quantile: use skipna=None (#6303)

* quantile: use skipna=None

* better term

* move whats new entry

* remove duplicated entry

doc/whats-new.rst

@@ -34,6 +34,9 @@ Deprecations
 Bug fixes
 ~~~~~~~~~
 
+- Set ``skipna=None`` for all ``quantile`` methods (e.g. :py:meth:`Dataset.quantile`) and
+  ensure it skips missing values for float dtypes (consistent with other methods). This should
+  not change the behavior (:pull:`6303`). By `Mathias Hauser <https://github.com/mathause>`_.
 
 Documentation
 ~~~~~~~~~~~~~
@@ -86,7 +89,6 @@ Deprecations
 Bug fixes
 ~~~~~~~~~
 
-
 - Variables which are chunked using dask in larger (but aligned) chunks than the target zarr chunk size
   can now be stored using `to_zarr()` (:pull:`6258`) By `Tobias Kölling <https://github.com/d70-t>`_.
 - Multi-file datasets containing encoded :py:class:`cftime.datetime` objects can be read in parallel again (:issue:`6226`, :pull:`6249`, :pull:`6305`).  By `Martin Bergemann <https://github.com/antarcticrainforest>`_ and `Stan West <https://github.com/stanwest>`_.

xarray/core/dataarray.py

@@ -3440,7 +3440,7 @@ def quantile(
         dim: str | Sequence[Hashable] | None = None,
         method: QUANTILE_METHODS = "linear",
         keep_attrs: bool = None,
-        skipna: bool = True,
+        skipna: bool = None,
         interpolation: QUANTILE_METHODS = None,
     ) -> DataArray:
         """Compute the qth quantile of the data along the specified dimension.
@@ -3486,7 +3486,10 @@ def quantile(
             the original object to the new one.  If False (default), the new
             object will be returned without attributes.
         skipna : bool, optional
-            Whether to skip missing values when aggregating.
+            If True, skip missing values (as marked by NaN). By default, only
+            skips missing values for float dtypes; other dtypes either do not
+            have a sentinel missing value (int) or skipna=True has not been
+            implemented (object, datetime64 or timedelta64).
 
         Returns
         -------

xarray/core/dataset.py

@@ -6160,7 +6160,7 @@ def quantile(
         method: QUANTILE_METHODS = "linear",
         numeric_only: bool = False,
         keep_attrs: bool = None,
-        skipna: bool = True,
+        skipna: bool = None,
         interpolation: QUANTILE_METHODS = None,
     ):
         """Compute the qth quantile of the data along the specified dimension.
@@ -6209,7 +6209,10 @@ def quantile(
         numeric_only : bool, optional
             If True, only apply ``func`` to variables with a numeric dtype.
         skipna : bool, optional
-            Whether to skip missing values when aggregating.
+            If True, skip missing values (as marked by NaN). By default, only
+            skips missing values for float dtypes; other dtypes either do not
+            have a sentinel missing value (int) or skipna=True has not been
+            implemented (object, datetime64 or timedelta64).
 
         Returns
         -------

xarray/core/groupby.py

@@ -554,7 +554,7 @@ def quantile(
         dim=None,
         method="linear",
         keep_attrs=None,
-        skipna=True,
+        skipna=None,
         interpolation=None,
     ):
         """Compute the qth quantile over each array in the groups and
@@ -597,7 +597,10 @@ def quantile(
             version 1.22.0.
 
         skipna : bool, optional
-            Whether to skip missing values when aggregating.
+            If True, skip missing values (as marked by NaN). By default, only
+            skips missing values for float dtypes; other dtypes either do not
+            have a sentinel missing value (int) or skipna=True has not been
+            implemented (object, datetime64 or timedelta64).
 
         Returns
         -------

xarray/core/variable.py

@@ -1978,7 +1978,7 @@ def quantile(
         dim: str | Sequence[Hashable] | None = None,
         method: QUANTILE_METHODS = "linear",
         keep_attrs: bool = None,
-        skipna: bool = True,
+        skipna: bool = None,
         interpolation: QUANTILE_METHODS = None,
     ) -> Variable:
         """Compute the qth quantile of the data along the specified dimension.
@@ -2024,6 +2024,11 @@ def quantile(
             If True, the variable's attributes (`attrs`) will be copied from
             the original object to the new one.  If False (default), the new
             object will be returned without attributes.
+        skipna : bool, optional
+            If True, skip missing values (as marked by NaN). By default, only
+            skips missing values for float dtypes; other dtypes either do not
+            have a sentinel missing value (int) or skipna=True has not been
+            implemented (object, datetime64 or timedelta64).
 
