Update V2 codec pipeline to use concrete classes (#2244)

The previous implementation used the codec config, rather than the codec
itself.

Author: TomAugspurger

src/zarr/codecs/_v2.py

@@ -8,16 +8,18 @@
 
 from zarr.abc.codec import ArrayArrayCodec, ArrayBytesCodec
 from zarr.core.buffer import Buffer, NDBuffer, default_buffer_prototype
-from zarr.core.common import JSON, to_thread
+from zarr.core.common import to_thread
 from zarr.registry import get_ndbuffer_class
 
 if TYPE_CHECKING:
+    import numcodecs.abc
+
     from zarr.core.array_spec import ArraySpec
 
 
 @dataclass(frozen=True)
 class V2Compressor(ArrayBytesCodec):
-    compressor: dict[str, JSON] | None
+    compressor: numcodecs.abc.Codec | None
 
     is_fixed_size = False
 
@@ -27,9 +29,8 @@ async def _decode_single(
         chunk_spec: ArraySpec,
     ) -> NDBuffer:
         if self.compressor is not None:
-            compressor = numcodecs.get_codec(self.compressor)
             chunk_numpy_array = ensure_ndarray(
-                await to_thread(compressor.decode, chunk_bytes.as_array_like())
+                await to_thread(self.compressor.decode, chunk_bytes.as_array_like())
             )
         else:
             chunk_numpy_array = ensure_ndarray(chunk_bytes.as_array_like())
@@ -47,14 +48,13 @@ async def _encode_single(
     ) -> Buffer | None:
         chunk_numpy_array = chunk_array.as_numpy_array()
         if self.compressor is not None:
-            compressor = numcodecs.get_codec(self.compressor)
             if (
                 not chunk_numpy_array.flags.c_contiguous
                 and not chunk_numpy_array.flags.f_contiguous
             ):
                 chunk_numpy_array = chunk_numpy_array.copy(order="A")
             encoded_chunk_bytes = ensure_bytes(
-                await to_thread(compressor.encode, chunk_numpy_array)
+                await to_thread(self.compressor.encode, chunk_numpy_array)
             )
         else:
             encoded_chunk_bytes = ensure_bytes(chunk_numpy_array)

src/zarr/core/metadata/v2.py

@@ -100,6 +100,8 @@ def _json_convert(
                     return o.str
                 else:
                     return o.descr
+            if isinstance(o, numcodecs.abc.Codec):
+                return o.get_config()
             if np.isscalar(o):
                 out: Any
                 if hasattr(o, "dtype") and o.dtype.kind == "M" and hasattr(o, "view"):

tests/v3/test_v2.py

@@ -2,7 +2,10 @@
 
 import numpy as np
 import pytest
+from numcodecs import Delta
+from numcodecs.blosc import Blosc
 
+import zarr
 from zarr import Array
 from zarr.store import MemoryStore, StorePath
 
@@ -26,3 +29,20 @@ def test_simple(store: StorePath) -> None:
 
     a[:, :] = data
     assert np.array_equal(data, a[:, :])
+
+
+def test_codec_pipeline() -> None:
+    # https://github.com/zarr-developers/zarr-python/issues/2243
+    store = MemoryStore(mode="w")
+    array = zarr.create(
+        store=store,
+        shape=(1,),
+        dtype="i4",
+        zarr_format=2,
+        filters=[Delta(dtype="i4").get_config()],
+        compressor=Blosc().get_config(),
+    )
+    array[:] = 1
+    result = array[:]
+    expected = np.ones(1)
+    np.testing.assert_array_equal(result, expected)