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916 lines (739 loc) · 31.5 KB
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from __future__ import annotations
import pickle
from typing import TYPE_CHECKING, Any, Literal, cast
import numpy as np
import pytest
import zarr
from zarr import Array, AsyncArray, AsyncGroup, Group
from zarr.abc.store import Store
from zarr.core.buffer import default_buffer_prototype
from zarr.core.common import JSON, ZarrFormat
from zarr.core.group import GroupMetadata
from zarr.core.sync import sync
from zarr.errors import ContainsArrayError, ContainsGroupError
from zarr.store import LocalStore, MemoryStore, StorePath
from zarr.store.common import make_store_path
from .conftest import parse_store
if TYPE_CHECKING:
from _pytest.compat import LEGACY_PATH
@pytest.fixture(params=["local", "memory", "zip"])
async def store(request: pytest.FixtureRequest, tmpdir: LEGACY_PATH) -> Store:
result = await parse_store(request.param, str(tmpdir))
if not isinstance(result, Store):
raise TypeError("Wrong store class returned by test fixture! got " + result + " instead")
return result
@pytest.fixture(params=[True, False])
def exists_ok(request: pytest.FixtureRequest) -> bool:
result = request.param
if not isinstance(result, bool):
raise TypeError("Wrong type returned by test fixture.")
return result
@pytest.fixture(params=[2, 3], ids=["zarr2", "zarr3"])
def zarr_format(request: pytest.FixtureRequest) -> ZarrFormat:
result = request.param
if result not in (2, 3):
raise ValueError("Wrong value returned from test fixture.")
return cast(ZarrFormat, result)
def test_group_init(store: Store, zarr_format: ZarrFormat) -> None:
"""
Test that initializing a group from an asyncgroup works.
"""
agroup = sync(AsyncGroup.from_store(store=store, zarr_format=zarr_format))
group = Group(agroup)
assert group._async_group == agroup
def test_group_name_properties(store: Store, zarr_format: ZarrFormat) -> None:
"""
Test basic properties of groups
"""
root = Group.from_store(store=store, zarr_format=zarr_format)
assert root.path == ""
assert root.name == "/"
assert root.basename == ""
foo = root.create_group("foo")
assert foo.path == "foo"
assert foo.name == "/foo"
assert foo.basename == "foo"
bar = root.create_group("foo/bar")
assert bar.path == "foo/bar"
assert bar.name == "/foo/bar"
assert bar.basename == "bar"
def test_group_members(store: Store, zarr_format: ZarrFormat) -> None:
"""
Test that `Group.members` returns correct values, i.e. the arrays and groups
(explicit and implicit) contained in that group.
"""
path = "group"
agroup = AsyncGroup(
metadata=GroupMetadata(zarr_format=zarr_format),
store_path=StorePath(store=store, path=path),
)
group = Group(agroup)
members_expected: dict[str, Array | Group] = {}
members_expected["subgroup"] = group.create_group("subgroup")
# make a sub-sub-subgroup, to ensure that the children calculation doesn't go
# too deep in the hierarchy
subsubgroup = members_expected["subgroup"].create_group("subsubgroup")
subsubsubgroup = subsubgroup.create_group("subsubsubgroup")
members_expected["subarray"] = group.create_array(
"subarray", shape=(100,), dtype="uint8", chunk_shape=(10,), exists_ok=True
)
# add an extra object to the domain of the group.
# the list of children should ignore this object.
sync(
store.set(f"{path}/extra_object-1", default_buffer_prototype().buffer.from_bytes(b"000000"))
)
