Merge branch 'main' into normanrz-patch-2

Author: dstansby

docs/release.rst

@@ -41,6 +41,10 @@ Fixes
 ~~~~~
 * Fixes issue with ``Delta`` Zarr 3 codec not working with ``astype``.
   By :user:`Norman Rzepka <normanrz>`, :issue:`664`
+* Cleanup ``PCodec`` soft dependency.
+  Previously importing ``numcodecs.pcodec`` would work if ``pcodec`` is not installed,
+  but now it will fail to import. This mirrors the behaviour of other optional dependencies.
+  By :user:`John Kirkham <jakirkham>`, :issue:`647`
 * Fixes issues with the upcoming ``zarr`` 3.0.0 release.
   By :user:`Norman Rzepka <normanrz>`, :issue:`675`
 

numcodecs/delta.py

@@ -63,12 +63,7 @@ def encode(self, buf):
         enc[0] = arr[0]
 
         # compute differences
-        # using np.subtract for in-place operations
-        if arr.dtype == bool:
-            np.not_equal(arr[1:], arr[:-1], out=enc[1:])
-        else:
-            np.subtract(arr[1:], arr[:-1], out=enc[1:])
-
+        enc[1:] = np.diff(arr)
         return enc
 
     def decode(self, buf, out=None):

numcodecs/pcodec.py

@@ -2,12 +2,7 @@
 
 from numcodecs.abc import Codec
 from numcodecs.compat import ensure_contiguous_ndarray
-
-try:
-    from pcodec import ChunkConfig, DeltaSpec, ModeSpec, PagingSpec, standalone
-except ImportError:  # pragma: no cover
-    standalone = None
-
+from pcodec import ChunkConfig, DeltaSpec, ModeSpec, PagingSpec, standalone
 
 DEFAULT_MAX_PAGE_N = 262144
 
@@ -58,9 +53,6 @@ def __init__(
         delta_encoding_order: int | None = None,
         equal_pages_up_to: int = DEFAULT_MAX_PAGE_N,
     ):
-        if standalone is None:  # pragma: no cover
-            raise ImportError("pcodec must be installed to use the PCodec codec.")
-
         # note that we use `level` instead of `compression_level` to
         # match other codecs
         self.level = level

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)
 

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()