[Numpy-svn] r5844 - in branches/clean_math_config: . doc numpy numpy/core numpy/distutils/command numpy/f2py numpy/f2py/doc numpy/lib numpy/linalg numpy/ma numpy/ma/tests numpy/oldnumeric numpy/testing
numpy-svn at scipy.org
numpy-svn at scipy.org
Sat Sep 20 07:40:24 EDT 2008
Author: cdavid
Date: 2008-09-20 06:39:20 -0500 (Sat, 20 Sep 2008)
New Revision: 5844
Modified:
branches/clean_math_config/
branches/clean_math_config/doc/TESTS.txt
branches/clean_math_config/numpy/_import_tools.py
branches/clean_math_config/numpy/core/records.py
branches/clean_math_config/numpy/distutils/command/install.py
branches/clean_math_config/numpy/f2py/auxfuncs.py
branches/clean_math_config/numpy/f2py/cb_rules.py
branches/clean_math_config/numpy/f2py/cfuncs.py
branches/clean_math_config/numpy/f2py/common_rules.py
branches/clean_math_config/numpy/f2py/crackfortran.py
branches/clean_math_config/numpy/f2py/doc/collectinput.py
branches/clean_math_config/numpy/f2py/f2py2e.py
branches/clean_math_config/numpy/f2py/f2py_testing.py
branches/clean_math_config/numpy/f2py/f90mod_rules.py
branches/clean_math_config/numpy/f2py/func2subr.py
branches/clean_math_config/numpy/f2py/use_rules.py
branches/clean_math_config/numpy/lib/index_tricks.py
branches/clean_math_config/numpy/lib/twodim_base.py
branches/clean_math_config/numpy/lib/utils.py
branches/clean_math_config/numpy/linalg/linalg.py
branches/clean_math_config/numpy/ma/bench.py
branches/clean_math_config/numpy/ma/core.py
branches/clean_math_config/numpy/ma/extras.py
branches/clean_math_config/numpy/ma/mrecords.py
branches/clean_math_config/numpy/ma/tests/test_core.py
branches/clean_math_config/numpy/ma/tests/test_extras.py
branches/clean_math_config/numpy/ma/tests/test_mrecords.py
branches/clean_math_config/numpy/ma/testutils.py
branches/clean_math_config/numpy/ma/timer_comparison.py
branches/clean_math_config/numpy/oldnumeric/arrayfns.py
branches/clean_math_config/numpy/oldnumeric/compat.py
branches/clean_math_config/numpy/oldnumeric/mlab.py
branches/clean_math_config/numpy/oldnumeric/rng.py
branches/clean_math_config/numpy/testing/noseclasses.py
Log:
Merged revisions 5812-5843 via svnmerge from
http://svn.scipy.org/svn/numpy/trunk
........
r5821 | alan.mcintyre | 2008-09-14 03:04:57 +0900 (Sun, 14 Sep 2008) | 3 lines
Removed unused imports.
Standardize NumPy import as "import numpy as np".
........
r5822 | alan.mcintyre | 2008-09-14 03:10:48 +0900 (Sun, 14 Sep 2008) | 6 lines
Rewrapped __all__ definition to conform to PEP8.
Standardize NumPy import as "import numpy as np".
Removed unused imports.
Fixed undefined reference to ndarray (should be np.ndarray).
Fixed undefined references to exp (should be math.exp).
........
r5823 | alan.mcintyre | 2008-09-14 03:15:38 +0900 (Sun, 14 Sep 2008) | 3 lines
Removed unused imports.
Fixed undefined reference to "getpackage" (from nose.util).
........
r5824 | pierregm | 2008-09-14 06:17:09 +0900 (Sun, 14 Sep 2008) | 1 line
MaskedArray.__new__ : make sure that we inherit the _hardmask from data (if any) instead of reverting to default.
........
r5826 | alan.mcintyre | 2008-09-18 12:29:56 +0900 (Thu, 18 Sep 2008) | 4 lines
Added documentation for doctests and using the skipif and knownfailureif decorators.
Fixed indentation on the last sample snippet in the "__init__.py and setup.py"
section.
........
r5827 | alan.mcintyre | 2008-09-18 12:33:15 +0900 (Thu, 18 Sep 2008) | 3 lines
Rewrapped __all__ to conform with PEP8.
Removed unused imports.
........
r5828 | alan.mcintyre | 2008-09-18 12:33:58 +0900 (Thu, 18 Sep 2008) | 2 lines
Removed unused imports.
........
r5829 | alan.mcintyre | 2008-09-18 12:45:53 +0900 (Thu, 18 Sep 2008) | 3 lines
Removed unused/redundant imports.
PEP8 conformance (only one import per line).
........
r5830 | alan.mcintyre | 2008-09-18 12:57:47 +0900 (Thu, 18 Sep 2008) | 2 lines
Removed redundant import.
........
r5831 | pierregm | 2008-09-19 02:51:55 +0900 (Fri, 19 Sep 2008) | 1 line
median : fixed a bug in _median1D (there shouldn't have been an axis)
........
r5832 | jarrod.millman | 2008-09-19 03:53:53 +0900 (Fri, 19 Sep 2008) | 2 lines
ReSTified an URL
........
r5833 | rkern | 2008-09-19 06:48:57 +0900 (Fri, 19 Sep 2008) | 1 line
BUG: Override setuptools' install.run() method to correctly allow 'python setup.py install' to work.
........
r5834 | pierregm | 2008-09-19 12:33:40 +0900 (Fri, 19 Sep 2008) | 1 line
* fixing view to recognize dtype and type parameters, for consistency with regular ndarrays.
........
r5835 | pierregm | 2008-09-20 04:43:05 +0900 (Sat, 20 Sep 2008) | 8 lines
core:
* add dtype to the repr of masked arrays w/ flexible type
* prevent __getitem__ to return masked on flexible-type masked array
* make sure __str__ returns something sensible for flexible dtype w/ masked fields
* simplify the count method
mrecords:
* fixed a pb with fromrecords when the number of fields cannot be determined from the first element.
........
Property changes on: branches/clean_math_config
___________________________________________________________________
Name: svnmerge-integrated
- /branches/aligned_alloca:1-5127 /branches/build_with_scons:1-4676 /branches/cdavid:1-5257 /branches/cleanconfig_rtm:1-4677 /branches/distutils-revamp:1-2752 /branches/distutils_scons_command:1-4619 /branches/multicore:1-3687 /branches/numpy.scons:1-4484 /branches/vs_longstring:1-5656 /cleaned_math_config:1-5731 /trunk:1-5811
+ /branches/aligned_alloca:1-5127 /branches/build_with_scons:1-4676 /branches/cdavid:1-5257 /branches/cleanconfig_rtm:1-4677 /branches/distutils-revamp:1-2752 /branches/distutils_scons_command:1-4619 /branches/multicore:1-3687 /branches/numpy.scons:1-4484 /branches/vs_longstring:1-5656 /cleaned_math_config:1-5731 /trunk:1-5843
Modified: branches/clean_math_config/doc/TESTS.txt
===================================================================
--- branches/clean_math_config/doc/TESTS.txt 2008-09-20 10:53:27 UTC (rev 5843)
+++ branches/clean_math_config/doc/TESTS.txt 2008-09-20 11:39:20 UTC (rev 5844)
@@ -58,7 +58,7 @@
run_module_suite()
-Note that all classes that are inherited from ``TestCase`` class, are picked up by the test runner. For more detailed information on defining test classes see the official documentation for the [http://docs.python.org/lib/module-unittest.html Python Unit testing framework].
+Note that all classes that are inherited from ``TestCase`` class, are picked up by the test runner. For more detailed information on defining test classes see the official documentation for the `Python Unit testing framework <http://docs.python.org/lib/module-unittest.html>`__.
Using test functions with nose
------------------------------
@@ -150,6 +150,19 @@
Note that 'check_even' is not itself a test (no 'test' in the name), but 'test_evens' is a generator that returns a series of tests, using 'check_even', across a range of inputs. Nice.
+Doctests
+--------
+
+Doctests are a convenient way of documenting the behavior a function and allowing that behavior to be tested at the same time. The output of an interactive Python session can be included in the docstring of a function, and the test framework can run the example and compare the actual output to the expected output.
