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test(chunk-grids): sample the full rectilinear chunk grid declaration space (#4377)
* fix(chunk-grids): enforce one zero-length-axis invariant across model, clamps and metadata Invariant: a chunk edge length is always >= 1; a dimension's extent may be 0, in which case the dimension has zero chunks (ceildiv(0, size) == 0). Zero-length-axis bugs have recurred since 2017 (#150, #241, #303, #972, #1977, #2434, #3711, #4305, #4307, #4328) because the layers disagreed on this invariant and every span-derived chunk spelling clamped on its own: - The metadata layer (common.py, metadata/v3.py) required chunk edges >= 1, but the in-memory FixedDimension allowed size == 0 with four special-case branches left over from #2434, so normalization could build a grid the metadata constructor then rejected. FixedDimension now rejects size < 1 and the four `if self.size == 0` branches are gone. VaryingDimension already required edges > 0 and is unchanged. - `chunks=-1`, `chunks=False`, `chunks="auto"` (_guess_regular_chunks, both the typesize == 0 early return and the np.maximum line) and `shards="auto"` each derived "one chunk covering the axis" independently. They now all go through one helper, `_full_span_chunk_size(span) = max(span, 1)`, which is the single definition of that phrase for a possibly zero-length axis. - Zarr format 2 metadata had no chunk >= 1 check, so a legacy `chunks: [0]` document opened fine and read uninitialised memory after a resize. It now raises a clear ValueError at parse time, matching the format 3 grid. - Rectilinear grids had no creation-time spelling for a zero-length axis: normalize_chunks_1d required sum(edges) == span, which no list of positive edges can satisfy for span 0, even though the same state is reachable via resize((0,)) and round-trips through reopen. For span == 0 any non-empty list of positive edges is now accepted verbatim, producing the same VaryingDimension(edges, extent=0) that resize produces; the strict sum check is kept for span > 0. Tests: the per-spelling regression test from #4328 is replaced by one matrix over {-1, False, "auto", 1, (1,...), [[2, 2]]} x {(0,), (0, 4), (4, 0), (0, 0), ()} x {v2, v3} x {no shards, shards="auto" with and without a byte budget, explicit shards}, with separate small tests for each error case. Tests that constructed FixedDimension(size=0) now assert it raises, and a zero-extent test covers the behaviour the old special cases were guarding. Assisted-by: ClaudeCode:claude-fable-5-1 * fix(metadata): read a legacy v2 zero chunk edge on an empty axis as 1 zarr-python 2.18.7 writes `chunks: [0]` for `zarr.zeros((0,), chunks=False)` and for `chunks=(0,)`, so stores with that document exist. Rejecting them at open would turn a previously-readable array into an error; leaving the 0 in place read uninitialised memory after a resize. Normalize the edge to 1 with a ZarrUserWarning instead — the same grid every other "one chunk spans the axis" spelling produces — and keep rejecting a zero edge on an axis that has data. Assisted-by: ClaudeCode:claude-fable-5-1 * chore: rename changelog fragment to the PR number Assisted-by: ClaudeCode:claude-fable-5-1 * docs: state what 2.x actually did with a zero chunk edge Measured against zarr 2.18.7: `zeros((0,), chunks=False)`, `chunks=-1` and `chunks=(0,)` all write `chunks: [0]`, after which nchunks, read, write, append, resize and reopen-then-read every raise ZeroDivisionError. There was never a working behaviour to preserve; normalizing the edge to 1 makes such arrays usable for the first time. Say so in the comment and fragment instead of claiming the stores were previously readable. Assisted-by: ClaudeCode:claude-fable-5-1 * docs: qualify zero-chunk compatibility history Assisted-by: Codex:GPT-6 * test: sample the full rectilinear chunk grid declaration space The rectilinear hypothesis strategy returned one list of edges per dimension, so no property test ever saw a bare-int dimension, a grid mixing bare ints and edge lists, a run-length encoded declaration, or edges overhanging the extent. The first-element-only classifier that zarr 3.2.x shipped (#4374) was invisible to it. The strategies now cover two spaces. `rectilinear_chunks` samples the `chunks=` syntax: bare ints and flat edge lists in any arrangement, at least one list so the grid is rectilinear. `rectilinear_chunk_shape_ declarations` samples the stored metadata: bare-int steps (including larger than the extent), edge lists written in full or run-length encoded in canonical or arbitrary grouping, and overhanging edges. Each draw comes with the chunk_shapes it must parse to. `chunk_grids` and so `array_metadata` draw from the stored space; `arrays` passes grids the list syntax cannot express as the metadata object, and asserts the stored grid equals the declared one. Two property tests pin the properties that would have caught #4374: every stored declaration parses to its expanded edges and re-serializes to an equivalent grid, and every `chunks=` specification is stored in zarr.json as a "rectilinear" grid equal to the specification. test_unified_chunk_grid.py used a private copy of the old strategy; it now draws from the shared one. Assisted-by: ClaudeCode:claude-fable-5-1 * docs: add changelog fragment for #4377 Assisted-by: ClaudeCode:claude-fable-5-1 * fix(metadata): read a legacy zero chunk size on an empty axis in Zarr format 3 The compatibility policy for a stored chunk size of 0 on a zero-length axis covered Zarr format 2 only, so arrays written by zarr-python 3.0 and 3.1 with `chunk_shape: [0]` — or `[false]`, which 3.0 wrote for `chunks=False` — still could not be opened at all. `ArrayV3Metadata` now applies the same policy to a regular chunk grid: a stored chunk size of 0 on a zero-length axis is read as 1 with a `ZarrUserWarning`, and a zero chunk size on a positive-length axis is left for the chunk grid parser to reject. It runs in `__init__` rather than in the grid parser because the policy needs the array shape, which chunk grid metadata does not carry. Both warnings now say how to store a corrected chunk size — open the array writable and call `array.update_attributes({})`, which rewrites the whole document from the parsed metadata — from one shared constant. The Zarr format 2 warning also named only zarr-python 2.x; measured against real installs, every 3.x release before 3.4 wrote a zero chunk size for an empty array too (3.3.0 for `chunks=-1` and `chunks=False`). Tested against stores written by zarr 3.0.10, 3.1.6 and 3.3.0: they open, append without losing data, and re-save to a chunk size that reopens without a warning. Assisted-by: ClaudeCode:claude-opus-5 * refactor(metadata): check stored chunk shapes against the array shape in one routine The legacy zero-chunk policy was written out twice: inline in `ArrayV2Metadata.__init__`, and again in a Zarr format 3 helper. The V2 copy also zipped with `strict=False` and re-appended any trailing chunk entries only so that a separate length check, `parse_metadata`, could report a dimensionality mismatch after construction. `parse_stored_chunk_shape` in `zarr.core.metadata.common` is now the one place a stored chunk shape is checked against its array's shape, for both formats: one entry per axis, every integer chunk size at least 1, and a size of 0 (or JSON `false`) on a zero-length axis read as 1 with a warning that names the writer and how to re-save. Non-integer entries, such as edge lists, pass through for the caller's own parser. `ArrayV2Metadata.__init__` calls it directly and `parse_metadata` is gone. The Zarr format 3 adapter only locates a regular grid's `chunk_shape` in the stored document and hands it over; it still runs in `ArrayV3Metadata.