@mcmcjs/julia 0.11.1 → 0.11.3
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/dist/fitlib.jl +56 -48
- package/dist/julia-env/Manifest.toml +8 -141
- package/dist/julia-env/Project.toml +0 -1
- package/package.json +2 -2
package/dist/fitlib.jl
CHANGED
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@@ -1,15 +1,14 @@
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# MCMC.js fit library, shared by the one-shot driver (driver.jl) and the
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# persistent worker (worker.jl). handle_request runs one fit or predict request
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# (Turing or JuliaBUGS) and writes the draws as
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#
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#
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# (Turing or JuliaBUGS) and writes the draws as the @mcmcjs/core samples
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# artifact (a flat JSON wire). This is the only place that touches the backend
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# chain type (FlexiChains), so a chain-type change is contained here.
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using JSON
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using Logging
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using Random
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using StableRNGs
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using Turing
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using Turing: VarName
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using MCMCChains
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using SHA
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using Pkg
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# Imported (not `using`) so they do not pull `@model` etc. into Main and clash
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@@ -136,28 +135,59 @@ predict_namedtuple(data) = (; (Symbol(k) => to_missing(v) for (k, v) in data)...
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# A blanked target compiles to a latent node; JuliaBUGS drops scalar missings.
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bugs_predict_namedtuple(data) = (; (Symbol(k) => narrow(to_missing(v)) for (k, v) in data)...)
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# Rebuild a posterior
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#
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#
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-
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# Rebuild a posterior VNChain (latents only) from our samples wire so it can feed
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# Turing's predict. Scalar leaves are regrouped into their array-valued VarName
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# (theta[1..8] -> @varname(theta) holding an 8-vector), so predict matches the
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# model's parameters exactly instead of relying on leaf reconstruction. Target
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# outcome columns are excluded.
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function wire_to_vnchain(wire, targets)
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sz = wire["size"]
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nIter,
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nIter, total, nChains = Int(sz[1]), Int(sz[2]), Int(sz[3])
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flat = wire["value_flat"]
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-
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index = Dict(n => i for (i, n) in enumerate(wire["parameters"]))
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is_target(n) = any(t -> n == t || startswith(n, t * "["), targets)
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keep = [n for n in wire["name_map"]["parameters"] if !is_target(n)]
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cell(name, i, c) = begin
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p = index[name]
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v = flat[i + (p - 1) * nIter + (c - 1) * nIter * total]
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v === nothing ? NaN : Float64(v)
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end
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base_of(n) = (b = findfirst('[', n); b === nothing ? n : n[1:prevind(n, b)])
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idx_of(n) = begin
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b = findfirst('[', n)
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b === nothing && return Int[]
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inner = n[nextind(n, b):prevind(n, findlast(']', n))]
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parse.(Int, split(inner, ','))
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end
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groups = Dict{String,Vector{String}}()
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for n in keep
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push!(get!(groups, base_of(n), String[]), n)
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end
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dict = Dict{FlexiChains.ParameterOrExtra{<:VarName},Array}()
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for (base, names) in groups
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vn = eval(:(Turing.@varname($(Meta.parse(base)))))
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if length(names) == 1 && isempty(idx_of(names[1]))
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m = Matrix{Float64}(undef, nIter, nChains)
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for c in 1:nChains, i in 1:nIter
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m[i, c] = cell(names[1], i, c)
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end
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dict[FlexiChains.Parameter(vn)] = m
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else
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idxs = [idx_of(n) for n in names]
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D = length(idxs[1])
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dims = ntuple(d -> maximum(ix[d] for ix in idxs), D)
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m = Matrix{Array{Float64,D}}(undef, nIter, nChains)
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for c in 1:nChains, i in 1:nIter
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a = Array{Float64,D}(undef, dims...)
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for (n, ix) in zip(names, idxs)
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a[ix...] = cell(n, i, c)
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end
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m[i, c] = a
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end
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dict[FlexiChains.Parameter(vn)] = m
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end
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end
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-
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vmap = Dict{VarName,Symbol}(eval(:(Turing.@varname($(Meta.parse(n))))) => Symbol(n) for n in keep)
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return MCMCChains.Chains(arr, syms, Dict(:parameters => syms); info = (; varname_to_symbol = vmap))
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return FlexiChains.FlexiChain{VarName}(nIter, nChains, dict)
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end
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# Expand one sampler transition to canonical scalar leaves (theta -> theta[1], ...),
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@@ -268,8 +298,7 @@ end
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# FlexiChains-native wire writer. DimArray(chn) splits array-valued parameters
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# into scalar leaves (theta -> theta[1], theta[2]) in the (iter, chain, param)
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# orientation; Real-valued extras become the internals section
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# the MCMCChains bridge produced.
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# orientation; Real-valued extras become the internals section.
