Merge branch 'main' into rtd-doc-theme

.flake8

@@ -12,3 +12,4 @@ exclude =
     fixture,
     notebooks,
     numcodecs.egg-info,
+    numcodecs/version.py,

.github/workflows/ci-linux.yaml

@@ -12,11 +12,11 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
 
     steps:
       - name: Checkout source
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           submodules: recursive
 
@@ -50,7 +50,7 @@ jobs:
         run: |
           conda activate env
           export DISABLE_NUMCODECS_AVX2=""
-          python -m pip install -v -e .[test,msgpack,zfpy]
+          python -m pip install -v -e .[test,test_extras,msgpack,zfpy]
 
       - name: List installed packages
         shell: "bash -l {0}"

.github/workflows/ci-osx.yaml

@@ -12,11 +12,11 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
 
     steps:
       - name: Checkout source
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           submodules: recursive
 
@@ -49,8 +49,8 @@ jobs:
         shell: "bash -l {0}"
         run: |
           conda activate env
-          export CC=clang
-          python -m pip install -v -e .[test,msgpack,zfpy]
+          export DISABLE_NUMCODECS_AVX2=""
+          python -m pip install -v -e .[test,test_extras,msgpack,zfpy]
 
       - name: List installed packages
         shell: "bash -l {0}"

.github/workflows/ci-windows.yaml

@@ -12,11 +12,11 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
 
     steps:
       - name: Checkout source
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           submodules: recursive
 
@@ -42,7 +42,7 @@ jobs:
         shell: "bash -l {0}"
         run: |
           conda activate env
-          python -m pip install -v -e .[test,msgpack,zfpy]
+          python -m pip install -v -e .[test,test_extras,msgpack,zfpy]
 
       - name: List installed packages
         shell: "bash -l {0}"

.github/workflows/codeql-analysis.yml

@@ -32,7 +32,7 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       # Initializes the CodeQL tools for scanning.
       - name: Initialize CodeQL

.github/workflows/wheel.yaml

@@ -22,11 +22,11 @@ jobs:
       # note: CIBW_ENVIRONMENT is now set in pyproject.toml
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           submodules: true
 
-      - uses: pypa/cibuildwheel@v2.14.1
+      - uses: pypa/cibuildwheel@v2.16.2
 
       - uses: actions/upload-artifact@v3
         with:
@@ -37,7 +37,7 @@ jobs:
     name: Build source distribution
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           submodules: true
 

docs/release.rst

@@ -6,7 +6,6 @@ Release notes
     # to document your changes. On releases it will be
     # re-indented so that it does not show up in the notes.
 
-
 .. _unreleased:
 
 Unreleased
@@ -15,10 +14,41 @@ Unreleased
 Enhancements
 ~~~~~~~~~~~~
 
+Fix
+~~~
+
+Maintenance
+~~~~~~~~~~~
+
+.. _release_0.12.1:
+
+0.12.1
+------
+
+Fix
+~~~
+
+* ``Codec`` is now derived from ``abc.ABC``
+  By :user:`Mads R. B. Kristensen <madsbk>`, :issue:`472`.
+* Fix handling of entry points on older Python versions where ``importlib_metadata`` compatibility is concerned
+  By :user:`Vyas Ramasubramani <vyasr>`, :issue:`478`.
+* Make shuffle pyx functions ``noexcept``
+  By :user:`Martin Durant <martindurant>`, :issue:`477`.
+
+.. _release_0.12.0:
+
+0.12.0
+------
+
+Enhancements
+~~~~~~~~~~~~
+
 * Add ``fletcher32`` checksum codec
   By :user:`Martin Durant <martindurant>`, :issue:`410`.
 * Add ``jenkins_lookup3`` checksum codec
   By :user:`Mark Kittisopkul <mkitti>`, :issue:`445`.
+* Support Python 3.12.
+  By :user:`John Kirkham <jakirkham>`, :issue:`471`.
 
 Fix
 ~~~
@@ -31,7 +61,7 @@ Fix
 Maintenance
 ~~~~~~~~~~~
 
-* Cleanup ``import``s in ``adhoc/blosc_memleak_check.py``
+* Cleanup ``import``\ s in ``adhoc/blosc_memleak_check.py``
   By :user:`John Kirkham <jakirkham>`, :issue:`408`.
 
 .. _release_0.11.0:

numcodecs/_shuffle.pyx

@@ -8,7 +8,7 @@ cimport cython
 
 @cython.boundscheck(False)
 @cython.wraparound(False)
-cpdef void _doShuffle(const unsigned char[::1] src, unsigned char[::1] des, Py_ssize_t element_size) nogil:
+cpdef void _doShuffle(const unsigned char[::1] src, unsigned char[::1] des, Py_ssize_t element_size) noexcept nogil:
     cdef Py_ssize_t count, i, j, offset, byte_index
     count = len(src) // element_size
     for i in range(count):
@@ -20,7 +20,7 @@ cpdef void _doShuffle(const unsigned char[::1] src, unsigned char[::1] des, Py_s
 
 @cython.boundscheck(False)
 @cython.wraparound(False)
-cpdef void _doUnshuffle(const unsigned char[::1] src, unsigned char[::1] des, Py_ssize_t element_size) nogil:
+cpdef void _doUnshuffle(const unsigned char[::1] src, unsigned char[::1] des, Py_ssize_t element_size) noexcept nogil:
     cdef Py_ssize_t count, i, j, offset, byte_index
     count = len(src) // element_size
     for i in range(element_size):

numcodecs/abc.py

@@ -29,10 +29,10 @@
 """
 
 
-from abc import abstractmethod
+from abc import ABC, abstractmethod
 
 
-class Codec:
+class Codec(ABC):
     """Codec abstract base class."""
 
     # override in sub-class

numcodecs/jenkins.pyx

@@ -96,7 +96,7 @@ cpdef uint32_t jenkins_lookup3(const uint8_t[::1] _data, uint32_t initval=0):
     hash a variable-length key into a 32-bit value
 
     data   : the key (unaligned variable-length array of bytes)
-    initval : can be any 4-byte value, defualts to 0
+    initval : can be any 4-byte value, defaults to 0
 
     Returns a 32-bit value.  Every bit of the key affects every bit of
     the return value.  Two keys differing by one or two bits will have

numcodecs/registry.py

@@ -13,10 +13,10 @@ def run_entrypoints():
     eps = entry_points()
     if hasattr(eps, 'select'):
         # If entry_points() has a select method, use that. Python 3.10+
-        entries.update(eps.select(group="numcodecs.codecs"))
+        entries.update({e.name: e for e in eps.select(group="numcodecs.codecs")})
     else:
         # Otherwise, fallback to using get
-        entries.update(eps.get("numcodecs.codecs", []))
+        entries.update({e.name: e for e in eps.get("numcodecs.codecs", [])})
 
 
 run_entrypoints()

numcodecs/tests/test_entrypoints.py

@@ -19,6 +19,7 @@ def set_path():
     numcodecs.registry.codec_registry.pop("test")
 
 
-def test_entrypoint_codec(set_path):
+@pytest.mark.usefixtures("set_path")
+def test_entrypoint_codec():
     cls = numcodecs.registry.get_codec({"id": "test"})
     assert cls.codec_id == "test"

numcodecs/tests/test_entrypoints_backport.py

@@ -0,0 +1,32 @@
+import os.path
+import pkgutil
+import sys
+
+import pytest
+
+from multiprocessing import Process
+
+import numcodecs.registry
+
+if not pkgutil.find_loader("importlib_metadata"):  # pragma: no cover
+    pytest.skip("This test module requires importlib_metadata to be installed")
+
+here = os.path.abspath(os.path.dirname(__file__))
+
+
+def get_entrypoints_with_importlib_metadata_loaded():
+    # importlib_metadata patches importlib.metadata, which can lead to breaking changes
+    # to the APIs of EntryPoint objects used when registering entrypoints. Attempt to
+    # isolate those changes to just this test.
+    import importlib_metadata  # noqa: F401
+    sys.path.append(here)
+    numcodecs.registry.run_entrypoints()
+    cls = numcodecs.registry.get_codec({"id": "test"})
+    assert cls.codec_id == "test"
+
+
+def test_entrypoint_codec_with_importlib_metadata():
+    p = Process(target=get_entrypoints_with_importlib_metadata_loaded)
+    p.start()
+    p.join()
+    assert p.exitcode == 0

pyproject.toml

@@ -10,9 +10,8 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "numcodecs"
 description = """
-A Python package providing buffer compression and transformation codecs for use
-in data storage and communication applications.
-"""
+A Python package providing buffer compression and transformation codecs \
+for use in data storage and communication applications."""
 readme =  "README.rst"
 dependencies = [
     "numpy>=1.7",
@@ -58,6 +57,9 @@ test = [
     "pytest",
     "pytest-cov",
 ]
+test_extras = [
+    "importlib_metadata",
+]
 msgpack = [
     "msgpack",
 ]
@@ -115,9 +117,9 @@ norecursedirs = [
     "numcodecs.egg-info",
 ]
 [tool.cibuildwheel]
- environment = { DISABLE_NUMCODECS_AVX2=1 }
- [tool.cibuildwheel.macos]
- environment = { MACOSX_DEPLOYMENT_TARGET=10.9, CFLAGS="$CFLAGS -Wno-implicit-function-declaration" }
- [[tool.cibuildwheel.overrides]]
- select = "*-macosx_arm64"
- environment = { DISABLE_NUMCODECS_SSE2=1 }
+environment = { DISABLE_NUMCODECS_AVX2=1 }
+[tool.cibuildwheel.macos]
+environment = { MACOSX_DEPLOYMENT_TARGET=10.9, DISABLE_NUMCODECS_AVX2=1, CFLAGS="$CFLAGS -Wno-implicit-function-declaration" }
+[[tool.cibuildwheel.overrides]]
+select = "*-macosx_arm64"
+environment = { DISABLE_NUMCODECS_AVX2=1, DISABLE_NUMCODECS_SSE2=1 }