Merged revisions 6185-6187,6191-6221,6235-6238,6240-6241,6244,6250-6251,6253,6256,6258,6260-6261,6263,6265-6266,6268,6271,6283-6286,6291-6316,6320-6352,6354,6356,6358-6368,6370-6373,6398-6400,6410,6421-6424 via svnmerge from

http://svn.scipy.org/svn/numpy/trunk

................
  r6185 | cdavid | 2008-12-22 01:19:14 +0900 (Mon, 22 Dec 2008) | 1 line
  
  Add doc sources so that sdist tarball contains them.
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  r6186 | pierregm | 2008-12-22 19:01:51 +0900 (Mon, 22 Dec 2008) | 4 lines
  
  testutils:
  assert_array_compare : make sure that the comparison is performed on ndarrays, and make sure we use the np version of the comparison function.
  core:
  * Try not to touch the data in unary/binary ufuncs, (including inplace)
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  r6187 | pearu | 2008-12-22 19:05:00 +0900 (Mon, 22 Dec 2008) | 1 line
  
  Fix a bug.
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  r6191 | cdavid | 2008-12-23 13:10:59 +0900 (Tue, 23 Dec 2008) | 1 line
  
  Fix typos in the comments for manifest.
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  r6192 | cdavid | 2008-12-23 13:11:12 +0900 (Tue, 23 Dec 2008) | 1 line
  
  Use msvcrt values if available for manifest generation: only there starting from python 2.6.1.
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  r6193 | pearu | 2008-12-23 18:02:15 +0900 (Tue, 23 Dec 2008) | 1 line
  
  Fix issue 964: f2py python 2.6, 2.6.1 support.
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  r6194 | pierregm | 2008-12-24 08:43:43 +0900 (Wed, 24 Dec 2008) | 12 lines
  
  testutils:
  * assert_equal : use assert_equal_array on records
  * assert_array_compare : prevent the common mask to be back-propagated to the initial input arrays.
  * assert_equal_array : use operator.__eq__ instead of ma.equal
  * assert_equal_less: use operator.__less__ instead of ma.less
  
  core:
  * Fixed _check_fill_value for nested flexible types
  * Add a ndtype option to _make_mask_descr
  * Fixed mask_or for nested flexible types
  * Fixed the printing of masked arrays w/ flexible types.
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  r6195 | cdavid | 2008-12-26 21:16:45 +0900 (Fri, 26 Dec 2008) | 1 line
  
  Update to handle numscons 0.10.0 and above.
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  r6196 | cdavid | 2008-12-26 21:36:19 +0900 (Fri, 26 Dec 2008) | 1 line
  
  Do not import msvcrt globally in mingw32compiler module, since the module is imported on all platforms.
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  r6197 | cdavid | 2008-12-26 23:39:55 +0900 (Fri, 26 Dec 2008) | 1 line
  
  Do not test for functions already tested by python configure script.
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  r6198 | cdavid | 2008-12-27 14:56:58 +0900 (Sat, 27 Dec 2008) | 1 line
  
  BUG: Add a runtime check about endianness, to detect bug 4728 in python on Mac OS X.
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  r6199 | cdavid | 2008-12-27 19:06:25 +0900 (Sat, 27 Dec 2008) | 1 line
  
  Fix some typo/syntax errors when converting dict access to a function in manifest generation.
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  r6200 | cdavid | 2008-12-27 19:15:30 +0900 (Sat, 27 Dec 2008) | 1 line
  
  BUG (#970): fix a python 2.6 bug in distutils which caused an unhelpful Error:None message when trying to build with no VS installed and without the -c mingw32 option.
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  r6201 | cdavid | 2008-12-27 19:30:49 +0900 (Sat, 27 Dec 2008) | 1 line
  
  Improve the error message when initializing compiler failed.
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  r6202 | cdavid | 2008-12-27 19:32:05 +0900 (Sat, 27 Dec 2008) | 1 line
  
  Try to initialize the msvc compiler before the general code to detect the error early.
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  r6203 | cdavid | 2008-12-27 19:43:41 +0900 (Sat, 27 Dec 2008) | 1 line
  
  BUG (#970): this commit should fix the actual bug, which albeeit linked to commir r6200, was caused in anoter code path.
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  r6204 | cdavid | 2008-12-27 19:57:05 +0900 (Sat, 27 Dec 2008) | 1 line
  
  Fix manifest generation.
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  r6205 | cdavid | 2008-12-27 20:46:08 +0900 (Sat, 27 Dec 2008) | 1 line
  
  BUG (#827): close temp file before reopning them on windows, and make sure they are not automatically deleted on close either (2.6and higher specific).
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  r6206 | cdavid | 2008-12-27 21:18:47 +0900 (Sat, 27 Dec 2008) | 1 line
  
  Do not define the union for runtime endianness detection if we don't check endianness.
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  r6207 | cdavid | 2008-12-27 22:48:52 +0900 (Sat, 27 Dec 2008) | 1 line
  
  Start working on formatting failure on 2.6: copy how python does complex formatting.
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  r6208 | cdavid | 2008-12-27 23:44:11 +0900 (Sat, 27 Dec 2008) | 1 line
  
  Fix formatting for purely imaginary complex numbers.
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  r6209 | cdavid | 2008-12-27 23:53:15 +0900 (Sat, 27 Dec 2008) | 1 line
  
  More work on formatting float.
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  r6210 | cdavid | 2008-12-27 23:59:41 +0900 (Sat, 27 Dec 2008) | 1 line
  
  Finish formatting fixes for float scalar arrays.
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  r6211 | cdavid | 2008-12-28 00:12:20 +0900 (Sun, 28 Dec 2008) | 1 line
  
  Include umath_funcs_c99 in multiarray so that we can use isinf and co macros.
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  r6212 | cdavid | 2008-12-28 01:15:04 +0900 (Sun, 28 Dec 2008) | 1 line
  
  Include config.h before our C99 math compat layer.
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  r6213 | cdavid | 2008-12-28 01:15:41 +0900 (Sun, 28 Dec 2008) | 1 line
  
  Fix formatting.
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  r6214 | cdavid | 2008-12-28 01:16:18 +0900 (Sun, 28 Dec 2008) | 1 line
  
  Do not define FMTR and FMTI macros, as those are already defined on some platforms.
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  r6215 | cdavid | 2008-12-28 01:16:52 +0900 (Sun, 28 Dec 2008) | 1 line
  
  More formatting fixes.
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  r6216 | cdavid | 2008-12-28 01:17:27 +0900 (Sun, 28 Dec 2008) | 1 line
  
  Remove undef of removed macro.
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  r6217 | cdavid | 2008-12-28 01:33:40 +0900 (Sun, 28 Dec 2008) | 1 line
  
  Do not use PyOS_ascii_formatd, as it does not handle long double correctly.
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  r6218 | cdavid | 2008-12-28 02:19:40 +0900 (Sun, 28 Dec 2008) | 1 line
  
  Try ugly hack to circumvent long double brokenness with mingw.
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  r6219 | cdavid | 2008-12-28 02:25:50 +0900 (Sun, 28 Dec 2008) | 1 line
  
  Use ugly hack for mingw long double pb with complex format function as well.
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  r6220 | cdavid | 2008-12-28 12:18:20 +0900 (Sun, 28 Dec 2008) | 1 line
  
  Revert formatting changes: ascii_formatd only works for double, so we can't use it as it is for our formatting needs.
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  r6221 | cdavid | 2008-12-28 15:44:06 +0900 (Sun, 28 Dec 2008) | 1 line
  
  Do not add doc sources through add_data_dir: it will put the docs alongside numpy, as a separate package, which is not what we want. Use the manifest instead, since that's the only way I know of to include something in sdist-generated tarballs.
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  r6235 | cdavid | 2008-12-29 16:57:52 +0900 (Mon, 29 Dec 2008) | 13 lines
  
  Merged revisions 6233-6234 via svnmerge from 
  http://svn.scipy.org/svn/numpy/branches/fix_float_format
  
  ........
    r6233 | cdavid | 2008-12-29 12:49:09 +0900 (Mon, 29 Dec 2008) | 1 line
    
    Use parametric tests for format tests so that it is clearer which type is failing.
  ........
    r6234 | cdavid | 2008-12-29 12:49:27 +0900 (Mon, 29 Dec 2008) | 1 line
    
    Fix formatting tests: cfloat and cdouble as well as np.float and np.double are the same; make sure we test 4 bytes float.
  ........
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  r6236 | cdavid | 2008-12-29 17:02:15 +0900 (Mon, 29 Dec 2008) | 1 line
  
  Add nan/inf tests for formatting.
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  r6237 | cdavid | 2008-12-29 17:26:04 +0900 (Mon, 29 Dec 2008) | 1 line
  
  Add test for real float types locale independance.
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  r6238 | cdavid | 2008-12-29 17:35:06 +0900 (Mon, 29 Dec 2008) | 1 line
  
  Clearer error messages for formatting failures.
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  r6240 | cdavid | 2008-12-30 12:48:11 +0900 (Tue, 30 Dec 2008) | 1 line
  
  Add tests for print of float types.
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  r6241 | cdavid | 2008-12-30 12:56:54 +0900 (Tue, 30 Dec 2008) | 1 line
  
  Add print tests for complex types.
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  r6244 | cdavid | 2008-12-30 13:20:48 +0900 (Tue, 30 Dec 2008) | 1 line
  
  Fix test for print: forgot to make sure the value is a float before comparing it.
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  r6250 | cdavid | 2008-12-30 14:02:28 +0900 (Tue, 30 Dec 2008) | 17 lines
  
  Merged revisions 6247-6249 via svnmerge from 
  http://svn.scipy.org/svn/numpy/branches/fix_float_format
  
  ........
    r6247 | cdavid | 2008-12-30 13:41:37 +0900 (Tue, 30 Dec 2008) | 1 line
    
    Handle 1e10 specially, as it is the limit where exp notation is shorter than decimal for single precision, but not for double (python native one).
  ........
    r6248 | cdavid | 2008-12-30 13:47:38 +0900 (Tue, 30 Dec 2008) | 1 line
    
    Refactor a bit redirected output print test.
  ........
    r6249 | cdavid | 2008-12-30 13:49:31 +0900 (Tue, 30 Dec 2008) | 1 line
    
    Fix test for single precision print.
  ........
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  r6251 | cdavid | 2008-12-30 14:12:50 +0900 (Tue, 30 Dec 2008) | 1 line
  
  Use np.inf instead of float('inf'), as the later does not work on windows for python < 2.6.
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  r6253 | cdavid | 2008-12-30 14:15:09 +0900 (Tue, 30 Dec 2008) | 1 line
  
  Fix typo in test.
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  r6256 | cdavid | 2008-12-30 14:34:22 +0900 (Tue, 30 Dec 2008) | 1 line
  
  Special case float tests on windows: python 2.5 and below have >=3 digits in the exp.
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  r6258 | cdavid | 2008-12-30 14:42:03 +0900 (Tue, 30 Dec 2008) | 1 line
  
  Hardcode reference for inf/nan-involved values.
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  r6260 | cdavid | 2008-12-30 14:50:18 +0900 (Tue, 30 Dec 2008) | 1 line
  
  Fix more formatting tests on win32.
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  r6261 | cdavid | 2008-12-30 14:52:16 +0900 (Tue, 30 Dec 2008) | 1 line
  
  Fix some more redirected output print tests.
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  r6263 | cdavid | 2008-12-30 15:01:31 +0900 (Tue, 30 Dec 2008) | 1 line
  
  More fixes for print tests.
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  r6265 | cdavid | 2008-12-30 15:03:56 +0900 (Tue, 30 Dec 2008) | 1 line
  
  Fix typo.
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  r6266 | cdavid | 2008-12-30 15:08:06 +0900 (Tue, 30 Dec 2008) | 1 line
  
  Fix typo.
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  r6268 | cdavid | 2008-12-30 15:12:26 +0900 (Tue, 30 Dec 2008) | 1 line
  
  complex scalar arrays cannot be created from real/imag args: wrap init values in a complex.
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  r6271 | cdavid | 2008-12-30 15:32:03 +0900 (Tue, 30 Dec 2008) | 1 line
  
