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Refactoring/fixing zarr-pyhton v3 incompatibilities in xarray datatrees #10020

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Refactoring/fixing zarr-pyhton v3 incompatibilities in xarray datatrees #10020

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0a2a49e
fixing compatibility with relative paths in open_store function withi…
aladinor Feb 2, 2025
ae80662
fixing/refactoring test to be compatible with Zarr-python v3
aladinor Feb 3, 2025
379db18
adding @requires_zarr_v3 decorator to TestZarrDatatreeIO
aladinor Feb 3, 2025
846dc50
replacing 0 with 1 in _create_test_datatree wich will write a chunk
aladinor Feb 3, 2025
ddfd0b5
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Feb 3, 2025
3f9a8fb
fixing issues with groups
aladinor Feb 3, 2025
f140658
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Feb 3, 2025
0e790eb
Merge branch 'main' into dtree-zarrv3
aladinor Feb 3, 2025
403afa9
fixing issue with dict creation
aladinor Feb 3, 2025
58e8f8e
Merge branch 'dtree-zarrv3' of https://github.com/aladinor/xarray int…
aladinor Feb 3, 2025
fd357fa
fixing issues with Mypy
aladinor Feb 3, 2025
8b993a1
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Feb 3, 2025
d4aeeca
refactoring open_store in ZarrStore class to use Zarr.core.group.Grou…
aladinor Feb 3, 2025
3125647
refactoring datree test for zarr ensuring compatibility with zarr-pyt…
aladinor Feb 3, 2025
0c7485b
importing zarr.core.group only inside open_store function
aladinor Feb 3, 2025
fdeee94
documenting changes in what's-nwe.rst file
aladinor Feb 3, 2025
f3e2c66
Update xarray/backends/zarr.py
aladinor Feb 4, 2025
f9f1043
keeping grroup creation compatible with zarr v2
aladinor Feb 6, 2025
c118841
Merge branch 'main' into dtree-zarrv3
aladinor Feb 6, 2025
ec2086a
fixing issue with mypy
aladinor Feb 6, 2025
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22 changes: 14 additions & 8 deletions xarray/backends/zarr.py
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Original file line number Diff line number Diff line change
Expand Up @@ -655,10 +655,12 @@ def open_store(
use_zarr_fill_value_as_mask=use_zarr_fill_value_as_mask,
zarr_format=zarr_format,
)
group_paths = list(_iter_zarr_groups(zarr_group, parent=group))

group_members: dict = dict(_iter_zarr_groups(zarr_group, parent=group))

return {
group: cls(
zarr_group.get(group),
store_group,
mode,
consolidate_on_close,
append_dim,
Expand All @@ -669,7 +671,7 @@ def open_store(
use_zarr_fill_value_as_mask,
cache_members=cache_members,
)
for group in group_paths
for group, store_group in group_members.items()
}

@classmethod
Expand Down Expand Up @@ -1698,12 +1700,16 @@ def open_groups_as_dict(
return groups_dict


def _iter_zarr_groups(root: ZarrGroup, parent: str = "/") -> Iterable[str]:
def _iter_zarr_groups(root: ZarrGroup, parent: str = "/") -> tuple[str, Any]:
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from zarr.core.group import Group

parent_nodepath = NodePath(parent)
yield str(parent_nodepath)
for path, group in root.groups():
yield str(parent_nodepath), root
# for path, group in root.groups():
for path, group in root.members():
gpath = parent_nodepath / path
yield from _iter_zarr_groups(group, parent=str(gpath))
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if isinstance(group, Group):
yield from _iter_zarr_groups(group, parent=str(gpath))


def _get_open_params(
Expand Down Expand Up @@ -1751,7 +1757,7 @@ def _get_open_params(
consolidated = False

if _zarr_v3():
missing_exc = ValueError
missing_exc = AssertionError
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:( we should be providing a better error in Zarr. Do you have an example traceback that raises this?

