Merge branch 'main' into update-2874-release-note

Author: d-v-b

.github/workflows/test.yml

@@ -21,20 +21,20 @@ jobs:
     strategy:
       matrix:
         python-version: ['3.11', '3.12', '3.13']
-        numpy-version: ['1.25', '2.2']
+        numpy-version: ['1.26', '2.2']
         dependency-set: ["minimal", "optional"]
         os: ["ubuntu-latest"]
         include:
           - python-version: '3.11'
-            numpy-version: '1.25'
+            numpy-version: '1.26'
             dependency-set: 'optional'
             os: 'macos-latest'
           - python-version: '3.13'
             numpy-version: '2.2'
             dependency-set: 'optional'
             os: 'macos-latest'
           - python-version: '3.11'
-            numpy-version: '1.25'
+            numpy-version: '1.26'
             dependency-set: 'optional'
             os: 'windows-latest'
           - python-version: '3.13'

changes/3228.removal.rst

@@ -0,0 +1,16 @@
+Removes default chunk encoding settings (filters, serializer, compressors) from the global
+configuration object.
+
+This removal is justified on the basis that storing chunk encoding settings in the config required
+a brittle, confusing, and inaccurate categorization of array data types, which was particularly
+unsuitable after the recent addition of new data types that didn't fit naturally into the
+pre-existing categories.
+
+The default chunk encoding is the same (Zstandard compression, and the required object codecs for
+variable length data types), but the chunk encoding is now generated by functions that cannot be
+reconfigured at runtime. Users who relied on setting the default chunk encoding via the global configuration object should
+instead specify the desired chunk encoding explicitly when creating an array.
+
+This change also adds an extra validation step to the creation of Zarr V2 arrays, which ensures that
+arrays with a ``VariableLengthUTF8`` or ``VariableLengthBytes`` data type cannot be created without the
+correct "object codec".

changes/xxxx.feature.rst

@@ -0,0 +1 @@
+The minimum version of NumPy has increased to 1.26.

docs/user-guide/arrays.rst

@@ -246,16 +246,6 @@ built-in delta filter::
    >>> z.compressors
    (LZMA(codec_name='numcodecs.lzma', codec_config={'filters': [{'id': 3, 'dist': 4}, {'id': 33, 'preset': 1}]}),)
 
-The default compressor can be changed by setting the value of the using Zarr's
-:ref:`user-guide-config`, e.g.::
-
-   >>> with zarr.config.set({'array.v2_default_compressor.default': {'id': 'blosc'}}):
-   ...     z = zarr.create_array(store={}, shape=(100000000,), chunks=(1000000,), dtype='int32', zarr_format=2)
-   >>> z.filters
-   ()
-   >>> z.compressors
-   (Blosc(cname='lz4', clevel=5, shuffle=SHUFFLE, blocksize=0),)
-
 To disable compression, set ``compressors=None`` when creating an array, e.g.::
 
    >>> z = zarr.create_array(store='data/example-8.zarr', shape=(100000000,), chunks=(1000000,), dtype='int32', compressors=None)

docs/user-guide/config.rst

@@ -43,25 +43,7 @@ This is the current default configuration::
 
    >>> zarr.config.pprint()
    {'array': {'order': 'C',
-            'v2_default_compressor': {'default': {'checksum': False,
-                                                   'id': 'zstd',
-                                                   'level': 0},
-                                       'variable-length-string': {'checksum': False,
-                                                                  'id': 'zstd',
-                                                                  'level': 0}},
-            'v2_default_filters': {'default': None,
-                                    'variable-length-string': [{'id': 'vlen-utf8'}]},
-            'v3_default_compressors': {'default': [{'configuration': {'checksum': False,
-                                                                        'level': 0},
-                                                      'name': 'zstd'}],
-                                       'variable-length-string': [{'configuration': {'checksum': False,
-                                                                                       'level': 0},
-                                                                     'name': 'zstd'}]},
-            'v3_default_filters': {'default': [], 'variable-length-string': []},
-            'v3_default_serializer': {'default': {'configuration': {'endian': 'little'},
-                                                   'name': 'bytes'},
-                                       'variable-length-string': {'name': 'vlen-utf8'}},
-            'write_empty_chunks': False},
+              'write_empty_chunks': False},
    'async': {'concurrency': 10, 'timeout': None},
    'buffer': 'zarr.buffer.cpu.Buffer',
    'codec_pipeline': {'batch_size': 1,

docs/user-guide/installation.rst

@@ -8,7 +8,7 @@ Required dependencies include:
 
 - `Python <https://docs.python.org/3/>`_ (3.11 or later)
 - `packaging <https://packaging.pypa.io>`_ (22.0 or later)
-- `numpy <https://numpy.org>`_ (1.25 or later)
+- `numpy <https://numpy.org>`_ (1.26 or later)
 - `numcodecs[crc32c] <https://numcodecs.readthedocs.io>`_ (0.14 or later)
 - `typing_extensions <https://typing-extensions.readthedocs.io>`_ (4.9 or later)
 - `donfig <https://donfig.readthedocs.io>`_ (0.8 or later)

pyproject.toml

@@ -33,7 +33,7 @@ requires-python = ">=3.11"
 # If you add a new dependency here, please also add it to .pre-commit-config.yml
 dependencies = [
     'packaging>=22.0',
-    'numpy>=1.25',
+    'numpy>=1.26',
     'numcodecs[crc32c]>=0.14',
     'typing_extensions>=4.9',
     'donfig>=0.8',
@@ -154,7 +154,7 @@ features = ["test"]
 
 [[tool.hatch.envs.test.matrix]]
 python = ["3.11", "3.12", "3.13"]
-numpy = ["1.25", "2.2"]
+numpy = ["1.26", "2.2"]
 deps = ["minimal", "optional"]
 
 [tool.hatch.envs.test.overrides]
@@ -190,7 +190,7 @@ features = ["test", "gpu"]
 
 [[tool.hatch.envs.gputest.matrix]]
 python = ["3.11", "3.12", "3.13"]
-numpy = ["1.25", "2.2"]
+numpy = ["1.26", "2.2"]
 version = ["minimal"]
 
 [tool.hatch.envs.gputest.scripts]
@@ -246,7 +246,7 @@ python = "3.11"
 dependencies = [
     'zarr[remote]',
     'packaging==22.*',
-    'numpy==1.25.*',
+    'numpy==1.26.*',
     'numcodecs==0.14.*',  # 0.14 needed for zarr3 codecs
     'fsspec==2023.10.0',
     's3fs==2023.10.0',