  Do not use dict for reference: hashing on scalar arrays does not work as I expected.
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  r6283 | ptvirtan | 2008-12-31 10:14:47 +0900 (Wed, 31 Dec 2008) | 1 line
  
  Fix #951: make tests to clean temp files properly
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  r6284 | jarrod.millman | 2009-01-01 08:25:03 +0900 (Thu, 01 Jan 2009) | 2 lines
  
  ran reindent
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  r6285 | alan.mcintyre | 2009-01-01 08:46:34 +0900 (Thu, 01 Jan 2009) | 15 lines
  
  Remove the following deprecated items from numpy.testing:
  
  - ParametricTestCase 
  - The following arguments from numpy.testing.Tester.test(): level, 
  verbosity, 
    all, sys_argv, testcase_pattern
  - Path manipulation functions: set_package_path, set_local_path, 
  restore_path
  - NumpyTestCase, NumpyTest
  
  Also separated testing parameter setup from NoseTester.test into 
  NoseTester.prepare_test_args for use in a utility script for valgrind 
  testing (see NumPy ticket #784).
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  r6286 | jarrod.millman | 2009-01-01 16:56:53 +0900 (Thu, 01 Jan 2009) | 2 lines
  
  add default include dir for Fedora/Red Hat (see SciPy ticket 817)
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  r6291 | cdavid | 2009-01-04 19:57:39 +0900 (Sun, 04 Jan 2009) | 1 line
  
  Do not import md5 on python >= 2.6; use hashlib instead.
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  r6292 | cdavid | 2009-01-04 20:08:16 +0900 (Sun, 04 Jan 2009) | 1 line
  
  Do not use popen* but subprocess.Popen instead.
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  r6293 | cdavid | 2009-01-04 21:03:29 +0900 (Sun, 04 Jan 2009) | 1 line
  
  Revert md5 change: hashlib.md5 is not a drop-in replacement for md5.
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  r6294 | pierregm | 2009-01-05 05:16:00 +0900 (Mon, 05 Jan 2009) | 2 lines
  
  * adapted default_fill_value for flexible datatype
  * fixed max/minimum_fill_value for flexible datatype
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  r6295 | stefan | 2009-01-06 06:51:18 +0900 (Tue, 06 Jan 2009) | 1 line
  
  Credit more developers.
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  r6296 | pierregm | 2009-01-06 07:52:21 +0900 (Tue, 06 Jan 2009) | 1 line
  
  *moved the printing templates out of MaskedArray.__repr__
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  r6297 | stefan | 2009-01-06 19:09:00 +0900 (Tue, 06 Jan 2009) | 1 line
  
  Use new-style classes with multiple-inheritance to address bug in IronPython.
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  r6298 | pierregm | 2009-01-07 05:35:37 +0900 (Wed, 07 Jan 2009) | 1 line
  
  * Bugfix #961
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  r6299 | pierregm | 2009-01-08 03:14:12 +0900 (Thu, 08 Jan 2009) | 1 line
  
  * Fixed iadd/isub/imul when the base array has no mask but the other array does
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  r6300 | pierregm | 2009-01-08 07:34:51 +0900 (Thu, 08 Jan 2009) | 3 lines
  
  * Renamed `torecords` to `toflex`, keeping `torecords` as an alias
  * Introduced `fromflex`, to reconstruct a masked_array from the output of `toflex` (can?\226?\128?\153t `use fromrecords` as it would clash with `numpy.ma.mrecords.fromrecords`)
  * Fixed a bug in MaskedBinaryOperation (#979) (wrong array broadcasting)
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  r6301 | cdavid | 2009-01-08 18:19:00 +0900 (Thu, 08 Jan 2009) | 1 line
  
  Avoid putting things into stderr when errors occurs in f2py wrappers; put all the info in the python error string instead.
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  r6302 | cdavid | 2009-01-09 00:11:32 +0900 (Fri, 09 Jan 2009) | 1 line
  
  Fix python 2.4 issue.
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  r6303 | chanley | 2009-01-09 01:30:01 +0900 (Fri, 09 Jan 2009) | 1 line
  
  Fix test_print.py function _test_locale_independance() since str(1.2) does not use the LC_NUMERIC locale to convert numbers.  Fix from Mark Sienkiewicz.
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  r6304 | cdavid | 2009-01-09 04:22:21 +0900 (Fri, 09 Jan 2009) | 1 line
  
  Revert buggy test fix for locale independecce.
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  r6305 | pierregm | 2009-01-09 05:02:29 +0900 (Fri, 09 Jan 2009) | 2 lines
  
  * Add __eq__ and __ne__ for support of flexible arrays.
  * Fixed .filled for nested structures
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  r6306 | pierregm | 2009-01-09 06:51:04 +0900 (Fri, 09 Jan 2009) | 1 line
  
  * Remove a debugging print statement.
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  r6307 | jarrod.millman | 2009-01-09 11:14:35 +0900 (Fri, 09 Jan 2009) | 2 lines
  
  Updated license file
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  r6308 | cdavid | 2009-01-09 14:26:58 +0900 (Fri, 09 Jan 2009) | 1 line
  
  Tag formatting unit tests as known failures.
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  r6309 | jarrod.millman | 2009-01-09 17:59:29 +0900 (Fri, 09 Jan 2009) | 2 lines
  
  should be more reliable way to determine what bit platform
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  r6310 | jarrod.millman | 2009-01-09 18:14:17 +0900 (Fri, 09 Jan 2009) | 2 lines
  
  better default library paths for 64bit arch
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  r6311 | jarrod.millman | 2009-01-09 18:57:15 +0900 (Fri, 09 Jan 2009) | 2 lines
  
  simplification suggested by stefan
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  r6312 | jarrod.millman | 2009-01-09 19:02:09 +0900 (Fri, 09 Jan 2009) | 2 lines
  
  switch the order [lib,lib64] --> [lib64,lib] 
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  r6313 | jarrod.millman | 2009-01-09 19:18:29 +0900 (Fri, 09 Jan 2009) | 2 lines
  
  removed unneeded import
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  r6314 | jarrod.millman | 2009-01-10 04:37:16 +0900 (Sat, 10 Jan 2009) | 2 lines
  
  can't use append an int to a string
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  r6315 | pierregm | 2009-01-10 05:18:12 +0900 (Sat, 10 Jan 2009) | 2 lines
  
