Move AHMIntegration and PartitionedSampling separate packages

Author: oschulz

CITATION.bib

@@ -1,4 +1,3 @@
-% primary paper on BAT.jl as a whole
 @article{Schulz:2021BAT,
   author  = {Schulz, Oliver and Beaujean, Frederik and Caldwell, Allen and Grunwald, Cornelius and Hafych, Vasyl and Kr{\"o}ninger, Kevin and Cagnina, Salvatore La and R{\"o}hrig, Lars and Shtembari, Lolian},
   journal = {SN Computer Science},
@@ -13,27 +12,3 @@ @article{Schulz:2021BAT
   doi     = {10.1007/s42979-021-00626-4},
   url     = {https://doi.org/10.1007/s42979-021-00626-4},
 }
-
-% specific paper on the algorithm behind BAT.AHMIntegration
-@article{Caldwell:2020AHMI,
-  author    = {Caldwell, Allen and Eller, Philipp and Hafych, Vasyl and Schick, Rafael and Schulz, Oliver and Szalay, Marco},
-  journal   = {International Journal of Modern Physics A},
-  title     = {Integration with an adaptive harmonic mean algorithm},
-  year      = {2020},
-  number    = {24},
-  pages     = {2050142},
-  volume    = {35},
-  doi       = {10.1142/S0217751X20501420},
-  publisher = {World Scientific},
-}
-
-% specific paper on the algorithm behind BAT.PartitionedSampling
-@article{Hafych:2008.03098,
-  author        = {Hafych, Vasyl and Eller, Philipp and Caldwell, Allen and Schulz, Oliver},
-  title         = {Parallelizing MCMC Sampling via Space Partitioning},
-  year          = {2018},
-  month         = {8},
-  archiveprefix = {arXiv},
-  eprint        = {2008.03098},
-  primaryclass  = {stat.CO},
-}

Project.toml

@@ -7,12 +7,10 @@ AdaptiveRejectionSampling = "c75e803d-635f-53bd-ab7d-544e482d8c75"
 AdvancedHMC = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d"
 ArgCheck = "dce04be8-c92d-5529-be00-80e4d2c0e197"
 ArraysOfArrays = "65a8f2f4-9b39-5baf-92e2-a9cc46fdf018"
-CPUTime = "a9c8d775-2e2e-55fc-8582-045d282d599e"
 ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
 ChangesOfVariables = "9e997f8a-9a97-42d5-a9f1-ce6bfc15e2c0"
 Clustering = "aaaa29a8-35af-508c-8bc3-b662a17a0fe5"
 Colors = "5ae59095-9a9b-59fe-a467-6f913c188581"
-DataStructures = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
 Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
 DensityInterface = "b429d917-457f-4dbc-8f4c-0cc954292b1d"
 DiffResults = "163ba53b-c6d8-5494-b064-1a9d43ac40c5"
@@ -45,7 +43,6 @@ Parameters = "d96e819e-fc66-5662-9728-84c9c7592b0a"
 PositiveFactorizations = "85a6dd25-e78a-55b7-8502-1745935b8125"
 PrettyTables = "08abe8d2-0d0c-5749-adfa-8a2ac140af0d"
 Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
-ProgressMeter = "92933f4c-e287-5a05-a399-4b506db050ca"
 QuadGK = "1fd47b50-473d-5c70-9696-f719f8f3bcdc"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 Random123 = "74087812-796a-5b5d-8853-05524746bad3"
@@ -69,12 +66,10 @@ AdaptiveRejectionSampling = "0.1.1"
 AdvancedHMC = "0.3"
 ArgCheck = "1, 2.0"
 ArraysOfArrays = "0.4, 0.5"
-CPUTime = "1.0"
 ChainRulesCore = "0.9.44, 0.10, 1"
 ChangesOfVariables = "0.1.1"
 Clustering = "0.13, 0.14"
 Colors = "0.9,0.10,0.11, 0.12"
-DataStructures = "0.17, 0.18"
 DensityInterface = "0.4"
 DiffResults = "1"
 Distributions = "0.21.10, 0.22, 0.23, 0.24, 0.25"
@@ -102,7 +97,6 @@ ParallelProcessingTools = "0.4"
 Parameters = "0.12"
 PositiveFactorizations = "0.2"
 PrettyTables = "1"
-ProgressMeter = "1"
 QuadGK = "2"
 Random123 = "1.2"
 RecipesBase = "0.7, 0.8, 1.0"

