Add support for DataTree to xarray.merge()

doc/whats-new.rst

@@ -13,6 +13,9 @@ v2025.10.2 (unreleased)
 New Features
 ~~~~~~~~~~~~
 
+- :py:func:`merge` now supports merging :py:class:`DataTree` objects
+  (:issue:`9790`).
+  By `Stephan Hoyer <https://github.com/shoyer>`_.
 
 Breaking Changes
 ~~~~~~~~~~~~~~~~

xarray/core/datatree.py

@@ -37,7 +37,7 @@
 from xarray.core.dataset import Dataset
 from xarray.core.dataset_variables import DataVariables
 from xarray.core.datatree_mapping import (
-    _handle_errors_with_path_context,
+    add_path_context_to_errors,
     map_over_datasets,
 )
 from xarray.core.formatting import (
@@ -2213,8 +2213,8 @@ def _selective_indexing(
         result = {}
         for path, node in self.subtree_with_keys:
             node_indexers = {k: v for k, v in indexers.items() if k in node.dims}
-            func_with_error_context = _handle_errors_with_path_context(path)(func)
-            node_result = func_with_error_context(node.dataset, node_indexers)
+            with add_path_context_to_errors(path):
+                node_result = func(node.dataset, node_indexers)
             # Indexing datasets corresponding to each node results in redundant
             # coordinates when indexes from a parent node are inherited.
             # Ideally, we would avoid creating such coordinates in the first

xarray/core/datatree_mapping.py

@@ -1,6 +1,7 @@
 from __future__ import annotations
 
 from collections.abc import Callable, Mapping
+from contextlib import contextmanager
 from typing import TYPE_CHECKING, Any, cast, overload
 
 from xarray.core.dataset import Dataset
@@ -112,9 +113,8 @@ def map_over_datasets(
         for i, arg in enumerate(args):
             if not isinstance(arg, DataTree):
                 node_dataset_args.insert(i, arg)
-
-        func_with_error_context = _handle_errors_with_path_context(path)(func)
-        results = func_with_error_context(*node_dataset_args, **kwargs)
+        with add_path_context_to_errors(path):
+            results = func(*node_dataset_args, **kwargs)
         out_data_objects[path] = results
 
     num_return_values = _check_all_return_values(out_data_objects)
@@ -138,27 +138,14 @@ def map_over_datasets(
     )
 
 
-def _handle_errors_with_path_context(path: str):
-    """Wraps given function so that if it fails it also raises path to node on which it failed."""
-
-    def decorator(func):
-        def wrapper(*args, **kwargs):
-            try:
-                return func(*args, **kwargs)
-            except Exception as e:
-                # Add the context information to the error message
-                add_note(
-                    e, f"Raised whilst mapping function over node with path {path!r}"
-                )
-                raise
-
-        return wrapper
-
-    return decorator
-
-
-def add_note(err: BaseException, msg: str) -> None:
-    err.add_note(msg)
+@contextmanager
+def add_path_context_to_errors(path: str):
+    """Add path context to any errors."""
+    try:
+        yield
+    except Exception as e:
+        e.add_note(f"Raised whilst mapping function over node(s) with path {path!r}")
+        raise
 
 
 def _check_single_set_return_values(path_to_node: str, obj: Any) -> int | None:

xarray/core/treenode.py

@@ -4,11 +4,7 @@
 import sys
 from collections.abc import Iterator, Mapping
 from pathlib import PurePosixPath
-from typing import (
-    TYPE_CHECKING,
-    Any,
-    TypeVar,
-)
+from typing import TYPE_CHECKING, Any, TypeVar
 
 from xarray.core.types import Self
 from xarray.core.utils import Frozen, is_dict_like

xarray/structure/merge.py

@@ -3,7 +3,7 @@
 from collections import defaultdict
 from collections.abc import Hashable, Iterable, Mapping, Sequence
 from collections.abc import Set as AbstractSet
-from typing import TYPE_CHECKING, Any, NamedTuple, Union
+from typing import TYPE_CHECKING, Any, NamedTuple, Union, cast, overload
 
 import pandas as pd
 
@@ -34,6 +34,7 @@
     from xarray.core.coordinates import Coordinates
     from xarray.core.dataarray import DataArray
     from xarray.core.dataset import Dataset
+    from xarray.core.datatree import DataTree
     from xarray.core.types import (
         CombineAttrsOptions,
         CompatOptions,
@@ -793,18 +794,101 @@ def merge_core(
     return _MergeResult(variables, coord_names, dims, out_indexes, attrs)
 
