Resolve Mypy erorrs in v3 branch (#1692)

* refactor(v3): Using appropriate types

* fix(v3): Typing fixes + minor code fixes

* fix(v3): _sync_iter works with coroutines

* docs(v3/store/core.py): clearer comment

* fix(metadata.py): Use Any outside TYPE_CHECKING for Pydantic

* fix(zarr/v3): correct zarr format + remove unused method

* fix(v3/store/core.py): Potential suggestion on handling str store_like

* refactor(zarr/v3): Add more typing

* ci(.pre-commit-config.yaml): zarr v3 mypy checks turned on in pre-commit

Author: DahnJ

.pre-commit-config.yaml

@@ -31,7 +31,6 @@ repos:
     hooks:
       - id: mypy
         files: src
-        exclude: ^src/zarr/v3
         args: []
         additional_dependencies:
           - types-redis

src/zarr/v3/abc/metadata.py

@@ -5,11 +5,12 @@
     from typing import Dict
     from typing_extensions import Self
 
-from dataclasses import fields
+from dataclasses import fields, dataclass
 
 from zarr.v3.common import JSON
 
 
+@dataclass(frozen=True)
 class Metadata:
     def to_dict(self) -> JSON:
         """

src/zarr/v3/array.py

@@ -182,7 +182,7 @@ def shape(self) -> ChunkCoords:
 
     @property
     def size(self) -> int:
-        return np.prod(self.metadata.shape)
+        return np.prod(self.metadata.shape).item()
 
     @property
     def dtype(self) -> np.dtype:

src/zarr/v3/chunk_grids.py

@@ -20,7 +20,7 @@ class ChunkGrid(Metadata):
     @classmethod
     def from_dict(cls, data: Dict[str, JSON]) -> ChunkGrid:
         if isinstance(data, ChunkGrid):
-            return data  # type: ignore
+            return data
 
         name_parsed, _ = parse_named_configuration(data)
         if name_parsed == "regular":

src/zarr/v3/chunk_key_encodings.py

@@ -1,6 +1,6 @@
 from __future__ import annotations
 from abc import abstractmethod
-from typing import TYPE_CHECKING, Dict, Literal
+from typing import TYPE_CHECKING, Dict, Literal, cast
 from dataclasses import dataclass
 from zarr.v3.abc.metadata import Metadata
 
@@ -19,7 +19,7 @@
 def parse_separator(data: JSON) -> SeparatorLiteral:
     if data not in (".", "/"):
         raise ValueError(f"Expected an '.' or '/' separator. Got {data} instead.")
-    return data  # type: ignore
+    return cast(SeparatorLiteral, data)
 
 
 @dataclass(frozen=True)
@@ -35,7 +35,7 @@ def __init__(self, *, separator: SeparatorLiteral) -> None:
     @classmethod
     def from_dict(cls, data: Dict[str, JSON]) -> ChunkKeyEncoding:
         if isinstance(data, ChunkKeyEncoding):
-            return data  # type: ignore
+            return data
 
         name_parsed, configuration_parsed = parse_named_configuration(data)
         if name_parsed == "default":

src/zarr/v3/codecs/transpose.py

@@ -1,5 +1,5 @@
 from __future__ import annotations
-from typing import TYPE_CHECKING, Dict, Iterable
+from typing import TYPE_CHECKING, Dict, Iterable, Union, cast
 
 from dataclasses import dataclass, replace
 
@@ -16,12 +16,12 @@
 from zarr.v3.codecs.registry import register_codec
 
 
-def parse_transpose_order(data: JSON) -> Tuple[int]:
+def parse_transpose_order(data: Union[JSON, Iterable[int]]) -> Tuple[int, ...]:
     if not isinstance(data, Iterable):
         raise TypeError(f"Expected an iterable. Got {data} instead.")
     if not all(isinstance(a, int) for a in data):
         raise TypeError(f"Expected an iterable of integers. Got {data} instead.")
-    return tuple(data)  # type: ignore[return-value]
+    return tuple(cast(Iterable[int], data))
 
 
 @dataclass(frozen=True)
@@ -31,7 +31,7 @@ class TransposeCodec(ArrayArrayCodec):
     order: Tuple[int, ...]
 
     def __init__(self, *, order: ChunkCoordsLike) -> None:
-        order_parsed = parse_transpose_order(order)  # type: ignore[arg-type]
+        order_parsed = parse_transpose_order(order)
 
         object.__setattr__(self, "order", order_parsed)
 

src/zarr/v3/group.py

@@ -4,7 +4,7 @@
 import asyncio
 import json
 import logging
-from typing import Any, Dict, Literal, Optional, Union, AsyncIterator, Iterator, List
+from typing import Any, Dict, Literal, Optional, Union, AsyncIterator, List
 from zarr.v3.abc.metadata import Metadata
 
 from zarr.v3.array import AsyncArray, Array
@@ -46,11 +46,11 @@ def to_bytes(self) -> Dict[str, bytes]:
             return {ZARR_JSON: json.dumps(self.to_dict()).encode()}
         else:
             return {
-                ZGROUP_JSON: self.zarr_format,
+                ZGROUP_JSON: json.dumps({"zarr_format": 2}).encode(),
                 ZATTRS_JSON: json.dumps(self.attributes).encode(),
             }
 
-    def __init__(self, attributes: Dict[str, Any] = None, zarr_format: Literal[2, 3] = 3):
+    def __init__(self, attributes: Optional[Dict[str, Any]] = None, zarr_format: Literal[2, 3] = 3):
         attributes_parsed = parse_attributes(attributes)
         zarr_format_parsed = parse_zarr_format(zarr_format)
 
@@ -104,7 +104,7 @@ async def open(
         zarr_format: Literal[2, 3] = 3,
     ) -> AsyncGroup:
         store_path = make_store_path(store)
-        zarr_json_bytes = await (store_path / ZARR_JSON).get_async()
+        zarr_json_bytes = await (store_path / ZARR_JSON).get()
         assert zarr_json_bytes is not None
 
         # TODO: consider trying to autodiscover the zarr-format here
@@ -139,7 +139,7 @@ def from_dict(
         store_path: StorePath,
         data: Dict[str, Any],
         runtime_configuration: RuntimeConfiguration,
-    ) -> Group:
+    ) -> AsyncGroup:
         group = cls(
             metadata=GroupMetadata.from_dict(data),
             store_path=store_path,
@@ -168,10 +168,12 @@ async def getitem(
                 zarr_json = json.loads(zarr_json_bytes)
             if zarr_json["node_type"] == "group":
                 return type(self).from_dict(store_path, zarr_json, self.runtime_configuration)
-            if zarr_json["node_type"] == "array":
+            elif zarr_json["node_type"] == "array":
                 return AsyncArray.from_dict(
                     store_path, zarr_json, runtime_configuration=self.runtime_configuration
                 )
+            else:
+                raise ValueError(f"unexpected node_type: {zarr_json['node_type']}")
         elif self.metadata.zarr_format == 2:
             # Q: how do we like optimistically fetching .zgroup, .zarray, and .zattrs?
             # This guarantees that we will always make at least one extra request to the store
@@ -271,7 +273,7 @@ def __repr__(self):
     async def nchildren(self) -> int:
         raise NotImplementedError
 
-    async def children(self) -> AsyncIterator[AsyncArray, AsyncGroup]:
+    async def children(self) -> AsyncIterator[Union[AsyncArray, AsyncGroup]]:
         raise NotImplementedError
 
     async def contains(self, child: str) -> bool:
@@ -381,8 +383,12 @@ async def update_attributes_async(self, new_attributes: Dict[str, Any]) -> Group
         new_metadata = replace(self.metadata, attributes=new_attributes)
 
         # Write new metadata
-        await (self.store_path / ZARR_JSON).set_async(new_metadata.to_bytes())
-        return replace(self, metadata=new_metadata)
+        to_save = new_metadata.to_bytes()
+        awaitables = [(self.store_path / key).set(value) for key, value in to_save.items()]
+        await asyncio.gather(*awaitables)
+
+        async_group = replace(self._async_group, metadata=new_metadata)
+        return replace(self, _async_group=async_group)
 
     @property
     def metadata(self) -> GroupMetadata:
@@ -396,34 +402,38 @@ def attrs(self) -> Attributes:
     def info(self):
         return self._async_group.info
 
+    @property
+    def store_path(self) -> StorePath:
+        return self._async_group.store_path
+
     def update_attributes(self, new_attributes: Dict[str, Any]):
         self._sync(self._async_group.update_attributes(new_attributes))
         return self
 
     @property
     def nchildren(self) -> int:
-        return self._sync(self._async_group.nchildren)
+        return self._sync(self._async_group.nchildren())
 
