can not open zarr v3 datasets with scalar variables #895
Description
Hi all, i was trying to open zarr v3 datasets with scalar coordinates (e.g., a height coordinate). Peeking into the tests, i could construct a minimal example of the problem:
from virtualizarr.parsers import ZarrParser
from virtualizarr import open_virtual_dataset
from obspec_utils.registry import ObjectStoreRegistry
from obstore.store import LocalStore
import xarray as xr
# Create a small Dataset with a scalar
ds = xr.Dataset(
{"data": 42.0},
)
filepath = "/tmp/scalar.zarr"
ds.to_zarr(
filepath,
consolidated=False,
zarr_format=3,
mode="w",
)
store = LocalStore(prefix=filepath)
registry = ObjectStoreRegistry({f"file://{filepath}": store})
parser = ZarrParser()
vds = open_virtual_dataset(
url=filepath,
parser=parser,
registry=registry,
)This fails with TypeError: 'NoneType' object is not iterable somewhere in xarray because dims is None. Note that this works fine with zarr_format=2 or if i add a dimension, e.g., like this:
ds = xr.Dataset(
{"data": (("x",), [42.0])},
)Full traceback
---------------------------------------------------------------------------
TypeError Traceback (most recent call last)
Cell In[18], [line 28](vscode-notebook-cell:?execution_count=18&line=28)
25 registry = ObjectStoreRegistry({f"file://{filepath}": store})
26 parser = ZarrParser()
---> [28](vscode-notebook-cell:?execution_count=18&line=28) vds = open_virtual_dataset(
29 url=filepath,
30 parser=parser,
31 registry=registry,
32 )
File /mnt/CORDEX_CMIP6_tmp/user_tmp/lbuntemeyer/conda_envs/cordex-etl/lib/python3.13/site-packages/virtualizarr/xarray.py:228, in open_virtual_dataset(url, registry, parser, drop_variables, loadable_variables, decode_times)
221 filepath = validate_and_normalize_path_to_uri(url, fs_root=Path.cwd().as_uri())
223 manifest_store = parser(
224 url=filepath,
225 registry=registry,
226 )
--> [228](https://vscode-remote+ssh-002dremote-002bjsc-002dcordex.vscode-resource.vscode-cdn.net/mnt/CORDEX_CMIP6_tmp/user_tmp/lbuntemeyer/conda_envs/cordex-etl/lib/python3.13/site-packages/virtualizarr/xarray.py:228) ds = manifest_store.to_virtual_dataset(
229 loadable_variables=loadable_variables,
230 decode_times=decode_times,
231 )
232 return ds.drop_vars(list(drop_variables or ()))
File /mnt/CORDEX_CMIP6_tmp/user_tmp/lbuntemeyer/conda_envs/cordex-etl/lib/python3.13/site-packages/virtualizarr/manifests/store.py:328, in ManifestStore.to_virtual_dataset(self, group, loadable_variables, decode_times)
323 if loadable_variables and self._registry.map is None:
324 raise ValueError(
325 f"ManifestStore contains an empty store registry, but {loadable_variables} were provided as loadable variables. Must provide an ObjectStore instance in order to load variables."
326 )
--> [328](https://vscode-remote+ssh-002dremote-002bjsc-002dcordex.vscode-resource.vscode-cdn.net/mnt/CORDEX_CMIP6_tmp/user_tmp/lbuntemeyer/conda_envs/cordex-etl/lib/python3.13/site-packages/virtualizarr/manifests/store.py:328) return construct_virtual_dataset(
329 manifest_store=self,
330 group=group,
331 loadable_variables=loadable_variables,
332 decode_times=decode_times,
333 )
File /mnt/CORDEX_CMIP6_tmp/user_tmp/lbuntemeyer/conda_envs/cordex-etl/lib/python3.13/site-packages/virtualizarr/xarray.py:477, in construct_virtual_dataset(manifest_store, group, loadable_variables, decode_times, reader_options)
474 else:
475 manifestgroup = manifest_store._group
--> [477](https://vscode-remote+ssh-002dremote-002bjsc-002dcordex.vscode-resource.vscode-cdn.net/mnt/CORDEX_CMIP6_tmp/user_tmp/lbuntemeyer/conda_envs/cordex-etl/lib/python3.13/site-packages/virtualizarr/xarray.py:477) fully_virtual_ds = manifestgroup.to_virtual_dataset()
479 with xr.open_zarr(
480 manifest_store,
