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zarr-python

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chore(deps): bump the actions group across 1 directory with 9 updates (#4241) Bumps the actions group with 9 updates in the / directory: | Package | From | To | | --- | --- | --- | | [actions/checkout](https://github.com/actions/checkout) | `7.0.0` | `7.0.1` | | [astral-sh/setup-uv](https://github.com/astral-sh/setup-uv) | `8.3.2` | `9.0.0` | | [CodSpeedHQ/action](https://github.com/codspeedhq/action) | `4.18.5` | `5.0.1` | | [actions/setup-python](https://github.com/actions/setup-python) | `6.3.0` | `7.0.0` | | [scientific-python/issue-from-pytest-log-action](https://github.com/scientific-python/issue-from-pytest-log-action) | `1.6.0` | `1.6.1` | | [j178/prek-action](https://github.com/j178/prek-action) | `2.0.5` | `3.0.0` | | [actions/attest](https://github.com/actions/attest) | `4.2.0` | `4.2.1` | | [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish) | `1.14.0` | `1.14.2` | | [zizmorcore/zizmor-action](https://github.com/zizmorcore/zizmor-action) | `0.6.0` | `0.6.1` | Updates `actions/checkout` from 7.0.0 to 7.0.1 - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](https://github.com/actions/checkout/compare/9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0...3d3c42e5aac5ba805825da76410c181273ba90b1) Updates `astral-sh/setup-uv` from 8.3.2 to 9.0.0 - [Release notes](https://github.com/astral-sh/setup-uv/releases) - [Commits](https://github.com/astral-sh/setup-uv/compare/11f9893b081a58869d3b5fccaea48c9e9e46f990...c771a70e6277c0a99b617c7a806ffedaca235ff9) Updates `CodSpeedHQ/action` from 4.18.5 to 5.0.1 - [Release notes](https://github.com/codspeedhq/action/releases) - [Changelog](https://github.com/CodSpeedHQ/action/blob/main/CHANGELOG.md) - [Commits](https://github.com/codspeedhq/action/compare/f99becdce5e5d51fd556489ebef684f4ecfd6286...88472375d0a4572cf70a9f1fe3a4e0ab8da1b924) Updates `actions/setup-python` from 6.3.0 to 7.0.0 - [Release notes](https://github.com/actions/setup-python/releases) - [Commits](https://github.com/actions/setup-python/compare/ece7cb06caefa5fff74198d8649806c4678c61a1...5fda3b95a4ea91299a34e894583c3862153e4b97) Updates `scientific-python/issue-from-pytest-log-action` from 1.6.0 to 1.6.1 - [Release notes](https://github.com/scientific-python/issue-from-pytest-log-action/releases) - [Commits](https://github.com/scientific-python/issue-from-pytest-log-action/compare/87351a8f864e969567cda22a25a2f214cbe2340f...054799b34bd75a5fd6c86277a4a8a575224e60c6) Updates `j178/prek-action` from 2.0.5 to 3.0.0 - [Release notes](https://github.com/j178/prek-action/releases) - [Commits](https://github.com/j178/prek-action/compare/e98a699c41eb69ab013a45817a0406469a748f8d...4e14d07f9231acabce116ccfca13b13dd9755ece) Updates `actions/attest` from 4.2.0 to 4.2.1 - [Release notes](https://github.com/actions/attest/releases) - [Changelog](https://github.com/actions/attest/blob/main/RELEASE.md) - [Commits](https://github.com/actions/attest/compare/f7c74d28b9d84cb8768d0b8ca14a4bac6ef463e6...508db95dd578ae2727ebd6217d5ba78e4fbda05d) Updates `pypa/gh-action-pypi-publish` from 1.14.0 to 1.14.2 - [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases) - [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/cef221092ed1bacb1cc03d23a2d87d1d172e277b...dc37677b2e1c63e2034f94d8a5b11f265b73ba33) Updates `zizmorcore/zizmor-action` from 0.6.0 to 0.6.1 - [Release notes](https://github.com/zizmorcore/zizmor-action/releases) - [Commits](https://github.com/zizmorcore/zizmor-action/compare/6599ee8b7a49aef6a770f63d261d214911a7ce02...6fc4b006235f201fdab3722e17240ab420d580e5) --- updated-dependencies: - dependency-name: actions/checkout dependency-version: 7.0.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: astral-sh/setup-uv dependency-version: 9.0.0 dependency-type: direct:production update-type: version-update:semver-major dependency-group: actions - dependency-name: CodSpeedHQ/action dependency-version: 5.0.1 dependency-type: direct:production update-type: version-update:semver-major dependency-group: actions - dependency-name: actions/setup-python dependency-version: 7.0.0 dependency-type: direct:production update-type: version-update:semver-major dependency-group: actions - dependency-name: scientific-python/issue-from-pytest-log-action dependency-version: 1.6.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: j178/prek-action dependency-version: 3.0.0 dependency-type: direct:production update-type: version-update:semver-major dependency-group: actions - dependency-name: actions/attest dependency-version: 4.2.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: pypa/gh-action-pypi-publish dependency-version: 1.14.2 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: zizmorcore/zizmor-action dependency-version: 0.6.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Max Jones <14077947+maxrjones@users.noreply.github.com>

