numcodecs 0.14.1__cp312-cp312-macosx_11_0_arm64.whl → 0.15.0__cp312-cp312-macosx_11_0_arm64.whl

numcodecs/tests/test_pcodec.py

@@ -1,11 +1,8 @@
 import numpy as np
 import pytest
 
-from numcodecs.pcodec import PCodec
-
 try:
-    # initializing codec triggers ImportError
-    PCodec()
+    from numcodecs.pcodec import PCodec
 except ImportError:  # pragma: no cover
     pytest.skip("pcodec not available", allow_module_level=True)
 
@@ -23,8 +20,12 @@ codecs = [
     PCodec(level=1),
     PCodec(level=5),
     PCodec(level=9),
-    PCodec(mode_spec='classic'),
+    PCodec(mode_spec="classic"),
     PCodec(equal_pages_up_to=300),
+    PCodec(delta_encoding_order=2),
+    PCodec(delta_spec="try_lookback"),
+    PCodec(delta_spec="none"),
+    PCodec(delta_spec="try_consecutive", delta_encoding_order=1),
 ]
 
 
@@ -56,15 +57,24 @@ def test_config():
     check_config(codec)
 
 
-def test_invalid_config_error():
-    codec = PCodec(mode_spec='bogus')
+@pytest.mark.parametrize("param", ["mode_spec", "delta_spec", "paging_spec"])
+def test_invalid_config_error(param):
+    codec = PCodec(**{param: "bogus"})
+    with pytest.raises(ValueError):
+        check_encode_decode_array_to_bytes(arrays[0], codec)
+
+
+def test_invalid_delta_encoding_combo():
+    codec = PCodec(delta_encoding_order=2, delta_spec="none")
     with pytest.raises(ValueError):
         check_encode_decode_array_to_bytes(arrays[0], codec)
 
 
 def test_repr():
     check_repr(
-        "PCodec(delta_encoding_order=None, equal_pages_up_to=262144, level=3, mode_spec='auto')"
+        "PCodec(delta_encoding_order=None, delta_spec='auto',"
+        " equal_pages_up_to=262144, level=3, mode_spec='auto',"
+        " paging_spec='equal_pages_up_to')"
     )
 
 

numcodecs/tests/test_registry.py

@@ -26,7 +26,7 @@ def test_all_classes_registered():
 
     see #346 for more info
     """
-    missing = set(
+    missing = {
         obj.codec_id
         for _, submod in inspect.getmembers(numcodecs, inspect.ismodule)
         for _, obj in inspect.getmembers(submod)
@@ -36,7 +36,7 @@ def test_all_classes_registered():
             and obj.codec_id not in numcodecs.registry.codec_registry
             and obj.codec_id is not None  # remove `None`
         )
-    )
+    }
 
     if missing:
         raise Exception(f"these codecs are missing: {missing}")  # pragma: no cover

numcodecs/tests/test_shuffle.py

@@ -79,14 +79,12 @@ def test_eq():
 
 def _encode_worker(data):
     compressor = Shuffle()
-    enc = compressor.encode(data)
-    return enc
+    return compressor.encode(data)
 
 
 def _decode_worker(enc):
     compressor = Shuffle()
-    data = compressor.decode(enc)
-    return data
+    return compressor.decode(enc)
 
 
 @pytest.mark.parametrize('pool', [Pool, ThreadPool])

numcodecs/tests/test_vlen_bytes.py

@@ -84,6 +84,9 @@ def test_decode_errors():
         codec.decode(enc, out=np.zeros(10, dtype='i4'))
 
 
+# TODO: fix this test on GitHub actions somehow...
+# See https://github.com/zarr-developers/numcodecs/issues/683
+@pytest.mark.skip("Test is failing on GitHub actions.")
 def test_encode_none():
     a = np.array([b'foo', None, b'bar'], dtype=object)
     codec = VLenBytes()

numcodecs/tests/test_zarr3.py

@@ -66,17 +66,19 @@ def test_docstring(codec_class: type[numcodecs.zarr3._NumcodecsCodec]):
         numcodecs.zarr3.Shuffle,
     ],
 )
-def test_generic_codec_class(store: StorePath, codec_class: type[numcodecs.zarr3._NumcodecsCodec]):
+def test_generic_compressor(
+    store: StorePath, codec_class: type[numcodecs.zarr3._NumcodecsBytesBytesCodec]
+):
     data = np.arange(0, 256, dtype="uint16").reshape((16, 16))
 
     with pytest.warns(UserWarning, match=EXPECTED_WARNING_STR):
-        a = Array.create(
+        a = zarr.create_array(
             store / "generic",
             shape=data.shape,
-            chunk_shape=(16, 16),
+            chunks=(16, 16),
             dtype=data.dtype,
             fill_value=0,
-            codecs=[BytesCodec(), codec_class()],
+            compressors=[codec_class()],
         )
 
     a[:, :] = data.copy()
@@ -100,26 +102,25 @@ def test_generic_codec_class(store: StorePath, codec_class: type[numcodecs.zarr3
 )
 def test_generic_filter(
     store: StorePath,
-    codec_class: type[numcodecs.zarr3._NumcodecsCodec],
+    codec_class: type[numcodecs.zarr3._NumcodecsArrayArrayCodec],
     codec_config: dict[str, JSON],
 ):
     data = np.linspace(0, 10, 256, dtype="float32").reshape((16, 16))
 
     with pytest.warns(UserWarning, match=EXPECTED_WARNING_STR):
-        a = Array.create(
+        a = zarr.create_array(
             store / "generic",
             shape=data.shape,
-            chunk_shape=(16, 16),
+            chunks=(16, 16),
             dtype=data.dtype,
             fill_value=0,
-            codecs=[
+            filters=[
                 codec_class(**codec_config),
-                BytesCodec(),
             ],
         )
 
         a[:, :] = data.copy()
-        a = Array.open(store / "generic")
+        a = zarr.open_array(store / "generic", mode="r")
     np.testing.assert_array_equal(data, a[:, :])
 
 
@@ -127,17 +128,17 @@ def test_generic_filter_bitround(store: StorePath):
     data = np.linspace(0, 1, 256, dtype="float32").reshape((16, 16))
 
     with pytest.warns(UserWarning, match=EXPECTED_WARNING_STR):
-        a = Array.create(
+        a = zarr.create_array(
             store / "generic_bitround",
             shape=data.shape,
-            chunk_shape=(16, 16),
+            chunks=(16, 16),
             dtype=data.dtype,
             fill_value=0,
-            codecs=[numcodecs.zarr3.BitRound(keepbits=3), BytesCodec()],
+            filters=[numcodecs.zarr3.BitRound(keepbits=3)],
         )
 
         a[:, :] = data.copy()
-        a = Array.open(store / "generic_bitround")
+        a = zarr.open_array(store / "generic_bitround", mode="r")
     assert np.allclose(data, a[:, :], atol=0.1)
 
 
@@ -145,17 +146,17 @@ def test_generic_filter_quantize(store: StorePath):
     data = np.linspace(0, 10, 256, dtype="float32").reshape((16, 16))
 
     with pytest.warns(UserWarning, match=EXPECTED_WARNING_STR):
-        a = Array.create(
+        a = zarr.create_array(
             store / "generic_quantize",
             shape=data.shape,
-            chunk_shape=(16, 16),
+            chunks=(16, 16),
             dtype=data.dtype,
             fill_value=0,
-            codecs=[numcodecs.zarr3.Quantize(digits=3), BytesCodec()],
+            filters=[numcodecs.zarr3.Quantize(digits=3)],
         )
 
         a[:, :] = data.copy()
-        a = Array.open(store / "generic_quantize")
+        a = zarr.open_array(store / "generic_quantize", mode="r")
     assert np.allclose(data, a[:, :], atol=0.001)
 
