Merge branch 'pull-141'

* pull-141: (167 commits)
  ENH: missingdata: Make PyArray_Converter and PyArray_OutputConverter safer for legacy code
  DOC: missingdata: Add a mention of the design NEP, and masks vs bitpatterns
  DOC: missingdata: Updates from pull request feedback
  DOC: missingdata: Updates based on pull request feedback
  ENH: nditer: Change the Python nditer exposure to automatically add NPY_ITER_USE_MASKNA
  ENH: missingdata: Make comparisons with NA return NA(dtype='bool')
  BLD: core: onefile build fix and Python3 compatibility change
  DOC: Mention the update to np.all and np.any in the release notes
  TST: dtype: Adjust void dtype test to pass without raising a zero-size exception
  STY: Remove trailing whitespace
  TST: missingdata: Write some tests for the np.any and np.all NA behavior
  ENH: missingdata: Make numpy.all follow the NA && False == False rule
  ENH: missingdata: Make numpy.all follow the NA || True == True rule
  DOC: missingdata: Also show what assigning a non-NA value does in each case
  DOC: missingdata: Add introductory documentation for NA-masked arrays
  ENH: core: Rename PyArrayObject_fieldaccess to PyArrayObject_fields
  DOC: missingdata: Some tweaks to the NA mask documentation
  DOC: missingdata: Add example of a C-API function supporting NA masks
  DOC: missingdata: Documenting C API for NA-masked arrays
  ENH: missingdata: Finish adding C-API access to the NpyNA object
  ...

1 files changed, 85 insertions, 38 deletions

diff --git a/numpy/core/arrayprint.py b/numpy/core/arrayprint.py
index 508056a26..aad83500e 100644
--- a/numpy/core/arrayprint.py
+++ b/numpy/core/arrayprint.py
@@ -15,7 +15,7 @@ __docformat__ = 'restructuredtext'
 import sys
 import numerictypes as _nt
 from umath import maximum, minimum, absolute, not_equal, isnan, isinf
-from multiarray import format_longfloat, datetime_as_string, datetime_data
+from multiarray import format_longfloat, datetime_as_string, datetime_data, isna
 from fromnumeric import ravel
 
 
@@ -29,6 +29,7 @@ _float_output_suppress_small = False
 _line_width = 75
 _nan_str = 'nan'
 _inf_str = 'inf'
+_na_str = 'NA'
 _formatter = None  # formatting function for array elements
 
 if sys.version_info[0] >= 3:
@@ -36,7 +37,8 @@ if sys.version_info[0] >= 3:
 
 def set_printoptions(precision=None, threshold=None, edgeitems=None,
                      linewidth=None, suppress=None,
-                     nanstr=None, infstr=None, formatter=None):
+                     nanstr=None, infstr=None, nastr=None,
+                     formatter=None):
     """
     Set printing options.
 
@@ -63,6 +65,8 @@ def set_printoptions(precision=None, threshold=None, edgeitems=None,
         String representation of floating point not-a-number (default nan).
     infstr : str, optional
         String representation of floating point infinity (default inf).
+    nastr : str, optional
+        String representation of NA missing value (default NA).
     formatter : dict of callables, optional
         If not None, the keys should indicate the type(s) that the respective
         formatting function applies to.  Callables should return a string.
@@ -140,7 +144,7 @@ def set_printoptions(precision=None, threshold=None, edgeitems=None,
 
     global _summaryThreshold, _summaryEdgeItems, _float_output_precision, \
            _line_width, _float_output_suppress_small, _nan_str, _inf_str, \
-           _formatter
+           _na_str, _formatter
     if linewidth is not None:
         _line_width = linewidth
     if threshold is not None:
@@ -155,6 +159,8 @@ def set_printoptions(precision=None, threshold=None, edgeitems=None,
         _nan_str = nanstr
     if infstr is not None:
         _inf_str = infstr
+    if nastr is not None:
+        _na_str = nastr
     _formatter = formatter
 
 def get_printoptions():
@@ -189,6 +195,7 @@ def get_printoptions():
              suppress=_float_output_suppress_small,
              nanstr=_nan_str,
              infstr=_inf_str,
+             nastr=_na_str,
              formatter=_formatter)
     return d
 
