genieclust_1.3.0

1.3.0 (2026-02-23)

• The package was heavily refactored; common MST-related functions and classes
  as well as functions from the tools and plots modules were moved to
  the new deadwood package, which is
  now required.

• [BACKWARD INCOMPATIBILITY] Outlier detection based solely on whether
  a node is a leaf of a minimum spanning tree w.r.t. some mutual reachability
  distance turned out to be subpar in more detailed experiments,
  especially for smaller smoothing factors. Note that in the previous
  versions of the package, this feature was deemed merely experimental;
  Hence, detect_noise in genie.default and skip_leaves, preprocess,
  and postprocess elsewhere are no longer available. Instead, use the more
  universal deadwood package now.

• [BACKWARD INCOMPATIBILITY] quitefastmst version >= 0.9.1 is now required;
  the introduced backward-incompatible changes have been addressed.
  In particular, the definition of mutual reachability distances has changed.
  Unlike in Campello et al.'s 2013 paper, now the core distance is the
  distance to the M-th nearest neighbour, not the (M-1)-th one
  (not including self).

• [Python] [BACKWARD INCOMPATIBILITY] internal module was renamed core.

• [BACKWARD INCOMPATIBILITY] Deprecated functions such as mst_from_nn
  have been removed.

• [Python] [BACKWARD INCOMPATIBILITY] compute_full_tree is now always True.

• [BUGFIX] #92: Passing a non-square confusion matrix to
  normalized_pivoted_accuracy and normalized_clustering_accuracy
  yields an error as such objects are yet to be supported.

• [R] gclust and genie now return the computed MST via the mst
  object attribute. genie returns an object of the class mstclust.
  This makes it operable with deadwood.

• [Python] [BUGFIX] Modifying quitefastmst_params via set_state
  now invalidates the cached MST.

• [Python] [NEW FEATURE] plots.plot_scatter has new arguments:
  asp, markers, and colours. The module globals mrk and col were
  renamed accordingly. However, as mentioned above, plots was
  moved to deadwood.

• [Python] [BACKWARD INCOMPATIBILITY] compute_all_cuts in Genie was
  renamed coarser. If True, labels_ is still a vector representing
  the requested n_clusters. The coarser-grained labels are now stored
  in labels_matrix_ whose i-th row represents an (i+1)-partition.