+
+The doctests can be run by adding the ``doctests`` argument to the ``test()`` call; for example, to run all tests (including doctests) for numpy.lib::
+
+>>> import numpy as np
+>>> np.lib.test(doctests=True)
+
+The doctests are run as if they are in a fresh Python instance which has executed ``import numpy as np`` (tests that are part of the SciPy package also have an implicit ``import scipy as sp``).
+
+
``tests/``
----------
@@ -188,13 +201,12 @@
>>> import scipy
>>> scipy.xxx.test()
-Also, when invoking the entire SciPy test suite, your tests will be found and run:
+Also, when invoking the entire SciPy test suite, your tests will be found and run::
>>> import scipy
>>> scipy.test()
# your tests are included and run automatically!
-
Tips & Tricks
'''''''''''''
@@ -230,9 +242,29 @@
In this case, we wanted to test solving a linear algebra problem using matrices of several data types, using ``linalg.solve`` and ``linalg.inv``. The common test cases (for single-precision, double-precision, etc. matrices) are collected in ``LinalgTestCase``. Note that ``LinalgTestCase`` is not descended from ``TestCase``--if it were, then nose would attempt to run ``LinalgTestCase.test_single`` and ``LinalgTestCase.test_double``, which would fail because ``LinalgTestCase`` has no ``do`` method. Since ``TestSolve`` and ``TestInv`` inherit from ``LinalgTestCase`` and ``TestCase``, nose will run ``test_single`` and ``test_double`` for each class.
+Known failures & skipping tests
+-------------------------------
+Sometimes you might want to skip a test or mark it as a known failure, such as when the test suite is being written before the code it's meant to test, or if a test only fails on a particular architecture. The decorators from numpy.testing.dec can be used to do this.
+To skip a test, simply use ``skipif``::
+ from numpy.testing import *
+ @dec.skipif(SkipMyTest, "Skipping this test because...")
+ def test_something(foo):
+ ...
+The test is marked as skipped if ``SkipMyTest`` evaluates to nonzero, and the message in verbose test output is the second argument given to ``skipif``. Similarly, a test can be marked as a known failure by using ``knownfailureif``::
+ from numpy.testing import *
+
+ @dec.knownfailureif(MyTestFails, "This test is known to fail because...")
+ def test_something_else(foo):
+ ...
+
+Of course, a test can be unconditionally skipped or marked as a known failure by passing ``True`` as the first argument to ``skipif`` or ``knownfailureif``, respectively.
+
+A total of the number of skipped and known failing tests is displayed at the end of the test run. Skipped tests are marked as ``'S'`` in the test results (or ``'SKIPPED'`` for ``verbosity > 1``), and known failing tests are marked as ``'K'`` (or ``'KNOWN'`` if ``verbosity > 1``).
+
+
Modified: branches/clean_math_config/numpy/_import_tools.py
===================================================================
--- branches/clean_math_config/numpy/_import_tools.py 2008-09-20 10:53:27 UTC (rev 5843)
+++ branches/clean_math_config/numpy/_import_tools.py 2008-09-20 11:39:20 UTC (rev 5844)
@@ -1,7 +1,5 @@
-
import os
import sys
-import imp
__all__ = ['PackageLoader']
Modified: branches/clean_math_config/numpy/core/records.py
===================================================================
--- branches/clean_math_config/numpy/core/records.py 2008-09-20 10:53:27 UTC (rev 5843)
+++ branches/clean_math_config/numpy/core/records.py 2008-09-20 11:39:20 UTC (rev 5844)
@@ -448,17 +448,23 @@
else:
return self.setfield(val, *res)
- def view(self, obj):
- try:
- if issubclass(obj, ndarray):
- return ndarray.view(self, obj)
- except TypeError:
- pass
- dtype = sb.dtype(obj)
- if dtype.fields is None:
- return self.__array__().view(dtype)
- return ndarray.view(self, obj)
+ def view(self, dtype=None, type=None):
+ if dtype is None:
+ return ndarray.view(self, type)
+ elif type is None:
+ try:
+ if issubclass(dtype, ndarray):
+ return ndarray.view(self, dtype)
+ except TypeError:
+ pass
+ dtype = sb.dtype(dtype)
+ if dtype.fields is None:
+ return self.__array__().view(dtype)
+ return ndarray.view(self, dtype)
+ else:
+ return ndarray.view(self, dtype, type)
+
def fromarrays(arrayList, dtype=None, shape=None, formats=None,
names=None, titles=None, aligned=False, byteorder=None):
""" create a record array from a (flat) list of arrays
Modified: branches/clean_math_config/numpy/distutils/command/install.py
===================================================================
--- branches/clean_math_config/numpy/distutils/command/install.py 2008-09-20 10:53:27 UTC (rev 5843)
+++ branches/clean_math_config/numpy/distutils/command/install.py 2008-09-20 11:39:20 UTC (rev 5844)
@@ -1,8 +1,10 @@
import sys
if 'setuptools' in sys.modules:
import setuptools.command.install as old_install_mod
+ have_setuptools = True
else:
import distutils.command.install as old_install_mod
+ have_setuptools = False
old_install = old_install_mod.install
from distutils.file_util import write_file
@@ -12,8 +14,41 @@
old_install.finalize_options(self)
self.install_lib = self.install_libbase
+ def setuptools_run(self):
+ """ The setuptools version of the .run() method.
+
+ We must pull in the entire code so we can override the level used in the
+ _getframe() call since we wrap this call by one more level.
+ """
+ # Explicit request for old-style install? Just do it
+ if self.old_and_unmanageable or self.single_version_externally_managed:
+ return old_install_mod._install.run(self)
+
+ # Attempt to detect whether we were called from setup() or by another
+ # command. If we were called by setup(), our caller will be the
+ # 'run_command' method in 'distutils.dist', and *its* caller will be
+ # the 'run_commands' method. If we were called any other way, our
+ # immediate caller *might* be 'run_command', but it won't have been
+ # called by 'run_commands'. This is slightly kludgy, but seems to
+ # work.
+ #
+ caller = sys._getframe(3)
+ caller_module = caller.f_globals.get('__name__','')
+ caller_name = caller.f_code.co_name
+
+ if caller_module != 'distutils.dist' or caller_name!='run_commands':
+ # We weren't called from the command line or setup(), so we
+ # should run in backward-compatibility mode to support bdist_*
+ # commands.
