@mcmcjs/julia 0.14.0 → 0.15.0
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/index.cjs +164 -14
- package/dist/index.cjs.map +1 -1
- package/dist/index.js +193 -39
- package/dist/index.js.map +1 -1
- package/package.json +3 -3
- package/dist/driver.jl +0 -18
- package/dist/fitlib.jl +0 -869
- package/dist/julia-env/Manifest.toml +0 -1840
- package/dist/julia-env/Project.toml +0 -12
- package/dist/worker.jl +0 -102
package/dist/index.js
CHANGED
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@@ -53,7 +53,7 @@ var juliaEngine = {
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};
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// src/fit.ts
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import { existsSync as existsSync2, mkdirSync, mkdtempSync, readFileSync, rmSync, writeFileSync } from "fs";
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import { existsSync as existsSync2, mkdirSync as mkdirSync2, mkdtempSync, readFileSync, rmSync as rmSync2, writeFileSync as writeFileSync2 } from "fs";
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import { join as join3 } from "path";
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import {
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canonicalJson,
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@@ -63,27 +63,176 @@ import {
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// src/runner-common.ts
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import { createHash } from "crypto";
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import { existsSync } from "fs";
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import { tmpdir } from "os";
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import { existsSync, mkdirSync, renameSync, rmSync, writeFileSync } from "fs";
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import { homedir as homedir2, tmpdir } from "os";
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import { dirname, join as join2 } from "path";
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-
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// src/assets.generated.ts
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var JULIA_ASSETS = {
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"driver.jl": `# MCMC.js one-shot fit driver. Reads a run-request JSON file and runs it via
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# fitlib's handle_request. On success a single line of provenance JSON is
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# printed to stdout; failures print one-line JSON to stderr ({error, stage})
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# and exit nonzero. Progress streams to stderr as {"mcmcjs":"progress"} lines.
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include(joinpath(@__DIR__, "fitlib.jl"))
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function main()
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request = JSON.parsefile(ARGS[1])
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result = handle_request(request)
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if result["ok"]
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println(JSON.json(result["provenance"]))
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else
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println(stderr, JSON.json(Dict("error" => result["error"], "stage" => result["stage"])))
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exit(1)
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end
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end
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main()
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`,
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"worker.jl": `# MCMC.js persistent fit worker. Keeps Turing loaded between fits so warm
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# re-fits skip the cold start. Listens on a Unix domain socket (ARGS[1]); each
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# connection carries one JSON request line and receives {"mcmcjs":"progress"}
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# lines followed by one final handle_request result line. A {"mcmcjs":"stop"}
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# request shuts the worker down; so does half an hour of idleness.
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include(joinpath(@__DIR__, "fitlib.jl"))
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using Sockets
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const IDLE_TIMEOUT_S = 30 * 60
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# True while this process still owns the socket path: another worker stealing
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# the path (by binding over it) changes the inode, and a worker that lost the
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# path must never delete its successor's socket.
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function owns_socket(path, ino)
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try
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return stat(path).inode == ino
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catch
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return false
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end
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end
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function remove_if_owned(path, ino)
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if owns_socket(path, ino)
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rm(path; force = true)
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rm(path * ".pid"; force = true)
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end
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end
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function serve(path)
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mkpath(dirname(path))
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if ispath(path)
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# A live worker already serving this path wins; a dead socket file is cleared.
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try
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close(Sockets.connect(path))
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exit(0)
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catch
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rm(path; force = true)
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rm(path * ".pid"; force = true)
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end
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end
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server = Sockets.listen(path)
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ino = stat(path).inode
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# A pidfile beside the socket lets a cancelling client kill this worker
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# mid-fit (it cannot answer a polite stop while busy sampling).
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write(path * ".pid", string(getpid()))
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atexit(() -> remove_if_owned(path, ino))
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last_activity = Ref(time())
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busy = Ref(false)
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# The watchdog task is cooperative: it gets scheduled while the main task
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# blocks on accept. The busy guard is belt and braces for any future
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# multithreaded scheduling.
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@async while true
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sleep(30)
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if !busy[] && time() - last_activity[] > IDLE_TIMEOUT_S
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remove_if_owned(path, ino)
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exit(0)
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end
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end
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while true
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sock = Sockets.accept(server)
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busy[] = true
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stopping = false
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try
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line = readline(sock)
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if isempty(strip(line))
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close(sock)
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continue
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end
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request = JSON.parse(line)
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if get(request, "mcmcjs", "") == "stop"
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stopping = true
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println(sock, JSON.json(Dict("ok" => true, "stopped" => true)))
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else
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PROGRESS_IO[] = sock
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result = try
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handle_request(request)
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finally
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PROGRESS_IO[] = stderr
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end
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println(sock, JSON.json(result))
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end
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close(sock)
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catch err
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try
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println(sock, JSON.json(Dict("ok" => false, "error" => sprint(showerror, err), "stage" => "worker")))
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close(sock)
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catch
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end
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finally
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busy[] = false
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last_activity[] = time()
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end
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if stopping
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remove_if_owned(path, ino)
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exit(0)
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end
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end
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end
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serve(ARGS[1])
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`,
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"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\nto_namedtuple(data) = (; (Symbol(k) => v for (k, v) in data)...)\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\nbugs_namedtuple(data) = (; (Symbol(k) => narrow(v) for (k, v) in data)...)\n\n# JSON null arrives as `nothing`; map it to `missing` so a blanked outcome becomes\n# a sampling (predictive) statement in the model.\nto_missing(x) = x === nothing ? missing : (x isa AbstractVector ? map(to_missing, x) : x)\npredict_namedtuple(data) = (; (Symbol(k) => to_missing(v) for (k, v) in data)...)\n\n# A blanked target compiles to a latent node; JuliaBUGS drops scalar missings.