From 8da13336dfa60c2b4412097bc5e58488aebbb66c Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Sun, 31 May 2026 19:28:07 +0200 Subject: [PATCH 1/2] chore(deps): bump the actions group across 1 directory with 8 updates (#176) Bumps the actions group with 8 updates in the / directory: | Package | From | To | | --- | --- | --- | | [prefix-dev/setup-pixi](https://github.com/prefix-dev/setup-pixi) | `0.9.5` | `0.9.6` | | [codecov/codecov-action](https://github.com/codecov/codecov-action) | `6.0.0` | `6.0.1` | | [github/issue-metrics](https://github.com/github/issue-metrics) | `4.2.2` | `4.2.7` | | [j178/prek-action](https://github.com/j178/prek-action) | `2.0.3` | `2.0.4` | | [actions/upload-artifact](https://github.com/actions/upload-artifact) | `7.0.0` | `7.0.1` | | [actions/download-artifact](https://github.com/actions/download-artifact) | `7.0.0` | `8.0.1` | | [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish) | `1.13.0` | `1.14.0` | | [zizmorcore/zizmor-action](https://github.com/zizmorcore/zizmor-action) | `0.5.3` | `0.5.6` | Updates `prefix-dev/setup-pixi` from 0.9.5 to 0.9.6 - [Release notes](https://github.com/prefix-dev/setup-pixi/releases) - [Commits](https://github.com/prefix-dev/setup-pixi/compare/1b2de7f3351f171c8b4dfeb558c639cb58ed4ec0...5185adfbffb4bd703da3010310260805d89ebb11) Updates `codecov/codecov-action` from 6.0.0 to 6.0.1 - [Release notes](https://github.com/codecov/codecov-action/releases) - [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md) - [Commits](https://github.com/codecov/codecov-action/compare/57e3a136b779b570ffcdbf80b3bdc90e7fab3de2...e79a6962e0d4c0c17b229090214935d2e33f8354) Updates `github/issue-metrics` from 4.2.2 to 4.2.7 - [Release notes](https://github.com/github/issue-metrics/releases) - [Commits](https://github.com/github/issue-metrics/compare/c9e9838147fd355dace335ba787f01b6641a400a...1e38d5e62363e14db8019ed7d106b9855bdba6cc) Updates `j178/prek-action` from 2.0.3 to 2.0.4 - [Release notes](https://github.com/j178/prek-action/releases) - [Commits](https://github.com/j178/prek-action/compare/6ad80277337ad479fe43bd70701c3f7f8aa74db3...bdca6f102f98e2b4c7029491a53dfd366469e33d) Updates `actions/upload-artifact` from 7.0.0 to 7.0.1 - [Release notes](https://github.com/actions/upload-artifact/releases) - [Commits](https://github.com/actions/upload-artifact/compare/v7...043fb46d1a93c77aae656e7c1c64a875d1fc6a0a) Updates `actions/download-artifact` from 7.0.0 to 8.0.1 - [Release notes](https://github.com/actions/download-artifact/releases) - [Commits](https://github.com/actions/download-artifact/compare/v7...3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c) Updates `pypa/gh-action-pypi-publish` from 1.13.0 to 1.14.0 - [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases) - [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.13.0...cef221092ed1bacb1cc03d23a2d87d1d172e277b) Updates `zizmorcore/zizmor-action` from 0.5.3 to 0.5.6 - [Release notes](https://github.com/zizmorcore/zizmor-action/releases) - [Commits](https://github.com/zizmorcore/zizmor-action/compare/b1d7e1fb5de872772f31590499237e7cce841e8e...5f14fd08f7cf1cb1609c1e344975f152c7ee938d) --- updated-dependencies: - dependency-name: prefix-dev/setup-pixi dependency-version: 0.9.6 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: codecov/codecov-action dependency-version: 6.0.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: github/issue-metrics dependency-version: 4.2.7 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: j178/prek-action dependency-version: 2.0.4 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: actions/upload-artifact dependency-version: 7.0.