+ old_install_mod._install.run(self)
+ else:
+ self.do_egg_install()
+
def run(self):
- r = old_install.run(self)
+ if not have_setuptools:
+ r = old_install.run(self)
+ else:
+ r = self.setuptools_run()
if self.record:
# bdist_rpm fails when INSTALLED_FILES contains
# paths with spaces. Such paths must be enclosed
Modified: branches/clean_math_config/numpy/f2py/auxfuncs.py
===================================================================
--- branches/clean_math_config/numpy/f2py/auxfuncs.py 2008-09-20 10:53:27 UTC (rev 5843)
+++ branches/clean_math_config/numpy/f2py/auxfuncs.py 2008-09-20 11:39:20 UTC (rev 5844)
@@ -20,9 +20,7 @@
import pprint
import sys
-import time
import types
-import os
import cfuncs
Modified: branches/clean_math_config/numpy/f2py/cb_rules.py
===================================================================
--- branches/clean_math_config/numpy/f2py/cb_rules.py 2008-09-20 10:53:27 UTC (rev 5843)
+++ branches/clean_math_config/numpy/f2py/cb_rules.py 2008-09-20 11:39:20 UTC (rev 5844)
@@ -21,16 +21,13 @@
import pprint
import sys
-import time
import types
-import copy
errmess=sys.stderr.write
outmess=sys.stdout.write
show=pprint.pprint
from auxfuncs import *
import capi_maps
-#from capi_maps import *
import cfuncs
################## Rules for callback function ##############
Modified: branches/clean_math_config/numpy/f2py/cfuncs.py
===================================================================
--- branches/clean_math_config/numpy/f2py/cfuncs.py 2008-09-20 10:53:27 UTC (rev 5843)
+++ branches/clean_math_config/numpy/f2py/cfuncs.py 2008-09-20 11:39:20 UTC (rev 5844)
@@ -19,7 +19,9 @@
import __version__
f2py_version = __version__.version
-import types,sys,copy,os
+import types
+import sys
+import copy
errmess=sys.stderr.write
##################### Definitions ##################
Modified: branches/clean_math_config/numpy/f2py/common_rules.py
===================================================================
--- branches/clean_math_config/numpy/f2py/common_rules.py 2008-09-20 10:53:27 UTC (rev 5843)
+++ branches/clean_math_config/numpy/f2py/common_rules.py 2008-09-20 11:39:20 UTC (rev 5844)
@@ -20,16 +20,12 @@
import pprint
import sys
-import time
-import types
-import copy
errmess=sys.stderr.write
outmess=sys.stdout.write
show=pprint.pprint
from auxfuncs import *
import capi_maps
-import cfuncs
import func2subr
from crackfortran import rmbadname
##############
Modified: branches/clean_math_config/numpy/f2py/crackfortran.py
===================================================================
--- branches/clean_math_config/numpy/f2py/crackfortran.py 2008-09-20 10:53:27 UTC (rev 5843)
+++ branches/clean_math_config/numpy/f2py/crackfortran.py 2008-09-20 11:39:20 UTC (rev 5844)
@@ -15,7 +15,6 @@
__version__ = "$Revision: 1.177 $"[10:-1]
import __version__
-import string
f2py_version = __version__.version
"""
Modified: branches/clean_math_config/numpy/f2py/doc/collectinput.py
===================================================================
--- branches/clean_math_config/numpy/f2py/doc/collectinput.py 2008-09-20 10:53:27 UTC (rev 5843)
+++ branches/clean_math_config/numpy/f2py/doc/collectinput.py 2008-09-20 11:39:20 UTC (rev 5844)
@@ -23,7 +23,6 @@
stdoutflag=0
import sys
-import os
import fileinput
import re
import commands
Modified: branches/clean_math_config/numpy/f2py/f2py2e.py
===================================================================
--- branches/clean_math_config/numpy/f2py/f2py2e.py 2008-09-20 10:53:27 UTC (rev 5843)
+++ branches/clean_math_config/numpy/f2py/f2py2e.py 2008-09-20 11:39:20 UTC (rev 5844)
@@ -21,7 +21,6 @@
import sys
import os
import pprint
-import shutil
import types
import re
errmess=sys.stderr.write
@@ -31,11 +30,8 @@
import crackfortran
import rules
import cb_rules
-import common_rules
import auxfuncs
import cfuncs
-import capi_maps
-import func2subr
import f90mod_rules
outmess = auxfuncs.outmess
@@ -395,7 +391,7 @@
"""
Do it all in one call!
"""
- import tempfile,os,shutil
+ import tempfile
i = sys.argv.index('-c')
del sys.argv[i]
@@ -547,6 +543,7 @@
setup(ext_modules = [ext])
if remove_build_dir and os.path.exists(build_dir):
+ import shutil
outmess('Removing build directory %s\n'%(build_dir))
shutil.rmtree(build_dir)
Modified: branches/clean_math_config/numpy/f2py/f2py_testing.py
===================================================================
--- branches/clean_math_config/numpy/f2py/f2py_testing.py 2008-09-20 10:53:27 UTC (rev 5843)
+++ branches/clean_math_config/numpy/f2py/f2py_testing.py 2008-09-20 11:39:20 UTC (rev 5844)
@@ -1,4 +1,5 @@
-import os,sys,re,time
+import sys
+import re
from numpy.testing.utils import jiffies, memusage
Modified: branches/clean_math_config/numpy/f2py/f90mod_rules.py
===================================================================
--- branches/clean_math_config/numpy/f2py/f90mod_rules.py 2008-09-20 10:53:27 UTC (rev 5843)
+++ branches/clean_math_config/numpy/f2py/f90mod_rules.py 2008-09-20 11:39:20 UTC (rev 5844)
@@ -17,11 +17,8 @@
f2py_version='See `f2py -v`'
-import copy
import pprint
import sys
-import time
-import types
errmess=sys.stderr.write
outmess=sys.stdout.write
show=pprint.pprint
@@ -29,7 +26,6 @@
from auxfuncs import *
import numpy as np
import capi_maps
-import cfuncs
import rules
import func2subr
from crackfortran import undo_rmbadname, undo_rmbadname1
Modified: branches/clean_math_config/numpy/f2py/func2subr.py
===================================================================
--- branches/clean_math_config/numpy/f2py/func2subr.py 2008-09-20 10:53:27 UTC (rev 5843)
+++ branches/clean_math_config/numpy/f2py/func2subr.py 2008-09-20 11:39:20 UTC (rev 5844)
@@ -20,9 +20,6 @@
import pprint
import copy
import sys
-import time
-import types
-import copy
errmess=sys.stderr.write
outmess=sys.stdout.write
show=pprint.pprint
Modified: branches/clean_math_config/numpy/f2py/use_rules.py
===================================================================
--- branches/clean_math_config/numpy/f2py/use_rules.py 2008-09-20 10:53:27 UTC (rev 5843)
+++ branches/clean_math_config/numpy/f2py/use_rules.py 2008-09-20 11:39:20 UTC (rev 5844)
@@ -21,16 +21,11 @@
import pprint
import sys
-import time
-import types
-import copy
errmess=sys.stderr.write
outmess=sys.stdout.write
show=pprint.pprint
from auxfuncs import *
-import capi_maps
-import cfuncs
##############
usemodule_rules={
Modified: branches/clean_math_config/numpy/lib/index_tricks.py
===================================================================
--- branches/clean_math_config/numpy/lib/index_tricks.py 2008-09-20 10:53:27 UTC (rev 5843)
+++ branches/clean_math_config/numpy/lib/index_tricks.py 2008-09-20 11:39:20 UTC (rev 5844)
@@ -7,7 +7,7 @@
import sys
import numpy.core.numeric as _nx
-from numpy.core.numeric import asarray, ScalarType, array, dtype
+from numpy.core.numeric import asarray, ScalarType, array
from numpy.core.numerictypes import find_common_type
import math
Modified: branches/clean_math_config/numpy/lib/twodim_base.py
===================================================================
--- branches/clean_math_config/numpy/lib/twodim_base.py 2008-09-20 10:53:27 UTC (rev 5843)
+++ branches/clean_math_config/numpy/lib/twodim_base.py 2008-09-20 11:39:20 UTC (rev 5844)
@@ -6,7 +6,7 @@
'tril','vander','histogram2d']
from numpy.core.numeric import asanyarray, equal, subtract, arange, \
- zeros, arange, greater_equal, multiply, ones, asarray
+ zeros, greater_equal, multiply, ones, asarray
def fliplr(m):
"""
Modified: branches/clean_math_config/numpy/lib/utils.py
===================================================================
--- branches/clean_math_config/numpy/lib/utils.py 2008-09-20 10:53:27 UTC (rev 5843)
+++ branches/clean_math_config/numpy/lib/utils.py 2008-09-20 11:39:20 UTC (rev 5844)
@@ -4,9 +4,7 @@
import types
import re
-from numpy.core.numerictypes import obj2sctype, generic, issubclass_, \
- issubsctype, issubdtype
-from numpy.core.multiarray import dtype as _dtype
+from numpy.core.numerictypes import issubclass_, issubsctype, issubdtype
from numpy.core import product, ndarray
__all__ = ['issubclass_', 'get_numpy_include', 'issubsctype',
Modified: branches/clean_math_config/numpy/linalg/linalg.py
===================================================================
--- branches/clean_math_config/numpy/linalg/linalg.py 2008-09-20 10:53:27 UTC (rev 5843)
+++ branches/clean_math_config/numpy/linalg/linalg.py 2008-09-20 11:39:20 UTC (rev 5844)
@@ -9,16 +9,9 @@
zgetrf, dpotrf, zpotrf, dgeqrf, zgeqrf, zungqr, dorgqr.
