[Numpy-discussion] NA masks for NumPy are ready to test

Bruce Southey bsouthey@gmail....
Fri Aug 19 12:55:13 CDT 2011


On Fri, Aug 19, 2011 at 10:48 AM, Mark Wiebe <mwwiebe@gmail.com> wrote:
> On Fri, Aug 19, 2011 at 7:15 AM, Bruce Southey <bsouthey@gmail.com> wrote:
>>
>> On 08/18/2011 04:43 PM, Mark Wiebe wrote:
>>
>> It's taken a lot of changes to get the NA mask support to its current
>> point, but the code ready for some testing now. You can read the
>> work-in-progress release notes here:
>>
>> https://github.com/m-paradox/numpy/blob/missingdata/doc/release/2.0.0-notes.rst
>> To try it out, check out the missingdata branch from my github account,
>> here, and build in the standard way:
>> https://github.com/m-paradox/numpy
>> The things most important to test are:
>> * Confirm that existing code still works correctly. I've tested against
>> SciPy and matplotlib.
>> * Confirm that the performance of code not using NA masks is the same or
>> better.
>> * Try to do computations with the NA values, find places they don't work
>> yet, and nominate unimplemented functionality important to you to be next on
>> the development list. The release notes have a preliminary list of
>> implemented/unimplemented functions.
>> * Report any crashes, build problems, or unexpected behaviors.
>> In addition to adding the NA mask, I've also added features and done a few
>> performance changes here and there, like letting reductions like sum take
>> lists of axes instead of being a single axis or all of them. These changes
>> affect various bugs
>> like http://projects.scipy.org/numpy/ticket/1143 and http://projects.scipy.org/numpy/ticket/533.
>> Thanks!
>> Mark
>> Here's a small example run using NAs:
>> >>> import numpy as np
>> >>> np.__version__
>> '2.0.0.dev-8a5e2a1'
>> >>> a = np.random.rand(3,3,3)
>> >>> a.flags.maskna = True
>> >>> a[np.random.rand(3,3,3) < 0.5] = np.NA
>> >>> a
>> array([[[NA, NA,  0.11511708],
>>         [ 0.46661454,  0.47565512, NA],
>>         [NA, NA, NA]],
>>        [[NA,  0.57860351, NA],
>>         [NA, NA,  0.72012669],
>>         [ 0.36582123, NA,  0.76289794]],
>>        [[ 0.65322748,  0.92794386, NA],
>>         [ 0.53745165,  0.97520989,  0.17515083],
>>         [ 0.71219688,  0.5184328 ,  0.75802805]]])
>> >>> np.mean(a, axis=-1)
>> array([[NA, NA, NA],
>>        [NA, NA, NA],
>>        [NA,  0.56260412,  0.66288591]])
>> >>> np.std(a, axis=-1)
>> array([[NA, NA, NA],
>>        [NA, NA, NA],
>>        [NA,  0.32710662,  0.10384331]])
>> >>> np.mean(a, axis=-1, skipna=True)
>>
>> /home/mwiebe/installtest/lib64/python2.7/site-packages/numpy/core/fromnumeric.py:2474:
>> RuntimeWarning: invalid value encountered in true_divide
>>   um.true_divide(ret, rcount, out=ret, casting='unsafe')
>> array([[ 0.11511708,  0.47113483,         nan],
>>        [ 0.57860351,  0.72012669,  0.56435958],
>>        [ 0.79058567,  0.56260412,  0.66288591]])
>> >>> np.std(a, axis=-1, skipna=True)
>>
>> /home/mwiebe/installtest/lib64/python2.7/site-packages/numpy/core/fromnumeric.py:2707:
>> RuntimeWarning: invalid value encountered in true_divide
>>   um.true_divide(arrmean, rcount, out=arrmean, casting='unsafe')
>>
>> /home/mwiebe/installtest/lib64/python2.7/site-packages/numpy/core/fromnumeric.py:2730:
>> RuntimeWarning: invalid value encountered in true_divide
>>   um.true_divide(ret, rcount, out=ret, casting='unsafe')
>> array([[ 0.        ,  0.00452029,         nan],
>>        [ 0.        ,  0.        ,  0.19853835],
>>        [ 0.13735819,  0.32710662,  0.10384331]])
>> >>> np.std(a, axis=(1,2), skipna=True)
>> array([ 0.16786895,  0.15498008,  0.23811937])
>>
>> _______________________________________________
>> NumPy-Discussion mailing list
>> NumPy-Discussion@scipy.org
>> http://mail.scipy.org/mailman/listinfo/numpy-discussion
>>
>> Hi,
>> That is great news!
>> (Python2.x will be another email.)
>>
>> Python3.1 and Python3.2 failed with building 'multiarraymodule_onefile.o'
>> but I could not see any obvious reason.
>
> I've pushed a change to fix the Python 3 build, it was a use
> of Py_TPFLAGS_CHECKTYPES, which is no longer in Python3 but is always
> default now. Tested with 3.2.
> Thanks!
> Mark
>
>>
>> I had removed my build directory and then 'python3 setup.py build' but I
>> saw this message:
>> Running from numpy source directory.
>> numpy/core/setup_common.py:86: MismatchCAPIWarning: API mismatch detected,
>> the C API version numbers have to be updated. Current C api version is 6,
>> with checksum ef5688af03ffa23dd8e11734f5b69313, but recorded checksum for C
>> API version 6 in codegen_dir/cversions.txt is
>> e61d5dc51fa1c6459328266e215d6987. If functions were added in the C API, you
>> have to update C_API_VERSION  in numpy/core/setup_common.py.
>>   MismatchCAPIWarning)
>>
>> Upstream of the build log is below.
>>
>> Bruce
>>
>> In file included from
>> numpy/core/src/multiarray/multiarraymodule_onefile.c:53:0:
>> numpy/core/src/multiarray/na_singleton.c: At top level:
>> numpy/core/src/multiarray/na_singleton.c:708:25: error:
>> ‘Py_TPFLAGS_CHECKTYPES’ undeclared here (not in a function)
>> numpy/core/src/multiarray/common.c:48:1: warning: ‘_use_default_type’
>> defined but not used
>> numpy/core/src/multiarray/ctors.h:93:1: warning: ‘_arrays_overlap’
>> declared ‘static’ but never defined
>> numpy/core/src/multiarray/scalartypes.c.src:2251:1: warning:
>> ‘gentype_getsegcount’ defined but not used
>> numpy/core/src/multiarray/scalartypes.c.src:2269:1: warning:
>> ‘gentype_getcharbuf’ defined but not used
>> numpy/core/src/multiarray/mapping.c:110:1: warning: ‘_array_ass_item’
>> defined but not used
>> numpy/core/src/multiarray/number.c:266:1: warning: ‘array_divide’ defined
>> but not used
>> numpy/core/src/multiarray/number.c:464:1: warning: ‘array_inplace_divide’
>> defined but not used
>> numpy/core/src/multiarray/buffer.c:25:1: warning: ‘array_getsegcount’
>> defined but not used
>> numpy/core/src/multiarray/buffer.c:58:1: warning: ‘array_getwritebuf’
>> defined but not used
>> numpy/core/src/multiarray/buffer.c:71:1: warning: ‘array_getcharbuf’
>> defined but not used
>> numpy/core/src/multiarray/na_mask.c:681:1: warning:
>> ‘PyArray_GetMaskInversionFunction’ defined but not used
>> In file included from numpy/core/src/multiarray/scalartypes.c.src:25:0,
>>                  from
>> numpy/core/src/multiarray/multiarraymodule_onefile.c:10:
>> numpy/core/src/multiarray/_datetime.h:9:1: warning: function declaration
>> isnât a prototype
>> In file included from
>> numpy/core/src/multiarray/multiarraymodule_onefile.c:13:0:
>> numpy/core/src/multiarray/datetime.c:33:1: warning: function declaration
>> isnât a prototype
>> In file included from