__init__` because chunk grid metadata has no array shape. The Zarr format 3 import changes that existed only for the old helper are reverted. Tests for the policy now target the routine: one table of valid and legacy inputs, and one test per rejection (dimension mismatch, zero on a non-empty axis, negative). They replace metadata-level tests in test_v2.py and test_v3.py that only re-tested the same rules; the end-to-end tests still cover both formats' wiring against stored arrays. Assisted-by: ClaudeCode:claude-opus-5 * refactor(metadata): scope the stored chunk shape check to regular chunk grids `parse_stored_chunk_shape` passed non-integer entries through "for the caller's own parser", which made a regular-grid policy look like a general chunk shape routine and let it decide what a 0-length chunk means for grids it does not own. A rectilinear grid, or any other grid, is free to define its own semantics for 0-length chunks. It is now `parse_stored_regular_chunk_shape`, typed `Sequence[int]`, with no pass-through, and its docstring says it applies to Zarr format 2 `chunks` and Zarr format 3 `regular` grids only. The Zarr format 3 caller hands it a chunk shape only when the grid is named `regular` and every entry is an integer (`_is_regular_chunk_shape`); anything else is not a regular chunk shape and goes to the chunk grid parser untouched. Assisted-by: ClaudeCode:claude-opus-5 * test: tighten rectilinear strategy contracts from review - Document the `rectilinear_chunks` return type change in the changelog fragment, since `zarr.testing.strategies` is public. - Make the `RectilinearDimDeclaration` alias private. - Encode canonical RLE in the strategy instead of calling `compress_rle`, so the generator does not depend on the code under test. - Assert `rectilinear_chunks` gets a non-empty shape instead of returning a non-rectilinear `[]`. Assisted-by: ClaudeCode:claude-opus-5-5 * test: draw zero-length axes in the rectilinear declaration strategies With #4334 a rectilinear dimension of extent 0 takes any non-empty list of positive edges at creation, the same state 3.2.x wrote and resize(0) produces. The strategies asserted extent > 0 and `chunk_grids` fell back to a regular grid for any empty axis, so no property saw that state. Assisted-by: ClaudeCode:claude-opus-5-5 Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> * fix(metadata): read a stored zero chunk size on a grown axis as one spanning chunk A stored chunk size of 0 was tolerated only on a zero-length axis and rejected otherwise, because the metadata supposedly could not say how the stored chunks were laid out. But a chunk size of 0 gives a grid of zero chunks, so no release could store a chunk under it, and the writers of that metadata let the axis grow: 3.4.0 appends to a Zarr format 2 array created empty by 3.3.0 (shape grows, no chunk written), and 3.1.6 records a Zarr format 3 resize and the resize half of a failed append. Measured with real installs. Those arrays open in 3.4.0, attributes included; the rejection would have made them unopenable. `parse_stored_regular_chunk_shape` now reads a stored 0 (or JSON `false`) on any axis as one chunk spanning it, `max(extent, 1)`, which is what the `-1`/`False` spec that wrote it meant. On a grown axis the warning also says that data written to it was not saved. Negative sizes are still rejected. Assisted-by: ClaudeCode:claude-opus-5-5 Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> * test: a stateful test of one array's create/append/resize/write life The only state machine that touched arrays compared zarr on one store with zarr on a MemoryStore, so a chunk grid bug showed up identically on both sides; it had no append rule, covered Zarr format 3 only, and kept every empty axis at 0 when resizing, which is where the zero-length bugs live. `ArrayLifecycle` checks one array against a NumPy model across both formats, every chunk spelling (-1, False, "auto", ints, sharded, rectilinear) and the stored chunk size of 0 that releases before 3.4 wrote, including on an axis those releases grew. Rules append, resize (growing and shrinking to and from 0), write and re-save the metadata; the invariant reopens the array and compares shape, values and whether the legacy warning is due. Deliberately breaking the grown-axis policy, the legacy warning, or append on an empty axis each fails it. `resize` keeps partly retained chunks whole, so cells cut off by a shrink can come back with their old values when the axis grows (as in 2.x); the model marks such cells unknown until written instead of encoding that. Assisted-by: ClaudeCode:claude-opus-5-5 Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> * fix(metadata): stop the zero chunk size warning from naming writers The warning for a stored chunk size of 0 said which zarr-python releases wrote it. The check runs on every metadata construction, so metadata built in code, such as VirtualiZarr's kerchunk writer passing an empty array's shape as `chunks`, was told it came from zarr-python 2.x. The warning now says what the chunk size is read as and, on an axis of positive length, that the axis holds only the fill value. `legacy_writers` is gone, and the docstrings no longer narrate release history; the changelog keeps it. Assisted-by: ClaudeCode:claude-opus-5-5 Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> * chore(metadata): drop an orphaned comment in ArrayV2Metadata.__init__ The comment introduced a consistency check (`parse_metadata`) that this branch removed; the check now lives in `parse_stored_regular_chunk_shape`. Assisted-by: ClaudeCode:claude-opus-5-5 Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> * fix(chunk-grids): size a full-span shard as a multiple of the inner chunk One definition of "one chunk spanning the axis", full_span_chunk_size(span, unit), is the smallest positive multiple of unit covering span. shards=-1 and shards=False now use the inner chunk size as unit, so a zero-length axis, or one whose length is not a multiple of the inner chunk, gets a valid shard instead of a divisibility error. The zero-length array test drops the explicit-size spellings and keeps the spellings that derive a chunk from the span. Assisted-by: ClaudeCode:claude-opus-5-5 Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> * refactor(metadata): read invalid stored chunk sizes in one module of document upgrades The metadata constructors are strict again: a chunk edge length is an int of at least 1, so metadata built in code with 0 or True raises, without a warning. Stored documents are read leniently only in zarr.core.metadata.upgrades, whose upgrades map a stored array document to a valid one before the constructors run. ArrayV2Metadata.from_dict and ArrayV3Metadata.from_dict apply them, so opening an array and parsing consolidated metadata take the same path. The first upgrade reads a regular chunk size of 0 or JSON false as one chunk spanning the axis, a multiple of the inner chunk size when the array is sharded (this opens sharded stores with an outer chunk size of 0), and JSON true, which real releases wrote for chunks=(True,), as 1. Its one warning says what is invalid, how it is read, and how to re-save, including zarr.consolidate_metadata. Assisted-by: ClaudeCode:claude-opus-5-5 Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> * docs: rewrite the 4334 changelog fragment and trim restating docstrings The fragment now covers the full-span shard rule, strict constructors, and the stored-document upgrade (including JSON true) in two short paragraphs. Assisted-by: ClaudeCode:claude-opus-5-5 Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> * test: model exactly what the store holds in the array lifecycle state machine The model now tracks cells beyond the array's shape: a shrinking resize deletes exactly the chunks outside the new grid, kept chunks keep their out-of-bounds cells, and a write covering every in-bounds cell of an unsharded chunk resets its out-of-bounds cells to the fill value. A resize that never deletes chunks now fails the test. Sharding is its own chunk spelling, a stored chunk size of 0 applies to sharded arrays too (in the outer grid), re-saving metadata only runs when the store warns, and the test takes its settings from the repository's hypothesis profiles under the slow_hypothesis marker, like the other stateful tests. Assisted-by: ClaudeCode:claude-opus-5-5 Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> * test(strategies): drop the overhang parameter and trim rectilinear events No caller passed overhang=False, so edge lists that sum past the extent are always drawn. rectilinear_chunk_grids now builds the metadata from the drawn chunk shapes instead of parsing a drawn declaration with the code under test, and only the events whose reach is reported remain. Assisted-by: ClaudeCode:claude-opus-5-5 Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> * test: check rectilinear properties against the declaration, not zarr's parsing test_create_array_stores_declared_rectilinear_chunks compared the stored grid with a RectilinearChunkGridMetadata built from the same chunks=, so a constructor that collapsed uniform edges to a bare int passed on both sides. It now expands the stored JSON chunk_shapes with a test-local RLE expansion and compares them with the raw chunks= list. The block indexing properties work their block extents out from the declared chunk sizes instead of from the chunk grid under test. Assisted-by: ClaudeCode:claude-opus-5-5 Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> * test: round-trip data through a rectilinear zero-length axis as it grows Draws rectilinear chunks= over a shape with a zero-length axis, grows that axis by append or resize, also past the declared edges, and checks the values against NumPy before and after reopening. Assisted-by: ClaudeCode:claude-opus-5-5 Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> * test: draw the state machine's rectilinear chunks from the shared strategy Replaces the local _rectilinear_dim copy with zarr.testing's rectilinear_chunks, now that this branch builds on the state machine. Reach for zero-length rectilinear axes is unchanged or higher. Assisted-by: ClaudeCode:claude-opus-5-5 Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> * refactor(metadata): warn about an upgraded document only once it validates An upgrade now returns the upgraded document and how it read it, and `from_dict` warns with those readings after the metadata constructor accepts the upgraded document. A stored document that is still invalid after an upgrade raises its own error instead of first warning how it was read. Assisted-by: ClaudeCode:claude-opus-5-5 Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> * refactor(metadata): one per-axis rule for stored chunk sizes, one rule for edges Stored regular chunk shapes, in both formats and in a sharding codec's inner chunk shape, are read entry by entry by one rule in upgrades.py: an int >= 1 is kept, `true` is read as 1 (zarr 3.0.10 also wrote it as the inner chunk size of a shard, which the sharding codec used to read silently), and 0 or `false` as one chunk spanning the axis. Integral floats are not read: no release wrote a regular grid with them. A document warns once, naming the array where the caller knows its path. Metadata constructors check every chunk edge length with one function, `parse_chunk_edge`, which tells a wrong type (TypeError) from a wrong value (ValueError); this covers bare sizes, rectilinear edges, RLE sizes and the sharding codec's inner chunk shape. Assisted-by: ClaudeCode:claude-opus-5-5 Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> * refactor(chunk-grids): start chunk guessing from the one full-span rule `_guess_regular_chunks` clamped zero-length axes with `np.maximum`, restating `full_span_chunk_size` with unit 1. Fold the zero-span normalizer tests into the `normalize_chunks_1d` tables. Assisted-by: ClaudeCode:claude-opus-5-5 Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> * test: run the array lifecycle state machine in the slow Hypothesis job Add it to `just hypothesis`. Re-saving metadata is always enabled and must leave valid metadata unchanged; appends favour an axis stored with chunk size 0, which raises how often a legacy axis grows before it is re-saved. A fixed example pins that a write to a shard kept by a shrink leaves its cells beyond the shape alone. Assisted-by: ClaudeCode:claude-opus-5-5 Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> * test: draw distinct rectilinear dividers without rejection `st.lists(..., unique=True)` rejected about 12% of draws per dimension (Hypothesis invalid cases); drawing each divider by index into the unused positions never rejects. Assisted-by: ClaudeCode:claude-opus-5-5 Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> * refactor(testing): type rectilinear declarations with RectilinearDimSpecJSON Reuse the JSON type from the metadata module instead of a private copy, and type the test's stored grid document with RectilinearChunkGridMetadataJSON so its type: ignore goes. Assisted-by: ClaudeCode:claude-opus-5-5 Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> * test: draw the list form of rectilinear chunks= from rectilinear_chunks `arrays()` decided whether a drawn rectilinear grid could be passed as `chunks=` lists by restating the normalizer's sum rule. Draw the list form from `rectilinear_chunks` instead, which also reaches it about three times as often. Drop issue references from shipped testing code. Assisted-by: ClaudeCode:claude-opus-5-5 Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> * fix(array): store upgraded metadata before writing the first chunk An array read from a stored document that the upgrades had to correct (a chunk size of 0, `false` or `true`) wrote chunks under the corrected layout while the store kept the old document, so zarr 3.2.1-3.4.0 then read only the fill value, and tensorstore and zarrs could not open it. `from_dict` now marks the metadata it read from an upgraded document (`_stored_document_upgraded`, a field outside the document and equality), and `AsyncArray._set_selection`, which every chunk write goes through (`setitem` now included), stores that metadata first and keeps the stored copy. Concurrent first writes store the same document. The array lifecycle state machine now ends the legacy state on a write and checks that no chunk is stored under a document that is still upgraded on read; `resave_metadata` runs only while the stored document is invalid, and re-saving valid metadata is checked once, at creation. The changelog also says which releases stored a chunk size of 0 on an axis of positive length. Assisted-by: ClaudeCode:claude-opus-5-5 Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> * refactor(metadata): name an array one way in upgrade warnings Warnings about an upgraded document name the array by its store path, `str(StorePath(store, path))`, on every path that reads one: opening an array, `AsyncArray.from_dict`, a group read with or without consolidated metadata, and consolidated members, which were named relative to the group. `GroupMetadata.from_dict` and `ConsolidatedMetadata.from_dict` take the group's path for that. The consolidated test now also opens the group with `use_consolidated=False` and checks each array's name, so dropping the path on either read path fails a test. Assisted-by: ClaudeCode:claude-opus-5-5 Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> * refactor(metadata): one rule for bare sizes and edge lists; one noun in messages - `_validate_chunk_shapes` decides "edge list or bare size" with one `match`: a list or tuple is an edge list, anything else is a bare size checked by `parse_chunk_edge`, so a string dimension such as `"10"` is rejected as not an int instead of being iterated per character. Stored rectilinear `from_dict` makes the same JSON split and passes the dimension to `expand_rle`, so an invalid edge or RLE count inside a list names its dimension. - Messages say "dimension" throughout, lowercase after the colon ("Dimension 0: chunk edge length must be >= 1, got 0"); the upgrade warnings read "0 in dimension 0 as one chunk spanning the dimension". - The upgrades test for JSON arrays with `list` only (a stored document holds no tuples), and `_read_chunk_size` says what `span=None` means. - `ArrayV2Metadata.from_dict` copies the document once. - The rejected stored chunk shapes get one test per error case. Assisted-by: ClaudeCode:claude-opus-5-5 Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> * refactor(testing)!: remove chunks_param_from_rectilinear `arrays()` now draws its rectilinear `chunks=` argument from `rectilinear_chunks`, so nothing uses the metadata-to-`chunks=` converter. The rectilinear strategies are experimental; the removal is noted in the changelog. Assisted-by: ClaudeCode:claude-opus-5-5 Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> * refactor(testing): drop the extent-1 special case in rectilinear_dim_edges Both modes already draw [1] for an extent of 1. Assisted-by: ClaudeCode:claude-opus-5-5 Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> * perf(testing): bound the chunks a drawn rectilinear grid declares in total Every dimension could draw up to 20 chunks, so a 3-d grid reached 8000 chunks; rejection-free divider draws made the large counts common, and indexing property tests visit every chunk. Mean chunks per drawn grid went from ~23 (before the rewrite) to ~75, with a tail past 5000, and test_mask_indexing went from 3.2s to 11.8s CPU under the ci profile. Cap the product at 400 chunks: 20 per dimension up to 2-d, 7 for 3-d, 4 for 4-d. Every declaration kind is still drawn. Assisted-by: ClaudeCode:claude-opus-5-5 Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> * fix(array): store the upgrade of the current stored document before writing A handle read from an upgraded document upserts the upgrade of what the store holds on its first non-empty chunk write: a stale handle no longer rolls back newer metadata, and an empty write stores nothing. consolidate_metadata does the same for each upgraded member before writing the consolidated document. Both go through two internal primitives in zarr.core.metadata.io: diff_documents compares a node's stored documents with those its metadata would store, value by value, and upsert_metadata encodes first, then stores only the documents that differ and returns the changes. The upgraded-document flag is a ClassVar set on the instance by one helper, mark_upgraded, which also warns; the upgrades are keyed by Zarr