Merge branch 'main' into kyle/object-store

.github/workflows/test.yml

@@ -102,6 +102,11 @@ jobs:
     - name: Run Tests
       run: |
         hatch env run --env ${{ matrix.dependency-set }} run
+    - name: Upload coverage
+      uses: codecov/codecov-action@v5
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+        verbose: true # optional (default = false)
 
   doctests:
     name: doctests

changes/2665.feature.rst

@@ -0,0 +1 @@
+Adds functions for concurrently creating multiple arrays and groups.

changes/2847.fix.rst

@@ -0,0 +1 @@
+Fixed a bug where ``ArrayV2Metadata`` could save ``filters`` as an empty array.

changes/2851.bugfix.rst

@@ -0,0 +1 @@
+Fix a bug when setting values of a smaller last chunk.

docs/developers/contributing.rst

@@ -230,6 +230,27 @@ during development at `http://0.0.0.0:8000/ <http://0.0.0.0:8000/>`_. This can b
 
     $ hatch --env docs run serve
 
+.. _changelog:
+
+Changelog
+~~~~~~~~~
+
+zarr-python uses `towncrier`_ to manage release notes. Most pull requests should
+include at least one news fragment describing the changes. To add a release
+note, you'll need the GitHub issue or pull request number and the type of your
+change (``feature``, ``bugfix``, ``doc``, ``removal``, ``misc``). With that, run
+```towncrier create``` with your development environment, which will prompt you
+for the issue number, change type, and the news text::
+
+   towncrier create
+
+Alternatively, you can manually create the files in the ``changes`` directory
+using the naming convention ``{issue-number}.{change-type}.rst``.
+
+See the `towncrier`_ docs for more.
+
+.. _towncrier: https://towncrier.readthedocs.io/en/stable/tutorial.html
+
 Development best practices, policies and procedures
 ---------------------------------------------------
 

docs/quickstart.rst

@@ -119,6 +119,28 @@ Zarr allows you to create hierarchical groups, similar to directories::
 
 This creates a group with two datasets: ``foo`` and ``bar``.
 
+Batch Hierarchy Creation
+~~~~~~~~~~~~~~~~~~~~~~~~
+
+Zarr provides tools for creating a collection of arrays and groups with a single function call.
+Suppose we want to copy existing groups and arrays into a new storage backend:
+
+    >>> # Create nested groups and add arrays
+    >>> root = zarr.group("data/example-3.zarr", attributes={'name': 'root'})
+    >>> foo = root.create_group(name="foo")
+    >>> bar = root.create_array(
+    ...     name="bar", shape=(100, 10), chunks=(10, 10), dtype="f4"
+    ... )
+    >>> nodes = {'': root.metadata} | {k: v.metadata for k,v in root.members()}
+    >>> print(nodes)
+    >>> from zarr.storage import MemoryStore
+    >>> new_nodes = dict(zarr.create_hierarchy(store=MemoryStore(), nodes=nodes))
+    >>> new_root = new_nodes['']
+    >>> assert new_root.attrs == root.attrs
+
+Note that :func:`zarr.create_hierarchy` will only initialize arrays and groups -- copying array data must
+be done in a separate step.
+
 Persistent Storage
 ------------------
 

docs/release-notes.rst

@@ -3,6 +3,45 @@ Release notes
 
 .. towncrier release notes start
 
+3.0.3 (2025-02-14)
+------------------
+
+Features
+~~~~~~~~
+
+- Improves performance of FsspecStore.delete_dir for remote filesystems supporting concurrent/batched deletes, e.g., s3fs. (:issue:`2661`)
+- Added :meth:`zarr.config.enable_gpu` to update Zarr's configuration to use GPUs. (:issue:`2751`)
+- Avoid reading chunks during writes where possible. :issue:`757` (:issue:`2784`)
+- :py:class:`LocalStore` learned to ``delete_dir``. This makes array and group deletes more efficient. (:issue:`2804`)
+- Add `zarr.testing.strategies.array_metadata` to generate ArrayV2Metadata and ArrayV3Metadata instances. (:issue:`2813`)
+- Add arbitrary `shards` to Hypothesis strategy for generating arrays. (:issue:`2822`)
+
+
+Bugfixes
+~~~~~~~~
+
+- Fixed bug with Zarr using device memory, instead of host memory, for storing metadata when using GPUs. (:issue:`2751`)
+- The array returned by ``zarr.empty`` and an empty ``zarr.core.buffer.cpu.NDBuffer`` will now be filled with the
+  specified fill value, or with zeros if no fill value is provided.
+  This fixes a bug where Zarr format 2 data with no fill value was written with un-predictable chunk sizes. (:issue:`2755`)
+- Fix zip-store path checking for stores with directories listed as files. (:issue:`2758`)
+- Use removeprefix rather than replace when removing filename prefixes in `FsspecStore.list` (:issue:`2778`)
+- Enable automatic removal of `needs release notes` with labeler action (:issue:`2781`)
+- Use the proper label config (:issue:`2785`)
+- Alters the behavior of ``create_array`` to ensure that any groups implied by the array's name are created if they do not already exist. Also simplifies the type signature for any function that takes an ArrayConfig-like object. (:issue:`2795`)
+- Enitialise empty chunks to the default fill value during writing and add default fill values for datetime, timedelta, structured, and other (void* fixed size) data types (:issue:`2799`)
+- Ensure utf8 compliant strings are used to construct numpy arrays in property-based tests (:issue:`2801`)
+- Fix pickling for ZipStore (:issue:`2807`)
+- Update numcodecs to not overwrite codec configuration ever. Closes :issue:`2800`. (:issue:`2811`)
+- Fix fancy indexing (e.g. arr[5, [0, 1]]) with the sharding codec (:issue:`2817`)
+
+
+Improved Documentation
+~~~~~~~~~~~~~~~~~~~~~~
+
+- Added new user guide on :ref:`user-guide-gpu`. (:issue:`2751`)
+
+
 3.0.2 (2025-01-31)
 ------------------
 