\nbugs_predict_namedtuple(data) = (; (Symbol(k) => 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.\nfunction vnchain_to_wire(chn)\n da = DimensionalData.DimArray(chn)\n pnames = string.(collect(DimensionalData.lookup(da, :param)))\n arr = parent(da)\n nIter, nChains, nParams = size(arr)\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 in 1:nParams, i in 1:nIter\n flat[i + (p - 1) * nIter + (c - 1) * nIter * total] = cell(arr[i, c, p])\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# 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.\n# `initialize!` ignores a name it does not recognise, so an unknown one is an\n# error here rather than a silent no-op.\nfunction initialize_bugs_model(model, sampler)\n haskey(sampler, "initial_params") || return model\n known = Set(\n String(JuliaBUGS.AbstractPPL.getsym(vn)) for vn in JuliaBUGS.model_parameters(model)\n )\n for name in keys(sampler["initial_params"])\n name in known ||\n error("initial_params names $name, which is not a parameter of this model")\n end\n return Base.invokelatest(\n JuliaBUGS.initialize!, model, bugs_namedtuple(sampler["initial_params"]),\n )\nend\n\n# An environment-based sampler starts from the model\'s evaluation environment and\n# accepts on `logp_proposed - logp_current`, which is NaN when both are -Inf: from\n# an impossible starting point the chain can never move. Say so, with the fix,\n# rather than return draws that never left the start.\nfunction check_bugs_start(model, sampler)\n logp = try\n last(Base.invokelatest(JuliaBUGS.AbstractPPL.evaluate!!, model))\n catch\n -Inf\n end\n isfinite(logp) && return model\n detail = haskey(sampler, "initial_params") ?\n "the given initial_params have zero probability under the model" :\n "the model\'s default starting values have zero probability under the data; " *\n "set [sampler.initial_params] to a state the data allows"\n return error("$(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 mode_name === nothing || (base = set_bugs_mode(base, mode_name))\n base = initialize_bugs_model(base, sampler)\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 base\n adtype = haskey(sampler, "adtype") ? build_adtype(sampler["adtype"]) :\n model isa JuliaBUGS.BUGSModelWithGradient ? model.adtype :\n Turing.ADTypes.AutoForwardDiff()\n return Base.invokelatest(JuliaBUGS.BUGSModelWithGradient, base, adtype)\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\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 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" ? JuliaBUGS.IndependentMH() :\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 JuliaBUGS.Gibbs(model, JuliaBUGS.IndependentMH())\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(model, sampler, draws_per_chain::Int, batch_size::Int)\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)\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.\nfunction load_model_module(path)\n mod = Module(gensym(:UserModel))\n Base.include(mod, abspath(path))\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_predict_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(predict_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 model = Base.invokelatest(entry, data)\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 ) : 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)\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',
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"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',
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"julia-env/Manifest.toml": '# This file is machine-generated - editing it directly is not advised\n\njulia_version = "1.12.6"\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 = "7063ad1083578215c7c4bf410368150abe8d5524"\nuuid = "7d9f7c33-5ae7-4f3b-8dc6-eff91059b697"\nversion = "0.1.45"\n\n [deps.Accessors.extensions]\n AxisKeysExt = "AxisKeys"\n IntervalSetsExt = "IntervalSets"\n LinearAlgebraExt = "LinearAlgebra"\n StaticArraysExt = "StaticArrays"\n StructArraysExt = "StructArrays"\n TestExt = "Test"\n UnitfulExt = "Unitful"\n\n [deps.Accessors.weakdeps]\n AxisKeys = "94b1ba4f-4ee9-5380-92f1-94cde586c3c5"\n IntervalSets = "8197267c-284f-5f27-9208-e0e47529a953"\n LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"\n StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"\n StructArrays = "09ab397b-f2b6-538f-b94a-2f83cf4a842a"\n Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"\n Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"\n\n[[deps.Adapt]]\ndeps = ["LinearAlgebra"]\ngit-tree-sha1 = "daa72978cd7a624246e894a4f4f067706d4e17e2"\nuuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e"\nversion = "4.7.0"\nweakdeps = ["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 = 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"Statistics"\n\n[[deps.StaticArraysCore]]\ngit-tree-sha1 = "6ab403037779dae8c514bad259f32a447262455a"\nuuid = "1e83bf80-4336-4d27-bf5d-d5a4f845583c"\nversion = "1.4.4"\n\n[[deps.StatisticalTraits]]\ndeps = ["ScientificTypesBase"]\ngit-tree-sha1 = "89f86d9376acd18a1a4fbef66a56335a3a7633b8"\nuuid = "64bff920-2084-43da-a3e6-9bb72801c0c9"\nversion = "3.5.0"\n\n[[deps.Statistics]]\ndeps = ["LinearAlgebra"]\ngit-tree-sha1 = "ae3bb1eb3bba077cd276bc5cfc337cc65c3075c0"\nuuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"\nversion = "1.11.1"\nweakdeps = ["SparseArrays"]\n\n [deps.Statistics.extensions]\n SparseArraysExt = ["SparseArrays"]\n\n[[deps.StatsAPI]]\ndeps = ["LinearAlgebra"]\ngit-tree-sha1 = "178ed29fd5b2a2cfc3bd31c13375ae925623ff36"\nuuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0"\nversion = "1.8.0"\n\n[[deps.StatsBase]]\ndeps = ["AliasTables", "DataAPI", "DataStructures", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"]\ngit-tree-sha1 = "e4d7a1a0edc20af42689ea6f4f3587a2175d50ee"\nuuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"\nversion = "0.34.12"\n\n[[deps.StatsFuns]]\ndeps = ["HypergeometricFunctions", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"]\ngit-tree-sha1 = "91f091a8716a6bb38417a6e6f274602a19aaa685"\nuuid = "4c63d2b9-4356-54db-8cca-17b64c39e42c"\nversion = "1.5.2"\nweakdeps = ["ChainRulesCore", "InverseFunctions"]\n\n [deps.StatsFuns.extensions]\n StatsFunsChainRulesCoreExt = "ChainRulesCore"\n StatsFunsInverseFunctionsExt = "InverseFunctions"\n\n[[deps.StructUtils]]\ndeps = ["Dates", "UUIDs"]\ngit-tree-sha1 = "2d0fc55c61321ba245c47be599570d11bac50303"\nuuid = "ec057cc2-7a8d-4b58-b3b3-92acb9f63b42"\nversion = "2.8.5"\n\n [deps.StructUtils.extensions]\n StructUtilsMeasurementsExt = ["Measurements"]\n StructUtilsStaticArraysCoreExt = ["StaticArraysCore"]\n StructUtilsTablesExt = ["Tables"]\n\n [deps.StructUtils.weakdeps]\n Measurements = "eff96d63-e80a-5855-80a2-b1b0885c5ab7"\n StaticArraysCore = "1e83bf80-4336-4d27-bf5d-d5a4f845583c"\n Tables = "bd369af6-aec1-5ad0-b16a-f7cc5008161c"\n\n[[deps.StyledStrings]]\nuuid = "f489334b-da3d-4c2e-b8f0-e476e12c162b"\nversion = "1.11.0"\n\n[[deps.SuiteSparse]]\ndeps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"]\nuuid = "4607b0f0-06f3-5cda-b6b1-a6196a1729e9"\n\n[[deps.SuiteSparse_jll]]\ndeps = ["Artifacts", "Libdl", "libblastrampoline_jll"]\nuuid = "bea87d4a-7f5b-5778-9afe-8cc45184846c"\nversion = "7.8.3+2"\n\n[[deps.SymbolicIndexingInterface]]\ndeps = ["Accessors", "ArrayInterface", "RuntimeGeneratedFunctions", "StaticArraysCore"]\ngit-tree-sha1 = "2167b9913f3013a1485bdc9bb249123eb8b53cb0"\nuuid = "2efcf032-c050-4f8e-a9bb-153293bab1f5"\nversion = "0.3.54"\n\n [deps.SymbolicIndexingInterface.extensions]\n SymbolicIndexingInterfacePrettyTablesExt = "PrettyTables"\n\n [deps.SymbolicIndexingInterface.weakdeps]\n PrettyTables = "08abe8d2-0d0c-5749-adfa-8a2ac140af0d"\n\n[[deps.TOML]]\ndeps = ["Dates"]\nuuid = "fa267f1f-6049-4f14-aa54-33bafae1ed76"\nversion = "1.0.3"\n\n[[deps.TableTraits]]\ndeps = ["IteratorInterfaceExtensions"]\ngit-tree-sha1 = "c06b2f539df1c6efa794486abfb6ed2022561a39"\nuuid = "3783bdb8-4a98-5b6b-af9a-565f29a5fe9c"\nversion = "1.0.1"\n\n[[deps.Tables]]\ndeps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "OrderedCollections", "TableTraits"]\ngit-tree-sha1 = "0f38a06c83f0007bbab3cf911262841c9a0f07e0"\nuuid = "bd369af6-aec1-5ad0-b16a-f7cc5008161c"\nversion = "1.13.0"\n\n[[deps.Tar]]\ndeps = ["ArgTools", "SHA"]\nuuid = "a4e569a6-e804-4fa4-b0f3-eef7a1d5b13e"\nversion = "1.10.0"\n\n[[deps.TerminalLoggers]]\ndeps = ["LeftChildRightSiblingTrees", "Logging", "Markdown", "Printf", "ProgressLogging", "UUIDs"]\ngit-tree-sha1 = "81c9b4137edfe56a56efcdcb35d721b2ce3e2416"\nuuid = "5d786b92-1e48-4d6f-9151-6b4477ca9bed"\nversion = "0.1.8"\n\n[[deps.Test]]\ndeps = ["InteractiveUtils", "Logging", "Random", "Serialization"]\nuuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40"\nversion = "1.11.0"\n\n[[deps.TranscodingStreams]]\ngit-tree-sha1 = "0c45878dcfdcfa8480052b6ab162cdd138781742"\nuuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa"\nversion = "0.11.3"\n\n[[deps.Turing]]\ndeps = ["ADTypes", "AbstractMCMC", "AbstractPPL", "Accessors", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "Compat", "DataStructures", "Distributions", "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'
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};
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// src/runner-common.ts
|
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200
|
function sharedTmpParent() {
|
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201
|
const uid = typeof process.getuid === "function" ? `-${process.getuid()}` : "";
|
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202
|
return join2(tmpdir(), `mcmcjs${uid}`);
|
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|
}
|
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-
function
|
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75
|
-
const
|
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76
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-
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-
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function sharedCacheParent() {
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const base = process.env.XDG_CACHE_HOME || join2(homedir2(), ".cache");
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return join2(base, "mcmcjs");
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}
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function driverDir() {
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const digest = sha256(
|
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Object.entries(JULIA_ASSETS).map(([k, v]) => `${k}\0${v}`).join("\0")
|
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);
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const dir = join2(sharedCacheParent(), "driver", digest.slice(0, 16));
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if (existsSync(join2(dir, "driver.jl"))) return dir;
|
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const staging = `${dir}.${process.pid}.tmp`;
|
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|
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for (const [name, contents] of Object.entries(JULIA_ASSETS)) {
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const target = join2(staging, name);
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mkdirSync(dirname(target), { recursive: true });
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writeFileSync(target, contents);
|
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}
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mkdirSync(dirname(dir), { recursive: true });
|
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try {
|
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renameSync(staging, dir);
|
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} catch {
|
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rmSync(staging, { recursive: true, force: true });
|
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}
|
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return dir;
|
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|
function driverPath() {
|
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-
return
|
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|
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return join2(driverDir(), "driver.jl");
|
|
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230
|
}
|
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|
function workerPath() {
|
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-
return
|
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|
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return join2(driverDir(), "worker.jl");
|
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|
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|
function pinnedEnvDir() {
|
|
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|
-
return join2(
|
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return join2(driverDir(), "julia-env");
|
|
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236
|
}
|
|
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237
|
function sha256(text) {
|
|
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238
|
return createHash("sha256").update(text).digest("hex");
|
|
@@ -116,14 +265,18 @@ function toStage(value) {
|
|
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// src/fit.ts
|
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266
|
function makeRequestDir(kind) {
|
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|
const parent = sharedTmpParent();
|
|
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-
|
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+
mkdirSync2(parent, { recursive: true });
|
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269
|
return mkdtempSync(join3(parent, `${kind}-`));
|
|
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|
}
|
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|
function fitRequest(spec, outPath, opts) {
|
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return {
|
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|
schema_version: spec.schema_version,
|
|
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backend: { id: spec.backend.id },
|
|
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|
-
model: {
|
|
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|
+
model: {
|
|
276
|
+
file: spec.modelPath,
|
|
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|
+
entry: spec.model.entry,
|
|
278
|
+
...spec.model.evaluation_mode ? { evaluation_mode: spec.model.evaluation_mode } : {}
|
|
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|
+
},
|
|
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280
|
data: spec.data,
|
|
128
281
|
sampler: spec.sampler,
|
|
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282
|
seed: spec.seed,
|
|
@@ -170,7 +323,7 @@ function finalizeOkFit(spec, resolved, io, provenance, startedAt, elapsedMs) {
|
|
|
170
323
|
started_at: startedAt,
|
|
171
324
|
elapsed_ms: elapsedMs
|
|
172
325
|
};
|
|
173
|
-
|
|
326
|
+
writeFileSync2(io.recordPath ?? `${io.outPath}.run.json`, `${JSON.stringify(record, null, 2)}
|
|
174
327
|
`);
|
|
175
328
|
return {
|
|
176
329
|
status: "ok",
|
|
@@ -190,7 +343,7 @@ async function runFit(spec, resolved, io) {
|
|
|
190
343
|
const ownTmp = io.tmpDir === void 0;
|
|
191
344
|
const tmp = io.tmpDir ?? makeRequestDir("fit");
|
|
192
345
|
const requestPath = join3(tmp, "request.json");
|
|
193
|
-
|
|
346
|
+
writeFileSync2(
|
|
194
347
|
requestPath,
|
|
195
348
|
JSON.stringify(
|
|
196
349
|
fitRequest(spec, io.outPath, {
|
|
@@ -219,7 +372,7 @@ async function runFit(spec, resolved, io) {
|
|
|
219
372
|
signal: io.signal
|
|
220
373
|
}));
|
|
221
374
|
} finally {
|
|
222
|
-
if (ownTmp)
|
|
375
|
+
if (ownTmp) rmSync2(tmp, { recursive: true, force: true });
|
|
223
376
|
}
|
|
224
377
|
const elapsedMs = Math.round(performance.now() - start);
|
|
225
378
|
if (cancelled) {
|
|
@@ -235,7 +388,7 @@ async function runFit(spec, resolved, io) {
|
|
|
235
388
|
}
|
|
236
389
|
|
|
237
390
|
// src/loglik.ts
|
|
238
|
-
import { existsSync as existsSync3, readFileSync as readFileSync2, rmSync as
|
|
391
|
+
import { existsSync as existsSync3, readFileSync as readFileSync2, rmSync as rmSync3, writeFileSync as writeFileSync3 } from "fs";
|
|
239
392
|
import { join as join4 } from "path";
|
|
240
393
|
import {
|
|
241
394
|
canonicalJson as canonicalJson2,
|
|
@@ -249,7 +402,7 @@ async function runLogLik(spec, resolved, io) {
|
|
|
249
402
|
const ownTmp = io.tmpDir === void 0;
|
|
250
403
|
const tmp = io.tmpDir ?? makeRequestDir("loglik");
|
|
251
404
|
const requestPath = join4(tmp, "request.json");
|
|