     @property
-    def children(self) -> List[Array, Group]:
-        _children = self._sync_iter(self._async_group.children)
+    def children(self) -> List[Union[Array, Group]]:
+        _children = self._sync_iter(self._async_group.children())
         return [Array(obj) if isinstance(obj, AsyncArray) else Group(obj) for obj in _children]
 
     def __contains__(self, child) -> bool:
         return self._sync(self._async_group.contains(child))
 
-    def group_keys(self) -> Iterator[str]:
-        return self._sync_iter(self._async_group.group_keys)
+    def group_keys(self) -> List[str]:
+        return self._sync_iter(self._async_group.group_keys())
 
     def groups(self) -> List[Group]:
         # TODO: in v2 this was a generator that return key: Group
-        return [Group(obj) for obj in self._sync_iter(self._async_group.groups)]
+        return [Group(obj) for obj in self._sync_iter(self._async_group.groups())]
 
     def array_keys(self) -> List[str]:
-        return self._sync_iter(self._async_group.array_keys)
+        return self._sync_iter(self._async_group.array_keys())
 
     def arrays(self) -> List[Array]:
-        return [Array(obj) for obj in self._sync_iter(self._async_group.arrays)]
+        return [Array(obj) for obj in self._sync_iter(self._async_group.arrays())]
 
     def tree(self, expand=False, level=None) -> Any:
         return self._sync(self._async_group.tree(expand=expand, level=level))

src/zarr/v3/metadata.py

@@ -1,6 +1,6 @@
 from __future__ import annotations
 from enum import Enum
-from typing import TYPE_CHECKING, cast, Dict, Iterable
+from typing import TYPE_CHECKING, cast, Dict, Iterable, Any
 from dataclasses import dataclass, field
 import json
 import numpy as np
@@ -10,7 +10,7 @@
 
 
 if TYPE_CHECKING:
-    from typing import Any, Literal, Union, List, Optional, Tuple
+    from typing import Literal, Union, List, Optional, Tuple
     from zarr.v3.codecs.pipeline import CodecPipeline
 
 
@@ -244,7 +244,7 @@ class ArrayV2Metadata(Metadata):
     filters: Optional[List[Dict[str, Any]]] = None
     dimension_separator: Literal[".", "/"] = "."
     compressor: Optional[Dict[str, Any]] = None
-    attributes: Optional[Dict[str, Any]] = field(default_factory=dict)
+    attributes: Optional[Dict[str, Any]] = cast(Dict[str, Any], field(default_factory=dict))
     zarr_format: Literal[2] = field(init=False, default=2)
 
     def __init__(

src/zarr/v3/store/core.py

@@ -5,6 +5,7 @@
 
 from zarr.v3.common import BytesLike
 from zarr.v3.abc.store import Store
+from zarr.v3.store.local import LocalStore
 
 
 def _dereference_path(root: str, path: str) -> str:
@@ -24,10 +25,6 @@ def __init__(self, store: Store, path: Optional[str] = None):
         self.store = store
         self.path = path or ""
 
-    @classmethod
-    def from_path(cls, pth: Path) -> StorePath:
-        return cls(Store.from_path(pth))
-
     async def get(
         self, byte_range: Optional[Tuple[int, Optional[int]]] = None
     ) -> Optional[BytesLike]:
@@ -70,14 +67,6 @@ def make_store_path(store_like: StoreLike) -> StorePath:
         return store_like
     elif isinstance(store_like, Store):
         return StorePath(store_like)
-    # elif isinstance(store_like, Path):
-    #     return StorePath(Store.from_path(store_like))
     elif isinstance(store_like, str):
-        try:
-            from upath import UPath
-
-            return StorePath(Store.from_path(UPath(store_like)))
-        except ImportError as e:
-            raise e
-            # return StorePath(LocalStore(Path(store_like)))
+        return StorePath(LocalStore(Path(store_like)))
     raise TypeError

src/zarr/v3/store/local.py

@@ -146,7 +146,7 @@ async def list_prefix(self, prefix: str) -> List[str]:
         """
 
         def _list_prefix(root: Path, prefix: str) -> List[str]:
-            files = [p for p in (root / prefix).rglob("*") if p.is_file()]
+            files = [str(p) for p in (root / prefix).rglob("*") if p.is_file()]
             return files
 
         return await to_thread(_list_prefix, self.root, prefix)