format; the Metadata.to_dict and V2 from_dict changes are reverted. _append goes through AsyncArray.setitem and _setitem is removed. A chunk shape that is not a list or tuple is rejected as a whole, and every expand_rle error names its dimension. Assisted-by: ClaudeCode:claude-opus-5-5 Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> * test: prefer zero-length axes for stored chunk size 0 in the lifecycle machine An empty write stores no metadata, so it no longer ends the legacy state. Assisted-by: ClaudeCode:claude-opus-5-5 Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> * refactor(testing): declare the rectilinear chunk limits and per-axis draw once The per-dimension limit of 20 chunks is now one constant, used by both `_max_chunks_per_dim` and the `rectilinear_dim_edges` default, and `rectilinear_chunk_grids` and `rectilinear_chunk_shape_declarations` draw their `chunk_shapes` through one private helper. The strategies draw exactly what they drew before. Assisted-by: ClaudeCode:claude-opus-5-5 Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> * fix(metadata): keep accepting the chunk sizes zarr 3.4.0 accepted in metadata constructors (patch release) Nothing in a patch release may reject a chunk size that zarr 3.4.0 accepted. The one chunk edge rule (`parse_chunk_edge`, which also reads RLE repeat counts) now reads any integral number as the `int` it equals: an `int`, a `bool`, a NumPy integer or an integral float, so rectilinear grids written with float edges (`[[4.0, 2]]`) read again and the grid constructors accept NumPy integers; a fractional float is still rejected. A regular chunk shape may again be any iterable. `ArrayV2Metadata(chunks=...)` and `ShardingCodec(chunk_shape=...)` read their chunk shape with `parse_shapelike`, as in 3.4.0: a scalar, NumPy integers, bools and 0 are accepted, and a 0 is written back as given (the kerchunk writer in VirtualiZarr relies on `chunks=(0,)` for empty inlined arrays). Stored documents with a chunk size of 0 are still read by the upgrades. The strict rule returns in the next minor release. Assisted-by: ClaudeCode:claude-opus-5-5 Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> * fix(array): leave a valid stored document as written on a stale handle's first write A handle read from an upgraded document re-reads the stored document before its first chunk write. If that document no longer needs an upgrade, store nothing: re-encoding it could differ from how another implementation wrote it, and nothing about it needs fixing. Assisted-by: ClaudeCode:claude-opus-5-5 Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> * docs: describe the 4334 changes to metadata constructors for a patch release Assisted-by: ClaudeCode:claude-opus-5-5 Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> * fix(testing): keep chunks_param_from_rectilinear in zarr.testing (patch release) Revert 0d640f8: a patch release removes nothing from `zarr.testing`. The removal returns in the next minor release. Assisted-by: ClaudeCode:claude-opus-5-5 Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> * fix(testing): keep rectilinear_chunks drawing an edge list per dimension (patch release) A patch release keeps what `zarr.testing` strategies return. `rectilinear_chunks` again returns `list[list[int]]`, an explicit edge list for every dimension, and `[]` for a 0-d shape; it now also draws zero-length dimensions. The form mixing bare-int steps and edge lists moves to the private `_rectilinear_chunks`, which `arrays()`, `rectilinear_arrays()`, `block_test_arrays()` and the tests draw from. The public strategy takes the mixed form in the next minor release. Assisted-by: ClaudeCode:claude-opus-5-5 Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> * docs: describe the 4377 strategy changes as additive for a patch release Assisted-by: ClaudeCode:claude-opus-5-5 Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> * fix(metadata): read float edges only in stored rectilinear documents The patch release widened the one chunk edge rule to accept integral floats so that stored rectilinear grids written with float edges (`[[4.0, 2]]`, as zarr 3.2 wrote for float edges) keep opening. That also made a stored regular chunk shape `[10.0]` open, which zarr 3.4.0 rejected and the next minor release would reject again. The constructor rule now accepts integers of any integer type (`int`, `bool`, NumPy integers) and rejects floats. A new document upgrade reads an integral JSON float of at least 1 as an `int` where zarr 3.2 stored one: the explicit edges and run-length encoded sizes of a rectilinear chunk grid, with the standard warning. Bare sizes, repeat counts, regular chunk shapes and inner chunk shapes stay for the constructors to reject. Assisted-by: ClaudeCode:claude-opus-5-5 Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> * test(codecs): pickle a ShardingCodec with an inner chunk size of 0 Assisted-by: ClaudeCode:claude-opus-5-5 Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> * fix(group): build every node before create_hierarchy deletes or stores anything A node whose metadata no array or group can be built from now fails with the store untouched, even with overwrite=True. Assisted-by: ClaudeCode:claude-opus-5-5 Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> * fix(metadata): warn only where the user must act; guard and refresh upgraded copies - Readings that give what zarr 3.4.0 read (0/false on an empty axis, JSON true, float rectilinear edges) are silent; the metadata is still marked upgraded, so the first write re-saves it. - JSON true is read as 1 in stored rectilinear edges and RLE sizes and in nested sharding codecs' inner chunk shapes. - A write through a handle whose stored document now lays out chunks differently raises and stores nothing; with no stored document it writes as before. - Storing group metadata refreshes each upgraded consolidated member from its own stored document (the one place: save_metadata); consolidate_metadata no longer needs its own pass. - Metadata built in code with chunk size 0 is read through the upgrades, so an array can be built from it, as in 3.4.0. - Chunk edges in metadata follow the 3.4.0 integer rule (int; bool read as its value); a string or mapping is rejected as a chunk shape as a whole. Assisted-by: ClaudeCode:claude-opus-5-5 Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> * test: expect the lifecycle machine's upgrade warning only on non-empty axes Assisted-by: ClaudeCode:claude-opus-5-5 Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> * test: pin chunks_param_from_rectilinear returning lists, as zarr 3.4.0 did Assisted-by: ClaudeCode:claude-opus-5-5 Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> * fix(metadata): leave a sharded chunk size of 0 unread when the inner shape is invalid A stored outer chunk size of 0 of a sharded array is read in multiples of the inner chunk size. When that inner size is itself 0 or `false`, the unit is unknown: the upgrade now leaves the 0 for the constructor, which rejects it with the same `ValueError` zarr 3.4.0 raised, instead of a ZeroDivisionError. `_read_codec` now matches the sharding codec like `_inner_chunk_shape` does. Assisted-by: ClaudeCode:claude-opus-5-5 Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> * perf(metadata): read each upgraded member once, concurrently, and adopt it A group handle kept the consolidated copies of upgraded members flagged, so every later group write re-read every such member, one after another, and read each twice on the first write (once to parse, once to diff). - `save_metadata` returns the metadata it stored; `AsyncGroup._save_metadata` (attrs, `update_attributes`, `delitem`, `consolidate_metadata`) and `Group.update_attributes_async` adopt it, so later writes read no member. - The refresh visits only nested groups and flagged members, and reads them with one `asyncio.gather`. The documents it reads are the ones the upsert diffs against (`read_documents` + `upsert_metadata(..., stored)`), and the array write path does the same. - `parse_stored_array` (documents -> silently marked metadata) replaces `read_stored_array`'s `(metadata, bool)` tuple, and is the one "read, mark, don't warn" path, also for code-built metadata. - A flagged member whose own document is gone or cannot be read (invalid, replaced by a group) keeps its consolidated copy instead of failing every group write. - `parse_array_metadata` of a metadata object reads it as a stored document only when `ArrayV2Metadata.chunks` holds a 0, the one chunk size that constructors still accept and the upgrades change. This removes the per-construction `to_dict` + upgrade (AsyncArray() back to 3.4.0 speed) and building arrays from codec configurations holding NumPy scalars works again, as in 3.4.0. - `create_hierarchy` documents that it stores a group's consolidated metadata as given. - Tests: second group write reads no member; nested member refresh; member without a readable document; NumPy-scalar codec configuration; stale handle whose inner chunk shape alone changed (kills `_chunk_layout` returning only the outer grid). Assisted-by: ClaudeCode:claude-opus-5-5 Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> * fix(group): adopt refreshed consolidated members in place A group write replaced the handle's metadata with a copy holding the consolidated members it read again, so the handle no longer shared its consolidated dicts with subgroup handles taken earlier: an array deleted through such a subgroup was stored again by the parent's next write, and reappeared on reopen. `_refresh_consolidated` now returns, along with the copy it encodes, the members it replaced (with the consolidated dict that holds each), and `save_metadata` writes them back into those dicts once the store succeeds, unless the member was deleted or replaced meanwhile. `save_metadata` returns nothing again, and the group callers keep their metadata objects. A failed store leaves the members flagged, so a retry reads them again. Assisted-by: ClaudeCode:claude-opus-5-5 Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> * fix(metadata): raise the rectilinear flag error when refreshing a consolidated member A group write reads each upgraded consolidated member again from its own document, and kept the consolidated copy when that document could not be read. That also swallowed the rectilinear chunks flag error, so a member whose document now declares a rectilinear grid had its stale copy stored as valid. The flag error is now `RectilinearChunksDisabledError`, a `ValueError`, and the refresh lets it propagate: the group write raises and stores nothing. Unreadable documents keep their consolidated copy as before. Assisted-by: ClaudeCode:claude-opus-5-5 Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> * fix(group): store a group's documents only; keep upgraded members as stored Group writes (attributes, `update_attributes`, deleting a member, `consolidate_metadata`, `create_hierarchy`) read each upgraded member of the consolidated metadata again from its own document and stored its upgrade. Those member writes raced concurrent deletions: two concurrent `delitem`s on a consolidated group recreated a deleted array's metadata document in most runs, which zarr 3.4.0 never did. A group write now stores only the group's own documents and reads none. Array metadata read from a document that had to be upgraded keeps that document (`_stored_document`, set by `mark_upgraded`, replacing the `_stored_document_upgraded` flag), and consolidated metadata stores such a member as it was stored. Every reader of the consolidated metadata then reads the member as upgraded again, and the array's own first chunk write stores the upgrade of its current document (or refuses a changed chunk grid) as before: the only write that upgrades a member document. Removed: the refresh and adoption of consolidated members in `save_metadata` (`_refresh_consolidated`, `_refresh_array`, `_Refreshed`), and `Group.update_attributes_async`'s detour through `save_metadata`. Tests pinning the refresh are replaced by tests that a group write reads nothing and writes only the group's documents, stores the member's consolidated copy byte for byte as stored, that concurrent deletions leave no member, and that the first write through consolidated metadata stores the member's upgrade or refuses a changed grid. Assisted-by: ClaudeCode:claude-opus-5-5 Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> * docs(group): say what consolidated metadata stores for an upgraded array Assisted-by: ClaudeCode:claude-opus-5-5 Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> * fix(array): clear the stored document whenever an array stores its metadata Setting attributes of an array read from a document that had to be upgraded stored the upgraded document with the new attributes, but left the metadata marked with the document it was read from. A consolidated group handle shares that metadata, so its next write stored the old document in the consolidated metadata and the new attributes were lost from it (zarr 3.4.0 kept them). Every write of an array's own documents (creating, resizing, setting attributes) now goes through `AsyncArray._save_metadata`, which clears the mark afterwards, as the first chunk write does after storing the upgrade. Both clear it through `_stored_document_replaced`, the one place that declares it: the first chunk write clears it also when it stores nothing (the store already holds a valid document, or none), so it cannot be folded into the save. The deep copy in `mark_upgraded` stays: the metadata's attributes share objects with the document it was read from, which the caller also holds. A test pins it. Assisted-by: ClaudeCode:claude-opus-5-5 Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> * test(metadata): pin that a failed metadata save keeps the stored document mark Setting attributes on or resizing an array read from a document that needed an upgrade clears the `_stored_document` mark only after the store accepts the new metadata. A test now injects a store failure for the array's own document and checks the mark and the stored bytes survive, for Zarr formats 2 and 3. The `_save_metadata` docstring now says only what the method does. Assisted-by: ClaudeCode:claude-opus-5-5 Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> * fix(metadata): read a stored chunk size of 0 as 1, however long the axis A stored chunk size of 0 or `false` was read as one chunk spanning the axis at open time. On an axis that grew after the size was written, that made the chunk size depend on when the array was opened, and it could be very large: `chunks: [0, 100, 100]` on shape (10000, 100, 100) read as one 800 MB chunk. It is now read as the smallest valid chunk edge length (1, or the inner chunk size for a shard), which is what `chunks=-1` gives on a zero-length axis. A resize by software that kept the stored 0 no longer changes the layout a stale handle expects. Assisted-by: ClaudeCode:claude-opus-5-5 * fix(metadata): re-save only upgrades that move chunks, and read non-JSON input as is A stored `true` chunk size or an integral float edge is read as the value zarr already read it as, so chunks written under the upgraded metadata are where every reader looks. Marking such documents for re-saving turned a plain chunk write into a metadata write: in a ZipStore that adds a second `zarr.json` entry (a `UserWarning`, an error under `-W error`), and it opened a race with concurrent metadata writes that 3.4.0 did not have. Each upgrade now reports whether it moves chunks, and only those mark the metadata. The upgrades also detected changes by comparing JSON encodings, so `ArrayV3Metadata.from_dict` given metadata built in code (a codec instance, a NumPy integer in a sharding codec's `chunk_shape`) raised `TypeError`. Changes are now tracked where they are made. Assisted-by: ClaudeCode:claude-opus-5-5 * fix(metadata): recommend recreating an array whose stored chunk size was 0 The warning for a stored chunk size of 0 on an axis of positive length now says that the array holds only its fill value, so recreating it with the wanted chunk shape loses nothing, and gives the re-save as the way to keep it instead. A re-save freezes the smallest chunk size into an array that holds no data yet. Each reading now carries its own advice, so mark_upgraded appends no shared hint. Assisted-by: ClaudeCode:claude-fable-5-1 Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com> * fix(metadata): give the recipe for recreating an array read from a stored chunk size of 0 The warning names the call, zarr.from_array(array.store, name=array.path, data=array, chunks=..., overwrite=True, write_data=False), which keeps the data type, fill value, attributes and codecs, and a test pins the recipe on both formats. Assisted-by: ClaudeCode:claude-fable-5-1 Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com> * refactor(metadata): call the lenient readings of stored documents repairs, not upgrades The module is zarr.core.metadata.repair: repair_array_document, mark_repaired, ARRAY_REPAIRS and the Repair type, AsyncArray._store_repaired_document, and the test module test_repair.py. A reading that turns an invalid stored document into a valid one fixes it; it does not move it to a newer format. Assisted-by: ClaudeCode:claude-fable-5-1 Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com> --------- Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
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‎changes/4377.misc.md‎

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The hypothesis strategies in `zarr.testing.strategies` now sample the full space of rectilinear chunk grid declarations: `arrays()` passes a rectilinear grid to `create_array` either as metadata or as a `chunks=` specification mixing bare-int steps and explicit edge lists in any arrangement, and the new `rectilinear_chunk_shape_declarations` and `rectilinear_chunk_grids` cover stored metadata, including run-length encoded edge lists in canonical and arbitrary groupings and edges overhanging the array extent. `rectilinear_chunks` and `chunk_grids` also draw zero-length dimensions.

‎src/zarr/testing/strategies.py‎

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@@ -34,7 +34,11 @@
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from zarr.core.dtype.npy.structured import Struct
3535
from zarr.core.dtype.wrapper import TBaseDType, TBaseScalar, ZDType
3636
from zarr.core.metadata import ArrayV2Metadata, ArrayV3Metadata
37-
from zarr.core.metadata.v3 import RectilinearChunkGridMetadata, RegularChunkGridMetadata
37+
from zarr.core.metadata.v3 import (
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RectilinearChunkGridMetadata,
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RectilinearDimSpecJSON,
40+
RegularChunkGridMetadata,
41+
)
3842
from zarr.core.sync import sync
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from zarr.storage import MemoryStore, StoreLike
4044
from zarr.storage._utils import _join_paths, normalize_path
@@ -444,18 +448,27 @@ def arrays(
444448
array_path = _join_paths([path, name])
445449
root = zarr.open_group(store, mode=open_mode, zarr_format=zarr_format)
446450

447-
# Convert chunk grid metadata to a form create_array accepts:
448-
# - RegularChunkGridMetadata -> flat tuple of ints
449-
# - RectilinearChunkGridMetadata -> nested list of ints (triggers rectilinear path)
450-
# - v2 -> flat tuple of ints
451-
chunks_param: tuple[int, ...] | list[int | list[int]]
451+
chunks_param: tuple[int, ...] | list[int | list[int]] | RectilinearChunkGridMetadata
452452
shard_shape = None
453453
dim_names = None
454454
if zarr_format == 3:
455455
chunk_grid_meta = draw(st.none() | chunk_grids(shape=nparray.shape), label="chunk grid")
456456
dim_names = draw(dimension_names(ndim=nparray.ndim), label="dimension names")
457457
if isinstance(chunk_grid_meta, RectilinearChunkGridMetadata):
458-
chunks_param = chunks_param_from_rectilinear(chunk_grid_meta)
458+
# A rectilinear grid is passed either as the metadata object or in
459+
# the list form of `chunks=`, drawn from its own strategy. A 0-d
460+
# array has no dimension to hold an edge list.
461+
if nparray.ndim > 0 and draw(st.booleans(), label="chunks as lists"):
462+
event("rectilinear chunks= as lists")
463+
chunks_param = draw(_rectilinear_chunks(shape=nparray.shape), label="chunks")
464+
chunk_grid_meta = RectilinearChunkGridMetadata(
465+
chunk_shapes=tuple(
466+
dim if isinstance(dim, int) else tuple(dim) for dim in chunks_param
467+
)
468+
)
469+
else:
470+
event("rectilinear chunks= as metadata")
471+
chunks_param = chunk_grid_meta
459472
elif isinstance(chunk_grid_meta, RegularChunkGridMetadata):
460473
chunks_param = chunk_grid_meta.chunk_shape
461474
else:
@@ -505,7 +518,9 @@ def arrays(
505518
)
506519
assert shard_shape == a.shards
507520
else:
508-
assert isinstance(a.metadata.chunk_grid, RectilinearChunkGridMetadata)
521+
# The stored grid is exactly the declared one: bare ints stay bare
522+
# ints, edge lists keep their edges.
523+
assert a.metadata.chunk_grid == chunk_grid_meta
509524
assert shard_shape is None
510525

511526
assert a.basename == name, (a.basename, name)
@@ -546,59 +561,190 @@ def chunks_param_from_rectilinear(
546561
return [list(dim) if isinstance(dim, tuple) else dim for dim in meta.chunk_shapes]
547562