 
@@ -164,27 +165,27 @@ def test_generic_filter_packbits(store: StorePath):
     data[0:4, :] = True
 
     with pytest.warns(UserWarning, match=EXPECTED_WARNING_STR):
-        a = Array.create(
+        a = zarr.create_array(
             store / "generic_packbits",
             shape=data.shape,
-            chunk_shape=(16, 16),
+            chunks=(16, 16),
             dtype=data.dtype,
             fill_value=0,
-            codecs=[numcodecs.zarr3.PackBits(), BytesCodec()],
+            filters=[numcodecs.zarr3.PackBits()],
         )
 
         a[:, :] = data.copy()
-        a = Array.open(store / "generic_packbits")
+        a = zarr.open_array(store / "generic_packbits", mode="r")
     np.testing.assert_array_equal(data, a[:, :])
 
     with pytest.raises(ValueError, match=".*requires bool dtype.*"):
-        Array.create(
+        zarr.create_array(
             store / "generic_packbits_err",
             shape=data.shape,
-            chunk_shape=(16, 16),
+            chunks=(16, 16),
             dtype="uint32",
             fill_value=0,
-            codecs=[numcodecs.zarr3.PackBits(), BytesCodec()],
+            filters=[numcodecs.zarr3.PackBits()],
         )
 
 
@@ -198,26 +199,30 @@ def test_generic_filter_packbits(store: StorePath):
         numcodecs.zarr3.JenkinsLookup3,
     ],
 )
-def test_generic_checksum(store: StorePath, codec_class: type[numcodecs.zarr3._NumcodecsCodec]):
+def test_generic_checksum(
+    store: StorePath, codec_class: type[numcodecs.zarr3._NumcodecsBytesBytesCodec]
+):
     data = np.linspace(0, 10, 256, dtype="float32").reshape((16, 16))
 
     with pytest.warns(UserWarning, match=EXPECTED_WARNING_STR):
-        a = Array.create(
+        a = zarr.create_array(
             store / "generic_checksum",
             shape=data.shape,
-            chunk_shape=(16, 16),
+            chunks=(16, 16),
             dtype=data.dtype,
             fill_value=0,
-            codecs=[BytesCodec(), codec_class()],
+            compressors=[codec_class()],
         )
 
         a[:, :] = data.copy()
-        a = Array.open(store / "generic_checksum")
+        a = zarr.open_array(store / "generic_checksum", mode="r")
     np.testing.assert_array_equal(data, a[:, :])
 
 
 @pytest.mark.parametrize("codec_class", [numcodecs.zarr3.PCodec, numcodecs.zarr3.ZFPY])
-def test_generic_bytes_codec(store: StorePath, codec_class: type[numcodecs.zarr3._NumcodecsCodec]):
+def test_generic_bytes_codec(
+    store: StorePath, codec_class: type[numcodecs.zarr3._NumcodecsArrayBytesCodec]
+):
     try:
         codec_class()._codec  # noqa: B018
     except ValueError as e:
@@ -225,22 +230,45 @@ def test_generic_bytes_codec(store: StorePath, codec_class: type[numcodecs.zarr3
             pytest.xfail(f"{codec_class.codec_name} is not available: {e}")
         else:
             raise  # pragma: no cover
-    except ImportError as e:
+    except ImportError as e:  # pragma: no cover
         pytest.xfail(f"{codec_class.codec_name} is not available: {e}")
 
     data = np.arange(0, 256, dtype="float32").reshape((16, 16))
 
     with pytest.warns(UserWarning, match=EXPECTED_WARNING_STR):
-        a = Array.create(
+        a = zarr.create_array(
             store / "generic",
             shape=data.shape,
-            chunk_shape=(16, 16),
+            chunks=(16, 16),
             dtype=data.dtype,
             fill_value=0,
-            codecs=[
-                codec_class(),
-            ],
+            serializer=codec_class(),
         )
 
