Changes in version 1.1.2 (2026-05-22)                  

Bug fixes

  - calculate_performance() now passes as.factor(true_labels) and
    as.factor(clusters) to aricode::NMI(). As of aricode 1.1.0
    (currently shipping in Bioconductor 3.24), NMI() routes mixed-type
    inputs through sort_pairs(), which calls as.integer() on character
    labels — turning cell-type names such as "alpha" into NA and
    aborting with "NA are not supported.". Coercing both sides to factor
    keeps the computation well-defined and restores compatibility with
    the Bioconductor build farm. This was the underlying cause of the
    vignette failure that 1.1.1 surfaced but did not fix.

                 Changes in version 1.1.1 (2026-05-19)                  

Bug fixes

  - cluster_nmf() now falls back to k-means clustering when the NMF
    embedding has too few features or cells for SNN (variable-feature
    selection on low-dim embeddings was failing under Seurat 5.x). The
    number of k-means / hclust centers is now clamped to a feasible
    range, so grid search no longer fails silently on small reference
    splits.
  - CellMentor() now stops with a clear message if every parameter
    configuration in the grid search fails, instead of cascading to a
    cryptic switch() error during final-model training.
  - evaluate_params() warnings now include the underlying error message,
    so build logs surface the real cause of failures.
  - initialize_wh() validates that method is a single character string
    and reports a helpful error if not.

Documentation

  - Updated citation to the published Nature Communications paper
    (Hevdeli et al., 2026, doi:10.1038/s41467-025-67088-7).
  - Added inst/CITATION so citation("CellMentor") returns a structured
    bibliographic entry.

                 Changes in version 0.99.2 (2024-12-10)                 

CHANGES FOR BIOCONDUCTOR REVIEW

  - Replaced parallel package with BiocParallel for Bioconductor
    compliance
  - Renamed h.baron_dataset() to hBaronDataset() (old name deprecated)
  - Updated R version requirement to >= 4.5.0
  - Removed GeneExpression from biocViews (redundant with
    Transcriptomics)

                 Changes in version 0.99.1 (2024-10-27)                 

  - Initial Bioconductor submission of CellMentor.