252
|
-
|
|
405
|
+
writeFileSync3(
|
|
253
406
|
requestPath,
|
|
254
407
|
JSON.stringify({
|
|
255
408
|
mode: "loglik",
|
|
@@ -275,7 +428,7 @@ async function runLogLik(spec, resolved, io) {
|
|
|
275
428
|
try {
|
|
276
429
|
({ stdout, stderr, code } = await io.spawn(resolved.command, args));
|
|
277
430
|
} finally {
|
|
278
|
-
if (ownTmp)
|
|
431
|
+
if (ownTmp) rmSync3(tmp, { recursive: true, force: true });
|
|
279
432
|
}
|
|
280
433
|
const elapsedMs = Math.round(performance.now() - start);
|
|
281
434
|
if (code !== 0 || !existsSync3(io.outPath)) {
|
|
@@ -312,7 +465,7 @@ async function runLogLik(spec, resolved, io) {
|
|
|
312
465
|
started_at: startedAt,
|
|
313
466
|
elapsed_ms: elapsedMs
|
|
314
467
|
};
|
|
315
|
-
|
|
468
|
+
writeFileSync3(`${io.outPath}.run.json`, `${JSON.stringify(record, null, 2)}
|
|
316
469
|
`);
|
|
317
470
|
return {
|
|
318
471
|
status: "ok",
|
|
@@ -324,7 +477,7 @@ async function runLogLik(spec, resolved, io) {
|
|
|
324
477
|
}
|
|
325
478
|
|
|
326
479
|
// src/predict.ts
|
|
327
|
-
import { existsSync as existsSync4, readFileSync as readFileSync3, rmSync as
|
|
480
|
+
import { existsSync as existsSync4, readFileSync as readFileSync3, rmSync as rmSync4, writeFileSync as writeFileSync4 } from "fs";
|
|
328
481
|
import { join as join5 } from "path";
|
|
329
482
|
import {
|
|
330
483
|
canonicalJson as canonicalJson3,
|
|
@@ -349,7 +502,7 @@ async function runPredict(spec, resolved, io) {
|
|
|
349
502
|
const ownTmp = io.tmpDir === void 0;
|
|
350
503
|
const tmp = io.tmpDir ?? makeRequestDir("predict");
|
|
351
504
|
const requestPath = join5(tmp, "request.json");
|
|
352
|
-
|
|
505
|
+
writeFileSync4(
|
|
353
506
|
requestPath,
|
|
354
507
|
JSON.stringify({
|
|
355
508
|
mode: "predict",
|
|
@@ -376,7 +529,7 @@ async function runPredict(spec, resolved, io) {
|
|
|
376
529
|
try {
|
|
377
530
|
({ stdout, stderr, code } = await io.spawn(resolved.command, args));
|
|
378
531
|
} finally {
|
|
379
|
-
if (ownTmp)
|
|
532
|
+
if (ownTmp) rmSync4(tmp, { recursive: true, force: true });
|
|
380
533
|
}
|
|
381
534
|
const elapsedMs = Math.round(performance.now() - start);
|
|
382
535
|
if (code !== 0 || !existsSync4(io.outPath)) {
|
|
@@ -413,7 +566,7 @@ async function runPredict(spec, resolved, io) {
|
|
|
413
566
|
started_at: startedAt,
|
|
414
567
|
elapsed_ms: elapsedMs
|
|
415
568
|
};
|
|
416
|
-
|
|
569
|
+
writeFileSync4(`${io.outPath}.run.json`, `${JSON.stringify(record, null, 2)}
|
|
417
570
|
`);
|
|
418
571
|
return {
|
|
419
572
|
status: "ok",
|
|
@@ -425,8 +578,8 @@ async function runPredict(spec, resolved, io) {
|
|
|
425
578
|
}
|
|
426
579
|
|
|
427
580
|
// src/project.ts
|
|
428
|
-
import { copyFileSync, existsSync as existsSync5, mkdirSync as
|
|
429
|
-
import { homedir as
|
|
581
|
+
import { copyFileSync, existsSync as existsSync5, mkdirSync as mkdirSync3, readFileSync as readFileSync4, writeFileSync as writeFileSync5 } from "fs";
|
|
582
|
+
import { homedir as homedir3 } from "os";
|
|
430
583
|
import { join as join6 } from "path";
|
|
431
584
|
import { canonicalJson as canonicalJson4, DEFAULT_JULIA_CHANNEL } from "@mcmcjs/core";
|
|
432
585
|
import { createRunner as createRunner3 } from "@mcmcjs/engine";
|
|
@@ -437,6 +590,7 @@ var PACKAGES = [
|
|
|
437
590
|
"MCMCChains",
|
|
438
591
|
"JuliaBUGS",
|
|
439
592
|
"AdvancedHMC",
|
|
593
|
+
"SliceSampling",
|
|
440
594
|
"ForwardDiff",
|
|
441
595
|
"Mooncake",
|
|
442
596
|
"ReverseDiff",
|
|
@@ -466,7 +620,7 @@ function hasPins(pins) {
|
|
|
466
620
|
return pins !== void 0 && Object.keys(pins).length > 0;
|
|
467
621
|
}
|
|
468
622
|
function managedProjectDir(version, pins) {
|
|
469
|
-
const base = process.env.XDG_DATA_HOME || join6(
|
|
623
|
+
const base = process.env.XDG_DATA_HOME || join6(homedir3(), ".local", "share");
|
|
470
624
|
const root = join6(base, "mcmcjs", "julia", "env");
|
|
471
625
|
if (!version && !hasPins(pins)) return root;
|
|
472
626
|
let leaf = (version ?? "default").replace(/[^A-Za-z0-9._-]/g, "_");
|
|
@@ -476,7 +630,7 @@ function managedProjectDir(version, pins) {
|
|
|
476
630
|
function sentinelPath(dir) {
|
|
477
631
|
