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

Charles R Harris charlesr.harris@gmail....
Fri Aug 19 13:07:45 CDT 2011


On Fri, Aug 19, 2011 at 11:55 AM, Bruce Southey <bsouthey@gmail.com> wrote:

> 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)
>

The 3.2 test errors aren't new. I'd fix the tests except I'm not sure if
Mark wants to modify the datetime stuff instead.

Chuck
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.scipy.org/pipermail/numpy-discussion/attachments/20110819/61dfcff7/attachment-0001.html 


More information about the NumPy-Discussion mailing list