docs/user-guide/config.rst

@@ -32,6 +32,7 @@ Configuration options include the following:
 - Whether empty chunks are written to storage ``array.write_empty_chunks``
 - Async and threading options, e.g. ``async.concurrency`` and ``threading.max_workers``
 - Selections of implementations of codecs, codec pipelines and buffers
+- Enabling GPU support with ``zarr.config.enable_gpu()``. See :ref:`user-guide-gpu` for more.
 
 For selecting custom implementations of codecs, pipelines, buffers and ndbuffers,
 first register the implementations in the registry and then select them in the config.

docs/user-guide/gpu.rst

@@ -0,0 +1,37 @@
+.. _user-guide-gpu:
+
+Using GPUs with Zarr
+====================
+
+Zarr can use GPUs to accelerate your workload by running
+:meth:`zarr.config.enable_gpu`.
+
+.. note::
+
+   `zarr-python` currently supports reading the ndarray data into device (GPU)
+   memory as the final stage of the codec pipeline. Data will still be read into
+   or copied to host (CPU) memory for encoding and decoding.
+
+   In the future, codecs will be available compressing and decompressing data on
+   the GPU, avoiding the need to move data between the host and device for
+   compression and decompression.
+
+Reading data into device memory
+-------------------------------
+
+:meth:`zarr.config.enable_gpu` configures Zarr to use GPU memory for the data
+buffers used internally by Zarr.
+
+.. code-block:: python
+
+   >>> import zarr
+   >>> import cupy as cp  # doctest: +SKIP
+   >>> zarr.config.enable_gpu()  # doctest: +SKIP
+   >>> store = zarr.storage.MemoryStore()  # doctest: +SKIP
+   >>> z = zarr.create_array(  # doctest: +SKIP
+   ...     store=store, shape=(100, 100), chunks=(10, 10), dtype="float32",
+   ... )
+   >>> type(z[:10, :10])  # doctest: +SKIP
+   cupy.ndarray
+
+Note that the output type is a ``cupy.ndarray`` rather than a NumPy array.

docs/user-guide/groups.rst

@@ -75,6 +75,31 @@ For more information on groups see the :class:`zarr.Group` API docs.
 
 .. _user-guide-diagnostics:
 
+Batch Group Creation
+--------------------
+
+You can also create multiple groups concurrently with a single function call. :func:`zarr.create_hierarchy` takes
+a :class:`zarr.storage.Store` instance and a dict of ``key : metadata`` pairs, parses that dict, and
+writes metadata documents to storage:
+
+   >>> from zarr import create_hierarchy
+   >>> from zarr.core.group import GroupMetadata
+   >>> from zarr.storage import LocalStore
+   >>> node_spec = {'a/b/c': GroupMetadata()}
+   >>> nodes_created = dict(create_hierarchy(store=LocalStore(root='data'), nodes=node_spec))
+   >>> print(sorted(nodes_created.items(), key=lambda kv: len(kv[0])))
+   [('', <Group file://data>), ('a', <Group file://data/a>), ('a/b', <Group file://data/a/b>), ('a/b/c', <Group file://data/a/b/c>)]
+
+Note that we only specified a single group named ``a/b/c``, but 4 groups were created. These additional groups
+were created to ensure that the desired node ``a/b/c`` is connected to the root group ``''`` by a sequence
+of intermediate groups. :func:`zarr.create_hierarchy` normalizes the ``nodes`` keyword argument to
+ensure that the resulting hierarchy is complete, i.e. all groups or arrays are connected to the root
+of the hierarchy via intermediate groups.
+
+Because :func:`zarr.create_hierarchy` concurrently creates metadata documents, it's more efficient
+than repeated calls to :func:`create_group` or :func:`create_array`, provided you can statically define
+the metadata for the groups and arrays you want to create.
+
 Array and group diagnostics
 ---------------------------
 

docs/user-guide/index.rst

@@ -23,6 +23,7 @@ Advanced Topics
     performance
     consolidated_metadata
     extending
+    gpu
 
