jsonlite::fromJSON -> Rarr::read_zarr_attributes

[HelenaLC]

No description provided.

[Copilot]

Pull request overview

This PR updates SpatialData’s Zarr metadata handling by replacing direct .zattrs JSON parsing with Rarr::read_zarr_attributes(), and refactors coordinate-transformation/axes accessors and related documentation/tests accordingly.

Changes:

• Replace jsonlite::fromJSON() usage for Zarr attributes with Rarr::read_zarr_attributes() across readers.
• Introduce/refactor coordinate transformation helpers (CTlist(), updated CTdata()/axes() behavior) and improve Zattrs printing.
• Add data_type() generic/methods and update vignettes/man pages/tests to reflect the new structures and defaults.

Reviewed changes

Copilot reviewed 35 out of 36 changed files in this pull request and generated 7 comments.

Show a summary per file

File	Description
vignettes/SpatialData.Rmd	Updates vignette examples/output to match new Zarr attribute reading and Zattrs printing.
vignettes/SpatialData.html	Regenerated vignette HTML reflecting updated printing/output and session info.
tests/testthat/test-zattrs.R	Updates tests for new axes() return types and CT accessor changes.
tests/testthat/test-tables.R	Updates read defaults and comments out some valTable() colData checks.
tests/testthat/test-sdarray.R	Adds tests for new data_type() behavior.
tests/testthat/test-reading.R	Simplifies element-reading test to treat tables like other elements.
tests/testthat/test-query.R	Updates CT comparisons to use CTlist(); silences sf startup messages.
tests/testthat/test-PointFrame.R	Updates select() test to use all_of() for tidyselect correctness.
tests/testthat/test-methods.R	Restores/expands tests for character indexing and invalid indexing cases.
tests/testthat/test-mask.R	Updates read defaults to anndataR=TRUE.
tests/testthat/test-labelarray.R	Removes stray text and drops unused subsetting tests.
tests/testthat/test-imagearray.R	Drops unused subsetting tests.
R/Zattrs.R	Adds custom show() method for Zattrs and updates examples.
R/trans.R	Generalizes scale() to sdArray; updates translation handling and examples.
R/table_utils.R	Refactors hasTable()/getTable()/setTable() logic and resolves table() ambiguity.
R/SpatialData.R	Updates examples to use anndataR=TRUE.
R/sdArray.R	Adds data_type() methods and expands examples.
R/read.R	Switches metadata reading to read_zarr_attributes(); changes readSpatialData() default anndataR to TRUE.
R/misc.R	Fixes title text and expands examples; improves coordinate systems display header.
R/methods.R	Tightens [[ indexing validation and minor formatting updates.
R/ImageArray.R	Updates channels() dispatch, refactors multiscales path validation.
R/coord_utils.R	Introduces CTlist() generic and refactors CT/axes accessors and CT graph construction.
R/AllGenerics.R	Adds CTlist() and data_type() generics.
NAMESPACE	Adds imports/exports for new generics and Rarr/ZarrArray helpers; removes jsonlite import.
man/Zattrs.Rd	Updates rendered docs/examples for new Zattrs usage.
man/trans.Rd	Updates rendered docs/examples for transformed shape/point examples.
man/table-utils.Rd	Updates rendered docs/examples to match new defaults.
man/SpatialData.Rd	Updates rendered examples to use anndataR=TRUE.
man/readSpatialData.Rd	Updates rendered docs for new default and examples for element readers.
man/misc.Rd	Updates rendered docs title and examples.
man/ImageArray.Rd	Adds channels,Zattrs-method alias and usage in docs.
man/coord-utils.Rd	Documents CTlist() and updated CT accessors/examples.
man/Array-methods.Rd	Documents new data_type() methods and expands examples.
inst/NEWS	Adds release notes for 0.99.25 describing the metadata reader replacement and show method changes.
DESCRIPTION	Bumps version and swaps jsonlite import for Rarr.
.github/workflows/check-bioc.yml	Modifies CI triggers/matrix (notably removing PR trigger and commenting one config).

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[Copilot]

readSpatialData() now defaults to anndataR=TRUE (signature), but the parameter documentation earlier in this file still states the default is FALSE (and implies readTable() has an anndataR default). Please update the roxygen so the documented default/behavior matches the code.

[Copilot]

The manual table-loading branch for anndataR=FALSE is currently unreachable: if (!anndataR) tables <- FALSE makes tables FALSE, so the later condition if (!anndataR && !isFALSE(tables)) can never be true. If the intent is to still load tables via .readTables_basilisk() when the caller requested tables, preserve the original tables argument in a separate flag before overwriting it.

[Copilot]

The Zattrs show() method indexes CTdata(object)[[i]][[CTtype(object)[i]]], but CTdata() now takes an i argument and returns the data for a single transformation. As written, CTdata(object) (default i=1) can be NULL for identity, and the subsequent [[i]] will error or read the wrong structure. Consider using CTdata(object, i) (or CTlist(object)[[i]]) inside the loop instead of indexing into CTdata(object).

Suggested change

	f(CTdata(object)[[i]][[CTtype(object)[i]]])))
	f(CTdata(object, i)[[CTtype(object)[i]]])))

[Copilot]

The workflow no longer runs on pull requests because the pull_request: trigger was removed. This will prevent CI from validating PRs before merge; re-add the PR trigger (or document why CI should only run on push).

Suggested change

	push:
	push:
	pull_request:

[Copilot]

The generated HTML contains an aria-label attribute with no value (aria-label instead of aria-label="..."). This is invalid HTML and can confuse assistive technologies. Either remove the empty aria-label or provide a meaningful label value (and keep alt consistent).

[Artur-man]

oh boy we need to remove the html

[HelenaLC]

Why? I think it's nice to have during development because we can see it online...