DEPR: use_inf_as_na (#53494)

* DEPR: use_inf_as_na

* troubleshoot doc

* troubleshoot docbuild

* troubleshoot doc

* troubleshoot docs

Author: jbrockmendel

doc/source/user_guide/missing_data.rst

@@ -29,11 +29,6 @@ detect this value with data of different types: floating point, integer,
 boolean, and general object. In many cases, however, the Python ``None`` will
 arise and we wish to also consider that "missing" or "not available" or "NA".
 
-.. note::
-
-   If you want to consider ``inf`` and ``-inf`` to be "NA" in computations,
-   you can set ``pandas.options.mode.use_inf_as_na = True``.
-
 .. _missing.isna:
 
 .. ipython:: python

doc/source/whatsnew/v2.1.0.rst

@@ -275,6 +275,7 @@ Deprecations
 - Deprecated allowing arbitrary ``fill_value`` in :class:`SparseDtype`, in a future version the ``fill_value`` will need to be compatible with the ``dtype.subtype``, either a scalar that can be held by that subtype or ``NaN`` for integer or bool subtypes (:issue:`23124`)
 - Deprecated behavior of :func:`assert_series_equal` and :func:`assert_frame_equal` considering NA-like values (e.g. ``NaN`` vs ``None`` as equivalent) (:issue:`52081`)
 - Deprecated constructing :class:`SparseArray` from scalar data, pass a sequence instead (:issue:`53039`)
+- Deprecated option "mode.use_inf_as_na", convert inf entries to ``NaN`` before instead (:issue:`51684`)
 - Deprecated positional indexing on :class:`Series` with :meth:`Series.__getitem__` and :meth:`Series.__setitem__`, in a future version ``ser[item]`` will *always* interpret ``item`` as a label, not a position (:issue:`50617`)
 
 .. ---------------------------------------------------------------------------

pandas/_config/config.py

@@ -438,7 +438,7 @@ def __init__(self, *args) -> None:
         self.ops = list(zip(args[::2], args[1::2]))
 
     def __enter__(self) -> None:
-        self.undo = [(pat, _get_option(pat, silent=True)) for pat, val in self.ops]
+        self.undo = [(pat, _get_option(pat)) for pat, val in self.ops]
 
         for pat, val in self.ops:
             _set_option(pat, val, silent=True)

pandas/core/config_init.py

@@ -411,6 +411,8 @@ def is_terminal() -> bool:
     True means treat None, NaN, INF, -INF as NA (old way),
     False means None and NaN are null, but INF, -INF are not NA
     (new way).
+
+    This option is deprecated in pandas 2.1.0 and will be removed in 3.0.
 """
 
 # We don't want to start importing everything at the global context level
@@ -426,6 +428,12 @@ def use_inf_as_na_cb(key) -> None:
 with cf.config_prefix("mode"):
     cf.register_option("use_inf_as_na", False, use_inf_as_na_doc, cb=use_inf_as_na_cb)
 
+cf.deprecate_option(
+    # GH#51684
+    "mode.use_inf_as_na",
+    "use_inf_as_na option is deprecated and will be removed in a future "
+    "version. Convert inf values to NaN before operating instead.",
+)
 
 data_manager_doc = """
 : string

pandas/core/frame.py

@@ -10740,8 +10740,7 @@ def count(self, axis: Axis = 0, numeric_only: bool = False):
         """
         Count non-NA cells for each column or row.
 
-        The values `None`, `NaN`, `NaT`, and optionally `numpy.inf` (depending
-        on `pandas.options.mode.use_inf_as_na`) are considered NA.
+        The values `None`, `NaN`, `NaT`, ``pandas.NA`` are considered NA.
 
         Parameters
         ----------

pandas/core/indexes/base.py

@@ -2820,8 +2820,7 @@ def isna(self) -> npt.NDArray[np.bool_]:
         NA values, such as ``None``, :attr:`numpy.NaN` or :attr:`pd.NaT`, get
         mapped to ``True`` values.
         Everything else get mapped to ``False`` values. Characters such as
-        empty strings `''` or :attr:`numpy.inf` are not considered NA values
-        (unless you set ``pandas.options.mode.use_inf_as_na = True``).
+        empty strings `''` or :attr:`numpy.inf` are not considered NA values.
 
