Merge branch 'main' into main

Author: dstansby

.github/workflows/ci.yaml

@@ -12,7 +12,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.10", "3.11", "3.12"]
+        python-version: ["3.10", "3.11", "3.12", "3.13.0"]
         # macos-12 is an intel runner, macos-14 is a arm64 runner
         platform: [ubuntu-latest, windows-latest, macos-12, macos-14]
 
@@ -61,7 +61,15 @@ jobs:
           conda activate env
           export DISABLE_NUMCODECS_AVX2=""
           # TODO: put back zfpy import when it supports numpy 2.0
-          python -m pip install -v -e .[test,test_extras,msgpack,pcodec]
+          python -m pip install -v -e .[test,test_extras,msgpack]
+
+      - name: Install pcodec
+        if: matrix.python-version != '3.13.0'
+        shell: "bash -l {0}"
+        run: |
+            conda activate env
+            python -m pip install -v pcodec
+
 
       # This is used to test with zfpy, which does not yet support numpy 2.0
       - name: Install older numpy and zfpy

.github/workflows/wheel.yaml

@@ -17,7 +17,7 @@ jobs:
         os: [ubuntu-latest, windows-latest, macos-12, macos-14]
     env:
       CIBW_TEST_COMMAND: python -c "import numcodecs"
-      CIBW_BUILD: "cp310-* cp311-* cp312-*"
+      CIBW_BUILD: "cp310-* cp311-* cp312-* cp313-*"
       CIBW_SKIP: "pp* *-musllinux_* *win32 *_i686 *_s390x"
       # note: CIBW_ENVIRONMENT is now set in pyproject.toml
 
@@ -26,7 +26,7 @@ jobs:
         with:
           submodules: true
 
-      - uses: pypa/[email protected].0
+      - uses: pypa/[email protected].2
 
       - uses: actions/upload-artifact@v4
         with:
@@ -44,7 +44,7 @@ jobs:
       - uses: actions/setup-python@v5
         name: Install Python
         with:
-          python-version: '3.10'
+          python-version: "3.10"
 
       - name: Build sdist
         run: pipx run build --sdist

.pre-commit-config.yaml

@@ -1,3 +1,4 @@
+exclude: ^fixture/  # files with trailing whitespaces on purpose
 ci:
   autoupdate_commit_msg: "chore: update pre-commit hooks"
   autofix_commit_msg: "style: pre-commit fixes"
@@ -6,9 +7,21 @@ default_stages: [commit, push]
 default_language_version:
   python: python3
 repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0
+    hooks:
+    - id: trailing-whitespace
+    - id: check-yaml
+    - id: debug-statements
+
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: 'v0.6.5'
+    rev: v0.6.9
     hooks:
     - id: ruff
       args: ["--fix", "--show-fixes"]
     - id: ruff-format
+
+  - repo: https://github.com/scientific-python/cookie
+    rev: 2024.04.23
+    hooks:
+    - id: sp-repo-review

.pyup.yml

@@ -1,4 +1,4 @@
-# autogenerated pyup.io config file 
+# autogenerated pyup.io config file
 # see https://pyup.io/docs/configuration/ for all available options
 
 schedule: every month

README.rst

@@ -1,7 +1,7 @@
 Numcodecs
 =========
 
-Numcodecs is a Python package providing buffer compression and transformation 
+Numcodecs is a Python package providing buffer compression and transformation
 codecs for use in data storage and communication applications.
 
 .. image:: https://readthedocs.org/projects/numcodecs/badge/?version=latest

adhoc/blosc_memleak_check.py

@@ -1,13 +1,13 @@
 import sys
 
-import numcodecs
 import numpy as np
 from numpy.testing import assert_array_equal
 
+import numcodecs
 
 codec = numcodecs.Blosc()
 data = np.arange(int(sys.argv[1]))
-for i in range(int(sys.argv[2])):
+for _ in range(int(sys.argv[2])):
     enc = codec.encode(data)
     dec = codec.decode(enc)
     arr = np.frombuffer(dec, dtype=data.dtype)

c-blosc

@@ -13,9 +13,10 @@
 # serve to show the default.
 
 
-import sys
 import os
+import sys
 from unittest.mock import Mock as MagicMock
+
 import numcodecs
 
 

docs/conf.py

@@ -8,30 +8,31 @@ Release notes
 
 .. _unreleased:
 
-Unreleased
-----------
+0.13.1
+------
 
 Breaking changes
 ~~~~~~~~~~~~~~~~
 * `Zstd.default_level`, `Zstd.min_level`, and `Zstd.max_level` are now class methods
   instead of properties. This means they must now be called like ``Zstd.default_level()``
   instead of ``Zstd.default_level``. This breaking change has been made because Python 3.13
   removes support for class properties.
-  By :user:`David Stansby <dstansby>`
+  By :user:`David Stansby <dstansby>`, :issue:`576`.
 
 Enhancements
 ~~~~~~~~~~~~
 
-
-Fix
-~~~
-
+* Update bundled c-blosc to v1.26.1. This updates Zlib to v1.3.1
+  and Zstd to v1.5.6.
+  By :user:`David Stansby <dstansby>`, :issue:`560`.
+* Added support for Python 3.13 :user:`David Stansby <dstansby>`, :issue:`576`.
+* Cleaned up the table of contents in the documentation to list codecs by category
+  :user:`David Stansby <dstansby>`, :issue:`458`.
 
 Maintenance
 ~~~~~~~~~~~
 * Change format() and old string formatting to f-strings.
   By :user:`Dimitri Papadopoulos Orfanos <DimitriPapadopoulos>`, :issue:`439`.
-
 * Remove pin on Sphinx
   By :user:`Elliott Sales de Andrade <QuLogic>`, :issue:`552`.
 

docs/release.rst

@@ -25,6 +25,7 @@
    ],
    "source": [
     "import numpy as np\n",
+    "\n",
     "import numcodecs\n",
     "\n",
     "numcodecs.__version__"