Zarr v3

[HelenaLC]

No description provided.

[Copilot]

Pull request overview

This PR updates SpatialData’s Zarr attribute handling to support Zarr v3 layout differences (notably multiscales under ome), and reorganizes the test suite to cover both v2/v3 fixtures.

Changes:

• Added a version-aware multiscales() accessor and updated coordinate-transform utilities to use it.
• Updated image channel extraction and SpatialData reading logic for v3-compatible metadata/layout.
• Reorganized and expanded unit tests (new CT utils/graph tests, new read tests, reduced zattrs tests).

Reviewed changes

Copilot reviewed 14 out of 16 changed files in this pull request and generated 6 comments.

Show a summary per file

File	Description
tests/testthat/test-zattrs.R	Reworked zattrs tests to run against both v1 and v3 fixtures; added multiscales/channels checks
tests/testthat/test-read.R	Added tests for read*() element readers and readSpatialData() layer selection behavior
tests/testthat/test-PointFrame.R	Adjusted filter error test
tests/testthat/test-ctutils.R	Moved/added coordinate-transformation utility tests
tests/testthat/test-ctgraph.R	Added tests for CT graph/path/plot helpers
R/Zattrs.R	Added internal version-aware multiscales method (list-backed)
R/validity.R	Tweaked validity checks; removed label .zattrs validation from SpatialData validity
R/utils.R	Adjusted centroids(LabelArray) coordinate handling
R/read.R	Changed element discovery from list.files() to list.dirs()
R/ImageArray.R	Made channels(Zattrs) version-aware; refactored multiscales dataset path checks
R/CTutils.R	Updated axes/CT helpers to use multiscales() accessor; docs rename
R/AllGenerics.R	Added multiscales generic; reordered some generics
NAMESPACE	Added imports for SpatialExperiment/anndataR
man/CTutils.Rd	Updated generated Rd to match CTutils rename
inst/NEWS	Added 0.99.29 release notes mentioning v3 work and new fixture
DESCRIPTION	Bumped version to 0.99.29
.gitignore	Added ignore rule for R/_*

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[Copilot]

Pull request overview

Copilot reviewed 39 out of 41 changed files in this pull request and generated 3 comments.

Comments suppressed due to low confidence (2)

R/CTutils.R:148

• rmvCT() is now used alongside version-aware CTlist()/axes() (via multiscales()), but this method still mutates x$multiscales / top-level x$coordinateTransformations. For Zarr v3, coordinate transformations live under x$ome$multiscales[[1]]$coordinateTransformations, so rmvCT() won’t actually affect what CTlist() returns. Update the mutation path to follow the version-specific layout.
  R/CTutils.R:201
• Same issue as rmvCT(): addCT() currently writes to x$multiscales[[1]]$coordinateTransformations (or top-level) but Zarr v3 stores this under x$ome$multiscales[[1]]$coordinateTransformations. As a result, adding a CT on v3 metadata won’t be reflected in CTlist()/CTname(). Make the write-back logic version-aware (e.g., branch on spatialdata_attrs$version).

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