main

2 days ago

fix: make consolidated metadata nesting independent of persisted key order (#4227) * fix: make consolidated metadata nesting independent of persisted key order `ConsolidatedMetadata._flat_to_nested` grouped the flat keys with `itertools.groupby` over keys sorted by depth alone. `groupby` only groups *consecutive* runs, so when a parent's children were not adjacent it emitted several runs for the same parent and the surrounding dict comprehension kept only the last one. Every child in the earlier runs was silently never re-parented, and lingered as a bogus slash-containing key at the top level, making it unreachable through the consolidated metadata. The persisted key order is arbitrary, so nesting must not depend on it. Group by parent with an accumulating mapping instead. This is reachable from zarr-python itself: `to_dict` sorts keys by `(depth, NFKC-casefold(key))`, so sibling subtrees whose names differ only by case interleave and trigger exactly this pattern. Fixes #4226 Assisted-by: ClaudeCode:claude-opus-5 * docs: add changelog entry for 273 Assisted-by: ClaudeCode:claude-opus-5 * docs: renumber changelog fragment to the upstream PR number Assisted-by: ClaudeCode:claude-opus-5

main

9 days ago

refactor(chunk-grids): drop dead ndarray branch from is_regular_1d Since normalize_chunks_nd returns ChunkGrid dimensions instead of int64 arrays, is_regular_1d only ever receives plain Python sequences; the vectorized numpy path was unreachable in production code. Remove it and narrow the signatures of is_regular_1d / is_regular_nd to Sequence[int]. Assisted-by: ClaudeCode:claude-fable-5

d-v-b:claude/optimistic-diffie-2ef839

12 days ago

chore(deps): bump pillow from 12.2.0 to 12.3.0 (#4169) Bumps [pillow](https://github.com/python-pillow/Pillow) from 12.2.0 to 12.3.0. - [Release notes](https://github.com/python-pillow/Pillow/releases) - [Changelog](https://github.com/python-pillow/Pillow/blob/main/CHANGES.rst) - [Commits](https://github.com/python-pillow/Pillow/compare/12.2.0...12.3.0) --- updated-dependencies: - dependency-name: pillow dependency-version: 12.3.0 dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>

main

16 days ago

chore: refine link checker configuration (#4158)

main

23 days ago

test: bind moto server to an ephemeral port to fix xdist deadlock (#4139) * 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] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * test: bind moto server to an ephemeral port to fix xdist deadlock The session-scoped moto_server fixture bound a fixed port (5555). Under pytest-xdist, session-scoped fixtures run once per worker, so concurrent workers raced to bind the same port. The losers blocked forever inside ThreadedMotoServer.start(): its werkzeug thread dies on "Address already in use" before setting the ready event that start() waits on, and the wait has no timeout. Any multi-worker run whose s3 tests landed on 2+ workers deadlocked near the end of the suite at 0% CPU. CI never saw this because it runs the suite single-process. Bind port 0 instead and yield the actual endpoint from the fixture. Since the endpoint is now only known at runtime, test_fsspec.py's module-level endpoint_url constant becomes an endpoint_url fixture (replacing the s3_base alias), and its consumers take it as a parameter. With this fix the full suite completes in ~1 minute under -n auto on a 10-core machine, where it previously hung indefinitely. Assisted-by: ClaudeCode:claude-fable-5 * doc: add changelog fragment for moto ephemeral-port fix Assisted-by: ClaudeCode:claude-fable-5 --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

main

30 days ago

fix: keep element order when writing F-contiguous chunks with vlen codecs (#4116) * fix: keep element order when writing F-contiguous chunks with vlen codecs The numcodecs vlen codecs flatten their input with order='A', so an F-contiguous object-dtype chunk is encoded in transposed element order while decode reshapes in C order, silently scrambling the round-trip. Make both vlen codec wrappers pass a C-contiguous array to numcodecs; this copies only the object-pointer array and only when the chunk is not already C-contiguous. * docs: add changelog entry * fix: keep element order for numcodecs filter codecs too The generic numcodecs adapter codecs pass the chunk to numcodecs unchanged, so F-contiguous chunks hit the same order='A' flattening as the vlen codecs: Delta, FixedScaleOffset and PackBits all round-trip transposed data for an F-contiguous chunk that exactly covers the selection. Apply the same C-contiguity normalization in the array-array and array-bytes adapter encode paths. --------- Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>

main

1 month ago

docs: add reviewer guidance and author attestation to PR template (#4106) * docs: add reviewer guidance and author attestation to PR template * docs: recommend conventional commits style PR titles * docs: change example

main

1 month ago

Latest Branches

+12%

fix(chunk-grids): make array creation O(1) in per-dimension chunk count#4218

13 days ago

8c192b2

d-v-b:claude/optimistic-diffie-2ef839

×5.4

perf: cache lexicographic chunk coords in sharding codec#4012

2 months ago

c8e1ffa

d-v-b:perf-sharding-coord-cache

×3.3

perf: use sync methods for chunk encoding / decoding#3885

2 months ago

48ab6be

d-v-b:perf/prepared-write-v2

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