Deprecate the None argument

scipy · May 1, 2016 · 70bbb67 · 70bbb67
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commit 70bbb67
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Showing 2 changed files with 22 additions and 14 deletions.
diff --git a/scipy/stats/stats.py b/scipy/stats/stats.py
@@ -4385,20 +4385,20 @@ def mannwhitneyu(x, y, use_continuity=True, alternative=None):
     use_continuity : bool, optional
             Whether a continuity correction (1/2.) should be taken into
             account. Default is True.
-    alternative : None, 'less', 'two-sided', or 'greater'
+    alternative : None (deprecated), 'less', 'two-sided', or 'greater'
             Whether to get the p-value for the one-sided hypothesis ('less'
-            or 'greater'), or for the two-sided hypothesis ('two-sided').
+            or 'greater') or for the two-sided hypothesis ('two-sided').
             Defaults to None, which results in a p-value half the size of
-            the 'two-sided' p-value and a different U statistic. The default
-            behavior is not the same as using 'less' or 'greater', is not
-            recommended, and will soon be deprecated.
+            the 'two-sided' p-value and a different U statistic. The
+            default behavior is not the same as using 'less' or 'greater':
+            it only exists for backward compatibility and is deprecated.
 
     Returns
     -------
     statistic : float
         The Mann-Whitney U statistic, equal to min(U for x, U for y) if
-        `alternative` is equal to None (not recommended; to be deprecated),
-        and U for y otherwise.
+        `alternative` is equal to None (deprecated; exists for backward
+        compatibility), and U for y otherwise.
     pvalue : float
         p-value assuming an asymptotic normal distribution. One-sided or
         two-sided, depending on the choice of `alternative`.
@@ -4413,6 +4413,10 @@ def mannwhitneyu(x, y, use_continuity=True, alternative=None):
     This test corrects for ties and by default uses a continuity correction.
 
     """
+    if alternative is None:
+        warnings.warn("Calling `mannwhitneyu` without specifying "
+                      "`alternative` is deprecated.", DeprecationWarning)
+
     x = np.asarray(x)
     y = np.asarray(y)
     n1 = len(x)

diff --git a/scipy/stats/tests/test_stats.py b/scipy/stats/tests/test_stats.py
@@ -2760,9 +2760,11 @@ def test_mannwhitneyu_two_sided(self):
 
     def test_mannwhitneyu_default(self):
         # The default value for alternative is None
-        u1, p1 = stats.mannwhitneyu(self.X, self.Y)
-        u2, p2 = stats.mannwhitneyu(self.Y, self.X)
-        u3, p3 = stats.mannwhitneyu(self.X, self.Y, alternative=None)
+        with warnings.catch_warnings():
+            warnings.simplefilter("ignore", DeprecationWarning)
+            u1, p1 = stats.mannwhitneyu(self.X, self.Y)
+            u2, p2 = stats.mannwhitneyu(self.Y, self.X)
+            u3, p3 = stats.mannwhitneyu(self.X, self.Y, alternative=None)
 
         assert_equal(p1, p2)
         assert_equal(p1, p3)
@@ -2806,10 +2808,12 @@ def test_mannwhitneyu_no_correct_two_sided(self):
 
     def test_mannwhitneyu_no_correct_default(self):
         # The default value for alternative is None
-        u1, p1 = stats.mannwhitneyu(self.X, self.Y, False)
-        u2, p2 = stats.mannwhitneyu(self.Y, self.X, False)
-        u3, p3 = stats.mannwhitneyu(self.X, self.Y, False,
-                                    alternative=None)
+        with warnings.catch_warnings():
+            warnings.simplefilter("ignore", DeprecationWarning)
+            u1, p1 = stats.mannwhitneyu(self.X, self.Y, False)
+            u2, p2 = stats.mannwhitneyu(self.Y, self.X, False)
+            u3, p3 = stats.mannwhitneyu(self.X, self.Y, False,
+                                        alternative=None)
 
         assert_equal(p1, p2)
         assert_equal(p1, p3)