DataTree: selecting via [["a"]] suggests subset, which is missing

[mathause]

What happened?

calling dt[["a"]] suggests to use .subset which does not exist.

What did you expect to happen?

No response

Minimal Complete Verifiable Example

import xarray as xr
a = xr.Dataset(data_vars={"x": [10, 20]}, coords={"time": [0, 1]})

dt = xr.DataTree()
dt["a"] = a

dt[["a"]] # fails and suggests subset
dt.subset # fails

MVCE confirmation

• Minimal example — the example is as focused as reasonably possible to demonstrate the underlying issue in xarray.
• Complete example — the example is self-contained, including all data and the text of any traceback.
• Verifiable example — the example copy & pastes into an IPython prompt or Binder notebook, returning the result.
• New issue — a search of GitHub Issues suggests this is not a duplicate.
• Recent environment — the issue occurs with the latest version of xarray and its dependencies.

Relevant log output

Anything else we need to know?

No response

Environment

master

[eschalkargans]

Xarray issue: DataTree: selecting via [["a"]] suggests subset, which is missing

#10014

Setup

import xarray as xr

xr.show_versions()

INSTALLED VERSIONS
------------------
commit: None
python: 3.13.1 (main, Feb 10 2025, 10:59:30) [GCC 9.4.0]
python-bits: 64
OS: Linux
OS-release: 5.15.0-134-generic
machine: x86_64
processor: x86_64
byteorder: little
LC_ALL: None
LANG: en_US.UTF-8
LOCALE: ('en_US', 'UTF-8')
libhdf5: 1.14.2
libnetcdf: 4.9.4-development

xarray: 2025.3.0
pandas: 2.2.3
numpy: 2.2.4
scipy: 1.15.2
netCDF4: 1.7.2
pydap: None
h5netcdf: None
h5py: None
zarr: None
cftime: 1.6.4.post1
nc_time_axis: None
iris: None
bottleneck: None
dask: None
distributed: None
matplotlib: 3.10.1
cartopy: None
seaborn: None
numbagg: None
fsspec: None
cupy: None
pint: None
sparse: None
flox: None
numpy_groupies: None
setuptools: None
pip: 23.2.1
conda: None
pytest: 8.3.5
mypy: 1.15.0
IPython: 8.32.0
sphinx: None

With Dataset

xds = xr.Dataset({"a": xr.DataArray([0], dims="x")})
print(xds)

<xarray.Dataset> Size: 8B
Dimensions:  (x: 1)
Dimensions without coordinates: x
Data variables:
    a        (x) int64 8B 0

print(xds["a"])

<xarray.DataArray 'a' (x: 1)> Size: 8B
array([0])
Dimensions without coordinates: x

print(xds[["a"]])

<xarray.Dataset> Size: 8B
Dimensions:  (x: 1)
Dimensions without coordinates: x
Data variables:
    a        (x) int64 8B 0

Example of trying to select a subset of variables, with a variable not in the dataset:

print(xds[["a", "not in dataset!"]])

---------------------------------------------------------------------------

KeyError                                  Traceback (most recent call last)

.venv/lib/python3.13/site-packages/xarray/core/dataset.py in ?(self, names)
   1168                 variables[name] = self._variables[name]
   1169             except KeyError:
-> 1170                 ref_name, var_name, var = _get_virtual_variable(
   1171                     self._variables, name, self.sizes


KeyError: 'not in dataset!'


During handling of the above exception, another exception occurred:


KeyError                                  Traceback (most recent call last)

Cell In[17], line 1
----> 1 print(xds[["a", "not in dataset!"]])


File .venv/lib/python3.13/site-packages/xarray/core/dataset.py:1321, in Dataset.__getitem__(self, key)
   1318         raise KeyError(message) from e
   1320 if utils.iterable_of_hashable(key):
-> 1321     return self._copy_listed(key)
   1322 raise ValueError(f"Unsupported key-type {type(key)}")


File .venv/lib/python3.13/site-packages/xarray/core/dataset.py:1170, in Dataset._copy_listed(self, names)
   1168     variables[name] = self._variables[name]
   1169 except KeyError:
-> 1170     ref_name, var_name, var = _get_virtual_variable(
   1171         self._variables, name, self.sizes
   1172     )
   1173     variables[var_name] = var
   1174     if ref_name in self._coord_names or ref_name in self.dims:


File .venv/lib/python3.13/site-packages/xarray/core/dataset_utils.py:79, in _get_virtual_variable(variables, key, dim_sizes)
     77 split_key = key.split(".", 1)
     78 if len(split_key) != 2:
---> 79     raise KeyError(key)
     81 ref_name, var_name = split_key
     82 ref_var = variables[ref_name]


KeyError: 'not in dataset!'