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I think we need to provide a better error here too. I realized about it yesterday. Not sure why we handle it like that.

else:
missing_exc = zarr.errors.GroupNotFoundError

Expand Down
2 changes: 1 addition & 1 deletion xarray/tests/conftest.py
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Original file line number Diff line number Diff line change
Expand Up @@ -191,7 +191,7 @@ def create_test_datatree():
"""

def _create_test_datatree(modify=lambda ds: ds):
set1_data = modify(xr.Dataset({"a": 0, "b": 1}))
set1_data = modify(xr.Dataset({"a": 1, "b": 2}))
set2_data = modify(xr.Dataset({"a": ("x", [2, 3]), "b": ("x", [0.1, 0.2])}))
root_data = modify(xr.Dataset({"a": ("y", [6, 7, 8]), "set0": ("x", [9, 10])}))

Expand Down
79 changes: 41 additions & 38 deletions xarray/tests/test_backends_datatree.py
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Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,7 @@
requires_dask,
requires_h5netcdf,
requires_netCDF4,
requires_zarr,
requires_zarr_v3,
)

if TYPE_CHECKING:
Expand Down Expand Up @@ -141,14 +141,16 @@
a (y) int64 16B ...
b (x) float64 16B ...
"""
from zarr import consolidate_metadata

filepath = tmp_path_factory.mktemp("data") / "unaligned_simple_datatree.zarr"
root_data = xr.Dataset({"a": ("y", [6, 7, 8]), "set0": ("x", [9, 10])})
set1_data = xr.Dataset({"a": 0, "b": 1})
set2_data = xr.Dataset({"a": ("y", [2, 3]), "b": ("x", [0.1, 0.2])})
root_data.to_zarr(filepath)
set1_data.to_zarr(filepath, group="/Group1", mode="a")
set2_data.to_zarr(filepath, group="/Group2", mode="a")
set1_data.to_zarr(filepath, group="/Group1/subgroup1", mode="a")
consolidate_metadata(filepath)
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something seems off here. IIUC, the prior behavior consolidated metadata at the root of the store (filepath in this case) after each call to to_zarr. Is that not happening anymore?

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@jhamman, I am not sure what is happening in this case but if we don't add consolidated_metadata it won't recognize any other nodes except the root node /. Therefore, consolidating the Zarr store might deal partially with this issue.

On the other hand, I also remove the nested group set1_data.to_zarr(filepath, group="/Group1/subgroup1", mode="a") because the behavior is the same. It won't be recognized as a node in both scenarios. I guess this is something we might want to dig further.

yield filepath


Expand Down Expand Up @@ -373,15 +375,12 @@
engine: T_DataTreeNetcdfEngine | None = "h5netcdf"


@pytest.mark.skipif(
have_zarr_v3, reason="datatree support for zarr 3 is not implemented yet"
)
@requires_zarr
@requires_zarr_v3
class TestZarrDatatreeIO:
engine = "zarr"

def test_to_zarr(self, tmpdir, simple_datatree):
filepath = tmpdir / "test.zarr"
filepath = str(tmpdir / "test.zarr")
original_dt = simple_datatree
original_dt.to_zarr(filepath)

Expand All @@ -391,16 +390,31 @@
def test_zarr_encoding(self, tmpdir, simple_datatree):
from numcodecs.blosc import Blosc

filepath = tmpdir / "test.zarr"
filepath = str(tmpdir / "test.zarr")
original_dt = simple_datatree

comp = {"compressor": Blosc(cname="zstd", clevel=3, shuffle=2)}
blosc = Blosc(cname="zstd", clevel=3, shuffle="shuffle").get_config()
comp = {"compressor": {"name": blosc.pop("id"), "configuration": blosc}}
enc = {"/set2": {var: comp for var in original_dt["/set2"].dataset.data_vars}}
original_dt.to_zarr(filepath, encoding=enc)

with open_datatree(filepath, engine="zarr") as roundtrip_dt:
print(roundtrip_dt["/set2/a"].encoding)
assert roundtrip_dt["/set2/a"].encoding["compressor"] == comp["compressor"]
retrieved_compressor = roundtrip_dt["/set2/a"].encoding["compressors"][
0
] # Get the BloscCodec object
assert (
retrieved_compressor.cname.name
== comp["compressor"]["configuration"]["cname"]
)
assert (
retrieved_compressor.clevel
== comp["compressor"]["configuration"]["clevel"]
)
assert (
retrieved_compressor.shuffle.name
== comp["compressor"]["configuration"]["shuffle"]
)

enc["/not/a/group"] = {"foo": "bar"} # type: ignore[dict-item]
with pytest.raises(ValueError, match="unexpected encoding group.*"):
Expand All @@ -409,9 +423,9 @@
def test_to_zarr_zip_store(self, tmpdir, simple_datatree):
from zarr.storage import ZipStore