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: actions/download-artifact dependency-version: 8.0.1 dependency-type: direct:production update-type: version-update:semver-major dependency-group: actions - dependency-name: pypa/gh-action-pypi-publish dependency-version: 1.14.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: actions - dependency-name: zizmorcore/zizmor-action dependency-version: 0.5.6 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- .github/workflows/downstream.yml | 2 +- .github/workflows/gpu_test.yml | 2 +- .github/workflows/hypothesis.yaml | 2 +- .github/workflows/issue-metrics.yml | 2 +- .github/workflows/lint.yml | 2 +- .github/workflows/test.yml | 4 ++-- .github/workflows/zarr-metadata-release.yml | 12 ++++++------ .github/workflows/zizmor.yml | 2 +- 8 files changed, 14 insertions(+), 14 deletions(-) diff --git a/.github/workflows/downstream.yml b/.github/workflows/downstream.yml index 74026233c4..3eb6898895 100644 --- a/.github/workflows/downstream.yml +++ b/.github/workflows/downstream.yml @@ -34,7 +34,7 @@ jobs: persist-credentials: false - name: Set up pixi - uses: prefix-dev/setup-pixi@1b2de7f3351f171c8b4dfeb558c639cb58ed4ec0 # v0.9.5 + uses: prefix-dev/setup-pixi@5185adfbffb4bd703da3010310260805d89ebb11 # v0.9.6 with: manifest-path: xarray/pixi.toml diff --git a/.github/workflows/gpu_test.yml b/.github/workflows/gpu_test.yml index 403441b306..333769cb9e 100644 --- a/.github/workflows/gpu_test.yml +++ b/.github/workflows/gpu_test.yml @@ -76,7 +76,7 @@ jobs: hatch env run --env "$HATCH_ENV" run-coverage - name: Upload coverage - uses: codecov/codecov-action@57e3a136b779b570ffcdbf80b3bdc90e7fab3de2 # v6.0.0 + uses: codecov/codecov-action@e79a6962e0d4c0c17b229090214935d2e33f8354 # v6.0.1 with: token: ${{ secrets.CODECOV_TOKEN }} flags: gpu diff --git a/.github/workflows/hypothesis.yaml b/.github/workflows/hypothesis.yaml index 4f9467be7d..a456b2aa0a 100644 --- a/.github/workflows/hypothesis.yaml +++ b/.github/workflows/hypothesis.yaml @@ -93,7 +93,7 @@ jobs: key: cache-hypothesis-${{ runner.os }}-${{ github.run_id }} - name: Upload coverage - uses: codecov/codecov-action@57e3a136b779b570ffcdbf80b3bdc90e7fab3de2 # v6.0.0 + uses: codecov/codecov-action@e79a6962e0d4c0c17b229090214935d2e33f8354 # v6.0.1 with: token: ${{ secrets.CODECOV_TOKEN }} flags: tests diff --git a/.github/workflows/issue-metrics.yml b/.github/workflows/issue-metrics.yml index 14fba5b9ec..510849ef3e 100644 --- a/.github/workflows/issue-metrics.yml +++ b/.github/workflows/issue-metrics.yml @@ -33,7 +33,7 @@ jobs: echo "last_month=$first_day..$last_day" >> "$GITHUB_ENV" - name: Run issue-metrics tool - uses: github/issue-metrics@c9e9838147fd355dace335ba787f01b6641a400a # v4.2.2 + uses: github/issue-metrics@1e38d5e62363e14db8019ed7d106b9855bdba6cc # v4.2.7 env: GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} SEARCH_QUERY: 'repo:zarr-developers/zarr-python is:issue created:${{ env.last_month }} -reason:"not planned"' diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml index 768e660ec2..fec211b4dd 100644 --- a/.github/workflows/lint.yml +++ b/.github/workflows/lint.yml @@ -30,4 +30,4 @@ jobs: uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0 with: enable-cache: true - - uses: j178/prek-action@6ad80277337ad479fe43bd70701c3f7f8aa74db3 # v2.0.3 + - uses: j178/prek-action@bdca6f102f98e2b4c7029491a53dfd366469e33d # v2.0.4 diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 03143d3e5b..62e571856b 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -78,7 +78,7 @@ jobs: hatch env run --env "$HATCH_ENV" run-coverage - name: Upload coverage if: ${{ matrix.dependency-set == 'optional' && matrix.os == 'ubuntu-latest' }} - uses: codecov/codecov-action@57e3a136b779b570ffcdbf80b3bdc90e7fab3de2 # v6.0.0 + uses: codecov/codecov-action@e79a6962e0d4c0c17b229090214935d2e33f8354 # v6.0.1 with: token: ${{ secrets.CODECOV_TOKEN }} flags: tests @@ -125,7 +125,7 @@ jobs: run: | hatch env run --env "$HATCH_ENV" run-coverage - name: Upload coverage - uses: codecov/codecov-action@57e3a136b779b570ffcdbf80b3bdc90e7fab3de2 # v6.0.0 + uses: codecov/codecov-action@e79a6962e0d4c0c17b229090214935d2e33f8354 # v6.0.1 with: token: ${{ secrets.CODECOV_TOKEN }} flags: tests diff --git a/.github/workflows/zarr-metadata-release.yml b/.github/workflows/zarr-metadata-release.yml index 809d502f16..9639fcfdd3 100644 --- a/.github/workflows/zarr-metadata-release.yml +++ b/.github/workflows/zarr-metadata-release.yml @@ -35,7 +35,7 @@ jobs: - name: Build run: hatch build - - uses: actions/upload-artifact@bbbca2ddaa5d8feaa63e36b76fdaad77386f024f # v7.0.0 + - uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7.0.1 with: name: zarr-metadata-dist path: packages/zarr-metadata/dist @@ -45,7 +45,7 @@ jobs: needs: [build] runs-on: ubuntu-latest steps: - - uses: actions/download-artifact@37930b1c2abaa49bbe596cd826c3c89aef350131 # v7.0.0 + - uses: actions/download-artifact@3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c # v8.0.1 with: name: zarr-metadata-dist path: dist @@ -76,7 +76,7 @@ jobs: id-token: write # required for OIDC trusted publishing attestations: write # required for artifact attestations steps: - - uses: actions/download-artifact@37930b1c2abaa49bbe596cd826c3c89aef350131 # v7.0.0 + - uses: actions/download-artifact@3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c # v8.0.1 with: name: zarr-metadata-dist path: dist @@ -87,7 +87,7 @@ jobs: subject-path: dist/* - name: Publish package to PyPI - uses: pypa/gh-action-pypi-publish@ed0c53931b1dc9bd32cbe73a98c7f6766f8a527e # v1.13.0 + uses: pypa/gh-action-pypi-publish@cef221092ed1bacb1cc03d23a2d87d1d172e277b # v1.14.0 upload_testpypi: name: Upload to TestPyPI @@ -101,7 +101,7 @@ jobs: id-token: write attestations: write steps: - - uses: actions/download-artifact@37930b1c2abaa49bbe596cd826c3c89aef350131 # v7.0.0 + - uses: actions/download-artifact@3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c # v8.0.1 with: name: zarr-metadata-dist path: dist @@ -112,6 +112,6 @@ jobs: subject-path: dist/* - name: Publish package to TestPyPI - uses: pypa/gh-action-pypi-publish@ed0c53931b1dc9bd32cbe73a98c7f6766f8a527e # v1.13.0 + uses: pypa/gh-action-pypi-publish@cef221092ed1bacb1cc03d23a2d87d1d172e277b # v1.14.0 with: repository-url: https://test.pypi.org/legacy/ diff --git a/.github/workflows/zizmor.yml b/.github/workflows/zizmor.yml index da19f22421..7ac4fe5d0e 100644 --- a/.github/workflows/zizmor.yml +++ b/.github/workflows/zizmor.yml @@ -32,4 +32,4 @@ jobs: persist-credentials: false - name: Run zizmor - uses: zizmorcore/zizmor-action@b1d7e1fb5de872772f31590499237e7cce841e8e # v0.5.3 + uses: zizmorcore/zizmor-action@5f14fd08f7cf1cb1609c1e344975f152c7ee938d # v0.5.6 From 433e836984acc600062e206758e7bd7576084e1b Mon Sep 17 00:00:00 2001 From: Davis Vann Bennett Date: Fri, 12 Jun 2026 13:32:23 +0200 Subject: [PATCH 2/2] Python 3.12 modernizations: itertools.batched, collections.abc.Buffer, math.prod, pathlib - Replace hand-rolled batched() in codec_pipeline.py with itertools.batched (stdlib 3.12+) - Replace typing_extensions.Buffer with collections.abc.Buffer in crc32c_.py - Remove unused ParamSpec / P from core/sync.py - Replace functools.reduce(operator.mul) with math.prod in common.product(), indexing.py CoordinateIndexer.__init__, array.AsyncArray.size, and chunk_grids._guess_num_chunks_per_axis_shard - Replace os.path.exists / os.path.getsize with pathlib equivalents in storage/_local.py Co-Authored-By: Claude Fable 5 --- src/zarr/codecs/crc32c_.py | 10 +++------- src/zarr/core/array.py | 3 ++- src/zarr/core/chunk_grids.py | 2 +- src/zarr/core/codec_pipeline.py | 10 +--------- src/zarr/core/common.py | 4 +--- src/zarr/core/indexing.py | 6 +++--- src/zarr/core/sync.py | 4 ---- src/zarr/storage/_local.py | 4 ++-- 8 files changed, 13 insertions(+), 30 deletions(-) diff --git a/src/zarr/codecs/crc32c_.py b/src/zarr/codecs/crc32c_.py index ebe2ac8f7a..7d41e11637 100644 --- a/src/zarr/codecs/crc32c_.py +++ b/src/zarr/codecs/crc32c_.py @@ -1,11 +1,11 @@ from __future__ import annotations +from collections.abc import Buffer as ABCBuffer from dataclasses import dataclass from typing import TYPE_CHECKING, cast import google_crc32c import numpy as np -import typing_extensions from zarr.abc.codec import BytesBytesCodec from zarr.core.common import JSON, parse_named_configuration @@ -41,9 +41,7 @@ def _decode_sync( inner_bytes = data[:-4] # Need to do a manual cast until https://github.com/numpy/numpy/issues/26783 is resolved - computed_checksum = np.uint32( - google_crc32c.value(cast("typing_extensions.Buffer", inner_bytes)) - ).tobytes() + computed_checksum = np.uint32(google_crc32c.value(cast(ABCBuffer, inner_bytes))).tobytes() stored_checksum = bytes(crc32_bytes) if computed_checksum != stored_checksum: raise ValueError( @@ -65,9 +63,7 @@ def _encode_sync( ) -> Buffer | None: data = chunk_bytes.as_numpy_array() # Calculate the checksum and "cast" it to a numpy array - checksum = np.array( - [google_crc32c.value(cast("typing_extensions.Buffer", data))], dtype=np.uint32 - ) + checksum = np.array([google_crc32c.value(cast(ABCBuffer, data))], dtype=np.uint32) # Append the checksum (as bytes) to the data return chunk_spec.prototype.buffer.from_array_like(np.append(data, checksum.view("B"))) diff --git a/src/zarr/core/array.py b/src/zarr/core/array.py index d15c70064b..9087007c33 100644 --- a/src/zarr/core/array.py +++ b/src/zarr/core/array.py @@ -1,5 +1,6 @@ from __future__ import annotations +import math import warnings from asyncio import gather from collections.abc import Iterable, Mapping, Sequence @@ -905,7 +906,7 @@ def size(self) -> int: int Total number of elements in the array """ - return np.prod(self.metadata.shape).item() + return math.prod(self.metadata.shape) @property def filters(self) -> tuple[Numcodec, ...] | tuple[ArrayArrayCodec, ...]: diff --git a/src/zarr/core/chunk_grids.py b/src/zarr/core/chunk_grids.py index 7459908e0a..2cb9762775 100644 --- a/src/zarr/core/chunk_grids.py +++ b/src/zarr/core/chunk_grids.py @@ -852,7 +852,7 @@ def _guess_num_chunks_per_axis_shard( ------- The number of chunks per axis. """ - bytes_per_chunk = np.prod(chunk_shape) * item_size + bytes_per_chunk = math.prod(chunk_shape) * item_size if max_bytes < bytes_per_chunk: return 1 num_axes = len(chunk_shape) diff --git a/src/zarr/core/codec_pipeline.py b/src/zarr/core/codec_pipeline.py index 