# add an extra object under a directory-like prefix in the domain of the group.
# this creates a directory with a random key in it
# this should not show up as a member
sync(
store.set(
f"{path}/extra_directory/extra_object-2",
default_buffer_prototype().buffer.from_bytes(b"000000"),
)
)
members_observed = group.members()
# members are not guaranteed to be ordered, so sort before comparing
assert sorted(dict(members_observed)) == sorted(members_expected)
# partial
members_observed = group.members(max_depth=1)
members_expected["subgroup/subsubgroup"] = subsubgroup
# members are not guaranteed to be ordered, so sort before comparing
assert sorted(dict(members_observed)) == sorted(members_expected)
# total
members_observed = group.members(max_depth=None)
members_expected["subgroup/subsubgroup/subsubsubgroup"] = subsubsubgroup
# members are not guaranteed to be ordered, so sort before comparing
assert sorted(dict(members_observed)) == sorted(members_expected)
with pytest.raises(ValueError, match="max_depth"):
members_observed = group.members(max_depth=-1)
def test_group(store: Store, zarr_format: ZarrFormat) -> None:
"""
Test basic Group routines.
"""
store_path = StorePath(store)
agroup = AsyncGroup(metadata=GroupMetadata(zarr_format=zarr_format), store_path=store_path)
group = Group(agroup)
assert agroup.metadata is group.metadata
assert agroup.store_path == group.store_path == store_path
# create two groups
foo = group.create_group("foo")
bar = foo.create_group("bar", attributes={"baz": "qux"})
# create an array from the "bar" group
data = np.arange(0, 4 * 4, dtype="uint16").reshape((4, 4))
arr = bar.create_array(
"baz", shape=data.shape, dtype=data.dtype, chunk_shape=(2, 2), exists_ok=True
)
arr[:] = data
# check the array
assert arr == bar["baz"]
assert arr.shape == data.shape
assert arr.dtype == data.dtype
# TODO: update this once the array api settles down
assert arr.chunks == (2, 2)
bar2 = foo["bar"]
assert dict(bar2.attrs) == {"baz": "qux"}
# update a group's attributes
bar2.attrs.update({"name": "bar"})
# bar.attrs was modified in-place
assert dict(bar2.attrs) == {"baz": "qux", "name": "bar"}
# and the attrs were modified in the store
bar3 = foo["bar"]
assert dict(bar3.attrs) == {"baz": "qux", "name": "bar"}
def test_group_create(store: Store, exists_ok: bool, zarr_format: ZarrFormat) -> None:
"""
Test that `Group.from_store` works as expected.
"""
attributes = {"foo": 100}
group = Group.from_store(
store, attributes=attributes, zarr_format=zarr_format, exists_ok=exists_ok
)
assert group.attrs == attributes
if not exists_ok:
with pytest.raises(ContainsGroupError):
group = Group.from_store(
store, attributes=attributes, exists_ok=exists_ok, zarr_format=zarr_format
)
def test_group_open(store: Store, zarr_format: ZarrFormat, exists_ok: bool) -> None:
"""
Test the `Group.open` method.
"""
spath = StorePath(store)
# attempt to open a group that does not exist
with pytest.raises(FileNotFoundError):
Group.open(store)
# create the group
attrs = {"path": "foo"}
group_created = Group.from_store(
store, attributes=attrs, zarr_format=zarr_format, exists_ok=exists_ok
)
assert group_created.attrs == attrs
assert group_created.metadata.zarr_format == zarr_format
assert group_created.store_path == spath
# attempt to create a new group in place, to test exists_ok
new_attrs = {"path": "bar"}
if not exists_ok:
with pytest.raises(ContainsGroupError):
Group.from_store(store, attributes=attrs, zarr_format=zarr_format, exists_ok=exists_ok)
else:
group_created_again = Group.from_store(
store, attributes=new_attrs, zarr_format=zarr_format, exists_ok=exists_ok
)
assert group_created_again.attrs == new_attrs
assert group_created_again.metadata.zarr_format == zarr_format
assert group_created_again.store_path == spath
def test_group_getitem(store: Store, zarr_format: ZarrFormat) -> None:
"""
Test the `Group.__getitem__` method.
