Changes in version 0.99.4                        

  - Added \value section to TCR_summary-class documentation to resolve R
    CMD check warning about empty/missing \value sections

                       Changes in version 0.99.3                        

  - Addressed Bioconductor reviewer feedback
  - Updated R dependency to >= 4.6.0
  - Converted TCR_summary from S3 class to formal S4 class with show
    method
  - Added ORCID to Authors@R
  - Replaced \dontrun{} with \donttest{} in all examples except
    runSoNNia (kept as \dontrun{} due to upstream soNNia/numpy
    incompatibility)
  - Removed redundant tryCatch/stop() pattern in huggingModel();
    replaced with on.exit() cleanup
  - Extracted shared .run_in_basilisk() helper to reduce code repetition
    across calculate.* functions
  - Added @importFrom SummarizedExperiment colData and removed explicit
    :: qualifiers in runOLGA, runClustTCR, and runEmbeddings
  - Added n == 0L edge-condition guard for seq.int() in
    proteinEmbeddings()
  - Expanded vignette introductions with biological context and detailed
    prose descriptions for each code section
  - Removed GitHub installation instructions from vignettes
  - Added additional unit tests for S4 class structure, edge cases, and
    input validation

                       Changes in version 0.99.2                        

  - Removed the umbrella roxygen block from R/utils.R
  - Added skip_on_bioc_build() check directly inside skip_if_no_python()
    in tests/testthat/helper-immLynx.R

                       Changes in version 0.99.1                        

  - Switched example data from Seurat to SingleCellExperiment object
  - Replaced Seurat with scran/scater in vignettes
  - Removed Seurat dependency; functions now use SingleCellExperiment
    exclusively
  - Renamed return_seurat parameter to return_input in
    runMetaclonotypist()

                       Changes in version 0.99.0                        

  - Initial Bioconductor submission
  - Added runClustTCR() for TCR clustering via clusTCR
  - Added runTCRdist() for pairwise TCR distance calculations
  - Added runOLGA() and generateOLGA() for generation probability
  - Added runEmbeddings() for protein language model embeddings
  - Added runMetaclonotypist() for metaclone discovery
  - Added runHLAassociation() for HLA-metaclone associations
  - Added runSoNNia() for selection inference
  - Added utility functions: extractTCRdata(), validateTCRdata(),
    convertToTcrdist(), summarizeTCRrepertoire()
  - Added huggingModel(), tokenizeSequences(), and proteinEmbeddings()
    for custom embedding workflows