  * Added flatten_structured_arrays
  * Fixed _get_recordarray for nested structures
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  r6316 | pierregm | 2009-01-10 10:53:05 +0900 (Sat, 10 Jan 2009) | 1 line
  
  * Add flatten_structured_array to the namespace
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  r6320 | pierregm | 2009-01-14 06:01:58 +0900 (Wed, 14 Jan 2009) | 9 lines
  
  numpy.ma.core:
  * introduced baseclass, sharedmask and hardmask as readonly properties of MaskedArray
  * docstrings update
  
  numpy.ma.extras:
  * docstring updates
  
  docs/reference
  * introduced maskedarray, maskedarray.baseclass, maskedarray.generic
................
  r6321 | stefan | 2009-01-14 16:14:27 +0900 (Wed, 14 Jan 2009) | 2 lines
  
  Docstring: remove old floating point arithmetic, parallel
  execution and postponed import references.
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  r6322 | stefan | 2009-01-14 16:55:16 +0900 (Wed, 14 Jan 2009) | 1 line
  
  Fix printing of limits.
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  r6323 | stefan | 2009-01-14 16:56:10 +0900 (Wed, 14 Jan 2009) | 1 line
  
  Fix finfo to work on all instances, not just NumPy scalars.
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  r6324 | pierregm | 2009-01-17 09:15:15 +0900 (Sat, 17 Jan 2009) | 1 line
  
  * fixed _arraymethod.__call__ for structured arrays
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  r6325 | ptvirtan | 2009-01-18 06:24:13 +0900 (Sun, 18 Jan 2009) | 3 lines
  
  Make `trapz` accept 1-D `x` parameter for n-d `y`, even if axis != -1.
  
  Additional tests included.
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  r6326 | pierregm | 2009-01-19 17:53:53 +0900 (Mon, 19 Jan 2009) | 3 lines
  
  * renamed FlatIter to MaskedIterator
  * added __getitem__ to MaskedIterator
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  r6327 | pierregm | 2009-01-19 18:01:24 +0900 (Mon, 19 Jan 2009) | 2 lines
  
  * replace np.asarray by np.asanyarray in unique1d
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  r6328 | pierregm | 2009-01-19 18:04:20 +0900 (Mon, 19 Jan 2009) | 2 lines
  
  * add intersect1d, intersect1d_nu, setdiff1d, setmember1d, setxor1d, unique1d, union1d
  * use np.atleast1d instead of ma.atleast1d
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  r6329 | pierregm | 2009-01-20 06:22:52 +0900 (Tue, 20 Jan 2009) | 3 lines
  
  * lib     : introduced _iotools
  * lib.io : introduced genfromtxt, ndfromtxt, mafromtxt, recfromtxt, recfromcsv.
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  r6330 | pierregm | 2009-01-22 14:37:36 +0900 (Thu, 22 Jan 2009) | 1 line
  
  * genfromtxt : if names is True, accept a line starting with a comment character as header.
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  r6331 | pierregm | 2009-01-22 14:40:25 +0900 (Thu, 22 Jan 2009) | 1 line
  
  * added recfunctions, a collection of utilities to manipulate structured arrays.
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  r6332 | pierregm | 2009-01-23 03:21:32 +0900 (Fri, 23 Jan 2009) | 2 lines
  
  * fixed a machine-dependent issue on default int ('<i4' on OS X, '<i8' on linux) ?
  * fixed an machine-dependent issue on argsort ?
................
  r6333 | cdavid | 2009-01-24 17:02:14 +0900 (Sat, 24 Jan 2009) | 1 line
  
  Fix compilation error on 2.4.
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  r6334 | pierregm | 2009-01-27 06:04:26 +0900 (Tue, 27 Jan 2009) | 7 lines
  
  * _iotools.StringConverter :
      - add a _checked attribute to indicate whether the converter has been upgraded or not.
      - switched the default value for bool to False
  * io.genfromtxt:
      - fixed for the case where a whole column is masked: switch to bool or the common dtype (if needed)
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  r6335 | pierregm | 2009-01-27 11:46:26 +0900 (Tue, 27 Jan 2009) | 1 line
  
  * prevent MaskedBinaryOperation and DomainedBinaryOperation to shrink the mask of the output when at least one of the inputs has a mask full of False
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  r6336 | matthew.brett@gmail.com | 2009-01-30 09:26:44 +0900 (Fri, 30 Jan 2009) | 1 line
  
  New docstrings for byteorder and newbyteorder()
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  r6337 | pierregm | 2009-02-02 14:20:17 +0900 (Mon, 02 Feb 2009) | 2 lines
  
  * Added a 'autoconvert' option to stack_arrays.
  * Fixed 'stack_arrays' to work with fields with titles.
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  r6338 | pierregm | 2009-02-04 02:11:44 +0900 (Wed, 04 Feb 2009) | 1 line
  
  * Make sure that StringConverter.update sets the type to object if it can't define it.
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  r6339 | pierregm | 2009-02-05 05:52:36 +0900 (Thu, 05 Feb 2009) | 2 lines
  
  * test__iotools : prevent test_upgrademapper if dateutil is not installed
  * MaskedArray.__rmul__ : switch to multiply(self, other)
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  r6340 | pierregm | 2009-02-05 06:53:05 +0900 (Thu, 05 Feb 2009) | 1 line
  
  test_upgrademapper : got rid of the dateutil import
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  r6341 | pierregm | 2009-02-05 13:31:51 +0900 (Thu, 05 Feb 2009) | 2 lines
  
  *  genfromtxt : Fixed when a dtype involving objects is explicitly given. Raise a NotImplementedError if the dtype is nested.
  * _iotools : make sure StringConverter gets properly initiated when a function returning a np.object is used as input parameter.
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  r6342 | alan.mcintyre | 2009-02-06 05:11:40 +0900 (Fri, 06 Feb 2009) | 6 lines
  
