Refactor: introduce parameter groups 2 - #140

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refactor/introduce_parameter_groups_2

Commits on Apr 4, 2026

Commits on Apr 14, 2026

Refactored `automaticCOTANObjectCreation` function
trinetra75
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c2ca0f2

Commits on Apr 15, 2026

Fixed issue with `proceedToCoex()` dispatch
trinetra75
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64267a7
Solved documentation issues regarding the new parameter pack
trinetra75
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ba23f2c
Solved minor Note in checks
trinetra75
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03a69c5
Fixed minor bugs
trinetra75
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26a7b45
Expanded `calculateCoex()` to accept `ExecutionOptions`
trinetra75
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a853379
Extended usage of `ExecutionOptions` to the estimate dispersion function
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15e157a
Added to the class
trinetra75
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795cc92

Commits on Apr 16, 2026

Extended usage of ExecutionOptions to various calculate functions
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9631664
Expanded usage of ExecutioOptions to checkClusterUniformity() function
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17739e3
Finished refactoring of `checkClusterUniformity()` function
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d295d4d
Finished adding ExecutionOptions to Uniform Clusters functions
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d92c1a3
Extended ExecutionOptions usage to heatmap plot functions
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d6308c1
Dropped unused parameters
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e0e10b0
Final changes
trinetra75
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e0d4cb1

Commits on May 11, 2026

Merge branch 'devel' into refactor/introduce_parameter_groups
trinetra75
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ee157f2

Commits on May 20, 2026

Merge branch 'devel' into refactor/introduce_parameter_groups
trinetra75
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4d8834c

Commits on May 21, 2026

Introduction of `ReductionOptions` for parameters refactoring
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635ede3
Added `ReductionOptions` to function `calculateReducedDataMatrix()`
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aa988b8
Added ReductionOptions parameter to function `cellsUMAPPlot()`
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67c798e
Moved private function `seuratClustering()` to use ReductionOptions
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163f20d
Added `ResolutionOptions` to parameters of function `cellsUniformClustering()`
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4a48333
Moved examples, vignettes and tests to use the new `ReductionOptions`
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820dbac
Last fixes for Execution and Reduction options
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c4bee43
Added `ClusterDistanceOptions` class to handle clusters' distances parameters
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bd275f6
Added `ClusterDistanceOptions` to all remaing functions
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0cb508c
Finished add `ClusterDistanceOptions`
trinetra75
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be216a0
Added `ClusterTreeOptions` as superset of `ClusterDistanceOptions`
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ad3250f
Further integration with clusterTreeOptions
trinetra75
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72d4943
Fixed tests and vignettes
trinetra75
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b1a4f9a
Fixed tests
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f8ba645
Added CleaningOptions
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7fa6f6b
Further introduction of CleaningOptions
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468a9b7
Finalized addition of `CleaningOptions`
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e12e18d

Commits on May 22, 2026

Commits on Jun 8, 2026

Updated last calls into tests
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3c7f761

Commits on Jun 9, 2026

Fixed minor assert issue in `seuratClustering()`
trinetra75
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8b885f7

Commits on Jun 12, 2026

Merge branch 'devel' into refactor/introduce_parameter_groups_2
trinetra75
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f6f4ca7
Updated NEWS.md
trinetra75
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7f61c36