Merge branch 'zarr-developers:main' into main

Author: gorloffslava

.github/workflows/ci.yaml

@@ -13,8 +13,8 @@ jobs:
       fail-fast: false
       matrix:
         python-version: ["3.11", "3.12", "3.13"]
-        # macos-12 is an intel runner, macos-14 is a arm64 runner
-        platform: [ubuntu-latest, windows-latest, macos-12, macos-14]
+        # macos-13 is an intel runner, macos-14 is a arm64 runner
+        platform: [ubuntu-latest, windows-latest, macos-13, macos-14]
 
     steps:
       - name: Checkout source
@@ -23,7 +23,7 @@ jobs:
           submodules: recursive
 
       - name: Set up Conda
-        uses: conda-incubator/setup-miniconda@v3.0.4
+        uses: conda-incubator/setup-miniconda@v3.1.0
         with:
             channels: conda-forge
             miniforge-version: latest
@@ -45,7 +45,7 @@ jobs:
 
       - name: Install clang
         shell: "bash -l {0}"
-        if: matrix.platform == 'macos-12'
+        if: matrix.platform == 'macos-13'
         run: |
           conda activate env
           conda install -y 'clang>=12.0.1,<17'
@@ -70,14 +70,23 @@ jobs:
             conda activate env
             python -m pip install -v ".[pcodec]"
 
+      - 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
 
       # 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 "zfpy>=1" "numpy<2"
+          python -m pip install -v ".[zfpy]"
 
       - name: List installed packages
         shell: "bash -l {0}"

.github/workflows/wheel.yaml

@@ -13,8 +13,8 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        # macos-12 is an intel runner, macos-14 is a arm64 runner
-        os: [ubuntu-latest, windows-latest, macos-12, macos-14]
+        # macos-13 is an intel runner, macos-14 is a arm64 runner
+        os: [ubuntu-latest, windows-latest, macos-13, macos-14]
     env:
       CIBW_TEST_COMMAND: python -c "import numcodecs"
       CIBW_BUILD: "cp311-* cp312-* cp313-*"

.pre-commit-config.yaml

@@ -15,7 +15,7 @@ repos:
     - id: debug-statements
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.7.1
+    rev: v0.7.2
     hooks:
     - id: ruff
       args: ["--fix", "--show-fixes"]

.readthedocs.yaml

@@ -7,6 +7,9 @@ build:
   os: ubuntu-20.04
   tools:
     python: "3.12"
+  jobs:
+    post_install:
+      - python -m pip install --pre 'zarr'
 
 sphinx:
   configuration: docs/conf.py
@@ -19,3 +22,4 @@ python:
         - docs
         - msgpack
         - zfpy
+        - crc32c

docs/api.rst

@@ -10,3 +10,4 @@ API reference
     checksum32
     abc
     registry
+    zarr3

docs/release.rst

@@ -22,8 +22,10 @@ Fix
 
 Enhancements
 ~~~~~~~~~~~~
-* Add Crc32c checksum codec
+* Add Crc32c checksum codec.
   By :user:`Norman Rzepka <normanrz>`, :issue:`613`.
+* Add codec wrappers for Zarr 3.
+  By :user:`Norman Rzepka <normanrz>`, :issue:`524`
 
 Maintenance
 ~~~~~~~~~~~

docs/zarr3.rst

@@ -0,0 +1,99 @@
+Zarr 3 codecs
+=============
+.. automodule:: numcodecs.zarr3
+
+
+Bytes-to-bytes codecs
+---------------------
+.. autoclass:: Blosc()
+
+    .. autoattribute:: codec_name
+
+.. autoclass:: LZ4()
+
+    .. autoattribute:: codec_name
+
+.. autoclass:: Zstd()
+
+    .. autoattribute:: codec_name
+
+.. autoclass:: Zlib()
+
+    .. autoattribute:: codec_name
+
+.. autoclass:: GZip()
+
+    .. autoattribute:: codec_name
+
+.. autoclass:: BZ2()
+
+    .. autoattribute:: codec_name
+
+.. autoclass:: LZMA()
+
+    .. autoattribute:: codec_name
+
+.. autoclass:: Shuffle()
+
+    .. autoattribute:: codec_name
+
+
+Array-to-array codecs
+---------------------
+.. autoclass:: Delta()
+
+    .. autoattribute:: codec_name
+
+.. autoclass:: BitRound()
+
+    .. autoattribute:: codec_name
+
+.. autoclass:: FixedScaleOffset()
+
+    .. autoattribute:: codec_name
+
+.. autoclass:: Quantize()
+
+    .. autoattribute:: codec_name
+
+.. autoclass:: PackBits()
+
+    .. autoattribute:: codec_name
+
+.. autoclass:: AsType()
+
+    .. autoattribute:: codec_name
+
+
+Bytes-to-bytes checksum codecs
+------------------------------
+.. autoclass:: CRC32()
+
+    .. autoattribute:: codec_name
+
+.. autoclass:: CRC32C()
+
+    .. autoattribute:: codec_name
+
+.. autoclass:: Adler32()
+
+    .. autoattribute:: codec_name
+
+.. autoclass:: Fletcher32()
+
+    .. autoattribute:: codec_name
+
+.. autoclass:: JenkinsLookup3()
+
+    .. autoattribute:: codec_name
+
+
+Array-to-bytes codecs
+---------------------
+.. autoclass:: PCodec()
+
+    .. autoattribute:: codec_name
+
+.. autoclass:: ZFPY()
+
+    .. autoattribute:: codec_name

numcodecs/tests/test_compat.py

@@ -64,6 +64,9 @@ def test_ensure_bytes_invalid_inputs():
             ensure_bytes(e)
 
 
+@pytest.mark.filterwarnings(
+    "ignore:The 'u' type code is deprecated and will be removed in Python 3.16"
+)
 def test_ensure_contiguous_ndarray_invalid_inputs():
     # object array not allowed
     a = np.array(['Xin chào thế giới'], dtype=object)

numcodecs/tests/test_fixedscaleoffset.py

@@ -36,12 +36,20 @@ def test_encode_decode():
         check_encode_decode(arr, codec, precision=precision)
 
 
-def test_encode():
+@pytest.mark.parametrize(
+    ("offset", "scale", "expected"),
+    [
+        (1000, 10, [0, 6, 11, 17, 22, 28, 33, 39, 44, 50]),
+        (1002.5, 10, [-25, -19, -14, -8, -3, 3, 8, 14, 19, 25]),
+        (1000, 0.5, [0, 0, 1, 1, 1, 1, 2, 2, 2, 2]),
+    ],
+)
+def test_encode(offset: float, scale: float, expected: list[int]):
     dtype = '<f8'
-    astype = '|u1'
-    codec = FixedScaleOffset(scale=10, offset=1000, dtype=dtype, astype=astype)
-    arr = np.linspace(1000, 1001, 10, dtype=dtype)
-    expect = np.array([0, 1, 2, 3, 4, 6, 7, 8, 9, 10], dtype=astype)
+    astype = np.int16
+    codec = FixedScaleOffset(scale=scale, offset=offset, dtype=dtype, astype=astype)
+    arr = np.linspace(1000, 1005, 10, dtype=dtype)
+    expect = np.array(expected, dtype=astype)
     actual = codec.encode(arr)
     assert_array_equal(expect, actual)
     assert np.dtype(astype) == actual.dtype

numcodecs/tests/test_msgpacks.py

@@ -55,6 +55,9 @@ def test_backwards_compatibility():
     check_backwards_compatibility(codec.codec_id, arrays, [codec])
 
 
+@pytest.mark.filterwarnings(
+    "ignore:Creating an ndarray from ragged nested sequences .* is deprecated.*"
+)
 @pytest.mark.parametrize(
     ("input_data", "dtype"),
     [