See __getitem__ in the dataset.py:

xarray/xarray/core/dataset.py

Line 1268 in e8b1daf

return self._copy_listed(key)

When the passed object is iterable or hashable, it calls _copy_listed:

xarray/xarray/core/dataset.py

Line 1105 in e8b1daf

def _copy_listed(self, names: Iterable[Hashable]) -> Self:

With DataTree

xdt = xr.DataTree.from_dict({"/": xds})
print(xdt)

<xarray.DataTree>
Group: /
    Dimensions:  (x: 1)
    Dimensions without coordinates: x
    Data variables:
        a        (x) int64 8B 0

print(xdt["a"])

<xarray.DataArray 'a' (x: 1)> Size: 8B
array([0])
Dimensions without coordinates: x

print(xdt[["a"]])

---------------------------------------------------------------------------

NotImplementedError                       Traceback (most recent call last)

Cell In[20], line 1
----> 1 print(xdt[["a"]])


File .venv/lib/python3.13/site-packages/xarray/core/datatree.py:941, in DataTree.__getitem__(self, key)
    938     return self._get_item(path)
    939 elif utils.is_list_like(key):
    940     # iterable of variable names
--> 941     raise NotImplementedError(
    942         "Selecting via tags is deprecated, and selecting multiple items should be "
    943         "implemented via .subset"
    944     )
    945 else:
    946     raise ValueError(f"Invalid format for key: {key}")


NotImplementedError: Selecting via tags is deprecated, and selecting multiple items should be implemented via .subset

See __getitem__ in the datatree.py:

xarray/xarray/core/datatree.py

Line 942 in e8b1daf

raise NotImplementedError(

The error message comes from datatree itself and states:

NotImplementedError: Selecting via tags is deprecated, and selecting multiple items should be implemented via .subset

Trying to use .subset fails with an AttributeError:

print(xdt.subset(["a"]))

---------------------------------------------------------------------------

AttributeError                            Traceback (most recent call last)

Cell In[21], line 1
----> 1 print(xdt.subset(["a"]))


File .venv/lib/python3.13/site-packages/xarray/core/common.py:306, in AttrAccessMixin.__getattr__(self, name)
    304         with suppress(KeyError):
    305             return source[name]
--> 306 raise AttributeError(
    307     f"{type(self).__name__!r} object has no attribute {name!r}"
    308 )


AttributeError: 'DataTree' object has no attribute 'subset'

How can we select multiple groups in a DataTree, like we can in Dataset?

[eschalkargans]

Note: for now, the workaround I have been using is to always convert the DataTree to Dataset before selecting multiple variables:

print(xdt.to_dataset()[["a"]])

<xarray.Dataset> Size: 8B
Dimensions:  (x: 1)
Dimensions without coordinates: x
Data variables:
    a        (x) int64 8B 0

It only works to select variables, not groups:

xds = xr.Dataset({"a": xr.DataArray([0], dims="x")})
xdt = xr.DataTree.from_dict({"a": xds, "b": xds, "c": xds})
print(xdt)

<xarray.DataTree>
Group: /
├── Group: /a
│       Dimensions:  (x: 1)
│       Dimensions without coordinates: x
│       Data variables:
│           a        (x) int64 8B 0
├── Group: /b
│       Dimensions:  (x: 1)
│       Dimensions without coordinates: x
│       Data variables:
│           a        (x) int64 8B 0
└── Group: /c
        Dimensions:  (x: 1)
        Dimensions without coordinates: x
        Data variables:
            a        (x) int64 8B 0

print(xdt.to_dataset())

<xarray.Dataset> Size: 0B
Dimensions:  ()
Data variables:
    *empty*

The DataTree only contains groups, no varaibles, so this workaround will not work.

xdt.to_dataset()[["a", "b"]]

-> Fails with KeyError as the resulting Dataset is indeed empty.