         Returns
         -------
@@ -2059,7 +2064,10 @@ def quantile(
 
             method = interpolation
 
-        _quantile_func = np.nanquantile if skipna else np.quantile
+        if skipna or (skipna is None and self.dtype.kind in "cfO"):
+            _quantile_func = np.nanquantile
+        else:
+            _quantile_func = np.quantile
 
         if keep_attrs is None:
             keep_attrs = _get_keep_attrs(default=False)

xarray/tests/test_dataarray.py

@@ -2516,15 +2516,19 @@ def test_reduce_out(self):
         with pytest.raises(TypeError):
             orig.mean(out=np.ones(orig.shape))
 
-    @pytest.mark.parametrize("skipna", [True, False])
+    @pytest.mark.parametrize("skipna", [True, False, None])
     @pytest.mark.parametrize("q", [0.25, [0.50], [0.25, 0.75]])
     @pytest.mark.parametrize(
         "axis, dim", zip([None, 0, [0], [0, 1]], [None, "x", ["x"], ["x", "y"]])
     )
     def test_quantile(self, q, axis, dim, skipna) -> None:
-        actual = DataArray(self.va).quantile(q, dim=dim, keep_attrs=True, skipna=skipna)
-        _percentile_func = np.nanpercentile if skipna else np.percentile
-        expected = _percentile_func(self.dv.values, np.array(q) * 100, axis=axis)
+
+        va = self.va.copy(deep=True)
+        va[0, 0] = np.NaN
+
+        actual = DataArray(va).quantile(q, dim=dim, keep_attrs=True, skipna=skipna)
+        _percentile_func = np.nanpercentile if skipna in (True, None) else np.percentile
+        expected = _percentile_func(va.values, np.array(q) * 100, axis=axis)
         np.testing.assert_allclose(actual.values, expected)
         if is_scalar(q):
             assert "quantile" not in actual.dims

xarray/tests/test_dataset.py

@@ -4718,10 +4718,11 @@ def test_reduce_keepdims(self):
         )
         assert_identical(expected, actual)
 
-    @pytest.mark.parametrize("skipna", [True, False])
+    @pytest.mark.parametrize("skipna", [True, False, None])
     @pytest.mark.parametrize("q", [0.25, [0.50], [0.25, 0.75]])
     def test_quantile(self, q, skipna) -> None:
         ds = create_test_data(seed=123)
+        ds.var1.data[0, 0] = np.NaN
 
         for dim in [None, "dim1", ["dim1"]]:
             ds_quantile = ds.quantile(q, dim=dim, skipna=skipna)

xarray/tests/test_groupby.py

@@ -203,6 +203,17 @@ def test_da_groupby_quantile() -> None:
     actual = array.groupby("x").quantile([0, 1])
     assert_identical(expected, actual)
 
+    array = xr.DataArray(
+        data=[np.NaN, 2, 3, 4, 5, 6], coords={"x": [1, 1, 1, 2, 2, 2]}, dims="x"
+    )
+
+    for skipna in (True, False, None):
+        e = [np.NaN, 5] if skipna is False else [2.5, 5]
+
+        expected = xr.DataArray(data=e, coords={"x": [1, 2], "quantile": 0.5}, dims="x")
+        actual = array.groupby("x").quantile(0.5, skipna=skipna)
+        assert_identical(expected, actual)
+
     # Multiple dimensions
     array = xr.DataArray(
         data=[[1, 11, 26], [2, 12, 22], [3, 13, 23], [4, 16, 24], [5, 15, 25]],
@@ -306,6 +317,20 @@ def test_ds_groupby_quantile() -> None:
     actual = ds.groupby("x").quantile([0, 1])
     assert_identical(expected, actual)
 
+    ds = xr.Dataset(
+        data_vars={"a": ("x", [np.NaN, 2, 3, 4, 5, 6])},
+        coords={"x": [1, 1, 1, 2, 2, 2]},
+    )
+
+    for skipna in (True, False, None):
+        e = [np.NaN, 5] if skipna is False else [2.5, 5]
+
+        expected = xr.Dataset(
+            data_vars={"a": ("x", e)}, coords={"quantile": 0.5, "x": [1, 2]}
+        )
+        actual = ds.groupby("x").quantile(0.5, skipna=skipna)
+        assert_identical(expected, actual)
+
     # Multiple dimensions
     ds = xr.Dataset(
         data_vars={

xarray/tests/test_variable.py

@@ -1700,16 +1700,20 @@ def raise_if_called(*args, **kwargs):
         with set_options(use_bottleneck=False):
             v.min()
 
-    @pytest.mark.parametrize("skipna", [True, False])
+    @pytest.mark.parametrize("skipna", [True, False, None])
     @pytest.mark.parametrize("q", [0.25, [0.50], [0.25, 0.75]])
     @pytest.mark.parametrize(
         "axis, dim", zip([None, 0, [0], [0, 1]], [None, "x", ["x"], ["x", "y"]])
     )
     def test_quantile(self, q, axis, dim, skipna):
-        v = Variable(["x", "y"], self.d)
+
+        d = self.d.copy()
+        d[0, 0] = np.NaN
+
+        v = Variable(["x", "y"], d)
         actual = v.quantile(q, dim=dim, skipna=skipna)
-        _percentile_func = np.nanpercentile if skipna else np.percentile
-        expected = _percentile_func(self.d, np.array(q) * 100, axis=axis)
+        _percentile_func = np.nanpercentile if skipna in (True, None) else np.percentile
+        expected = _percentile_func(d, np.array(q) * 100, axis=axis)
         np.testing.assert_allclose(actual.values, expected)
 
     @requires_dask