Merge remote-tracking branch 'upstream/main' into tom/fix/info

pyproject.toml

@@ -153,7 +153,7 @@ run-coverage-gpu = "pip install cupy-cuda12x && pytest -m gpu --cov-config=pypro
 run = "run-coverage --no-cov"
 run-verbose = "run-coverage --verbose"
 run-mypy = "mypy src"
-run-hypothesis = "pytest --hypothesis-profile ci tests/v3/test_properties.py tests/v3/test_store/test_stateful*"
+run-hypothesis = "pytest --hypothesis-profile ci tests/test_properties.py tests/test_store/test_stateful*"
 list-env = "pip list"
 
 [tool.hatch.envs.gputest]
@@ -173,7 +173,7 @@ run-coverage = "pytest -m gpu --cov-config=pyproject.toml --cov=pkg --cov=tests"
 run = "run-coverage --no-cov"
 run-verbose = "run-coverage --verbose"
 run-mypy = "mypy src"
-run-hypothesis = "pytest --hypothesis-profile ci tests/v3/test_properties.py tests/v3/test_store/test_stateful*"
+run-hypothesis = "pytest --hypothesis-profile ci tests/test_properties.py tests/test_store/test_stateful*"
 list-env = "pip list"
 
 [tool.hatch.envs.docs]
@@ -282,18 +282,17 @@ ignore_errors = true
 
 [[tool.mypy.overrides]]
 module = [
-    "tests.v2.*",
-    "tests.v3.package_with_entrypoint.*",
-    "tests.v3.test_codecs.test_codecs",
-    "tests.v3.test_codecs.test_transpose",
-    "tests.v3.test_metadata.*",
-    "tests.v3.test_store.*",
-    "tests.v3.test_config",
-    "tests.v3.test_group",
-    "tests.v3.test_indexing",
-    "tests.v3.test_properties",
-    "tests.v3.test_sync",
-    "tests.v3.test_v2",
+    "tests.package_with_entrypoint.*",
+    "tests.test_codecs.test_codecs",
+    "tests.test_codecs.test_transpose",
+    "tests.test_metadata.*",
+    "tests.test_store.*",
+    "tests.test_config",
+    "tests.test_group",
+    "tests.test_indexing",
+    "tests.test_properties",
+    "tests.test_sync",
+    "tests.test_v2",
 ]
 ignore_errors = true
 

src/zarr/codecs/sharding.py

@@ -129,7 +129,7 @@ def get_chunk_slice(self, chunk_coords: ChunkCoords) -> tuple[int, int] | None:
         if (chunk_start, chunk_len) == (MAX_UINT_64, MAX_UINT_64):
             return None
         else:
-            return (int(chunk_start), int(chunk_start) + int(chunk_len))
+            return (int(chunk_start), int(chunk_len))
 
     def set_chunk_slice(self, chunk_coords: ChunkCoords, chunk_slice: slice | None) -> None:
         localized_chunk = self._localize_chunk(chunk_coords)
@@ -203,7 +203,7 @@ def create_empty(
     def __getitem__(self, chunk_coords: ChunkCoords) -> Buffer:
         chunk_byte_slice = self.index.get_chunk_slice(chunk_coords)
         if chunk_byte_slice:
-            return self.buf[chunk_byte_slice[0] : chunk_byte_slice[1]]
+            return self.buf[chunk_byte_slice[0] : (chunk_byte_slice[0] + chunk_byte_slice[1])]
         raise KeyError
 
     def __len__(self) -> int:

src/zarr/testing/utils.py

@@ -1,6 +1,7 @@
 from __future__ import annotations
 
-from typing import TYPE_CHECKING, Any, cast
+from collections.abc import Callable, Coroutine
+from typing import TYPE_CHECKING, Any, TypeVar, cast
 
 import pytest
 
@@ -37,8 +38,16 @@ def has_cupy() -> bool:
         return False
 
 
+T_Callable = TypeVar("T_Callable", bound=Callable[[], Coroutine[Any, Any, None]])
+
+
 # Decorator for GPU tests
-def gpu_test(func: Any) -> Any:
-    return pytest.mark.gpu(
-        pytest.mark.skipif(not has_cupy(), reason="CuPy not installed or no GPU available")(func)
+def gpu_test(func: T_Callable) -> T_Callable:
+    return cast(
+        T_Callable,
+        pytest.mark.gpu(
+            pytest.mark.skipif(not has_cupy(), reason="CuPy not installed or no GPU available")(
+                func
+            )
+        ),
     )

tests/v3/test_codecs/test_sharding.py → tests/test_codecs/test_sharding.py

@@ -118,6 +118,42 @@ def test_sharding_partial(
     assert np.array_equal(data, read_data)
 
 
+@pytest.mark.parametrize("index_location", ["start", "end"])
+@pytest.mark.parametrize("store", ["local", "memory", "zip"], indirect=["store"])
+@pytest.mark.parametrize(
+    "array_fixture",
+    [
+        ArrayRequest(shape=(128,) * 3, dtype="uint16", order="F"),
+    ],
+    indirect=["array_fixture"],
+)
+def test_sharding_partial_readwrite(
+    store: Store, array_fixture: npt.NDArray[Any], index_location: ShardingCodecIndexLocation
+) -> None:
+    data = array_fixture
+    spath = StorePath(store)
+    a = Array.create(
+        spath,
+        shape=data.shape,
+        chunk_shape=data.shape,
+        dtype=data.dtype,
+        fill_value=0,
+        codecs=[
+            ShardingCodec(
+                chunk_shape=(1, data.shape[1], data.shape[2]),
+                codecs=[BytesCodec()],
+                index_location=index_location,
+            )
+        ],
+    )
+
+    a[:] = data
+
+    for x in range(data.shape[0]):
+        read_data = a[x, :, :]
+        assert np.array_equal(data[x], read_data)
+
+
 @pytest.mark.parametrize(
     "array_fixture",
     [

tests/v3/test_config.py → tests/test_config.py

@@ -87,7 +87,7 @@ class MockClass:
 
     assert (
         fully_qualified_name(MockClass)
-        == "tests.v3.test_config.test_fully_qualified_name.<locals>.MockClass"
+        == "tests.test_config.test_fully_qualified_name.<locals>.MockClass"
     )