Merge branch 'main' into feature/append-v3

.github/workflows/test.yml

@@ -43,3 +43,35 @@ jobs:
     - name: Run Tests
       run: |
         hatch env run --env test.py${{ matrix.python-version }}-${{ matrix.numpy-version }}-${{ matrix.dependency-set }} run
+
+  test-upstream-and-min-deps:
+    name: py=${{ matrix.python-version }}-${{ matrix.dependency-set }}
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.11', "3.13"]
+        dependency-set: ["upstream", "min_deps"]
+        exclude:
+          - python-version: "3.13"
+            dependency-set: min_deps
+          - python-version: "3.11"
+            dependency-set: upstream
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+        cache: 'pip'
+    - name: Install Hatch
+      run: |
+        python -m pip install --upgrade pip 
+        pip install hatch
+    - name: Set Up Hatch Env
+      run: |
+        hatch env create ${{ matrix.dependency-set }}
+        hatch env run -e ${{ matrix.dependency-set }} list-env
+    - name: Run Tests
+      run: |
+        hatch env run --env ${{ matrix.dependency-set }} run

.pre-commit-config.yaml

@@ -7,7 +7,7 @@ default_language_version:
   python: python3
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.6.9
+    rev: v0.7.0
     hooks:
     - id: ruff
       args: ["--fix", "--show-fixes"]
@@ -22,7 +22,7 @@ repos:
     hooks:
     - id: check-yaml
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.11.2
+    rev: v1.12.1
     hooks:
       - id: mypy
         files: src|tests

docs/guide/storage.rst

@@ -72,7 +72,7 @@ that implements the `AbstractFileSystem` API,
 .. code-block:: python
 
    >>> import zarr
-   >>> store = zarr.storage.RemoteStore("gs://foo/bar", mode="r")
+   >>> store = zarr.storage.RemoteStore.from_url("gs://foo/bar", mode="r")
    >>> zarr.open(store=store)
    <Array <RemoteStore(GCSFileSystem, foo/bar)> shape=(10, 20) dtype=float32>
 

pyproject.toml

@@ -28,12 +28,13 @@ requires-python = ">=3.11"
 dependencies = [
     'asciitree',
     'numpy>=1.25',
-    'numcodecs>=0.10.2',
-    'fsspec>2024',
-    'crc32c',
-    'typing_extensions',
-    'donfig',
+    'numcodecs>=0.13',
+    'fsspec>=2022.10.0',
+    'crc32c>=2.3',
+    'typing_extensions>=4.6',
+    'donfig>=0.8',
 ]
+
 dynamic = [
   "version",
 ]
@@ -98,7 +99,7 @@ extra = [
 ]
 optional = [
     'lmdb',
-    'universal-pathlib',
+    'universal-pathlib>=0.0.22',
 ]
 
 [project.urls]
@@ -183,6 +184,65 @@ features = ['docs']
 build = "cd docs && make html"
 serve = "sphinx-autobuild docs docs/_build --host 0.0.0.0"
 
+[tool.hatch.envs.upstream]
+python = "3.13"
+dependencies = [
+    'numpy',  # from scientific-python-nightly-wheels
+    'numcodecs @ git+https://github.com/zarr-developers/numcodecs',
+    'fsspec @ git+https://github.com/fsspec/filesystem_spec',
+    's3fs @ git+https://github.com/fsspec/s3fs',
+    'universal_pathlib @ git+https://github.com/fsspec/universal_pathlib',
+    'crc32c @ git+https://github.com/ICRAR/crc32c',
+    'typing_extensions @ git+https://github.com/python/typing_extensions',
+    'donfig @ git+https://github.com/pytroll/donfig',
+    # test deps
+    'hypothesis',
+    'pytest',
+    'pytest-cov',
+    'pytest-asyncio',
+    'moto[s3]',
+]
+
+[tool.hatch.envs.upstream.env-vars]
+PIP_INDEX_URL = "https://pypi.anaconda.org/scientific-python-nightly-wheels/simple/"
+PIP_EXTRA_INDEX_URL = "https://pypi.org/simple/"
+PIP_PRE = "1"
+
+[tool.hatch.envs.upstream.scripts]
+run = "pytest --verbose"
+run-mypy = "mypy src"
+run-hypothesis = "pytest --hypothesis-profile ci tests/test_properties.py tests/test_store/test_stateful*"
+list-env = "pip list"
+
+[tool.hatch.envs.min_deps]
+description = """Test environment for minimum supported dependencies
+
+See Spec 0000 for details and drop schedule: https://scientific-python.org/specs/spec-0000/
+"""
+python = "3.11"
+dependencies = [
+    'numpy==1.25.*',
+    'numcodecs==0.13.*',  # 0.13 needed for? (should be 0.11)
+    'fsspec==2022.10.0',
+    's3fs==2022.10.0',
+    'universal_pathlib==0.0.22',
+    'crc32c==2.3.*',
+    'typing_extensions==4.6.*',  # 4.5 needed for @deprecated, 4.6 for Buffer
+    'donfig==0.8.*',
+    # test deps
+    'hypothesis',
+    'pytest',
+    'pytest-cov',
+    'pytest-asyncio',
+    'moto[s3]',
+]
+
+[tool.hatch.envs.min_deps.scripts]
+run = "pytest --verbose"
+run-hypothesis = "pytest --hypothesis-profile ci tests/test_properties.py tests/test_store/test_stateful*"
+list-env = "pip list"
+
+
 [tool.ruff]
 line-length = 100
 force-exclude = true

