fix: allow writing to 0-dimensional arrays with sharding by NIK-TIGER-BILL · Pull Request #3966 · zarr-developers/zarr-python

NIK-TIGER-BILL · 2026-05-11T23:16:19Z

This PR fixes a bug where writing to a 0-dimensional array with sharding enabled would crash with an IndexError in the sharding codec's vectorized chunk slice lookup.

The root cause was that get_chunk_slices_vectorized in zarr/codecs/sharding.py assumed offsets_and_lengths was at least 2-dimensional, but for 0-dimensional arrays it has shape (2,) instead of (1, 2). This caused offsets_and_lengths[:, 0] to fail with "too many indices for array".

Fix: Add an early return in get_chunk_slices_vectorized to handle the 0-dimensional case by reshaping offsets_and_lengths to (1, 2) before slicing.

Test: Added test_sharding_zero_dimensional in tests/test_codecs/test_sharding.py as a regression test.

codecov · 2026-05-11T23:19:58Z

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 93.29%. Comparing base (eac9c86) to head (bb315a8).

Additional details and impacted files

@@ Coverage Diff @@## main #3966 +/- ##
==========================================
+ Coverage 93.28% 93.29% +0.01% 
==========================================
Files 87 87 Lines 11745 11752 +7 ==========================================
+ Hits 10956 10964 +8 + Misses 789 788 -1

Files with missing lines	Coverage Δ
src/zarr/codecs/sharding.py	`89.32% <100.00%> (+0.23%)`	⬆️

... and 1 file with indirect coverage changes

🚀 New features to boost your workflow:

❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

chuckwondo

Thanks @NIK-TIGER-BILL!

Would you mind also adding a test that covers your patch that handles the 0D case? The test you added shows that the original case no longer errors, but that case no longer enters the function that you patched, so your patch itself remains untested, hence the failed codecov run.

NIK-TIGER-BILL · 2026-05-13T03:11:56Z

@chuckwondo Good catch — the integration test bypassed the patched function. I just pushed a direct unit test that exercises _ShardIndex.get_chunk_slices_vectorized with a 0-D offsets_and_lengths array, covering both the written and unwritten chunk cases. This should satisfy codecov for the new branch. Let me know if you would like anything else adjusted!

chuckwondo · 2026-05-13T16:32:56Z

Thanks @NIK-TIGER-BILL. Would you mind updating your branch and addressing the ruff pre-commit error? (See https://results.pre-commit.ci/run/github/48049137/1778641889.s58oPP4KQbGdn7pJdtUPAg)

@maxrjones and/or @d-v-b, please review.

Signed-off-by: NIK-TIGER-BILL <nik.tiger.bill@github.com>

NIK-TIGER-BILL · 2026-05-13T23:01:20Z

@chuckwondo Done — rebased on latest upstream/main and fixed the ruff unused-variable error (prefixed ends_e with an underscore). CI should be green now. Let me know if anything else is needed!

NIK-TIGER-BILL · 2026-05-14T03:04:12Z

@chuckwondo I believe I've addressed all feedback — rebased on latest upstream/main and fixed the ruff unused-variable issue (prefixed with ). Could you please take another look when you have a moment? Thanks!

chuckwondo · 2026-05-14T10:43:19Z

@d-v-b, this is a very small PR. Looks good to me, but would you mind reviewing as well?

chuckwondo

Thanks @NIK-TIGER-BILL!

d-v-b · 2026-05-14T10:53:36Z

this looks good! there's some baseline code smell in these classes but this fix is appropriately targeted. I'll open an issue with my follow-up recommendations.

Resolve conflicts in tests/test_codecs/test_sharding.py: combine the imports from both sides (INDEX_LOCATION/IndexLocation/ShardingCodecIndexLocation from our deprecation work, plus MAX_UINT_64/_ShardIndex from zarr-developers#3966's 0-D sharding fix), and keep all added test functions from both branches. Other auto-merged files (src/zarr/codecs/sharding.py and src/zarr/core/buffer/core.py) merged cleanly: upstream's 0-D path and NDArrayLike protocol tightening sit alongside our enum deprecation changes without overlap. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* 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](prefix-dev/setup-pixi@1b2de7f...5185adf) 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](codecov/codecov-action@57e3a13...e79a696) Updates `github/issue-metrics` from 4.2.2 to 4.2.7 - [Release notes](https://github.com/github/issue-metrics/releases) - [Commits](github-community-projects/issue-metrics@c9e9838...1e38d5e) Updates `j178/prek-action` from 2.0.3 to 2.0.4 - [Release notes](https://github.com/j178/prek-action/releases) - [Commits](j178/prek-action@6ad8027...bdca6f1) Updates `actions/upload-artifact` from 7.0.0 to 7.0.1 - [Release notes](https://github.com/actions/upload-artifact/releases) - [Commits](actions/upload-artifact@v7...043fb46) Updates `actions/download-artifact` from 7.0.0 to 8.0.1 - [Release notes](https://github.com/actions/download-artifact/releases) - [Commits](actions/download-artifact@v7...3e5f45b) 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](pypa/gh-action-pypi-publish@v1.13.0...cef2210) Updates `zizmorcore/zizmor-action` from 0.5.3 to 0.5.6 - [Release notes](https://github.com/zizmorcore/zizmor-action/releases) - [Commits](zizmorcore/zizmor-action@b1d7e1f...5f14fd0) --- 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> * fix: byte-order handling for structured dtypes in the bytes codec (#220) * fix: byte-order handling for structured dtypes in the bytes codec The bytes codec neither byte-swapped structured-dtype fields to its configured endian on encode (numpy reports byteorder '|' for void dtypes, so the top-level byteorder comparison never detected a mismatch) nor honored its endian when decoding, silently corrupting any structured data whose field byte order differed from the stored one (e.g. virtual references to external big-endian data). Encode now detects byte-order mismatches by comparing full dtypes via newbyteorder, and decode reinterprets raw bytes in the stored byte order before converting to the data type's declared byte order, so the stored layout (codec state) and the in-memory layout (array data type) are independent. Closes#4141 Assisted-by: ClaudeCode:claude-fable-5 * test: fold structured byte-order cases into existing bytes codec tests Extend test_endian's parametrization with structured dtypes and test_bytes_codec_sync_roundtrip with endian/dtype parametrization plus stored-layout and decoded-dtype assertions, instead of adding parallel test functions for the same properties. Assisted-by: ClaudeCode:claude-fable-5 * refactor: rename stored_dtype to view_dtype in BytesCodec decode The variable is the dtype used to view the raw chunk bytes (byte order from the codec's endian configuration), not a property of the stored data or of the returned buffer, which always carries the array's declared dtype. Assisted-by: ClaudeCode:claude-fable-5 * docs: note that the decode-side byte-order conversion copies the chunk Assisted-by: ClaudeCode:claude-fable-5 * docs: 3.3.0 release notes Add missing changelog fragments for #3955 (datetime64/timedelta64 V3 metadata types), #3966 (writes to 0-dimensional sharded arrays), and the public alias renames that accompanied the #3963/#3968 enum deprecations, then build the 3.3.0 release notes with towncrier, consuming all fragments accumulated since v3.2.1. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Claude Fable 5 <noreply@anthropic.com>

github-actionsBot added the needs release notes Automatically applied to PRs which haven't added release notes label May 11, 2026

chuckwondo suggested changes May 12, 2026
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NIK-TIGER-BILL added 3 commits May 13, 2026 23:00

fix: allow writing to 0-dimensional arrays with sharding
1db4efb
Signed-off-by: NIK-TIGER-BILL <nik.tiger.bill@github.com>

test: directly cover get_chunk_slices_vectorized 0D path
0736110
Signed-off-by: NIK-TIGER-BILL <nik.tiger.bill@github.com>

fix: ruff unused variable in zero-dim sharding test
bb315a8
Signed-off-by: NIK-TIGER-BILL <nik.tiger.bill@github.com>

NIK-TIGER-BILL force-pushed the fix-3751-zero-dim-sharding branch from 411cf37 to bb315a8Compare May 13, 2026 23:01

chuckwondo approved these changes May 14, 2026
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d-v-b approved these changes May 14, 2026
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d-v-b merged commit fcb3cd3 into zarr-developers:mainMay 14, 2026
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d-v-b mentioned this pull request May 14, 2026
explicitly encode chunk grid shape in _ShardIndex #3974
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d-v-b mentioned this pull request Jul 15, 2026
docs: 3.3.0 release notes #4148
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github-actionsBot mentioned this pull request Jul 29, 2026
Link Checker Report d-v-b/zarr-python#265
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fix: allow writing to 0-dimensional arrays with sharding - #3966

fix: allow writing to 0-dimensional arrays with sharding#3966
d-v-b merged 3 commits into
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