docs/src/experimental_api.md

@@ -29,7 +29,6 @@ EllipsoidalNestedSampling
 ForwardDiffAD
 GridSampler
 HierarchicalDistribution
-PartitionedSampling
 PriorImportanceSampler
 ReactiveNestedSampling
 renormalize_density

docs/src/index.md

@@ -56,38 +56,6 @@ When using BAT.jl for research, teaching or similar, please cite
 }
 ```
 
-If you use [`BAT.AHMIntegration`](@ref) as an important part of your work, please also cite 
-*Caldwell et al. "Integration with an Adaptive Harmonic Mean Algorithm", [IJMPA (2020)](http://doi.org/10.1142/S0217751X20501420).*
-
-```
-@article{Caldwell:2020AHMI,
-  author    = {Caldwell, Allen and Eller, Philipp and Hafych, Vasyl and Schick, Rafael and Schulz, Oliver and Szalay, Marco},
-  journal   = {International Journal of Modern Physics A},
-  title     = {Integration with an adaptive harmonic mean algorithm},
-  year      = {2020},
-  number    = {24},
-  pages     = {2050142},
-  volume    = {35},
-  doi       = {10.1142/S0217751X20501420},
-  publisher = {World Scientific},
-}
-```
-
-If you use [`BAT.PartitionedSampling`](@ref) (experimental feature) as an important part of your work, please also cite 
-*Hafych et al. "Parallelizing MCMC Sampling via Space Partitioning", [arXiv:2008.03098 (2020)](https://arxiv.org/abs/2008.03098)*.
-
-```
-@article{Hafych:2008.03098,
-  author        = {Hafych, Vasyl and Eller, Philipp and Caldwell, Allen and Schulz, Oliver},
-  title         = {Parallelizing MCMC Sampling via Space Partitioning},
-  year          = {2018},
-  month         = {8},
-  archiveprefix = {arXiv},
-  eprint        = {2008.03098},
-  primaryclass  = {stat.CO},
-}
-```
-
 
 ## Learning (more about) Julia
 

docs/src/internal_api.md

@@ -35,7 +35,6 @@ Order = [:macro, :function]
 BAT.AbstractProposalDist
 BAT.AbstractSampleGenerator
 BAT.BasicMvStatistics
-BAT.DataSet
 BAT.ENSAutoProposal
 BAT.ENSBound
 BAT.ENSEllipsoidBound
@@ -45,40 +44,30 @@ BAT.ENSProposal
 BAT.ENSRandomWalk
 BAT.ENSSlice
 BAT.ENSUniformly
-BAT.HMIData
-BAT.HMISettings
-BAT.IntegrationVolume
-BAT.KDTreePartitioning
 BAT.LFDensity
 BAT.LFDensityWithGrad
 BAT.MCMCSampleGenerator
 BAT.OnlineMvCov
 BAT.OnlineMvMean
 BAT.OnlineUvMean
 BAT.OnlineUvVar
-BAT.PointCloud
 BAT.RenormalizedDensity
-BAT.SearchResult
-BAT.SpacePartTree
 BAT.StandardMvNormal
 BAT.StandardMvUniform
 BAT.StandardUvNormal
 BAT.StandardUvUniform
 BAT.TransformedDensity
-BAT.WhiteningResult
+
 BAT.WrappedNonBATDensity
 
 BAT.argchoice_msg
 BAT.bat_sampler
 BAT.bg_R_2sqr
 BAT.checked_logdensityof
-BAT.create_hypercube
-BAT.create_hyperrectangle
 BAT.default_val_numtype
 BAT.default_var_numtype
 BAT.density_valtype
 BAT.drop_low_weight_samples
-BAT.find_hypercube_centers
 BAT.find_marginalmodes
 BAT.fromuhc
 BAT.fromuhc!
@@ -87,21 +76,12 @@ BAT.get_bin_centers
 BAT.getlikelihood
 BAT.getprior
 BAT.gr_Rsqr
-BAT.hm_init
-BAT.hm_integrate!
-BAT.hm_whiteningtransformation!
-BAT.hyperrectangle_creationproccess!
-BAT.integrate_hyperrectangle_cov
 BAT.is_log_zero
 BAT.issymmetric_around_origin
 BAT.log_volume
 BAT.log_zero_density
-BAT.modify_hypercube!
-BAT.modify_integrationvolume!
-BAT.partition_space
 BAT.proposal_rand!
 BAT.proposaldist_logpdf
-BAT.reduced_volume_hm
 BAT.repetition_to_weights
 BAT.spatialvolume
 BAT.sum_first_dim

docs/src/list_of_algorithms.md

@@ -45,9 +45,9 @@ sampling_algorithm = EllipsoidalNestedSampling()
 ```
 
