Changelog¶

Version 0.3.0¶

Updated to the latest version of all C++ libraries in the assorthead package. This should not affect results except for MNN correction where the underlying algorithm has changed.
Updated to version 1.0.0 of igraph, which may result in some small changes to the graph clustering results.
Functions that previously returned a dedicated *Result dataclass will now return a BiocFrame or NamedList. This is simpler and improves consistency with the R package.
Added SummarizedExperiment-compatible wrappers for each function. These are identifiable by the *_se suffix in their name and will accept (and often return) a SummarizedExperiment for improved compatibility with BiocPy workflows.
Replaced the analyze() function with analyze_se(), which converts the analysis results in a more convenient format for downstream inspection.
Set collapse_search=True in run_all_neighbor_steps(), which improves speed at the cost of some reproducibility when compared to running each function separately.
Added a delayed= option to normalize_counts() to avoid returning a DelayedArray.
Transpose the arrays returned by run_tsne() and run_umap() so that each row corresponds to a cell and each column is a dimension.

Major refactor to use the new libscran C++ libraries. Functions are now aligned with those in the scrapper package.
Removed support for Python 3.8 (EOL).

Added overlord functions for basic, multi-modal and multi-sample analyses from matrices, SummarizedExperiments and SingleCellExperiments.