@mcmcjs/julia 0.21.1 → 0.21.2

package/dist/index.cjs

@@ -245,7 +245,7 @@ serve(ARGS[1])
 `,
   "fitlib.jl": '# MCMC.js fit library, shared by the one-shot driver (driver.jl) and the\n# persistent worker (worker.jl). handle_request runs one fit or predict request\n# (Turing or JuliaBUGS) and writes the draws as the @mcmcjs/core samples\n# artifact (a flat JSON wire). This is the only place that touches the backend\n# chain type (FlexiChains), so a chain-type change is contained here.\nusing JSON\nusing Logging\nimport Distributed\nusing Random\nusing StableRNGs\nusing Turing\nusing Turing: VarName\nusing SHA\nusing Pkg\n# Imported (not `using`) so they do not pull `@model` etc. into Main and clash\n# with Turing\'s exports, which would break Turing model files on include.\nimport JuliaBUGS\nimport AdvancedHMC\n# Loading SliceSampling activates JuliaBUGS\'s extension for its derivative-free samplers.\nimport SliceSampling\nimport ForwardDiff\n# Loading Mooncake activates AbstractPPL\'s native extension for AutoMooncake.\nimport Mooncake\n# Loading ReverseDiff activates the DynamicPPL extension for AutoReverseDiff.\nimport ReverseDiff\nimport FlexiChains\nimport DimensionalData\n\n# Workers include this file to mirror the master\'s definitions (ModelData, the\n# helpers a deserialized model may reference) when sampling MCMCDistributed.\nconst FITLIB_FILE = @__FILE__\n\n# AbstractMCMC reports sampling progress through ProgressLogging (reachable via\n# Turing\'s dependency, no extra package in the managed env).\nconst ProgressLogging = Turing.AbstractMCMC.ProgressLogging\n\n# Where progress JSON lines go: the driver leaves this on stderr; the worker\n# points it at the client socket for the duration of a request.\nconst PROGRESS_IO = Ref{IO}(stderr)\n\n# Translates ProgressLogging records into one JSON line per update\n# ({"mcmcjs":"progress",...}). The TypeScript side filters these out of the\n# failure protocol\'s stderr buffer. Info-and-above records pass through to a\n# plain console logger; Debug records (AdvancedHMC step-size search) are dropped.\nstruct JSONProgressLogger <: Logging.AbstractLogger\n    fallback::Logging.AbstractLogger\n    last::Dict{Int,Float64}\nend\nJSONProgressLogger() =\n    JSONProgressLogger(Logging.ConsoleLogger(stderr, Logging.Info), Dict{Int,Float64}())\n\nLogging.min_enabled_level(::JSONProgressLogger) = Logging.BelowMinLevel\nLogging.shouldlog(::JSONProgressLogger, args...) = true\nLogging.catch_exceptions(::JSONProgressLogger) = true\n\nfunction emit_progress(logger::JSONProgressLogger, name, fraction, done)\n    m = match(r"Chain (\\d+) of (\\d+)", String(name))\n    chain = m === nothing ? 1 : parse(Int, m.captures[1])\n    of = m === nothing ? 1 : parse(Int, m.captures[2])\n    f = done ? 1.0 : fraction === nothing ? 0.0 : Float64(fraction)\n    # AbstractMCMC already steps by 1%; the dedupe guards chattier emitters.\n    if done || f - get(logger.last, chain, -1.0) >= 0.01\n        logger.last[chain] = f\n        println(\n            PROGRESS_IO[],\n            JSON.json(\n                Dict(\n                    "mcmcjs" => "progress",\n                    "chain" => chain,\n                    "of" => of,\n                    "fraction" => round(f; digits = 4),\n                    "done" => done,\n                ),\n            ),\n        )\n        flush(PROGRESS_IO[])\n    end\nend\n\nfunction Logging.handle_message(\n    logger::JSONProgressLogger, level, message, _module, group, id, file, line; kwargs...\n)\n    progress = message isa ProgressLogging.ProgressString ? message.progress :\n        message isa ProgressLogging.Progress ? message : nothing\n    if progress !== nothing\n        emit_progress(logger, progress.name, progress.fraction, progress.done)\n        return\n    end\n    if haskey(kwargs, :progress) && (kwargs[:progress] isa Real || kwargs[:progress] == "done")\n        value = kwargs[:progress]\n        emit_progress(logger, string(message), value == "done" ? nothing : value, value == "done")\n        return\n    end\n    level >= Logging.Info || return\n    Logging.handle_message(logger.fallback, level, message, _module, group, id, file, line; kwargs...)\nend\n\n# A Turing model file may declare the AD backend it needs by exporting, e.g.,\n# `const MCMC_DEFAULTS = (; adtype = "mooncake")`. A spec or flag adtype wins;\n# the model default fills in only when the request leaves adtype unset.\nfunction apply_model_defaults(sampler, mod)\n    haskey(sampler, "adtype") && return sampler\n    # Only the gradient samplers take an AD backend.\n    get(sampler, "algorithm", "NUTS") in ("NUTS", "HMC", "HMCDA", "Gibbs", "External") ||\n        return sampler\n    Base.invokelatest(isdefined, mod, :MCMC_DEFAULTS) || return sampler\n    defaults = Base.invokelatest(getfield, mod, :MCMC_DEFAULTS)\n    hasproperty(defaults, :adtype) || return sampler\n    merged = copy(sampler)\n    merged["adtype"] = String(defaults.adtype)\n    return merged\nend\n\nfunction build_adtype(name)\n    name == "forwarddiff" && return Turing.ADTypes.AutoForwardDiff()\n    name == "reversediff" && return Turing.ADTypes.AutoReverseDiff()\n    name == "mooncake" && return Turing.ADTypes.AutoMooncake(; config = nothing)\n    error("unsupported adtype: $name")\nend\n\nfunction build_sampler(sampler, modelmod = nothing)\n    algorithm = get(sampler, "algorithm", "NUTS")\n    # Prior draws are iid: no warmup, no adaptation. The JuliaBUGS path samples\n    # ancestrally (sample_bugs_prior) instead of going through a sampler object.\n    algorithm == "Prior" && return Turing.Prior(), 0\n    warmup = Int(get(sampler, "warmup", 1000))\n    adapt_delta = Float64(get(sampler, "adapt_delta", 0.8))\n    algorithm == "MH" && return Turing.MH(), warmup\n    algorithm == "ESS" && return Turing.ESS(), warmup\n    algorithm == "SMC" && return Turing.SMC(), warmup\n    algorithm == "PG" && return Turing.PG(Int(sampler["particles"])), warmup\n    adkw = haskey(sampler, "adtype") ? (; adtype = build_adtype(sampler["adtype"])) : (;)\n    algorithm == "NUTS" && return Turing.NUTS(warmup, adapt_delta; adkw...), warmup\n    algorithm == "HMC" &&\n        return Turing.HMC(Float64(sampler["step_size"]), Int(sampler["leapfrog_steps"]); adkw...),\n        warmup\n    algorithm == "HMCDA" &&\n        return Turing.HMCDA(warmup, adapt_delta, Float64(sampler["lambda"]); adkw...), warmup\n    algorithm == "Gibbs" && return build_gibbs(sampler, adkw, warmup), warmup\n    if algorithm == "External"\n        modelmod === nothing && error("the External algorithm applies to Turing models only")\n        Base.invokelatest(isdefined, modelmod, :MCMC_SAMPLER) ||\n            error("algorithm External needs the model file to define MCMC_SAMPLER")\n        ext = Base.invokelatest(getfield, modelmod, :MCMC_SAMPLER)\n        return Turing.externalsampler(ext; adkw...), warmup\n    end\n    error("unsupported sampler algorithm: $algorithm")\nend\n\n# One Gibbs component: the block\'s variables get the block\'s sampler. A single\n# variable keys by symbol, several by tuple, matching Turing\'s constructor.\nfunction block_sampler(block, adkw, warmup)\n    algorithm = get(block, "algorithm", "NUTS")\n    adapt_delta = Float64(get(block, "adapt_delta", 0.8))\n    algorithm == "MH" && return Turing.MH()\n    algorithm == "ESS" && return Turing.ESS()\n    algorithm == "PG" && return Turing.PG(Int(block["particles"]))\n    algorithm == "NUTS" && return Turing.NUTS(warmup, adapt_delta; adkw...)\n    algorithm == "HMC" &&\n        return Turing.HMC(Float64(block["step_size"]), Int(block["leapfrog_steps"]); adkw...)\n    algorithm == "HMCDA" &&\n        return Turing.HMCDA(warmup, adapt_delta, Float64(block["lambda"]); adkw...)\n    error("unsupported Gibbs block algorithm: $algorithm")\nend\n\nfunction build_gibbs(sampler, adkw, warmup)\n    pairs = map(sampler["blocks"]) do block\n        vars = Symbol.(block["variables"])\n        key = length(vars) == 1 ? vars[1] : Tuple(vars)\n        key => block_sampler(block, adkw, warmup)\n    end\n    return Turing.Gibbs(pairs...)\nend\n\n# Extra keyword arguments for AbstractMCMC.sample, from the request\'s sampler\n# table: thinning, burn-in for the non-adaptive samplers (NUTS and HMCDA discard\n# their own adaptation), and named starting values replicated across chains.