>> numpy/core/src/multiarray/multiarraymodule_onefile.c:17:0:
>> numpy/core/src/multiarray/arraytypes.c.src: In function âVOID_getitemâ:
>> numpy/core/src/multiarray/arraytypes.c.src:643:9: warning: passing
>> argument 2 of âPyArray_SetBaseObjectâ from incompatible pointer type
>>
>> build/src.linux-x86_64-3.2/numpy/core/include/numpy/__multiarray_api.h:763:12:
>> note: expected âstruct PyObject *â but argument is of type âstruct
>> PyArrayObject *â
>> In file included from
>> numpy/core/src/multiarray/multiarraymodule_onefile.c:44:0:
>> numpy/core/src/multiarray/nditer_pywrap.c: In function
>> ânpyiter_subscriptâ:
>> numpy/core/src/multiarray/nditer_pywrap.c:2395:29: warning: passing
>> argument 1 of âPySlice_GetIndicesâ from incompatible pointer type
>> /usr/local/include/python3.2m/sliceobject.h:38:5: note: expected âstruct
>> PyObject *â but argument is of type âstruct PySliceObject *â
>> numpy/core/src/multiarray/nditer_pywrap.c: In function
>> ânpyiter_ass_subscriptâ:
>> numpy/core/src/multiarray/nditer_pywrap.c:2440:29: warning: passing
>> argument 1 of âPySlice_GetIndicesâ from incompatible pointer type
>> /usr/local/include/python3.2m/sliceobject.h:38:5: note: expected âstruct
>> PyObject *â but argument is of type âstruct PySliceObject *â
>> In file included from
>> numpy/core/src/multiarray/multiarraymodule_onefile.c:53:0:
>> numpy/core/src/multiarray/na_singleton.c: At top level:
>> numpy/core/src/multiarray/na_singleton.c:708:25: error:
>> âPy_TPFLAGS_CHECKTYPESâ undeclared here (not in a function)
>> numpy/core/src/multiarray/common.c:48:1: warning: â_use_default_typeâ
>> defined but not used
>> numpy/core/src/multiarray/ctors.h:93:1: warning: â_arrays_overlapâ
>> declared âstaticâ but never defined
>> numpy/core/src/multiarray/scalartypes.c.src:2251:1: warning:
>> âgentype_getsegcountâ defined but not used
>> numpy/core/src/multiarray/scalartypes.c.src:2269:1: warning:
>> âgentype_getcharbufâ defined but not used
>> numpy/core/src/multiarray/mapping.c:110:1: warning: â_array_ass_itemâ
>> defined but not used
>> numpy/core/src/multiarray/number.c:266:1: warning: âarray_divideâ defined
>> but not used
>> numpy/core/src/multiarray/number.c:464:1: warning: âarray_inplace_divideâ
>> defined but not used
>> numpy/core/src/multiarray/buffer.c:25:1: warning: âarray_getsegcountâ
>> defined but not used
>> numpy/core/src/multiarray/buffer.c:58:1: warning: âarray_getwritebufâ
>> defined but not used
>> numpy/core/src/multiarray/buffer.c:71:1: warning: âarray_getcharbufâ
>> defined but not used
>> numpy/core/src/multiarray/na_mask.c:681:1: warning:
>> âPyArray_GetMaskInversionFunctionâ defined but not used
>> error: Command "gcc -pthread -DNDEBUG -g -fwrapv -O3 -Wall
>> -Wstrict-prototypes -fPIC -Inumpy/core/include
>> -Ibuild/src.linux-x86_64-3.2/numpy/core/include/numpy
>> -Inumpy/core/src/private -Inumpy/core/src -Inumpy/core
>> -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath
>> -Inumpy/core/src/npysort -Inumpy/core/include
>> -I/usr/local/include/python3.2m
>> -Ibuild/src.linux-x86_64-3.2/numpy/core/src/multiarray
>> -Ibuild/src.linux-x86_64-3.2/numpy/core/src/umath -c
>> numpy/core/src/multiarray/multiarraymodule_onefile.c -o
>> build/temp.linux-x86_64-3.2/numpy/core/src/multiarray/multiarraymodule_onefile.o"
>> failed with exit status 1
>>
>>
>>
>>
Thanks for the prompt responses.

