Merge branch 'main' into refactor-open-group

Author: d-v-b

.github/workflows/nightly_wheels.yml

@@ -0,0 +1,37 @@
+name: Nightly Wheels
+
+on:
+  schedule:
+    # Run nightly at 2 AM UTC
+    - cron: '0 2 * * *'
+  workflow_dispatch:
+
+jobs:
+  build_and_upload_nightly:
+    name: Build and upload nightly wheels
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v5
+        with:
+          submodules: true
+          fetch-depth: 0
+
+      - uses: actions/setup-python@v6
+        name: Install Python
+        with:
+          python-version: '3.13'
+
+      - name: Install build dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install hatch
+
+      - name: Build wheel and sdist
+        run: hatch build
+
+      - name: Upload nightly wheels
+        uses: scientific-python/upload-nightly-action@b36e8c0c10dbcfd2e05bf95f17ef8c14fd708dbf
+        with:
+          artifacts_path: dist
+          anaconda_nightly_upload_token: ${{ secrets.ANACONDA_ORG_UPLOAD_TOKEN }}

changes/3422.bugfix.rst

@@ -0,0 +1,4 @@
+Fix a potential race condition when using :func:`zarr.create_array` with the ``data`` parameter
+set to a NumPy array. Previously Zarr was iterating over the newly created array with a granularity
+that was too low. Now Zarr chooses a granularity that matches the size of the stored objects for
+that array.

changes/3448.bugfix.rst

@@ -0,0 +1,3 @@
+Setting ``fill_value`` to a float like ``0.0`` when the data type of the array is an integer is a common
+mistake. This change lets Zarr Python read arrays with this erroneous metadata, although Zarr Python
+will not create such arrays.

changes/3449.misc.rst

@@ -0,0 +1 @@
+Publish nightly wheels to https://anaconda.org/scientific-python-nightly-wheels/.

docs/user-guide/installation.rst

@@ -42,6 +42,19 @@ Zarr is also published to `conda-forge <https://conda-forge.org>`_. Install it u
 Conda does not support optional dependencies, so you will have to manually install any packages
 needed to enable extra functionality.
 
+Nightly wheels
+--------------
+
+Development wheels are built nightly and published to the `scientific-python-nightly-wheels <https://anaconda.org/scientific-python-nightly-wheels>`_ index. To install the latest nightly build:
+
+.. code-block:: console
+
+    $ pip install --pre \
+        --extra-index-url https://pypi.anaconda.org/scientific-python-nightly-wheels/simple \
+        zarr
+
+Note that nightly wheels may be unstable and are intended for testing purposes.
+
 Dependency support
 ------------------
 Zarr has endorsed `Scientific-Python SPEC 0 <https://scientific-python.org/specs/spec-0000/>`_ and now follows the version support window as outlined below:

src/zarr/api/asynchronous.py

@@ -250,14 +250,23 @@ async def consolidate_metadata(
 
 
 async def copy(*args: Any, **kwargs: Any) -> tuple[int, int, int]:
+    """
+    Not implemented.
+    """
     raise NotImplementedError
 
 
 async def copy_all(*args: Any, **kwargs: Any) -> tuple[int, int, int]:
+    """
+    Not implemented.
+    """
     raise NotImplementedError
 
 
 async def copy_store(*args: Any, **kwargs: Any) -> tuple[int, int, int]:
+    """
+    Not implemented.
+    """
     raise NotImplementedError
 
 

src/zarr/api/synchronous.py

@@ -112,14 +112,23 @@ def consolidate_metadata(
 
 
 def copy(*args: Any, **kwargs: Any) -> tuple[int, int, int]:
+    """
+    Not implemented.
+    """
     return sync(async_api.copy(*args, **kwargs))
 
 
 def copy_all(*args: Any, **kwargs: Any) -> tuple[int, int, int]:
+    """
+    Not implemented.
+    """
     return sync(async_api.copy_all(*args, **kwargs))
 
 
 def copy_store(*args: Any, **kwargs: Any) -> tuple[int, int, int]:
+    """
+    Not implemented.
+    """
     return sync(async_api.copy_store(*args, **kwargs))
 
 

src/zarr/core/array.py

@@ -4421,7 +4421,7 @@ async def _copy_arraylike_region(chunk_coords: slice, _data: NDArrayLike) -> Non
 
             # Stream data from the source array to the new array
             await concurrent_map(
-                [(region, data) for region in result._iter_chunk_regions()],
+                [(region, data) for region in result._iter_shard_regions()],
                 _copy_arraylike_region,
                 zarr.core.config.config.get("async.concurrency"),
             )

src/zarr/core/dtype/npy/common.py

@@ -9,6 +9,7 @@
     Any,
     Final,
     Literal,
+    NewType,
     SupportsComplex,
     SupportsFloat,
     SupportsIndex,
@@ -54,6 +55,9 @@
     "generic",
 )
 
+IntishFloat = NewType("IntishFloat", float)
+"""A type for floats that represent integers, like 1.0 (but not 1.1)."""
+
 NumpyEndiannessStr = Literal[">", "<", "="]
 NUMPY_ENDIANNESS_STR: Final = ">", "<", "="
 
@@ -467,6 +471,23 @@ def check_json_int(data: JSON) -> TypeGuard[int]:
     return bool(isinstance(data, int))
 
 
+def check_json_intish_float(data: JSON) -> TypeGuard[IntishFloat]:
+    """
+    Check if a JSON value is an "intish float", i.e. a float that represents an integer, like 0.0.
+
+    Parameters
+    ----------
+    data : JSON
+        The JSON value to check.
+
+    Returns
+    -------
+    Bool
+        True if the data is an intish float, False otherwise.
+    """
+    return isinstance(data, float) and data.is_integer()
+
+
 def check_json_str(data: JSON) -> TypeGuard[str]:
     """
     Check if a JSON value is a string.

src/zarr/core/dtype/npy/int.py

@@ -25,6 +25,7 @@
 )
 from zarr.core.dtype.npy.common import (
     check_json_int,
+    check_json_intish_float,
     endianness_to_numpy_str,
     get_endianness_from_numpy_dtype,
 )
@@ -206,6 +207,8 @@ def from_json_scalar(self, data: JSON, *, zarr_format: ZarrFormat) -> TIntScalar
         """
         if check_json_int(data):
             return self._cast_scalar_unchecked(data)
+        if check_json_intish_float(data):
+            return self._cast_scalar_unchecked(int(data))
         raise TypeError(f"Invalid type: {data}. Expected an integer.")
 
     def to_json_scalar(self, data: object, *, zarr_format: ZarrFormat) -> int: