Update version to 1.19.2, introduce 'append_samples()' method for com…

[stemangiola]

…bining SingleCellExperiment objects, and deprecate 'bind_rows()' in favor of the new method. Update documentation and examples accordingly.

[Copilot]

Pull Request Overview

This PR updates the package to version 1.19.2 by soft-deprecating the existing bind_rows() method in favor of a new append_samples() method for combining SingleCellExperiment objects by their samples. It also updates documentation, examples, tests, and the NEWS file to reflect this change.

• Deprecate bind_rows.SingleCellExperiment() and introduce append_samples.SingleCellExperiment()
• Update vignettes, README, and test code to use append_samples() instead of bind_rows()
• Remove old bind_rows.Rd man page and add a new append_samples.Rd along with version bump in DESCRIPTION

Reviewed Changes

Copilot reviewed 10 out of 10 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
vignettes/introduction.Rmd	Added a “Combining datasets” section and replaced bind_rows calls with append_samples
tests/testthat/test-dplyr_methods.R	Renamed tests to target append_samples() instead of bind_rows()
man/bind_rows.Rd	Removed deprecated documentation for bind_rows()
man/append_samples.Rd	Added documentation for append_samples()
inst/NEWS.rd	Added NEWS entry for version 1.19.2 and noted deprecation
README.md	Updated usage examples to use append_samples()
README.Rmd	Updated usage examples to use append_samples()
R/dplyr_methods.R	Deprecated bind_rows.SingleCellExperiment and implemented append_samples.SingleCellExperiment
NAMESPACE	Exported append_samples S3 method and imported new functions
DESCRIPTION	Bumped package version to 1.19.2

Comments suppressed due to low confidence (4)

tests/testthat/test-dplyr_methods.R:27

• Consider adding a test for bind_rows() to verify it emits the deprecation warning and suggests append_samples(), ensuring coverage of the soft-deprecation behavior.

test_that("append_samples()", {

README.md:741

• Switching from bind_rows to append_samples on tibbles will break, as append_samples only handles SingleCellExperiment inputs. Either restore bind_rows for data frames or ensure these inputs are converted back to SCE before using append_samples.

            map_dfr(~ append_samples(as_tibble(.x)))

README.Rmd:464

• In this context .x is a tibble, so append_samples will not dispatch. It may be better to keep using bind_rows() here or coerce back to a SingleCellExperiment before appending.

            map_dfr(~ append_samples(as_tibble(.x)))