 ### Partitioned Sampling (experimental)
-BAT.jl sampling algorithm type: [`PartitionedSampling`](@ref)
+BAT.jl sampling algorithm type: `PartitionedSampling`, requires [PartitionedParallelSampling.jl](https://github.com/bat/PartitionedParallelSampling.jl).
 ```julia
-sampling_algorithm = ReactiveNestedSampling()
+sampling_algorithm = PartitionedParallelSampling.PartitionedSampling()
 ```
 
 
@@ -79,9 +79,9 @@ integral = bat_integrate(sampleable, integration_algorithm).result
 ```
 
 ### Adaptive Harmonic Mean Integration (AHMI)]
-BAT.jl integration algorithm type: [`AHMIntegration`](@ref) 
+BAT.jl integration algorithm type: `AHMI.AHMIntegration`, requires [AHMI.jl](https://github.com/bat/AHMI.jl).
 ```julia
-integration_algorithm = AHMIntegration()
+integration_algorithm = AHMI.AHMIntegration()
 ```
 
 ### Vegas Integration

docs/src/stable_api.md

@@ -54,7 +54,6 @@ AbstractTransformedDensity
 AbstractTransformToInfinite
 AbstractTransformToUnitspace
 AdaptiveMHTuning
-AHMIntegration
 AnyDensityLike
 AnyIIDSampleable
 AnySampleable

examples/benchmarks/benchmarks.jl

@@ -1,4 +1,5 @@
 using BAT, ValueShapes, IntervalSets, Distributions, Plots, EmpiricalDistributions
+using AHMI
 using StatsBase, ArraysOfArrays, LinearAlgebra, LaTeXStrings, QuadGK, PrettyTables, HypothesisTests, Statistics
 ENV["JULIA_DEBUG"] = "BAT"
 

examples/paper-example/paper_example.jl

@@ -10,6 +10,7 @@ using ArraysOfArrays
 using TypedTables
 using CSV
 import Cuba
+using AHMI
 
 
 function log_pdf_poisson(λ::T, k::U) where {T<:Real,U<:Real}

src/BAT.jl

@@ -37,7 +37,6 @@ using ParallelProcessingTools
 using Parameters
 using PDMats
 using PositiveFactorizations
-using ProgressMeter
 using RecipesBase
 using Requires
 using StaticArrays
@@ -67,12 +66,10 @@ import ZygoteRules
 
 using ChainRulesCore: AbstractTangent, Tangent, NoTangent, ZeroTangent, AbstractThunk, unthunk
 
-#for AHMI
-using DataStructures
-using QuadGK
-
-#for Space Partitioning
-import CPUTime
+# For GaussianShell:
+import AdaptiveRejectionSampling
+import QuadGK
+import SpecialFunctions
 
 
 include("utils/utils.jl")

src/algodefaults/default_integration_algorithm.jl

@@ -1,5 +1,5 @@
 # This file is a part of BAT.jl, licensed under the MIT License (MIT).
 
 
-bat_default(::typeof(bat_integrate), ::Val{:algorithm}, ::AnySampleable) = AHMIntegration()
+# ToDo: bat_default(::typeof(bat_integrate), ::Val{:algorithm}, ::AnySampleable) = BridgeSampling()
 bat_default(::typeof(bat_integrate), ::Val{:algorithm}, ::SampledDensity) = BridgeSampling()

src/distributions/gaussian_shell.jl

@@ -1,8 +1,5 @@
 # This file is a part of BAT.jl, licensed under the MIT License (MIT).
 
-using SpecialFunctions
-using Random123 
-import AdaptiveRejectionSampling
 
 """
     struct BAT.GaussianShell <: Distribution{Multivariate,Continuous}