src/zarr/abc/store.py

@@ -168,7 +168,7 @@ def with_mode(self, mode: AccessModeLiteral) -> Self:
 
         Returns
         -------
-        store:
+        store
             A new store of the same type with the new mode.
 
         Examples

src/zarr/api/asynchronous.py

@@ -712,7 +712,7 @@ async def create(
     dtype: npt.DTypeLike | None = None,
     compressor: dict[str, JSON] | None = None,  # TODO: default and type change
     fill_value: Any | None = 0,  # TODO: need type
-    order: MemoryOrder | None = None,  # TODO: default change
+    order: MemoryOrder | None = None,
     store: str | StoreLike | None = None,
     synchronizer: Any | None = None,
     overwrite: bool = False,
@@ -761,6 +761,7 @@ async def create(
         Default value to use for uninitialized portions of the array.
     order : {'C', 'F'}, optional
         Memory layout to be used within each chunk.
+        Default is set in Zarr's config (`array.order`).
     store : Store or str
         Store or path to directory in file system or name of zip file.
     synchronizer : object, optional
@@ -834,12 +835,6 @@ async def create(
         else:
             chunk_shape = shape
 
-    if order is not None:
-        warnings.warn(
-            "order is deprecated, use config `array.order` instead",
-            DeprecationWarning,
-            stacklevel=2,
-        )
     if synchronizer is not None:
         warnings.warn("synchronizer is not yet implemented", RuntimeWarning, stacklevel=2)
     if chunk_store is not None:
@@ -889,6 +884,7 @@ async def create(
         codecs=codecs,
         dimension_names=dimension_names,
         attributes=attributes,
+        order=order,
         **kwargs,
     )
 

src/zarr/codecs/zstd.py

@@ -3,10 +3,11 @@
 import asyncio
 from dataclasses import dataclass
 from functools import cached_property
-from importlib.metadata import version
 from typing import TYPE_CHECKING
 
+import numcodecs
 from numcodecs.zstd import Zstd
+from packaging.version import Version
 
 from zarr.abc.codec import BytesBytesCodec
 from zarr.core.buffer.cpu import as_numpy_array_wrapper
@@ -43,8 +44,8 @@ class ZstdCodec(BytesBytesCodec):
 
     def __init__(self, *, level: int = 0, checksum: bool = False) -> None:
         # numcodecs 0.13.0 introduces the checksum attribute for the zstd codec
-        _numcodecs_version = tuple(map(int, version("numcodecs").split(".")))
-        if _numcodecs_version < (0, 13, 0):  # pragma: no cover
+        _numcodecs_version = Version(numcodecs.__version__)
+        if _numcodecs_version < Version("0.13.0"):
             raise RuntimeError(
                 "numcodecs version >= 0.13.0 is required to use the zstd codec. "
                 f"Version {_numcodecs_version} is currently installed."

src/zarr/core/array.py

@@ -33,6 +33,7 @@
     ZARRAY_JSON,
     ZATTRS_JSON,
     ChunkCoords,
+    MemoryOrder,
     ShapeLike,
     ZarrFormat,
     concurrent_map,
@@ -203,29 +204,29 @@ class AsyncArray(Generic[T_ArrayMetadata]):
     metadata: T_ArrayMetadata
     store_path: StorePath
     codec_pipeline: CodecPipeline = field(init=False)
-    order: Literal["C", "F"]
+    order: MemoryOrder
 
     @overload
     def __init__(
         self: AsyncArray[ArrayV2Metadata],
         metadata: ArrayV2Metadata | ArrayV2MetadataDict,
         store_path: StorePath,
-        order: Literal["C", "F"] | None = None,
+        order: MemoryOrder | None = None,
     ) -> None: ...
 
     @overload
     def __init__(
         self: AsyncArray[ArrayV3Metadata],
         metadata: ArrayV3Metadata | ArrayV3MetadataDict,
         store_path: StorePath,
-        order: Literal["C", "F"] | None = None,
+        order: MemoryOrder | None = None,
     ) -> None: ...
 
     def __init__(
         self,
         metadata: ArrayMetadata | ArrayMetadataDict,
         store_path: StorePath,
-        order: Literal["C", "F"] | None = None,
+        order: MemoryOrder | None = None,
     ) -> None:
         if isinstance(metadata, dict):
             zarr_format = metadata["zarr_format"]
@@ -261,7 +262,7 @@ async def create(
         attributes: dict[str, JSON] | None = None,
         chunks: ShapeLike | None = None,
         dimension_separator: Literal[".", "/"] | None = None,
-        order: Literal["C", "F"] | None = None,
+        order: MemoryOrder | None = None,
         filters: list[dict[str, JSON]] | None = None,
         compressor: dict[str, JSON] | None = None,
         # runtime
@@ -350,7 +351,7 @@ async def create(
         # v2 only
         chunks: ShapeLike | None = None,
         dimension_separator: Literal[".", "/"] | None = None,
-        order: Literal["C", "F"] | None = None,
+        order: MemoryOrder | None = None,
         filters: list[dict[str, JSON]] | None = None,
         compressor: dict[str, JSON] | None = None,
         # runtime
@@ -382,7 +383,7 @@ async def create(
         # v2 only
         chunks: ShapeLike | None = None,
         dimension_separator: Literal[".", "/"] | None = None,
-        order: Literal["C", "F"] | None = None,
+        order: MemoryOrder | None = None,
         filters: list[dict[str, JSON]] | None = None,
         compressor: dict[str, JSON] | None = None,
         # runtime
@@ -422,7 +423,6 @@ async def create(
             V2 only. V3 arrays cannot have a dimension separator.
         order : Literal["C", "F"], optional
             The order of the array (default is None).
-            V2 only. V3 arrays should not have 'order' parameter.
         filters : list[dict[str, JSON]], optional
             The filters used to compress the data (default is None).
             V2 only. V3 arrays should not have 'filters' parameter.
@@ -471,10 +471,6 @@ async def create(
                 raise ValueError(
                     "dimension_separator cannot be used for arrays with version 3. Use chunk_key_encoding instead."
                 )
-            if order is not None:
-                raise ValueError(
-                    "order cannot be used for arrays with version 3. Use a transpose codec instead."
-                )
             if filters is not None:
                 raise ValueError(
                     "filters cannot be used for arrays with version 3. Use array-to-array codecs instead."
@@ -494,6 +490,7 @@ async def create(
                 dimension_names=dimension_names,
                 attributes=attributes,
                 exists_ok=exists_ok,
+                order=order,
             )
         elif zarr_format == 2:
             if dtype is str or dtype == "str":
@@ -545,6 +542,7 @@ async def _create_v3(
         dtype: npt.DTypeLike,
         chunk_shape: ChunkCoords,
         fill_value: Any | None = None,
+        order: MemoryOrder | None = None,
         chunk_key_encoding: (
             ChunkKeyEncoding
             | tuple[Literal["default"], Literal[".", "/"]]
@@ -588,7 +586,7 @@ async def _create_v3(
             attributes=attributes or {},
         )
 
-        array = cls(metadata=metadata, store_path=store_path)
+        array = cls(metadata=metadata, store_path=store_path, order=order)
         await array._save_metadata(metadata, ensure_parents=True)
         return array
 
@@ -602,16 +600,17 @@ async def _create_v2(
         chunks: ChunkCoords,
         dimension_separator: Literal[".", "/"] | None = None,
         fill_value: None | float = None,
-        order: Literal["C", "F"] | None = None,
+        order: MemoryOrder | None = None,
         filters: list[dict[str, JSON]] | None = None,
         compressor: dict[str, JSON] | None = None,
         attributes: dict[str, JSON] | None = None,
         exists_ok: bool = False,
     ) -> AsyncArray[ArrayV2Metadata]:
         if not exists_ok:
             await ensure_no_existing_node(store_path, zarr_format=2)
+
         if order is None:
-            order = "C"
+            order = parse_indexing_order(config.get("array.order"))
 
         if dimension_separator is None:
             dimension_separator = "."
@@ -627,7 +626,7 @@ async def _create_v2(
             filters=filters,
             attributes=attributes,
         )
-        array = cls(metadata=metadata, store_path=store_path)
+        array = cls(metadata=metadata, store_path=store_path, order=order)
         await array._save_metadata(metadata, ensure_parents=True)
         return array
 
@@ -1236,7 +1235,7 @@ def create(
         # v2 only
         chunks: ChunkCoords | None = None,
         dimension_separator: Literal[".", "/"] | None = None,
-        order: Literal["C", "F"] | None = None,
+        order: MemoryOrder | None = None,
         filters: list[dict[str, JSON]] | None = None,
         compressor: dict[str, JSON] | None = None,
         # runtime
@@ -1432,7 +1431,7 @@ def store_path(self) -> StorePath:
         return self._async_array.store_path
 
     @property
-    def order(self) -> Literal["C", "F"]:
+    def order(self) -> MemoryOrder:
         return self._async_array.order
 
     @property