@@ -212,9 +219,19 @@ def _leading_trailing(a):
     return b
 
 def _boolFormatter(x):
-    if x: return ' True'
-    else: return 'False'
+    if isna(x):
+        return str(x).replace('NA', _na_str, 1)
+    elif x:
+        return ' True'
+    else:
+        return 'False'
+
 
+def repr_format(x):
+    if isna(x):
+        return str(x).replace('NA', _na_str, 1)
+    else:
+        return repr(x)
 
 def _array2string(a, max_line_width, precision, suppress_small, separator=' ',
                   prefix="", formatter=None):
@@ -247,8 +264,9 @@ def _array2string(a, max_line_width, precision, suppress_small, separator=' ',
                   'longcomplexfloat' : LongComplexFormat(precision),
                   'datetime' : DatetimeFormat(data),
                   'timedelta' : TimedeltaFormat(data),
-                  'numpystr' : repr,
+                  'numpystr' : repr_format,
                   'str' : str}
+
     if formatter is not None:
         fkeys = [k for k in formatter.keys() if formatter[k] is not None]
         if 'all' in fkeys:
@@ -419,16 +437,20 @@ def array2string(a, max_line_width=None, precision=None,
 
     if a.shape == ():
         x = a.item()
-        try:
-            lst = a._format(x)
-            msg = "The `_format` attribute is deprecated in Numpy 2.0 and " \
-                  "will be removed in 2.1. Use the `formatter` kw instead."
-            import warnings
-            warnings.warn(msg, DeprecationWarning)
-        except AttributeError:
-            if isinstance(x, tuple):
-                x = _convert_arrays(x)
-            lst = style(x)
+        if isna(x):
+            lst = str(x).replace('NA', _na_str, 1)
+        else:
+            try:
+                lst = a._format(x)
+                msg = "The `_format` attribute is deprecated in Numpy " \
+                      "2.0 and will be removed in 2.1. Use the " \
+                      "`formatter` kw instead."
+                import warnings
+                warnings.warn(msg, DeprecationWarning)
+            except AttributeError:
+                if isinstance(x, tuple):
+                    x = _convert_arrays(x)
+                lst = style(x)
     elif reduce(product, a.shape) == 0:
         # treat as a null array if any of shape elements == 0
         lst = "[]"
@@ -531,14 +553,17 @@ class FloatFormat(object):
         import numeric as _nc
         errstate = _nc.seterr(all='ignore')
         try:
-            special = isnan(data) | isinf(data)
-            non_zero = absolute(data.compress(not_equal(data, 0) & ~special))
+            special = isnan(data) | isinf(data) | isna(data)
+            special[isna(data)] = False
+            valid = not_equal(data, 0) & ~special
+            valid[isna(data)] = False
+            non_zero = absolute(data.compress(valid))
             if len(non_zero) == 0:
                 max_val = 0.
                 min_val = 0.
             else:
-                max_val = maximum.reduce(non_zero)
-                min_val = minimum.reduce(non_zero)
+                max_val = maximum.reduce(non_zero, skipna=True)
+                min_val = minimum.reduce(non_zero, skipna=True)
                 if max_val >= 1.e8:
                     self.exp_format = True
                 if not self.suppress_small and (min_val < 0.0001
@@ -569,7 +594,8 @@ class FloatFormat(object):
             if _nc.any(special):
                 self.max_str_len = max(self.max_str_len,
                                        len(_nan_str),
-                                       len(_inf_str)+1)
+                                       len(_inf_str)+1,
+                                       len(_na_str))
             if self.sign:
                 format = '%#+'
             else:
@@ -583,7 +609,9 @@ class FloatFormat(object):
         import numeric as _nc
         err = _nc.seterr(invalid='ignore')
         try:
-            if isnan(x):
+            if isna(x):
+                return self.special_fmt % (str(x).replace('NA', _na_str, 1),)
+            elif isnan(x):
                 if self.sign:
                     return self.special_fmt % ('+' + _nan_str,)
                 else:
@@ -626,16 +654,21 @@ _MININT = -sys.maxint-1
 class IntegerFormat(object):
     def __init__(self, data):
         try:
-            max_str_len = max(len(str(maximum.reduce(data))),
-                              len(str(minimum.reduce(data))))
+            max_str_len = max(len(str(maximum.reduce(data, skipna=True))),
+                              len(str(minimum.reduce(data, skipna=True))))
             self.format = '%' + str(max_str_len) + 'd'
         except TypeError, NotImplementedError:
             # if reduce(data) fails, this instance will not be called, just
             # instantiated in formatdict.
             pass
+        except ValueError:
+            # this occurs when everything is NA
+            pass
 
