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feat(zarr-metadata): draw whole v3 documents - #439

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feat(zarr-metadata): draw whole v3 documents#439
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Added array_documents, group_documents and consolidated_group_documents to zarr_metadata.testing.strategies, which draw whole Zarr v3 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. pipelines now takes spellings, as declarations does.

How the document strategies work

  • A drawn document is read by the package's reader before it is returned, and one its definitions refuse raises a ValueError. Strategies with nothing to draw a required member from raise a LookupError that names what is missing.
  • A data type that no array -> bytes codec in the strategies takes is not drawn. If that is every data type they hold, Hypothesis reports the strategy as unsatisfiable.
  • spellings="canonical" applies to declarations. A fill value is drawn in every spelling its data type's spec gives it, either way.
  • A member the spec does not define is always an object that says must_understand is false, so a reader may ignore it.
  • A consolidated listing is flat, and each node's parent is a group it also lists. A listed group has no listing of its own, or the empty one the reference implementation writes.
  • A shape has each number of axes up to 8 about as often as any other, and axes that are zero, short, or up to 2**63 - 1.
  • A document's data type is drawn first. Drawn after the shape, the first data type in the list made up about a fifth of all documents.

Tests

  • Each document is read in ZARR_PYTHON_CONTEXT. Arrays and groups are read as drawn and after a JSON round trip, and consolidated listings as drawn.
  • Reach tests cover every definition, each optional member present and absent, no axes, a zero-length axis, a shard over a rectilinear grid, a listed node below a listed group, and a listed group with and without an empty listing.
  • Share tests bound how often a few hundred examples hold no axes, more than five axes, a zero-length axis, an axis past 32 bits, and the first data type. The bounds are wide, because a share can move a few points between processes.
  • The agent planted bugs in the new module and in the later sampling fixes, and the suite catches each of them. Three name-filter bugs survived at first, so the strategies now draw reserved names on purpose and filter them out.
  • just check is green on Python 3.11 and 3.14 (3587 passed, 3 skipped; 3590 passed).

Left open

  • storage_transformers is drawn only as empty, because no strategy defines one.
  • A listed group never holds a non-empty listing of its own.
  • A definition that claims an extra field has no way to be drawn. A custom strategy cannot add one yet.
  • v2 documents are planned as a separate PR.
Stack

PR 3 of the strategies stack, based on claude/zarr-metadata-nested-strategies (#416, upstream zarr-developers#4597). Merge that first, then retarget this to main.

🤖 Generated with Claude Code

d-v-b added a commit that referenced this pull request Nov 3, 2026
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chore(zarr-metadata): number the document strategies changelog fragme…
f15c9d3 
…nt after #439

Assisted-by: ClaudeCode:claude-opus-5-5
d-v-b added a commit that referenced this pull request Nov 3, 2026
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chore(zarr-metadata): number the document strategies changelog fragme…
c211013 
…nt after #439

Assisted-by: ClaudeCode:claude-opus-5-5
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d-v-b force-pushed the claude/zarr-metadata-document-strategies branch from f15c9d3 to c211013 Compare November 3, 2026 21:48
d-v-b added a commit that referenced this pull request Nov 3, 2026
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chore(zarr-metadata): number the document strategies changelog fragme…
55b3331 
…nt after #439

Assisted-by: ClaudeCode:claude-opus-5-5
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d-v-b force-pushed the claude/zarr-metadata-document-strategies branch from c211013 to 1b955ce Compare November 3, 2026 22:46
d-v-b added a commit that referenced this pull request Nov 3, 2026
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chore(zarr-metadata): number the document strategies changelog fragme…
9ca1a8c 
…nt after #439

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d-v-b force-pushed the claude/zarr-metadata-document-strategies branch from 1b955ce to e9bc2fb Compare November 3, 2026 23:21
d-v-b added a commit that referenced this pull request Nov 4, 2026
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chore(zarr-metadata): number the document strategies changelog fragme…
656c61f 
…nt after #439

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d-v-b force-pushed the claude/zarr-metadata-document-strategies branch from e9bc2fb to e8ef016 Compare November 4, 2026 07:51
d-v-b and others added 7 commits November 4, 2026 09:58
@d-v-b
feat(zarr-metadata): draw nested fields and codec pipelines (zarr-dev…
630bf36 
…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
@d-v-b
feat(zarr-metadata)!: replace scope update with copy(update=...) and …
94dcfd1 
…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
@pre-commit-ci @d-v-b
chore: update pre-commit hooks (zarr-developers#4594)
4a804a7 
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>
@d-v-b
feat(zarr-metadata): draw whole v3 documents
3653351 
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
@d-v-b
chore(zarr-metadata): number the document strategies changelog fragme…
0afeada 
…nt after #439

Assisted-by: ClaudeCode:claude-opus-5-5
@d-v-b
fix(zarr-metadata): sample document shapes, listings and data types e…
e916dc1 
…venly

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
@d-v-b
chore(zarr-metadata): number the document strategies changelog fragme…
032a0b4 
…nt after zarr-developers#4602

Assisted-by: ClaudeCode:claude-opus-5-5
@d-v-b
d-v-b force-pushed the claude/zarr-metadata-document-strategies branch from e8ef016 to 032a0b4 Compare November 6, 2026 13:21
d-v-b added a commit that referenced this pull request Nov 6, 2026
@d-v-b
feat(zarr-metadata): draw whole v3 documents (zarr-developers#4602)
4fdafb2 
* 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

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