Repository navigation
Conversation
…elopers#4597) * feat(zarr-metadata): draw nested fields and codec pipelines Add Hypothesis strategies for struct, cast_value and sharding_indexed, which draw the fields they hold from the same Strategies mapping, and a `pipelines` strategy that walks a codec pipeline, drawing each codec for the chunk the codec before it hands on via its definition's transition. A shard's inner and index pipelines are drawn for the chunks its definition's `pipelines` gives. Shards and structs nest at most one level deep, and strategies are wrapped in a mapping with a short repr so Hypothesis's error notes stay under its 30,000-character warning. Every strategy record's functions now take the Strategies mapping as their last argument. Assisted-by: ClaudeCode:claude-opus-5-5 * fix(zarr-metadata): reject non-numeric data types in arithmetic codecs `NOT_NUMBERS` predates the zarr-python data types, so `cast_value` and `scale_offset` accepted `fixed_length_utf32`, `null_terminated_bytes`, `raw_bytes` and `variable_length_bytes`, and the strategies drew them. The cast_value spec defines the codec only for floating-point and integral data types. Assisted-by: ClaudeCode:claude-opus-5-5 * fix(zarr-metadata): let the later of two same-named strategies win `_scope` documented this but raised `ScopeConflictError`, so `declarations` failed for any definition named as a default, which worked before this branch. Pipelines and data type names now draw only the definition that claims a name, and `declarations` reads a draw with its own definition claiming the name. Assisted-by: ClaudeCode:claude-opus-5-5 * test(zarr-metadata): check a same-named definition reads its own draws The test compared a draw with the bare name, which depended on the example Hypothesis returned and said nothing of which definition read it. Every spelling is now read by the definition it was drawn for. Assisted-by: ClaudeCode:claude-opus-5-5 * chore(zarr-metadata): number the nested strategies changelog fragments after zarr-developers#4597 Assisted-by: ClaudeCode:claude-opus-5-5 * fix(zarr-metadata): keep same-named definitions out of nested draws The struct and shard strategies removed the default definition by identity before drawing what they hold. A custom definition with the same name stayed in the inner strategies, so it could claim the name there and be drawn, and the default then refused the result with a ValueError. Filter by name instead. Assisted-by: ClaudeCode:claude-opus-5-5 * fix(zarr-metadata): draw long runs in rectilinear dimensions A run held at most 4 chunks, so the `[size, count]` spelling was never drawn for what it is for, and a long dimension was covered by a few small chunks and one huge one. Draw counts sized to the dimension, and always write a run too long to list as a pair. Reach tests now cover each spelling of a dimension, not only that a pair is drawn at all. Assisted-by: ClaudeCode:claude-opus-5-5 * fix(zarr-metadata): sample float fills, shard factors and struct fields evenly A measured audit found strategies that drew valid metadata from little of what they could. Hex float fills came from a small-biased integer, so 83% of float64 fills were subnormal and few were normal. Integer float fills stopped at the limit of the narrowest type. Rectilinear edges rarely shared a factor, so 70% of a shard's axes held inner chunks of length 1. A struct field's type was drawn after its name, which made the first data type about a fifth of all fields. Draw hex fills from floats, infinities and NaN payloads as well as raw bits, limit integers by width, draw edges with a common factor, and draw a field's type first. Divisor search is now bounded, so a very long shard no longer takes billions of steps. New tests measure shares at the number of examples a test runs, which plain reach tests do not see. Assisted-by: ClaudeCode:claude-opus-5-5 * fix(zarr-metadata): keep regular chunk lengths within a signed 64-bit size Axes can be up to 2**63 - 1 long, but regular and bare rectilinear chunk lengths reached twice that, which a reader indexing with int64 cannot hold. Cap them. A rectilinear last edge needs no cap: the runs before it cover at least one factor, so rounding up cannot pass the axis. Correct two docstrings, and require a covering run to count more than one chunk in its reach test, since the leftover edge passed it on its own. Assisted-by: ClaudeCode:claude-opus-5-5 * fix(zarr-metadata): draw non-finite and hex scale_offset values An offset and a scale are fill values of the chunk's data type, but the strategy drew only finite floats, and never an integer spelling. It now draws every spelling a fill value takes, and still never a scale of zero. Assisted-by: ClaudeCode:claude-opus-5-5
…add definitions with union (zarr-developers#4598) * feat(zarr-metadata)!: replace scope update with copy(update=...) and add definitions with union `ZarrV3Context.update(**slots)` and `ZarrV2Context.update(**slots)` read as a merge, but replace each slot whole, so passing one new definition silently dropped every default. They become `copy(*, update=None)`, after pydantic's `model_copy(update=...)`, whose replace-whole meaning pydantic users already know. Adding definitions is `union`, which keeps every definition the scope has and refuses a conflicting one; the docs, docstrings and call sites now use it instead of splicing a slot's definitions back in. Fixes #424 Assisted-by: ClaudeCode:claude-opus-5-5 * docs(zarr-metadata): number the scope copy changelog fragment after its PR Assisted-by: ClaudeCode:claude-opus-5-5 * test(zarr-metadata): check copy refuses another format's definition and name copy in scope docstrings Assisted-by: ClaudeCode:claude-opus-5-5