         Returns
         -------
@@ -2876,8 +2875,7 @@ def notna(self) -> npt.NDArray[np.bool_]:
 
         Return a boolean same-sized object indicating if the values are not NA.
         Non-missing values get mapped to ``True``. Characters such as empty
-        strings ``''`` or :attr:`numpy.inf` are not considered NA values
-        (unless you set ``pandas.options.mode.use_inf_as_na = True``).
+        strings ``''`` or :attr:`numpy.inf` are not considered NA values.
         NA values, such as None or :attr:`numpy.NaN`, get mapped to ``False``
         values.
 

pandas/tests/arrays/categorical/test_missing.py

@@ -137,18 +137,20 @@ def test_fillna_array(self):
     )
     def test_use_inf_as_na(self, values, expected):
         # https://github.com/pandas-dev/pandas/issues/33594
-        with pd.option_context("mode.use_inf_as_na", True):
-            cat = Categorical(values)
-            result = cat.isna()
-            tm.assert_numpy_array_equal(result, expected)
+        msg = "use_inf_as_na option is deprecated"
+        with tm.assert_produces_warning(FutureWarning, match=msg):
+            with pd.option_context("mode.use_inf_as_na", True):
+                cat = Categorical(values)
+                result = cat.isna()
+                tm.assert_numpy_array_equal(result, expected)
 
-            result = Series(cat).isna()
-            expected = Series(expected)
-            tm.assert_series_equal(result, expected)
+                result = Series(cat).isna()
+                expected = Series(expected)
+                tm.assert_series_equal(result, expected)
 
-            result = DataFrame(cat).isna()
-            expected = DataFrame(expected)
-            tm.assert_frame_equal(result, expected)
+                result = DataFrame(cat).isna()
+                expected = DataFrame(expected)
+                tm.assert_frame_equal(result, expected)
 
     @pytest.mark.parametrize(
         "values, expected",
@@ -164,17 +166,19 @@ def test_use_inf_as_na_outside_context(self, values, expected):
         # Using isna directly for Categorical will fail in general here
         cat = Categorical(values)
 
-        with pd.option_context("mode.use_inf_as_na", True):
-            result = isna(cat)
-            tm.assert_numpy_array_equal(result, expected)
+        msg = "use_inf_as_na option is deprecated"
+        with tm.assert_produces_warning(FutureWarning, match=msg):
+            with pd.option_context("mode.use_inf_as_na", True):
+                result = isna(cat)
+                tm.assert_numpy_array_equal(result, expected)
 
-            result = isna(Series(cat))
-            expected = Series(expected)
-            tm.assert_series_equal(result, expected)
+                result = isna(Series(cat))
+                expected = Series(expected)
+                tm.assert_series_equal(result, expected)
 
-            result = isna(DataFrame(cat))
-            expected = DataFrame(expected)
-            tm.assert_frame_equal(result, expected)
+                result = isna(DataFrame(cat))
+                expected = DataFrame(expected)
+                tm.assert_frame_equal(result, expected)
 
     @pytest.mark.parametrize(
         "a1, a2, categories",

pandas/tests/arrays/string_/test_string.py

@@ -492,17 +492,19 @@ def test_value_counts_with_normalize(dtype):
 def test_use_inf_as_na(values, expected, dtype):
     # https://github.com/pandas-dev/pandas/issues/33655
     values = pd.array(values, dtype=dtype)
-    with pd.option_context("mode.use_inf_as_na", True):
-        result = values.isna()
-        tm.assert_numpy_array_equal(result, expected)
-
-        result = pd.Series(values).isna()
-        expected = pd.Series(expected)
-        tm.assert_series_equal(result, expected)
-
-        result = pd.DataFrame(values).isna()
-        expected = pd.DataFrame(expected)
-        tm.assert_frame_equal(result, expected)
+    msg = "use_inf_as_na option is deprecated"
+    with tm.assert_produces_warning(FutureWarning, match=msg):
+        with pd.option_context("mode.use_inf_as_na", True):
+            result = values.isna()
+            tm.assert_numpy_array_equal(result, expected)
+
+            result = pd.Series(values).isna()
+            expected = pd.Series(expected)
+            tm.assert_series_equal(result, expected)
+
+            result = pd.DataFrame(values).isna()
+            expected = pd.DataFrame(expected)
+            tm.assert_frame_equal(result, expected)
 
 
 def test_memory_usage(dtype):

pandas/tests/dtypes/test_missing.py

@@ -53,21 +53,24 @@ def test_notna_notnull(notna_f):
     assert not notna_f(None)
     assert not notna_f(np.NaN)
 
-    with cf.option_context("mode.use_inf_as_na", False):
-        assert notna_f(np.inf)
-        assert notna_f(-np.inf)
+    msg = "use_inf_as_na option is deprecated"
+    with tm.assert_produces_warning(FutureWarning, match=msg):
+        with cf.option_context("mode.use_inf_as_na", False):
+            assert notna_f(np.inf)
+            assert notna_f(-np.inf)
 
-        arr = np.array([1.5, np.inf, 3.5, -np.inf])
-        result = notna_f(arr)
-        assert result.all()
+            arr = np.array([1.5, np.inf, 3.5, -np.inf])
+            result = notna_f(arr)
+            assert result.all()
 