5c26681d6b..23b45a69ed 100644 --- a/src/zarr/core/codec_pipeline.py +++ b/src/zarr/core/codec_pipeline.py @@ -1,7 +1,7 @@ from __future__ import annotations from dataclasses import dataclass, field -from itertools import islice, pairwise +from itertools import batched, pairwise from typing import TYPE_CHECKING, Any from warnings import warn @@ -42,14 +42,6 @@ def _unzip2[T, U](iterable: Iterable[tuple[T, U]]) -> tuple[list[T], list[U]]: return (out0, out1) -def batched[T](iterable: Iterable[T], n: int) -> Iterable[tuple[T, ...]]: - if n < 1: - raise ValueError("n must be at least one") - it = iter(iterable) - while batch := tuple(islice(it, n)): - yield batch - - def resolve_batched(codec: Codec, chunk_specs: Iterable[ArraySpec]) -> Iterable[ArraySpec]: return [codec.resolve_metadata(chunk_spec) for chunk_spec in chunk_specs] diff --git a/src/zarr/core/common.py b/src/zarr/core/common.py index eafffa1818..67e0416778 100644 --- a/src/zarr/core/common.py +++ b/src/zarr/core/common.py @@ -1,9 +1,7 @@ from __future__ import annotations import asyncio -import functools import math -import operator import warnings from collections.abc import Iterable, Mapping, Sequence from enum import Enum @@ -83,7 +81,7 @@ class NamedRequiredConfig[TName: str, TConfig: Mapping[str, object]](TypedDict): def product(tup: tuple[int, ...]) -> int: - return functools.reduce(operator.mul, tup, 1) + return math.prod(tup) def ceildiv(a: float, b: float) -> int: diff --git a/src/zarr/core/indexing.py b/src/zarr/core/indexing.py index cb81164209..4b2fa0f9fc 100644 --- a/src/zarr/core/indexing.py +++ b/src/zarr/core/indexing.py @@ -1,12 +1,12 @@ from __future__ import annotations import itertools +import math import numbers -import operator from collections.abc import Iterator, Sequence from dataclasses import dataclass from enum import Enum -from functools import lru_cache, reduce +from functools import lru_cache from types import EllipsisType from typing import ( TYPE_CHECKING, @@ -1187,7 +1187,7 @@ def __init__( cdata_shape = (1,) else: cdata_shape = tuple(g.nchunks for g in dim_grids) - nchunks = reduce(operator.mul, cdata_shape, 1) + nchunks = math.prod(cdata_shape) # some initial normalization selection_normalized = cast("CoordinateSelectionNormalized", ensure_tuple(selection)) diff --git a/src/zarr/core/sync.py b/src/zarr/core/sync.py index 260d4ad841..160950ba64 100644 --- a/src/zarr/core/sync.py +++ b/src/zarr/core/sync.py @@ -8,8 +8,6 @@ from concurrent.futures import ThreadPoolExecutor, wait from typing import TYPE_CHECKING -from typing_extensions import ParamSpec - from zarr.core.config import config if TYPE_CHECKING: @@ -19,8 +17,6 @@ logger = logging.getLogger(__name__) -P = ParamSpec("P") - # From https://github.com/fsspec/filesystem_spec/blob/master/fsspec/asyn.py iothread: list[threading.Thread | None] = [None] # dedicated IO thread diff --git a/src/zarr/storage/_local.py b/src/zarr/storage/_local.py index 3d9882d3db..1627c1a6b5 100644 --- a/src/zarr/storage/_local.py +++ b/src/zarr/storage/_local.py @@ -363,10 +363,10 @@ async def move(self, dest_root: Path | str) -> None: if isinstance(dest_root, str): dest_root = Path(dest_root) os.makedirs(dest_root.parent, exist_ok=True) - if os.path.exists(dest_root): + if dest_root.exists(): raise FileExistsError(f"Destination root {dest_root} already exists.") shutil.move(self.root, dest_root) self.root = dest_root async def getsize(self, key: str) -> int: - return os.path.getsize(self.root / key) + return (self.root / key).stat().st_size