"""
group = Group.from_store(store, zarr_format=zarr_format)
subgroup = group.create_group(name="subgroup")
subarray = group.create_array(name="subarray", shape=(10,), chunk_shape=(10,))
assert group["subgroup"] == subgroup
assert group["subarray"] == subarray
with pytest.raises(KeyError):
group["nope"]
def test_group_delitem(store: Store, zarr_format: ZarrFormat) -> None:
"""
Test the `Group.__delitem__` method.
"""
if not store.supports_deletes:
pytest.skip("store does not support deletes")
group = Group.from_store(store, zarr_format=zarr_format)
subgroup = group.create_group(name="subgroup")
subarray = group.create_array(name="subarray", shape=(10,), chunk_shape=(10,))
assert group["subgroup"] == subgroup
assert group["subarray"] == subarray
del group["subgroup"]
with pytest.raises(KeyError):
group["subgroup"]
del group["subarray"]
with pytest.raises(KeyError):
group["subarray"]
def test_group_iter(store: Store, zarr_format: ZarrFormat) -> None:
"""
Test the `Group.__iter__` method.
"""
group = Group.from_store(store, zarr_format=zarr_format)
with pytest.raises(NotImplementedError):
list(group)
def test_group_len(store: Store, zarr_format: ZarrFormat) -> None:
"""
Test the `Group.__len__` method.
"""
group = Group.from_store(store, zarr_format=zarr_format)
with pytest.raises(NotImplementedError):
len(group)
def test_group_setitem(store: Store, zarr_format: ZarrFormat) -> None:
"""
Test the `Group.__setitem__` method.
"""
group = Group.from_store(store, zarr_format=zarr_format)
with pytest.raises(NotImplementedError):
group["key"] = 10
def test_group_contains(store: Store, zarr_format: ZarrFormat) -> None:
"""
Test the `Group.__contains__` method
"""
group = Group.from_store(store, zarr_format=zarr_format)
assert "foo" not in group
_ = group.create_group(name="foo")
assert "foo" in group
def test_group_child_iterators(store: Store, zarr_format: ZarrFormat):
group = Group.from_store(store, zarr_format=zarr_format)
expected_group_keys = ["g0", "g1"]
expected_group_values = [group.create_group(name=name) for name in expected_group_keys]
expected_groups = list(zip(expected_group_keys, expected_group_values, strict=False))
expected_group_values[0].create_group("subgroup")
expected_group_values[0].create_array("subarray", shape=(1,))
expected_array_keys = ["a0", "a1"]
expected_array_values = [
group.create_array(name=name, shape=(1,)) for name in expected_array_keys
]
expected_arrays = list(zip(expected_array_keys, expected_array_values, strict=False))
assert sorted(group.groups(), key=lambda x: x[0]) == expected_groups
assert sorted(group.group_keys()) == expected_group_keys
assert sorted(group.group_values(), key=lambda x: x.name) == expected_group_values
assert sorted(group.arrays(), key=lambda x: x[0]) == expected_arrays
assert sorted(group.array_keys()) == expected_array_keys
assert sorted(group.array_values(), key=lambda x: x.name) == expected_array_values
def test_group_update_attributes(store: Store, zarr_format: ZarrFormat) -> None:
"""
Test the behavior of `Group.update_attributes`
"""
attrs = {"foo": 100}
group = Group.from_store(store, zarr_format=zarr_format, attributes=attrs)
assert group.attrs == attrs
new_attrs = {"bar": 100}
new_group = group.update_attributes(new_attrs)
assert new_group.attrs == new_attrs
async def test_group_update_attributes_async(store: Store, zarr_format: ZarrFormat) -> None:
"""
Test the behavior of `Group.update_attributes_async`
"""
attrs = {"foo": 100}
group = Group.from_store(store, zarr_format=zarr_format, attributes=attrs)
assert group.attrs == attrs
new_attrs = {"bar": 100}
new_group = await group.update_attributes_async(new_attrs)
assert new_group.attrs == new_attrs
@pytest.mark.parametrize("method", ["create_array", "array"])
def test_group_create_array(
store: Store,
zarr_format: ZarrFormat,
exists_ok: bool,
method: Literal["create_array", "array"],
) -> None:
"""
Test `Group.from_store`
"""
group = Group.from_store(store, zarr_format=zarr_format)
shape = (10, 10)
dtype = "uint8"
data = np.arange(np.prod(shape)).reshape(shape).astype(dtype)
if method == "create_array":
array = group.create_array(name="array", shape=shape, dtype=dtype, data=data)
elif method == "array":
with pytest.warns(DeprecationWarning):
array = group.array(name="array", shape=shape, dtype=dtype, data=data)
else:
raise AssertionError
if not exists_ok:
if method == "create_array":
with pytest.raises(ContainsArrayError):
group.create_array(name="array", shape=shape, dtype=dtype, data=data)
elif method == "array":
with pytest.raises(ContainsArrayError), pytest.warns(DeprecationWarning):
group.array(name="array", shape=shape, dtype=dtype, data=data)
assert array.shape == shape
assert array.dtype == np.dtype(dtype)
assert np.array_equal(array[:], data)
def test_group_array_creation(
store: Store,
zarr_format: ZarrFormat,
):
group = Group.from_store(store, zarr_format=zarr_format)
shape = (10, 10)
empty_array = group.empty(name="empty", shape=shape)
assert isinstance(empty_array, Array)
assert empty_array.fill_value == 0
assert empty_array.shape == shape
assert empty_array.store_path.store == store
empty_like_array = group.empty_like(name="empty_like", prototype=empty_array)
assert isinstance(empty_like_array, Array)
assert empty_like_array.fill_value == 0
assert empty_like_array.shape == shape
assert empty_like_array.store_path.store == store
empty_array_bool = group.empty(name="empty_bool", shape=shape, dtype=np.dtype("bool"))
assert isinstance(empty_array_bool, Array)
assert not empty_array_bool.fill_value
assert empty_array_bool.shape == shape
assert empty_array_bool.store_path.store == store
empty_like_array_bool = group.empty_like(name="empty_like_bool", prototype=empty_array_bool)
assert isinstance(empty_like_array_bool, Array)
assert not empty_like_array_bool.fill_value
assert empty_like_array_bool.shape == shape
assert empty_like_array_bool.store_path.store == store
zeros_array = group.zeros(name="zeros", shape=shape)
assert isinstance(zeros_array, Array)
assert zeros_array.fill_value == 0
assert zeros_array.shape == shape
assert zeros_array.store_path.store == store
zeros_like_array = group.zeros_like(name="zeros_like", prototype=zeros_array)
assert isinstance(zeros_like_array, Array)
assert zeros_like_array.fill_value == 0
assert zeros_like_array.shape == shape
assert zeros_like_array.store_path.store == store
ones_array = group.ones(name="ones", shape=shape)
assert isinstance(ones_array, Array)
assert ones_array.fill_value == 1
assert ones_array.shape == shape
assert ones_array.store_path.store == store
ones_like_array = group.ones_like(name="ones_like", prototype=ones_array)
assert isinstance(ones_like_array, Array)
assert ones_like_array.fill_value == 1
assert ones_like_array.shape == shape
assert ones_like_array.store_path.store == store
full_array = group.full(name="full", shape=shape, fill_value=42)
assert isinstance(full_array, Array)
assert full_array.fill_value == 42
assert full_array.shape == shape
assert full_array.store_path.store == store
full_like_array = group.full_like(name="full_like", prototype=full_array, fill_value=43)
assert isinstance(full_like_array, Array)
assert full_like_array.fill_value == 43
assert full_like_array.shape == shape
assert full_like_array.store_path.store == store
@pytest.mark.parametrize("store", ["local", "memory", "zip"], indirect=["store"])
@pytest.mark.parametrize("zarr_format", [2, 3])
@pytest.mark.parametrize("exists_ok", [True, False])
@pytest.mark.parametrize("extant_node", ["array", "group"])
def test_group_creation_existing_node(
store: Store,
zarr_format: ZarrFormat,
exists_ok: bool,
extant_node: Literal["array", "group"],
) -> None:
"""
Check that an existing array or group is handled as expected during group creation.