\nfunction sampling_kwargs(sampler, warmup, chains)\n    kw = (;)\n    thin = Int(get(sampler, "thin", 1))\n    thin > 1 && (kw = merge(kw, (; thinning = thin)))\n    algorithm = get(sampler, "algorithm", "NUTS")\n    if algorithm in ("MH", "HMC", "ESS", "PG", "Gibbs", "External") && warmup > 0\n        kw = merge(kw, (; discard_initial = warmup))\n    end\n    # AdvancedHMC-style external samplers adapt only when told how many steps to\n    # use; without n_adapts a chain can freeze at its initial point.\n    if algorithm == "External" && warmup > 0\n        kw = merge(kw, (; n_adapts = warmup))\n    end\n    # NUTS/HMCDA blocks inside Gibbs adapt only through the sample-level nadapts\n    # keyword (the constructor\'s count is ignored there); without it the block\n    # never tunes its step size and can freeze.\n    if algorithm == "Gibbs" && warmup > 0\n        blocks = get(sampler, "blocks", Any[])\n        if any(get(b, "algorithm", "NUTS") in ("NUTS", "HMCDA") for b in blocks)\n            kw = merge(kw, (; nadapts = warmup))\n        end\n    end\n    if haskey(sampler, "initial_params")\n        nt = (; (Symbol(k) => narrow(v) for (k, v) in sampler["initial_params"])...)\n        strategy = Turing.DynamicPPL.InitFromParams(nt)\n        kw = merge(kw, (; initial_params = fill(strategy, chains)))\n    end\n    return kw\nend\n\n# Binds the data so a model can read a variable as a property (`data.y`) or by\n# index (`data["y"]` / `data[:y]`), with `haskey`/`keys` supported, so models\n# written in either idiom run unchanged. The underlying NamedTuple is reached\n# via getfield to avoid colliding with a data variable also named `nt`.\nstruct ModelData\n    nt::NamedTuple\nend\nBase.getproperty(d::ModelData, k::Symbol) = getproperty(getfield(d, :nt), k)\nBase.getindex(d::ModelData, k::Symbol) = getproperty(getfield(d, :nt), k)\nBase.getindex(d::ModelData, k::AbstractString) = getproperty(getfield(d, :nt), Symbol(k))\nBase.haskey(d::ModelData, k::Symbol) = haskey(getfield(d, :nt), k)\nBase.haskey(d::ModelData, k::AbstractString) = haskey(getfield(d, :nt), Symbol(k))\nBase.keys(d::ModelData) = keys(getfield(d, :nt))\nBase.propertynames(d::ModelData) = propertynames(getfield(d, :nt))\n\n# JuliaBUGS requires dense arrays with a concrete numeric eltype, but JSON parses\n# them as Vector{Any} (and nested arrays as vectors of vectors). narrow promotes a\n# numeric array to a concrete eltype and stacks equal-sized nested arrays into a\n# dense array; an empty array becomes Float64[].\nfunction narrow(v::AbstractVector)\n    isempty(v) && return Float64[]\n    elems = [narrow(x) for x in v]\n    if all(e -> e isa AbstractArray, elems) && allequal(size.(elems))\n        return stack(elems; dims = 1)\n    end\n    return eltype(elems) <: Real && !isconcretetype(eltype(elems)) ? float.(elems) : elems\nend\nnarrow(x) = x\n\n# JSON null arrives as `nothing`; map it to `missing`, which both PPLs read as an\n# unobserved entry: a sampling statement rather than an observation.\nto_missing(x) = x === nothing ? missing : (x isa AbstractVector ? map(to_missing, x) : x)\nto_namedtuple(data) = (; (Symbol(k) => to_missing(v) for (k, v) in data)...)\n\n# JuliaBUGS backs an array\'s unobserved entries with the eltype of its observed\n# ones, so an integer censoring time would leave a continuous latent an Int slot\n# to live in. Float64 holds a count just as exactly, so it holds either.\nfunction allow_missing(v::AbstractArray)\n    any(ismissing, v) || return v\n    return convert(AbstractArray{Union{Missing,Float64}}, v)\nend\nallow_missing(x) = x\n\nbugs_namedtuple(data) =\n    (; (Symbol(k) => allow_missing(narrow(to_missing(v))) for (k, v) in data)...)\n\n# Rebuild a posterior VNChain (latents only) from our samples wire so it can feed\n# Turing\'s predict. Scalar leaves are regrouped into their array-valued VarName\n# (theta[1..8] -> @varname(theta) holding an 8-vector), so predict matches the\n# model\'s parameters exactly instead of relying on leaf reconstruction. Target\n# outcome columns are excluded.\nfunction wire_to_vnchain(wire, targets)\n    sz = wire["size"]\n    nIter, total, nChains = Int(sz[1]), Int(sz[2]), Int(sz[3])\n    flat = wire["value_flat"]\n    index = Dict(n => i for (i, n) in enumerate(wire["parameters"]))\n    is_target(n) = any(t -> n == t || startswith(n, t * "["), targets)\n    keep = [n for n in wire["name_map"]["parameters"] if !is_target(n)]\n    cell(name, i, c) = begin\n        p = index[name]\n        v = flat[i + (p - 1) * nIter + (c - 1) * nIter * total]\n        v === nothing ? NaN : Float64(v)\n    end\n    base_of(n) = (b = findfirst(\'[\', n); b === nothing ? n : n[1:prevind(n, b)])\n    idx_of(n) = begin\n        b = findfirst(\'[\', n)\n        b === nothing && return Int[]\n        inner = n[nextind(n, b):prevind(n, findlast(\']\', n))]\n        parse.(Int, split(inner, \',\'))\n    end\n    groups = Dict{String,Vector{String}}()\n    for n in keep\n        push!(get!(groups, base_of(n), String[]), n)\n    end\n    dict = Dict{FlexiChains.ParameterOrExtra{<:VarName},Array}()\n    for (base, names) in groups\n        vn = eval(:(Turing.@varname($(Meta.parse(base)))))\n        if length(names) == 1 && isempty(idx_of(names[1]))\n            m = Matrix{Float64}(undef, nIter, nChains)\n            for c in 1:nChains, i in 1:nIter\n                m[i, c] = cell(names[1], i, c)\n            end\n            dict[FlexiChains.Parameter(vn)] = m\n        else\n            idxs = [idx_of(n) for n in names]\n            D = length(idxs[1])\n            dims = ntuple(d -> maximum(ix[d] for ix in idxs), D)\n            m = Matrix{Array{Float64,D}}(undef, nIter, nChains)\n            for c in 1:nChains, i in 1:nIter\n                a = Array{Float64,D}(undef, dims...)\n                for (n, ix) in zip(names, idxs)\n                    a[ix...] = cell(n, i, c)\n                end\n                m[i, c] = a\n            end\n            dict[FlexiChains.Parameter(vn)] = m\n        end\n    end\n    return FlexiChains.FlexiChain{VarName}(nIter, nChains, dict)\nend\n\n# Expand one sampler transition to canonical scalar leaves (theta -> theta[1], ...),\n# the same names the final samples file uses, so streamed batches reconstruct it.\n# Sampler statistics (acceptance rate, tree depth, ...) ride along under the same\n# names the samples file records as internals, so consumers get per-draw\n# diagnostics without a second channel; Bool stats become 0/1.\nfunction flatten_draw(transition)\n    out = Pair{String,Float64}[]\n    for (vn, val) in pairs(transition.params)\n        for (leaf, leafval) in Turing.DynamicPPL.varname_and_value_leaves(vn, val)\n            push!(out, string(leaf) => Float64(leafval))\n        end\n    end\n    if hasproperty(transition, :stats)\n        for (name, value) in pairs(transition.stats)\n            value isa Real && push!(out, string(name) => Float64(value))\n        end\n    end\n    return out\nend\n\n# A per-draw callback that emits {"mcmcjs":"draws",...} batches on PROGRESS_IO as\n# sampling proceeds. AbstractMCMC passes the 1-based chain index as `chain_number`;\n# each batch carries a per-chain monotonic seq, and a chain\'s batches concatenate\n# (by leaf name) to the final samples file. Assumes the callback is not invoked\n# concurrently across chains (true for the MCMCSerial path build_and_sample uses).\nfunction draw_streamer(draws_per_chain::Int, batch_size::Int)\n    chain = Ref(-1)\n    seq = Ref(0)\n    names = String[]\n    buffer = Dict{String,Vector{Float64}}()\n    filled = Ref(0)\n    function emit(iteration)\n        filled[] == 0 && return\n        cols = Dict{String,Vector{Float64}}(n => copy(buffer[n]) for n in names)\n        println(\n            PROGRESS_IO[],\n            JSON.json(\n                Dict(\n                    "mcmcjs" => "draws",\n                    "chain" => chain[],\n                    "seq" => seq[],\n                    "iteration" => iteration,\n                    "draws" => cols,\n                ),\n            ),\n        )\n        flush(PROGRESS_IO[])\n        seq[] += 1\n        for n in names\n            empty!(buffer[n])\n        end\n        filled[] = 0\n    end\n    return function (_rng, _model, _sampler, transition, _state, iteration; chain_number = 1, _kwargs...)\n        c = Int(chain_number) - 1\n        if c != chain[]\n            chain[] = c\n            seq[] = 0\n        end\n        leaves = flatten_draw(transition)\n        if isempty(names)\n            for (n, _) in leaves\n                push!(names, n)\n                buffer[n] = Float64[]\n            end\n        end\n        for (n, v) in leaves\n            push!(get!(buffer, n, Float64[]), v)\n        end\n        filled[] += 1\n        if filled[] >= batch_size || iteration >= draws_per_chain\n            emit(iteration)\n        end\n    end\nend\n\n# Turing observes a variable only when its name is a model argument. A dict-reading\n# model (`y = data["y"]; y[i] ~ dist`) would otherwise SAMPLE its outcome instead of\n# observing it, so condition the built model on the data columns to turn each such\n# `~` into an observation. Columns that are already model arguments are skipped: they\n# are observed by construction, and conditioning one that is also an argument errors.\n# Do not probe the model to find latent columns (e.g. via VarInfo): evaluating a\n# dict-reading model assigns prior draws into the array the data is read from,\n# corrupting it before we condition. Predictor columns carry no `~`, so conditioning\n# on them is a harmless no-op.\nfunction condition_on_data(model, data)\n    nt = data isa ModelData ? getfield(data, :nt) : data\n    nt isa NamedTuple || return model\n    argnames = keys(model.args)\n    pairs = [k => getproperty(nt, k) for k in keys(nt) if Base.isidentifier(string(k)) && !(k in argnames)]\n    isempty(pairs) && return model\n    return Turing.DynamicPPL.condition(model, (; pairs...))\nend\n\n# Build the model and sample in one call so both run in the latest world age:\n# the model methods are defined by `include` at runtime, so a plain call from\n# this (older) world would fail with "method too new". invokelatest fixes that.\n# Returns Turing\'s default chain type, a FlexiChain. With a callback, draws stream.\nfunction build_and_sample(\n    entry, data, sampler, draws, chains, rng; callback = nothing, extra = (;), parallel = "serial"\n)\n    model = condition_on_data(entry(data), data)\n    kw = callback === nothing ? extra : merge(extra, (; callback))\n    ensemble = parallel == "threads" ? MCMCThreads() :\n        parallel == "distributed" ? MCMCDistributed() : MCMCSerial()\n    return Logging.with_logger(JSONProgressLogger()) do\n        sample(rng, model, sampler, ensemble, draws, chains; progress = true, kw...)\n    end\nend\n\n# Distributed chains need the model\'s definitions on every process: workers get\n# this file (ModelData and friends), then all processes include the model file\n# into Main so the serialized model\'s references resolve identically everywhere.\nfunction setup_distributed(chains, model_file)\n    missing_workers = chains - Distributed.nworkers()\n    if Distributed.nprocs() == 1 || missing_workers > 0\n        Distributed.addprocs(\n            Distributed.nprocs() == 1 ? chains : missing_workers;\n            exeflags = ["--project=$(Base.active_project())", "--startup-file=no"],\n        )\n        Distributed.remotecall_eval(\n            Main, Distributed.workers(), :(Base.include(Main, $FITLIB_FILE))\n        )\n    end\n    Distributed.remotecall_eval(Main, Distributed.procs(), :(Base.include(Main, $model_file)))\nend\n\n# The internals section: one scalar column per sampler statistic, as\n# (name, (iter, chain) -> value) pairs. An array-valued statistic (a slice\n# sampler reports a proposal count per coordinate) splits into name[i] columns\n# the way array parameters do, so nothing the sampler reported is dropped.\nfunction extra_columns(chn)\n    cols = Tuple{String,Function}[]\n    for e in FlexiChains.extras(chn)\n        m = chn[e]\n        name = string(Symbol(e))\n        if eltype(m) <: Union{Missing,Real}\n            push!(cols, (name, (i, c) -> m[i, c]))\n        elseif eltype(m) <: AbstractArray && eltype(eltype(m)) <: Union{Missing,Real}\n            for idx in eachindex(m[1, 1])\n                push!(cols, ("$name[$idx]", (i, c) -> m[i, c][idx]))\n            end\n        end\n    end\n    return cols\nend\n\n# FlexiChains-native wire writer. DimArray(chn) splits array-valued parameters\n# into scalar leaves (theta -> theta[1], theta[2]) in the (iter, chain, param)\n# orientation; the sampler\'s statistics become the internals section. `keep`\n# decides by leaf name which columns are written; nothing keeps them all.\nfunction vnchain_to_wire(chn; keep = nothing)\n    da = DimensionalData.DimArray(chn)\n    names = string.(collect(DimensionalData.lookup(da, :param)))\n    arr = parent(da)\n    nIter, nChains, _ = size(arr)\n    kept = keep === nothing ? eachindex(names) : findall(keep, names)\n    pnames = names[kept]\n    nParams = length(kept)\n\n    extras = extra_columns(chn)\n    enames = first.(extras)\n    total = nParams + length(extras)\n\n    flat = Vector{Union{Float64,Nothing}}(undef, nIter * total * nChains)\n    # JSON has no Inf/NaN; a non-finite draw (e.g. 1/sqrt(tau) under a diffuse\n    # prior) becomes null, which the samples parser reads back as NaN.\n    cell(v) = v === missing || !isfinite(v) ? nothing : Float64(v)\n    for c in 1:nChains, (p, src) in enumerate(kept), i in 1:nIter\n        flat[i + (p - 1) * nIter + (c - 1) * nIter * total] = cell(arr[i, c, src])\n    end\n    for (k, (_, draw)) in enumerate(extras)\n        p = nParams + k\n        for c in 1:nChains, i in 1:nIter\n            flat[i + (p - 1) * nIter + (c - 1) * nIter * total] = cell(draw(i, c))\n        end\n    end\n\n    return Dict(\n        "size" => [nIter, total, nChains],\n        "value_flat" => flat,\n        "parameters" => vcat(pnames, enames),\n        "name_map" => Dict("parameters" => pnames, "internals" => enames),\n    )\nend\n\n# A BUGSModel carries its own `base_model` field (the unconditioned model, or\n# nothing), so unwrapping has to test the wrapper\'s type, not for the field.\nbase_bugs(model) = model isa JuliaBUGS.BUGSModelWithGradient ? model.base_model : model\n\n# `[model].monitor` names the deterministic quantities worth storing; the model\'s\n# parameters are always stored. Unset keeps every column the chain carries. The\n# graph\'s parameter list is read rather than `model_parameters`, which in the\n# marginalized mode leaves out the discrete latents the chain still carries.\nfunction bugs_column_filter(request, model)\n    monitor = get(request["model"], "monitor", nothing)\n    monitor === nothing && return nothing\n    keep = Set{String}(String.(monitor))\n    for vn in base_bugs(model).graph_evaluation_data.model_parameters\n        push!(keep, String(JuliaBUGS.AbstractPPL.getsym(vn)))\n    end\n    return name -> first(split(name, \'[\'; limit = 2)) in keep\nend\n\n# JuliaBUGS samplers that propose in the evaluation environment, so they move the\n# discrete latents themselves rather than needing them summed out.\nconst ENV_BASED_BUGS_SAMPLERS = ("MH", "Gibbs")\n\n# Switches a model to the evaluation mode the spec names. The generated and\n# marginalized modes read parameters in unconstrained space, so both need a\n# transformed model first. invokelatest is needed because JuliaBUGS `Core.eval`s\n# the model\'s node functions while compiling, putting them in a newer world than\n# this frame; the generated mode `Core.eval`s a log-density function here too.\nfunction set_bugs_mode(model, name)\n    name == "graph" &&\n        return Base.invokelatest(JuliaBUGS.set_evaluation_mode, model, JuliaBUGS.UseGraph())\n    mode = name == "generated" ? JuliaBUGS.UseGeneratedLogDensityFunction() :\n        name == "marginalized" ? JuliaBUGS.UseAutoMarginalization() :\n        error("unsupported evaluation mode: $name")\n    return Base.invokelatest(\n        JuliaBUGS.set_evaluation_mode, JuliaBUGS.settrans(model, true), mode,\n    )\nend\n\n# Named starting values, in constrained space, as the spec records them. A name\n# the model does not have at all is an error, since `initialize!` would ignore it\n# silently. A name that is a variable but not a parameter, an observed node or a\n# deterministic one, is left out, as BUGS does with such initial values; the\n# published inits of the classic examples carry them.