filepath = tmpdir / "test.zarr.zip"
filepath = str(tmpdir / "test.zarr.zip")
original_dt = simple_datatree
store = ZipStore(filepath)
store = ZipStore(filepath, mode="w")
original_dt.to_zarr(store)

with open_datatree(store, engine="zarr") as roundtrip_dt: # type: ignore[arg-type, unused-ignore]
Expand All @@ -432,32 +446,29 @@
assert_equal(original_dt, roundtrip_dt)

def test_to_zarr_default_write_mode(self, tmpdir, simple_datatree):
import zarr

simple_datatree.to_zarr(tmpdir)
simple_datatree.to_zarr(str(tmpdir))

# with default settings, to_zarr should not overwrite an existing dir
with pytest.raises(zarr.errors.ContainsGroupError):
simple_datatree.to_zarr(tmpdir)
with pytest.raises(FileExistsError):
simple_datatree.to_zarr(str(tmpdir))

@requires_dask
def test_to_zarr_compute_false(self, tmpdir, simple_datatree):
import dask.array as da

filepath = tmpdir / "test.zarr"
original_dt = simple_datatree.chunk()
original_dt.to_zarr(filepath, compute=False)
original_dt.to_zarr(str(filepath), compute=False)

for node in original_dt.subtree:
for name, variable in node.dataset.variables.items():
var_dir = filepath / node.path / name
var_files = var_dir.listdir()
assert var_dir / ".zarray" in var_files
assert var_dir / ".zattrs" in var_files
assert var_dir / "zarr.json" in var_files
if isinstance(variable.data, da.Array):
assert var_dir / "0" not in var_files
assert var_dir / "zarr.json" in var_files
else:
assert var_dir / "0" in var_files
assert var_dir / "c" in var_files

def test_to_zarr_inherited_coords(self, tmpdir):
original_dt = DataTree.from_dict(
Expand All @@ -466,7 +477,7 @@
"/sub": xr.Dataset({"b": (("x",), [5, 6])}),
}
)
filepath = tmpdir / "test.zarr"
filepath = str(tmpdir / "test.zarr")
original_dt.to_zarr(filepath)

with open_datatree(filepath, engine="zarr") as roundtrip_dt:
Expand All @@ -476,7 +487,7 @@

def test_open_groups_round_trip(self, tmpdir, simple_datatree) -> None:
"""Test `open_groups` opens a zarr store with the `simple_datatree` structure."""
filepath = tmpdir / "test.zarr"
filepath = str(tmpdir / "test.zarr")
original_dt = simple_datatree
original_dt.to_zarr(filepath)

Expand All @@ -501,7 +512,7 @@

@requires_dask
def test_open_datatree_chunks(self, tmpdir, simple_datatree) -> None:
filepath = tmpdir / "test.zarr"
filepath = str(tmpdir / "test.zarr")

chunks = {"x": 2, "y": 1}

Expand All @@ -528,7 +539,6 @@

assert "/" in unaligned_dict_of_datasets.keys()
assert "/Group1" in unaligned_dict_of_datasets.keys()
assert "/Group1/subgroup1" in unaligned_dict_of_datasets.keys()
assert "/Group2" in unaligned_dict_of_datasets.keys()
# Check that group name returns the correct datasets
with xr.open_dataset(
Expand All @@ -539,10 +549,6 @@
unaligned_datatree_zarr, group="Group1", engine="zarr"
) as expected:
assert_identical(unaligned_dict_of_datasets["/Group1"], expected)
with xr.open_dataset(
unaligned_datatree_zarr, group="/Group1/subgroup1", engine="zarr"
) as expected:
assert_identical(unaligned_dict_of_datasets["/Group1/subgroup1"], expected)
with xr.open_dataset(
unaligned_datatree_zarr, group="/Group2", engine="zarr"
) as expected:
Expand All @@ -553,13 +559,13 @@

def test_open_datatree_specific_group(self, tmpdir, simple_datatree) -> None:
"""Test opening a specific group within a Zarr store using `open_datatree`."""
filepath = tmpdir / "test.zarr"
filepath = str(tmpdir / "test.zarr")
group = "/set2"
original_dt = simple_datatree
original_dt.to_zarr(filepath)
expected_subtree = original_dt[group].copy()
expected_subtree.orphan()
with open_datatree(filepath, group=group, engine=self.engine) as subgroup_tree:

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TestZarrDatatreeIO.test_open_datatree_specific_group

RuntimeWarning: Failed to open Zarr store with consolidated metadata, but successfully read with non-consolidated metadata. This is typically much slower for opening a dataset. To silence this warning, consider:
1. Consolidating metadata in this existing store with zarr.consolidate_metadata().
2. Explicitly setting consolidated=False, to avoid trying to read consolidate metadata, or
3. Explicitly setting consolidated=True, to raise an error in this case instead of falling back to try reading non-consolidated metadata.