-    with cf.option_context("mode.use_inf_as_na", True):
-        assert not notna_f(np.inf)
-        assert not notna_f(-np.inf)
+    with tm.assert_produces_warning(FutureWarning, match=msg):
+        with cf.option_context("mode.use_inf_as_na", True):
+            assert not notna_f(np.inf)
+            assert not notna_f(-np.inf)
 
-        arr = np.array([1.5, np.inf, 3.5, -np.inf])
-        result = notna_f(arr)
-        assert result.sum() == 2
+            arr = np.array([1.5, np.inf, 3.5, -np.inf])
+            result = notna_f(arr)
+            assert result.sum() == 2
 
 
 @pytest.mark.parametrize("null_func", [notna, notnull, isna, isnull])
@@ -82,8 +85,10 @@ def test_notna_notnull(notna_f):
     ],
 )
 def test_null_check_is_series(null_func, ser):
-    with cf.option_context("mode.use_inf_as_na", False):
-        assert isinstance(null_func(ser), Series)
+    msg = "use_inf_as_na option is deprecated"
+    with tm.assert_produces_warning(FutureWarning, match=msg):
+        with cf.option_context("mode.use_inf_as_na", False):
+            assert isinstance(null_func(ser), Series)
 
 
 class TestIsNA:
@@ -214,8 +219,10 @@ def test_isna_old_datetimelike(self):
         objs = [dta, dta.tz_localize("US/Eastern"), dta - dta, dta.to_period("D")]
 
         for obj in objs:
-            with cf.option_context("mode.use_inf_as_na", True):
-                result = isna(obj)
+            msg = "use_inf_as_na option is deprecated"
+            with tm.assert_produces_warning(FutureWarning, match=msg):
+                with cf.option_context("mode.use_inf_as_na", True):
+                    result = isna(obj)
 
             tm.assert_numpy_array_equal(result, expected)
 

pandas/tests/extension/base/missing.py

@@ -154,6 +154,8 @@ def test_fillna_fill_other(self, data):
     def test_use_inf_as_na_no_effect(self, data_missing):
         ser = pd.Series(data_missing)
         expected = ser.isna()
-        with pd.option_context("mode.use_inf_as_na", True):
-            result = ser.isna()
+        msg = "use_inf_as_na option is deprecated"
+        with tm.assert_produces_warning(FutureWarning, match=msg):
+            with pd.option_context("mode.use_inf_as_na", True):
+                result = ser.isna()
         self.assert_series_equal(result, expected)

pandas/tests/frame/methods/test_dtypes.py

@@ -96,10 +96,12 @@ def test_dtypes_gh8722(self, float_string_frame):
         tm.assert_series_equal(result, expected)
 
         # compat, GH 8722
-        with option_context("use_inf_as_na", True):
-            df = DataFrame([[1]])
-            result = df.dtypes
-            tm.assert_series_equal(result, Series({0: np.dtype("int64")}))
+        msg = "use_inf_as_na option is deprecated"
+        with tm.assert_produces_warning(FutureWarning, match=msg):
+            with option_context("use_inf_as_na", True):
+                df = DataFrame([[1]])
+                result = df.dtypes
+                tm.assert_series_equal(result, Series({0: np.dtype("int64")}))
 
     def test_dtypes_timedeltas(self):
         df = DataFrame(

pandas/tests/frame/methods/test_sort_index.py

@@ -769,8 +769,10 @@ def test_sort_index_use_inf_as_na(self):
             {"col1": [1, 2, 3], "col2": [3, 4, 5]},
             index=pd.date_range("2020", periods=3),
         )
-        with pd.option_context("mode.use_inf_as_na", True):
-            result = expected.sort_index()
+        msg = "use_inf_as_na option is deprecated"
+        with tm.assert_produces_warning(FutureWarning, match=msg):
+            with pd.option_context("mode.use_inf_as_na", True):
+                result = expected.sort_index()
         tm.assert_frame_equal(result, expected)
 
     @pytest.mark.parametrize(

pandas/tests/frame/test_repr_info.py

@@ -400,30 +400,36 @@ def test_to_records_with_na_record(self):
 
     def test_to_records_with_inf_as_na_record(self):
         # GH 48526
-        with option_context("use_inf_as_na", True):
-            df = DataFrame(
-                [[np.inf, "b"], [np.nan, np.nan], ["e", "f"]], columns=[np.nan, np.inf]
-            )
-            df["record"] = df[[np.nan, np.inf]].to_records()
-            expected = """   NaN  inf         record
+        expected = """   NaN  inf         record
 0  NaN    b    [0, inf, b]
 1  NaN  NaN  [1, nan, nan]
 2    e    f      [2, e, f]"""
-            result = repr(df)
+        msg = "use_inf_as_na option is deprecated"
+        with tm.assert_produces_warning(FutureWarning, match=msg):
+            with option_context("use_inf_as_na", True):
+                df = DataFrame(
+                    [[np.inf, "b"], [np.nan, np.nan], ["e", "f"]],
+                    columns=[np.nan, np.inf],
+                )
+                df["record"] = df[[np.nan, np.inf]].to_records()
+                result = repr(df)
         assert result == expected
 