I would like to be able to select by paths, to select indistinctively groups or variables (eg below group b and variable c/a)

print(xdt[["/b", "/c/a"]])

---

The closest form of subset is using .filter, but only works on groups, not actual concrete variables

xds = xr.Dataset({"a": xr.DataArray([0], dims="x")})
xdt = xr.DataTree.from_dict({"toto/tata/a": xds, "toto/tete/a": xds, "toto/tutu/a": xds})
print(xdt)

<xarray.DataTree>
Group: /
└── Group: /toto
    ├── Group: /toto/tata
    │   └── Group: /toto/tata/a
    │           Dimensions:  (x: 1)
    │           Dimensions without coordinates: x
    │           Data variables:
    │               a        (x) int64 8B 0
    ├── Group: /toto/tete
    │   └── Group: /toto/tete/a
    │           Dimensions:  (x: 1)
    │           Dimensions without coordinates: x
    │           Data variables:
    │               a        (x) int64 8B 0
    └── Group: /toto/tutu
        └── Group: /toto/tutu/a
                Dimensions:  (x: 1)
                Dimensions without coordinates: x
                Data variables:
                    a        (x) int64 8B 0

print(xdt.filter(lambda node: node.path in ["/toto/tata", "/toto/tete/a"]))

<xarray.DataTree>
Group: /
└── Group: /toto
    ├── Group: /toto/tata
    └── Group: /toto/tete
        └── Group: /toto/tete/a
                Dimensions:  (x: 1)
                Dimensions without coordinates: x
                Data variables:
                    a        (x) int64 8B 0

Note that the resulting selected group is devoid of variables: /toto/tata is empty.

A more complex filter function to achieve group selection can be used, but seems a bit cumbersome, and still does not select variables:

xds = xr.Dataset({"a": xr.DataArray([0], dims="x"), "b": xr.DataArray([1], dims="y")})
xdt = xr.DataTree.from_dict(
    {
        "/toto/tata/bar": xds,
        "/toto/tete/bar": xds,
        "/toto/tutu/bar": xds,
        "/toto/tata/foo": xds,
        "/toto/tete/foo": xds,
        "/toto/tutu/foo": xds,
    }
)
print(xdt)

<xarray.DataTree>
Group: /
└── Group: /toto
    ├── Group: /toto/tata
    │   ├── Group: /toto/tata/bar
    │   │       Dimensions:  (x: 1, y: 1)
    │   │       Dimensions without coordinates: x, y
    │   │       Data variables:
    │   │           a        (x) int64 8B 0
    │   │           b        (y) int64 8B 1
    │   └── Group: /toto/tata/foo
    │           Dimensions:  (x: 1, y: 1)
    │           Dimensions without coordinates: x, y
    │           Data variables:
    │               a        (x) int64 8B 0
    │               b        (y) int64 8B 1
    ├── Group: /toto/tete
    │   ├── Group: /toto/tete/bar
    │   │       Dimensions:  (x: 1, y: 1)
    │   │       Dimensions without coordinates: x, y
    │   │       Data variables:
    │   │           a        (x) int64 8B 0
    │   │           b        (y) int64 8B 1
    │   └── Group: /toto/tete/foo
    │           Dimensions:  (x: 1, y: 1)
    │           Dimensions without coordinates: x, y
    │           Data variables:
    │               a        (x) int64 8B 0
    │               b        (y) int64 8B 1
    └── Group: /toto/tutu
        ├── Group: /toto/tutu/bar
        │       Dimensions:  (x: 1, y: 1)
        │       Dimensions without coordinates: x, y
        │       Data variables:
        │           a        (x) int64 8B 0
        │           b        (y) int64 8B 1
        └── Group: /toto/tutu/foo
                Dimensions:  (x: 1, y: 1)
                Dimensions without coordinates: x, y
                Data variables:
                    a        (x) int64 8B 0
                    b        (y) int64 8B 1

def select(xdt: xr.DataTree, paths: list[str]) -> xr.DataTree:
    return xdt.filter(lambda node: any(node.path.startswith(p) for p in paths))


sel = select(
    xdt,
    [
        "/toto/tata",  # Whole tata group selected with bar and foo
        "/toto/tete/bar",  # Only bar subgroup is selected
        "/toto/tutu/foo/a",  # Nothing selected!
    ],
)
print(sel)

<xarray.DataTree>
Group: /
└── Group: /toto
    ├── Group: /toto/tata
    │   ├── Group: /toto/tata/bar
    │   │       Dimensions:  (x: 1, y: 1)
    │   │       Dimensions without coordinates: x, y
    │   │       Data variables:
    │   │           a        (x) int64 8B 0
    │   │           b        (y) int64 8B 1
    │   └── Group: /toto/tata/foo
    │           Dimensions:  (x: 1, y: 1)
    │           Dimensions without coordinates: x, y
    │           Data variables:
    │               a        (x) int64 8B 0
    │               b        (y) int64 8B 1
    └── Group: /toto/tete
        └── Group: /toto/tete/bar
                Dimensions:  (x: 1, y: 1)
                Dimensions without coordinates: x, y
                Data variables:
                    a        (x) int64 8B 0
                    b        (y) int64 8B 1