That fixes the build problem for both Python3.1 and Python3.2.

I got some test errors below but I guess you are working on those.


Bruce



$ python3 -c "import numpy; numpy.test()"
Running unit tests for numpy
NumPy version 2.0.0.dev-965a5c6
NumPy is installed in /usr/lib64/python3.2/site-packages/numpy
Python version 3.2 (r32:88445, Feb 21 2011, 21:11:06) [GCC 4.6.0
20110212 (Red Hat 4.6.0-0.7)]
nose version 1.0.0
..............S.......EFF.....E............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................K...................................................................................................................................................................................................K..................................................................................................K......................K..........................................................................................................S......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................./usr/lib64/python3.2/site-packages/numpy/lib/format.py:575:
ResourceWarning: unclosed file <_io.BufferedReader
name='/tmp/tmpfmmo7x'>
  mode=mode, offset=offset)
......................................................................................................................................................................................................................../usr/lib64/python3.2/subprocess.py:460:
ResourceWarning: unclosed file <_io.BufferedReader name=3>
  return Popen(*popenargs, **kwargs).wait()
/usr/lib64/python3.2/subprocess.py:460: ResourceWarning: unclosed file
<_io.BufferedReader name=8>
  return Popen(*popenargs, **kwargs).wait()
....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
======================================================================
ERROR: test_datetime_array_str (test_datetime.TestDateTime)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib64/python3.2/site-packages/numpy/core/tests/test_datetime.py",
line 510, in test_datetime_array_str
    assert_equal(str(a), "['2011-03-16' '1920-01-01' '2013-05-19']")
  File "/usr/lib64/python3.2/site-packages/numpy/core/numeric.py",
line 1400, in array_str
    return array2string(a, max_line_width, precision, suppress_small,
' ', "", str)
  File "/usr/lib64/python3.2/site-packages/numpy/core/arrayprint.py",
line 459, in array2string
    separator, prefix, formatter=formatter)
  File "/usr/lib64/python3.2/site-packages/numpy/core/arrayprint.py",
line 331, in _array2string
    _summaryEdgeItems, summary_insert)[:-1]
  File "/usr/lib64/python3.2/site-packages/numpy/core/arrayprint.py",
line 502, in _formatArray
    word = format_function(a[-i]) + separator
  File "/usr/lib64/python3.2/site-packages/numpy/core/arrayprint.py",
line 770, in __call__
    casting=self.casting)
TypeError: Cannot create a local timezone-based date string from a
NumPy datetime without forcing 'unsafe' casting

======================================================================
ERROR: test_datetime_divide (test_datetime.TestDateTime)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib64/python3.2/site-packages/numpy/core/tests/test_datetime.py",
line 926, in test_datetime_divide
    assert_equal(tda / tdb, 6.0 / 9.0)
TypeError: internal error: could not find appropriate datetime inner
loop in true_divide ufunc

======================================================================
FAIL: test_datetime_as_string (test_datetime.TestDateTime)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib64/python3.2/site-packages/numpy/core/tests/test_datetime.py",
line 1166, in test_datetime_as_string
    '1959')
  File "/usr/lib64/python3.2/site-packages/numpy/testing/utils.py",
line 313, in assert_equal
    raise AssertionError(msg)
AssertionError:
Items are not equal:
 ACTUAL: b'1959'
 DESIRED: '1959'

======================================================================
FAIL: test_datetime_as_string_timezone (test_datetime.TestDateTime)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib64/python3.2/site-packages/numpy/core/tests/test_datetime.py",
line 1277, in test_datetime_as_string_timezone
    '2010-03-15T06:30Z')
  File "/usr/lib64/python3.2/site-packages/numpy/testing/utils.py",
line 313, in assert_equal
    raise AssertionError(msg)
AssertionError:
Items are not equal:
 ACTUAL: b'2010-03-15T06:30Z'
 DESIRED: '2010-03-15T06:30Z'

----------------------------------------------------------------------
Ran 3063 tests in 37.701s

FAILED (KNOWNFAIL=4, SKIP=2, errors=2, failures=2)


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