Fix sortby descending order placing NaNs at beginning instead of end

Use duck_array_ops.notnull as additional sort keys to ensure null values
sort to the end in descending order. This is cleaner than the previous
approach of manually tracking NaN positions.

Fixes #7358

Co-Authored-By: Claude <noreply@anthropic.com>

Author: kkollsga

doc/whats-new.rst

@@ -30,6 +30,9 @@ Bug Fixes
   Dask chunk boundaries must now align with shard boundaries, not just internal
   Zarr chunk boundaries (:issue:`10831`).
 
+- Fix :py:meth:`Dataset.sortby` and :py:meth:`DataArray.sortby` placing NaN values
+  at the beginning instead of the end when using ``ascending=False`` (:issue:`7358`).
+  By `Kristian Kollsgård <https://github.com/kkollsga>`_.
 
 Documentation
 ~~~~~~~~~~~~~

xarray/core/dataset.py

@@ -8129,8 +8129,21 @@ def sortby(
 
         indices = {}
         for key, arrays in vars_by_dim.items():
-            order = np.lexsort(tuple(reversed(arrays)))
-            indices[key] = order if ascending else order[::-1]
+            if ascending:
+                indices[key] = np.lexsort(tuple(reversed(arrays)))
+            else:
+                # For descending order, we need to keep NaNs at the end.
+                # By adding notnull(arr) as additional sort keys, null values
+                # sort to the beginning (False=0 < True=1), then reversing
+                # puts them at the end. See https://github.com/pydata/xarray/issues/7358
+                indices[key] = np.lexsort(
+                    tuple(
+                        [
+                            *reversed(arrays),
+                            *[duck_array_ops.notnull(arr) for arr in reversed(arrays)],
+                        ]
+                    )
+                )[::-1]
         return aligned_self.isel(indices)
 
     def quantile(

xarray/tests/test_dataset.py

@@ -7236,6 +7236,47 @@ def test_sortby(self) -> None:
         actual = ds.sortby(["x", "y"], ascending=False)
         assert_equal(actual, ds)
 
+    def test_sortby_descending_nans(self) -> None:
+        # Regression test for https://github.com/pydata/xarray/issues/7358
+        # NaN values should remain at the end when sorting in descending order
+        ds = Dataset({"var": ("x", [3.0, np.nan, 4.0, 2.0, np.nan])})
+
+        # Ascending: NaNs at end
+        result_asc = ds.sortby("var", ascending=True)
+        assert_array_equal(result_asc["var"].values[:3], [2.0, 3.0, 4.0])
+        assert np.all(np.isnan(result_asc["var"].values[3:]))
+
+        # Descending: NaNs should also be at end (not beginning)
+        result_desc = ds.sortby("var", ascending=False)
+        assert_array_equal(result_desc["var"].values[:3], [4.0, 3.0, 2.0])
+        assert np.all(np.isnan(result_desc["var"].values[3:]))
+
+    def test_sortby_descending_nans_multi_key(self) -> None:
+        # Test sortby with multiple keys where one has NaN values
+        # Regression test for https://github.com/pydata/xarray/issues/7358
+        ds = Dataset(
+            {
+                "A": (("x", "y"), [[1, 2, 3], [4, 5, 6]]),
+                "B": (("x", "y"), [[7, 8, 9], [10, 11, 12]]),
+            },
+            coords={"x": ["b", "a"], "y": [np.nan, 1, 0]},
+        )
+
+        # Sort by multiple keys in descending order
+        result = ds.sortby(["x", "y"], ascending=False)
+
+        # x should be sorted descending: ["b", "a"]
+        assert_array_equal(result["x"].values, ["b", "a"])
+
+        # y should be sorted descending with NaN at end: [1, 0, nan]
+        assert_array_equal(result["y"].values[:2], [1, 0])
+        assert np.isnan(result["y"].values[2])
+
+        # Verify data is reordered correctly
+        # Original y=[nan, 1, 0] -> sorted y=[1, 0, nan] means columns reordered [1, 2, 0]
+        assert_array_equal(result["A"].values, [[2, 3, 1], [5, 6, 4]])
+        assert_array_equal(result["B"].values, [[8, 9, 7], [11, 12, 10]])
+
     def test_attribute_access(self) -> None:
         ds = create_test_data(seed=1)
         for key in ["var1", "var2", "var3", "time", "dim1", "dim2", "dim3", "numbers"]: