Changes in version 1.1.1                        

  - Aligned version with Bioconductor release
  - Switched default branch to devel for Bioconductor compatibility
  - Updated CI workflows to target devel branch
  - Converted NEWS to NEWS.md format
  - Added automated GitHub Release workflow via tags
  - Ibex_matrix() now accepts character vectors of amino acid sequences
    directly
  - Removed rlang from Imports, added lifecycle
  - As per basilisk documentation:
      - Add .BBSoptions with UnsupportedPlatforms: win32
      - Add configure and configure.win scripts
  - Add Docker infrastructure with Dockerfile and
    .devcontainer/devcontainer.json
  - Improved testthat compatibility across platforms
  - Improve adherence to verbosity arguments

                        Changes in version 1.0.0                        

Major Underlying Changes

  - Integration of Ibex with immApex
  - Updated Seurat object to v5
  - Runs using basilisk instead of reticulate - no installation of
    python packages

Feature Changes

  - Renamed Ibex.matrix() to Ibex_matrix()
  - Updated support for SCE format for runIbex()
  - Update CoNGAfy() to function with all versions of Seurat
  - Updated quietBCRgenes() to use VariableFeatures() call for SeuratV5
    and backward compatibility
  - Add getHumanIgPseudoGenes() to return a list of human Immunoglobulin
    Pseudo genes that are kept by quietBCRgenes()

New Models

  - Added New Light and Heavy Chain Models
  - Encoding methods now accepted: "OHE", "atchleyFactors",
    "crucianiProperties", "kideraFactors", "MSWHIM", "tScales",
    "zScales"
  - Sequence input:
      - Human Heavy: 10000000
      - Human Light: 5000000
      - Human Heavy-Expanded: 5000000
      - Human Light-Expanded: 2500000
      - Mouse Heavy: 5000000
      - Mouse Heavy-Expanded: 5000000
  - Trained convolutional and variational autoencoders for Heavy/Light
    chains
      - Architecture: 512-256-128-256-512
      - Parameters:
          - Batch Size = 128
          - Latent Dimensions = 128
          - Epochs = 100
          - Loss = Mean Squared Error (CNN) & KL Divergence (VAE)
          - Activation = relu
          - Learning rate = 1e-6
      - Optimizers: Adam
      - Early stopping was set to patients of 10 for minimal validation
        loss and restoration of best weights
      - CNN autoencoders have batch normalization layers between the
        dense layers

                       Changes in version 0.99.31                       

  - ibex_ensure_basilisk_external_dir no longer importsFrom
    basilisk.utils directly
  - Moved data processing script out of vignette to inst/scripts
  - Added ibex_ensure_basilisk_external_dir with basilisk.utils
  - Adding internal .OnLoad() function to handle basilisk lock dir issue
  - Deprecated quietBCRgenes()
  - Converted Ibex.matrix() to Ibex_matrix()
  - Added Install Instructions for Bioconductor on README and Vignette
  - Removed references to Keras3 Installation

                       Changes in version 0.99.5                        

  - Initial commit and early development
  - Added detection of chain length to function call
  - Added support for direct output of combineBCR()
  - Modified quietBCR() to include constant regions and J-chains
  - Updated models to include radam optimization, early stop, trained
    on 800,000 unique cdr3s
  - quietBCRgenes() now does not remove human Ig pseudogenes
  - Updated models for manuscript revision
  - Added chain.checker() function to allow for uncapitalized chain
    calls
  - Trained classical and variational autoencoders for light/heavy
    chains (architecture: 256-128-30-128-256)
  - Integration of Ibex with immApex
  - Updated Seurat object to v5
  - Updated support for SCE format for runIbex()
  - Update CoNGAfy() to function with all versions of Seurat
  - Updated quietBCRgenes() to use VariableFeatures() call for SeuratV5
    and backward compatibility
  - Added getHumanIgPseudoGenes() to return a list of human
    Immunoglobulin Pseudo genes
  - Added new light and heavy chain models with encoding methods: OHE,
    atchleyFactors, crucianiProperties, kideraFactors, MSWHIM, tScales,
    zScales
  - Trained convolutional and variational autoencoders
    (architecture: 512-256-128-256-512)
  - Implementing GitHub action workflows
  - Adding testthat framework
  - Deprecated clonalCommunity
  - Added geometric encoding using the BLOSUM62 matrix
  - Added information to example data
  - Examples now check if python is installed and running
  - Updated example data to 2k HEL BEAM-Ab from 10x
  - Converted ibex_example into SCE object for compliance
  - Large revision of vignette to fit new data/format
  - Added species argument to runIbex
  - Implementing GitHub action workflows
  - Adding testthat framework
  - Deprecating clonalCommunity
  - Added geometric encoding using the BLOSUM62 matrix
  - Added chain.checker() function to allow for uncapitalized chain
    calls
  - Updated models for manuscript revision
  - Updated models to include radam optimization, early stop, trained
    on 800,000 unique cdr3s
  - quietBCRgenes() now does not remove human Ig pseudogenes
  - Added detection of chain length to function call
  - Added support for direct output of combineBCR()
  - Modified quietBCR() to include constant regions and J-chains
  - Initial commit
  - Deprecated quietBCRgenes()
  - Converted Ibex.matrix() to Ibex_matrix()
  - Added Install Instructions for Bioconductor on README and Vignette
  - Removed references to Keras3 Installation
  - Moved data processing script out of vignette to inst/scripts
  - Added ibex_ensure_basilisk_external_dir with basilisk.utils
  - Adding internal .OnLoad() function to handle basilisk lock dir issue