 
+def merge_trees(
+    trees: Iterable[DataTree],
+    compat: CompatOptions | CombineKwargDefault = _COMPAT_DEFAULT,
+    join: JoinOptions | CombineKwargDefault = _JOIN_DEFAULT,
+    fill_value: object = dtypes.NA,
+    combine_attrs: CombineAttrsOptions = "override",
+) -> DataTree:
+    """Merge specialized to DataTree objects."""
+    from xarray.core.dataset import Dataset
+    from xarray.core.datatree import DataTree
+    from xarray.core.datatree_mapping import add_path_context_to_errors
+
+    if fill_value is not dtypes.NA:
+        # fill_value support dicts, which probably should be mapped to sub-groups?
+        raise NotImplementedError(
+            "fill_value is not yet supported for DataTree objects in merge"
+        )
+
+    node_lists: defaultdict[str, list[DataTree]] = defaultdict(list)
+    for tree in trees:
+        for key, node in tree.subtree_with_keys:
+            node_lists[key].append(node)
+
+    root_datasets = [node.dataset for node in node_lists.pop(".")]
+    with add_path_context_to_errors("."):
+        root_ds = merge(
+            root_datasets, compat=compat, join=join, combine_attrs=combine_attrs
+        )
+    result = DataTree(dataset=root_ds)
+
+    def level(kv):
+        # all trees with the same path have the same level
+        _, trees = kv
+        return trees[0].level
+
+    for key, nodes in sorted(node_lists.items(), key=level):
+        # Merge datasets, including inherited indexes to ensure alignment.
+        datasets = [node.dataset for node in nodes]
+        with add_path_context_to_errors(key):
+            merge_result = merge_core(
+                datasets,
+                compat=compat,
+                join=join,
+                combine_attrs=combine_attrs,
+            )
+        # Remove inherited coordinates/indexes/dimensions.
+        for var_name in list(merge_result.coord_names):
+            if not any(var_name in node._coord_variables for node in nodes):
+                del merge_result.variables[var_name]
+                merge_result.coord_names.remove(var_name)
+        for index_name in list(merge_result.indexes):
+            if not any(index_name in node._node_indexes for node in nodes):
+                del merge_result.indexes[index_name]
+        for dim in list(merge_result.dims):
+            if not any(dim in node._node_dims for node in nodes):
+                del merge_result.dims[dim]
+
+        merged_ds = Dataset._construct_direct(**merge_result._asdict())
+        result[key] = DataTree(dataset=merged_ds)
+
+    return result
+
+
+@overload
+def merge(
+    objects: Iterable[DataTree],
+    compat: CompatOptions | CombineKwargDefault = ...,
+    join: JoinOptions | CombineKwargDefault = ...,
+    fill_value: object = ...,
+    combine_attrs: CombineAttrsOptions = ...,
+) -> DataTree: ...
+
+
+@overload
+def merge(
+    objects: Iterable[DataArray | Dataset | Coordinates | dict],
+    compat: CompatOptions | CombineKwargDefault = ...,
+    join: JoinOptions | CombineKwargDefault = ...,
+    fill_value: object = ...,
+    combine_attrs: CombineAttrsOptions = ...,
+) -> Dataset: ...
+
+
 def merge(
-    objects: Iterable[DataArray | CoercibleMapping],
+    objects: Iterable[DataTree | DataArray | Dataset | Coordinates | dict],
     compat: CompatOptions | CombineKwargDefault = _COMPAT_DEFAULT,
     join: JoinOptions | CombineKwargDefault = _JOIN_DEFAULT,
     fill_value: object = dtypes.NA,
     combine_attrs: CombineAttrsOptions = "override",
-) -> Dataset:
+) -> DataTree | Dataset:
     """Merge any number of xarray objects into a single Dataset as variables.
 
