Merge branch 'main' into mkitti-zstd-stream-decompress

Author: mkitti

.github/workflows/ci.yaml

@@ -13,8 +13,8 @@ jobs:
       fail-fast: false
       matrix:
         python-version: ["3.11", "3.12", "3.13"]
-        # macos-13 is an intel runner, macos-14 is a arm64 runner
-        platform: [ubuntu-latest, windows-latest, macos-13, macos-14]
+        # macos-13 is an intel runner, macos-14 is an arm64 runner
+        platform: [ubuntu-latest, ubuntu-22.04-arm, windows-latest, macos-13, macos-14]
 
     defaults:
       run:
@@ -28,7 +28,7 @@ jobs:
           fetch-depth: 0 # required for version resolution
 
       - name: Set up Conda
-        uses: conda-incubator/[email protected].0
+        uses: conda-incubator/[email protected].1
         with:
           channels: conda-forge
           miniforge-version: latest
@@ -56,8 +56,7 @@ jobs:
         # Since zarr v3 requires numpy >= 1.25, on Python 3.11 leave it out
         # so we can have some tests of our minimum version of numpy (1.24)
         if: matrix.python-version != '3.11'
-        # TODO: remove --pre option when zarr v3 is out
-        run: python -m pip install --pre zarr>=3.0.0b2
+        run: python -m pip install zarr>=3
 
       - name: List installed packages
         run: python -m pip list

.github/workflows/wheel.yaml

@@ -13,8 +13,8 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        # macos-13 is an intel runner, macos-14 is a arm64 runner
-        os: [ubuntu-latest, windows-latest, macos-13, macos-14]
+        # macos-13 is an intel runner, macos-14 is an arm64 runner
+        os: [ubuntu-latest, ubuntu-22.04-arm, windows-latest, macos-13, macos-14]
     env:
       CIBW_TEST_COMMAND: python -c "import numcodecs"
       CIBW_BUILD: "cp311-* cp312-* cp313-*"
@@ -26,7 +26,7 @@ jobs:
         with:
           submodules: true
 
-      - uses: pypa/cibuildwheel@v2.22.0
+      - uses: pypa/cibuildwheel@v2.23.2
 
       - uses: actions/upload-artifact@v4
         with:

.pre-commit-config.yaml

@@ -14,20 +14,20 @@ repos:
     - id: debug-statements
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.9.4
+    rev: v0.11.12
     hooks:
     - id: ruff
       args: ["--fix", "--show-fixes"]
     - id: ruff-format
 
   - repo: https://github.com/scientific-python/cookie
-    rev: 2025.01.22
+    rev: 2025.05.02
     hooks:
     - id: sp-repo-review
 
   -   repo: https://github.com/pre-commit/mirrors-mypy
-      rev: v1.14.1
+      rev: v1.16.0
       hooks:
       -   id: mypy
           args: [--config-file, pyproject.toml]
-          additional_dependencies: [numpy, pytest, crc32c, zfpy, 'zarr>=3.0.0rc1']
+          additional_dependencies: [numpy, pytest, crc32c, zfpy, 'zarr>=3']

docs/contributing.rst

@@ -203,12 +203,11 @@ contributors.
 Merging pull requests
 ~~~~~~~~~~~~~~~~~~~~~
 
-Pull requests submitted by an external contributor should be reviewed and approved by at least
-one core developers before being merged. Ideally, pull requests submitted by a core developer
-should be reviewed and approved by at least one other core developers before being merged.
+Pull requests should be reviewed and approved by at least one core developer
+(other than the pull request author) before being merged.
 
-Pull requests should not be merged until all CI checks have passed (Travis, AppVeyor,
-Codecov) against code that has had the latest main merged in.
+Pull requests should not be merged until all CI checks have passed against code
+that has had the latest main merged in.
 
 Compatibility and versioning policies
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -278,6 +277,10 @@ hard-and-fast rules, e.g., it is fine to make a minor release to make a single n
 feature available; equally, it is fine to make a minor release that includes a number of
 changes.
 
+When making a minor release, open an issue stating your intention so other developers
+know that a release is planned. At least a week's notice should be given for other
+developers to be aware of and possibly add to the contents of the release.
+
 Major releases obviously need to be given careful consideration, and should be done as
 infrequently as possible, as they will break existing code and/or affect data
 compatibility in some way.

docs/release.rst

@@ -17,6 +17,82 @@ Release notes
 Unreleased
 ----------
 
+Enhancements
+~~~~~~~~~~~~
+
+Improvements
+~~~~~~~~~~~~
+
+* In ``vlen``, define and use ``const`` ``HEADER_LENGTH``.
+  By :user:`John Kirkham <jakirkham>`, :issue:`723`
+* All codecs are now pickleable.
+  By :user:`Tom Nicholas <TomNicholas>`, :issue:`744`
+
+Fixes
+~~~~~
+
+* Fix ``const`` discard warnings in ``fletcher32``.
+  By :user:`John Kirkham <jakirkham>`, :issue:`728`
+
+* Update ``license*`` metadata and include third-party licenses.
+  By :user:`John Kirkham <jakirkham>`, :issue:`729`
+
+* Add ``#ifndef`` guard around ``PyBytes_RESIZE``.
+  By :user:`John Kirkham <jakirkham>`, :issue:`732`
+
+* Remove ``typesize`` from ``Blosc.get_config`` output
+  By :user:`Ilan Gold <ilan-gold>`
+
+Maintenance
+~~~~~~~~~~~
+
+
+0.16.0
+------
+
+Enhancements
+~~~~~~~~~~~~
+
+* Add ``typesize`` argument to ``Blosc`` to allow for buffers that are passed to ``encode``
+  use that information.  zarr v3 currently has its Blosc codec as bytes-to-bytes but does retain
+  the size information so using it here allows for massive compression ratio gains.
+  By :user:`Ilan Gold <ilan-gold>`
+* Add support for the Linux aarch64 architecture,
+  By :user:`Agriya Khetarpal <agriyakhetarpal>`, :issue:`288`.
+* Preallocate output buffers and resize directly as needed.
+  By :user:`John Kirkham <jakirkham>`, :issue:`656`
+* ``Checksum32`` is now an abstract base clase, with ``checksum()`` as an abstract method.
+  This helps ensure that any subclasses implement the ``checksum()`` method.
+  :issue:`711`
+
+Removals
+~~~~~~~~
+
+The following ``blosc`` funcitons are removed, with no replacement.
+This is because they were not intended to be public API.
+
+- ``numcodecs.blosc.init``
+- ``numcodecs.blosc.destroy``
+- ``numcodecs.blosc.compname_to_compcode``
+- ``numcodecs.blosc.cbuffer_sizes``
+- ``numcodecs.blosc.cbuffer_metainfo``
+
+In addition, ``numcodecs.blosc.decompress_partial`` is removed as
+has always been experimental and there is no equivalent in the official
+blsoc Python package.
+By :user:`David Stansby <dstansby>`, :issue:`712`
+
+Maintenance
+~~~~~~~~~~~
+* Replace internal ``Buffer`` usage with ``memoryview``\ s.
+  By :user:`John Kirkham <jakirkham>`, :issue:`656`
+* Bump the minimum macOS deployment target for x86_64 to 10.13.
+  By :user:`Agriya Khetarpal <agriyakhetarpal>`, :issue:`288`.
+
+
+0.15.1
+------
+
 Improvements
 ~~~~~~~~~~~~
 * Add streaming decompression for ZSTD (:issue:`699`)
@@ -42,7 +118,7 @@ Breaking changes
 
 Deprecations
 ~~~~~~~~~~~~
-The following ``blosc`` funcitons are deprecated, with no replacement.
+The following ``blosc`` functions are deprecated, with no replacement.
 This is because they are not intended to be public API.
 
 - ``numcodecs.blosc.init``
@@ -54,7 +130,7 @@ This is because they are not intended to be public API.
 In addition, ``numcodecs.blosc.decompress_partial`` is deprecated as
 has always been experimental and there is no equivalent in the official
 blsoc Python package.
-By :user:`David Stansby <dstansby>`, :issue`619`
+By :user:`David Stansby <dstansby>`, :issue:`619`
 
 Fixes
 ~~~~~

numcodecs/__init__.py

@@ -51,7 +51,7 @@
     ncores = 1
 blosc._init()
 blosc.set_nthreads(min(8, ncores))
-atexit.register(blosc.destroy)
+atexit.register(blosc._destroy)
 
 from numcodecs import zstd as zstd
 from numcodecs.zstd import Zstd