numpy · mattip · Jun 13, 2019 · May 26, 2019 · Jun 7, 2019
diff --git a/doc/release/1.17.0-notes.rst b/doc/release/1.17.0-notes.rst
@@ -43,6 +43,13 @@ from python.
 This deprecation should not affect many users since arrays created in such
 a manner are very rare in practice and only available through the NumPy C-API.
 
+`numpy.nonzero` should no longer be called on 0d arrays
+-------------------------------------------------------
+The behavior of nonzero on 0d arrays was surprising, making uses of it almost
+always incorrect. If the old behavior was intended, it can be preserved without
+a warning by using ``nonzero(atleast_1d(arr))`` instead of ``nonzero(arr)``.
+In a future release, it is most likely this will raise a `ValueError`.
+
 
 Future Changes
 ==============

diff --git a/numpy/core/fromnumeric.py b/numpy/core/fromnumeric.py
@@ -1764,17 +1764,17 @@ def nonzero(a):
     Returns a tuple of arrays, one for each dimension of `a`,
     containing the indices of the non-zero elements in that
     dimension. The values in `a` are always tested and returned in
-    row-major, C-style order. The corresponding non-zero
-    values can be obtained with::
+    row-major, C-style order.
 
-        a[nonzero(a)]
+    To group the indices by element, rather than dimension, use `argwhere`,
+    which returns a row for each non-zero element.
 
-    To group the indices by element, rather than dimension, use::
-
-        transpose(nonzero(a))
+    .. note::
+        When called on a zero-d array or scalar, ``nonzero(a)`` is treated
+        as ``nonzero(atleast1d(a))``.
 
-    The result of this is always a 2-D array, with a row for
-    each non-zero element.
+        ..deprecated:: 1.17.0
+            Use `atleast1d` explicitly if this behavior is deliberate.
 
     Parameters
     ----------
@@ -1795,11 +1795,12 @@ def nonzero(a):
         Equivalent ndarray method.
     count_nonzero :
         Counts the number of non-zero elements in the input array.
-        
+
     Notes
     -----
-    To obtain the non-zero values, it is recommended to use ``x[x.astype(bool)]`` 
-    which will correctly handle 0-d arrays. 
+    While the nonzero values can be obtained with ``a[nonzero(a)]``, it is
+    recommended to use ``x[x.astype(bool)]`` or ``x[x != 0]`` instead, which
+    will correctly handle 0-d arrays.
 
     Examples
     --------

diff --git a/numpy/core/src/multiarray/item_selection.c b/numpy/core/src/multiarray/item_selection.c
@@ -2208,8 +2208,26 @@ PyArray_Nonzero(PyArrayObject *self)
     NpyIter_GetMultiIndexFunc *get_multi_index;
     char **dataptr;
 
-    /* Special case - nonzero(zero_d) is nonzero(atleast1d(zero_d)) */
+    /* Special case - nonzero(zero_d) is nonzero(atleast_1d(zero_d)) */
     if (ndim == 0) {
+        char const* msg;
+        if (PyArray_ISBOOL(self)) {
+            msg =
+                "Calling nonzero on 0d arrays is deprecated, as it behaves "
+                "surprisingly. Use `atleast_1d(cond).nonzero()` if the old "
+                "behavior was intended. If the context of this warning is of "
+                "the form `arr[nonzero(cond)]`, just use `arr[cond]`.";
+        }
+        else {
+            msg =
+                "Calling nonzero on 0d arrays is deprecated, as it behaves "
+                "surprisingly. Use `atleast_1d(arr).nonzero()` if the old "
+                "behavior was intended.";
+        }
+        if (DEPRECATE(msg) < 0) {
+            return NULL;
+        }
+
         static npy_intp const zero_dim_shape[1] = {1};
         static npy_intp const zero_dim_strides[1] = {0};
 

diff --git a/numpy/core/tests/test_deprecations.py b/numpy/core/tests/test_deprecations.py
@@ -541,3 +541,10 @@ class TestShape1Fields(_DeprecationTestCase):
     # 2019-05-20, 1.17.0
     def test_shape_1_fields(self):
         self.assert_deprecated(np.dtype, args=([('a', int, 1)],))
+
+
+class TestNonZero(_DeprecationTestCase):
+    # 2019-05-26, 1.17.0
+    def test_zerod(self):
+        self.assert_deprecated(lambda: np.nonzero(np.array(0)))
+        self.assert_deprecated(lambda: np.nonzero(np.array(1)))
diff --git a/numpy/core/tests/test_numeric.py b/numpy/core/tests/test_numeric.py
@@ -976,12 +976,24 @@ def test_nonzero_trivial(self):
         assert_equal(np.count_nonzero(np.array([], dtype='?')), 0)
         assert_equal(np.nonzero(np.array([])), ([],))
 
+        assert_equal(np.count_nonzero(np.array([0])), 0)
+        assert_equal(np.count_nonzero(np.array([0], dtype='?')), 0)
+        assert_equal(np.nonzero(np.array([0])), ([],))
+
+        assert_equal(np.count_nonzero(np.array([1])), 1)
+        assert_equal(np.count_nonzero(np.array([1], dtype='?')), 1)
+        assert_equal(np.nonzero(np.array([1])), ([0],))
+
+    def test_nonzero_zerod(self):
         assert_equal(np.count_nonzero(np.array(0)), 0)
         assert_equal(np.count_nonzero(np.array(0, dtype='?')), 0)
-        assert_equal(np.nonzero(np.array(0)), ([],))
+        with assert_warns(DeprecationWarning):
+            assert_equal(np.nonzero(np.array(0)), ([],))
+
         assert_equal(np.count_nonzero(np.array(1)), 1)
         assert_equal(np.count_nonzero(np.array(1, dtype='?')), 1)
-        assert_equal(np.nonzero(np.array(1)), ([0],))
+        with assert_warns(DeprecationWarning):
+            assert_equal(np.nonzero(np.array(1)), ([0],))
 
     def test_nonzero_onedim(self):
         x = np.array([1, 0, 2, -1, 0, 0, 8])