\nfunction initialize_bugs_model(model, sampler)\n    haskey(sampler, "initial_params") || return model\n    gd = base_bugs(model).graph_evaluation_data\n    name(vn) = String(JuliaBUGS.AbstractPPL.getsym(vn))\n    parameters = Set(name.(gd.model_parameters))\n    known = Set(name.(gd.sorted_nodes))\n    for k in keys(sampler["initial_params"])\n        k in known || error("initial_params names $k, which is not a variable of this model")\n    end\n    inits = Dict(k => v for (k, v) in sampler["initial_params"] if k in parameters)\n    isempty(inits) && return model\n    # A JSON `0` arrives as an integer, and a continuous parameter initialized with it\n    # gets an integer slot that the generated log density cannot write a float into.\n    types = bugs_node_types(base_bugs(model))\n    continuous(k) = all(t == :continuous for (vn, t) in types if name(vn) == k)\n    as_float(v) = v isa AbstractArray{<:Real} || v isa Real ? float(v) : v\n    values = bugs_namedtuple(inits)\n    values = (; (k => (continuous(String(k)) ? as_float(v) : v) for (k, v) in pairs(values))...)\n    model = Base.invokelatest(JuliaBUGS.initialize!, model, values)\n    return finite_start(model, Set(String.(keys(values))))\nend\n\n# Published initial values rarely cover every parameter, and the rest come from prior\n# draws, which under vague priors put Magnesium\'s start at -Inf every time. A start that\n# is not finite has those uncovered parameters redrawn uniformly on (-2, 2) in\n# unconstrained space, as Stan starts, keeping the given values.\nfunction finite_start(model, given; attempts = 50)\n    model.transformed || return model\n    LDP = JuliaBUGS.LogDensityProblems\n    x = Base.invokelatest(JuliaBUGS.getparams, model)\n    isfinite(Base.invokelatest(LDP.logdensity, model, x)) && return model\n    vars = model.evaluation_mode isa JuliaBUGS.UseAutoMarginalization ?\n        model.marginalization_cache.continuous_model_parameters :\n        Base.invokelatest(JuliaBUGS.model_parameters, model)\n    rng = StableRNG(1)\n    for _ in 1:attempts\n        z = copy(x)\n        pos = 1\n        for vn in vars\n            len = model.transformed_var_lengths[vn]\n            String(JuliaBUGS.AbstractPPL.getsym(vn)) in given ||\n                (z[pos:(pos + len - 1)] .= 4 .* rand(rng, len) .- 2)\n            pos += len\n        end\n        isfinite(Base.invokelatest(LDP.logdensity, model, z)) &&\n            return Base.invokelatest(JuliaBUGS.initialize!, model, z)\n    end\n    return model\nend\n\n# With no evaluation mode chosen, a gradient sampler gets the discrete finite\n# latents summed out of the log density, since it cannot move them itself. A model\n# that is discrete throughout has nothing left for it to sample.\nfunction marginalize_if_discrete(base)\n    base.evaluation_mode isa JuliaBUGS.UseGraph || return base\n    marginalized = set_bugs_mode(base, "marginalized")\n    cache = marginalized.marginalization_cache\n    (cache === nothing || cache.n_discrete_finite == 0) && return base\n    Base.invokelatest(JuliaBUGS.LogDensityProblems.dimension, marginalized) == 0 && error(\n        "every parameter of this model is discrete, which a gradient sampler cannot move; use the MH sampler",\n    )\n    return marginalized\nend\n\n# An environment-based sampler starts from the model\'s evaluation environment and\n# accepts on `logp_proposed - logp_current`, which is NaN when both are -Inf: from\n# an impossible starting point the chain can never move. Say so, with the fix,\n# rather than return draws that never left the start.\nfunction check_bugs_start(model, sampler)\n    logp = try\n        last(Base.invokelatest(JuliaBUGS.AbstractPPL.evaluate!!, model))\n    catch\n        -Inf\n    end\n    isfinite(logp) && return model\n    detail = haskey(sampler, "initial_params") ?\n        "the given initial_params have zero probability under the model" :\n        "the model\'s default starting values have zero probability under the data; " *\n        "set [sampler.initial_params] to a state the data allows"\n    return error("$(get(sampler, "algorithm", "MH")) cannot start: $detail")\nend\n\n# Applies the request\'s options to a compiled model: the spec\'s evaluation mode\n# over whatever the model file chose, the initial values, and the AD backend. The\n# gradient wrapper holds a prepared gradient over one base model, so it is rebuilt\n# whenever the base changes.\nfunction prepare_bugs_model(model, sampler, mode_name)\n    base = base_bugs(model)\n    if get(sampler, "algorithm", "NUTS") in ENV_BASED_BUGS_SAMPLERS\n        # Marginalizing would sum out the very latents these samplers propose, so\n        # they always run against the plain model under graph evaluation.\n        base = initialize_bugs_model(set_bugs_mode(base, "graph"), sampler)\n        return check_bugs_start(base, sampler)\n    end\n    base = mode_name === nothing ? marginalize_if_discrete(base) : set_bugs_mode(base, mode_name)\n    # A derivative-free sampler wants the plain model: preparing a gradient it\n    # never calls costs a compile, which for Mooncake runs into minutes.\n    get(sampler, "algorithm", "NUTS") == "Slice" && return initialize_bugs_model(base, sampler)\n    if !haskey(sampler, "adtype") && !(model isa JuliaBUGS.BUGSModelWithGradient) &&\n       mode_name === nothing\n        checked = checked_gradient(base, sampler)\n        checked === nothing || return checked\n    end\n    adtype = haskey(sampler, "adtype") ? build_adtype(sampler["adtype"]) :\n        model isa JuliaBUGS.BUGSModelWithGradient ? model.adtype :\n        Turing.ADTypes.AutoForwardDiff()\n    base = initialize_bugs_model(base, sampler)\n    return Base.invokelatest(JuliaBUGS.BUGSModelWithGradient, base, adtype)\nend\n\n# With neither an evaluation mode nor an AD backend chosen, each candidate gradient is\n# tried fastest first, and the first whose gradient at the starting point matches central\n# differences of the same function is used. On the BUGS examples the generated log\n# density under Mooncake takes 10 to 740 times less per gradient than ForwardDiff on the\n# graph, and on marginalized models ForwardDiff is the faster by 13 to 18 times.\n# Neither is right everywhere: ForwardDiff\'s Poisson derivative at rate zero is NaN\n# (Leuk, Hearts) and Mooncake\'s Birats gradient is 6% off. Returns nothing when no\n# candidate passes, and the model is then fitted as before.\nfunction checked_gradient(base, sampler)\n    forwarddiff = Turing.ADTypes.AutoForwardDiff()\n    mooncake = Turing.ADTypes.AutoMooncake(; config = nothing)\n    candidates = if base.evaluation_mode isa JuliaBUGS.UseGraph\n        (("generated", mooncake),)\n    elseif base.evaluation_mode isa JuliaBUGS.UseAutoMarginalization\n        ((nothing, forwarddiff), (nothing, mooncake))\n    else\n        ()\n    end\n    for (mode, adtype) in candidates\n        try\n            # The generated function writes into the evaluation environment\'s arrays,\n            # so each attempt gets its own copy and a failed one leaves `base` unchanged.\n            candidate = deepcopy(base)\n            if mode !== nothing\n                candidate = set_bugs_mode(candidate, mode)\n                candidate.evaluation_mode isa JuliaBUGS.UseGeneratedLogDensityFunction || continue\n            end\n            candidate = initialize_bugs_model(candidate, sampler)\n            wrapped = Base.invokelatest(JuliaBUGS.BUGSModelWithGradient, candidate, adtype)\n            x = Base.invokelatest(JuliaBUGS.getparams, candidate)\n            gradient_matches_differences(wrapped, x) && return wrapped\n        catch\n        end\n    end\n    return nothing\nend\n\nfunction gradient_matches_differences(wrapped, x; rtol = 1e-4)\n    LDP = JuliaBUGS.LogDensityProblems\n    ld, grad = Base.invokelatest(LDP.logdensity_and_gradient, wrapped, x)\n    (isfinite(ld) && all(isfinite, grad)) || return false\n    f(z) = Base.invokelatest(LDP.logdensity, wrapped, z)\n    diffs = similar(x)\n    for i in eachindex(x)\n        h = 1e-6 * max(1.0, abs(x[i]))\n        step = zero(x)\n        step[i] = h\n        diffs[i] = (f(x .+ step) - f(x .- step)) / 2h\n    end\n    all(isfinite, diffs) || return false\n    return sqrt(sum(abs2, grad .- diffs)) <= rtol * max(sqrt(sum(abs2, diffs)), 1.0)\nend\n\n# AdvancedHMC starts from a fresh draw unless handed a starting vector, so an\n# initialized model\'s values reach a gradient sampler through this. The\n# environment-based samplers start from the model\'s own environment, which\n# `initialize!