deprecate: expression_matrix_class across createGiottoObject + read helpers#372
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jiajic merged 1 commit intoMay 26, 2026
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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>
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| cores = determine_cores(), | ||
| raw_exprs = NULL, | ||
| expression_matrix_class = c("dgCMatrix", "DelayedArray"), | ||
| expression_matrix_class = deprecated(), |
| images <- c(images, largeImages) | ||
| } | ||
|
|
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| if (is_present(expression_matrix_class)) { |
| "DelayedArray", | ||
| "dbSparseMatrix" | ||
| )) { | ||
| expression_matrix_class = deprecated()) { |
|
|
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| if (is_present(expression_matrix_class)) { | ||
| warning(sprintf( | ||
| "[createGiottoObject] param '%s' is deprecated", |
| if (identical(expression_matrix_class, "dbSparseMatrix")) { | ||
| stop("File conversion to dbMatrix is not yet supported") | ||
| if (is_present(expression_matrix_class)) { | ||
| warning(sprintf( |
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May 26, 2026
Cascade giotto-suite#372 (expression_matrix_class deprecation) + giotto-suite#374 (flip overlapPointDT[i] / [,j] default ids = TRUE → FALSE) into gmulti.
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`expression_matrix_class` was already deprecated in `createExprObj` but still had real defaults on `createGiottoObject`, `readExprData`, and `readExprMatrix`. `createGiottoObject` forwarded its default through `readExprData` → `.read_expression_data` → `createExprObj`, where `is_present()` matched and emitted the deprecation warning on every default `createGiottoObject` call. The test suite was generating ~3000 of these warnings per run as a result.
What changes
Same pattern as the existing `createExprObj` deprecation, applied to the rest of the chain:
Tests
Full suite: 967 / 0. Warning count dropped from ~4700 to 1449 with this cleanup.
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