Merge pull request #250 from Julia-Tempering/miguelbiron-patch-1

drop a couple of dependencies we are not using

Project.toml

@@ -4,14 +4,11 @@ authors = ["Alexandre Bouchard-Côté <[email protected]>, Nikola Surjanovic
 version = "0.4.2"
 
 [deps]
-ConcreteStructs = "2569d6c7-a4a2-43d3-a901-331e8e4be471"
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
-DataStructures = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
 Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
 DocStringExtensions = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
 Expect = "6a31a4e8-6e70-5a2d-b005-bc2d500d80a5"
-ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
 Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6"
 Interpolations = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59"
 JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
@@ -22,10 +19,9 @@ LogExpFunctions = "2ab3a3ac-af41-5b50-aa03-7779005ae688"
 MPI = "da04e1cc-30fd-572f-bb4f-1f8673147195"
 MPIPreferences = "3da0fdf6-3ccc-4f1b-acd9-58baa6c99267"
 MacroTools = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09"
-OnlineStats = "a15396b6-48d5-5d58-9928-6d29437db91e"
+OnlineStatsBase = "925886fa-5bf2-5e8e-b522-a9147a512338"
 OrderedCollections = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
 Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
-Preferences = "21216c6a-2e73-6563-6e65-726566657250"
 Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 RecipesBase = "3cdcf5f2-1ef4-517c-9805-6587b60abb01"
@@ -34,7 +30,7 @@ Roots = "f2b01f46-fcfa-551c-844a-d8ac1e96c665"
 Serialization = "9e88b42a-f829-5b0c-bbe9-9e923198166b"
 SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b"
 SplittableRandoms = "8efc31e9-3fb0-4277-b18c-5a3d5d07abad"
-StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
+StaticArraysCore = "1e83bf80-4336-4d27-bf5d-d5a4f845583c"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
 ZipFile = "a5390f91-8eb1-5f08-bee0-b1d1ffed6cea"
@@ -53,14 +49,11 @@ PigeonsMCMCChainsExt = "MCMCChains"
 
 [compat]
 BridgeStan = "2"
-ConcreteStructs = "0.2"
 DataFrames = "1"
-DataStructures = "0.18"
 Distributions = "0.25"
 DocStringExtensions = "0.9"
 DynamicPPL = "0.23, 0.24, 0.25, 0.26, 0.27, 0.28"
 Expect = "0.3"
-ForwardDiff = "0.10"
 Graphs = "1"
 HypothesisTests = "0.11"
 Interpolations = "0.14, 0.15"
@@ -72,15 +65,14 @@ MCMCChains = "6"
 MPI = "0.20"
 MPIPreferences = "0.1"
 MacroTools = "0.5"
-OnlineStats = "1"
+OnlineStatsBase = "1"
 OrderedCollections = "1"
-Preferences = "1"
 RecipesBase = "1"
 Requires = "1"
 Roots = "2"
 SpecialFunctions = "2"
 SplittableRandoms = "0.1"
-StaticArrays = "1"
+StaticArraysCore = "1"
 Statistics = "1"
 StatsBase = "0.33, 0.34"
 ZipFile = "0.10"
@@ -89,4 +81,5 @@ julia = "1.8"
 [extras]
 BridgeStan = "c88b6f0a-829e-4b0b-94b7-f06ab5908f5a"
 DynamicPPL = "366bfd00-2699-11ea-058f-f148b4cae6d8"
+HypothesisTests = "09f84164-cd44-5f33-b23f-e6b0d136a0d5"
 MCMCChains = "c7f686f2-ff18-58e9-bc7b-31028e88f75d"

docs/Project.toml

@@ -5,6 +5,7 @@ DistributionsAD = "ced4e74d-a319-5a8a-b0ac-84af2272839c"
 DocStringExtensions = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 DynamicPPL = "366bfd00-2699-11ea-058f-f148b4cae6d8"
+ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
 LogDensityProblems = "6fdf6af0-433a-55f7-b3ed-c6c6e0b8df7c"
 MCMCChains = "c7f686f2-ff18-58e9-bc7b-31028e88f75d"
 OnlineStats = "a15396b6-48d5-5d58-9928-6d29437db91e"

