Assisted-by: ClaudeCode:claude-opus-4.8

The hatch run-coverage / run-coverage-html / run-hypothesis (and
gputest run-coverage) scripts passed --source=src to coverage run, which
excluded the index-transform algebra after its move to
packages/zarr-transforms/src — it was measured before the move. Declare the
measured source trees in [tool.coverage.run] source instead, so every
coverage run invocation measures both src and the workspace package
consistently, and drop the CLI flag from all four scripts.

Assisted-by: ClaudeCode:claude-opus-4.8

…anges

zarr-transforms is a hard runtime dependency of zarr with no CI. Add
`zarr-transforms.yml` (push/PR path-filtered test/ruff/pyright, mirroring
zarr-metadata; the test job runs from the repo root because the transform
tests import zarr) and `zarr-transforms-release.yml` (tag-triggered publish
on `zarr_transforms-v*`). Extend `check_changelogs.yml` to check the
package's changes directory.

Bump the package `requires-python` floor to >=3.12 (consistent with the
repo; nothing tested 3.11) and update its classifiers, ruff target, and
pyright pythonVersion to match. Extend the root hatch `--match v*` comment
to note the `zarr_transforms-v*` tags it also excludes.

Disclose the two deliberate eager-path changes in the 3906 changelog: the
Array repr `domain={...}` suffix and the 0-d iteration TypeError matching
NumPy. Fix a stale comment in array.py that claimed pop_fields yields []
for no fields (it now yields None).

Assisted-by: ClaudeCode:claude-fable-5

Mirrors zarr_metadata's importlib.metadata idiom; the release
workflow's isolated-wheel check imports it.

Assisted-by: ClaudeCode:claude-fable-5

…ansforms

The ArrayMap (fancy) branch of iter_chunk_transforms enumerated the dense
range(min_chunk, max_chunk + 1) bounding box and ran transform.intersect
against every candidate chunk, making sparse fancy/vindex chunk resolution
scale O(n_chunks) instead of O(n_touched). The exact touched chunk ids were
already computed and then discarded in favor of min/max.

Enumerate each fancy dimension's distinct touched chunk ids (np.unique)
instead; the cartesian product then spans only touched-per-dimension
combinations. Constant/Dimension dims keep their contiguous ranges. Semantics
are unchanged: the dense range only ever added empty intersections, which
intersect already skipped.

Sparse vindex (2 far-apart coords) goes from 15.9x slower than eager at 1k
chunks / 65.5x at 4k to ~1.1x at both, flat in grid size. Dense fancy
selections are unchanged.

Assisted-by: ClaudeCode:claude-fable-5

Vendored, unmodified, from ndsel branch fix/slice-origin-trunc
(commit c132b4c1caa3205830ce35a42502363171f650a7). PROVENANCE.md records
the source URL, commit SHA, and do-not-edit note. The corpus is the
language-agnostic fixture set every ndsel implementation runs against.

Assisted-by: ClaudeCode:claude-opus-4.8

Add a pure JSON->JSON message layer (messages.py: parse_ndsel,
normalize_ndsel, NdselError) implementing the ndsel draft wire format,
which adapts TensorStore's IndexTransform. It accepts all five kinds
(point/box/slice/points/transform), normalizes to the canonical transform
body (spec 4.3), and enforces the full error taxonomy. Verified against the
vendored conformance corpus.

Rework json.py into the engine/lowering layer: transform_{to,from}_canonical
(re-pointed from index_transform_{to,from}_json). Engine constraints live
here only (reject infinite bounds, implicit-lowers-by-value). Fix the oindex
wire format so index_array maps no longer carry input_dimension (rejected by
ndsel and TensorStore); degenerate all-singleton arrays collapse to constant
maps, and input_dimension is reconstructed from array dependency axes on load.

Cross-checked against a real tensorstore (importorskip) for a set of finite
canonical bodies.

Assisted-by: ClaudeCode:claude-opus-4.8

The pyright job added alongside zarr-metadata's config had never actually
run before an external PR triggered it, and fails with 68 errors on this
branch's HEAD.

Downgrade reportUnknownVariableType/Argument/Member/ParameterType to
warnings: the strict config was copied from zarr-metadata's JSON/dataclass
code, but numpy's stubs return partially-unknown types even at fully-typed
call sites, so this numpy-heavy package can't reasonably satisfy that
family. CI only fails on errors, so warnings keep the signal visible
without blocking the build.

Fix the genuine findings in code:
- reportUnnecessaryIsInstance (14 sites across transform.py,
  composition.py, json.py, chunk_resolution.py): replace tautological
  final isinstance arms (pyright proves them always-true once prior
  branches exhaust the union) with `else:` plus a comment naming the
  narrowed type. Two sites in composition.py and one in json.py also drop
  a `# pragma: no cover`-marked dead `raise TypeError` that followed.
- reportPrivateUsage (2 sites): chunk_resolution.py's
  `chunk_grid._dimensions` (declared on the ChunkGridLike Protocol for
  structural typing against zarr's ChunkGrid) and json.py's cross-module
  import of transform.py's `_array_map_dependency_axes`. Both are
  suppressed with `# pyright: ignore[reportPrivateUsage]` plus a comment;
  renaming either is left as an open pre-publish API decision.

Zero behavior change. Verified: pyright 0 errors (was 68); pytest 266
passed, 1 skipped; mypy clean; ruff clean.

Assisted-by: ClaudeCode:claude-fable-5

Fixtures verified byte-identical to the merged c59bc556c; only the
reference moves off the deleted feature branch.

Assisted-by: ClaudeCode:claude-fable-5

…nsforms

The fast path bound 'm' as ArrayMap before the general loop rebinds it
to the OutputIndexMap union, which mypy rejects (and treats the
ConstantMap arm as unreachable). packages/ is outside the pre-commit
mypy scope, so #234's CI could not catch this.

Assisted-by: ClaudeCode:claude-fable-5

…ndexing

# Conflicts:
#	pyproject.toml
#	src/zarr/core/array.py
#	uv.lock

…indexing

Pre-publish rename: the in-tree zarr-transforms workspace package is not
yet published, so this is a safe, purely mechanical rename with zero
behavior change. Distribution name is now zarr-indexing; import name is
now zarr_indexing.

Covers: the package directory and src layout, the package's own
pyproject.toml (name, tag-pattern, wheel packages, towncrier package),
the root pyproject.toml (workspace member, uv source, runtime
dependency, coverage source, pytest testpaths, hatch version comment),
all imports across src/zarr, tests, and the package's own tests, the
zarr-transforms(-release).yml workflows (renamed to zarr-indexing(-release).yml
with matching job names, path filters, tag pattern, environment names,
artifact names, and smoke test), check_changelogs.yml's package path,
changelog fragments (root changes/3906.feature.md and the package's own
changes/), and the regenerated uv.lock.

Assisted-by: ClaudeCode:claude-fable-5

…classes

Identity (non-view) arrays now render with the legacy 3.x repr with no
`domain={...}` suffix, byte-identical across `Array` and `AsyncArray`.
The suffix appears only on non-identity lazy views, and `AsyncArray`
gains it for views (reachable via `translate_by` and friends). Restores
the doctests and repr tests that had been rewritten to expect the
unconditional suffix on identity arrays.

Assisted-by: ClaudeCode:claude-opus-4.8

`get_coordinate_selection(out=...)` requires a flat `(n,)` buffer on
eager/identity arrays but the broadcast selection shape on lazy views.
Document both sides in the `out` parameter docstring and note that the
broadcast-shape contract is the long-term direction. No behavior change.

Assisted-by: ClaudeCode:claude-opus-4.8

…nning docs)

- name the zarr-indexing changelog fragment by PR number (3906) so the
  integer-issue check passes
- drop :class: sphinx roles from the indexing-program docstrings
  (mkdocs markdown; caught by main's new ci/lint_docs.py)
- untrack docs/superpowers/ planning documents: upstream main gitignores
  that path (agent planning notes are local-only by convention), which
  also removes them from markdownlint's scope; files remain on disk

Assisted-by: ClaudeCode:claude-fable-5

…dLike Protocol

Pre-publish API cleanup (option 2): iter_chunk_transforms now accepts
Sequence[DimensionGridLike] directly, so the published contract contains
only public names. zarr's integration layer passes its own private
chunk_grid._dimensions, keeping the private access inside zarr where it
belongs; both pyright reportPrivateUsage suppressions tied to the old
Protocol are gone.

Assisted-by: ClaudeCode:claude-fable-5

The copy predates the merge from main that bumped setup-uv to v8.3.2
and attest to v4.1.1 in the zarr-metadata release workflow.

Assisted-by: ClaudeCode:claude-fable-5

…y paths

`Order.check` differenced adjacent elements with `np.diff`, so on an unsigned
dtype a descending step wrapped around to a large positive value and the
selection was classified as increasing. `IntArrayDimIndexer` then took the
no-reorder fast path and read the wrong region out of each chunk.

Unsigned arrays also reached the chunk-relative arithmetic, where NumPy
promotes `uint64` mixed with a signed offset to `float64`, yielding a float
chunk selection and `IndexError: arrays used as indices must be of integer (or
boolean) type`.

`Order.check` now compares adjacent elements instead of differencing them, and
both eager entry points (`IntArrayDimIndexer` for oindex, `CoordinateIndexer`
for vindex) cast unsigned index arrays to `np.intp` before any order check or
chunk arithmetic. A value too large for `np.intp` cannot index any array, so it
raises `BoundsCheckError` rather than wrapping to a negative index. Signed
input is untouched. The lazy path already normalized to `np.intp` at its
boundary and is unaffected.

Assisted-by: ClaudeCode:claude-fable-5