Fix Series.isin dtype and value semantics for masked (nullable) dtypes

python/cudf/cudf/core/column/numerical.py

@@ -40,6 +40,7 @@
     find_common_type,
     get_dtype_of_same_kind,
     is_pandas_nullable_extension_dtype,
+    is_pandas_nullable_numpy_dtype,
     min_signed_type,
     min_unsigned_type,
 )
@@ -926,6 +927,104 @@ def nan_count(self) -> int:
             return super().nan_count
         return self.isnan().sum()
 
+    def isin(self, values: Sequence | ColumnBase) -> ColumnBase:
+        if isinstance(self.dtype, np.dtype) or not (
+            is_pandas_nullable_numpy_dtype(self.dtype)
+        ):
+            return super().isin(values)
+        # Mirror pandas' BaseMaskedArray.isin for masked (nullable
+        # integer/float/boolean) dtypes:
+        #  * matching is done on the underlying numpy values, so e.g. a
+        #    boolean element equals the integer 1,
+        #  * an NA element is considered present only when pd.NA itself
+        #    is one of the passed values (a plain NaN/None/NaT does not
+        #    match), and
+        #  * the result is a nullable BooleanDtype with no missing values.
+        # Validity-only nulls (ColumnBase.isnull): a genuine NaN value in a
+        # masked float column is data, not NA - it must keep matching a NaN
+        # needle instead of being folded into the mask
+        # (NumericalColumn.isnull would count it as null).
+        na_mask = ColumnBase.isnull(self)
+        # View the column through its numpy dtype (identical physical
+        # layout). astype is not used because casting a masked column with
+        # nulls to numpy raises in pandas-compatible mode, and its
+        # short-circuit mutates the live column's dtype in place; fillna is
+        # not used because it folds genuine NaN values into the fill. Null
+        # rows come back False from ``isin`` (the needles below never
+        # contain nulls) and are then corrected from ``na_mask``.
+        data_col = ColumnBase.create(self.plc_column, self.dtype.numpy_dtype)
+        cleaned_values, values_have_na = self._process_values_for_masked_isin(
+            values
+        )
+        if len(cleaned_values) == 0:
+            # Nothing can match; also avoids the object-dtype column an
+            # empty needle list produces, which an all-null data column
+            # cannot be compared against in pandas-compatible mode.
+            result = as_column(
+                False, length=len(self), dtype=np.dtype(np.bool_)
+            )
+        else:
+            result = data_col.isin(cleaned_values)
+        if na_mask.any():
+            result = result | na_mask if values_have_na else result & ~na_mask
+        return result.astype(pd.BooleanDtype())
+
+    @staticmethod
+    def _process_values_for_masked_isin(
+        values: Sequence | ColumnBase,
+    ) -> tuple[Sequence, bool]:
+        """Normalize ``values`` for a masked ``isin``.
+
+        Drops NA-like needles (they are handled through the mask by the
+        caller) and reports whether ``pd.NA`` itself was among them.
+        """
+        # The normalization below rebinds across container types, so use a
+        # loosely typed alias.
+        host_values: Any = values
+        # Bring device-backed ``values`` to host in a single transfer; the
+        # per-element inspection below would otherwise read them
+        # element-wise or fail on non-iterable cudf objects.
+        if isinstance(host_values, (ColumnBase, cudf.Series, cudf.Index)):
+            host_values = host_values.to_pandas()
+        elif isinstance(host_values, cp.ndarray):
+            host_values = cp.asnumpy(host_values)
+        elif isinstance(host_values, (pa.Array, pa.ChunkedArray)):
+            host_values = host_values.to_pylist()
+        if isinstance(
+            host_values,
+            (pd.Series, pd.Index, pd.api.extensions.ExtensionArray),
+        ):
+            # np.asarray mirrors pandas' BaseMaskedArray.isin: a masked (or
+            # other extension) container decays to numpy, where pd.NA
+            # becomes NaN and no longer matches NA rows - only object
+            # containers can carry pd.NA identity.
+            host_values = np.asarray(host_values)
+        elif not isinstance(host_values, np.ndarray):
+            # Materialize one-shot iterators so the single pass below is
+            # the only traversal.
+            host_values = list(host_values)
+        # NA-like sentinels never match a real value and would otherwise
+        # raise when mixed with numeric values, so they are dropped from
+        # the needles; NA rows are handled by the caller through the mask
+        # instead.
+        if isinstance(host_values, np.ndarray) and host_values.dtype != object:
+            # A non-object array cannot hold pd.NA, and NaT is the only
+            # NA-like value it can hold (NaN is a matchable value), so no
+            # Python-level scan is needed.
+            if host_values.dtype.kind in "mM":
+                host_values = host_values[~np.isnat(host_values)]
+            return cast("Sequence", host_values), False
+        # ``host_values`` is a list or an object array here; a single
+        # Python pass mirrors pandas' pd.NA identity scan.
+        cleaned: list[Any] = []
+        values_have_na = False
+        for value in host_values:
+            if value is pd.NA:
+                values_have_na = True
+            elif not is_na_like(value):
+                cleaned.append(value)
+        return cleaned, values_have_na
+
     def _process_values_for_isin(
         self, values: Sequence | ColumnBase
     ) -> tuple[ColumnBase, ColumnBase]:
@@ -943,6 +1042,22 @@ def _process_values_for_isin(
                 rhs = rhs.astype(lhs.dtype)
             elif lhs.can_cast_safely(rhs.dtype):
                 lhs = lhs.astype(rhs.dtype)
+            elif (
+                isinstance(lhs.dtype, np.dtype)
+                and isinstance(rhs.dtype, np.dtype)
+                and lhs.dtype.kind in "biuf"
+                and rhs.dtype.kind in "biuf"
+                and "b" in (lhs.dtype.kind, rhs.dtype.kind)
+            ):
+                # A boolean column compares by value against numeric needles
+                # (``True == 1``) like numpy/pandas. ``can_cast_safely`` reports
+                # bool<->numeric as unsafe, so promote the boolean side to the
+                # numeric dtype (a bool always fits) rather than bailing out to
+                # an all-False result.
+                if lhs.dtype.kind == "b":
+                    lhs = lhs.astype(rhs.dtype)
+                else:
+                    rhs = rhs.astype(lhs.dtype)
         return lhs, rhs
 
     def _can_return_nan(self, skipna: bool | None = None) -> bool:

python/cudf/cudf/core/series.py

@@ -3133,8 +3133,10 @@ def isin(self, values):
                 f"to isin(), you passed a [{type(values).__name__}]"
             )
 
+        result_col = self._column.isin(values)
+
         return Series._from_column(
-            self._column.isin(values),
+            result_col,
             name=self.name,
             index=self.index,
             attrs=self.attrs,

python/cudf/cudf/pandas/scripts/pandas-testing-plugin.py

@@ -3931,18 +3931,6 @@ def pytest_unconfigure(config):
     "tests/series/methods/test_info.py::test_info_series[False]": "TODO: Add a reason for failure",
     "tests/series/methods/test_info.py::test_info_series[True]": "TODO: Add a reason for failure",
     "tests/series/methods/test_info.py::test_info_show_counts_false": "assert '<class 'pand...: 140.0 bytes' == '<class 'pand...ge: 8.0 bytes'",
-    "tests/series/methods/test_isin.py::TestSeriesIsIn::test_isin_masked_types[data0-values0-expected0-Float64]": "TODO: Add a reason for failure",
-    "tests/series/methods/test_isin.py::TestSeriesIsIn::test_isin_masked_types[data0-values0-expected0-Int64]": "TODO: Add a reason for failure",
-    "tests/series/methods/test_isin.py::TestSeriesIsIn::test_isin_masked_types[data0-values0-expected0-boolean]": "TODO: Add a reason for failure",
-    "tests/series/methods/test_isin.py::TestSeriesIsIn::test_isin_masked_types[data2-values2-expected2-Float64]": "TODO: Add a reason for failure",
-    "tests/series/methods/test_isin.py::TestSeriesIsIn::test_isin_masked_types[data2-values2-expected2-Int64]": "TODO: Add a reason for failure",
-    "tests/series/methods/test_isin.py::TestSeriesIsIn::test_isin_masked_types[data2-values2-expected2-boolean]": "TODO: Add a reason for failure",
-    "tests/series/methods/test_isin.py::TestSeriesIsIn::test_isin_masked_types[data4-values4-expected4-Float64]": "TODO: Add a reason for failure",
-    "tests/series/methods/test_isin.py::TestSeriesIsIn::test_isin_masked_types[data4-values4-expected4-Int64]": "TODO: Add a reason for failure",
-    "tests/series/methods/test_isin.py::TestSeriesIsIn::test_isin_masked_types[data4-values4-expected4-boolean]": "TODO: Add a reason for failure",
-    "tests/series/methods/test_isin.py::TestSeriesIsIn::test_isin_masked_types[data5-values5-expected5-Int64]": "TODO: Add a reason for failure",
-    "tests/series/methods/test_isin.py::TestSeriesIsIn::test_isin_masked_types[data5-values5-expected5-boolean]": "TODO: Add a reason for failure",
-    "tests/series/methods/test_isin.py::test_isin_large_series_and_pdNA[boolean-data3-values3-expected3]": "AssertionError: Attributes of Series are different",
     "tests/series/methods/test_map.py::test_map_callable[MockEngineDecorator]": "AssertionError: assert Index([], dtype='object', name='bar') is Index([], dtype='object', name='bar')",
     "tests/series/methods/test_map.py::test_map_callable[None]": "AssertionError: assert Index([], dtype='object', name='bar') is Index([], dtype='object', name='bar')",
     "tests/series/methods/test_map.py::test_map_categorical_na_action[None-expected0]": "TODO: Add a reason for failure",

python/cudf/cudf/tests/series/methods/test_isin.py

@@ -1,6 +1,7 @@
 # SPDX-FileCopyrightText: Copyright (c) 2025-2026, NVIDIA CORPORATION & AFFILIATES. All rights reserved.
 # SPDX-License-Identifier: Apache-2.0
 
+import cupy as cp
 import numpy as np
 import pandas as pd
 import pyarrow as pa
@@ -162,6 +163,190 @@ def test_isin_categorical(data, values):
     assert_eq(got, expected)
 
 
+@pytest.mark.parametrize("dtype", ["boolean", "Int64", "Float64"])
+@pytest.mark.parametrize(
+    "data,values",
+    [
+        ([0, 1, 0], [1]),
+        ([0, 1, 0], [1, pd.NA]),
+        ([0, pd.NA, 0], [1, 0]),
+        ([0, 1, pd.NA], [1, pd.NA]),
+        ([0, 1, pd.NA], [1, np.nan]),
+        ([0, pd.NA, pd.NA], [np.nan, pd.NaT, None]),
+    ],
+)
+def test_isin_masked_types(dtype, data, values):
+    # Series.isin on a pandas masked (nullable integer/float/boolean) dtype
+    # returns a nullable BooleanDtype result and matches pandas' NA semantics:
+    #  * comparison is done on the underlying values (a boolean element equals
+    #    the integer 1), and
+    #  * an NA element is considered present only when pd.NA itself is one of
+    #    ``values`` (a plain NaN/None/NaT does not match).
+    psr = pd.Series(data, dtype=dtype)
+    gsr = cudf.Series(data, dtype=dtype)
+
+    got = gsr.isin(values)
+    expected = psr.isin(values)
+
+    assert got.dtype == pd.BooleanDtype()
+    assert_eq(got, expected)
+
+
+@pytest.mark.parametrize(
+    "values",
+    [[1], [0], [1, 0], [2], [1.0], [1.5], [True], [False]],
+)
+def test_isin_bool_against_numeric(values):
+    # A boolean Series compares equal to the integers/floats 0 and 1, matching
+    # numpy/pandas value semantics (previously cudf returned all-False for a
+    # numeric ``values`` argument).
+    psr = pd.Series([True, False, False, True])
+    gsr = cudf.Series([True, False, False, True])
+
+    got = gsr.isin(values)
+    assert got.dtype == np.dtype("bool")
+    assert_eq(got, psr.isin(values))
+
+
+@pytest.mark.parametrize(
+    "values",
+    [
+        lambda: (value for value in [1, 2]),
+        lambda: cudf.Series([1, 2]),
+        lambda: cudf.Index([1, 2]),
+        lambda: cp.array([1, 2]),
+        lambda: pa.chunked_array([[1, 2]]),
+    ],
+    ids=["generator", "cudf-series", "cudf-index", "cupy", "pyarrow"],
+)
+def test_isin_masked_values_containers(values):
+    # ``values`` is materialized on host once for masked dtypes:
+    # device-backed inputs are moved in a single transfer instead of
+    # element-wise reads (cudf objects are not Python-iterable at all).
+    psr = pd.Series([0, 1, pd.NA], dtype="Int64")
+    gsr = cudf.Series([0, 1, pd.NA], dtype="Int64")
+
+    assert_eq(gsr.isin(values()), psr.isin([1, 2]))
+
+
+@pytest.mark.parametrize(
+    "values",
+    [
+        pd.Series([1, pd.NA], dtype="Int64"),
+        pd.Index([1, pd.NA], dtype="Int64"),
+        pd.array([1, pd.NA], dtype="Int64"),
+    ],
+    ids=["pd-series", "pd-index", "pd-array"],
+)
+def test_isin_masked_values_container_NA_does_not_match(values):
+    # pandas materializes pandas-container ``values`` with np.asarray, where
+    # pd.NA decays to NaN: an NA needle inside a masked container does NOT
+    # match NA rows, unlike a literal pd.NA in a list.
+    psr = pd.Series([0, 1, pd.NA], dtype="Int64")
+    gsr = cudf.Series([0, 1, pd.NA], dtype="Int64")
+
+    assert_eq(gsr.isin(values), psr.isin(values))
+
+
+def test_isin_masked_one_shot_iterator_with_NA():
+    # A one-shot iterator must not be exhausted before the pd.NA
+    # inspection: the NA row still matches when pd.NA is one of ``values``.
+    psr = pd.Series([0, 1, pd.NA], dtype="Int64")
+    gsr = cudf.Series([0, 1, pd.NA], dtype="Int64")
+
+    got = gsr.isin(value for value in [1, pd.NA])
+    expected = psr.isin([1, pd.NA])
+    assert_eq(got, expected)
+
+
+def test_isin_masked_nan_is_value_not_na():
+    # A genuine NaN value in a masked float column is data, not NA: it
+    # matches a NaN needle and does not match pd.NA (mirrors pandas, where
+    # only the mask is NA).
+    psr = pd.Series(
+        pd.arrays.FloatingArray(
+            np.array([np.nan, 1.0, 0.0]),
+            np.array([False, False, True]),
+        )
+    )
+    gsr = cudf.Series([np.nan, 1.0, None], dtype="Float64", nan_as_null=False)
+
+    assert_eq(gsr.isin([np.nan]), psr.isin([np.nan]))
+    assert_eq(gsr.isin([pd.NA]), psr.isin([pd.NA]))
+
+
+def test_isin_masked_pandas_compatible_mode():
+    # The masked path must work in pandas-compatible mode (the
+    # masked-with-nulls to numpy astype guard must not trigger) and must
+    # not mutate the input Series' dtype via the in-place astype
+    # short-circuit.
+    with cudf.option_context("mode.pandas_compatible", True):
+        gsr = cudf.Series([1, pd.NA], dtype="Int64")
+        got = gsr.isin([1])
+        assert gsr.dtype == pd.Int64Dtype()
+        assert got.dtype == pd.BooleanDtype()
+        assert got.to_pandas().tolist() == [True, False]
+
+        gsr = cudf.Series([True, pd.NA], dtype="boolean")
+        got = gsr.isin([True])
+        assert gsr.dtype == pd.BooleanDtype()
+        assert got.to_pandas().tolist() == [True, False]
+
+        gsr = cudf.Series([1.5, 2.5], dtype="Float64")
+        got = gsr.isin([1.5])
+        assert gsr.dtype == pd.Float64Dtype()
+        assert got.to_pandas().tolist() == [True, False]
+
+
+@pytest.mark.parametrize("values", [[], [pd.NA], [None], [1]])
+def test_isin_masked_all_na(values):
+    # An all-NA masked Series with needles that clean to empty used to
+    # raise in pandas-compatible mode (an empty needle list produces an
+    # object-dtype column that an all-null column cannot be cast to there).
+    psr = pd.Series([pd.NA, pd.NA], dtype="Int64")
+    expected = psr.isin(values)
+
+    gsr = cudf.Series([pd.NA, pd.NA], dtype="Int64")
+    assert_eq(gsr.isin(values), expected)
+
+    with cudf.option_context("mode.pandas_compatible", True):
+        gsr = cudf.Series([pd.NA, pd.NA], dtype="Int64")
+        got = gsr.isin(values)
+    assert_eq(got, expected)
+
+
+def test_isin_masked_does_not_mutate_dtype():
+    # Regression test: the astype in the masked path used to flip the
+    # input's dtype from Int64 to int64 in pandas-compatible mode.
+    gsr = cudf.Series([1, 2], dtype="Int64")
+    gsr.isin([1])
+    assert gsr.dtype == pd.Int64Dtype()
+
+    with cudf.option_context("mode.pandas_compatible", True):
+        gsr = cudf.Series([1, 2], dtype="Int64")
+        gsr.isin([1])
+        assert gsr.dtype == pd.Int64Dtype()
+
+
+@pytest.mark.parametrize(
+    "psr",
+    [
+        pd.Series([0, 1, 0], dtype=pd.ArrowDtype(pa.int64())),
+        pd.Series([1.0, 2.0, None], dtype=pd.ArrowDtype(pa.float64())),
+        pd.Series([True, False, True], dtype=pd.ArrowDtype(pa.bool_())),
+        pd.Series(["a", "b", "a"], dtype="category"),
+    ],
+)
+def test_isin_non_masked_extension_returns_numpy_bool(psr):
+    # Arrow and categorical inputs yield a numpy bool result (only masked
+    # numeric/boolean dtypes upgrade to nullable boolean).
+    gsr = cudf.from_pandas(psr)
+
+    got = gsr.isin([psr.iloc[0]])
+    assert got.dtype == np.dtype("bool")
+    assert_eq(got, psr.isin([psr.iloc[0]]))
+
+
 @pytest.mark.parametrize(
     "dtype",
     [