     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 = zarr.create_array(
+            store / "generic",
+            shape=data.shape,
+            chunks=(16, 16),
+            dtype=data.dtype,
+            fill_value=0,
+            filters=[
+                numcodecs.zarr3.Delta(dtype="i8", astype="i2"),  # type: ignore[arg-type]
+            ],
+        )
+
+        a[:, :] = data.copy()
+        a = zarr.open_array(store / "generic", mode="r")
+    np.testing.assert_array_equal(data, a[:, :])
+
+
+def test_repr():
+    codec = numcodecs.zarr3.LZ4(level=5)
+    assert repr(codec) == "LZ4(codec_name='numcodecs.lz4', codec_config={'level': 5})"

numcodecs/version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.14.1'
-__version_tuple__ = version_tuple = (0, 14, 1)
+__version__ = version = '0.15.0'
+__version_tuple__ = version_tuple = (0, 15, 0)

numcodecs/zarr3.py

@@ -8,12 +8,13 @@ You can use codecs from :py:mod:`numcodecs` by constructing codecs from :py:mod:
 >>> import zarr
 >>> import numcodecs.zarr3
 >>>
->>> codecs = [zarr.codecs.BytesCodec(), numcodecs.zarr3.BZ2(level=5)]
->>> array = zarr.open(
-...   "data.zarr", mode="w",
-...   shape=(1024, 1024), chunks=(64, 64),
+>>> array = zarr.create_array(
+...   store="data.zarr",
+...   shape=(1024, 1024),
+...   chunks=(64, 64),
 ...   dtype="uint32",
-...   codecs=codecs)
+...   filters=[numcodecs.zarr3.Delta()],
+...   compressors=[numcodecs.zarr3.BZ2(level=5)])
 >>> array[:] = np.arange(*array.shape).astype(array.dtype)
 
 .. note::
@@ -40,8 +41,10 @@ try:
 
     if zarr.__version__ < "3.0.0":  # pragma: no cover
         raise ImportError("zarr 3.0.0 or later is required to use the numcodecs zarr integration.")
-except ImportError:  # pragma: no cover
-    raise ImportError("zarr 3.0.0 or later is required to use the numcodecs zarr integration.")
+except ImportError as e:  # pragma: no cover
+    raise ImportError(
+        "zarr 3.0.0 or later is required to use the numcodecs zarr integration."
+    ) from e
 
 from zarr.abc.codec import ArrayArrayCodec, ArrayBytesCodec, BytesBytesCodec
 from zarr.abc.metadata import Metadata
@@ -95,6 +98,7 @@ class _NumcodecsCodec(Metadata):
             "Numcodecs codecs are not in the Zarr version 3 specification and "
             "may not be supported by other zarr implementations.",
             category=UserWarning,
+            stacklevel=2,
         )
 
     @cached_property
@@ -116,6 +120,12 @@ class _NumcodecsCodec(Metadata):
     def compute_encoded_size(self, input_byte_length: int, chunk_spec: ArraySpec) -> int:
         raise NotImplementedError  # pragma: no cover
 
+    # Override __repr__ because dynamically constructed classes don't seem to work otherwise
+    def __repr__(self) -> str:
+        codec_config = self.codec_config.copy()
+        codec_config.pop("id", None)
+        return f"{self.__class__.__name__}(codec_name={self.codec_name!r}, codec_config={codec_config!r})"
+
 
 class _NumcodecsBytesBytesCodec(_NumcodecsCodec, BytesBytesCodec):
     def __init__(self, **codec_config: JSON) -> None:
@@ -266,7 +276,19 @@ class Shuffle(_NumcodecsBytesBytesCodec):
 
 
 # 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"
 )
@@ -355,25 +377,25 @@ PCodec = _add_docstring(_make_array_bytes_codec("pcodec", "PCodec"), "numcodecs.
 ZFPY = _add_docstring(_make_array_bytes_codec("zfpy", "ZFPY"), "numcodecs.zfpy.ZFPY")
 
 __all__ = [
-    "Blosc",
-    "LZ4",
-    "Zstd",
-    "Zlib",
-    "GZip",
     "BZ2",
-    "LZMA",
-    "Shuffle",
-    "Delta",
-    "BitRound",
-    "FixedScaleOffset",
-    "Quantize",
-    "PackBits",
-    "AsType",
     "CRC32",
     "CRC32C",
+    "LZ4",
+    "LZMA",
+    "ZFPY",
     "Adler32",
+    "AsType",
+    "BitRound",
+    "Blosc",
+    "Delta",
+    "FixedScaleOffset",
     "Fletcher32",
+    "GZip",
     "JenkinsLookup3",
     "PCodec",
-    "ZFPY",
+    "PackBits",
+    "Quantize",
+    "Shuffle",
+    "Zlib",
+    "Zstd",
 ]

numcodecs/zfpy.py

@@ -13,7 +13,7 @@ with suppress(PackageNotFoundError):
 if _zfpy_version:
     # Check NumPy version
     _numpy_version: tuple = tuple(map(int, version("numpy").split('.')))
-    if _numpy_version >= (2, 0, 0) and _zfpy_version <= (1, 0, 1):  # pragma: no cover
+    if _numpy_version >= (2, 0, 0) and _zfpy_version < (1, 0, 1):  # pragma: no cover
         _zfpy_version = ()
         warnings.warn(
             "NumPy version >= 2.0.0 detected. The zfpy library is incompatible with this version of NumPy. "

{numcodecs-0.14.1.dist-info → numcodecs-0.15.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: numcodecs
-Version: 0.14.1
+Version: 0.15.0
 Summary: A Python package providing buffer compression and transformation codecs for use in data storage and communication applications.
 Maintainer-email: Alistair Miles <alimanfoo@googlemail.com>
 License: MIT
@@ -22,6 +22,7 @@ Requires-Python: >=3.11
 Description-Content-Type: text/x-rst
 License-File: LICENSE.txt
 Requires-Dist: numpy>=1.24
+Requires-Dist: deprecated
 Provides-Extra: docs
 Requires-Dist: sphinx; extra == "docs"
 Requires-Dist: sphinx-issues; extra == "docs"
@@ -37,9 +38,8 @@ Provides-Extra: msgpack
 Requires-Dist: msgpack; extra == "msgpack"
 Provides-Extra: zfpy
 Requires-Dist: zfpy>=1.0.0; extra == "zfpy"
-Requires-Dist: numpy<2.0.0; extra == "zfpy"
 Provides-Extra: pcodec
-Requires-Dist: pcodec<0.3,>=0.2; extra == "pcodec"
+Requires-Dist: pcodec<0.4,>=0.3; extra == "pcodec"
 Provides-Extra: crc32c
 Requires-Dist: crc32c>=2.7; extra == "crc32c"
 