     Parameters
     ----------
-    objects : iterable of Dataset or iterable of DataArray or iterable of dict-like
+    objects : iterable of DataArray, Dataset, DataTree or dict
         Merge together all variables from these objects. If any of them are
         DataArray objects, they must have a name.
     compat : {"identical", "equals", "broadcast_equals", "no_conflicts", \
@@ -859,8 +943,9 @@ def merge(
 
     Returns
     -------
-    Dataset
-        Dataset with combined variables from each object.
+    Dataset or DataTree
+        Objects with combined variables from the inputs. If any inputs are a
+        DataTree, this will also be a DataTree. Otherwise it will be a Dataset.
 
     Examples
     --------
@@ -1023,13 +1108,31 @@ def merge(
     from xarray.core.coordinates import Coordinates
     from xarray.core.dataarray import DataArray
     from xarray.core.dataset import Dataset
+    from xarray.core.datatree import DataTree
+
+    objects = list(objects)
+
+    if any(isinstance(obj, DataTree) for obj in objects):
+        if not all(isinstance(obj, DataTree) for obj in objects):
+            raise TypeError(
+                "merge does not support mixed type arguments when one argument "
+                f"is a DataTree: {objects}"
+            )
+        trees = cast(list[DataTree], objects)
+        return merge_trees(
+            trees,
+            compat=compat,
+            join=join,
+            combine_attrs=combine_attrs,
+            fill_value=fill_value,
+        )
 
     dict_like_objects = []
     for obj in objects:
         if not isinstance(obj, DataArray | Dataset | Coordinates | dict):
             raise TypeError(
-                "objects must be an iterable containing only "
-                "Dataset(s), DataArray(s), and dictionaries."
+                "objects must be an iterable containing only DataTree(s), "
+                f"Dataset(s), DataArray(s), and dictionaries: {objects}"
             )
 
         if isinstance(obj, DataArray):

xarray/tests/test_datatree.py

@@ -2219,13 +2219,17 @@ def test_sel_isel_error_has_node_info(self) -> None:
 
         with pytest.raises(
             KeyError,
-            match="Raised whilst mapping function over node with path 'second'",
+            match=re.escape(
+                "Raised whilst mapping function over node(s) with path 'second'"
+            ),
         ):
             tree.sel(x=1)
 
         with pytest.raises(
             IndexError,
-            match="Raised whilst mapping function over node with path 'first'",
+            match=re.escape(
+                "Raised whilst mapping function over node(s) with path 'first'"
+            ),
         ):
             tree.isel(x=4)
 

xarray/tests/test_datatree_mapping.py

@@ -192,7 +192,7 @@ def fail_on_specific_node(ds):
         with pytest.raises(
             ValueError,
             match=re.escape(
-                r"Raised whilst mapping function over node with path 'set1'"
+                r"Raised whilst mapping function over node(s) with path 'set1'"
             ),
         ):
             dt.map_over_datasets(fail_on_specific_node)