` has already set.\nfunction bugs_initial_params(model, sampler)\n    haskey(sampler, "initial_params") || return nothing\n    get(sampler, "algorithm", "NUTS") in ENV_BASED_BUGS_SAMPLERS && return nothing\n    return Base.invokelatest(JuliaBUGS.getparams, base_bugs(model))\nend\n\n# The AdvancedHMC sampler for a NUTS/HMC/HMCDA configuration, whole or per Gibbs\n# block; nothing for any other algorithm. Adaptation runs off `sample`\'s n_adapts,\n# so no constructor here takes a step count.\nfunction bugs_hmc_sampler(conf)\n    algorithm = get(conf, "algorithm", "NUTS")\n    adapt_delta = Float64(get(conf, "adapt_delta", 0.8))\n    algorithm == "NUTS" && return AdvancedHMC.NUTS(adapt_delta)\n    algorithm == "HMC" &&\n        return AdvancedHMC.HMC(Float64(conf["step_size"]), Int(conf["leapfrog_steps"]))\n    algorithm == "HMCDA" && return AdvancedHMC.HMCDA(adapt_delta, Float64(conf["lambda"]))\n    return nothing\nend\n\n# SliceSampling\'s univariate samplers move one coordinate at a time, so a\n# multi-parameter target needs a multivariate strategy around them. RandPermGibbs\n# cycles the coordinates in a random order, and reduces to the plain univariate\n# update when a Gibbs block leaves only one.\nfunction bugs_slice_sampler(conf)\n    width = Float64(conf["slice_width"])\n    return SliceSampling.RandPermGibbs(SliceSampling.SliceSteppingOut(width))\nend\n\n# The support of each variable, as `Gibbs` itself classifies it. The stored value\n# does not say: JuliaBUGS keeps a latent count in a Float64 array, so a count\n# reads as continuous and would draw a Gaussian proposal it cannot represent.\nfunction bugs_node_types(model)\n    gd = model.graph_evaluation_data\n    return Dict(zip(gd.sorted_nodes, Base.invokelatest(JuliaBUGS.Model._compute_node_types, model)))\nend\n\n# A Gaussian step never lands on an integer, so a block of counts gets a lattice\n# walk. `Gibbs` draws a finite discrete block exactly instead, whatever it is\n# given here.\nfunction bugs_mh_kernel(model, vns, node_types)\n    expanded = JuliaBUGS.expand_variables(vns, model.graph_evaluation_data.model_parameters)\n    all(vn -> get(node_types, vn, :continuous) === :discrete_infinite, expanded) ||\n        return JuliaBUGS.AdvancedMH.RobustAdaptiveMetropolis()\n    return JuliaBUGS.AdvancedMH.RWMH([DiscreteUniform(-1, 1) for _ in expanded])\nend\n\n# One block per parameter, each with the kernel its own support calls for. The\n# convenience `Gibbs(model, sampler)` gives every block the same one.\nfunction bugs_single_site_mh(model)\n    node_types = bugs_node_types(model)\n    pairs = [\n        vn => bugs_mh_kernel(model, [vn], node_types) for\n        vn in JuliaBUGS.model_parameters(model)\n    ]\n    return JuliaBUGS.Gibbs(model, JuliaBUGS.OrderedDict(pairs))\nend\n\nbugs_varname(name) = eval(:(Turing.@varname($(Meta.parse(name)))))\n\n# One spec block becomes one entry of JuliaBUGS\'s sampler map, keyed by the\n# block\'s variables together; gradient blocks must carry their AD backend as a\n# tuple. JuliaBUGS checks that the map covers every parameter exactly once.\nfunction build_bugs_gibbs(sampler, model)\n    adtype = build_adtype(get(sampler, "adtype", "forwarddiff"))\n    node_types = bugs_node_types(model)\n    pairs = map(sampler["blocks"]) do block\n        vars = [bugs_varname(v) for v in block["variables"]]\n        key = length(vars) == 1 ? vars[1] : vars\n        algorithm = get(block, "algorithm", "NUTS")\n        component = algorithm == "MH" ? bugs_mh_kernel(model, vars, node_types) :\n            algorithm == "Slice" ? bugs_slice_sampler(block) :\n            (bugs_hmc_sampler(block), adtype)\n        key => component\n    end\n    return JuliaBUGS.Gibbs(model, JuliaBUGS.OrderedDict(pairs))\nend\n\n# Unlike the Turing path this needs the model: JuliaBUGS\'s Gibbs validates its\n# sampler map against the model\'s parameters as it is constructed.\nfunction build_bugs_sampler(sampler, model)\n    hmc = bugs_hmc_sampler(sampler)\n    hmc === nothing || return hmc\n    algorithm = get(sampler, "algorithm", "NUTS")\n    algorithm == "Slice" && return bugs_slice_sampler(sampler)\n    # Single-site Metropolis over every parameter: the WinBUGS-shaped sampler, and\n    # the route to discrete latents that marginalization declines.\n    algorithm == "MH" && return bugs_single_site_mh(model)\n    algorithm == "Gibbs" && return build_bugs_gibbs(sampler, model)\n    return error("the juliabugs backend does not support the $algorithm sampler")\nend\n\n# JuliaBUGS compiles the model at runtime, so building and sampling must run in\n# separate latest-world frames; merging them reintroduces a world-age error.\n# Returns a FlexiChain like the Turing path; gen_chains recovers generated\n# quantities (unobserved nodes with no observed descendants) after sampling.\n# With a callback, draws stream (see bugs_draw_streamer).\nfunction sample_bugs(\n    model, sampler, warmup, draws, chains, rng;\n    callback = nothing, thin = 1, threads = false, initial_params = nothing,\n)\n    kw = callback === nothing ? (;) : (; callback)\n    thin > 1 && (kw = merge(kw, (; thinning = thin)))\n    # Ensemble sampling wants one starting point per chain; every chain starts from\n    # the values the spec named, and diverges from there through its own stream.\n    initial_params === nothing ||\n        (kw = merge(kw, (; initial_params = fill(initial_params, chains))))\n    ensemble = threads ? JuliaBUGS.AbstractMCMC.MCMCThreads() : JuliaBUGS.AbstractMCMC.MCMCSerial()\n    return Logging.with_logger(JSONProgressLogger()) do\n        JuliaBUGS.AbstractMCMC.sample(\n            rng, model, sampler, ensemble, draws, chains;\n            chain_type = FlexiChains.VNChain, n_adapts = warmup, discard_initial = warmup,\n            progress = true, kw...,\n        )\n    end\nend\n\n# JuliaBUGS prior sampling: each draw is one ancestral pass (evaluate!! with an\n# rng samples every unobserved stochastic node from its prior and recomputes the\n# deterministic ones; observed data stays fixed). The collected variables are the\n# model parameters plus generated quantities, the same columns a posterior fit\n# produces through gen_chains.\nfunction sample_bugs_prior(model, draws, chains, rng)\n    model = base_bugs(model)\n    APPL = JuliaBUGS.AbstractPPL\n    vars = vcat(JuliaBUGS.model_parameters(model), JuliaBUGS.generated_quantities(model))\n    isempty(vars) && error("the model has no parameters or generated quantities to sample")\n    grab(env, vn) = (v = APPL.getvalue(env, vn); v isa AbstractArray ? copy(v) : v)\n    columns = Dict(vn => Vector{Any}(undef, draws * chains) for vn in vars)\n    for c in 1:chains, i in 1:draws\n        env, _ = APPL.evaluate!!(rng, model)\n        for vn in vars\n            columns[vn][i + (c - 1) * draws] = grab(env, vn)\n        end\n    end\n    dict = Dict{FlexiChains.ParameterOrExtra{<:VarName},Array}(\n        FlexiChains.Parameter(vn) =>\n            [columns[vn][i + (c - 1) * draws] for i in 1:draws, c in 1:chains] for vn in vars\n    )\n    return FlexiChains.FlexiChain{VarName}(draws, chains, dict)\nend\n\n# The JuliaBUGS counterpart to draw_streamer. A JuliaBUGS transition carries an\n# unconstrained parameter vector (or, for the environment-based samplers, an\n# evaluation environment), so (unlike the Turing path) draws cannot be read off it\n# directly: the generated quantities and any marginalized discrete latents are\n# reconstructed only when the draws are laid out. Per batch we therefore build a\n# small FlexiChain through the same bundle_transitions + vnchain_to_wire path the\n# final file uses, so the streamed leaf names match the file exactly, on a copy of\n# the model so reconstruction never perturbs the sampler\'s state. AbstractMCMC\n# passes the 1-based chain index as chain_number; each chain\'s batches carry a\n# per-chain monotonic seq.