Merge pull request #3818 from markotoplak/scipy-1.2

Update tests for scipy.stats.mode workaround

Orange/statistics/util.py

@@ -479,7 +479,11 @@ def nanmedian_sparse(x):
 
 
 def nanmode(x, axis=0):
-    """ A temporary replacement for a buggy scipy.stats.stats.mode from scipy < 1.2.0"""
+    """ A temporary replacement for a scipy.stats.mode.
+
+    This function returns mode NaN if all values are NaN (scipy<1.2.0 wrongly
+    returns zero). Also, this function returns count NaN if all values are NaN
+    (scipy=1.3.0 returns some number)."""
     nans = np.isnan(np.array(x)).sum(axis=axis, keepdims=True) == x.shape[axis]
     res = scipy.stats.stats.mode(x, axis)
     return scipy.stats.stats.ModeResult(np.where(nans, np.nan, res.mode),

Orange/tests/test_statistics.py

@@ -645,14 +645,18 @@ def test_nanunique_ignores_nans_in_counts(self, array):
         np.testing.assert_equal(nanunique(x, return_counts=True)[1], expected)
 
 
-class TestNanModeAppVeyor(unittest.TestCase):
-    def test_appveyour_still_not_onscipy_1_2_0(self):
-        import scipy
-        from distutils.version import StrictVersion
-        import os
-
-        if os.getenv("APPVEYOR") and \
-                StrictVersion(scipy.__version__) >= StrictVersion("1.2.0"):
-            self.fail("Appveyor now uses Scipy 1.2.0; revert changes in "
-                      "the last three commits (bde2cbe, 7163448, ab0f31d) "
-                      "of gh-3480. Then, remove this test.")
+class TestNanModeFixedInScipy(unittest.TestCase):
+
+    @unittest.expectedFailure
+    def test_scipy_nanmode_still_wrong(self):
+        import scipy.stats
+        X = np.array([[np.nan, np.nan, 1, 1],
+                      [2, np.nan, 1, 1]])
+        mode, count = scipy.stats.mode(X, 0)
+        np.testing.assert_array_equal(mode, [[2, np.nan, 1, 1]])
+        np.testing.assert_array_equal(count, [[1, np.nan, 2, 2]])
+        mode, count = scipy.stats.mode(X, 1)
+        np.testing.assert_array_equal(mode, [[1], [1]])
+        np.testing.assert_array_equal(count, [[2], [2]])
+        # When Scipy's scipy.stats.mode works correcly, remove Orange.statistics.util.nanmode
+        # and this test. Also update requirements.

Orange/widgets/data/owfeaturestatistics.py

@@ -252,7 +252,7 @@ def __mode(x, *args, **kwargs):
             if sp.issparse(x):
                 x = x.todense(order="C")
             # return ss.mode(x, *args, **kwargs)[0]
-            return ut.nanmode(x, *args, **kwargs)[0]  # Temporary replacement for scipy < 1.2.0
+            return ut.nanmode(x, *args, **kwargs)[0]  # Temporary replacement for scipy
 
         self._center = self.__compute_stat(
             matrices,