"""
-__all__ = ['matrix_power', 'solve', 'tensorsolve', 'tensorinv',
- 'inv', 'cholesky',
- 'eigvals',
- 'eigvalsh', 'pinv',
- 'det', 'svd',
- 'eig', 'eigh','lstsq', 'norm',
- 'qr',
- 'cond',
- 'LinAlgError'
- ]
+__all__ = ['matrix_power', 'solve', 'tensorsolve', 'tensorinv', 'inv',
+ 'cholesky', 'eigvals', 'eigvalsh', 'pinv', 'det', 'svd',
+ 'eig', 'eigh','lstsq', 'norm', 'qr', 'cond', 'LinAlgError']
from numpy.core import array, asarray, zeros, empty, transpose, \
intc, single, double, csingle, cdouble, inexact, complexfloating, \
@@ -27,7 +20,7 @@
isfinite, size
from numpy.lib import triu
from numpy.linalg import lapack_lite
-from numpy.core.defmatrix import matrix_power, matrix
+from numpy.core.defmatrix import matrix_power
fortran_int = intc
Modified: branches/clean_math_config/numpy/ma/bench.py
===================================================================
--- branches/clean_math_config/numpy/ma/bench.py 2008-09-20 10:53:27 UTC (rev 5843)
+++ branches/clean_math_config/numpy/ma/bench.py 2008-09-20 11:39:20 UTC (rev 5844)
@@ -6,9 +6,9 @@
#ip = IPython.ipapi.get()
#from IPython import ipmagic
import numpy
-from numpy import ma
-from numpy.ma import filled
-from numpy.ma.testutils import assert_equal
+#from numpy import ma
+#from numpy.ma import filled
+#from numpy.ma.testutils import assert_equal
#####---------------------------------------------------------------------------
Modified: branches/clean_math_config/numpy/ma/core.py
===================================================================
--- branches/clean_math_config/numpy/ma/core.py 2008-09-20 10:53:27 UTC (rev 5843)
+++ branches/clean_math_config/numpy/ma/core.py 2008-09-20 11:39:20 UTC (rev 5844)
@@ -57,17 +57,14 @@
'var', 'where',
'zeros']
-import sys
-import types
import cPickle
import operator
import numpy as np
-from numpy import ndarray, typecodes, amax, amin, iscomplexobj,\
- bool_, complex_, float_, int_, object_, str_
+from numpy import ndarray, amax, amin, iscomplexobj, bool_, complex_, float_,\
+ int_, object_
from numpy import array as narray
-
import numpy.core.umath as umath
import numpy.core.numerictypes as ntypes
from numpy import expand_dims as n_expand_dims
@@ -1237,7 +1234,7 @@
def __new__(cls, data=None, mask=nomask, dtype=None, copy=False,
subok=True, ndmin=0, fill_value=None,
- keep_mask=True, hard_mask=False, flag=None, shrink=True,
+ keep_mask=True, hard_mask=None, flag=None, shrink=True,
**options):
"""Create a new masked array from scratch.
@@ -1341,7 +1338,10 @@
if fill_value is not None:
_data._fill_value = _check_fill_value(fill_value, _data.dtype)
# Process extra options ..
- _data._hardmask = hard_mask
+ if hard_mask is None:
+ _data._hardmask = getattr(data, '_hardmask', False)
+ else:
+ _data._hardmask = hard_mask
_data._baseclass = _baseclass
return _data
#
@@ -1479,15 +1479,22 @@
# if getmask(indx) is not nomask:
# msg = "Masked arrays must be filled before they can be used as indices!"
# raise IndexError, msg
- dout = ndarray.__getitem__(self.view(ndarray), indx)
+ dout = ndarray.__getitem__(ndarray.view(self,ndarray), indx)
# We could directly use ndarray.__getitem__ on self...
# But then we would have to modify __array_finalize__ to prevent the
# mask of being reshaped if it hasn't been set up properly yet...
# So it's easier to stick to the current version
_mask = self._mask
if not getattr(dout,'ndim', False):
+ # A record ................
+ if isinstance(dout, np.void):
+ mask = _mask[indx]
+ if mask.view((bool,len(mask.dtype))).any():
+ dout = masked_array(dout, mask=mask)
+ else:
+ return dout
# Just a scalar............
- if _mask is not nomask and _mask[indx]:
+ elif _mask is not nomask and _mask[indx]:
return masked
else:
# Force dout to MA ........
@@ -1896,7 +1903,15 @@
res = self._data
else:
if m.shape == ():
- if m:
+ if m.dtype.names:
+ m = m.view((bool, len(m.dtype)))
+ if m.any():
+ r = np.array(self._data.tolist(), dtype=object)
+ np.putmask(r, m, f)
+ return str(tuple(r))
+ else:
+ return str(self._data)
+ elif m:
return str(f)
else:
return str(self._data)
@@ -1933,21 +1948,31 @@
mask = %(mask)s,
fill_value=%(fill)s)
"""
+ with_mask_flx = """\
+masked_%(name)s(data =
+ %(data)s,
+ mask =
+ %(mask)s,
+ fill_value=%(fill)s,
+ dtype=%(dtype)s)
+"""
+ with_mask1_flx = """\
+masked_%(name)s(data = %(data)s,
+ mask = %(mask)s,
+ fill_value=%(fill)s
+ dtype=%(dtype)s)
+"""
n = len(self.shape)
name = repr(self._data).split('(')[0]
- if n <= 1:
- return with_mask1 % {
- 'name': name,
- 'data': str(self),
- 'mask': str(self._mask),
- 'fill': str(self.fill_value),
- }
- return with_mask % {
- 'name': name,
- 'data': str(self),
- 'mask': str(self._mask),
- 'fill': str(self.fill_value),
- }
+ parameters = dict(name=name, data=str(self), mask=str(self._mask),
+ fill=str(self.fill_value), dtype=str(self.dtype))
+ if self.dtype.names:
+ if n<= 1:
+ return with_mask1_flx % parameters
+ return with_mask_flx % parameters
+ elif n <= 1:
+ return with_mask1 % parameters
+ return with_mask % parameters
#............................................
def __add__(self, other):
"Add other to self, and return a new masked array."
@@ -3509,6 +3534,8 @@
return data
def count(a, axis = None):
+ if isinstance(a, MaskedArray):
+ return a.count(axis)
return masked_array(a, copy=False).count(axis)
count.__doc__ = MaskedArray.count.__doc__
Modified: branches/clean_math_config/numpy/ma/extras.py
===================================================================
--- branches/clean_math_config/numpy/ma/extras.py 2008-09-20 10:53:27 UTC (rev 5843)
+++ branches/clean_math_config/numpy/ma/extras.py 2008-09-20 11:39:20 UTC (rev 5844)
@@ -415,7 +415,7 @@
"""
def _median1D(data):
- counts = filled(count(data, axis),0)
+ counts = filled(count(data),0)
(idx, rmd) = divmod(counts, 2)
if rmd:
choice = slice(idx, idx+1)
Modified: branches/clean_math_config/numpy/ma/mrecords.py
===================================================================
--- branches/clean_math_config/numpy/ma/mrecords.py 2008-09-20 10:53:27 UTC (rev 5843)
+++ branches/clean_math_config/numpy/ma/mrecords.py 2008-09-20 11:39:20 UTC (rev 5844)
@@ -16,23 +16,21 @@
__author__ = "Pierre GF Gerard-Marchant"
import sys
-import types
import numpy as np
-from numpy import bool_, complex_, float_, int_, str_, object_, dtype, \
- chararray, ndarray, recarray, record, array as narray
+from numpy import bool_, dtype, \
+ ndarray, recarray, array as narray
import numpy.core.numerictypes as ntypes
-from numpy.core.records import find_duplicate, format_parser
from numpy.core.records import fromarrays as recfromarrays, \
- fromrecords as recfromrecords
+ fromrecords as recfromrecords
_byteorderconv = np.core.records._byteorderconv
_typestr = ntypes._typestr
import numpy.ma as ma
from numpy.ma import MAError, MaskedArray, masked, nomask, masked_array,\
- make_mask, mask_or, getdata, getmask, getmaskarray, filled, \
- default_fill_value, masked_print_option
+ getdata, getmaskarray, filled
+
_check_fill_value = ma.core._check_fill_value
import warnings
@@ -153,10 +151,9 @@
return self
#......................................................
