/usr/X11R6/include --x-libraries=/usr/X11R6/lib --program-suffix=-fsf-4.5 --enable-lto Thread-Modell: posix gcc-Version 4.5.2 (GCC)
Can you send me the _test_ext_module_5403-f2pywrappers.f file. It should exist there when the compilation fails. Pearu
On Thu, Mar 24, 2011 at 12:34 AM, Derek Homeier <derek@astro.physik.uni-goettingen.de> wrote:
Hi again,
On 23 Mar 2011, at 17:07, Ralf Gommers wrote:
I am pleased to announce the availability of the first beta of NumPy 1.6.0. Due to the extensive changes in the Numpy core for this release, the beta testing phase will last at least one month. Please test this beta and report any problems on the Numpy mailing list.
tests with the fink-installed pythons on MacOS X mostly succeeded, with one failure in python2.4 and a couple of issues seemingly related to PPC floating point accuracy, as below:
OSX/Python 2.4 2.5 2.6 2.7 3.1 3.2 10.5/i386 FAIL[1] pass pass pass pass pass 10.5/ppc FAIL[1,2] FAIL[2] FAIL[2] FAIL[2] FAIL[2] FAIL[2] 10.6/x86_64 n/a pass pass pass pass pass
Failures: [1] Python 2.4.4 (#1, Jan 5 2011, 03:05:41) [GCC 4.0.1 (Apple Inc. build 5493)] on darwin Type "help", "copyright", "credits" or "license" for more information. >>> import numpy >>> numpy.test('full') Running unit tests for numpy NumPy version 1.6.0b1 NumPy is installed in /sw/lib/python2.4/site-packages/numpy Python version 2.4.4 (#1, Jan 5 2011, 03:05:41) [GCC 4.0.1 (Apple Inc. build 5493)] nose version 1.0.0 ........ FAIL: test_iterator.test_iter_broadcasting_errors ---------------------------------------------------------------------- Traceback (most recent call last): File "/sw/lib/python2.4/site-packages/nose/case.py", line 187, in runTest self.test(*self.arg) File "/sw/lib/python2.4/site-packages/numpy/core/tests/ test_iterator.py", line 639, in test_iter_broadcasting_errors 'Message "%s" doesn\'t contain operand shape (2,3)' % msg) File "/sw/lib/python2.4/site-packages/numpy/testing/utils.py", line 34, in assert_ raise AssertionError(msg) AssertionError: Message "non-broadcastable output operand with shape (%zd,%zd) doesn't match the broadcast shape (%zd,%zd,%zd)" doesn't contain operand shape (2,3)
Mark just committed a fix for this, could you test the current 1.6.x branch to see if that worked and report on http://projects.scipy.org/numpy/ticket/1780? Thanks, Ralf
In article <AANLkTi=eeg8KL7639imRTL-iHg1ncqYoLDDSiD5tfYvs@mail.gmail.com>, Ralf Gommers <ralf.gommers@googlemail.com> wrote:
Hi,
I am pleased to announce the availability of the first beta of NumPy 1.6.0. Due to the extensive changes in the Numpy core for this release, the beta testing phase will last at least one month. Please test this beta and report any problems on the Numpy mailing list.
Sources and binaries can be found at: http://sourceforge.net/projects/numpy/files/NumPy/1.6.0b1/ For (preliminary) release notes see below.
Great! FYI: it works for me on MacOS X 10.5.8 with python.org python 2.6.6: python setup.py build --fcompiler=gnu95 python setup.py install cd .. python -Wd -c 'import numpy; numpy.test()' NumPy version 1.6.0b1 NumPy is installed in /Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-pack ages/numpy Python version 2.6.6 (r266:84374, Aug 31 2010, 11:00:51) [GCC 4.0.1 (Apple Inc. build 5493)] nose version 0.11.4 ... Ran 3399 tests in 25.474s OK (KNOWNFAIL=3, SKIP=1) -- Russell
On Wed, Mar 30, 2011 at 7:22 AM, Russell E. Owen <rowen@uw.edu> wrote:
In article <AANLkTi=eeg8KL7639imRTL-iHg1ncqYoLDDSiD5tfYvs@mail.gmail.com>, Ralf Gommers <ralf.gommers@googlemail.com> wrote:
Hi,
I am pleased to announce the availability of the first beta of NumPy 1.6.0. Due to the extensive changes in the Numpy core for this release, the beta testing phase will last at least one month. Please test this beta and report any problems on the Numpy mailing list.
Sources and binaries can be found at: http://sourceforge.net/projects/numpy/files/NumPy/1.6.0b1/ For (preliminary) release notes see below.