 
 .. Coming soon

pyproject.toml

@@ -214,11 +214,7 @@ dependencies = [
     'donfig @ git+https://github.com/pytroll/donfig',
     'obstore @ git+https://github.com/developmentseed/obstore@main#subdirectory=obstore',
     # test deps
-    'hypothesis',
-    'pytest',
-    'pytest-cov',
-    'pytest-asyncio',
-    'moto[s3]',
+    'zarr[test]',
 ]
 
 [tool.hatch.envs.upstream.env-vars]
@@ -230,6 +226,9 @@ PIP_PRE = "1"
 run = "pytest --verbose"
 run-mypy = "mypy src"
 run-hypothesis = "pytest --hypothesis-profile ci tests/test_properties.py tests/test_store/test_stateful*"
+run-coverage = "pytest --cov-config=pyproject.toml --cov=pkg --cov-report xml --cov=src --junitxml=junit.xml -o junit_family=legacy"
+run-coverage-gpu = "pip install cupy-cuda12x && pytest -m gpu --cov-config=pyproject.toml --cov=pkg --cov-report xml --cov=src --junitxml=junit.xml -o junit_family=legacy"
+run-coverage-html = "pytest --cov-config=pyproject.toml --cov=pkg --cov-report html --cov=src"
 list-env = "pip list"
 
 [tool.hatch.envs.min_deps]
@@ -249,18 +248,16 @@ dependencies = [
     'typing_extensions==4.9.*',
     'donfig==0.8.*',
     # test deps
-    'hypothesis',
-    'pytest',
-    'pytest-cov',
-    'pytest-asyncio',
-    'moto[s3]',
+    'zarr[test]',
 ]
 
 [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"
-
+run-coverage = "pytest --cov-config=pyproject.toml --cov=pkg --cov-report xml --cov=src --junitxml=junit.xml -o junit_family=legacy"
+run-coverage-gpu = "pip install cupy-cuda12x && pytest -m gpu --cov-config=pyproject.toml --cov=pkg --cov-report xml --cov=src --junitxml=junit.xml -o junit_family=legacy"
+run-coverage-html = "pytest --cov-config=pyproject.toml --cov=pkg --cov-report html --cov=src"
 
 [tool.ruff]
 line-length = 100

src/zarr/__init__.py

@@ -8,6 +8,7 @@
     create,
     create_array,
     create_group,
+    create_hierarchy,
     empty,
     empty_like,
     full,
@@ -50,6 +51,7 @@
     "create",
     "create_array",
     "create_group",
+    "create_hierarchy",
     "empty",
     "empty_like",
     "full",

src/zarr/api/asynchronous.py

@@ -10,7 +10,7 @@
 from typing_extensions import deprecated
 
 from zarr.core.array import Array, AsyncArray, create_array, get_array_metadata
-from zarr.core.array_spec import ArrayConfig, ArrayConfigLike
+from zarr.core.array_spec import ArrayConfig, ArrayConfigLike, ArrayConfigParams
 from zarr.core.buffer import NDArrayLike
 from zarr.core.common import (
     JSON,
@@ -23,7 +23,12 @@
     _warn_write_empty_chunks_kwarg,
     parse_dtype,
 )
-from zarr.core.group import AsyncGroup, ConsolidatedMetadata, GroupMetadata
+from zarr.core.group import (
+    AsyncGroup,
+    ConsolidatedMetadata,
+    GroupMetadata,
+    create_hierarchy,
+)
 from zarr.core.metadata import ArrayMetadataDict, ArrayV2Metadata, ArrayV3Metadata
 from zarr.core.metadata.v2 import _default_compressor, _default_filters
 from zarr.errors import NodeTypeValidationError
@@ -48,6 +53,7 @@
     "copy_store",
     "create",
     "create_array",
+    "create_hierarchy",
     "empty",
     "empty_like",
     "full",
@@ -856,7 +862,7 @@ async def create(
     codecs: Iterable[Codec | dict[str, JSON]] | None = None,
     dimension_names: Iterable[str] | None = None,
     storage_options: dict[str, Any] | None = None,
-    config: ArrayConfig | ArrayConfigLike | None = None,
+    config: ArrayConfigLike | None = None,
     **kwargs: Any,
 ) -> AsyncArray[ArrayV2Metadata] | AsyncArray[ArrayV3Metadata]:
     """Create an array.
@@ -1018,7 +1024,7 @@ async def create(
         mode = "a"
     store_path = await make_store_path(store, path=path, mode=mode, storage_options=storage_options)
 
-    config_dict: ArrayConfigLike = {}
+    config_dict: ArrayConfigParams = {}
 
     if write_empty_chunks is not None:
         if config is not None: