Append samples

[stemangiola]

No description provided.

[Copilot]

Pull Request Overview

This PR introduces a new append_samples() method for combining SummarizedExperiment objects by samples, deprecates the existing bind_rows() method in favor of the new API, and updates related documentation, tests, and examples.

• Soft-deprecate bind_rows.SummarizedExperiment() and add a lifecycle warning pointing to append_samples().
• Implement append_samples.SummarizedExperiment(), add its Rd file, and update the vignette with usage examples.
• Remove the old bind_rows.Rd, update tests to target append_samples(), bump package version to 1.19.5 and update dependencies.

Reviewed Changes

Copilot reviewed 8 out of 8 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
R/dplyr_methods.R	Added append_samples.SummarizedExperiment(), deprecation warning in bind_rows
man/append_samples.Rd	New documentation for append_samples()
man/bind_rows.Rd	Removed deprecated bind_rows documentation
tests/testthat/test-dplyr_methods.R	Switched tests to append_samples() and basic result assertions
vignettes/introduction.Rmd	Added vignette section demonstrating append_samples()
inst/NEWS.rd	News entry deprecating bind_rows() in favor of append_samples()
DESCRIPTION	Bumped version to 1.19.5, updated ttservice dependency
NAMESPACE	Exported append_samples S3 method and updated imports

Comments suppressed due to low confidence (3)

tests/testthat/test-dplyr_methods.R:13

• Add a test case for a scenario where append_samples() produces duplicated sample names to verify that a warning is issued and that colnames() are made unique as intended.

    expect_true(inherits(pasilla_bind, "SummarizedExperiment"))

R/dplyr_methods.R:88

• [nitpick] The variable name tts is ambiguous. Rename it to a more descriptive name like se_list or experiments to improve readability.

    tts <- flatten_if(list(x, ...), is_spliced)

[Copilot]

Directly accessing the @listData slot is discouraged. Instead, consider using assays(new_obj) as a SimpleList and applying lapply() over its elements, then reassigning via SimpleList() to avoid relying on internal slots.

Suggested change

	assays(new_obj) <- assays(new_obj)@listData |> lapply(function(.x) {
	assays(new_obj) <- lapply(assays(new_obj), function(.x) {