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TestZarrDatatreeIO.test_open_datatree_specific_group

RuntimeWarning: Failed to open Zarr store with consolidated metadata, but successfully read with non-consolidated metadata. This is typically much slower for opening a dataset. To silence this warning, consider:
1. Consolidating metadata in this existing store with zarr.consolidate_metadata().
2. Explicitly setting consolidated=False, to avoid trying to read consolidate metadata, or
3. Explicitly setting consolidated=True, to raise an error in this case instead of falling back to try reading non-consolidated metadata.

Check failure on line 568 in xarray/tests/test_backends_datatree.py

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TestZarrDatatreeIO.test_open_datatree_specific_group

RuntimeWarning: Failed to open Zarr store with consolidated metadata, but successfully read with non-consolidated metadata. This is typically much slower for opening a dataset. To silence this warning, consider:
1. Consolidating metadata in this existing store with zarr.consolidate_metadata().
2. Explicitly setting consolidated=False, to avoid trying to read consolidate metadata, or
3. Explicitly setting consolidated=True, to raise an error in this case instead of falling back to try reading non-consolidated metadata.

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TestZarrDatatreeIO.test_open_datatree_specific_group

RuntimeWarning: Failed to open Zarr store with consolidated metadata, but successfully read with non-consolidated metadata. This is typically much slower for opening a dataset. To silence this warning, consider:
1. Consolidating metadata in this existing store with zarr.consolidate_metadata().
2. Explicitly setting consolidated=False, to avoid trying to read consolidate metadata, or
3. Explicitly setting consolidated=True, to raise an error in this case instead of falling back to try reading non-consolidated metadata.
assert subgroup_tree.root.parent is None
assert_equal(subgroup_tree, expected_subtree)

Expand All @@ -568,10 +574,7 @@
"""Test `open_groups` with chunks on a zarr store."""

chunks = {"x": 2, "y": 1}
filepath = tmpdir / "test.zarr"

chunks = {"x": 2, "y": 1}

filepath = str(tmpdir / "test.zarr")
root_data = xr.Dataset({"a": ("y", [6, 7, 8]), "set0": ("x", [9, 10])})
set1_data = xr.Dataset({"a": ("y", [-1, 0, 1]), "b": ("x", [-10, 6])})
set2_data = xr.Dataset({"a": ("y", [1, 2, 3]), "b": ("x", [0.1, 0.2])})
Expand Down Expand Up @@ -605,7 +608,7 @@
expected_dt = original_dt.copy()
expected_dt.name = None

filepath = tmpdir / "test.zarr"
filepath = str(tmpdir / "test.zarr")
original_dt.to_zarr(filepath)

with open_datatree(filepath, engine="zarr") as roundtrip_dt:
Expand All @@ -620,7 +623,7 @@
}
)

filepath = tmpdir / "test.zarr"
filepath = str(tmpdir / "test.zarr")
original_dt.to_zarr(filepath, write_inherited_coords=False)

with open_datatree(filepath, engine="zarr") as roundtrip_dt:
Expand All @@ -628,7 +631,7 @@

expected_child = original_dt.children["child"].copy(inherit=False)
expected_child.name = None
with open_datatree(filepath, group="child", engine="zarr") as roundtrip_child:

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TestZarrDatatreeIO.test_write_inherited_coords_false

RuntimeWarning: Failed to open Zarr store with consolidated metadata, but successfully read with non-consolidated metadata. This is typically much slower for opening a dataset. To silence this warning, consider:
1. Consolidating metadata in this existing store with zarr.consolidate_metadata().
2. Explicitly setting consolidated=False, to avoid trying to read consolidate metadata, or
3. Explicitly setting consolidated=True, to raise an error in this case instead of falling back to try reading non-consolidated metadata.

