Merge branch 'main' into minor-contrib-improvement

Author: d-v-b

.github/dependabot.yml

@@ -1,15 +1,7 @@
 ---
 version: 2
 updates:
-  # Updates for v3 branch (the default branch)
-  - package-ecosystem: "pip"
-    directory: "/"
-    schedule:
-      interval: "daily"
-    groups:
-      actions:
-        patterns:
-          - "*"
+  # Updates for main
   - package-ecosystem: "github-actions"
     directory: "/"
     schedule:
@@ -19,19 +11,19 @@ updates:
         patterns:
           - "*"
 
-  # Same updates, but for main branch
+  # Updates for support/v2 branch
   - package-ecosystem: "pip"
     directory: "/"
-    target-branch: "main"
+    target-branch: "support/v2"
     schedule:
-      interval: "daily"
+      interval: "weekly"
     groups:
       requirements:
         patterns:
           - "*"
   - package-ecosystem: "github-actions"
     directory: "/"
-    target-branch: "main"
+    target-branch: "support/v2"
     schedule:
       interval: "weekly"
     groups:

.github/labeler.yml

@@ -1,2 +1,2 @@
 needs release notes:
-- all: ['!docs/release.rst']
+- all: ['!docs/release-notes.rst']

.github/workflows/needs_release_notes.yml

@@ -8,7 +8,7 @@ jobs:
     if: ${{ github.event.pull_request.user.login != 'dependabot[bot]' }} && ${{ github.event.pull_request.user.login != 'pre-commit-ci[bot]' }}
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/labeler@main
+    - uses: actions/labeler@8558fd74291d67161a8a78ce36a881fa63b766a9  # v5.0.0
       with:
         repo-token: ${{ secrets.GITHUB_TOKEN }}
         sync-labels: true

.pre-commit-config.yaml

@@ -6,7 +6,7 @@ ci:
 default_stages: [pre-commit, pre-push]
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.8.6
+    rev: v0.9.1
     hooks:
     - id: ruff
       args: ["--fix", "--show-fixes"]

docs/conf.py

@@ -15,15 +15,12 @@
 
 import os
 import sys
+from importlib.metadata import version as get_version
 from typing import Any
 
 import sphinx
 import sphinx.application
 
-from importlib.metadata import version as get_version
-
-import sphinx
-
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.

docs/release-notes.rst

@@ -4,30 +4,58 @@ Release notes
 Unreleased
 ----------
 
-New features
-~~~~~~~~~~~~
+Bug fixes
+~~~~~~~~~
+
+Features
+~~~~~~~~
+
+Documentation
+~~~~~~~~~~~~~
+
+Other
+~~~~~
+
+3.0.1 (Jan. 17, 2025)
+---------------------
 
 Bug fixes
 ~~~~~~~~~
 * Fixes ``order`` argument for Zarr format 2 arrays (:issue:`2679`).
 
-* Fixes a bug that prevented reading Zarr format 2 data with consolidated metadata written using ``zarr-python`` version 2 (:issue:`2694`).
+* Fixes a bug that prevented reading Zarr format 2 data with consolidated
+  metadata written using ``zarr-python`` version 2 (:issue:`2694`).
+
+* Ensure that compressor=None results in no compression when writing Zarr
+  format 2 data (:issue:`2708`).
+
+* Fix for empty consolidated metadata dataset: backwards compatibility with
+  Zarr-Python 2 (:issue:`2695`).
+
+Documentation
+~~~~~~~~~~~~~
+* Add v3.0.0 release announcement banner (:issue:`2677`).
 
-* Ensure that compressor=None results in no compression when writing Zarr format 2 data (:issue:`2708`)
+* Quickstart guide alignment with V3 API (:issue:`2697`).
 
-Behaviour changes
-~~~~~~~~~~~~~~~~~
+* Fix doctest failures related to numcodecs 0.15 (:issue:`2727`).
 
 Other
 ~~~~~
 * Removed some unnecessary files from the source distribution
-  to reduce its size. (:issue:`2686`)
+  to reduce its size. (:issue:`2686`).
+
+* Enable codecov in GitHub actions (:issue:`2682`).
+
+* Speed up hypothesis tests (:issue:`2650`).
+
+* Remove multiple imports for an import name (:issue:`2723`).
 