return join6(dir, ".mcmcjs-packages.json");
|
|
478
632
|
}
|
|
479
|
-
var PROVISION_GENERATION =
|
|
633
|
+
var PROVISION_GENERATION = 2;
|
|
480
634
|
function expectedSentinel(pins) {
|
|
481
635
|
return canonicalJson4({
|
|
482
636
|
gen: PROVISION_GENERATION,
|
|
@@ -507,7 +661,7 @@ function usesPinnedEnv(version, pins) {
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|
|
507
661
|
async function ensureProject(juliaBin, run = createRunner3(30 * 6e4), dir = managedProjectDir(), pins, opts) {
|
|
508
662
|
validatePins(pins);
|
|
509
663
|
if (managedProjectReady(dir, pins)) return dir;
|
|
510
|
-
|
|
664
|
+
mkdirSync3(dir, { recursive: true });
|
|
511
665
|
if (usesPinnedEnv(opts?.version, pins)) {
|
|
512
666
|
copyFileSync(join6(pinnedEnvDir(), "Project.toml"), join6(dir, "Project.toml"));
|
|
513
667
|
copyFileSync(join6(pinnedEnvDir(), "Manifest.toml"), join6(dir, "Manifest.toml"));
|
|
@@ -521,7 +675,7 @@ async function ensureProject(juliaBin, run = createRunner3(30 * 6e4), dir = mana
|
|
|
521
675
|
const code = `using Pkg; Pkg.add(${packageSpecsCode(pins)}); Pkg.precompile()`;
|
|
522
676
|
await run(juliaBin, ["--startup-file=no", `--project=${dir}`, "-e", code]);
|
|
523
677
|
}
|
|
524
|
-
|
|
678
|
+
writeFileSync5(sentinelPath(dir), expectedSentinel(pins));
|
|
525
679
|
return dir;
|
|
526
680
|
}
|
|
527
681
|
|
|
@@ -715,7 +869,7 @@ function assertVersionsInstalled(channels, installed) {
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|
|
715
869
|
|
|
716
870
|
// src/worker.ts
|
|
717
871
|
import { spawn } from "child_process";
|
|
718
|
-
import { mkdirSync as
|
|
872
|
+
import { mkdirSync as mkdirSync4, readdirSync, readFileSync as readFileSync5, rmdirSync, rmSync as rmSync5, statSync } from "fs";
|
|
719
873
|
import { createConnection } from "net";
|
|
720
874
|
import { join as join8 } from "path";
|
|
721
875
|
import { parseDrawBatchLine, parseProgressLine } from "@mcmcjs/engine";
|
|
@@ -746,13 +900,13 @@ function killWorker(socket) {
|
|
|
746
900
|
}
|
|
747
901
|
} catch {
|
|
748
902
|
}
|
|
749
|
-
|
|
750
|
-
|
|
903
|
+
rmSync5(socket, { force: true });
|
|
904
|
+
rmSync5(pidPath, { force: true });
|
|
751
905
|
}
|
|
752
906
|
function workersDir() {
|
|
753
907
|
const runtime = process.env.XDG_RUNTIME_DIR;
|
|
754
908
|
const dir = runtime ? join8(runtime, "mcmcjs") : join8(sharedTmpParent(), "workers");
|
|
755
|
-
|
|
909
|
+
mkdirSync4(dir, { recursive: true, mode: 448 });
|
|
756
910
|
return dir;
|
|
757
911
|
}
|
|
758
912
|
function workerSocketPath(command, projectDir) {
|
|
@@ -780,13 +934,13 @@ var delay = (ms) => new Promise((resolve) => setTimeout(resolve, ms));
|
|
|
780
934
|
function acquireStartLock(socketPath) {
|
|
781
935
|
const lock = `${socketPath}.start`;
|
|
782
936
|
try {
|
|
783
|
-
|
|
937
|
+
mkdirSync4(lock);
|
|
784
938
|
return true;
|
|
785
939
|
} catch {
|
|
786
940
|
try {
|
|
787
941
|
if (Date.now() - statSync(lock).mtimeMs > START_WAIT_MS) {
|
|
788
942
|
rmdirSync(lock);
|
|
789
|
-
|
|
943
|
+
mkdirSync4(lock);
|
|
790
944
|
return true;
|
|
791
945
|
}
|
|
792
946
|
} catch {
|
|
@@ -811,7 +965,7 @@ async function ensureWorker(resolved, projectDir, notify, signal) {
|
|
|
811
965
|
const startedHere = acquireStartLock(path);
|
|
812
966
|
if (startedHere) {
|
|
813
967
|
try {
|
|
814
|
-
|
|
968
|
+
rmSync5(path, { force: true });
|
|
815
969
|
notify?.("starting the Julia worker (first use loads Turing, can take a minute)...");
|
|
816
970
|
const child = spawn(
|
|
817
971
|
resolved.command,
|
|
@@ -1023,7 +1177,7 @@ async function stopWorker(socket) {
|
|
|
1023
1177
|
try {
|
|
1024
1178
|
sock = await connectOnce(socket);
|
|
1025
1179
|
} catch {
|
|
1026
|
-
|
|
1180
|
+
rmSync5(socket, { force: true });
|
|
1027
1181
|
return "stale";
|
|
1028
1182
|
}
|
|
1029
1183
|
const acked = await new Promise((resolve) => {
|
|
@@ -1039,7 +1193,7 @@ async function stopWorker(socket) {
|
|
|
1039
1193
|
});
|
|
1040
1194
|
sock.destroy();
|
|
1041
1195
|
if (!acked) return "pending";
|
|
1042
|
-
|
|
1196
|
+
rmSync5(socket, { force: true });
|
|
1043
1197
|
return "stopped";
|
|
1044
1198
|
}
|
|
1045
1199
|
export {
|