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Fix reading partial shards #2397

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merged 2 commits into from
Oct 18, 2024
Merged

Fix reading partial shards #2397

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0cdc04b
fix reading partial shards
normanrz Oct 18, 2024
a6ea397
Merge remote-tracking branch 'origin/main' into fix-sharding-ranges
normanrz Oct 18, 2024
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4 changes: 2 additions & 2 deletions src/zarr/codecs/sharding.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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)
Expand Down Expand Up @@ -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:
Expand Down
36 changes: 36 additions & 0 deletions tests/test_codecs/test_sharding.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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",
[
Expand Down