Merge branch 'main' into setup-emscripten-ci

Author: agriyakhetarpal

.github/workflows/ci.yaml

@@ -16,89 +16,55 @@ jobs:
         # macos-13 is an intel runner, macos-14 is a arm64 runner
         platform: [ubuntu-latest, windows-latest, macos-13, macos-14]
 
+    defaults:
+      run:
+        shell: bash -el {0}
+
     steps:
       - name: Checkout source
         uses: actions/checkout@v4
         with:
           submodules: recursive
+          fetch-depth: 0 # required for version resolution
 
       - name: Set up Conda
         uses: conda-incubator/[email protected]
         with:
-            channels: conda-forge
-            miniforge-version: latest
-            python-version: ${{ matrix.python-version }}
+          channels: conda-forge
+          miniforge-version: latest
+          python-version: ${{ matrix.python-version }}
 
-      - name: Show info about `base` environment
-        shell: "bash -l {0}"
-        run: |
-          conda info
-          conda config --show-sources
-          conda list --show-channel-urls
-
-      - name: Set up `env`
-        shell: "bash -l {0}"
-        run: >
-          conda create -n env
-          c-compiler cxx-compiler
-          python=${{matrix.python-version}} wheel pip
+      - name: Install compilers
+        run: conda install -y c-compiler cxx-compiler
 
       - name: Install clang
-        shell: "bash -l {0}"
         if: matrix.platform == 'macos-13'
-        run: |
-          conda activate env
-          conda install -y 'clang>=12.0.1,<17'
+        run: conda install -y 'clang>=12.0.1,<17'
 
-      - name: Show info about `env` environment
-        shell: "bash -l {0}"
+      - name: Show conda environment info
         run: |
-          conda list --show-channel-urls -n env
+          conda info
+          conda config --show-sources
+          conda list --show-channel-urls
 
       - name: Install numcodecs
-        shell: "bash -l {0}"
         run: |
-          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,crc32c]
-
-      - name: Install pcodec
-        if: matrix.python-version != '3.13'
-        shell: "bash -l {0}"
-        run: |
-            conda activate env
-            python -m pip install -v ".[pcodec]"
+          python -m pip install -v -e .[test,test_extras,msgpack,crc32c,pcodec,zfpy]
 
       - name: Install zarr-python
-        shell: "bash -l {0}"
         # 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'
-        run: |
-          conda activate env
-          # TODO: remove --pre option when zarr v3 is out
-          python -m pip install --pre zarr>=3.0.0b2
-
-      # This is used to test with zfpy, which does not yet support numpy 2.0
-      - name: Install older numpy and zfpy
-        if: matrix.python-version == '3.11'
-        shell: "bash -l {0}"
-        run: |
-          conda activate env
-          python -m pip install -v ".[zfpy]"
+        # TODO: remove --pre option when zarr v3 is out
+        run: python -m pip install --pre zarr>=3.0.0b2
 
       - name: List installed packages
-        shell: "bash -l {0}"
-        run: |
-          conda activate env
-          python -m pip list
+        run: python -m pip list
 
       - name: Run tests
         shell: "bash -l {0}"
-        run: |
-          conda activate env
-          pytest -v
+        run: pytest -v
 
       - uses: codecov/codecov-action@v5
         with:

.pre-commit-config.yaml

@@ -14,20 +14,20 @@ repos:
     - id: debug-statements
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.8.4
+    rev: v0.9.4
     hooks:
     - id: ruff
       args: ["--fix", "--show-fixes"]
     - id: ruff-format
 
   - repo: https://github.com/scientific-python/cookie
-    rev: 2024.08.19
+    rev: 2025.01.22
     hooks:
     - id: sp-repo-review
 
   -   repo: https://github.com/pre-commit/mirrors-mypy
-      rev: v1.14.0
+      rev: v1.14.1
       hooks:
       -   id: mypy
           args: [--config-file, pyproject.toml]
-          additional_dependencies: [numpy, pytest, crc32c, zfpy, 'zarr>=3.0.0b2']
+          additional_dependencies: [numpy, pytest, crc32c, zfpy, 'zarr>=3.0.0rc1']

docs/compression/blosc.rst

@@ -18,15 +18,9 @@ Blosc
 Helper functions
 ----------------
 
-.. autofunction:: init
-.. autofunction:: destroy
-.. autofunction:: compname_to_compcode
 .. autofunction:: list_compressors
 .. autofunction:: get_nthreads
 .. autofunction:: set_nthreads
-.. autofunction:: cbuffer_sizes
 .. autofunction:: cbuffer_complib
-.. autofunction:: cbuffer_metainfo
 .. autofunction:: compress
 .. autofunction:: decompress
-.. autofunction:: decompress_partial

docs/release.rst

@@ -11,23 +11,64 @@ Release notes
     Unreleased
     ----------
 
+
 .. _unreleased:
 
 Unreleased
 ----------
 
+Improvements
+~~~~~~~~~~~~
+* Raise a custom `UnknownCodecError` when trying to retrieve an unavailable codec.
+  By :user:`Cas Wognum <cwognum>`.
+
+Fixes
+~~~~~
+* Remove redundant ``id`` from codec metadata serialization in Zarr3 codecs.
+  By :user:`Norman Rzepka <normanrz>`, :issue:`685`
+
+.. _release_0.15.0:
+
+0.15.0
+------
+
 Breaking changes
 ~~~~~~~~~~~~~~~~
 * All arguments to the ``PCodec`` constructor except for ``level``
   are now keyword only, to support the updated API.
   By :user:`Sam Levang <slevang>`, :issue:`623`
 
+Deprecations
+~~~~~~~~~~~~
+The following ``blosc`` funcitons are deprecated, with no replacement.
+This is because they are 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 deprecated as
+has always been experimental and there is no equivalent in the official
+blsoc Python package.
+By :user:`David Stansby <dstansby>`, :issue`619`
 
 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`
+
+* Removed Version Check: The previous code included a check for the `NumPy` version
+  and a warning if the version was incompatible with `zfpy`.
+  This check has been removed because `zfpy` now supports the newer versions of `NumPy`.
+  By :user:`Meher Gajula <me-her>`, :issue:`672`
 
 Improvements
 ~~~~~~~~~~~~
@@ -44,6 +85,7 @@ Improvements
   are still silently caught.
   By :user:`David Stansby <dstansby>`, :issue:`550`.
 
+.. _release_0.14.1:
 
 0.14.1
 ------

docs/zarr3.rst

@@ -5,8 +5,8 @@ Zarr 3 codecs
 .. automodule:: numcodecs.zarr3
 
 
-Bytes-to-bytes codecs
----------------------
+Compressors (bytes-to-bytes codecs)
+-----------------------------------
 .. autoclass:: Blosc()
 
     .. autoattribute:: codec_name
@@ -40,58 +40,61 @@ Bytes-to-bytes codecs
     .. autoattribute:: codec_name
 
 
-Array-to-array codecs
----------------------
-.. autoclass:: Delta()
+Checksum codecs (bytes-to-bytes codecs)
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Need to be used as ``compressors`` in zarr-python.
+
+.. autoclass:: CRC32()
 
     .. autoattribute:: codec_name
 
-.. autoclass:: BitRound()
+.. autoclass:: CRC32C()
 
     .. autoattribute:: codec_name
 
-.. autoclass:: FixedScaleOffset()
+.. autoclass:: Adler32()
 
     .. autoattribute:: codec_name
 
-.. autoclass:: Quantize()
+.. autoclass:: Fletcher32()
 
     .. autoattribute:: codec_name
 
-.. autoclass:: PackBits()
+.. autoclass:: JenkinsLookup3()
 
     .. autoattribute:: codec_name
 
-.. autoclass:: AsType()
 
-    .. autoattribute:: codec_name
+Filters (array-to-array codecs)
+-------------------------------
+.. autoclass:: Delta()
 
+    .. autoattribute:: codec_name
 
-Bytes-to-bytes checksum codecs
-------------------------------
-.. autoclass:: CRC32()
+.. autoclass:: BitRound()
 
     .. autoattribute:: codec_name
 
-.. autoclass:: CRC32C()
+.. autoclass:: FixedScaleOffset()
 
     .. autoattribute:: codec_name
 
-.. autoclass:: Adler32()
+.. autoclass:: Quantize()
 
     .. autoattribute:: codec_name
 
-.. autoclass:: Fletcher32()
+.. autoclass:: PackBits()
 
     .. autoattribute:: codec_name
 
-.. autoclass:: JenkinsLookup3()
+.. autoclass:: AsType()
 
     .. autoattribute:: codec_name
 
 
-Array-to-bytes codecs
----------------------
+
+Serializers (array-to-bytes codecs)
+-----------------------------------
 .. autoclass:: PCodec()
 
     .. autoattribute:: codec_name

numcodecs/__init__.py

@@ -49,7 +49,7 @@
     ncores = multiprocessing.cpu_count()
 except OSError:  # pragma: no cover
     ncores = 1
-blosc.init()
+blosc._init()
 blosc.set_nthreads(min(8, ncores))
 atexit.register(blosc.destroy)