LogicComm 0.12.1

LogicComm 0.12.1

Documentation

• All user-facing docs were rewritten to the v0.12 cell-type co-expression API:
  the README and the LogicComm-intro, Seurat_demo, and
  PBMC_multisample_demo vignettes. The neighborhood/KNN-as-default workflow is
  removed, discover_celltype_communication() is presented as the recommended
  one-call entry point, permutation examples use the axis-level null, and the
  deprecated graph arguments (knn_mat, mode, graph_name,
  graph_symmetrize, edge_weight_mode, remove_self_edges) are dropped from
  all examples.

Fixes

• summarize_spatial_communication() no longer silently ignores its spatial
  graph. The v0.12 rewrite removed the per-cell graph scorer it relied on, so it
  was returning non-spatial cell-type co-expression without notice; it now warns
  that graph-based spatial scoring is pending a dedicated re-implementation and
  returns cell-type co-expression. build_spatial_graph() and
  plot_spatial_logic() are unaffected.