Merge pull request numpy#476 from njsmith/copy-memory-order

[FIX] preserve memory order in np.copy()

numpy/add_newdocs.py

@@ -3222,10 +3222,13 @@ def luf(lamdaexpr, *args, **kwargs):
         Controls the memory layout of the copy. 'C' means C-order,
         'F' means F-order, 'A' means 'F' if `a` is Fortran contiguous,
         'C' otherwise. 'K' means match the layout of `a` as closely
-        as possible.
+        as possible. (Note that this function and :func:numpy.copy are very
+        similar, but have different default values for their order=
+        arguments.)
 
     See also
     --------
+    numpy.copy
     numpy.copyto
 
     Examples

numpy/lib/function_base.py

@@ -778,7 +778,7 @@ def select(condlist, choicelist, default=0):
             S = S*ones(asarray(pfac).shape, S.dtype)
     return choose(S, tuple(choicelist))
 
-def copy(a, order='C'):
+def copy(a, order='K'):
     """
     Return an array copy of the given object.
 
@@ -790,7 +790,9 @@ def copy(a, order='C'):
         Controls the memory layout of the copy. 'C' means C-order,
         'F' means F-order, 'A' means 'F' if `a` is Fortran contiguous,
         'C' otherwise. 'K' means match the layout of `a` as closely
-        as possible.
+        as possible. (Note that this function and :meth:ndarray.copy are very
+        similar, but have different default values for their order=
+        arguments.)
 
     Returns
     -------

numpy/lib/tests/test_function_base.py

@@ -42,6 +42,32 @@ def test_nd(self):
         assert_array_equal(np.alltrue(y1, axis=1), [0, 0, 1])
 
 
+class TestCopy(TestCase):
+    def test_basic(self):
+        a = np.array([[1, 2], [3, 4]])
+        a_copy = np.copy(a)
+        assert_array_equal(a, a_copy)
+        a_copy[0, 0] = 10
+        assert_equal(a[0, 0], 1)
+        assert_equal(a_copy[0, 0], 10)
+
+    def test_order(self):
+        # It turns out that people rely on np.copy() preserving order by
+        # default; changing this broke scikit-learn:
+        #   https://github.com/scikit-learn/scikit-learn/commit/7842748cf777412c506a8c0ed28090711d3a3783
+        a = np.array([[1, 2], [3, 4]])
+        assert_(a.flags.c_contiguous)
+        assert_(not a.flags.f_contiguous)
+        a_fort = np.array([[1, 2], [3, 4]], order="F")
+        assert_(not a_fort.flags.c_contiguous)
+        assert_(a_fort.flags.f_contiguous)
+        a_copy = np.copy(a)
+        assert_(a_copy.flags.c_contiguous)
+        assert_(not a_copy.flags.f_contiguous)
+        a_fort_copy = np.copy(a_fort)
+        assert_(not a_fort_copy.flags.c_contiguous)
+        assert_(a_fort_copy.flags.f_contiguous)
+
 class TestAverage(TestCase):
     def test_basic(self):
         y1 = np.array([1, 2, 3])