chore: cascade dev → gsource (expression_matrix_class deprecation + overlap ids flip)#373
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…elpers The expression_matrix_class param was already deprecated in createExprObj but still had real defaults on createGiottoObject, readExprData, and readExprMatrix. createGiottoObject forwarded the default into readExprData → .read_expression_data → createExprObj, which then matched is_present() and emitted the deprecation warning on every default createGiottoObject call — generating thousands of warnings across the test suite. Three changes, same pattern as createExprObj: - Default changed from a real character vector to lifecycle::deprecated() - is_present() check emits the deprecation warning when the param is actually supplied by the caller - Param is no longer forwarded to downstream helpers .read_expression_data (internal) drops the param entirely — no external callers, no longer plumbed through. The DelayedArray / dbSparseMatrix branches in readExprMatrix are removed since the param can no longer influence return type; the function now always returns the default sparse class. Acceptable behavior change for a deprecated parameter — surfaced via the warning. Test suite: 967 / 0 (was previously generating ~3000 deprecation warnings on every run from the cascade; warning count down to 1449). Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
…ression-matrix-class deprecate: expression_matrix_class across createGiottoObject + read helpers
- pulls `expression_matrix_class ` deprecation and a docs change
Default subset on a single axis now returns an overlapPointDT subset object, matching overlapIntensityDT (which has no ids param and always subsets) and SpatVector (legacy storage). The selection-query form (integer indices) is still available via `ovlp[i, ids = TRUE]`. Why: callers consistently want subset semantics — `.subset_overlaps_poly`, `.subset_overlaps_feat`, and the broken-then-reverted-then-broken "ids = FALSE" workarounds all converge on subset. The default returning indices was the unusual case (only documented + tested, no external callers found). Flipping it removes a footgun. Internal callers updated: - `.subset_overlaps_poly`: `[i, ids = FALSE]` → `[i]` - `.subset_overlaps_feat`: `[, i, ids = FALSE]` → `[, i]` Selection-query callers explicit: - test-aggregate.R: now uses `ovlp[i, ids = TRUE]` for the indices form, plus new test asserting `ovlp[i]` default returns overlapPointDT. Docs in classes-overlaps.R updated to reflect the new default. Side benefit: standalone polygon loads (e.g. GiottoData::loadSubObjectMini) that carry legacy SpatVector @overlaps now subset cleanly — SpatVector's [i] already returns a subset SpatVector, so .subset_overlaps_poly works without needing the ids workaround that SpatVector's [ doesn't support. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
flip overlapPointDT[i] / [,j] default: ids = TRUE → FALSE
Cascade giotto-suite#374 (flip overlapPointDT ids default TRUE → FALSE) up to gsource.
jiajic
changed the title
New S4 generic for the "filter form" complement to relate() — returns x narrowed by a spatial predicate rather than a relation matrix. The eager method on (giottoSpatial, giottoSpatial) wraps relate() + subset; the on- disk lazy form lives in GiottoDisk via methods on parquetGeomBase. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Five tests covering the eager filter-form contract: returns same class as x, narrowed to features satisfying the predicate; default relation is intersects; predicate choice affects narrowing; empty result is a zero-row giottoSpatial. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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Cascade the recent
devchanges up togsource:expression_matrix_classdeprecationoverlapPointDT[i] / [,j]default (ids = TRUE→ids = FALSE)Test plan
backendparameter work intact alongside the deprecation.