I see a segfault on Ubuntu 64 bits for the test TestAssumedShapeSumExample in numpy/f2py/tests/test_assumed_shape.py. Am I the only one seeing it ? David
On Thu, Mar 31, 2011 at 12:19 PM, David Cournapeau <cournape@gmail.com>wrote:
On Wed, Mar 30, 2011 at 7:22 AM, Russell E. Owen <rowen@uw.edu> wrote:
In article <AANLkTi=eeg8KL7639imRTL-iHg1ncqYoLDDSiD5tfYvs@mail.gmail.com>, Ralf Gommers <ralf.gommers@googlemail.com> wrote:
Hi,
I am pleased to announce the availability of the first beta of NumPy 1.6.0. Due to the extensive changes in the Numpy core for this release, the beta testing phase will last at least one month. Please test this beta and report any problems on the Numpy mailing list.
Sources and binaries can be found at: http://sourceforge.net/projects/numpy/files/NumPy/1.6.0b1/ For (preliminary) release notes see below.
I see a segfault on Ubuntu 64 bits for the test TestAssumedShapeSumExample in numpy/f2py/tests/test_assumed_shape.py. Am I the only one seeing it ?
The test work here ok on Ubuntu 64 with numpy master. Could you try the maintenance/1.6.x branch where the related bugs are fixed. Pearu
On 31 March 2011 11:37, Pearu Peterson <pearu.peterson@gmail.com> wrote:
On Thu, Mar 31, 2011 at 12:19 PM, David Cournapeau <cournape@gmail.com> wrote:
On Wed, Mar 30, 2011 at 7:22 AM, Russell E. Owen <rowen@uw.edu> wrote:
In article <AANLkTi=eeg8KL7639imRTL-iHg1ncqYoLDDSiD5tfYvs@mail.gmail.com>, Ralf Gommers <ralf.gommers@googlemail.com> wrote:
Hi,
I am pleased to announce the availability of the first beta of NumPy 1.6.0. Due to the extensive changes in the Numpy core for this release, the beta testing phase will last at least one month. Please test this beta and report any problems on the Numpy mailing list.
Sources and binaries can be found at: http://sourceforge.net/projects/numpy/files/NumPy/1.6.0b1/ For (preliminary) release notes see below.
I see a segfault on Ubuntu 64 bits for the test TestAssumedShapeSumExample in numpy/f2py/tests/test_assumed_shape.py. Am I the only one seeing it ?
The test work here ok on Ubuntu 64 with numpy master. Could you try the maintenance/1.6.x branch where the related bugs are fixed.
For what it's worth, the maintenance/1.6.x branch works for me on 64-bit Ubuntu: (numpy-1.6.x)scott@godzilla:~$ python -c "import numpy; numpy.test()" Running unit tests for numpy NumPy version 1.6.0b2.dev-a172fd6 NumPy is installed in /home/scott/.virtualenvs/numpy-1.6.x/lib/python2.6/site-packages/numpy Python version 2.6.6 (r266:84292, Sep 15 2010, 16:22:56) [GCC 4.4.5] nose version 1.0.0 <snip...> ---------------------------------------------------------------------- Ran 3406 tests in 16.889s OK (KNOWNFAIL=3, SKIP=4) Cheers, Scott
On Thu, Mar 31, 2011 at 1:00 PM, Scott Sinclair <scott.sinclair.za@gmail.com
wrote:
On 31 March 2011 11:37, Pearu Peterson <pearu.peterson@gmail.com> wrote:
On Thu, Mar 31, 2011 at 12:19 PM, David Cournapeau <cournape@gmail.com> wrote:
On Wed, Mar 30, 2011 at 7:22 AM, Russell E. Owen <rowen@uw.edu> wrote:
In article <AANLkTi=eeg8KL7639imRTL-iHg1ncqYoLDDSiD5tfYvs@mail.gmail.com>, Ralf Gommers <ralf.gommers@googlemail.com> wrote:
Hi,
I am pleased to announce the availability of the first beta of NumPy 1.6.0. Due to the extensive changes in the Numpy core for this release, the beta testing phase will last at least one month. Please test this beta and report any problems on the Numpy mailing list.
Sources and binaries can be found at: http://sourceforge.net/projects/numpy/files/NumPy/1.6.0b1/ For (preliminary) release notes see below.
I see a segfault on Ubuntu 64 bits for the test TestAssumedShapeSumExample in numpy/f2py/tests/test_assumed_shape.py. Am I the only one seeing it ?
The test work here ok on Ubuntu 64 with numpy master. Could you try the maintenance/1.6.x branch where the related bugs are fixed.