def __array_finalize__(self,obj):
- MaskedArray._update_from(self,obj)
# Make sure we have a _fieldmask by default ..
- _fieldmask = getattr(obj, '_fieldmask', None)
- if _fieldmask is None:
+ _mask = getattr(obj, '_mask', None)
+ if _mask is None:
objmask = getattr(obj, '_mask', nomask)
_dtype = ndarray.__getattribute__(self,'dtype')
if objmask is nomask:
@@ -165,15 +162,15 @@
mdescr = ma.make_mask_descr(_dtype)
_mask = narray([tuple([m]*len(mdescr)) for m in objmask],
dtype=mdescr).view(recarray)
- else:
- _mask = _fieldmask
# Update some of the attributes
- _locdict = self.__dict__
- if _locdict['_baseclass'] == ndarray:
- _locdict['_baseclass'] = recarray
- _locdict.update(_mask=_mask, _fieldmask=_mask)
+ _dict = self.__dict__
+ _dict.update(_mask=_mask, _fieldmask=_mask)
+ self._update_from(obj)
+ if _dict['_baseclass'] == ndarray:
+ _dict['_baseclass'] = recarray
return
+
def _getdata(self):
"Returns the data as a recarray."
return ndarray.view(self,recarray)
@@ -250,7 +247,6 @@
# Get the list of names ......
fielddict = ndarray.__getattribute__(self,'dtype').fields or {}
# Check the attribute
-##### _localdict = self.__dict__
if attr not in fielddict:
return ret
if newattr: # We just added this one
@@ -284,8 +280,8 @@
"""Returns all the fields sharing the same fieldname base.
The fieldname base is either `_data` or `_mask`."""
_localdict = self.__dict__
- _mask = _localdict['_fieldmask']
- _data = self._data
+ _mask = ndarray.__getattribute__(self,'_mask')
+ _data = ndarray.view(self, _localdict['_baseclass'])
# We want a field ........
if isinstance(indx, basestring):
#!!!: Make sure _sharedmask is True to propagate back to _fieldmask
@@ -473,7 +469,7 @@
dtype=dtype, shape=shape, formats=formats,
names=names, titles=titles, aligned=aligned,
byteorder=byteorder).view(mrecarray)
- _array._fieldmask.flat = zip(*masklist)
+ _array._mask.flat = zip(*masklist)
if fill_value is not None:
_array.fill_value = fill_value
return _array
@@ -507,13 +503,17 @@
mask : {nomask, sequence}, optional.
External mask to apply on the data.
-*Notes*:
+ Notes
+ -----
Lists of tuples should be preferred over lists of lists for faster processing.
"""
# Grab the initial _fieldmask, if needed:
_fieldmask = getattr(reclist, '_fieldmask', None)
# Get the list of records.....
- nfields = len(reclist[0])
+ try:
+ nfields = len(reclist[0])
+ except TypeError:
+ nfields = len(reclist[0].dtype)
if isinstance(reclist, ndarray):
# Make sure we don't have some hidden mask
if isinstance(reclist,MaskedArray):
@@ -656,7 +656,7 @@
set to 'fi', where `i` is the number of existing fields.
"""
_data = mrecord._data
- _mask = mrecord._fieldmask
+ _mask = mrecord._mask
if newfieldname is None or newfieldname in reserved_fields:
newfieldname = 'f%i' % len(_data.dtype)
newfield = ma.array(newfield)
Modified: branches/clean_math_config/numpy/ma/tests/test_core.py
===================================================================
--- branches/clean_math_config/numpy/ma/tests/test_core.py 2008-09-20 10:53:27 UTC (rev 5843)
+++ branches/clean_math_config/numpy/ma/tests/test_core.py 2008-09-20 11:39:20 UTC (rev 5844)
@@ -173,10 +173,12 @@
def test_asarray(self):
(x, y, a10, m1, m2, xm, ym, z, zm, xf) = self.d
xm.fill_value = -9999
+ xm._hardmask = True
xmm = asarray(xm)
assert_equal(xmm._data, xm._data)
assert_equal(xmm._mask, xm._mask)
assert_equal(xmm.fill_value, xm.fill_value)
+ assert_equal(xmm._hardmask, xm._hardmask)
def test_fix_invalid(self):
"Checks fix_invalid."
@@ -2370,8 +2372,24 @@
test = a.view((float,2), np.matrix)
assert_equal(test, data)
assert(isinstance(test, np.matrix))
+ #
+ def test_getitem(self):
+ ndtype = [('a',float), ('b',float)]
+ a = array(zip(np.random.rand(10),np.arange(10)), dtype=ndtype)
+ a.mask = np.array(zip([0,0,0,0,0,0,0,0,1,1],
+ [1,0,0,0,0,0,0,0,1,0]),
+ dtype=[('a',bool),('b',bool)])
+ # No mask
+ assert(isinstance(a[1], np.void))
+ # One element masked
+ assert(isinstance(a[0], MaskedArray))
+ assert_equal_records(a[0]._data, a._data[0])
+ assert_equal_records(a[0]._mask, a._mask[0])
+ # All element masked
+ assert(isinstance(a[-2], MaskedArray))
+ assert_equal_records(a[-2]._data, a._data[-2])
+ assert_equal_records(a[-2]._mask, a._mask[-2])
-
###############################################################################
#------------------------------------------------------------------------------
if __name__ == "__main__":
Modified: branches/clean_math_config/numpy/ma/tests/test_extras.py
===================================================================
--- branches/clean_math_config/numpy/ma/tests/test_extras.py 2008-09-20 10:53:27 UTC (rev 5843)
+++ branches/clean_math_config/numpy/ma/tests/test_extras.py 2008-09-20 11:39:20 UTC (rev 5844)
@@ -11,7 +11,7 @@
__revision__ = "$Revision: 3473 $"
__date__ = '$Date: 2007-10-29 17:18:13 +0200 (Mon, 29 Oct 2007) $'
-import numpy
+import numpy as np
from numpy.testing import TestCase, run_module_suite
from numpy.ma.testutils import *
from numpy.ma.core import *
@@ -332,25 +332,36 @@
def test_2d(self):
"Tests median w/ 2D"
(n,p) = (101,30)
- x = masked_array(numpy.linspace(-1.,1.,n),)
+ x = masked_array(np.linspace(-1.,1.,n),)
x[:10] = x[-10:] = masked
- z = masked_array(numpy.empty((n,p), dtype=numpy.float_))
+ z = masked_array(np.empty((n,p), dtype=float))
z[:,0] = x[:]
- idx = numpy.arange(len(x))
+ idx = np.arange(len(x))
for i in range(1,p):
- numpy.random.shuffle(idx)
+ np.random.shuffle(idx)
z[:,i] = x[idx]
assert_equal(median(z[:,0]), 0)
- assert_equal(median(z), numpy.zeros((p,)))
+ assert_equal(median(z), 0)
+ assert_equal(median(z, axis=0), np.zeros(p))
+ assert_equal(median(z.T, axis=1), np.zeros(p))
#
+ def test_2d_waxis(self):
+ "Tests median w/ 2D arrays and different axis."