numcodecs-0.15.0.dist-info/RECORD

@@ -0,0 +1,78 @@
+numcodecs-0.15.0.dist-info/RECORD,,
+numcodecs-0.15.0.dist-info/WHEEL,sha256=VujM3ypTCyUW6hcTDdK2ej0ARVMxlU1Djlh_zWnDgqk,109
+numcodecs-0.15.0.dist-info/entry_points.txt,sha256=3W3FHKrwE52X3fLq8KdioOtf93lh5KaoGV5t2D10DBI,919
+numcodecs-0.15.0.dist-info/top_level.txt,sha256=JkHllzt6IuVudg4Tk--wF-yfPPsdVOiMTag1tjGIihw,10
+numcodecs-0.15.0.dist-info/LICENSE.txt,sha256=lJysaEeeE7bJeSRjUVC04e9eaXZq2eRy6oWgjBV2u5Y,1124
+numcodecs-0.15.0.dist-info/METADATA,sha256=Ex3f5L-JE6Kr2Bm9v148Lu1xeLTFWkH7k0k9kbL2iGM,2934
+numcodecs/jenkins.cpython-312-darwin.so,sha256=stBwHYuFEtIBUbVxTzswor1XQBSuCmEKOmtfL6WOZZc,203712
+numcodecs/lzma.py,sha256=6XeJ-c-lTJN1EVrIOb5cEFEiMGlNHsS4c_OentmUox0,2257
+numcodecs/astype.py,sha256=pfdFqjNvb-PETswa2_UxZm632O-y2Lex-g_68IJpiuk,2099
+numcodecs/gzip.py,sha256=DJuc87g8neqn-SYEeCEQwPSdEN5oZGgDUan9MTI6Fb4,1436
+numcodecs/zstd.cpython-312-darwin.so,sha256=GjtWPxPsFr2g5hTc-moRJPvHw0qgSPUYsZnNRQosBZo,731304
+numcodecs/base64.py,sha256=79BSqVvloKc8JYenUQfqdPm0a0JAZhd9Zld7k5Cp2lc,752
+numcodecs/bz2.py,sha256=4Ups3IMVsjvBlXyaeYONPdE14TaK9V-4LH5LSNe7AGc,1174
+numcodecs/version.py,sha256=oHv-EAjiXbJma3jZ0Tq6UPimiWYyyw2Ao9S8zdq9uWs,413
+numcodecs/compat.py,sha256=JadagE6pTEcrX3V8wDml0n1tdkHvOWo6D21J3a4P0mw,6505
+numcodecs/_shuffle.cpython-312-darwin.so,sha256=vYgu77B9fV3u1XK1SHG4JfCEOW7J3r1ZmdrmchtqCuE,182736
+numcodecs/checksum32.py,sha256=L4BxbQZZ556EvJlYyxCQgZ3fvIZFxva_rycOx7FEBdY,5435
+numcodecs/ndarray_like.py,sha256=fVupUg_K_rDZNRlUmTiRp53OmF6YHb-yNyixJNFR8ME,1883
+numcodecs/quantize.py,sha256=UcQPVsWvx7fHb5mWfOd7VvhCc-MI8C2B3afBG4KYUFM,3026
+numcodecs/registry.py,sha256=76qBMok0wR_eeffFZNNEiFxysjHNVI_76AxFGi9p5PI,1831
+numcodecs/blosc.cpython-312-darwin.so,sha256=gg9Yhwf9gS5soVCJuZ5mobcz813EuQJWDsF9oDRPTDs,1059640
+numcodecs/pickles.py,sha256=LtcMa6cK-V5TUYJNR4dRDsWWRmLfNv0syZddbrbRv3A,1290
+numcodecs/fixedscaleoffset.py,sha256=fQwP_H-P3Mq4_LXtMQw5CLYeMjCBUdTtV-AKWVAIzkY,4188
+numcodecs/lz4.cpython-312-darwin.so,sha256=ZjHr9Ctnc2dTfo5Y6qNrTvfVJ_mVbLuezCHyi4j4HY0,248632
+numcodecs/__init__.py,sha256=LzVQQ8X8Mk7mXvOX9tu5tlwmQwIVhuhXMofXdFJJNjo,3103
+numcodecs/bitround.py,sha256=4lei39ZG4G2GGkDxl12q29nR5_8a4Icx4T-OgP1A1D4,2845
+numcodecs/vlen.cpython-312-darwin.so,sha256=ae8EJfWvX1uLF5QozWFykov4UEftkbrrpSDHA_S4xC0,261560
+numcodecs/zlib.py,sha256=gLPUICEQc5p6DICC_63nOsbUqxzJH_5ynuzenTQXzOQ,1049
+numcodecs/shuffle.py,sha256=hYOFJOCEeDSNI-TqT1JrbQxbprkQD4R8VfSzD4IPI3I,1575
+numcodecs/zarr3.py,sha256=lBBOVkoVmZ1YPU4z1RxdRHXaS4LXlD6ys_YobQ1gZM8,14712
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{numcodecs-0.14.1.dist-info → numcodecs-0.15.0.dist-info}/WHEEL

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 Wheel-Version: 1.0
-Generator: setuptools (75.6.0)
+Generator: setuptools (75.8.0)
 Root-Is-Purelib: false
 Tag: cp312-cp312-macosx_11_0_arm64
 

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