  Issue #957:
  - Fix problems with test decorators when used on test generators.  
  - The skip/fail arguments for skipif and knownfailureif can now be 
    either a bool or a callable that returns a bool.
  - Added tests for the test decorators. 
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  r6343 | ptvirtan | 2009-02-06 09:27:08 +0900 (Fri, 06 Feb 2009) | 1 line
  
  doc/numpydoc: work better together with Sphinx's  config option
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  r6344 | ptvirtan | 2009-02-06 09:51:41 +0900 (Fri, 06 Feb 2009) | 1 line
  
  doc: Move maskedarray docs upward in TOC
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  r6345 | oliphant | 2009-02-06 15:25:50 +0900 (Fri, 06 Feb 2009) | 1 line
  
  Avoid re-creating the sequence when there is only one field in the regular expression.
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  r6346 | oliphant | 2009-02-06 15:31:11 +0900 (Fri, 06 Feb 2009) | 1 line
  
  Removed an unneccessary return statement in a unit test.
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  r6347 | pearu | 2009-02-06 23:36:58 +0900 (Fri, 06 Feb 2009) | 1 line
  
  Fix a bug: python system_info.py failed because _pkg_config_info defined section to be None.
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  r6348 | pearu | 2009-02-06 23:38:57 +0900 (Fri, 06 Feb 2009) | 1 line
  
  Fix another bug, see last commit.
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  r6349 | pierregm | 2009-02-07 18:19:12 +0900 (Sat, 07 Feb 2009) | 2 lines
  
  MaskedArray.resize : systematically raise a TypeError exception, as a masked array never owns its data
  MaskedIterator : fixed to allow .flat on masked matrices
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  r6350 | pierregm | 2009-02-08 03:51:31 +0900 (Sun, 08 Feb 2009) | 1 line
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  r6351 | ptvirtan | 2009-02-10 05:18:08 +0900 (Tue, 10 Feb 2009) | 1 line
  
  Fix #955: fix errobj leak in scalarmath floating point error handling
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  r6352 | pierregm | 2009-02-10 09:42:40 +0900 (Tue, 10 Feb 2009) | 1 line
  
  * prevent modifications to the mask to be back-propagated w/ __array_wrap__
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  r6354 | cdavid | 2009-02-10 19:44:01 +0900 (Tue, 10 Feb 2009) | 1 line
  
  Fix hyphen (patch from debian package).
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  r6356 | pierregm | 2009-02-11 10:51:28 +0900 (Wed, 11 Feb 2009) | 1 line
  
  * MaskedArray.__array_wrap__ : forces the domain (if any) to a ndarray (fill with True)
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  r6358 | oliphant | 2009-02-12 13:22:03 +0900 (Thu, 12 Feb 2009) | 1 line
  
  Add multiple-field access by making a copy of the array and filling with the selected fields.
................
  r6359 | stefan | 2009-02-12 14:44:07 +0900 (Thu, 12 Feb 2009) | 2 lines
  
  Trust user's specification of MACOSX_DEPLOYMENT_TARGET [patch by Brian
  Granger].
................
  r6360 | cdavid | 2009-02-14 23:54:26 +0900 (Sat, 14 Feb 2009) | 1 line
  
  Merge fix_float_format branch into the trunk.
................
  r6361 | cdavid | 2009-02-15 00:02:39 +0900 (Sun, 15 Feb 2009) | 1 line
  
  Fix typo in multiarray tests.
................
  r6362 | cdavid | 2009-02-15 00:03:22 +0900 (Sun, 15 Feb 2009) | 1 line
  
  Remove leftover in TestIO.
................
  r6363 | cdavid | 2009-02-15 02:03:51 +0900 (Sun, 15 Feb 2009) | 1 line
  
  Include C99 math compatbility layer in multiarray - isnan and co needed by numpyos.c
................
  r6364 | ptvirtan | 2009-02-15 07:09:26 +0900 (Sun, 15 Feb 2009) | 1 line
  
  More add_newdocs entries, and make add_newdoc capable of adding docs also to normal Python objects.
................
  r6365 | ptvirtan | 2009-02-15 07:10:24 +0900 (Sun, 15 Feb 2009) | 1 line
  
  Move (un)packbits docstrings to add_newdocs.py. Fix typos.
................
  r6366 | ptvirtan | 2009-02-15 07:11:19 +0900 (Sun, 15 Feb 2009) | 1 line
  
  Document constants in numpy.doc.constants
................
  r6367 | ptvirtan | 2009-02-15 07:38:32 +0900 (Sun, 15 Feb 2009) | 1 line
  
  Move numpy.lib __doc__ back to info.py; was moved to __init__.py by mistake.
................
  r6368 | pierregm | 2009-02-15 07:42:29 +0900 (Sun, 15 Feb 2009) | 1 line
  
  * genfromtxt : fixed case when using explicit converters and explicit dtype.
................
  r6370 | ptvirtan | 2009-02-16 00:44:47 +0900 (Mon, 16 Feb 2009) | 1 line
  
  sphinxext: clean up plot directive, and merge some features from matplotlib
................
  r6371 | charris | 2009-02-18 06:19:10 +0900 (Wed, 18 Feb 2009) | 2 lines
  
  Coding style cleanups.
................
  r6372 | cdavid | 2009-02-18 14:06:57 +0900 (Wed, 18 Feb 2009) | 1 line
  
  Fix some const issues in NumPyOs_ascii_strtod.
................
  r6373 | charris | 2009-02-18 14:36:35 +0900 (Wed, 18 Feb 2009) | 1 line
  
  Coding style cleanups.
................
  r6398 | charris | 2009-02-19 05:54:52 +0900 (Thu, 19 Feb 2009) | 2 lines
  
  Coding style cleanups.
................
  r6399 | charris | 2009-02-19 09:45:14 +0900 (Thu, 19 Feb 2009) | 2 lines
  
  Coding style cleanups.
................
  r6400 | charris | 2009-02-19 13:58:23 +0900 (Thu, 19 Feb 2009) | 1 line
  
  Coding style cleanups.
................
  r6410 | cdavid | 2009-02-19 19:05:28 +0900 (Thu, 19 Feb 2009) | 1 line
  
  Tag known failure on win32.
................
  r6421 | stefan | 2009-02-20 04:28:08 +0900 (Fri, 20 Feb 2009) | 1 line
  
  Fix tests using strptime to be Python 2.4 compatible.
................
  r6422 | charris | 2009-02-20 08:25:01 +0900 (Fri, 20 Feb 2009) | 2 lines
  
  Coding style cleanups.
................
  r6423 | charris | 2009-02-20 12:40:53 +0900 (Fri, 20 Feb 2009) | 1 line
  
  Coding style cleanups.
................
  r6424 | cdavid | 2009-02-20 22:30:20 +0900 (Fri, 20 Feb 2009) | 1 line
  
  Unhelpful message for compaq fortran compiler.
................

