Merge remote-tracking branch 'origin/main' into zarr3-codecs

Author: normanrz

.pep8speaks.yml

@@ -15,7 +15,7 @@ repos:
     - id: debug-statements
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.6.9
+    rev: v0.7.0
     hooks:
     - id: ruff
       args: ["--fix", "--show-fixes"]

.pre-commit-config.yaml

@@ -8,6 +8,17 @@ Release notes
 
 .. _unreleased:
 
+Unreleased
+----------
+
+Fix
+~~~
+* Fix in-place mutation of input array in `BitRound`.
+  By :user:`Sam Levang <slevang>`, :issue:`608`
+
+
+.. _release_0.13.1:
+
 0.13.1
 ------
 

docs/release.rst

@@ -1,4 +1,4 @@
-# ruff: noqa: E402,F401
+# ruff: noqa: E402
 """Numcodecs is a Python package providing buffer compression and
 transformation codecs for use in data storage and communication
 applications. These include:
@@ -21,8 +21,9 @@
 import multiprocessing
 from contextlib import suppress
 
-from numcodecs.registry import get_codec, register_codec
-from numcodecs.version import version as __version__
+from numcodecs.registry import get_codec as get_codec
+from numcodecs.registry import register_codec
+from numcodecs.version import version as __version__  # noqa: F401
 from numcodecs.zlib import Zlib
 
 register_codec(Zlib)
@@ -55,13 +56,13 @@
     atexit.register(blosc.destroy)
 
 with suppress(ImportError):
-    from numcodecs import zstd
+    from numcodecs import zstd as zstd
     from numcodecs.zstd import Zstd
 
     register_codec(Zstd)
 
 with suppress(ImportError):
-    from numcodecs import lz4
+    from numcodecs import lz4 as lz4
     from numcodecs.lz4 import LZ4
 
     register_codec(LZ4)
@@ -127,7 +128,7 @@
 register_codec(JSON)
 
 with suppress(ImportError):
-    from numcodecs import vlen
+    from numcodecs import vlen as vlen
     from numcodecs.vlen import VLenArray, VLenBytes, VLenUTF8
 
     register_codec(VLenUTF8)

numcodecs/__init__.py

@@ -1,7 +1,5 @@
-# ruff: noqa: F401
 import array
 import codecs
-import functools
 
 import numpy as np
 

numcodecs/compat.py

@@ -29,9 +29,6 @@ class PackBits(Codec):
 
     codec_id = 'packbits'
 
-    def __init__(self):
-        pass
-
     def encode(self, buf):
         # normalise input
         arr = ensure_ndarray(buf).view(bool)

numcodecs/packbits.py

@@ -8,7 +8,7 @@
 here = os.path.abspath(os.path.dirname(__file__))
 
 
-@pytest.fixture()
+@pytest.fixture
 def set_path():
     sys.path.append(here)
     numcodecs.registry.run_entrypoints()

numcodecs/tests/test_entrypoints.py

@@ -57,8 +57,8 @@ def test_config():
 
 
 def test_invalid_config_error():
+    codec = PCodec(mode_spec='bogus')
     with pytest.raises(ValueError):
-        codec = PCodec(mode_spec='bogus')
         check_encode_decode_array_to_bytes(arrays[0], codec)
 
 

numcodecs/tests/test_pcodec.py

@@ -162,7 +162,7 @@ def test_expected_result():
 
 
 def test_incompatible_elementsize():
+    arr = np.arange(1001, dtype='u1')
+    codec = Shuffle(elementsize=4)
     with pytest.raises(ValueError):
-        arr = np.arange(1001, dtype='u1')
-        codec = Shuffle(elementsize=4)
         codec.encode(arr)

numcodecs/tests/test_shuffle.py

@@ -162,22 +162,29 @@ line-length = 100
 [tool.ruff.lint]
 extend-select = [
     "B",
+    "FLY",
+    "FURB",
+    "G",
     "I",
+    "PERF",
     "PGH",
     "PIE",
     "PT",
+    "PYI",
     "RSE",
     "RUF",
     "UP",
+    # "W",  https://github.com/astral-sh/ruff/issues/13763
 ]
 ignore = [
     "B028",
     "B904",
+    "FURB101",
+    "FURB103",
     "PT001",
     "PT004",  # deprecated
     "PT005",  # deprecated
     "PT011",
-    "PT012",
 	"RUF001",
     "UP007",
     "UP027",  # deprecated