+ x = masked_array(np.arange(30).reshape(10,3))
+ x[:3] = x[-3:] = masked
+ assert_equal(median(x), 14.5)
+ assert_equal(median(x, axis=0), [13.5,14.5,15.5])
+ assert_equal(median(x,axis=1), [0,0,0,10,13,16,19,0,0,0])
+ assert_equal(median(x,axis=1).mask, [1,1,1,0,0,0,0,1,1,1])
+ #
def test_3d(self):
"Tests median w/ 3D"
- x = numpy.ma.arange(24).reshape(3,4,2)
+ x = np.ma.arange(24).reshape(3,4,2)
x[x%3==0] = masked
assert_equal(median(x,0), [[12,9],[6,15],[12,9],[18,15]])
x.shape = (4,3,2)
assert_equal(median(x,0),[[99,10],[11,99],[13,14]])
- x = numpy.ma.arange(24).reshape(4,3,2)
+ x = np.ma.arange(24).reshape(4,3,2)
x[x%5==0] = masked
assert_equal(median(x,0), [[12,10],[8,9],[16,17]])
@@ -483,9 +494,9 @@
def test_polyfit(self):
"Tests polyfit"
# On ndarrays
- x = numpy.random.rand(10)
- y = numpy.random.rand(20).reshape(-1,2)
- assert_almost_equal(polyfit(x,y,3),numpy.polyfit(x,y,3))
+ x = np.random.rand(10)
+ y = np.random.rand(20).reshape(-1,2)
+ assert_almost_equal(polyfit(x,y,3),np.polyfit(x,y,3))
# ON 1D maskedarrays
x = x.view(MaskedArray)
x[0] = masked
@@ -493,17 +504,17 @@
y[0,0] = y[-1,-1] = masked
#
(C,R,K,S,D) = polyfit(x,y[:,0],3,full=True)
- (c,r,k,s,d) = numpy.polyfit(x[1:], y[1:,0].compressed(), 3, full=True)
+ (c,r,k,s,d) = np.polyfit(x[1:], y[1:,0].compressed(), 3, full=True)
for (a,a_) in zip((C,R,K,S,D),(c,r,k,s,d)):
assert_almost_equal(a, a_)
#
(C,R,K,S,D) = polyfit(x,y[:,-1],3,full=True)
- (c,r,k,s,d) = numpy.polyfit(x[1:-1], y[1:-1,-1], 3, full=True)
+ (c,r,k,s,d) = np.polyfit(x[1:-1], y[1:-1,-1], 3, full=True)
for (a,a_) in zip((C,R,K,S,D),(c,r,k,s,d)):
assert_almost_equal(a, a_)
#
(C,R,K,S,D) = polyfit(x,y,3,full=True)
- (c,r,k,s,d) = numpy.polyfit(x[1:-1], y[1:-1,:], 3, full=True)
+ (c,r,k,s,d) = np.polyfit(x[1:-1], y[1:-1,:], 3, full=True)
for (a,a_) in zip((C,R,K,S,D),(c,r,k,s,d)):
assert_almost_equal(a, a_)
Modified: branches/clean_math_config/numpy/ma/tests/test_mrecords.py
===================================================================
--- branches/clean_math_config/numpy/ma/tests/test_mrecords.py 2008-09-20 10:53:27 UTC (rev 5843)
+++ branches/clean_math_config/numpy/ma/tests/test_mrecords.py 2008-09-20 11:39:20 UTC (rev 5844)
@@ -8,23 +8,19 @@
__revision__ = "$Revision: 3473 $"
__date__ = '$Date: 2007-10-29 17:18:13 +0200 (Mon, 29 Oct 2007) $'
-import types
-
import numpy as np
from numpy import recarray
from numpy.core.records import fromrecords as recfromrecords, \
- fromarrays as recfromarrays
+ fromarrays as recfromarrays
import numpy.ma.testutils
from numpy.ma.testutils import *
import numpy.ma as ma
-from numpy.ma import masked, nomask, getdata, getmaskarray
+from numpy.ma import masked, nomask
-import numpy.ma.mrecords
-reload(numpy.ma.mrecords)
-from numpy.ma.mrecords import MaskedRecords, mrecarray,\
- fromarrays, fromtextfile, fromrecords, addfield
+from numpy.ma.mrecords import MaskedRecords, mrecarray, fromarrays, \
+ fromtextfile, fromrecords, addfield
#..............................................................................
class TestMRecords(TestCase):
@@ -207,8 +203,8 @@
#
def test_set_elements(self):
base = self.base.copy()
- mbase = base.view(mrecarray)
# Set an element to mask .....................
+ mbase = base.view(mrecarray).copy()
mbase[-2] = masked
assert_equal(mbase._fieldmask.tolist(),
np.array([(0,0,0),(1,1,1),(0,0,0),(1,1,1),(1,1,1)],
@@ -432,7 +428,6 @@
'strings',4,-1e-10,,,1
"""
import os
- from datetime import datetime
import tempfile
(tmp_fd,tmp_fl) = tempfile.mkstemp()
os.write(tmp_fd, fcontent)
Modified: branches/clean_math_config/numpy/ma/testutils.py
===================================================================
--- branches/clean_math_config/numpy/ma/testutils.py 2008-09-20 10:53:27 UTC (rev 5843)
+++ branches/clean_math_config/numpy/ma/testutils.py 2008-09-20 11:39:20 UTC (rev 5844)
@@ -16,12 +16,10 @@
from numpy import ndarray, float_
import numpy.core.umath as umath
from numpy.testing import *
-from numpy.testing.utils import build_err_msg, rand
import numpy.testing.utils as utils
-import core
-from core import mask_or, getmask, getmaskarray, masked_array, nomask, masked
-from core import fix_invalid, filled, equal, less
+from core import mask_or, getmask, masked_array, nomask, masked, filled, \
+ equal, less
#------------------------------------------------------------------------------
def approx (a, b, fill_value=True, rtol=1.e-5, atol=1.e-8):
Modified: branches/clean_math_config/numpy/ma/timer_comparison.py
===================================================================
--- branches/clean_math_config/numpy/ma/timer_comparison.py 2008-09-20 10:53:27 UTC (rev 5843)
+++ branches/clean_math_config/numpy/ma/timer_comparison.py 2008-09-20 11:39:20 UTC (rev 5844)
@@ -1,17 +1,15 @@
-
import timeit
-import numpy
-from numpy import int_, float_, bool_
-import numpy.core.fromnumeric as fromnumeric
+import numpy as np
+from numpy import float_
+import np.core.fromnumeric as fromnumeric
-from numpy.testing.utils import build_err_msg, rand
+from np.testing.utils import build_err_msg
+np.seterr(all='ignore')
-numpy.seterr(all='ignore')
+pi = np.pi
-pi = numpy.pi
-
class moduletester:
#-----------------------------------
def __init__(self, module):
@@ -61,15 +59,15 @@
y = self.filled(self.masked_array(yf, mask=m), fill_value)
if (x.dtype.char != "O"):
x = x.astype(float_)
- if isinstance(x, numpy.ndarray) and x.size > 1:
- x[numpy.isnan(x)] = 0
- elif numpy.isnan(x):
+ if isinstance(x, np.ndarray) and x.size > 1:
+ x[np.isnan(x)] = 0
+ elif np.isnan(x):
x = 0
if (y.dtype.char != "O"):
y = y.astype(float_)
- if isinstance(y, numpy.ndarray) and y.size > 1:
- y[numpy.isnan(y)] = 0
- elif numpy.isnan(y):
+ if isinstance(y, np.ndarray) and y.size > 1:
+ y[np.isnan(y)] = 0
+ elif np.isnan(y):
y = 0
try:
cond = (x.shape==() or y.shape==()) or x.shape == y.shape
@@ -110,23 +108,23 @@
#----------------------------------
def test_0(self):
"Tests creation"
- x = numpy.array([1.,1.,1.,-2., pi/2.0, 4., 5., -10., 10., 1., 2., 3.])
+ x = np.array([1.,1.,1.,-2., pi/2.0, 4., 5., -10., 10., 1., 2., 3.])
m = [1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0]
xm = self.masked_array(x, mask=m)
xm[0]
#----------------------------------
def test_1(self):
"Tests creation"
- x = numpy.array([1.,1.,1.,-2., pi/2.0, 4., 5., -10., 10., 1., 2., 3.])
- y = numpy.array([5.,0.,3., 2., -1., -4., 0., -10., 10., 1., 0., 3.])
+ x = np.array([1.,1.,1.,-2., pi/2.0, 4., 5., -10., 10., 1., 2., 3.])