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function vnchain_to_wire(chn)
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da = DimensionalData.DimArray(chn)
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pnames = string.(collect(DimensionalData.lookup(da, :param)))
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@@ -460,32 +489,11 @@ function predict_bugs(model, posterior, targets, rng)
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)
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end
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# Build the exact wire object parseMCMCChainsJson consumes: value_flat is indexed
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# i + p*nIter + c*nIter*nParams (column-major over [iteration, parameter, chain]).
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function chains_to_wire(chn)
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arr = Array(chn.value)
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nIter, nParams, nChains = size(arr)
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flat = Vector{Union{Float64,Nothing}}(undef, nIter * nParams * nChains)
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for c in 1:nChains, p in 1:nParams, i in 1:nIter
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v = arr[i, p, c]
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flat[i + (p - 1) * nIter + (c - 1) * nIter * nParams] = v === missing ? nothing : Float64(v)
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end
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return Dict(
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"size" => [nIter, nParams, nChains],
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"value_flat" => flat,
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"parameters" => string.(names(chn)),
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"name_map" => Dict(
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"parameters" => string.(get(chn.name_map, :parameters, Symbol[])),
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"internals" => string.(get(chn.name_map, :internals, Symbol[])),
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),
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)
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end
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function provenance()
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packages = Dict{String,String}()
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for (_, info) in Pkg.dependencies()
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if info.name in
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("Turing", "FlexiChains", "
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("Turing", "FlexiChains", "DynamicPPL", "AbstractMCMC", "JuliaBUGS", "AdvancedHMC", "ForwardDiff", "Mooncake", "ADTypes") &&
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info.version !== nothing
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packages[info.name] = string(info.version)
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end
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else
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model = Base.invokelatest(entry, ModelData(predict_namedtuple(request["data"])))
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stage = "load_samples"
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rchn =
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rchn = wire_to_vnchain(JSON.parsefile(request["samples"]), request["predict"]["targets"])
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stage = "predict"
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pp = Base.invokelatest(predict, rng, model, rchn)
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isempty(
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pp = Base.invokelatest(predict, rng, model, rchn; include_all = false)
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isempty(FlexiChains.parameters(pp)) &&
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error("no variables predicted; check that [predict].targets name unconditioned outcomes")
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vnchain_to_wire(pp)
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end
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else
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data = backend == "juliabugs" ? bugs_namedtuple(request["data"]) : ModelData(to_namedtuple(request["data"]))
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julia_version = "1.12.6"
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manifest_format = "2.0"
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project_hash = "
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project_hash = "53fe6fe905b54b27f87eac7040ed8686b3f8b8c1"
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[[deps.ADTypes]]
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git-tree-sha1 = "ec6be48a85c93d995563b84bff8a86bc98df45ce"
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@@ -231,18 +231,6 @@ version = "7.27.0"
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uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33"
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version = "1.11.0"
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deps = ["LinearAlgebra", "Random", "SparseArrays", "WoodburyMatrices"]
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git-tree-sha1 = "01b8ccb13d68535d73d2b0c23e39bd23155fb712"
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deps = ["Dates", "IntervalSets", "IterTools", "RangeArrays"]
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git-tree-sha1 = "4126b08903b777c88edf1754288144a0492c05ad"
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uuid = "39de3d68-74b9-583c-8d2d-e117c070f3a9"
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version = "0.4.8"
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[[deps.BangBang]]
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deps = ["Accessors", "ConstructionBase", "InitialValues", "LinearAlgebra"]
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git-tree-sha1 = "cceb62468025be98d42a5dc581b163c20896b040"
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ConstructionBaseLinearAlgebraExt = "LinearAlgebra"
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ConstructionBaseStaticArraysExt = "StaticArrays"
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[[deps.Crayons]]
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deps = ["AbstractFFTs", "DocStringExtensions", "LinearAlgebra", "MuladdMacro", "Primes", "Random", "Reexport"]
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GraphsSharedArraysExt = "SharedArrays"
