Make typing strict (#1879)

* Disallow subclassing any

* Disallow returning any

* Enable strict

* Fix literal import

* pre-commit fixes

* Remove old group imports

Author: dstansby

.pre-commit-config.yaml

@@ -31,3 +31,5 @@ repos:
           - types-setuptools
           - pytest
           - numpy
+          - numcodecs
+          - zstandard

pyproject.toml

@@ -187,21 +187,7 @@ python_version = "3.10"
 ignore_missing_imports = true
 namespace_packages = false
 
-warn_unused_configs = true
-warn_redundant_casts = true
-warn_unused_ignores = true
-strict_equality = true
-strict_concatenate = true
-
-check_untyped_defs = true
-disallow_untyped_decorators = true
-disallow_any_generics = true
-
-disallow_incomplete_defs = true
-disallow_untyped_calls = true
-
-disallow_untyped_defs = true
-no_implicit_reexport = true
+strict = true
 
 
 [[tool.mypy.overrides]]
@@ -238,6 +224,13 @@ module = [
 disallow_untyped_defs = false
 
 
+[[tool.mypy.overrides]]
+module = [
+    "zarr.metadata",
+    "zarr.store.remote"
+]
+warn_return_any = false
+
 [tool.pytest.ini_options]
 minversion = "7"
 testpaths = ["tests"]

src/zarr/codecs/sharding.py

@@ -101,7 +101,7 @@ def is_all_empty(self) -> bool:
         return bool(np.array_equiv(self.offsets_and_lengths, MAX_UINT_64))
 
     def get_full_chunk_map(self) -> npt.NDArray[np.bool_]:
-        return self.offsets_and_lengths[..., 0] != MAX_UINT_64
+        return np.not_equal(self.offsets_and_lengths[..., 0], MAX_UINT_64)
 
     def get_chunk_slice(self, chunk_coords: ChunkCoords) -> tuple[int, int] | None:
         localized_chunk = self._localize_chunk(chunk_coords)

src/zarr/codecs/zstd.py

@@ -55,11 +55,11 @@ def to_dict(self) -> dict[str, JSON]:
 
     def _compress(self, data: npt.NDArray[Any]) -> bytes:
         ctx = ZstdCompressor(level=self.level, write_checksum=self.checksum)
-        return ctx.compress(data)
+        return ctx.compress(data.tobytes())
 
     def _decompress(self, data: npt.NDArray[Any]) -> bytes:
         ctx = ZstdDecompressor()
-        return ctx.decompress(data)
+        return ctx.decompress(data.tobytes())
 
     async def _decode_single(
         self,

src/zarr/common.py

@@ -7,7 +7,15 @@
 from collections.abc import Iterable
 from dataclasses import dataclass
 from enum import Enum
-from typing import TYPE_CHECKING, Any, Literal, ParamSpec, TypeVar, overload
+from typing import (
+    TYPE_CHECKING,
+    Any,
+    Literal,
+    ParamSpec,
+    TypeVar,
+    cast,
+    overload,
+)
 
 if TYPE_CHECKING:
     from collections.abc import Awaitable, Callable, Iterator
@@ -178,5 +186,5 @@ def parse_fill_value(data: Any) -> Any:
 
 def parse_order(data: Any) -> Literal["C", "F"]:
     if data in ("C", "F"):
-        return data
+        return cast(Literal["C", "F"], data)
     raise ValueError(f"Expected one of ('C', 'F'), got {data} instead.")

src/zarr/config.py

@@ -1,6 +1,6 @@
 from __future__ import annotations
 
-from typing import Any, Literal
+from typing import Any, Literal, cast
 
 from donfig import Config
 
@@ -18,6 +18,6 @@
 
 def parse_indexing_order(data: Any) -> Literal["C", "F"]:
     if data in ("C", "F"):
-        return data
+        return cast(Literal["C", "F"], data)
     msg = f"Expected one of ('C', 'F'), got {data} instead."
     raise ValueError(msg)

src/zarr/group.py

@@ -5,7 +5,7 @@
 import logging
 from collections.abc import Iterator
 from dataclasses import asdict, dataclass, field, replace
-from typing import TYPE_CHECKING, overload
+from typing import TYPE_CHECKING, Literal, cast, overload
 
 import numpy.typing as npt
 
@@ -37,7 +37,7 @@
 
 def parse_zarr_format(data: Any) -> ZarrFormat:
     if data in (2, 3):
-        return data
+        return cast(Literal[2, 3], data)
     msg = msg = f"Invalid zarr_format. Expected one 2 or 3. Got {data}."
     raise ValueError(msg)
 

src/zarr/v2/n5.py

@@ -780,7 +780,7 @@ def compressor_config_to_zarr(compressor_config: Dict[str, Any]) -> Optional[Dic
     return zarr_config
 
 
-class N5ChunkWrapper(Codec):
+class N5ChunkWrapper(Codec):  # type: ignore[misc]
     codec_id = "n5_wrapper"
 
     def __init__(self, dtype, chunk_shape, compressor_config=None, compressor=None):

src/zarr/v2/util.py

@@ -444,7 +444,7 @@ def get_type(self):
         return type(self.obj).__name__
 
 
-class TreeTraversal(Traversal):
+class TreeTraversal(Traversal):  # type: ignore[misc]
     def get_children(self, node):
         return node.get_children()