docs/src/input-julia.md

@@ -95,12 +95,14 @@ nothing # hide
 
 ## Changing the explorer 
 
-Here is an example using [`AutoMALA`](@ref) instead of the default 
-[`SliceSampler`](@ref). We only need to add methods to make 
+Here is an example using [`AutoMALA`](@ref)—a gradient-based sampler—instead of the default 
+[`SliceSampler`](@ref). For simplicity, we'll use the ForwardDiff backend; many others are supported by the [LogDensityProblemsAD.jl](https://github.com/tpapp/LogDensityProblemsAD.jl) interface.
+We only need to add methods to make 
 our custom type `MyLogPotential` conform the 
 [LogDensityProblems interface](https://github.com/tpapp/LogDensityProblems.jl):
 
 ```@example julia
+using ForwardDiff
 using LogDensityProblems
 
 LogDensityProblems.dimension(lp::MyLogPotential) = 2

ext/PigeonsBridgeStanExt/interface.jl

@@ -6,7 +6,7 @@ The `data` argument can be a path with a file with `.json` suffix or the json st
 See `BridgeStan` for details.
 """
 function Pigeons.StanLogPotential(stan_file, data, extra_information = nothing)
-    model = BridgeStan.StanModel(; stan_file, data, make_args = stan_threads_options())
+    model = BridgeStan.StanModel(stan_file, data; make_args = stan_threads_options())
     result = StanLogPotential(
         model,
         stan_file,

src/Pigeons.jl

@@ -10,52 +10,39 @@ import MPI: Comm, Allreduce, Comm_rank,
             Allgather, Comm_split, isend, recv,
             bcast, tag_ub
 
-
-using Base: Forward
 using DataFrames
-using Distributions
-using StatsBase
-using Interpolations
-using Roots
 using Dates
-using OnlineStats
-using MacroTools
+using Distributions
 using DocStringExtensions
-using LinearAlgebra
-using SpecialFunctions
-using Serialization
-using ConcreteStructs
-using Random
-using Graphs
-using DataStructures
-using Preferences
-using MPIPreferences
 using Expect
+using Graphs
+using Interpolations
+using JSON
+using LinearAlgebra
+using LogDensityProblems
+using LogDensityProblemsAD
 using LogExpFunctions
-using StaticArrays
+using MPIPreferences
+using MacroTools
+using OnlineStatsBase
+using OrderedCollections
 using Printf
-using Statistics
+using Random
 using RecipesBase
+using Roots
+using Serialization
+using SpecialFunctions: beta
+using StaticArraysCore
+using Statistics
+using StatsBase
 using ZipFile
-using ForwardDiff
-using LogDensityProblems
-using LogDensityProblemsAD
-using JSON
 
-import Serialization.serialize
-import Serialization.deserialize
-import Base.@kwdef
-import Base.show
-import Base.print
+import Base: Forward, @kwdef, show, print, merge, keys
 import Base.Threads.@threads
-import OnlineStats._fit!
-import OnlineStats.value
-import OnlineStats._merge!
+import OnlineStatsBase: _fit!, value, _merge!
 import Random.rand!
-import Base.keys
-import Statistics.mean
-import Statistics.var
-import Base.merge
+import Serialization: serialize, deserialize
+import Statistics: mean, var
 
 
 const use_auto_exec_folder = "use_auto_exec_folder"

src/paths/ScaledPrecisionNormalPath.jl

@@ -54,7 +54,7 @@ Known cumulative barrier used for testing,
 from [Predescu et al., 2003](https://aip.scitation.org/doi/10.1063/1.1644093).
 """
 function analytic_cumulativebarrier(path::ScaledPrecisionNormalPath)
-    b = beta(path.dim / 2.0, path.dim / 2.0)
+    b = beta(path.dim / 2.0, path.dim / 2.0) # NB: this is the beta function in SpecialFunctions.jl 
     function cumulativebarrier(beta)
         sigma0 = 1.0 / sqrt(path.precision0)
         sigmab = 1.0 / sqrt(precision(path, beta))

src/recorders/LogSum.jl

@@ -5,14 +5,14 @@ end
 
 LogSum(T::Type{<:Number} = Float64) = LogSum(-inf(T), 0)
 
-OnlineStats.value(stat::LogSum, args...; kw...) = stat.value 
+OnlineStatsBase.value(stat::LogSum, args...; kw...) = stat.value 
 
-function OnlineStats._fit!(stat::LogSum, y)
+function OnlineStatsBase._fit!(stat::LogSum, y)
     stat.value = LogExpFunctions.logaddexp(stat.value, y)
     stat.n += 1
 end
 
-function _merge!(stat1::LogSum, stat2::LogSum)
+function OnlineStatsBase._merge!(stat1::LogSum, stat2::LogSum)
     stat1.value = LogExpFunctions.logaddexp(stat1.value, stat2.value)
     stat1.n += stat2.n
 end

src/recorders/recorder.jl

@@ -51,7 +51,7 @@ recorder_values(pt::PT, recorder_name::Symbol) =
     recorder_values(pt.reduced_recorders, recorder_name::Symbol)
 recorder_values(reduced_recorders, recorder_name::Symbol) = 
     recorder_values(reduced_recorders[recorder_name])
-recorder_values(recorder::GroupBy) = (value(v) for v in values(value(recorder)))
+recorder_values(recorder::OnlineStatsBase.GroupBy) = (value(v) for v in values(value(recorder)))
 
 """ 
 Average MH swap acceptance probabilities for each pairs 

src/utils/@auto.jl

@@ -32,7 +32,7 @@ macro auto(expr)
 end
 
 
-# Parse whole struct definition for the @concrete macro
+# Parse whole struct definition for the @auto macro
 function _concretize(expr)
     expr isa Expr && expr.head == :struct || error("Invalid usage of @auto")
 

test/test_DistributionLogPotential.jl

@@ -67,7 +67,7 @@ end
                 n_local_mpi_processes = n_mpis,
                 n_threads = 1,
                 mpiexec_args = extra_mpi_args(),
-                dependencies = [Bijectors,BridgeStan]
+                dependencies = [Bijectors,BridgeStan,ForwardDiff]
             )
         )
         @test true

test/test_src_sortable.jl

@@ -1,5 +1,5 @@
 @testset "src-sortable" begin
     cd(dirname(dirname(pathof(Pigeons)))) do
-        @assert length(Pigeons.sort_includes("Pigeons.jl")) > 1
+        @test length(Pigeons.sort_includes("Pigeons.jl")) > 1
     end
 end