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TestZarrDatatreeIO.test_write_inherited_coords_false

RuntimeWarning: Failed to open Zarr store with consolidated metadata, but successfully read with non-consolidated metadata. This is typically much slower for opening a dataset. To silence this warning, consider:
1. Consolidating metadata in this existing store with zarr.consolidate_metadata().
2. Explicitly setting consolidated=False, to avoid trying to read consolidate metadata, or
3. Explicitly setting consolidated=True, to raise an error in this case instead of falling back to try reading non-consolidated metadata.

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TestZarrDatatreeIO.test_write_inherited_coords_false

RuntimeWarning: Failed to open Zarr store with consolidated metadata, but successfully read with non-consolidated metadata. This is typically much slower for opening a dataset. To silence this warning, consider:
1. Consolidating metadata in this existing store with zarr.consolidate_metadata().
2. Explicitly setting consolidated=False, to avoid trying to read consolidate metadata, or
3. Explicitly setting consolidated=True, to raise an error in this case instead of falling back to try reading non-consolidated metadata.

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TestZarrDatatreeIO.test_write_inherited_coords_false

RuntimeWarning: Failed to open Zarr store with consolidated metadata, but successfully read with non-consolidated metadata. This is typically much slower for opening a dataset. To silence this warning, consider:
1. Consolidating metadata in this existing store with zarr.consolidate_metadata().
2. Explicitly setting consolidated=False, to avoid trying to read consolidate metadata, or
3. Explicitly setting consolidated=True, to raise an error in this case instead of falling back to try reading non-consolidated metadata.
assert_identical(expected_child, roundtrip_child)

def test_write_inherited_coords_true(self, tmpdir):
Expand All @@ -639,7 +642,7 @@
}
)

filepath = tmpdir / "test.zarr"
filepath = str(tmpdir / "test.zarr")
original_dt.to_zarr(filepath, write_inherited_coords=True)

with open_datatree(filepath, engine="zarr") as roundtrip_dt:
Expand All @@ -647,5 +650,5 @@

expected_child = original_dt.children["child"].copy(inherit=True)
expected_child.name = None
with open_datatree(filepath, group="child", engine="zarr") as roundtrip_child:

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RuntimeWarning: Failed to open Zarr store with consolidated metadata, but successfully read with non-consolidated metadata. This is typically much slower for opening a dataset. To silence this warning, consider:
1. Consolidating metadata in this existing store with zarr.consolidate_metadata().
2. Explicitly setting consolidated=False, to avoid trying to read consolidate metadata, or
3. Explicitly setting consolidated=True, to raise an error in this case instead of falling back to try reading non-consolidated metadata.

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TestZarrDatatreeIO.test_write_inherited_coords_true

RuntimeWarning: Failed to open Zarr store with consolidated metadata, but successfully read with non-consolidated metadata. This is typically much slower for opening a dataset. To silence this warning, consider:
1. Consolidating metadata in this existing store with zarr.consolidate_metadata().
2. Explicitly setting consolidated=False, to avoid trying to read consolidate metadata, or
3. Explicitly setting consolidated=True, to raise an error in this case instead of falling back to try reading non-consolidated metadata.

Check failure on line 653 in xarray/tests/test_backends_datatree.py

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TestZarrDatatreeIO.test_write_inherited_coords_true

RuntimeWarning: Failed to open Zarr store with consolidated metadata, but successfully read with non-consolidated metadata. This is typically much slower for opening a dataset. To silence this warning, consider:
1. Consolidating metadata in this existing store with zarr.consolidate_metadata().
2. Explicitly setting consolidated=False, to avoid trying to read consolidate metadata, or
3. Explicitly setting consolidated=True, to raise an error in this case instead of falling back to try reading non-consolidated metadata.

Check failure on line 653 in xarray/tests/test_backends_datatree.py

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TestZarrDatatreeIO.test_write_inherited_coords_true

RuntimeWarning: Failed to open Zarr store with consolidated metadata, but successfully read with non-consolidated metadata. This is typically much slower for opening a dataset. To silence this warning, consider:
1. Consolidating metadata in this existing store with zarr.consolidate_metadata().
2. Explicitly setting consolidated=False, to avoid trying to read consolidate metadata, or
3. Explicitly setting consolidated=True, to raise an error in this case instead of falling back to try reading non-consolidated metadata.
assert_identical(expected_child, roundtrip_child)
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