+ y = np.array([5.,0.,3., 2., -1., -4., 0., -10., 10., 1., 0., 3.])
a10 = 10.
m1 = [1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0]
m2 = [0, 0, 1, 0, 0, 1, 1, 0, 0, 0 ,0, 1]
xm = self.masked_array(x, mask=m1)
ym = self.masked_array(y, mask=m2)
- z = numpy.array([-.5, 0., .5, .8])
+ z = np.array([-.5, 0., .5, .8])
zm = self.masked_array(z, mask=[0,1,0,0])
- xf = numpy.where(m1, 1.e+20, x)
+ xf = np.where(m1, 1.e+20, x)
xm.set_fill_value(1.e+20)
#.....
assert((xm-ym).filled(0).any())
@@ -146,13 +144,13 @@
#----------------------------------
def test_2(self):
"Tests conversions and indexing"
- x1 = numpy.array([1,2,4,3])
+ x1 = np.array([1,2,4,3])
x2 = self.array(x1, mask=[1,0,0,0])
x3 = self.array(x1, mask=[0,1,0,1])
x4 = self.array(x1)
# test conversion to strings
junk, garbage = str(x2), repr(x2)
-# assert_equal(numpy.sort(x1), self.sort(x2, fill_value=0))
+# assert_equal(np.sort(x1), self.sort(x2, fill_value=0))
# tests of indexing
assert type(x2[1]) is type(x1[1])
assert x1[1] == x2[1]
@@ -178,12 +176,12 @@
x4[:] = self.masked_array([1,2,3,4],[0,1,1,0])
# assert self.allequal(self.getmask(x4), self.array([0,1,1,0]))
# assert self.allequal(x4, self.array([1,2,3,4]))
- x1 = numpy.arange(5)*1.0
+ x1 = np.arange(5)*1.0
x2 = self.masked_values(x1, 3.0)
# assert self.allequal(x1,x2)
# assert self.allequal(self.array([0,0,0,1,0], self.MaskType), x2.mask)
x1 = self.array([1,'hello',2,3],object)
- x2 = numpy.array([1,'hello',2,3],object)
+ x2 = np.array([1,'hello',2,3],object)
s1 = x1[1]
s2 = x2[1]
assert x1[1:1].shape == (0,)
@@ -216,15 +214,15 @@
def test_4(self):
"Test of take, transpose, inner, outer products"
x = self.arange(24)
- y = numpy.arange(24)
+ y = np.arange(24)
x[5:6] = self.masked
x = x.reshape(2,3,4)
y = y.reshape(2,3,4)
- assert self.allequal(numpy.transpose(y,(2,0,1)), self.transpose(x,(2,0,1)))
- assert self.allequal(numpy.take(y, (2,0,1), 1), self.take(x, (2,0,1), 1))
- assert self.allequal(numpy.inner(self.filled(x,0), self.filled(y,0)),
+ assert self.allequal(np.transpose(y,(2,0,1)), self.transpose(x,(2,0,1)))
+ assert self.allequal(np.take(y, (2,0,1), 1), self.take(x, (2,0,1), 1))
+ assert self.allequal(np.inner(self.filled(x,0), self.filled(y,0)),
self.inner(x, y))
- assert self.allequal(numpy.outer(self.filled(x,0), self.filled(y,0)),
+ assert self.allequal(np.outer(self.filled(x,0), self.filled(y,0)),
self.outer(x, y))
y = self.array(['abc', 1, 'def', 2, 3], object)
y[2] = self.masked
@@ -396,8 +394,8 @@
self.assert_array_equal(self.average(x, axis=0), 2.5)
self.assert_array_equal(self.average(x, axis=0, weights=w1), 2.5)
y = self.array([self.arange(6), 2.0*self.arange(6)])
- self.assert_array_equal(self.average(y, None), numpy.add.reduce(numpy.arange(6))*3./12.)
- self.assert_array_equal(self.average(y, axis=0), numpy.arange(6) * 3./2.)
+ self.assert_array_equal(self.average(y, None), np.add.reduce(np.arange(6))*3./12.)
+ self.assert_array_equal(self.average(y, axis=0), np.arange(6) * 3./2.)
self.assert_array_equal(self.average(y, axis=1), [self.average(x,axis=0), self.average(x,axis=0) * 2.0])
self.assert_array_equal(self.average(y, None, weights=w2), 20./6.)
self.assert_array_equal(self.average(y, axis=0, weights=w2), [0.,1.,2.,3.,4.,10.])
@@ -420,7 +418,7 @@
#------------------------
def test_A(self):
x = self.arange(24)
- y = numpy.arange(24)
+ y = np.arange(24)
x[5:6] = self.masked
x = x.reshape(2,3,4)
@@ -431,10 +429,10 @@
setup_base = "from __main__ import moduletester \n"\
"import numpy\n" \
"tester = moduletester(module)\n"
-# setup_new = "import numpy.ma.core_ini as module\n"+setup_base
- setup_cur = "import numpy.ma.core as module\n"+setup_base
-# setup_alt = "import numpy.ma.core_alt as module\n"+setup_base
-# setup_tmp = "import numpy.ma.core_tmp as module\n"+setup_base
+# setup_new = "import np.ma.core_ini as module\n"+setup_base
+ setup_cur = "import np.ma.core as module\n"+setup_base
+# setup_alt = "import np.ma.core_alt as module\n"+setup_base
+# setup_tmp = "import np.ma.core_tmp as module\n"+setup_base
(nrepeat, nloop) = (10, 10)
@@ -445,10 +443,10 @@
cur = timeit.Timer(func, setup_cur).repeat(nrepeat, nloop*10)
# alt = timeit.Timer(func, setup_alt).repeat(nrepeat, nloop*10)
# tmp = timeit.Timer(func, setup_tmp).repeat(nrepeat, nloop*10)
-# new = numpy.sort(new)
- cur = numpy.sort(cur)
-# alt = numpy.sort(alt)
-# tmp = numpy.sort(tmp)
+# new = np.sort(new)
+ cur = np.sort(cur)
+# alt = np.sort(alt)
+# tmp = np.sort(tmp)
print "#%i" % i +50*'.'
print eval("moduletester.test_%i.__doc__" % i)
# print "core_ini : %.3f - %.3f" % (new[0], new[1])
Modified: branches/clean_math_config/numpy/oldnumeric/arrayfns.py
===================================================================
--- branches/clean_math_config/numpy/oldnumeric/arrayfns.py 2008-09-20 10:53:27 UTC (rev 5843)
+++ branches/clean_math_config/numpy/oldnumeric/arrayfns.py 2008-09-20 11:39:20 UTC (rev 5844)
@@ -1,10 +1,11 @@
"""Backward compatible with arrayfns from Numeric
"""
-__all__ = ['array_set', 'construct3', 'digitize', 'error', 'find_mask', 'histogram', 'index_sort',
- 'interp', 'nz', 'reverse', 'span', 'to_corners', 'zmin_zmax']
+__all__ = ['array_set', 'construct3', 'digitize', 'error', 'find_mask',
+ 'histogram', 'index_sort', 'interp', 'nz', 'reverse', 'span',
+ 'to_corners', 'zmin_zmax']
-import numpy as nx
+import numpy as np
from numpy import asarray
class error(Exception):
@@ -14,7 +15,7 @@
indices = asarray(indices)
if indices.ndim != 1:
raise ValueError, "index array must be 1-d"
- if not isinstance(vals1, ndarray):
+ if not isinstance(vals1, np.ndarray):
raise TypeError, "vals1 must be an ndarray"
vals1 = asarray(vals1)
vals2 = asarray(vals2)
@@ -31,7 +32,7 @@
def interp(y, x, z, typ=None):
"""y(z) interpolated by treating y(x) as piecewise function
"""
- res = numpy.interp(z, x, y)
+ res = np.interp(z, x, y)
if typ is None or typ == 'd':
return res
if typ == 'f':
@@ -40,17 +41,17 @@
raise error, "incompatible typecode"
def nz(x):
- x = asarray(x,dtype=nx.ubyte)
+ x = asarray(x,dtype=np.ubyte)
if x.ndim != 1:
raise TypeError, "intput must have 1 dimension."