1 files changed, 261 insertions, 101 deletions

diff --git a/numpy/ma/extras.py b/numpy/ma/extras.py
index cf80180e4..b2f06ea6c 100644
--- a/numpy/ma/extras.py
+++ b/numpy/ma/extras.py
@@ -19,11 +19,14 @@ __all__ = ['apply_along_axis', 'atleast_1d', 'atleast_2d', 'atleast_3d',
            'ediff1d',
            'flatnotmasked_contiguous', 'flatnotmasked_edges',
            'hsplit', 'hstack',
+           'intersect1d', 'intersect1d_nu',
            'mask_cols', 'mask_rowcols', 'mask_rows', 'masked_all',
            'masked_all_like', 'median', 'mr_',
            'notmasked_contiguous', 'notmasked_edges',
            'polyfit',
            'row_stack',
+           'setdiff1d', 'setmember1d', 'setxor1d',
+           'unique1d', 'union1d',
            'vander', 'vstack',
            ]
 
@@ -45,22 +48,19 @@ from numpy.linalg import lstsq
 #...............................................................................
 def issequence(seq):
     """Is seq a sequence (ndarray, list or tuple)?"""
-    if isinstance(seq, ndarray):
-        return True
-    elif isinstance(seq, tuple):
-        return True
-    elif isinstance(seq, list):
+    if isinstance(seq, (ndarray, tuple, list)):
         return True
     return False
 
 def count_masked(arr, axis=None):
-    """Count the number of masked elements along the given axis.
+    """
+    Count the number of masked elements along the given axis.
 
     Parameters
     ----------
-        axis : int, optional
-            Axis along which to count.
-            If None (default), a flattened version of the array is used.
+    axis : int, optional
+        Axis along which to count.
+        If None (default), a flattened version of the array is used.
 
     """
     m = getmaskarray(arr)
@@ -136,9 +136,12 @@ class _fromnxfunction:
                 res.append(masked_array(_d, mask=_m))
             return res
 
-atleast_1d = _fromnxfunction('atleast_1d')
-atleast_2d = _fromnxfunction('atleast_2d')
-atleast_3d = _fromnxfunction('atleast_3d')
+#atleast_1d = _fromnxfunction('atleast_1d')
+#atleast_2d = _fromnxfunction('atleast_2d')
+#atleast_3d = _fromnxfunction('atleast_3d')
+atleast_1d = np.atleast_1d
+atleast_2d = np.atleast_2d
+atleast_3d = np.atleast_3d
 
 vstack = row_stack = _fromnxfunction('vstack')
 hstack = _fromnxfunction('hstack')
@@ -252,7 +255,8 @@ apply_along_axis.__doc__ = np.apply_along_axis.__doc__
 
 
 def average(a, axis=None, weights=None, returned=False):
-    """Average the array over the given axis.
+    """
+    Average the array over the given axis.
 
     Parameters
     ----------
@@ -440,10 +444,10 @@ def median(a, axis=None, out=None, overwrite_input=False):
 #..............................................................................
 def compress_rowcols(x, axis=None):
     """
-    Suppress the rows and/or columns of a 2D array that contains
+    Suppress the rows and/or columns of a 2D array that contain
     masked values.
 
-    The suppression behavior is selected with the `axis`parameter.
+    The suppression behavior is selected with the `axis` parameter.
 
         - If axis is None, rows and columns are suppressed.
         - If axis is 0, only rows are suppressed.
@@ -482,13 +486,15 @@ def compress_rowcols(x, axis=None):
     return x._data[idxr][:,idxc]
 
 def compress_rows(a):
-    """Suppress whole rows of a 2D array that contain masked values.
+    """
+    Suppress whole rows of a 2D array that contain masked values.
 
     """
     return compress_rowcols(a, 0)
 
 def compress_cols(a):
-    """Suppress whole columnss of a 2D array that contain masked values.
+    """
+    Suppress whole columns of a 2D array that contain masked values.
 
     """
     return compress_rowcols(a, 1)
@@ -530,30 +536,35 @@ def mask_rowcols(a, axis=None):
     return a
 
 def mask_rows(a, axis=None):
-    """Mask whole rows of a 2D array that contain masked values.
+    """
+    Mask whole rows of a 2D array that contain masked values.
 
     Parameters
     ----------
-        axis : int, optional
-            Axis along which to perform the operation.
-            If None, applies to a flattened version of the array.
+    axis : int, optional
+        Axis along which to perform the operation.
+        If None, applies to a flattened version of the array.
+
     """
     return mask_rowcols(a, 0)
 
 def mask_cols(a, axis=None):
-    """Mask whole columns of a 2D array that contain masked values.
+    """
+    Mask whole columns of a 2D array that contain masked values.
 
     Parameters
     ----------
-        axis : int, optional
-            Axis along which to perform the operation.
-            If None, applies to a flattened version of the array.
+    axis : int, optional
+        Axis along which to perform the operation.
+        If None, applies to a flattened version of the array.
+
     """
     return mask_rowcols(a, 1)
 
 
 def dot(a,b, strict=False):
-    """Return the dot product of two 2D masked arrays a and b.
+    """
+    Return the dot product of two 2D masked arrays a and b.
 
     Like the generic numpy equivalent, the product sum is over the last
     dimension of a and the second-to-last dimension of b.  If strict is True,
@@ -582,72 +593,211 @@ def dot(a,b, strict=False):
     m = ~np.dot(am, bm)
     return masked_array(d, mask=m)
 
-#...............................................................................
-def ediff1d(array, to_end=None, to_begin=None):
-    """Return the differences between consecutive elements of an
-    array, possibly with prefixed and/or appended values.
+#####--------------------------------------------------------------------------
+#---- --- arraysetops ---
+#####--------------------------------------------------------------------------
 
-    Parameters
-    ----------
-        array : {array}
-            Input array,  will be flattened before the difference is taken.
-        to_end : {number}, optional
-            If provided, this number will be tacked onto the end of the returned
-            differences.
-        to_begin : {number}, optional
-            If provided, this number will be taked onto the beginning of the
-            returned differences.
+def ediff1d(arr, to_end=None, to_begin=None):
+    """
+    Computes the differences between consecutive elements of an array.
+
+    This function is the equivalent of `numpy.ediff1d` that takes masked
+    values into account.
+
+    See Also
+    --------
+    numpy.eddif1d : equivalent function for ndarrays.
 
     Returns
     -------
-          ed : {array}
-            The differences. Loosely, this will be (ary[1:] - ary[:-1]).
-
+    output : MaskedArray
+    
     """
-    a = masked_array(array, copy=True)
-    if a.ndim > 1:
-        a.reshape((a.size,))
-    (d, m, n) = (a._data, a._mask, a.size-1)
-    dd = d[1:]-d[:-1]
-    if m is nomask:
-        dm = nomask
-    else:
-        dm = m[1:]-m[:-1]
+    arr = ma.asanyarray(arr).flat
+    ed = arr[1:] - arr[:-1]
+    arrays = [ed]
     #
+    if to_begin is not None:
+        arrays.insert(0, to_begin)
     if to_end is not None:
-        to_end = asarray(to_end)
-        nend = to_end.size
-        if to_begin is not None:
-            to_begin = asarray(to_begin)
-            nbegin = to_begin.size
-            r_data = np.empty((n+nend+nbegin,), dtype=a.dtype)
-            r_mask = np.zeros((n+nend+nbegin,), dtype=bool)
-            r_data[:nbegin] = to_begin._data
-            r_mask[:nbegin] = to_begin._mask
-            r_data[nbegin:-nend] = dd
-            r_mask[nbegin:-nend] = dm
-        else:
-            r_data = np.empty((n+nend,), dtype=a.dtype)
-            r_mask = np.zeros((n+nend,), dtype=bool)
-            r_data[:-nend] = dd
-            r_mask[:-nend] = dm
-        r_data[-nend:] = to_end._data
-        r_mask[-nend:] = to_end._mask
+        arrays.append(to_end)
+    #
+    if len(arrays) != 1:
+        # We'll save ourselves a copy of a potentially large array in the common
+        # case where neither to_begin or to_end was given.
+        ed = hstack(arrays)
+    #
+    return ed
+
+
+def unique1d(ar1, return_index=False, return_inverse=False):
+    """
+    Finds the unique elements of an array.
+
+    Masked values are considered the same element (masked).
+
+    The output array is always a MaskedArray.
+
+    See Also
+    --------
+    np.unique1d : equivalent function for ndarrays.
+    """
+    output = np.unique1d(ar1,
+                         return_index=return_index,
+                         return_inverse=return_inverse)
+    if isinstance(output, tuple):
+        output = list(output)
+        output[0] = output[0].view(MaskedArray)
+        output = tuple(output)
+    else:
+        output = output.view(MaskedArray)
+    return output
+
+
+def intersect1d(ar1, ar2):
+    """
+    Returns the repeated or unique elements belonging to the two arrays.
+
+    Masked values are assumed equals one to the other.
+    The output is always a masked array
+
+    See Also
+    --------
+    numpy.intersect1d : equivalent function for ndarrays.
+
+    Examples
+    --------
+    >>> x = array([1, 3, 3, 3], mask=[0, 0, 0, 1])
+    >>> y = array([3, 1, 1, 1], mask=[0, 0, 0, 1])
+    >>> intersect1d(x, y)
+    masked_array(data = [1 1 3 3 --],
+                 mask = [False False False False  True],
+           fill_value = 999999)
+    """
+    aux = ma.concatenate((ar1,ar2))
+    aux.sort()
+    return aux[aux[1:] == aux[:-1]]
+
+
+
+def intersect1d_nu(ar1, ar2):
+    """
+    Returns the unique elements common to both arrays.
+
+    Masked values are considered equal one to the other.
+    The output is always a masked array.
+
+    See Also
+    --------
+    intersect1d : Returns repeated or unique common elements.
+    numpy.intersect1d_nu : equivalent function for ndarrays.
+
+    Examples
+    --------
+    >>> x = array([1, 3, 3, 3], mask=[0, 0, 0, 1])
+    >>> y = array([3, 1, 1, 1], mask=[0, 0, 0, 1])
+    >>> intersect1d_nu(x, y)
+    masked_array(data = [1 3 --],
+                 mask = [False False  True],
+           fill_value = 999999)
+
+    """
+    # Might be faster than unique1d( intersect1d( ar1, ar2 ) )?
+    aux = ma.concatenate((unique1d(ar1), unique1d(ar2)))
+    aux.sort()
+    return aux[aux[1:] == aux[:-1]]
+
+
+
+def setxor1d(ar1, ar2):
+    """
+    Set exclusive-or of 1D arrays with unique elements.
+
+    See Also
+    --------
+    numpy.setxor1d : equivalent function for ndarrays
+
+    """
+    aux = ma.concatenate((ar1, ar2))
+    if aux.size == 0:
+        return aux
+    aux.sort()
+    auxf = aux.filled()
+#    flag = ediff1d( aux, to_end = 1, to_begin = 1 ) == 0
+    flag = ma.concatenate(([True], (auxf[1:] != auxf[:-1]), [True]))
+#    flag2 = ediff1d( flag ) == 0
+    flag2 = (flag[1:] == flag[:-1])
+    return aux[flag2]
+
+
+def setmember1d(ar1, ar2):
+    """
+    Return a boolean array set True where first element is in second array.
+
+    See Also
+    --------
+    numpy.setmember1d : equivalent function for ndarrays.
+
+    """
+    ar1 = ma.asanyarray(ar1)
+    ar2 = ma.asanyarray( ar2 )
+    ar = ma.concatenate((ar1, ar2 ))
+    b1 = ma.zeros(ar1.shape, dtype = np.int8)
+    b2 = ma.ones(ar2.shape, dtype = np.int8)
+    tt = ma.concatenate((b1, b2))
+
+    # We need this to be a stable sort, so always use 'mergesort' here. The
+    # values from the first array should always come before the values from the
+    # second array.
+    perm = ar.argsort(kind='mergesort')
+    aux = ar[perm]
+    aux2 = tt[perm]
+#    flag = ediff1d( aux, 1 ) == 0
+    flag = ma.concatenate((aux[1:] == aux[:-1], [False]))
+    ii = ma.where( flag * aux2 )[0]
+    aux = perm[ii+1]
+    perm[ii+1] = perm[ii]
+    perm[ii] = aux
     #
-    elif to_begin is not None:
-        to_begin = asarray(to_begin)
-        nbegin = to_begin.size
-        r_data = np.empty((n+nbegin,), dtype=a.dtype)
-        r_mask = np.zeros((n+nbegin,), dtype=bool)
-        r_data[:nbegin] = to_begin._data
-        r_mask[:nbegin] = to_begin._mask
-        r_data[nbegin:] = dd
-        r_mask[nbegin:] = dm
+    indx = perm.argsort(kind='mergesort')[:len( ar1 )]
     #
+    return flag[indx]
+
+
+def union1d(ar1, ar2):
+    """
+    Union of 1D arrays with unique elements.
+
+    See also
+    --------
+    numpy.union1d : equivalent function for ndarrays.
+
+    """
+    return unique1d(ma.concatenate((ar1, ar2)))
+
+
+def setdiff1d(ar1, ar2):
+    """
+    Set difference of 1D arrays with unique elements.
+
+    See Also
+    --------
+    numpy.setdiff1d : equivalent function for ndarrays
+
+    """
+    aux = setmember1d(ar1,ar2)
+    if aux.size == 0:
+        return aux
     else:
-        r_data = dd
-        r_mask = dm
-    return masked_array(r_data, mask=r_mask)
+        return ma.asarray(ar1)[aux == 0]
+
+
+
+#####--------------------------------------------------------------------------
+#---- --- Covariance ---
+#####--------------------------------------------------------------------------
+
+
 
 
 def _covhelper(x, y=None, rowvar=True, allow_masked=True):
@@ -747,7 +897,8 @@ def cov(x, y=None, rowvar=True, bias=False, allow_masked=True):
 
 
 def corrcoef(x, y=None, rowvar=True, bias=False, allow_masked=True):
-    """The correlation coefficients formed from the array x, where the
+    """
+    The correlation coefficients formed from the array x, where the
     rows are the observations, and the columns are variables.
 
     corrcoef(x,y) where x and y are 1d arrays is the same as
@@ -818,7 +969,8 @@ def corrcoef(x, y=None, rowvar=True, bias=False, allow_masked=True):
 #####--------------------------------------------------------------------------
 
 class MAxisConcatenator(AxisConcatenator):
-    """Translate slice objects to concatenation along an axis.
+    """
+    Translate slice objects to concatenation along an axis.
 
     """
 
@@ -877,11 +1029,13 @@ class MAxisConcatenator(AxisConcatenator):
         return self._retval(res)
 
 class mr_class(MAxisConcatenator):
-    """Translate slice objects to concatenation along the first axis.
+    """
+    Translate slice objects to concatenation along the first axis.
 
-    For example:
-        >>> np.ma.mr_[np.ma.array([1,2,3]), 0, 0, np.ma.array([4,5,6])]
-        array([1, 2, 3, 0, 0, 4, 5, 6])
+    Examples
+    --------
+    >>> np.ma.mr_[np.ma.array([1,2,3]), 0, 0, np.ma.array([4,5,6])]
+    array([1, 2, 3, 0, 0, 4, 5, 6])
 
     """
     def __init__(self):
@@ -894,7 +1048,8 @@ mr_ = mr_class()
 #####--------------------------------------------------------------------------
 
 def flatnotmasked_edges(a):
-    """Find the indices of the first and last not masked values in a
+    """
+    Find the indices of the first and last not masked values in a
     1D masked array.  If all values are masked, returns None.
 
     """
@@ -907,8 +1062,10 @@ def flatnotmasked_edges(a):
     else:
         return None
 
+
 def notmasked_edges(a, axis=None):
-    """Find the indices of the first and last not masked values along
+    """
+    Find the indices of the first and last not masked values along
     the given axis in a masked array.
 
     If all values are masked, return None.  Otherwise, return a list
@@ -917,9 +1074,10 @@ def notmasked_edges(a, axis=None):
 
     Parameters
     ----------
-        axis : int, optional
-            Axis along which to perform the operation.
-            If None, applies to a flattened version of the array.
+    axis : int, optional
+        Axis along which to perform the operation.
+        If None, applies to a flattened version of the array.
+
     """
     a = asarray(a)
     if axis is None or a.ndim == 1:
@@ -929,8 +1087,10 @@ def notmasked_edges(a, axis=None):
     return [tuple([idx[i].min(axis).compressed() for i in range(a.ndim)]),
             tuple([idx[i].max(axis).compressed() for i in range(a.ndim)]),]
 
+
 def flatnotmasked_contiguous(a):
-    """Find contiguous unmasked data in a flattened masked array.
+    """
+    Find contiguous unmasked data in a flattened masked array.
 
     Return a sorted sequence of slices (start index, end index).
 
@@ -950,22 +1110,22 @@ def flatnotmasked_contiguous(a):
     return result
 
 def notmasked_contiguous(a, axis=None):
-    """Find contiguous unmasked data in a masked array along the given
-    axis.
+    """
+    Find contiguous unmasked data in a masked array along the given axis.
 
     Parameters
     ----------
-        axis : int, optional
-            Axis along which to perform the operation.
-            If None, applies to a flattened version of the array.
+    axis : int, optional
+        Axis along which to perform the operation.
+        If None, applies to a flattened version of the array.
 
     Returns
     -------
-        A sorted sequence of slices (start index, end index).
+    A sorted sequence of slices (start index, end index).
 
     Notes
     -----
-        Only accepts 2D arrays at most.
+    Only accepts 2D arrays at most.
 
     """
     a = asarray(a)