SeuratIntegrate (development version)

Fix AnnData initialization: the var argument for features is now a data.frame
Fix overestimation of number of zeros in sparse matrices: remaining 0s in the matrix values are discarded before counting non-zero values (src/n_zeros_matrix.cpp)
Fix choose_matrix_format() (utils.R)
Created a first set of unit tests covering utils.R (testthat)
Add method to preserve a Graph object's attributes when using as.Graph on a Graph object
Fix deprecation warning in GetNeighborsPerBatch (Graph method)
Minor fixes in docstrings

SeuratIntegrate 0.4.1

Revised score rescaling with a new option enabling min-max rescaling of ranks (default) rather than scores directly (as in Luecken et al., 2021)
Speed up Dijkstra's algorithm-like used in ExpandNeighbours with a new c++ implementation
The most suited matrix format is automatically chosen for corrected counts output by integration methods (should be dense matrix most of the time)
Add support for scGraph metric (Wang et al., 2024)
Improved speed of CreateIntegrationGroups for non-SCT assay in unambiguous cases