updates: - [github.com/astral-sh/ruff-pre-commit: v0.16.10 → v0.17.3](astral-sh/ruff-pre-commit@v0.16.10...v0.17.3) - [github.com/DavidAnson/markdownlint-cli2: v0.23.3 → v0.24.0](DavidAnson/markdownlint-cli2@v0.23.3...v0.24.0) - [github.com/zizmorcore/zizmor-pre-commit: v1.30.1 → v1.31.1](zizmorcore/zizmor-pre-commit@v1.30.1...v1.31.1) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
* feat(zarr-metadata): draw whole v3 documents Add `array_documents`, `group_documents` and `consolidated_group_documents`. An array's members are drawn to fit each other: the chunk grid for the shape, the fill value for the data type, and the codecs for the grid's chunks of that data type. A consolidated listing holds each node's parent, as a group, before the node. `pipelines` takes `spellings`, as `declarations` does. A drawn document its definitions refuse raises a ValueError, and strategies with nothing to draw some member from raise a LookupError. `Spellings` and `CHARACTERS` move to `_strategy` so the new module can share them. Assisted-by: ClaudeCode:claude-opus-5-5 * chore(zarr-metadata): number the document strategies changelog fragment after #439 Assisted-by: ClaudeCode:claude-opus-5-5 * fix(zarr-metadata): sample document shapes, listings and data types evenly Shapes capped axes at 2**16 and rank at 5, with a quarter of documents rank 0 and few holding a zero-length axis. Draw each rank about as often, up to 8, and axes that are zero, short, or past 32 bits. Draw a document's data type first: drawn after the shape, the first in the list was a fifth of all documents. A listed group now sometimes holds the empty listing the reference implementation writes, a fresh one for each group. New tests bound these shares. Assisted-by: ClaudeCode:claude-opus-5-5 * chore(zarr-metadata): number the document strategies changelog fragment after zarr-developers#4602 Assisted-by: ClaudeCode:claude-opus-5-5
) Bumps the actions group with 3 updates: [astral-sh/setup-uv](https://github.com/astral-sh/setup-uv), [scientific-python/upload-nightly-action](https://github.com/scientific-python/upload-nightly-action) and [zizmorcore/zizmor-action](https://github.com/zizmorcore/zizmor-action). Updates `astral-sh/setup-uv` from 10.3.2 to 10.3.3 - [Release notes](https://github.com/astral-sh/setup-uv/releases) - [Commits](astral-sh/setup-uv@07a047e...68559e9) Updates `scientific-python/upload-nightly-action` from 0.6.5 to 0.6.6 - [Release notes](https://github.com/scientific-python/upload-nightly-action/releases) - [Commits](scientific-python/upload-nightly-action@16fa02e...5a74a2a) Updates `zizmorcore/zizmor-action` from 0.7.1 to 0.8.0 - [Release notes](https://github.com/zizmorcore/zizmor-action/releases) - [Commits](zizmorcore/zizmor-action@85b2b9f...53290ba) --- updated-dependencies: - dependency-name: astral-sh/setup-uv dependency-version: 10.3.3 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: scientific-python/upload-nightly-action dependency-version: 0.6.6 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: zizmorcore/zizmor-action dependency-version: 0.8.0 dependency-type: direct:production update-type: version-update:semver-minor 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: Davis Bennett <davis.v.bennett@gmail.com>
…dices When the flat in-hull positions are non-decreasing (the usual C-order case), repeats are adjacent and the last occurrence of each can be found in O(n) without np.unique. When there are no repeats at all, return a full slice so callers index without a gather copy. Assisted-by: ClaudeCode:claude-opus-5-5 Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Assisted-by: ClaudeCode:claude-opus-5-5 Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
…s#4603 Assisted-by: ClaudeCode:claude-opus-5-5 Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
This branch has not been deployed
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
🤖 AI text below 🤖
Writes whose indices land on a chunk in sorted order no longer sort them to drop repeated indices, so deduplication is linear in the number of points; writes without repeats also skip a gather copy. Unsorted indices behave as before.
_last_occurrencesnow checks in O(n) whether the flat positions are non-decreasing, the usual case since a chunk's points arrive in C order. If they are, repeats are adjacent and the last of each run is kept vianp.flatnonzero(np.append(flat[1:] != flat[:-1], True)). If there are no repeats, or fewer than two positions, it returnsslice(None), so_scatter_numpyand_scatter_plannedindex without copying. Unsorted input still goes throughnp.unique. Callers only use the result to pick matching rows of coordinates and values, so the order of the kept positions doesn't matter. The sorted-input check is borrowed from thelast_occurrenceshelper that Bhaskar Gurram (bhaskargurram-ai) wrote in upstream zarr-developers#4601; credit for the idea goes to them.A new parametrized test,
test_last_occurrences_matches_sequential_assignment, checks empty, single, sorted, sorted-with-repeats, unsorted-with-repeats and reversed input against sequential NumPy assignment.Timing for
_last_occurrenceson 5Mintppositions (NumPy 2.5.1, Python 3.13, macOS arm64, best of 5):The zarr-indexing suite passes on Python 3.13 (1745 passed), and
just typecheckandjust lintare clean. On Python 3.15, four tests fail onmaintoo, because they match the__index__error message that 3.15 changed.🤖 Generated with Claude Code