548563

564+
# The most chunks a drawn rectilinear grid declares along one axis, and over
565+
# the array, all axes together. Indexing tests visit every chunk, so the
566+
# product is what costs time.
567+
_RECTILINEAR_MAX_CHUNKS_PER_DIM = 20
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_RECTILINEAR_CHUNK_BUDGET = 400
569+
570+
571+
def _max_chunks_per_dim(ndim: int) -> int:
572+
"""At most `_RECTILINEAR_MAX_CHUNKS_PER_DIM` chunks per dimension, and at
573+
most `_RECTILINEAR_CHUNK_BUDGET` in total over `ndim` dimensions."""
574+
return max(
575+
k
576+
for k in range(1, _RECTILINEAR_MAX_CHUNKS_PER_DIM + 1)
577+
if k**ndim <= _RECTILINEAR_CHUNK_BUDGET
578+
)
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580+
581+
@st.composite
582+
def rectilinear_dim_edges(
583+
draw: st.DrawFn, *, extent: int, max_chunks: int = _RECTILINEAR_MAX_CHUNKS_PER_DIM
584+
) -> list[int]:
585+
"""Explicit chunk edge lengths summing exactly to `extent`.
586+
587+
A zero `extent` has no chunks for edges to cover, and no non-empty list
588+
of positive edges sums to 0; its edges are the chunks the axis grows into
589+
on `append` or `resize`, so any non-empty list of positive edges is drawn.
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591+
Two modes: "uneven" cuts the extent at random dividers; "uniform" repeats
592+
one size with an optional remainder, optionally shuffled so equal edges
593+
are not all adjacent. At most `max_chunks` chunks keeps property tests
594+
fast.
595+
"""
596+
assert extent >= 0
597+
if extent == 0:
598+
event("rectilinear edges: zero extent")
599+
return draw(st.lists(st.integers(min_value=1, max_value=10), min_size=1, max_size=5))
600+
if draw(st.booleans(), label="uneven edges"):
601+
nchunks = draw(st.integers(min_value=1, max_value=min(extent, max_chunks)))
602+
# Draw distinct dividers by index into the unused positions: no
603+
# rejection, unlike `st.lists(..., unique=True)`.
604+
positions = list(range(1, extent))
605+
dividers = sorted(
606+
positions.pop(draw(st.integers(min_value=0, max_value=len(positions) - 1)))
607+
for _ in range(nchunks - 1)
608+
)
609+
return [b - a for a, b in zip([0, *dividers], [*dividers, extent], strict=True)]
610+
size = draw(st.integers(min_value=math.ceil(extent / max_chunks), max_value=extent))
611+
edges = [size] * (extent // size)
612+
if extent % size:
613+
edges.append(extent % size)
614+
if draw(st.booleans(), label="shuffle uniform edges"):
615+
return list(draw(st.permutations(edges)))
616+
return edges
617+
618+
619+
def _rectilinear_step(draw: st.DrawFn, *, extent: int, max_chunks: int) -> int:
620+
"""A bare-int chunk size for one dimension: a step that repeats to cover
621+
the extent, with the last chunk possibly smaller. A step larger than the
622+
extent (one overhanging chunk) is allowed, as for a regular grid."""
623+
step = draw(st.integers(min_value=max(1, math.ceil(extent / max_chunks)), max_value=extent + 3))
624+
if step > extent:
625+
event("rectilinear step: larger than extent")
626+
return step
627+
628+
549629
@st.composite
550630
def rectilinear_chunks(draw: st.DrawFn, *, shape: tuple[int, ...]) -> list[list[int]]:
551-
"""Generate valid rectilinear chunk shapes for a given array shape.
631+
"""A `chunks=` specification declaring a rectilinear grid over `shape`, as an
632+
explicit edge list per dimension summing to the extent (any edges, for a zero
633+
extent). A 0-d `shape` gives `[]`.
634+
635+
To also draw bare-int steps, see `_rectilinear_chunks`.
636+
"""
637+
max_chunks = _max_chunks_per_dim(len(shape))
638+
return [draw(rectilinear_dim_edges(extent=e, max_chunks=max_chunks)) for e in shape]
552639

553-
Uses two modes per dimension:
554-
- "expanded": random divider points create arbitrary chunk sizes
555-
- "rle": uniform chunks with optional remainder, optionally shuffled
556640

557-
Keeps max chunks per dimension <= 20 to avoid performance issues
558-
in property tests. With higher dimensions, the total chunk count
559-
grows multiplicatively.
641+
@st.composite
642+
def _rectilinear_chunks(draw: st.DrawFn, *, shape: tuple[int, ...]) -> list[int | list[int]]:
643+
"""A `chunks=` specification declaring a rectilinear grid over `shape`.
644+
645+
Each dimension is either a bare int (a step size; the last chunk may be
646+
smaller) or an explicit edge list summing to the extent (any edges, for a
647+
zero extent). At least one dimension is an edge list, since bare ints
648+
alone declare a regular grid.
649+
Run-length encoding is not part of the `chunks=` syntax; it belongs to
650+
stored metadata, see `rectilinear_chunk_shape_declarations`.
651+
652+
`shape` must have at least one dimension: a 0-d array has no dimension
653+
to hold an edge list, so it cannot have a rectilinear grid.
560654
"""
561-
chunk_shapes: list[list[int]] = []
562-
for size in shape:
563-
assert size > 0
564-
if size > 1:
565-
mode = draw(st.sampled_from(["expanded", "rle"]))
566-
if mode == "expanded":
567-
event("rectilinear expanded")
568-
max_chunks = min(size - 1, 20)
569-
nchunks = draw(st.integers(min_value=1, max_value=max_chunks))
570-
dividers = sorted(
571-
draw(
572-
st.lists(
573-
st.integers(min_value=1, max_value=size - 1),
574-
min_size=nchunks - 1,
575-
max_size=nchunks - 1,
576-
unique=True,
577-
)
578-
)
579-
)
580-
chunk_shapes.append(
581-
[a - b for a, b in zip(dividers + [size], [0] + dividers, strict=False)]
582-
)
583-
else:
584-
# RLE mode: uniform chunks with optional remainder
585-
max_chunk_size = min(size, 20)
586-
chunk_size = draw(st.integers(min_value=1, max_value=max_chunk_size))
587-
n_full = size // chunk_size
588-
remainder = size % chunk_size
589-
chunks_list = [chunk_size] * n_full
590-
if remainder > 0:
591-
chunks_list.append(remainder)
592-
# Optionally shuffle to create non-contiguous duplicate patterns
593-
if draw(st.booleans()):
594-
event("rectilinear rle shuffled")
595-
chunks_list = draw(st.permutations(chunks_list))
596-
else:
597-
event("rectilinear rle")
598-
chunk_shapes.append(list(chunks_list))
655+
assert shape, "a rectilinear grid needs at least one dimension"
656+
max_chunks = _max_chunks_per_dim(len(shape))
657+
forced_list = draw(st.integers(min_value=0, max_value=len(shape) - 1))
658+
chunks: list[int | list[int]] = []
659+
for i, extent in enumerate(shape):
660+
if i != forced_list and draw(st.booleans(), label="bare int"):
661+
chunks.append(_rectilinear_step(draw, extent=extent, max_chunks=max_chunks))
599662
else:
600-
chunk_shapes.append([1])
601-
return chunk_shapes
663+
chunks.append(draw(rectilinear_dim_edges(extent=extent, max_chunks=max_chunks)))
664+
return chunks
665+
666+
667+
def _rle_encode(draw: st.DrawFn, edges: list[int]) -> list[int | list[int]]:
668+
"""Run-length encode `edges` as the spec allows: a mix of bare ints and
669+
`[size, count]` pairs. Either the canonical form (each run as one pair,
670+
a run of one as a bare int) or an arbitrary grouping, which may split a
671+
run across pairs and use `count == 1`."""
672+
canonical = draw(st.booleans(), label="canonical rle")
673+
if not canonical:
674+
event("rectilinear rle: arbitrary grouping")
675+
encoded: list[int | list[int]] = []
676+
i = 0
677+
while i < len(edges):
678+
run = 1
679+
while i + run < len(edges) and edges[i + run] == edges[i]:
680+
run += 1
681+
if canonical:
682+
count = run
683+
bare = run == 1
684+
else:
685+
count = draw(st.integers(min_value=1, max_value=run))
686+
bare = count == 1 and draw(st.booleans(), label="bare edge")
687+
encoded.append(edges[i] if bare else [edges[i], count])
688+
i += count
689+
return encoded
690+
691+
692+
def _rectilinear_chunk_shapes(
693+
draw: st.DrawFn, shape: tuple[int, ...]
694+
) -> tuple[int | tuple[int, ...], ...]:
695+
"""The `chunk_shapes` of a stored rectilinear grid over `shape`: per
696+
dimension a bare-int step, or explicit edges. Edges may sum beyond the
697+
extent, which the spec allows and a shrinking resize produces."""
698+
max_chunks = _max_chunks_per_dim(len(shape))
699+
chunk_shapes: list[int | tuple[int, ...]] = []
700+
for extent in shape:
701+
if draw(st.booleans(), label="bare int"):
702+
chunk_shapes.append(_rectilinear_step(draw, extent=extent, max_chunks=max_chunks))
703+
continue
704+
edges = draw(rectilinear_dim_edges(extent=extent, max_chunks=max_chunks))
705+
if extent > 0 and draw(st.booleans(), label="overhang"):
706+
event("rectilinear edges: overhang")
707+
if draw(st.booleans(), label="trailing edge"):
708+
edges = [*edges, draw(st.integers(min_value=1, max_value=5))]
709+
else:
710+
edges[-1] += draw(st.integers(min_value=1, max_value=5))
711+
chunk_shapes.append(tuple(edges))
712+
return tuple(chunk_shapes)
713+
714+
715+
@st.composite
716+
def rectilinear_chunk_shape_declarations(
717+
draw: st.DrawFn, *, shape: tuple[int, ...]
718+
) -> tuple[list[RectilinearDimSpecJSON], tuple[int | tuple[int, ...], ...]]:
719+
"""The `chunk_shapes` of a stored rectilinear chunk grid, with its meaning.
720+
721+
Samples the whole declaration space of the spec. Per dimension: a bare
722+
int step, or an edge list written in full or run-length encoded
723+
(canonically, or with arbitrary grouping). Edge lists may sum beyond the
724+
extent.
725+
726+
Returns `(declaration, chunk_shapes)`: the JSON value to store, and the
727+
`chunk_shapes` that parsing it must produce.
728+
"""
729+
chunk_shapes = _rectilinear_chunk_shapes(draw, shape)
730+
declaration: list[RectilinearDimSpecJSON] = [
731+
dim
732+
if isinstance(dim, int)
733+
else list(dim)
734+
if draw(st.booleans(), label="write edges in full")
735+
else _rle_encode(draw, list(dim))
736+
for dim in chunk_shapes
737+
]
738+
return declaration, chunk_shapes
739+
740+
741+
@st.composite
742+
def rectilinear_chunk_grids(
743+
draw: st.DrawFn, *, shape: tuple[int, ...]
744+
) -> RectilinearChunkGridMetadata:
745+
"""A `RectilinearChunkGridMetadata` over `shape`, per dimension a bare-int
746+
step or explicit edges, which may sum beyond the extent."""
747+
return RectilinearChunkGridMetadata(chunk_shapes=_rectilinear_chunk_shapes(draw, shape))
602748