\nfunction bugs_draw_streamer(\n    model, sampler, draws_per_chain::Int, batch_size::Int; keep = nothing,\n)\n    recon = deepcopy(model)\n    side_rng = StableRNG(0)\n    chain = Ref(-1)\n    seq = Ref(0)\n    transitions = Any[]\n    function emit(iteration)\n        isempty(transitions) && return\n        chn = JuliaBUGS.bundle_transitions(\n            FlexiChains.VNChain, recon, transitions, sampler; rng = side_rng,\n        )\n        wire = vnchain_to_wire(chn; keep)\n        nIter, total, _ = wire["size"]\n        flat = wire["value_flat"]\n        params = wire["parameters"]\n        cols = Dict(params[p] => [flat[i + (p - 1) * nIter] for i in 1:nIter] for p in 1:total)\n        println(\n            PROGRESS_IO[],\n            JSON.json(\n                Dict(\n                    "mcmcjs" => "draws",\n                    "chain" => chain[],\n                    "seq" => seq[],\n                    "iteration" => iteration,\n                    "draws" => cols,\n                ),\n            ),\n        )\n        flush(PROGRESS_IO[])\n        seq[] += 1\n        empty!(transitions)\n    end\n    return function (_rng, _model, _sampler, transition, _state, iteration; chain_number = 1, _kwargs...)\n        c = Int(chain_number) - 1\n        if c != chain[]\n            chain[] = c\n            seq[] = 0\n            empty!(transitions)\n        end\n        push!(transitions, deepcopy(transition))\n        if length(transitions) >= batch_size || iteration >= draws_per_chain\n            emit(iteration)\n        end\n    end\nend\n\n# JuliaBUGS pointwise log-likelihood: restore each posterior draw into the\n# evaluation environment, recompute the deterministic nodes in topological\n# order, and record logpdf per observed node. Every unobserved stochastic node\n# must be covered by the posterior columns, or log p(y | theta) would not be a\n# function of the draw.\nfunction loglik_bugs(model, posterior)\n    model = base_bugs(model)\n    APPL = JuliaBUGS.AbstractPPL\n    gd = model.graph_evaluation_data\n\n    sz = posterior["size"]\n    nIter, nCols, nChains = Int(sz[1]), Int(sz[2]), Int(sz[3])\n    flat = posterior["value_flat"]\n    col = Dict(n => i for (i, n) in enumerate(posterior["parameters"]))\n    posterior_names = Set(posterior["name_map"]["parameters"])\n    cell(i, p, c) = begin\n        v = flat[i + (p - 1) * nIter + (c - 1) * nIter * nCols]\n        v === nothing ? NaN : Float64(v)\n    end\n\n    restore = Tuple{APPL.VarName,Int}[]\n    for vn in JuliaBUGS.model_parameters(model)\n        leaves = collect(APPL.varname_leaves(vn, APPL.getvalue(model.evaluation_env, vn)))\n        found = count(l -> string(l) in posterior_names, leaves)\n        found == length(leaves) ||\n            error("the posterior samples do not cover $(vn); were they produced by fitting this spec?")\n        append!(restore, [(l, col[string(l)]) for l in leaves])\n    end\n    observed = [\n        (vn, i) for (i, vn) in enumerate(gd.sorted_nodes) if\n        gd.is_stochastic_vals[i] && gd.is_observed_vals[i]\n    ]\n    isempty(observed) && error("the model has no observed variables to compute a log-likelihood for")\n\n    pnames = string.(first.(observed))\n    n = length(pnames)\n    flat_out = Vector{Union{Float64,Nothing}}(undef, nIter * n * nChains)\n    for c in 1:nChains, i in 1:nIter\n        env = model.evaluation_env\n        for (leaf, p) in restore\n            env = JuliaBUGS.BangBang.setindex!!(env, cell(i, p, c), leaf)\n        end\n        for (k, node) in enumerate(gd.sorted_nodes)\n            if !gd.is_stochastic_vals[k]\n                env = JuliaBUGS.BangBang.setindex!!(\n                    env, gd.node_function_vals[k](env, gd.loop_vars_vals[k]), node,\n                )\n            end\n        end\n        for (k, (vn, idx)) in enumerate(observed)\n            dist = gd.node_function_vals[idx](env, gd.loop_vars_vals[idx])\n            v = logpdf(dist, APPL.getvalue(env, vn))\n            flat_out[i + (k - 1) * nIter + (c - 1) * nIter * n] = isfinite(v) ? Float64(v) : nothing\n        end\n    end\n    return Dict(\n        "size" => [nIter, n, nChains],\n        "value_flat" => flat_out,\n        "parameters" => pnames,\n        "name_map" => Dict("parameters" => pnames, "internals" => String[]),\n    )\nend\n\n# JuliaBUGS posterior prediction: condition the (target-blanked) model on the\n# posterior parameter columns, then evaluate!! ancestral-samples the remaining\n# latents once per posterior draw. No sampler or gradient runs.\nfunction predict_bugs(model, posterior, targets, rng)\n    model = base_bugs(model)\n    APPL = JuliaBUGS.AbstractPPL\n    target_syms = Set(Symbol.(targets))\n    is_target(vn) = APPL.getsym(vn) in target_syms\n\n    sz = posterior["size"]\n    nIter, nCols, nChains = Int(sz[1]), Int(sz[2]), Int(sz[3])\n    flat = posterior["value_flat"]\n    col = Dict(n => i for (i, n) in enumerate(posterior["parameters"]))\n    posterior_names = Set(posterior["name_map"]["parameters"])\n    cell(i, p, c) = begin\n        v = flat[i + (p - 1) * nIter + (c - 1) * nIter * nCols]\n        v === nothing ? NaN : Float64(v)\n    end\n\n    # Nodes fully covered by posterior columns are conditioned; anything\n    # uncovered stays latent and is forward-sampled, like Turing.predict.\n    gd = model.graph_evaluation_data\n    conditioned = APPL.VarName[]\n    restore = Tuple{APPL.VarName,Int}[]\n    for (i, vn) in enumerate(gd.sorted_nodes)\n        (gd.is_stochastic_vals[i] && !gd.is_observed_vals[i] && !is_target(vn)) || continue\n        leaves = collect(APPL.varname_leaves(vn, APPL.getvalue(model.evaluation_env, vn)))\n        found = count(l -> string(l) in posterior_names, leaves)\n        if found == length(leaves)\n            push!(conditioned, vn)\n            append!(restore, [(l, col[string(l)]) for l in leaves])\n        elseif found > 0\n            error("the posterior samples cover $(vn) only partially; refit before predicting")\n        end\n    end\n    isempty(conditioned) &&\n        error("the posterior samples share no parameters with the model; were they produced by fitting this spec?")\n    cond = APPL.condition(model, conditioned)\n\n    any(is_target, cond.graph_evaluation_data.sorted_nodes) ||\n        error("no variables predicted; check that [predict].targets name model variables")\n\n    out_leaves = APPL.VarName[]\n    arr = Array{Float64,3}(undef, 0, 0, 0)\n    for c in 1:nChains, i in 1:nIter\n        env = cond.evaluation_env\n        for (leaf, p) in restore\n            env = JuliaBUGS.BangBang.setindex!!(env, cell(i, p, c), leaf)\n        end\n        cond = JuliaBUGS.BangBang.setproperty!!(cond, :evaluation_env, env)\n        drawn, _ = APPL.evaluate!!(rng, cond)\n        if isempty(out_leaves)\n            out_leaves = [\n                l for vn in cond.graph_evaluation_data.sorted_nodes if is_target(vn)\n                for l in APPL.varname_leaves(vn, APPL.getvalue(drawn, vn))\n            ]\n            arr = Array{Float64,3}(undef, nIter, length(out_leaves), nChains)\n        end\n        for (k, leaf) in enumerate(out_leaves)\n            arr[i, k, c] = Float64(APPL.getvalue(drawn, leaf))\n        end\n    end\n\n    pnames = string.(out_leaves)\n    n = length(pnames)\n    flat_out = Vector{Union{Float64,Nothing}}(undef, nIter * n * nChains)\n    for c in 1:nChains, p in 1:n, i in 1:nIter\n        v = arr[i, p, c]\n        flat_out[i + (p - 1) * nIter + (c - 1) * nIter * n] = isfinite(v) ? v : nothing\n    end\n    return Dict(\n        "size" => [nIter, n, nChains],\n        "value_flat" => flat_out,\n        "parameters" => pnames,\n        "name_map" => Dict("parameters" => pnames, "internals" => String[]),\n    )\nend\n\nfunction provenance()\n    packages = Dict{String,String}()\n    for (_, info) in Pkg.dependencies()\n        if info.name in\n           ("Turing", "FlexiChains", "DynamicPPL", "AbstractMCMC", "JuliaBUGS", "AdvancedHMC", "SliceSampling", "ForwardDiff", "Mooncake", "ADTypes") &&\n           info.version !== nothing\n            packages[info.name] = string(info.version)\n        end\n    end\n    manifest = joinpath(dirname(Base.active_project()), "Manifest.toml")\n    return Dict(\n        "julia_version" => string(VERSION),\n        "packages" => packages,\n        "manifest_sha256" => isfile(manifest) ? bytes2hex(sha256(read(manifest))) : "",\n    )\nend\n\n# Resolve the model entry function: use the requested name, falling back to the\n# conventional build_model. This lets a request leave the entry implicit, or name a\n# custom entry that a given model file does not define (then build_model is used).\n# Load the user\'s model file into a throwaway module. Isolation keeps repeated\n# requests in the persistent worker from colliding on names (e.g. two models each\n# defining `const model_def`), and confines the model\'s globals to their own scope.\n# Compiling draws every parameter it is not given from its prior, and a draw from a\n# vague prior such as dgamma(0.001, 0.001) can underflow into a Weibull scale of zero\n# or a Poisson rate of NaN before sampling starts. An entry that takes the starting\n# values as a second argument gets them at compile time.\nfunction build_bugs_model(entry, data, sampler)\n    haskey(sampler, "initial_params") && applicable(entry, data, (;)) || return entry(data)\n    return entry(data, bugs_namedtuple(sampler["initial_params"]))\nend\n\nfunction load_model_module(path)\n    mod = Module(gensym(:UserModel))\n    if endswith(lowercase(path), ".bugs")\n        # A bare BUGS program, parsed as the string form of `@bugs` parses it with\n        # dotted names kept, and given the entry a Julia model file would define.\n        model_def = JuliaBUGS.Parser._bugs_string_input(read(abspath(path), String), false)\n        Core.eval(mod, :(using JuliaBUGS))\n        Core.eval(mod, :(const model_def = $(Meta.quot(model_def))))\n        Core.eval(\n            mod, :(build_model(data, inits = (;)) = JuliaBUGS.compile(model_def, data, inits)),\n        )\n    else\n        Base.include(mod, abspath(path))\n    end\n    return mod\nend\n\nfunction resolve_entry(mod, requested)\n    for name in (requested, "build_model")\n        name === nothing && continue\n        sym = Symbol(name)\n        # The model was just include\'d, so its bindings live in a newer world than\n        # this frame; resolve them in the latest world to avoid a Julia 1.12\n        # world-age warning on the access.\n        Base.invokelatest(isdefined, mod, sym) && return Base.invokelatest(getfield, mod, sym)\n    end\n    error("model file defines no entry function (looked for $(requested) and build_model)")\nend\n\n# Runs one request end to end. Returns {"ok": true, "provenance": ...} or\n# {"ok": false, "error": ..., "stage": ...}; never throws.\nfunction handle_request(request)\n    out = request["out"]\n    mode = get(request, "mode", "fit")\n    backend = get(get(request, "backend", Dict()), "id", "turing")\n    stage = "compile"\n    try\n        Random.seed!(Int(request["seed"]))\n        rng = StableRNG(Int(request["seed"]))\n        modelmod = load_model_module(request["model"]["file"])\n        entry = resolve_entry(modelmod, get(request["model"], "entry", nothing))\n\n        wire = if mode == "loglik"\n            if backend == "juliabugs"\n                model = Base.invokelatest(entry, bugs_namedtuple(request["data"]))\n                stage = "load_samples"\n                posterior = JSON.parsefile(request["samples"])\n                stage = "loglik"\n                Base.invokelatest(loglik_bugs, model, posterior)\n            else\n                data = ModelData(to_namedtuple(request["data"]))\n                model = Base.invokelatest(entry, data)\n                model = Base.invokelatest(condition_on_data, model, data)\n                stage = "load_samples"\n                chn = wire_to_vnchain(JSON.parsefile(request["samples"]), String[])\n                stage = "loglik"\n                pll = Base.invokelatest(Turing.DynamicPPL.pointwise_loglikelihoods, model, chn)\n                isempty(FlexiChains.parameters(pll)) &&\n                    error("the model has no observed variables to compute a log-likelihood for")\n                vnchain_to_wire(pll)\n            end\n        elseif mode == "predict"\n            if backend == "juliabugs"\n                model = Base.invokelatest(entry, bugs_namedtuple(request["data"]))\n                stage = "load_samples"\n                posterior = JSON.parsefile(request["samples"])\n                stage = "predict"\n                Base.invokelatest(predict_bugs, model, posterior, request["predict"]["targets"], rng)\n            else\n                model = Base.invokelatest(entry, ModelData(to_namedtuple(request["data"])))\n                stage = "load_samples"\n                rchn = wire_to_vnchain(JSON.parsefile(request["samples"]), request["predict"]["targets"])\n                stage = "predict"\n                pp = Base.invokelatest(predict, rng, model, rchn; include_all = false)\n                isempty(FlexiChains.parameters(pp)) &&\n                    error("no variables predicted; check that [predict].targets name unconditioned outcomes")\n                vnchain_to_wire(pp)\n            end\n        else\n            data = backend == "juliabugs" ? bugs_namedtuple(request["data"]) : ModelData(to_namedtuple(request["data"]))\n            parallel = get(request["sampler"], "parallel", "serial")\n            chains = Int(get(request["sampler"], "chains", 4))\n            if parallel == "distributed" && backend != "juliabugs"\n                # Every process needs the model\'s definitions under the same\n                # names; the module-per-request isolation gives way to Main.\n                stage = "distribute"\n                Base.invokelatest(setup_distributed, chains, request["model"]["file"])\n                modelmod = Main\n                entry = resolve_entry(Main, get(request["model"], "entry", nothing))\n            end\n            sampler_conf = apply_model_defaults(request["sampler"], modelmod)\n            draws = Int(request["sampler"]["draws"])\n            stage = "sample"\n            if backend == "juliabugs"\n                stage = "compile"\n                model = Base.invokelatest(build_bugs_model, entry, data, sampler_conf)\n                stage = "sample"\n                chn = if get(sampler_conf, "algorithm", "NUTS") == "Prior"\n                    Base.invokelatest(sample_bugs_prior, model, draws, chains, rng)\n                else\n                    model = Base.invokelatest(\n                        prepare_bugs_model, model, sampler_conf,\n                        get(request["model"], "evaluation_mode", nothing),\n                    )\n                    sampler = Base.invokelatest(build_bugs_sampler, sampler_conf, model)\n                    warmup = Int(get(sampler_conf, "warmup", 1000))\n                    threads = parallel == "threads"\n                    # Reconstruction reads the plain BUGSModel; a gradient sampler runs wrapped.\n                    cb = get(request, "stream_draws", false) && !threads ?\n                        bugs_draw_streamer(\n                            base_bugs(model), sampler, draws,\n                            Int(get(request, "draw_batch_size", 25));\n                            keep = bugs_column_filter(request, model),\n                        ) : nothing\n                    Base.invokelatest(\n                        sample_bugs, model, sampler, warmup, draws, chains, rng;\n                        callback = cb, thin = Int(get(request["sampler"], "thin", 1)), threads,\n                        initial_params = Base.invokelatest(\n                            bugs_initial_params, model, sampler_conf,\n                        ),\n                    )\n                end\n                vnchain_to_wire(chn; keep = bugs_column_filter(request, model))\n            else\n                sampler, warmup = build_sampler(sampler_conf, modelmod)\n                # The draw streamer assumes chains arrive one at a time; with\n                # concurrent chains the caller must not request streaming.\n                cb = get(request, "stream_draws", false) && parallel == "serial" ?\n                    draw_streamer(draws, Int(get(request, "draw_batch_size", 25))) : nothing\n                extra = sampling_kwargs(request["sampler"], warmup, chains)\n                chn = Base.invokelatest(\n                    build_and_sample, entry, data, sampler, draws, chains, rng;\n                    callback = cb, extra, parallel,\n                )\n                vnchain_to_wire(chn)\n            end\n        end\n\n        stage = "write"\n        tmp = out * ".tmp"\n        open(tmp, "w") do io\n            JSON.print(io, wire)\n        end\n        mv(tmp, out; force = true)\n\n        return Dict("ok" => true, "provenance" => provenance())\n    catch err\n        return Dict("ok" => false, "error" => sprint(showerror, err), "stage" => stage)\n    end\nend\n',
   "julia-env/Project.toml": '[deps]\nAdvancedHMC = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d"\nDimensionalData = "0703355e-b756-11e9-17c0-8b28908087d0"\nFlexiChains = "4a37a8b9-6e57-4b92-8664-298d46e639f7"\nForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"\nJSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"\nJuliaBUGS = "ba9fb4c0-828e-4473-b6a1-cd2560fee5bf"\nMooncake = "da2b9cff-9c12-43a0-ae48-6db2b0edb7d6"\nReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267"\nSliceSampling = "43f4d3e8-9711-4a8c-bd1b-03ac73a255cf"\nStableRNGs = "860ef19b-820b-49d6-a774-d7a799459cd3"\nStatsFuns = "4c63d2b9-4356-54db-8cca-17b64c39e42c"\nTuring = "fce5fe82-541a-59a6-adf8-730c64b5f9a0"\n',
-  "julia-env/Manifest.toml": '# This file is machine-generated - editing it directly is not advised\n\njulia_version = "1.12.7"\nmanifest_format = "2.0"\nproject_hash = "ea3a76551fb06c81495151e9f5037ca1e9513b81"\n\n[[deps.ADTypes]]\ngit-tree-sha1 = "5970c86505ae9c07bf5bc521ef2bbbb3849e8b7b"\nuuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b"\nversion = "1.23.0"\n\n    [deps.ADTypes.extensions]\n    ADTypesChainRulesCoreExt = "ChainRulesCore"\n    ADTypesConstructionBaseExt = "ConstructionBase"\n    ADTypesEnzymeCoreExt = "EnzymeCore"\n\n    [deps.ADTypes.weakdeps]\n    ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"\n    ConstructionBase = "187b0558-2788-49d3-abe0-74a17ed4e7c9"\n    EnzymeCore = "f151be2c-9106-41f4-ab19-57ee4f262869"\n\n[[deps.ANSIColoredPrinters]]\ngit-tree-sha1 = "574baf8110975760d391c710b6341da1afa48d8c"\nuuid = "a4c015fc-c6ff-483c-b24f-f7ea428134e9"\nversion = "0.0.1"\n\n[[deps.AbstractFFTs]]\ndeps = ["LinearAlgebra"]\ngit-tree-sha1 = "d92ad398961a3ed262d8bf04a1a2b8340f915fef"\nuuid = "621f4979-c628-5d54-868e-fcf4e3e8185c"\nversion = "1.5.0"\nweakdeps = ["ChainRulesCore", "Test"]\n\n    [deps.AbstractFFTs.extensions]\n    AbstractFFTsChainRulesCoreExt = "ChainRulesCore"\n    AbstractFFTsTestExt = "Test"\n\n[[deps.AbstractMCMC]]\ndeps = ["BangBang", "ConsoleProgressMonitor", "Dates", "Distributed", "LogDensityProblems", "Logging", "LoggingExtras", "ProgressLogging", "Random", "StatsBase", "TerminalLoggers", "UUIDs"]\ngit-tree-sha1 = "328c7d50f307c66308a915abb20d9889e5aab48b"\nuuid = "80f14c24-f653-4e6a-9b94-39d6b0f70001"\nversion = "5.16.0"\n\n    [deps.AbstractMCMC.extensions]\n    AbstractMCMCOnlineStatsExt = "OnlineStats"\n    AbstractMCMCTensorBoardLoggerExt = "TensorBoardLogger"\n\n    [deps.AbstractMCMC.weakdeps]\n    OnlineStats = "a15396b6-48d5-5d58-9928-6d29437db91e"\n    TensorBoardLogger = "899adc3e-224a-11e9-021f-63837185c80f"\n\n[[deps.AbstractPPL]]\ndeps = ["ADTypes", "AbstractMCMC", "Accessors", "BangBang", "DensityInterface", "JSON", "LinearAlgebra", "MacroTools", "OrderedCollections", "Random", "StatsBase"]\ngit-tree-sha1 = "31fb177c9952267ac2dc54a44868cb768390e6ef"\nuuid = "7a57a42e-76ec-4ea3-a279-07e840d6d9cf"\nversion = "0.15.5"\nweakdeps = ["DiffResults", "DifferentiationInterface", "Distributions", "ForwardDiff", "Mooncake", "Test"]\n\n    [deps.AbstractPPL.extensions]\n    AbstractPPLDifferentiationInterfaceExt = ["DifferentiationInterface"]\n    AbstractPPLDistributionsExt = ["Distributions", "LinearAlgebra"]\n    AbstractPPLForwardDiffExt = ["ForwardDiff", "DiffResults"]\n    AbstractPPLMooncakeExt = ["Mooncake"]\n    AbstractPPLTestExt = ["Test"]\n\n[[deps.AbstractTrees]]\ngit-tree-sha1 = "2d9c9a55f9c93e8887ad391fbae72f8ef55e1177"\nuuid = "1520ce14-60c1-5f80-bbc7-55ef81b5835c"\nversion = "0.4.5"\n\n[[deps.Accessors]]\ndeps = ["CompositionsBase", "ConstructionBase", "Dates", "InverseFunctions", "MacroTools"]\ngit-tree-sha1 = 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["SparseArrays", "StaticArrays"]\n\n    [deps.Adapt.extensions]\n    AdaptSparseArraysExt = "SparseArrays"\n    AdaptStaticArraysExt = "StaticArrays"\n\n[[deps.AdvancedHMC]]\ndeps = ["AbstractMCMC", "ArgCheck", "DocStringExtensions", "IrrationalConstants", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "LogExpFunctions", "ProgressMeter", "Random", "Setfield", "Statistics", "StatsBase"]\ngit-tree-sha1 = "3a188c0f280dd237a03b29b2d9023859ef85a429"\nuuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d"\nversion = "0.8.5"\n\n    [deps.AdvancedHMC.extensions]\n    AdvancedHMCADTypesExt = "ADTypes"\n    AdvancedHMCCUDAExt = "CUDA"\n    AdvancedHMCComponentArraysExt = "ComponentArrays"\n    AdvancedHMCMCMCChainsExt = "MCMCChains"\n    AdvancedHMCOrdinaryDiffEqSymplecticRKExt = "OrdinaryDiffEqSymplecticRK"\n\n    [deps.AdvancedHMC.weakdeps]\n    ADTypes = "47edcb42-4c32-4615-8424-f2b9edc5f35b"\n    CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba"\n    ComponentArrays = "b0b7db55-cfe3-40fc-9ded-d10e2dbeff66"\n    MCMCChains = "c7f686f2-ff18-58e9-bc7b-31028e88f75d"\n    OrdinaryDiffEqSymplecticRK = "fa646aed-7ef9-47eb-84c4-9443fc8cbfa8"\n\n[[deps.AdvancedMH]]\ndeps = ["AbstractMCMC", "Distributions", "DocStringExtensions", "FillArrays", "LinearAlgebra", "LogDensityProblems", "Random", "Requires"]\ngit-tree-sha1 = "62ddbccf0ce5c26f8ef3cebe4bedef6b1599d616"\nuuid = "5b7e9947-ddc0-4b3f-9b55-0d8042f74170"\nversion = "0.8.10"\n\n    [deps.AdvancedMH.extensions]\n    AdvancedMHForwardDiffExt = ["DiffResults", "ForwardDiff"]\n    AdvancedMHMCMCChainsExt = "MCMCChains"\n    AdvancedMHStructArraysExt = "StructArrays"\n\n    [deps.AdvancedMH.weakdeps]\n    DiffResults = "163ba53b-c6d8-5494-b064-1a9d43ac40c5"\n    ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"\n    MCMCChains = "c7f686f2-ff18-58e9-bc7b-31028e88f75d"\n    StructArrays = "09ab397b-f2b6-538f-b94a-2f83cf4a842a"\n\n[[deps.AdvancedPS]]\ndeps = ["AbstractMCMC", "Distributions", "Random", "Random123", "Requires", "SSMProblems", "StatsFuns"]\ngit-tree-sha1 = "d92dd3fb4cc2748860ae8d5dd1d324cf0715a53b"\nuuid = "576499cb-2369-40b2-a588-c64705576edc"\nversion = "0.7.2"\nweakdeps = ["Libtask"]\n\n    [deps.AdvancedPS.extensions]\n    AdvancedPSLibtaskExt = "Libtask"\n\n[[deps.AdvancedVI]]\ndeps = ["ADTypes", "AbstractPPL", "Accessors", "ChainRulesCore", "DiffResults", "Distributions", "DocStringExtensions", "FillArrays", "Functors", "LinearAlgebra", "LogDensityProblems", "Optimisers", "ProgressMeter", "Random", "StatsBase"]\ngit-tree-sha1 = "fc42c29943eae508fd28ec620d1faa4d2c1ce044"\nuuid = "b5ca4192-6429-45e5-a2d9-87aec30a685c"\nversion = "0.7.0"\n\n    [deps.AdvancedVI.extensions]\n    AdvancedVIDynamicPPLExt = ["DynamicPPL", "Accessors", "Distributions", "LogDensityProblems"]\n    AdvancedVIEnzymeExt = ["Enzyme", "ChainRulesCore"]\n    AdvancedVIMooncakeExt = ["Mooncake", "ChainRulesCore"]\n    AdvancedVIReverseDiffExt = ["ReverseDiff", "ChainRulesCore"]\n\n    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"DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "FlexiChains", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "Optimization", "OptimizationOptimJL", "OrderedCollections", "Printf", "Random", "Reexport", "SciMLBase", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"]\ngit-tree-sha1 = "36243b86c346ac2329f931b31d00c0f147f77381"\nuuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0"\nversion = "0.46.0"\n\n    [deps.Turing.extensions]\n    TuringDynamicHMCExt = "DynamicHMC"\n    TuringMCMCChainsExt = "MCMCChains"\n\n    [deps.Turing.weakdeps]\n    DynamicHMC = "bbc10e6e-7c05-544b-b16e-64fede858acb"\n    MCMCChains = "c7f686f2-ff18-58e9-bc7b-31028e88f75d"\n\n[[deps.UUIDs]]\ndeps = ["Random", "SHA"]\nuuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4"\nversion = "1.11.0"\n\n[[deps.Unicode]]\nuuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5"\nversion = "1.11.0"\n\n[[deps.Zlib_jll]]\ndeps = ["Libdl"]\nuuid = "83775a58-1f1d-513f-b197-d71354ab007a"\nversion = "1.3.1+2"\n\n[[deps.libblastrampoline_jll]]\ndeps = ["Artifacts", "Libdl"]\nuuid = "8e850b90-86db-534c-a0d3-1478176c7d93"\nversion = "5.15.0+0"\n\n[[deps.nghttp2_jll]]\ndeps = ["Artifacts", "Libdl"]\nuuid = "8e850ede-7688-5339-a07c-302acd2aaf8d"\nversion = "1.64.0+1"\n\n[[deps.p7zip_jll]]\ndeps = ["Artifacts", "CompilerSupportLibraries_jll", "Libdl"]\nuuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0"\nversion = "17.7.0+0"\n'
 };
 
 // src/runner-common.ts