Changes in version 0.5.8                        

03/02/2026

  - BUGFIX: Fixed critical bug in cellMarkers() where min_cells
    filtering was non-functional due to incorrect operator precedence.
  - Improved numerical stability across all core functions:
      - Protected against division by zero in dotprod(), equalweight(),
        scaleSphere()
      - Added input clamping for acos() to prevent NaN from
        floating-point errors
      - Added singular matrix detection in deconv()
      - Fixed NA handling in outlier detection during multi-pass
        deconvolution
      - Added robust error handling in rstudent() and cooks.distance()
        methods
  - Fixed edge case in balance_cores() when cores = 1.
  - Unified code style: consistent spacing around operators throughout
    codebase.
  - Added comprehensive test suite with 69+ tests covering:
      - Core mathematical functions
      - Scientific accuracy validation
      - Edge cases and numerical stability
      - Integration tests for full deconvolution workflow
  - Updated maintainer and repository information.

                 Changes in version 0.5.7 (2025-12-11)                  

11/12/2025

  - Change log argument in deconvolute() to logged_bulk. NB. this is a
    change of logic.

                        Changes in version 0.5.6                        

07/10/2025

  - Add residuals.deconv() to allow recalculation of full residuals
    matrix.

                        Changes in version 0.5.5                        

10/09/2025

  - Fix bug in mergeMarkers() if cellMarkers object has no cell grouping
    vector.

                 Changes in version 0.5.4 (2025-09-15)                  

09/09/2025

  - Fix CRAN checks
  - Switch from using cat() to message()

                        Changes in version 0.5.3                        

26/08/2025

  - Massive speed up (4-5x) in compensation optimisation

                        Changes in version 0.5.2                        

30/07/2025

  - Expanded to 3 methods for identifying outlier genes (var.e, Cook's
    distance, Studentized residuals)
  - Improved (nested) parallelisation of tune_deconv()
  - Rewrite weights code (faster)

                        Changes in version 0.5.0                        

14/07/2025

  - Calculation of SE
  - Detection and multipass removal of problematic genes with extreme
    residuals

                        Changes in version 0.2.0                        

24/01/2025

  - This is the initial build of cellGeometry