For what it's worth, the maintenance/1.6.x branch works for me on 64-bit Ubuntu:
(numpy-1.6.x)scott@godzilla:~$ python -c "import numpy; numpy.test()"
You might want to run python -c "import numpy; numpy.test('full')" as the corresponding test is decorated as slow. Pearu
On 31 March 2011 12:18, Pearu Peterson <pearu.peterson@gmail.com> wrote:
On Thu, Mar 31, 2011 at 1:00 PM, Scott Sinclair <scott.sinclair.za@gmail.com> wrote:
For what it's worth, the maintenance/1.6.x branch works for me on 64-bit Ubuntu:
(numpy-1.6.x)scott@godzilla:~$ python -c "import numpy; numpy.test()"
You might want to run
python -c "import numpy; numpy.test('full')"
as the corresponding test is decorated as slow.
python -c "import numpy; numpy.test('full')" Running unit tests for numpy NumPy version 1.6.0b2.dev-a172fd6 NumPy is installed in /home/scott/.virtualenvs/numpy-1.6.x/lib/python2.6/site-packages/numpy Python version 2.6.6 (r266:84292, Sep 15 2010, 16:22:56) [GCC 4.4.5] nose version 1.0.0 <snip...> Ran 3423 tests in 28.713s OK (KNOWNFAIL=3, SKIP=4) Cheers, Scott
On 03/31/2011 06:37 PM, Pearu Peterson wrote:
On Thu, Mar 31, 2011 at 12:19 PM, David Cournapeau <cournape@gmail.com <mailto:cournape@gmail.com>> wrote:
On Wed, Mar 30, 2011 at 7:22 AM, Russell E. Owen <rowen@uw.edu <mailto:rowen@uw.edu>> wrote: > In article > <AANLkTi=eeg8KL7639imRTL-iHg1ncqYoLDDSiD5tfYvs@mail.gmail.com <mailto:eeg8KL7639imRTL-iHg1ncqYoLDDSiD5tfYvs@mail.gmail.com>>, > Ralf Gommers <ralf.gommers@googlemail.com <mailto:ralf.gommers@googlemail.com>> wrote: > >> Hi, >> >> I am pleased to announce the availability of the first beta of NumPy >> 1.6.0. Due to the extensive changes in the Numpy core for this >> release, the beta testing phase will last at least one month. Please >> test this beta and report any problems on the Numpy mailing list. >> >> Sources and binaries can be found at: >> http://sourceforge.net/projects/numpy/files/NumPy/1.6.0b1/ >> For (preliminary) release notes see below.
I see a segfault on Ubuntu 64 bits for the test TestAssumedShapeSumExample in numpy/f2py/tests/test_assumed_shape.py. Am I the only one seeing it ?
The test work here ok on Ubuntu 64 with numpy master. Could you try the maintenance/1.6.x branch where the related bugs are fixed.
I did test that as well, and got the same issue, but could not reproduce it on another machine. I do get the error every time on my main work machine, though. I will look more into it, but it is most likely something due to my machine, cheers, David
Ralf Gommers, on 2011-03-23 17:07, wrote:
Please test this beta and report any problems on the Numpy mailing list.
Hi, I reopened http://projects.scipy.org/numpy/ticket/1768, as 'test_chisquare' still fails for me on a 32 bit machine. Lowering the precision from 14 to 13 decimals makes the test pass, however. Other than that: NumPy version 1.6.0b1 NumPy is installed in /home/pi/.local/lib/python2.6/site-packages/numpy Python version 2.6.5 (r265:79063, Apr 16 2010, 13:09:56) [GCC 4.4.3] nose version 0.11.1 --snip-- Ran 3399 tests in 23.052s FAILED (KNOWNFAIL=3, SKIP=4, failures=1) best, -- Paul Ivanov 314 address only used for lists, off-list direct email at: http://pirsquared.org | GPG/PGP key id: 0x0F3E28F7
Hi, I'd like to backport the following fixes to the 1.6.x branch for b2: ef46a091 89db53b1 They're bugs in PEP 3118 format string generation, of the brown paper-pag variety. Pauli
On Sat, Apr 2, 2011 at 12:41 PM, Pauli Virtanen <pav@iki.fi> wrote:
Hi,
I'd like to backport the following fixes to the 1.6.x branch for b2:
ef46a091 89db53b1
They're bugs in PEP 3118 format string generation, of the brown paper-pag variety.
Go ahead. For bug fixes I think you can always just backport (at least before the RC stage), no need to check. Cheers, Ralf
participants (10)
-
Bruce Southey -
David -
David Cournapeau -
Derek Homeier -
Paul Ivanov -
Pauli Virtanen -
Pearu Peterson -
Ralf Gommers -
Russell E. Owen -
Scott Sinclair