481 group=group,
(...) 485 decode_times=decode_times,
486 ) as loadable_ds:
487 return replace_virtual_with_loadable_vars(
488 fully_virtual_ds, loadable_ds, loadable_variables
489 )
File /mnt/CORDEX_CMIP6_tmp/user_tmp/lbuntemeyer/conda_envs/cordex-etl/lib/python3.13/site-packages/virtualizarr/manifests/group.py:120, in ManifestGroup.to_virtual_dataset(self)
116 attributes = metadata_dict["attributes"]
117 coord_names = attributes.pop("coordinates", [])
119 virtual_vars = {
--> [120](https://vscode-remote+ssh-002dremote-002bjsc-002dcordex.vscode-resource.vscode-cdn.net/mnt/CORDEX_CMIP6_tmp/user_tmp/lbuntemeyer/conda_envs/cordex-etl/lib/python3.13/site-packages/virtualizarr/manifests/group.py:120) name: marr.to_virtual_variable() for name, marr in self.arrays.items()
121 }
123 return construct_fully_virtual_dataset(
124 virtual_vars=virtual_vars,
125 coord_names=coord_names,
126 attrs=attributes,
127 )
File /mnt/CORDEX_CMIP6_tmp/user_tmp/lbuntemeyer/conda_envs/cordex-etl/lib/python3.13/site-packages/virtualizarr/manifests/array.py:292, in ManifestArray.to_virtual_variable(self)
285 stripped_metadata = utils.copy_and_replace_metadata(
286 self.metadata, new_dimension_names=None, new_attributes={}
287 )
288 stripped_marr = ManifestArray(
289 chunkmanifest=self.manifest, metadata=stripped_metadata
290 )
--> [292](https://vscode-remote+ssh-002dremote-002bjsc-002dcordex.vscode-resource.vscode-cdn.net/mnt/CORDEX_CMIP6_tmp/user_tmp/lbuntemeyer/conda_envs/cordex-etl/lib/python3.13/site-packages/virtualizarr/manifests/array.py:292) return xr.Variable(
293 data=stripped_marr,
294 dims=dims,
295 attrs=attrs,
296 )
File /mnt/CORDEX_CMIP6_tmp/user_tmp/lbuntemeyer/conda_envs/cordex-etl/lib/python3.13/site-packages/xarray/core/variable.py:399, in Variable.__init__(self, dims, data, attrs, encoding, fastpath)
371 def __init__(
372 self,
373 dims,
(...) 377 fastpath=False,
378 ):
379 """
380 Parameters
381 ----------
(...) 397 unrecognized encoding items.
398 """
--> [399](https://vscode-remote+ssh-002dremote-002bjsc-002dcordex.vscode-resource.vscode-cdn.net/mnt/CORDEX_CMIP6_tmp/user_tmp/lbuntemeyer/conda_envs/cordex-etl/lib/python3.13/site-packages/xarray/core/variable.py:399) super().__init__(
400 dims=dims, data=as_compatible_data(data, fastpath=fastpath), attrs=attrs
401 )
403 self._encoding: dict[Any, Any] | None = None
404 if encoding is not None:
File /mnt/CORDEX_CMIP6_tmp/user_tmp/lbuntemeyer/conda_envs/cordex-etl/lib/python3.13/site-packages/xarray/namedarray/core.py:261, in NamedArray.__init__(self, dims, data, attrs)
254 def __init__(
255 self,
256 dims: _DimsLike,
257 data: duckarray[Any, _DType_co],
258 attrs: _AttrsLike = None,
259 ):
260 self._data = data
--> [261](https://vscode-remote+ssh-002dremote-002bjsc-002dcordex.vscode-resource.vscode-cdn.net/mnt/CORDEX_CMIP6_tmp/user_tmp/lbuntemeyer/conda_envs/cordex-etl/lib/python3.13/site-packages/xarray/namedarray/core.py:261) self._dims = self._parse_dimensions(dims)
262 self._attrs = dict(attrs) if attrs else None
File /mnt/CORDEX_CMIP6_tmp/user_tmp/lbuntemeyer/conda_envs/cordex-etl/lib/python3.13/site-packages/xarray/namedarray/core.py:503, in NamedArray._parse_dimensions(self, dims)
502 def _parse_dimensions(self, dims: _DimsLike) -> _Dims:
--> [503](https://vscode-remote+ssh-002dremote-002bjsc-002dcordex.vscode-resource.vscode-cdn.net/mnt/CORDEX_CMIP6_tmp/user_tmp/lbuntemeyer/conda_envs/cordex-etl/lib/python3.13/site-packages/xarray/namedarray/core.py:503) dims = (dims,) if isinstance(dims, str) else tuple(dims)
504 if len(dims) != self.ndim:
505 raise ValueError(
506 f"dimensions {dims} must have the same length as the "
507 f"number of data dimensions, ndim={self.ndim}"
508 )
TypeError: 'NoneType' object is not iterable