NEWS

# harmony v1.2.0 - Oct 12 2023
  - Major performance enhancements, using indexes for the regression
  - update_R - Generate blocks correctly #214
  - lambda optimization - Lambda as a function of E.
  - New alpha parameter to estimate lambda during runtime
  - fail-safe for < 40 cells dataset . Setting block_size=0.2. Refuse to run with < 6 cells.
  - added progress bar for the integration step.
# harmony v1.1.0 - Oct 12 2023
  - update_R bug - All cells are corrected exactly once per invocation
  - Improved documentation RunHarmony generc
  - Fix lambda failing on multiple covariates
  - verbose option suppresses all messages  
# harmony v1.0.0 - Jul 27 2023
* API changes
  - removed do_pca functionality
  - removed reference_values functionality
  - removed cluster_prior functionality
  - beta feature: automatic parameterization of lambda when it is set to NULL
  - ncore parameter controls the use of multiple processors when parallelized BLAS exists.
  - Moved several parameters to the .options. Now they are accessible through harmony_options()
* Documentation
  - Updated seurat vignette
  - Removed mudan Seurat2 and Seurat3 vignettes
* Name changes
  - Integrated HarmonyMatrix function to the RunHarmony generic
  - HarmonyMatrix is deprecated
* Backend changes
  - Sparse matrix coercion to yield performance enhancements
  - L2-normalization using armadillo routines
  - Supports parallel versions of BLAS.
* Fixes
  - RunHarmony() for Seurat considers dimension set
  - RunHarmony() for SingleCellExperiment works
  - custom ceiling function to avoid conflicts for some block_size
  - Coercing covariate to factor when levels are numbers
  
* New features
  - Automatic parameterization of lambda
  - Updated convergence plot


# harmony v0.1.0
* Initial release to CRAN

# harmony v0.1.1
* Updates pow to harmony_pow to avoid collision with new Armadillo pow function