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deps = ["Adapt", "AxisAlgorithms", "ChainRulesCore", "LinearAlgebra", "OffsetArrays", "Random", "Ratios", "SharedArrays", "SparseArrays", "StaticArrays", "WoodburyMatrices"]
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InterpolationsForwardDiffExt = "ForwardDiff"
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InterpolationsUnitfulExt = "Unitful"
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ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
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git-tree-sha1 = "42d5f897009e7ff2cf88db414a389e5ed1bdd023"
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uuid = "c8e1da08-722c-5040-9ed9-7db0dc04731e"
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-
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-
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[[deps.IteratorInterfaceExtensions]]
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git-tree-sha1 = "a3f24677c21f5bbe9d2a714f95dcd58337fb2856"
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@@ -933,17 +889,6 @@ deps = ["StyledStrings"]
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|
uuid = "ac6e5ff7-fb65-4e79-a425-ec3bc9c03011"
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|
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[[deps.KernelDensity]]
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-
deps = ["Distributions", "DocStringExtensions", "FFTA", "Interpolations", "StatsBase"]
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[[deps.LazilyInitializedFields]]
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@@ -1063,12 +1008,6 @@ git-tree-sha1 = "f00544d95982ea270145636c181ceda21c4e2575"
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[[deps.MCMCChains]]
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-
deps = ["AbstractMCMC", "AxisArrays", "DataAPI", "Dates", "Distributions", "IteratorInterfaceExtensions", "KernelDensity", "LinearAlgebra", "MCMCDiagnosticTools", "MLJModelInterface", "NaturalSort", "OrderedCollections", "PrettyTables", "Random", "RecipesBase", "Statistics", "StatsBase", "StatsFuns", "TableTraits", "Tables"]
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[[deps.MCMCDiagnosticTools]]
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deps = ["AbstractFFTs", "DataAPI", "DataStructures", "Distributions", "LinearAlgebra", "MLJModelInterface", "Random", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns", "Tables"]
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-
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-
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|
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[[deps.NaturalSort]]
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[[deps.NetworkOptions]]
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@@ -1693,11 +1575,6 @@ git-tree-sha1 = "c5391c6ace3bc430ca630251d02ea9687169ca68"
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[[deps.SimpleTraits]]
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|
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|
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1709
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StatsFunsChainRulesCoreExt = "ChainRulesCore"
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StatsFunsInverseFunctionsExt = "InverseFunctions"
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-
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|
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1712
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[[deps.StructUtils]]
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|
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|
git-tree-sha1 = "82bee338d650aa515f31866c460cb7e3bcef90b8"
|
|
@@ -1872,11 +1743,13 @@ deps = ["Accessors", "ArrayInterface", "RuntimeGeneratedFunctions", "StaticArray
|
|
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1872
1743
|
git-tree-sha1 = "72d6d882fa1e59c699f1b22d846db94c5600295c"
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|
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|
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|
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|
-
weakdeps = ["PrettyTables"]
|
|
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|
|
|
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1747
|
[deps.SymbolicIndexingInterface.extensions]
|
|
1878
1748
|
SymbolicIndexingInterfacePrettyTablesExt = "PrettyTables"
|
|
1879
1749
|
|
|
1750
|
+
[deps.SymbolicIndexingInterface.weakdeps]
|
|
1751
|
+
PrettyTables = "08abe8d2-0d0c-5749-adfa-8a2ac140af0d"
|
|
1752
|
+
|
|
1880
1753
|
[[deps.TOML]]
|
|
1881
1754
|
deps = ["Dates"]
|
|
1882
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|
uuid = "fa267f1f-6049-4f14-aa54-33bafae1ed76"
|
|
@@ -1944,12 +1817,6 @@ version = "1.11.0"
|
|
|
1944
1817
|
uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5"
|
|
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1818
|
version = "1.11.0"
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|
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1819
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|
-
[[deps.WoodburyMatrices]]
|
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1948
|
-
deps = ["LinearAlgebra", "SparseArrays"]
|
|
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|
-
git-tree-sha1 = "248a7031b3da79a127f14e5dc5f417e26f9f6db7"
|
|
1950
|
-
uuid = "efce3f68-66dc-5838-9240-27a6d6f5f9b6"
|
|
1951
|
-
version = "1.1.0"
|
|
1952
|
-
|
|
1953
1820
|
[[deps.Zlib_jll]]
|
|
1954
1821
|
deps = ["Libdl"]
|
|
1955
1822
|
uuid = "83775a58-1f1d-513f-b197-d71354ab007a"
|
|
@@ -5,7 +5,6 @@ FlexiChains = "4a37a8b9-6e57-4b92-8664-298d46e639f7"
|
|
|
5
5
|
ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
|
|
6
6
|
JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
|
|
7
7
|
JuliaBUGS = "ba9fb4c0-828e-4473-b6a1-cd2560fee5bf"
|
|
8
|
-
MCMCChains = "c7f686f2-ff18-58e9-bc7b-31028e88f75d"
|
|
9
8
|
Mooncake = "da2b9cff-9c12-43a0-ae48-6db2b0edb7d6"
|
|
10
9
|
StableRNGs = "860ef19b-820b-49d6-a774-d7a799459cd3"
|
|
11
10
|
StatsFuns = "4c63d2b9-4356-54db-8cca-17b64c39e42c"
|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@mcmcjs/julia",
|
|
3
|
-
"version": "0.11.
|
|
3
|
+
"version": "0.11.3",
|
|
4
4
|
"description": "Julia toolchain detection and the inference runner for MCMC.js.",
|
|
5
5
|
"keywords": [
|
|
6
6
|
"mcmc",
|
|
@@ -46,7 +46,7 @@
|
|
|
46
46
|
"access": "public"
|
|
47
47
|
},
|
|
48
48
|
"dependencies": {
|
|
49
|
-
"@mcmcjs/core": "0.
|
|
49
|
+
"@mcmcjs/core": "0.8.0",
|
|
50
50
|
"@mcmcjs/engine": "0.6.0"
|
|
51
51
|
},
|
|
52
52
|
"scripts": {
|