xarray/tests/test_merge.py

@@ -1,5 +1,6 @@
 from __future__ import annotations
 
+import re
 import warnings
 
 import numpy as np
@@ -867,3 +868,95 @@ def test_merge_auto_align(self):
         with set_options(use_new_combine_kwarg_defaults=True):
             with pytest.raises(ValueError, match="might be related to new default"):
                 expected.identical(ds2.merge(ds1))
+
+
+class TestMergeDataTree:
+    def test_mixed(self) -> None:
+        tree = xr.DataTree()
+        ds = xr.Dataset()
+        with pytest.raises(
+            TypeError,
+            match="merge does not support mixed type arguments when one argument is a DataTree",
+        ):
+            xr.merge([tree, ds])  # type: ignore[list-item]
+
+    def test_distinct(self) -> None:
+        tree1 = xr.DataTree.from_dict({"/a/b/c": 1})
+        tree2 = xr.DataTree.from_dict({"/a/d/e": 2})
+        expected = xr.DataTree.from_dict({"/a/b/c": 1, "/a/d/e": 2})
+        merged = xr.merge([tree1, tree2])
+        assert_equal(merged, expected)
+
+    def test_overlap(self) -> None:
+        tree1 = xr.DataTree.from_dict({"/a/b": 1})
+        tree2 = xr.DataTree.from_dict({"/a/c": 2})
+        tree3 = xr.DataTree.from_dict({"/a/d": 3})
+        expected = xr.DataTree.from_dict({"/a/b": 1, "/a/c": 2, "/a/d": 3})
+        merged = xr.merge([tree1, tree2, tree3])
+        assert_equal(merged, expected)
+
+    def test_inherited(self) -> None:
+        tree1 = xr.DataTree.from_dict({"/a/b": ("x", [1])}, coords={"x": [0]})
+        tree2 = xr.DataTree.from_dict({"/a/c": ("x", [2])})
+        expected = xr.DataTree.from_dict(
+            {"/a/b": ("x", [1]), "a/c": ("x", [2])}, coords={"x": [0]}
+        )
+        merged = xr.merge([tree1, tree2])
+        assert_equal(merged, expected)
+
+    def test_inherited_join(self) -> None:
+        tree1 = xr.DataTree.from_dict({"/a/b": ("x", [0, 1])}, coords={"x": [0, 1]})
+        tree2 = xr.DataTree.from_dict({"/a/c": ("x", [1, 2])}, coords={"x": [1, 2]})
+
+        expected = xr.DataTree.from_dict(
+            {"/a/b": ("x", [0, 1]), "a/c": ("x", [np.nan, 1])}, coords={"x": [0, 1]}
+        )
+        merged = xr.merge([tree1, tree2], join="left")
+        assert_equal(merged, expected)
+
+        expected = xr.DataTree.from_dict(
+            {"/a/b": ("x", [1, np.nan]), "a/c": ("x", [1, 2])}, coords={"x": [1, 2]}
+        )
+        merged = xr.merge([tree1, tree2], join="right")
+        assert_equal(merged, expected)
+
+        expected = xr.DataTree.from_dict(
+            {"/a/b": ("x", [1]), "a/c": ("x", [1])}, coords={"x": [1]}
+        )
+        merged = xr.merge([tree1, tree2], join="inner")
+        assert_equal(merged, expected)
+
+        expected = xr.DataTree.from_dict(
+            {"/a/b": ("x", [0, 1, np.nan]), "a/c": ("x", [np.nan, 1, 2])},
+            coords={"x": [0, 1, 2]},
+        )
+        merged = xr.merge([tree1, tree2], join="outer")
+        assert_equal(merged, expected)
+
+        with pytest.raises(
+            xr.AlignmentError,
+            match=re.escape("cannot align objects with join='exact'"),
+        ):
+            xr.merge([tree1, tree2], join="exact")
+
+    def test_merge_error_includes_path(self) -> None:
+        tree1 = xr.DataTree.from_dict({"/a/b": ("x", [0, 1])})
+        tree2 = xr.DataTree.from_dict({"/a/b": ("x", [1, 2])})
+        with pytest.raises(
+            xr.MergeError,
+            match=re.escape(
+                "Raised whilst mapping function over node(s) with path 'a'"
+            ),
+        ):
+            xr.merge([tree1, tree2], join="exact")
+
+    def test_fill_value_errors(self) -> None:
+        trees = [xr.DataTree(), xr.DataTree()]
+
+        with pytest.raises(
+            NotImplementedError,
+            match=re.escape(
+                "fill_value is not yet supported for DataTree objects in merge"
+            ),
+        ):
+            xr.merge(trees, fill_value=None)