"""
spath = StorePath(store)
group = Group.from_store(spath, zarr_format=zarr_format)
expected_exception: type[ContainsArrayError | ContainsGroupError]
attributes: dict[str, JSON] = {"old": True}
if extant_node == "array":
expected_exception = ContainsArrayError
_ = group.create_array("extant", shape=(10,), dtype="uint8", attributes=attributes)
elif extant_node == "group":
expected_exception = ContainsGroupError
_ = group.create_group("extant", attributes=attributes)
else:
raise AssertionError
new_attributes = {"new": True}
if exists_ok:
node_new = Group.from_store(
spath / "extant",
attributes=new_attributes,
zarr_format=zarr_format,
exists_ok=exists_ok,
)
assert node_new.attrs == new_attributes
else:
with pytest.raises(expected_exception):
node_new = Group.from_store(
spath / "extant",
attributes=new_attributes,
zarr_format=zarr_format,
exists_ok=exists_ok,
)
async def test_asyncgroup_create(
store: Store,
exists_ok: bool,
zarr_format: ZarrFormat,
) -> None:
"""
Test that `AsyncGroup.from_store` works as expected.
"""
spath = StorePath(store=store)
attributes = {"foo": 100}
agroup = await AsyncGroup.from_store(
store,
attributes=attributes,
exists_ok=exists_ok,
zarr_format=zarr_format,
)
assert agroup.metadata == GroupMetadata(zarr_format=zarr_format, attributes=attributes)
assert agroup.store_path == await make_store_path(store)
if not exists_ok:
with pytest.raises(ContainsGroupError):
agroup = await AsyncGroup.from_store(
spath,
attributes=attributes,
exists_ok=exists_ok,
zarr_format=zarr_format,
)
# create an array at our target path
collision_name = "foo"
_ = await AsyncArray.create(
spath / collision_name, shape=(10,), dtype="uint8", zarr_format=zarr_format
)
with pytest.raises(ContainsArrayError):
_ = await AsyncGroup.from_store(
StorePath(store=store) / collision_name,
attributes=attributes,
exists_ok=exists_ok,
zarr_format=zarr_format,
)
async def test_asyncgroup_attrs(store: Store, zarr_format: ZarrFormat) -> None:
attributes = {"foo": 100}
agroup = await AsyncGroup.from_store(store, zarr_format=zarr_format, attributes=attributes)
assert agroup.attrs == agroup.metadata.attributes == attributes
async def test_asyncgroup_info(store: Store, zarr_format: ZarrFormat) -> None:
agroup = await AsyncGroup.from_store( # noqa: F841
store,
zarr_format=zarr_format,
)
pytest.xfail("Info is not implemented for metadata yet")
# assert agroup.info == agroup.metadata.info
async def test_asyncgroup_open(
store: Store,
zarr_format: ZarrFormat,
) -> None:
"""
Create an `AsyncGroup`, then ensure that we can open it using `AsyncGroup.open`
"""
attributes = {"foo": 100}
group_w = await AsyncGroup.from_store(
store=store,
attributes=attributes,
exists_ok=False,
zarr_format=zarr_format,
)
group_r = await AsyncGroup.open(store=store, zarr_format=zarr_format)
assert group_w.attrs == group_w.attrs == attributes
assert group_w == group_r
async def test_asyncgroup_open_wrong_format(
store: Store,
zarr_format: ZarrFormat,
) -> None:
_ = await AsyncGroup.from_store(store=store, exists_ok=False, zarr_format=zarr_format)
zarr_format_wrong: ZarrFormat
# try opening with the wrong zarr format
if zarr_format == 3:
zarr_format_wrong = 2
elif zarr_format == 2:
zarr_format_wrong = 3
else:
raise AssertionError
with pytest.raises(FileNotFoundError):
await AsyncGroup.open(store=store, zarr_format=zarr_format_wrong)
# todo: replace the dict[str, Any] type with something a bit more specific
# should this be async?
@pytest.mark.parametrize(
"data",
[
{"zarr_format": 3, "node_type": "group", "attributes": {"foo": 100}},
{"zarr_format": 2, "attributes": {"foo": 100}},
],
)
def test_asyncgroup_from_dict(store: Store, data: dict[str, Any]) -> None:
"""
Test that we can create an AsyncGroup from a dict
"""
path = "test"
store_path = StorePath(store=store, path=path)
group = AsyncGroup.from_dict(store_path, data=data)
assert group.metadata.zarr_format == data["zarr_format"]
assert group.metadata.attributes == data["attributes"]
# todo: replace this with a declarative API where we model a full hierarchy
async def test_asyncgroup_getitem(store: Store, zarr_format: ZarrFormat) -> None:
"""
Create an `AsyncGroup`, then create members of that group, and ensure that we can access those
members via the `AsyncGroup.getitem` method.
"""
agroup = await AsyncGroup.from_store(store=store, zarr_format=zarr_format)
array_name = "sub_array"
sub_array = await agroup.create_array(
name=array_name, shape=(10,), dtype="uint8", chunk_shape=(2,)
)
assert await agroup.getitem(array_name) == sub_array
sub_group_path = "sub_group"
sub_group = await agroup.create_group(sub_group_path, attributes={"foo": 100})
assert await agroup.getitem(sub_group_path) == sub_group
# check that asking for a nonexistent key raises KeyError
with pytest.raises(KeyError):
await agroup.getitem("foo")
async def test_asyncgroup_delitem(store: Store, zarr_format: ZarrFormat) -> None:
if not store.supports_deletes:
pytest.skip("store does not support deletes")
agroup = await AsyncGroup.from_store(store=store, zarr_format=zarr_format)
array_name = "sub_array"
_ = await agroup.create_array(
name=array_name, shape=(10,), dtype="uint8", chunk_shape=(2,), attributes={"foo": 100}
)
await agroup.delitem(array_name)
# todo: clean up the code duplication here
if zarr_format == 2:
assert not await agroup.store_path.store.exists(array_name + "/" + ".zarray")
assert not await agroup.store_path.store.exists(array_name + "/" + ".zattrs")
elif zarr_format == 3:
assert not await agroup.store_path.store.exists(array_name + "/" + "zarr.json")
else:
raise AssertionError
sub_group_path = "sub_group"
_ = await agroup.create_group(sub_group_path, attributes={"foo": 100})
await agroup.delitem(sub_group_path)
if zarr_format == 2:
assert not await agroup.store_path.store.exists(array_name + "/" + ".zgroup")
assert not await agroup.store_path.store.exists(array_name + "/" + ".zattrs")
elif zarr_format == 3:
assert not await agroup.store_path.store.exists(array_name + "/" + "zarr.json")
else:
raise AssertionError
async def test_asyncgroup_create_group(
store: Store,
zarr_format: ZarrFormat,
) -> None:
agroup = await AsyncGroup.from_store(store=store, zarr_format=zarr_format)
sub_node_path = "sub_group"
attributes = {"foo": 999}
subnode = await agroup.create_group(name=sub_node_path, attributes=attributes)
assert isinstance(subnode, AsyncGroup)
assert subnode.attrs == attributes
assert subnode.store_path.path == sub_node_path
assert subnode.store_path.store == store
assert subnode.metadata.zarr_format == zarr_format
async def test_asyncgroup_create_array(
store: Store, zarr_format: ZarrFormat, exists_ok: bool
) -> None:
"""
Test that the AsyncGroup.create_array method works correctly. We ensure that array properties
specified in create_array are present on the resulting array.
"""
agroup = await AsyncGroup.from_store(store=store, zarr_format=zarr_format)
if not exists_ok:
with pytest.raises(ContainsGroupError):
agroup = await AsyncGroup.from_store(store=store, zarr_format=zarr_format)
shape = (10,)
dtype = "uint8"
chunk_shape = (4,)
attributes: dict[str, JSON] = {"foo": 100}
sub_node_path = "sub_array"
subnode = await agroup.create_array(
name=sub_node_path,
shape=shape,
dtype=dtype,
chunk_shape=chunk_shape,
attributes=attributes,
)
assert isinstance(subnode, AsyncArray)
assert subnode.attrs == attributes
assert subnode.store_path.path == sub_node_path
assert subnode.store_path.store == store
assert subnode.shape == shape
assert subnode.dtype == dtype
# todo: fix the type annotation of array.metadata.chunk_grid so that we get some autocomplete
# here.
assert subnode.metadata.chunk_grid.chunk_shape == chunk_shape
assert subnode.metadata.zarr_format == zarr_format
async def test_asyncgroup_update_attributes(store: Store, zarr_format: ZarrFormat) -> None:
"""
Test that the AsyncGroup.update_attributes method works correctly.
"""
attributes_old = {"foo": 10}
attributes_new = {"baz": "new"}
agroup = await AsyncGroup.from_store(
store=store, zarr_format=zarr_format, attributes=attributes_old
)
agroup_new_attributes = await agroup.update_attributes(attributes_new)
assert agroup_new_attributes.attrs == attributes_new
@pytest.mark.parametrize("store", ["local"], indirect=["store"])
@pytest.mark.parametrize("zarr_format", [2, 3])
async def test_serializable_async_group(store: LocalStore, zarr_format: ZarrFormat) -> None:
expected = await AsyncGroup.from_store(
store=store, attributes={"foo": 999}, zarr_format=zarr_format
)
p = pickle.dumps(expected)
actual = pickle.loads(p)
assert actual == expected
@pytest.mark.parametrize("store", ["local"], indirect=["store"])
@pytest.mark.parametrize("zarr_format", [2, 3])
def test_serializable_sync_group(store: LocalStore, zarr_format: ZarrFormat) -> None:
expected = Group.from_store(store=store, attributes={"foo": 999}, zarr_format=zarr_format)
p = pickle.dumps(expected)
actual = pickle.loads(p)
assert actual == expected
async def test_group_members_async(store: LocalStore | MemoryStore) -> None:
group = AsyncGroup(
GroupMetadata(),
store_path=StorePath(store=store, path="root"),
)
a0 = await group.create_array("a0", shape=(1,))
g0 = await group.create_group("g0")
a1 = await g0.create_array("a1", shape=(1,))
g1 = await g0.create_group("g1")
a2 = await g1.create_array("a2", shape=(1,))
g2 = await g1.create_group("g2")
# immediate children
children = sorted([x async for x in group.members()], key=lambda x: x[0])
assert children == [
("a0", a0),
("g0", g0),
]
nmembers = await group.nmembers()
assert nmembers == 2
# partial
children = sorted([x async for x in group.members(max_depth=1)], key=lambda x: x[0])
expected = [
("a0", a0),
("g0", g0),
("g0/a1", a1),
("g0/g1", g1),
]
assert children == expected
nmembers = await group.nmembers(max_depth=1)
assert nmembers == 4
# all children
all_children = sorted([x async for x in group.members(max_depth=None)], key=lambda x: x[0])
expected = [
("a0", a0),
("g0", g0),
("g0/a1", a1),
("g0/g1", g1),
("g0/g1/a2", a2),
("g0/g1/g2", g2),
]
assert all_children == expected
nmembers = await group.nmembers(max_depth=None)
assert nmembers == 6
with pytest.raises(ValueError, match="max_depth"):
[x async for x in group.members(max_depth=-1)]
async def test_require_group(store: LocalStore | MemoryStore, zarr_format: ZarrFormat) -> None:
