Merge branch 'main' into update-pcodec

Author: dstansby

.pre-commit-config.yaml

@@ -15,7 +15,7 @@ repos:
     - id: debug-statements
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.8.0
+    rev: v0.8.1
     hooks:
     - id: ruff
       args: ["--fix", "--show-fixes"]

docs/release.rst

@@ -22,12 +22,28 @@ Breaking changes
   are now keyword only, to support the updated API.
   By :user:`Sam Levang <slevang>`, :issue:`623`
 
-Enhancements
+
+Fixes
+~~~~~
+* Fixes issue with ``Delta`` Zarr 3 codec not working with ``astype``.
+  By :user:`Norman Rzepka <normanrz>`, :issue:`664`
+
+
+Improvements
 ~~~~~~~~~~~~
 * Add support for ``pcodec`` 0.3. This exposes the new ``delta_spec``
   and ``paging_spec`` arguments, but maintains full backwards
   compatibility for data written with older package versions.
   By :user:`Sam Levang <slevang>`, :issue:`623`
+* If an import error is raised when trying to define a codec that is *not*
+  an optional dependency, it is no longer silently caught. Instead it will
+  be propagated to the user, as this indicates an issue with the installed
+  package.
+
+  Import errors caused by optional dependencies (ZFPY, MsgPack, CRC32C, and PCodec)
+  are still silently caught.
+  By :user:`David Stansby <dstansby>`, :issue:`550`.
+
 
 0.14.1
 ------

docs/zarr3.rst

@@ -1,3 +1,5 @@
+.. _Zarr 3 codecs:
+
 Zarr 3 codecs
 =============
 .. automodule:: numcodecs.zarr3

numcodecs/__init__.py

@@ -36,41 +36,32 @@
 
 register_codec(BZ2)
 
-with suppress(ImportError):
-    from numcodecs.lzma import LZMA
+from numcodecs.lzma import LZMA
 
-    register_codec(LZMA)
+register_codec(LZMA)
 
-with suppress(ImportError):
-    from numcodecs import blosc
-    from numcodecs.blosc import Blosc
-
-    register_codec(Blosc)
-    # initialize blosc
-    try:
-        ncores = multiprocessing.cpu_count()
-    except OSError:  # pragma: no cover
-        ncores = 1
-    blosc.init()
-    blosc.set_nthreads(min(8, ncores))
-    atexit.register(blosc.destroy)
+from numcodecs import blosc
+from numcodecs.blosc import Blosc
 
-with suppress(ImportError):
-    from numcodecs import zstd as zstd
-    from numcodecs.zstd import Zstd
+register_codec(Blosc)
+# initialize blosc
+try:
+    ncores = multiprocessing.cpu_count()
+except OSError:  # pragma: no cover
+    ncores = 1
+blosc.init()
+blosc.set_nthreads(min(8, ncores))
+atexit.register(blosc.destroy)
 
-    register_codec(Zstd)
+from numcodecs import zstd as zstd
+from numcodecs.zstd import Zstd
 
-with suppress(ImportError):
-    from numcodecs import lz4 as lz4
-    from numcodecs.lz4 import LZ4
+register_codec(Zstd)
 
-    register_codec(LZ4)
+from numcodecs import lz4 as lz4
+from numcodecs.lz4 import LZ4
 
-with suppress(ImportError):
-    from numcodecs.zfpy import ZFPY
-
-    register_codec(ZFPY)
+register_codec(LZ4)
 
 from numcodecs.astype import AsType
 
@@ -112,38 +103,44 @@
 
 register_codec(BitRound)
 
-with suppress(ImportError):
-    from numcodecs.msgpacks import MsgPack
-
-    register_codec(MsgPack)
-
 from numcodecs.checksum32 import CRC32, Adler32, JenkinsLookup3
 
 register_codec(CRC32)
 register_codec(Adler32)
 register_codec(JenkinsLookup3)
 
-with suppress(ImportError):
-    from numcodecs.checksum32 import CRC32C
-
-    register_codec(CRC32C)
-
 from numcodecs.json import JSON
 
 register_codec(JSON)
 
-with suppress(ImportError):
-    from numcodecs import vlen as vlen
-    from numcodecs.vlen import VLenArray, VLenBytes, VLenUTF8
+from numcodecs import vlen as vlen
+from numcodecs.vlen import VLenArray, VLenBytes, VLenUTF8
 
-    register_codec(VLenUTF8)
-    register_codec(VLenBytes)
-    register_codec(VLenArray)
+register_codec(VLenUTF8)
+register_codec(VLenBytes)
+register_codec(VLenArray)
 
 from numcodecs.fletcher32 import Fletcher32
 
 register_codec(Fletcher32)
 
-from numcodecs.pcodec import PCodec
+# Optional depenedencies
+with suppress(ImportError):
+    from numcodecs.zfpy import ZFPY
+
+    register_codec(ZFPY)
+
+with suppress(ImportError):
+    from numcodecs.msgpacks import MsgPack
+
+    register_codec(MsgPack)
+
+with suppress(ImportError):
+    from numcodecs.checksum32 import CRC32C
+
+    register_codec(CRC32C)
+
+with suppress(ImportError):
+    from numcodecs.pcodec import PCodec
 
-register_codec(PCodec)
+    register_codec(PCodec)

numcodecs/tests/test_zarr3.py

@@ -244,3 +244,24 @@ def test_generic_bytes_codec(store: StorePath, codec_class: type[numcodecs.zarr3
 
     a[:, :] = data.copy()
     np.testing.assert_array_equal(data, a[:, :])
+
+
+def test_delta_astype(store: StorePath):
+    data = np.linspace(0, 10, 256, dtype="i8").reshape((16, 16))
+
+    with pytest.warns(UserWarning, match=EXPECTED_WARNING_STR):
+        a = Array.create(
+            store / "generic",
+            shape=data.shape,
+            chunk_shape=(16, 16),
+            dtype=data.dtype,
+            fill_value=0,
+            codecs=[
+                numcodecs.zarr3.Delta(dtype="i8", astype="i2"),  # type: ignore[arg-type]
+                BytesCodec(),
+            ],
+        )
+
+        a[:, :] = data.copy()
+        a = Array.open(store / "generic")
+    np.testing.assert_array_equal(data, a[:, :])

numcodecs/zarr3.py

@@ -266,7 +266,19 @@ def evolve_from_array_spec(self, array_spec: ArraySpec) -> Shuffle:
 
 
 # array-to-array codecs ("filters")
-Delta = _add_docstring(_make_array_array_codec("delta", "Delta"), "numcodecs.delta.Delta")
+@_add_docstring_wrapper("numcodecs.delta.Delta")
+class Delta(_NumcodecsArrayArrayCodec):
+    codec_name = f"{CODEC_PREFIX}delta"
+
+    def __init__(self, **codec_config: dict[str, JSON]) -> None:
+        super().__init__(**codec_config)
+
+    def resolve_metadata(self, chunk_spec: ArraySpec) -> ArraySpec:
+        if astype := self.codec_config.get("astype"):
+            return replace(chunk_spec, dtype=np.dtype(astype))  # type: ignore[arg-type]
+        return chunk_spec
+
+
 BitRound = _add_docstring(
     _make_array_array_codec("bitround", "BitRound"), "numcodecs.bitround.BitRound"
 )