@mcmcjs/stan 0.1.0

package/dist/index.js.map

@@ -0,0 +1 @@
+{"version":3,"sources":["../src/compile.ts","../src/environment.ts","../src/csv.ts","../src/doctor.ts","../src/engine.ts","../src/fit.ts","../src/runner.ts","../src/matrix.ts","../src/predict.ts","../src/setup.ts","../src/versions.ts"],"sourcesContent":["import { createHash } from \"node:crypto\";\nimport { existsSync, mkdirSync, readFileSync, writeFileSync } from \"node:fs\";\nimport { dirname, isAbsolute, join } from \"node:path\";\nimport type { CommandRunner } from \"@mcmcjs/engine\";\nimport { createRunner } from \"@mcmcjs/engine\";\nimport type { CmdStanInstall } from \"./environment\";\nimport { managedStanRoot } from \"./environment\";\n\nexport interface CompiledModel {\n  /** Path to the compiled model executable. */\n  binaryPath: string;\n  /** True when a previously compiled binary was reused. */\n  cached: boolean;\n}\n\nexport interface CompileOptions {\n  /** Runs make; injectable for tests. Compiles can take minutes. */\n  runner?: CommandRunner;\n  /** Cache root; defaults to `<managed>/models`. */\n  cacheRoot?: string;\n}\n\n/**\n * Concatenates the source with any #include'd files (resolved against the\n * model's directory) so include edits invalidate the compile cache. Nested\n * includes resolve a few levels deep; unresolvable paths are left to stanc.\n */\nexport function cacheKeySource(source: string, modelDir: string, depth = 4): string {\n  if (depth === 0) return source;\n  const parts = [source];\n  for (const match of source.matchAll(/^\\s*#include\\s+[<\"']?([^>\"'\\s]+)[>\"']?/gm)) {\n    const file = match[1];\n    if (!file) continue;\n    try {\n      const included = readFileSync(isAbsolute(file) ? file : join(modelDir, file), \"utf8\");\n      parts.push(cacheKeySource(included, modelDir, depth - 1));\n    } catch {\n      // stanc reports missing includes with a proper error at compile time\n    }\n  }\n  return parts.join(\"\\n\");\n}\n\n/** The compile cache directory for a model source on a CmdStan version. */\nexport function modelCacheDir(source: string, version: string, cacheRoot?: string): string {\n  const key = createHash(\"sha256\").update(`${version}\\n${source}`).digest(\"hex\").slice(0, 16);\n  return join(cacheRoot ?? join(managedStanRoot(), \"models\"), key);\n}\n\n/**\n * Compiles a Stan model to an executable through CmdStan's make, cached by\n * source content and CmdStan version so edits recompile and reruns are instant.\n */\nexport async function compileModel(\n  install: CmdStanInstall,\n  modelPath: string,\n  options: CompileOptions = {},\n): Promise<CompiledModel> {\n  const { runner = createRunner(10 * 60_000), cacheRoot } = options;\n  const source = readFileSync(modelPath, \"utf8\");\n  const modelDir = dirname(modelPath);\n  const dir = modelCacheDir(cacheKeySource(source, modelDir), install.version, cacheRoot);\n  const binaryPath = join(dir, \"model\");\n  // The sentinel is written only after a successful make, so an interrupted\n  // compile never gets reused as a valid binary.\n  const okPath = join(dir, \".ok\");\n  if (existsSync(okPath) && existsSync(binaryPath)) return { binaryPath, cached: true };\n\n  mkdirSync(dir, { recursive: true });\n  writeFileSync(join(dir, \"model.stan\"), source);\n  // CmdStan's pattern rules build targets outside its tree by absolute path;\n  // includes still resolve against the original model's directory.