     def __call__(self, x):
-        if _MININT < x < _MAXINT:
+        if isna(x):
+            return str(x).replace('NA', _na_str, 1)
+        elif _MININT < x < _MAXINT:
             return self.format % x
         else:
             return "%s" % x
@@ -648,7 +681,9 @@ class LongFloatFormat(object):
         self.sign = sign
 
     def __call__(self, x):
-        if isnan(x):
+        if isna(x):
+            return str(x).replace('NA', _na_str, 1)
+        elif isnan(x):
             if self.sign:
                 return '+' + _nan_str
             else:
@@ -676,9 +711,12 @@ class LongComplexFormat(object):
         self.imag_format = LongFloatFormat(precision, sign=True)
 
     def __call__(self, x):
-        r = self.real_format(x.real)
-        i = self.imag_format(x.imag)
-        return r + i + 'j'
+        if isna(x):
+            return str(x).replace('NA', _na_str, 1)
+        else:
+            r = self.real_format(x.real)
+            i = self.imag_format(x.imag)
+            return r + i + 'j'
 
 
 class ComplexFormat(object):
@@ -688,14 +726,17 @@ class ComplexFormat(object):
                                        sign=True)
 
     def __call__(self, x):
-        r = self.real_format(x.real, strip_zeros=False)
-        i = self.imag_format(x.imag, strip_zeros=False)
-        if not self.imag_format.exp_format:
-            z = i.rstrip('0')
-            i = z + 'j' + ' '*(len(i)-len(z))
+        if isna(x):
+            return str(x).replace('NA', _na_str, 1)
         else:
-            i = i + 'j'
-        return r + i
+            r = self.real_format(x.real, strip_zeros=False)
+            i = self.imag_format(x.imag, strip_zeros=False)
+            if not self.imag_format.exp_format:
+                z = i.rstrip('0')
+                i = z + 'j' + ' '*(len(i)-len(z))
+            else:
+                i = i + 'j'
+            return r + i
 
 class DatetimeFormat(object):
     def __init__(self, x, unit=None,
@@ -720,7 +761,10 @@ class DatetimeFormat(object):
         self.casting = casting
 
     def __call__(self, x):
-        return "'%s'" % datetime_as_string(x,
+        if isna(x):
+            return str(x).replace('NA', _na_str, 1)
+        else:
+            return "'%s'" % datetime_as_string(x,
                                         unit=self.unit,
                                         timezone=self.timezone,
                                         casting=self.casting)
@@ -734,5 +778,8 @@ class TimedeltaFormat(object):
             self.format = '%' + str(max_str_len) + 'd'
 
     def __call__(self, x):
-        return self.format % x.astype('i8')
+        if isna(x):
+            return str(x).replace('NA', _na_str, 1)
+        else:
+            return self.format % x.astype('i8')