root = await AsyncGroup.from_store(store=store, zarr_format=zarr_format)
# create foo group
_ = await root.create_group("foo", attributes={"foo": 100})
# test that we can get the group using require_group
foo_group = await root.require_group("foo")
assert foo_group.attrs == {"foo": 100}
# test that we can get the group using require_group and overwrite=True
foo_group = await root.require_group("foo", overwrite=True)
_ = await foo_group.create_array(
"bar", shape=(10,), dtype="uint8", chunk_shape=(2,), attributes={"foo": 100}
)
# test that overwriting a group w/ children fails
# TODO: figure out why ensure_no_existing_node is not catching the foo.bar array
#
# with pytest.raises(ContainsArrayError):
# await root.require_group("foo", overwrite=True)
# test that requiring a group where an array is fails
with pytest.raises(TypeError):
await foo_group.require_group("bar")
async def test_require_groups(store: LocalStore | MemoryStore, zarr_format: ZarrFormat) -> None:
root = await AsyncGroup.from_store(store=store, zarr_format=zarr_format)
# create foo group
_ = await root.create_group("foo", attributes={"foo": 100})
# create bar group
_ = await root.create_group("bar", attributes={"bar": 200})
foo_group, bar_group = await root.require_groups("foo", "bar")
assert foo_group.attrs == {"foo": 100}
assert bar_group.attrs == {"bar": 200}
# get a mix of existing and new groups
foo_group, spam_group = await root.require_groups("foo", "spam")
assert foo_group.attrs == {"foo": 100}
assert spam_group.attrs == {}
# no names
no_group = await root.require_groups()
assert no_group == ()
async def test_create_dataset(store: LocalStore | MemoryStore, zarr_format: ZarrFormat) -> None:
root = await AsyncGroup.from_store(store=store, zarr_format=zarr_format)
with pytest.warns(DeprecationWarning):
foo = await root.create_dataset("foo", shape=(10,), dtype="uint8")
assert foo.shape == (10,)
with pytest.raises(ContainsArrayError), pytest.warns(DeprecationWarning):
await root.create_dataset("foo", shape=(100,), dtype="int8")
_ = await root.create_group("bar")
with pytest.raises(ContainsGroupError), pytest.warns(DeprecationWarning):
await root.create_dataset("bar", shape=(100,), dtype="int8")
async def test_require_array(store: LocalStore | MemoryStore, zarr_format: ZarrFormat) -> None:
root = await AsyncGroup.from_store(store=store, zarr_format=zarr_format)
foo1 = await root.require_array("foo", shape=(10,), dtype="i8", attributes={"foo": 101})
assert foo1.attrs == {"foo": 101}
foo2 = await root.require_array("foo", shape=(10,), dtype="i8")
assert foo2.attrs == {"foo": 101}
# exact = False
_ = await root.require_array("foo", shape=10, dtype="f8")
# errors w/ exact True
with pytest.raises(TypeError, match="Incompatible dtype"):
await root.require_array("foo", shape=(10,), dtype="f8", exact=True)
with pytest.raises(TypeError, match="Incompatible shape"):
await root.require_array("foo", shape=(100, 100), dtype="i8")
with pytest.raises(TypeError, match="Incompatible dtype"):
await root.require_array("foo", shape=(10,), dtype="f4")
_ = await root.create_group("bar")
with pytest.raises(TypeError, match="Incompatible object"):
await root.require_array("bar", shape=(10,), dtype="int8")
async def test_open_mutable_mapping():
group = await zarr.api.asynchronous.open_group(store={}, mode="w")
assert isinstance(group.store_path.store, MemoryStore)
def test_open_mutable_mapping_sync():
group = zarr.open_group(store={}, mode="w")
assert isinstance(group.store_path.store, MemoryStore)