 
 .. _release_3.0.0:
 
-3.0.0
------
+3.0.0 (Jan. 9, 2025)
+--------------------
 
 3.0.0 is a new major release of Zarr-Python, with many breaking changes.
 See the :ref:`v3 migration guide` for a listing of what's changed.

docs/user-guide/arrays.rst

@@ -241,7 +241,7 @@ built-in delta filter::
    >>> data = np.arange(100000000, dtype='int32').reshape(10000, 10000)
    >>> z = zarr.create_array(store='data/example-7.zarr', shape=data.shape, dtype=data.dtype, chunks=(1000, 1000), compressors=compressors)
    >>> z.compressors
-   (_make_bytes_bytes_codec.<locals>._Codec(codec_name='numcodecs.lzma', codec_config={'id': 'lzma', 'filters': [{'id': 3, 'dist': 4}, {'id': 33, 'preset': 1}]}),)
+   (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.::
@@ -292,7 +292,7 @@ Here is an example using a delta filter with the Blosc compressor::
    Order              : C
    Read-only          : False
    Store type         : LocalStore
-   Filters            : (_make_array_array_codec.<locals>._Codec(codec_name='numcodecs.delta', codec_config={'id': 'delta', 'dtype': 'int32'}),)
+   Filters            : (Delta(codec_name='numcodecs.delta', codec_config={'dtype': 'int32'}),)
    Serializer         : BytesCodec(endian=<Endian.little: 'little'>)
    Compressors        : (BloscCodec(typesize=4, cname=<BloscCname.zstd: 'zstd'>, clevel=1, shuffle=<BloscShuffle.shuffle: 'shuffle'>, blocksize=0),)
    No. bytes          : 400000000 (381.5M)

pyproject.toml

@@ -230,11 +230,12 @@ See Spec 0000 for details and drop schedule: https://scientific-python.org/specs
 """
 python = "3.11"
 dependencies = [
+    'zarr[remote]',
     'packaging==22.*',
     'numpy==1.25.*',
     'numcodecs==0.14.*',  # 0.14 needed for zarr3 codecs
-    'fsspec==2022.10.0',
-    's3fs==2022.10.0',
+    'fsspec==2023.10.0',
+    's3fs==2023.10.0',
     'universal_pathlib==0.0.22',
     'typing_extensions==4.9.*',
     'donfig==0.8.*',
@@ -328,8 +329,6 @@ ignore = [
     "Q003",
     "COM812",
     "COM819",
-    "ISC001",
-    "ISC002",
 ]
 
 [tool.ruff.lint.extend-per-file-ignores]

src/zarr/codecs/sharding.py

@@ -86,9 +86,9 @@ async def get(
         self, prototype: BufferPrototype, byte_range: ByteRequest | None = None
     ) -> Buffer | None:
         assert byte_range is None, "byte_range is not supported within shards"
-        assert (
-            prototype == default_buffer_prototype()
-        ), f"prototype is not supported within shards currently. diff: {prototype} != {default_buffer_prototype()}"
+        assert prototype == default_buffer_prototype(), (
+            f"prototype is not supported within shards currently. diff: {prototype} != {default_buffer_prototype()}"
+        )
         return self.shard_dict.get(self.chunk_coords)
 
 

src/zarr/core/array.py

@@ -112,7 +112,6 @@
     _parse_bytes_bytes_codec,
     get_pipeline_class,
 )
-from zarr.storage import StoreLike
 from zarr.storage._common import StorePath, ensure_no_existing_node, make_store_path
 
 if TYPE_CHECKING: