DEPR: Enforce alignment with numpy ufuncs (#50455)

* DEPR: Enforce alignment with numpy ufuncs

* fix other test

doc/source/whatsnew/v2.0.0.rst

@@ -527,6 +527,7 @@ Removal of prior version deprecations/changes
 - Removed deprecated :func:`pandas.api.types.is_categorical`; use :func:`pandas.api.types.is_categorical_dtype` instead  (:issue:`33385`)
 - Removed deprecated :meth:`Index.asi8` (:issue:`37877`)
 - Enforced deprecation changing behavior when passing ``datetime64[ns]`` dtype data and timezone-aware dtype to :class:`Series`, interpreting the values as wall-times instead of UTC times, matching :class:`DatetimeIndex` behavior (:issue:`41662`)
+- Enforced deprecation changing behavior when applying a numpy ufunc on multiple non-aligned (on the index or columns) :class:`DataFrame` that will now align the inputs first (:issue:`39239`)
 - Removed deprecated :meth:`DataFrame._AXIS_NUMBERS`, :meth:`DataFrame._AXIS_NAMES`, :meth:`Series._AXIS_NUMBERS`, :meth:`Series._AXIS_NAMES` (:issue:`33637`)
 - Removed deprecated :meth:`Index.to_native_types`, use ``obj.astype(str)`` instead (:issue:`36418`)
 - Removed deprecated :meth:`Series.iteritems`, :meth:`DataFrame.iteritems`, use ``obj.items`` instead (:issue:`45321`)

pandas/core/arraylike.py

@@ -8,13 +8,11 @@
 
 import operator
 from typing import Any
-import warnings
 
 import numpy as np
 
 from pandas._libs import lib
 from pandas._libs.ops_dispatch import maybe_dispatch_ufunc_to_dunder_op
-from pandas.util._exceptions import find_stack_level
 
 from pandas.core.dtypes.generic import ABCNDFrame
 
@@ -166,81 +164,6 @@ def __rpow__(self, other):
 # Helpers to implement __array_ufunc__
 
 
-def _is_aligned(frame, other):
-    """
-    Helper to check if a DataFrame is aligned with another DataFrame or Series.
-    """
-    from pandas import DataFrame
-
-    if isinstance(other, DataFrame):
-        return frame._indexed_same(other)
-    else:
-        # Series -> match index
-        return frame.columns.equals(other.index)
-
-
-def _maybe_fallback(ufunc: np.ufunc, method: str, *inputs: Any, **kwargs: Any):
-    """
-    In the future DataFrame, inputs to ufuncs will be aligned before applying
-    the ufunc, but for now we ignore the index but raise a warning if behaviour
-    would change in the future.
-    This helper detects the case where a warning is needed and then fallbacks
-    to applying the ufunc on arrays to avoid alignment.
-
-    See https://github.com/pandas-dev/pandas/pull/39239
-    """
-    from pandas import DataFrame
-    from pandas.core.generic import NDFrame
-
-    n_alignable = sum(isinstance(x, NDFrame) for x in inputs)
-    n_frames = sum(isinstance(x, DataFrame) for x in inputs)
-
-    if n_alignable >= 2 and n_frames >= 1:
-        # if there are 2 alignable inputs (Series or DataFrame), of which at least 1
-        # is a DataFrame -> we would have had no alignment before -> warn that this
-        # will align in the future
-
-        # the first frame is what determines the output index/columns in pandas < 1.2
-        first_frame = next(x for x in inputs if isinstance(x, DataFrame))
-
-        # check if the objects are aligned or not
-        non_aligned = sum(
-            not _is_aligned(first_frame, x) for x in inputs if isinstance(x, NDFrame)
-        )
-
-        # if at least one is not aligned -> warn and fallback to array behaviour
-        if non_aligned:
-            warnings.warn(
-                "Calling a ufunc on non-aligned DataFrames (or DataFrame/Series "
-                "combination). Currently, the indices are ignored and the result "
-                "takes the index/columns of the first DataFrame. In the future , "
-                "the DataFrames/Series will be aligned before applying the ufunc.\n"
-                "Convert one of the arguments to a NumPy array "
-                "(eg 'ufunc(df1, np.asarray(df2)') to keep the current behaviour, "
-                "or align manually (eg 'df1, df2 = df1.align(df2)') before passing to "
-                "the ufunc to obtain the future behaviour and silence this warning.",
-                FutureWarning,
-                stacklevel=find_stack_level(),
-            )
-
-            # keep the first dataframe of the inputs, other DataFrame/Series is
-            # converted to array for fallback behaviour
-            new_inputs = []
-            for x in inputs:
-                if x is first_frame:
-                    new_inputs.append(x)
-                elif isinstance(x, NDFrame):
-                    new_inputs.append(np.asarray(x))
-                else:
-                    new_inputs.append(x)
-
-            # call the ufunc on those transformed inputs
-            return getattr(ufunc, method)(*new_inputs, **kwargs)
-
-    # signal that we didn't fallback / execute the ufunc yet
-    return NotImplemented
-
-
 def array_ufunc(self, ufunc: np.ufunc, method: str, *inputs: Any, **kwargs: Any):
     """
     Compatibility with numpy ufuncs.
@@ -260,11 +183,6 @@ def array_ufunc(self, ufunc: np.ufunc, method: str, *inputs: Any, **kwargs: Any)
 
     kwargs = _standardize_out_kwarg(**kwargs)
 
-    # for backwards compatibility check and potentially fallback for non-aligned frames
-    result = _maybe_fallback(ufunc, method, *inputs, **kwargs)
-    if result is not NotImplemented:
-        return result
-
     # for binary ops, use our custom dunder methods
     result = maybe_dispatch_ufunc_to_dunder_op(self, ufunc, method, *inputs, **kwargs)
     if result is not NotImplemented:

pandas/tests/frame/test_ufunc.py

@@ -118,21 +118,18 @@ def test_binary_input_aligns_columns(request, dtype_a, dtype_b):
 
     if isinstance(dtype_a, dict) and isinstance(dtype_b, dict):
         dtype_b["C"] = dtype_b.pop("B")
-
     df2 = pd.DataFrame({"A": [1, 2], "C": [3, 4]}).astype(dtype_b)
-    with tm.assert_produces_warning(FutureWarning):
-        result = np.heaviside(df1, df2)
-    # Expected future behaviour:
-    # expected = np.heaviside(
-    #     np.array([[1, 3, np.nan], [2, 4, np.nan]]),
-    #     np.array([[1, np.nan, 3], [2, np.nan, 4]]),
-    # )
-    # expected = pd.DataFrame(expected, index=[0, 1], columns=["A", "B", "C"])
-    expected = pd.DataFrame([[1.0, 1.0], [1.0, 1.0]], columns=["A", "B"])
+    # As of 2.0, align first before applying the ufunc
+    result = np.heaviside(df1, df2)
+    expected = np.heaviside(
+        np.array([[1, 3, np.nan], [2, 4, np.nan]]),
+        np.array([[1, np.nan, 3], [2, np.nan, 4]]),
+    )
+    expected = pd.DataFrame(expected, index=[0, 1], columns=["A", "B", "C"])
     tm.assert_frame_equal(result, expected)
 
-    # ensure the expected is the same when applying with numpy array
     result = np.heaviside(df1, df2.values)
+    expected = pd.DataFrame([[1.0, 1.0], [1.0, 1.0]], columns=["A", "B"])
     tm.assert_frame_equal(result, expected)
 
 
@@ -146,35 +143,29 @@ def test_binary_input_aligns_index(request, dtype):
         )
     df1 = pd.DataFrame({"A": [1, 2], "B": [3, 4]}, index=["a", "b"]).astype(dtype)
     df2 = pd.DataFrame({"A": [1, 2], "B": [3, 4]}, index=["a", "c"]).astype(dtype)
-    with tm.assert_produces_warning(FutureWarning):
-        result = np.heaviside(df1, df2)
-    # Expected future behaviour:
-    # expected = np.heaviside(
-    #     np.array([[1, 3], [3, 4], [np.nan, np.nan]]),
-    #     np.array([[1, 3], [np.nan, np.nan], [3, 4]]),
-    # )
-    # # TODO(FloatArray): this will be Float64Dtype.
-    # expected = pd.DataFrame(expected, index=["a", "b", "c"], columns=["A", "B"])
-    expected = pd.DataFrame(
-        [[1.0, 1.0], [1.0, 1.0]], columns=["A", "B"], index=["a", "b"]
+    result = np.heaviside(df1, df2)
+    expected = np.heaviside(
+        np.array([[1, 3], [3, 4], [np.nan, np.nan]]),
+        np.array([[1, 3], [np.nan, np.nan], [3, 4]]),
     )
+    # TODO(FloatArray): this will be Float64Dtype.
+    expected = pd.DataFrame(expected, index=["a", "b", "c"], columns=["A", "B"])
     tm.assert_frame_equal(result, expected)
 
-    # ensure the expected is the same when applying with numpy array
     result = np.heaviside(df1, df2.values)
+    expected = pd.DataFrame(
+        [[1.0, 1.0], [1.0, 1.0]], columns=["A", "B"], index=["a", "b"]
+    )
     tm.assert_frame_equal(result, expected)
 
 
-@pytest.mark.filterwarnings("ignore:Calling a ufunc on non-aligned:FutureWarning")
 def test_binary_frame_series_raises():
     # We don't currently implement
     df = pd.DataFrame({"A": [1, 2]})
-    # with pytest.raises(NotImplementedError, match="logaddexp"):
-    with pytest.raises(ValueError, match=""):
+    with pytest.raises(NotImplementedError, match="logaddexp"):
         np.logaddexp(df, df["A"])
 
-    # with pytest.raises(NotImplementedError, match="logaddexp"):
-    with pytest.raises(ValueError, match=""):
+    with pytest.raises(NotImplementedError, match="logaddexp"):
         np.logaddexp(df["A"], df)
 
 
@@ -206,7 +197,8 @@ def test_frame_outer_disallowed():
         np.subtract.outer(df, df)
 
 
-def test_alignment_deprecation():
+def test_alignment_deprecation_enforced():
+    # Enforced in 2.0
     # https://github.com/pandas-dev/pandas/issues/39184
     df1 = pd.DataFrame({"a": [1, 2, 3], "b": [4, 5, 6]})
     df2 = pd.DataFrame({"b": [1, 2, 3], "c": [4, 5, 6]})
@@ -221,12 +213,11 @@ def test_alignment_deprecation():
         result = np.add(df1, df1)
     tm.assert_frame_equal(result, expected)
 
-    with tm.assert_produces_warning(FutureWarning):
-        # non-aligned -> warns
-        result = np.add(df1, df2)
+    result = np.add(df1, df2.values)
     tm.assert_frame_equal(result, expected)
 
-    result = np.add(df1, df2.values)
+    result = np.add(df1, df2)
+    expected = pd.DataFrame({"a": [np.nan] * 3, "b": [5, 7, 9], "c": [np.nan] * 3})
     tm.assert_frame_equal(result, expected)
 
     result = np.add(df1.values, df2)
@@ -241,20 +232,23 @@ def test_alignment_deprecation():
         result = np.add(df1, s1)
     tm.assert_frame_equal(result, expected)
 
-    with tm.assert_produces_warning(FutureWarning):
-        result = np.add(df1, s2)
+    result = np.add(df1, s2.values)
     tm.assert_frame_equal(result, expected)
 
-    with tm.assert_produces_warning(FutureWarning):
-        result = np.add(s2, df1)
+    expected = pd.DataFrame(
+        {"a": [np.nan] * 3, "b": [5.0, 6.0, 7.0], "c": [np.nan] * 3}
+    )
+    result = np.add(df1, s2)
     tm.assert_frame_equal(result, expected)
 
-    result = np.add(df1, s2.values)
-    tm.assert_frame_equal(result, expected)
+    msg = "Cannot apply ufunc <ufunc 'add'> to mixed DataFrame and Series inputs."
+    with pytest.raises(NotImplementedError, match=msg):
+        np.add(s2, df1)
 
 
 @td.skip_if_no("numba")
-def test_alignment_deprecation_many_inputs(request):
+def test_alignment_deprecation_many_inputs_enforced():
+    # Enforced in 2.0
     # https://github.com/pandas-dev/pandas/issues/39184
     # test that the deprecation also works with > 2 inputs -> using a numba
     # written ufunc for this because numpy itself doesn't have such ufuncs
@@ -271,31 +265,34 @@ def my_ufunc(x, y, z):
     df2 = pd.DataFrame({"b": [1, 2, 3], "c": [4, 5, 6]})
     df3 = pd.DataFrame({"a": [1, 2, 3], "c": [4, 5, 6]})
 
-    with tm.assert_produces_warning(FutureWarning):
-        result = my_ufunc(df1, df2, df3)
-    expected = pd.DataFrame([[3.0, 12.0], [6.0, 15.0], [9.0, 18.0]], columns=["a", "b"])
+    result = my_ufunc(df1, df2, df3)
+    expected = pd.DataFrame(np.full((3, 3), np.nan), columns=["a", "b", "c"])
     tm.assert_frame_equal(result, expected)
 
     # all aligned -> no warning
     with tm.assert_produces_warning(None):
         result = my_ufunc(df1, df1, df1)
+    expected = pd.DataFrame([[3.0, 12.0], [6.0, 15.0], [9.0, 18.0]], columns=["a", "b"])
     tm.assert_frame_equal(result, expected)
 
     # mixed frame / arrays
-    with tm.assert_produces_warning(FutureWarning):
-        result = my_ufunc(df1, df2, df3.values)
-    tm.assert_frame_equal(result, expected)
+    msg = (
+        r"operands could not be broadcast together with shapes \(3,3\) \(3,3\) \(3,2\)"
+    )
+    with pytest.raises(ValueError, match=msg):
+        my_ufunc(df1, df2, df3.values)
 
     # single frame -> no warning
     with tm.assert_produces_warning(None):
         result = my_ufunc(df1, df2.values, df3.values)
     tm.assert_frame_equal(result, expected)
 
     # takes indices of first frame
-    with tm.assert_produces_warning(FutureWarning):
-        result = my_ufunc(df1.values, df2, df3)
-    expected = expected.set_axis(["b", "c"], axis=1)
-    tm.assert_frame_equal(result, expected)
+    msg = (
+        r"operands could not be broadcast together with shapes \(3,2\) \(3,3\) \(3,3\)"
+    )
+    with pytest.raises(ValueError, match=msg):
+        my_ufunc(df1.values, df2, df3)
 
 
 def test_array_ufuncs_for_many_arguments():

pandas/tests/series/test_ufunc.py

@@ -426,14 +426,10 @@ def test_np_matmul():
     # GH26650
     df1 = pd.DataFrame(data=[[-1, 1, 10]])
     df2 = pd.DataFrame(data=[-1, 1, 10])
-    expected_result = pd.DataFrame(data=[102])
+    expected = pd.DataFrame(data=[102])
 
-    with tm.assert_produces_warning(FutureWarning, match="on non-aligned"):
-        result = np.matmul(df1, df2)
-    tm.assert_frame_equal(
-        expected_result,
-        result,
-    )
+    result = np.matmul(df1, df2)
+    tm.assert_frame_equal(expected, result)
 
 
 def test_array_ufuncs_for_many_arguments():