603749

604750
@st.composite
@@ -613,16 +759,9 @@ def chunk_grids(
613759
614760
This allows property tests to exercise both chunk grid types.
615761
"""
616-
# RectilinearChunkGridMetadata doesn't support zero-sized dimensions,
617-
# so use RegularChunkGridMetadata if any dimension is 0
618-
if any(s == 0 for s in shape):
619-
event("using RegularChunkGridMetadata (zero-sized dimensions)")
620-
return RegularChunkGridMetadata(chunk_shape=draw(chunk_shapes(shape=shape)))
621-
622762
if zarr.config.get("array.rectilinear_chunks") and draw(st.booleans()):
623-
chunks = draw(rectilinear_chunks(shape=shape))
624763
event("using RectilinearChunkGridMetadata")
625-
return RectilinearChunkGridMetadata(chunk_shapes=tuple(tuple(dim) for dim in chunks))
764+
return draw(rectilinear_chunk_grids(shape=shape))
626765
else:
627766
event("using RegularChunkGridMetadata")
628767
return RegularChunkGridMetadata(chunk_shape=draw(chunk_shapes(shape=shape)))
@@ -640,7 +779,7 @@ def rectilinear_arrays(
640779
) -> Any:
641780
"""Generate a zarr v3 array with rectilinear (variable) chunk grid."""
642781
shape = draw(shapes)
643-
chunk_shapes = draw(rectilinear_chunks(shape=shape))
782+
chunk_shapes = draw(_rectilinear_chunks(shape=shape))
644783

645784
np_dtype = draw(dtypes())
646785
nparray = draw(numpy_arrays(shapes=st.just(shape), dtype=np_dtype))
@@ -943,7 +1082,7 @@ def block_test_arrays(
9431082
``zarray.write_chunk_sizes`` — the array's *outer* (block / shard) grid, which
9441083
is exactly the grid ``Array.blocks`` addresses; the caller reads it directly.
9451084
"""
946-
chunks: tuple[int, ...] | list[list[int]]
1085+
chunks: tuple[int, ...] | list[int | list[int]]
9471086
if draw(st.booleans()):
9481087
# regular arm, optionally sharded
9491088
nparray, chunks = draw(
@@ -960,7 +1099,7 @@ def block_test_arrays(
9601099
# rectilinear arm, always unsharded
9611100
event("block rectilinear")
9621101
shape = draw(_rectilinear_shapes)
963-
chunks = draw(rectilinear_chunks(shape=shape))
1102+
chunks = draw(_rectilinear_chunks(shape=shape))
9641103
nparray = draw(numpy_arrays(shapes=st.just(shape), dtype=draw(dtypes())))
9651104
shards, rectilinear = None, True
9661105

‎tests/conftest.py‎

Lines changed: 16 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,6 @@
11
from __future__ import annotations
22

3+
import itertools
34
import math
45
import os
56
import pathlib
@@ -574,6 +575,21 @@ def deep_nan_equal(a: object, b: object) -> bool:
574575
return nan_equal(a, b)
575576

576577

578+
def declared_chunk_data_sizes(declared: int | Sequence[int], extent: int) -> tuple[int, ...]:
579+
"""The data sizes of the chunks one declared chunk grid dimension places
580+
over `extent`, worked out from the declaration alone: a bare int repeats
581+
to cover the extent, explicit edges are clipped to it. An oracle that does
582+
not go through zarr's chunk grid code."""
583+
sizes: list[int] = []
584+
offset = 0
585+
for edge in itertools.repeat(declared) if isinstance(declared, int) else declared:
586+
if offset >= extent:
587+
break
588+
sizes.append(min(edge, extent - offset))
589+
offset += edge
590+
return tuple(sizes)
591+
592+
577593
def gzip_streams_equal_except_mtime(a: bytes, b: bytes) -> bool:
578594
"""Compare two gzip streams, ignoring the MTIME field of the header.
579595

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