     def test_to_records_with_inf_record(self):
         # GH 48526
-        with option_context("use_inf_as_na", False):
-            df = DataFrame(
-                [[np.inf, "b"], [np.nan, np.nan], ["e", "f"]], columns=[np.nan, np.inf]
-            )
-            df["record"] = df[[np.nan, np.inf]].to_records()
-            expected = """   NaN  inf         record
+        expected = """   NaN  inf         record
 0  inf    b    [0, inf, b]
 1  NaN  NaN  [1, nan, nan]
 2    e    f      [2, e, f]"""
-            result = repr(df)
+        msg = "use_inf_as_na option is deprecated"
+        with tm.assert_produces_warning(FutureWarning, match=msg):
+            with option_context("use_inf_as_na", False):
+                df = DataFrame(
+                    [[np.inf, "b"], [np.nan, np.nan], ["e", "f"]],
+                    columns=[np.nan, np.inf],
+                )
+                df["record"] = df[[np.nan, np.inf]].to_records()
+                result = repr(df)
         assert result == expected
 
     def test_masked_ea_with_formatter(self):

pandas/tests/io/parser/common/test_inf.py

@@ -62,7 +62,9 @@ def test_read_csv_with_use_inf_as_na(all_parsers):
     # https://github.com/pandas-dev/pandas/issues/35493
     parser = all_parsers
     data = "1.0\nNaN\n3.0"
-    with option_context("use_inf_as_na", True):
-        result = parser.read_csv(StringIO(data), header=None)
+    msg = "use_inf_as_na option is deprecated"
+    with tm.assert_produces_warning(FutureWarning, match=msg):
+        with option_context("use_inf_as_na", True):
+            result = parser.read_csv(StringIO(data), header=None)
     expected = DataFrame([1.0, np.nan, 3.0])
     tm.assert_frame_equal(result, expected)

pandas/tests/reductions/test_reductions.py

@@ -562,8 +562,10 @@ def test_sum_inf(self):
         arr = np.random.randn(100, 100).astype("f4")
         arr[:, 2] = np.inf
 
-        with pd.option_context("mode.use_inf_as_na", True):
-            tm.assert_almost_equal(s.sum(), s2.sum())
+        msg = "use_inf_as_na option is deprecated"
+        with tm.assert_produces_warning(FutureWarning, match=msg):
+            with pd.option_context("mode.use_inf_as_na", True):
+                tm.assert_almost_equal(s.sum(), s2.sum())
 
         res = nanops.nansum(arr, axis=1)
         assert np.isinf(res).all()
@@ -1102,13 +1104,15 @@ def test_idxminmax_with_inf(self):
         assert s.idxmax() == 2
         assert np.isnan(s.idxmax(skipna=False))
 
-        # Using old-style behavior that treats floating point nan, -inf, and
-        # +inf as missing
-        with pd.option_context("mode.use_inf_as_na", True):
-            assert s.idxmin() == 0
-            assert np.isnan(s.idxmin(skipna=False))
-            assert s.idxmax() == 0
-            np.isnan(s.idxmax(skipna=False))
+        msg = "use_inf_as_na option is deprecated"
+        with tm.assert_produces_warning(FutureWarning, match=msg):
+            # Using old-style behavior that treats floating point nan, -inf, and
+            # +inf as missing
+            with pd.option_context("mode.use_inf_as_na", True):
+                assert s.idxmin() == 0
+                assert np.isnan(s.idxmin(skipna=False))
+                assert s.idxmax() == 0
+                np.isnan(s.idxmax(skipna=False))
 
     def test_sum_uint64(self):
         # GH 53401

pandas/tests/series/methods/test_count.py

@@ -5,6 +5,7 @@
     Categorical,
     Series,
 )
+import pandas._testing as tm
 
 
 class TestSeriesCount:
@@ -15,9 +16,13 @@ def test_count(self, datetime_series):
 
         assert datetime_series.count() == np.isfinite(datetime_series).sum()
 
+    def test_count_inf_as_na(self):
         # GH#29478
-        with pd.option_context("use_inf_as_na", True):
-            assert Series([pd.Timestamp("1990/1/1")]).count() == 1
+        ser = Series([pd.Timestamp("1990/1/1")])
+        msg = "use_inf_as_na option is deprecated"
+        with tm.assert_produces_warning(FutureWarning, match=msg):
+            with pd.option_context("use_inf_as_na", True):
+                assert ser.count() == 1
 
     def test_count_categorical(self):
         ser = Series(