- indxs = nx.flatnonzero(x != 0)
+ indxs = np.flatnonzero(x != 0)
return indxs[-1].item()+1
def reverse(x, n):
x = asarray(x,dtype='d')
if x.ndim != 2:
raise ValueError, "input must be 2-d"
- y = nx.empty_like(x)
+ y = np.empty_like(x)
if n == 0:
y[...] = x[::-1,:]
elif n == 1:
@@ -58,11 +59,11 @@
return y
def span(lo, hi, num, d2=0):
- x = linspace(lo, hi, num)
+ x = np.linspace(lo, hi, num)
if d2 <= 0:
return x
else:
- ret = empty((d2,num),x.dtype)
+ ret = np.empty((d2,num),x.dtype)
ret[...] = x
return ret
@@ -71,15 +72,15 @@
ireg = asarray(ireg, dtype=int)
if z.shape != ireg.shape or z.ndim != 2:
raise ValueError, "z and ireg must be the same shape and 2-d"
- ix, iy = nx.nonzero(ireg)
+ ix, iy = np.nonzero(ireg)
# Now, add more indices
x1m = ix - 1
y1m = iy-1
i1 = x1m>=0
i2 = y1m>=0
i3 = i1 & i2
- nix = nx.r_[ix, x1m[i1], x1m[i1], ix[i2] ]
- niy = nx.r_[iy, iy[i1], y1m[i3], y1m[i2]]
+ nix = np.r_[ix, x1m[i1], x1m[i1], ix[i2] ]
+ niy = np.r_[iy, iy[i1], y1m[i3], y1m[i2]]
# remove any negative indices
zres = z[nix,niy]
return zres.min().item(), zres.max().item()
Modified: branches/clean_math_config/numpy/oldnumeric/compat.py
===================================================================
--- branches/clean_math_config/numpy/oldnumeric/compat.py 2008-09-20 10:53:27 UTC (rev 5843)
+++ branches/clean_math_config/numpy/oldnumeric/compat.py 2008-09-20 11:39:20 UTC (rev 5844)
@@ -12,7 +12,7 @@
import numpy.core.multiarray as multiarray
import numpy.core.umath as um
-from numpy.core.numeric import array, correlate
+from numpy.core.numeric import array
import functions
import sys
Modified: branches/clean_math_config/numpy/oldnumeric/mlab.py
===================================================================
--- branches/clean_math_config/numpy/oldnumeric/mlab.py 2008-09-20 10:53:27 UTC (rev 5843)
+++ branches/clean_math_config/numpy/oldnumeric/mlab.py 2008-09-20 11:39:20 UTC (rev 5844)
@@ -1,6 +1,10 @@
# This module is for compatibility only. All functions are defined elsewhere.
-__all__ = ['rand', 'tril', 'trapz', 'hanning', 'rot90', 'triu', 'diff', 'angle', 'roots', 'ptp', 'kaiser', 'randn', 'cumprod', 'diag', 'msort', 'LinearAlgebra', 'RandomArray', 'prod', 'std', 'hamming', 'flipud', 'max', 'blackman', 'corrcoef', 'bartlett', 'eye', 'squeeze', 'sinc', 'tri', 'cov', 'svd', 'min', 'median', 'fliplr', 'eig', 'mean']
+__all__ = ['rand', 'tril', 'trapz', 'hanning', 'rot90', 'triu', 'diff', 'angle',
+ 'roots', 'ptp', 'kaiser', 'randn', 'cumprod', 'diag', 'msort',
+ 'LinearAlgebra', 'RandomArray', 'prod', 'std', 'hamming', 'flipud',
+ 'max', 'blackman', 'corrcoef', 'bartlett', 'eye', 'squeeze', 'sinc',
+ 'tri', 'cov', 'svd', 'min', 'median', 'fliplr', 'eig', 'mean']
import numpy.oldnumeric.linear_algebra as LinearAlgebra
import numpy.oldnumeric.random_array as RandomArray
@@ -12,7 +16,7 @@
from numpy.linalg import eig, svd
from numpy.random import rand, randn
-import numpy as nn
+import numpy as np
from typeconv import convtypecode
@@ -22,7 +26,7 @@
"""
dtype = convtypecode(typecode, dtype)
if M is None: M = N
- m = nn.equal(nn.subtract.outer(nn.arange(N), nn.arange(M)),-k)
+ m = np.equal(np.subtract.outer(np.arange(N), np.arange(M)),-k)
if m.dtype != dtype:
return m.astype(dtype)
@@ -32,7 +36,7 @@
"""
dtype = convtypecode(typecode, dtype)
if M is None: M = N
- m = nn.greater_equal(nn.subtract.outer(nn.arange(N), nn.arange(M)),-k)
+ m = np.greater_equal(np.subtract.outer(np.arange(N), np.arange(M)),-k)
if m.dtype != dtype:
return m.astype(dtype)
Modified: branches/clean_math_config/numpy/oldnumeric/rng.py
===================================================================
--- branches/clean_math_config/numpy/oldnumeric/rng.py 2008-09-20 10:53:27 UTC (rev 5843)
+++ branches/clean_math_config/numpy/oldnumeric/rng.py 2008-09-20 11:39:20 UTC (rev 5844)
@@ -4,9 +4,9 @@
# It is for backwards compatibility only.
-__all__ = ['CreateGenerator','ExponentialDistribution','LogNormalDistribution','NormalDistribution',
- 'UniformDistribution', 'error', 'default_distribution', 'random_sample', 'ranf',
- 'standard_generator']
+__all__ = ['CreateGenerator','ExponentialDistribution','LogNormalDistribution',
+ 'NormalDistribution', 'UniformDistribution', 'error', 'ranf',
+ 'default_distribution', 'random_sample', 'standard_generator']
import numpy.random.mtrand as mt
import math
@@ -44,7 +44,7 @@
return 0.0
else:
lambda_ = self._args[0]
- return lambda_*exp(-lambda_*x)
+ return lambda_*math.exp(-lambda_*x)
class LogNormalDistribution(Distribution):
def __init__(self, m, s):
@@ -61,7 +61,7 @@
def density(x):
m,s = self._args
y = (math.log(x)-self._mn)/self._sn
- return self._fac*exp(-0.5*y*y)/x
+ return self._fac*math.exp(-0.5*y*y)/x
class NormalDistribution(Distribution):
@@ -76,7 +76,7 @@
def density(x):
m,s = self._args
y = (x-m)/s
- return self._fac*exp(-0.5*y*y)
+ return self._fac*math.exp(-0.5*y*y)
class UniformDistribution(Distribution):
def __init__(self, a, b):
Modified: branches/clean_math_config/numpy/testing/noseclasses.py
===================================================================
--- branches/clean_math_config/numpy/testing/noseclasses.py 2008-09-20 10:53:27 UTC (rev 5843)
+++ branches/clean_math_config/numpy/testing/noseclasses.py 2008-09-20 11:39:20 UTC (rev 5844)
@@ -9,7 +9,7 @@
from nose.plugins import doctests as npd
from nose.plugins.errorclass import ErrorClass, ErrorClassPlugin
from nose.plugins.base import Plugin
-from nose.util import src, tolist
+from nose.util import src, getpackage
import numpy
from nosetester import get_package_name
import inspect
@@ -79,10 +79,11 @@
# doctests in extension modules.
# Local shorthands
- from inspect import isroutine, isclass, ismodule
+ from inspect import isroutine, isclass, ismodule, isfunction, \
+ ismethod
# Look for tests in a module's contained objects.
- if inspect.ismodule(obj) and self._recurse:
+ if ismodule(obj) and self._recurse:
for valname, val in obj.__dict__.items():
valname1 = '%s.%s' % (name, valname)
if ( (isroutine(val) or isclass(val))
@@ -93,7 +94,7 @@
# Look for tests in a class's contained objects.
- if inspect.isclass(obj) and self._recurse:
+ if isclass(obj) and self._recurse:
#print 'RECURSE into class:',obj # dbg
for valname, val in obj.__dict__.items():
#valname1 = '%s.%s' % (name, valname) # dbg
@@ -105,9 +106,8 @@
val = getattr(obj, valname).im_func
# Recurse to methods, properties, and nested classes.
- if ((inspect.isfunction(val) or inspect.isclass(val) or
- inspect.ismethod(val) or
- isinstance(val, property)) and
+ if ((isfunction(val) or isclass(val) or
+ ismethod(val) or isinstance(val, property)) and
self._from_module(module, val)):
valname = '%s.%s' % (name, valname)
self._find(tests, val, valname, module, source_lines,
@@ -175,7 +175,6 @@
def configure(self, options, config):
Plugin.configure(self, options, config)
self.doctest_tests = True
-# self.extension = tolist(options.doctestExtension)
self.finder = NumpyDocTestFinder()
self.parser = doctest.DocTestParser()
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