\n  await runner(\"make\", [\"-C\", install.home, `STANCFLAGS=--include-paths=${modelDir}`, binaryPath]);\n  if (!existsSync(binaryPath)) {\n    throw new Error(\"make reported success but produced no model executable\");\n  }\n  writeFileSync(okPath, \"\");\n  return { binaryPath, cached: false };\n}\n","import { existsSync, readdirSync, readFileSync } from \"node:fs\";\nimport { homedir } from \"node:os\";\nimport { basename, join } from \"node:path\";\nimport { type CommandRunner, createRunner, type ToolInfo } from \"@mcmcjs/engine\";\n\nexport type { CommandRunner, ToolInfo } from \"@mcmcjs/engine\";\nexport { createRunner } from \"@mcmcjs/engine\";\n\nconst defaultRunner = createRunner();\n\nimport { DEFAULT_CMDSTAN_CHANNEL } from \"@mcmcjs/core\";\n\n/** The spec channel meaning \"use whatever CmdStan is installed locally\". */\nexport const INSTALLED_CMDSTAN_CHANNEL = DEFAULT_CMDSTAN_CHANNEL;\n\n/** The CmdStan version `mcmc setup --engine stan` provisions. */\nexport const PINNED_CMDSTAN_VERSION = \"2.39.0\";\n\n/** A CmdStan installation found on this machine. */\nexport interface CmdStanInstall {\n  version: string;\n  /** The cmdstan home directory (contains makefile, bin/stanc, examples/). */\n  home: string;\n}\n\n/** The managed root for CmdStan installs: `<data>/mcmcjs/stan`. */\nexport function managedStanRoot(): string {\n  const home = process.env.HOME || homedir();\n  const dataHome = process.env.XDG_DATA_HOME || join(home, \".local\", \"share\");\n  return join(dataHome, \"mcmcjs\", \"stan\");\n}\n\n/** A directory is a usable CmdStan home when the makefile and stanc are present. */\nexport function isCmdStanHome(dir: string): boolean {\n  return existsSync(join(dir, \"makefile\")) && existsSync(join(dir, \"bin\", \"stanc\"));\n}\n\nfunction versionFromDirName(dir: string): string | undefined {\n  return basename(dir).match(/^cmdstan-(\\d+\\.\\d+\\.\\d+(?:-rc\\d+)?)$/)?.[1];\n}\n\nfunction versionFromMakefile(home: string): string | undefined {\n  try {\n    const makefile = readFileSync(join(home, \"makefile\"), \"utf8\");\n    return makefile.match(/CMDSTAN_VERSION\\s*:?=\\s*(\\S+)/)?.[1];\n  } catch {\n    return undefined;\n  }\n}\n\nfunction installAt(home: string): CmdStanInstall | undefined {\n  if (!isCmdStanHome(home)) return undefined;\n  const version = versionFromDirName(home) ?? versionFromMakefile(home);\n  return version ? { version, home } : undefined;\n}\n\nfunction scanRoot(root: string): CmdStanInstall[] {\n  let entries: string[];\n  try {\n    entries = readdirSync(root);\n  } catch {\n    return [];\n  }\n  const installs: CmdStanInstall[] = [];\n  for (const name of entries) {\n    if (!name.startsWith(\"cmdstan-\")) continue;\n    const install = installAt(join(root, name));\n    if (install) installs.push(install);\n  }\n  return installs;\n}\n\nfunction compareVersions(a: string, b: string): number {\n  const parse = (v: string) => {\n    const [core, rc] = v.split(\"-rc\");\n    const nums = (core ?? \"\").split(\".\").map((p) => Number.parseInt(p, 10) || 0);\n    // A release candidate sorts before its final release.\n    return { nums, rc: rc === undefined ? Number.POSITIVE_INFINITY : Number.parseInt(rc, 10) || 0 };\n  };\n  const pa = parse(a);\n  const pb = parse(b);\n  for (let i = 0; i < Math.max(pa.nums.length, pb.nums.length); i++) {\n    const d = (pa.nums[i] ?? 0) - (pb.nums[i] ?? 0);\n    if (d !== 0) return d;\n  }\n  if (pa.rc === pb.rc) return 0;\n  return pa.rc < pb.rc ? -1 : 1;\n}\n\n/**\n * Every CmdStan install visible to mcmcjs, newest first: an explicit\n * MCMCJS_CMDSTAN/CMDSTAN home wins, then the managed root, then the\n * conventional `~/.cmdstan` used by other Stan interfaces.\n */\nexport function listCmdStanInstalls(): CmdStanInstall[] {\n  const explicit = process.env.MCMCJS_CMDSTAN || process.env.CMDSTAN;\n  if (explicit) {\n    const install = installAt(explicit);\n    if (!install) {\n      throw new Error(\n        `MCMCJS_CMDSTAN/CMDSTAN points at ${explicit}, which is not a CmdStan directory (expected a makefile and bin/stanc); unset it or point it at a CmdStan home.`,\n      );\n    }\n    return [install];\n  }\n  const home = process.env.HOME || homedir();\n  const installs = [...scanRoot(managedStanRoot()), ...scanRoot(join(home, \".cmdstan\"))];\n  return installs.sort((a, b) => compareVersions(b.version, a.version));\n}\n\n/**\n * Resolves the CmdStan install a fit runs on. `installed` (the default channel)\n * takes the newest local install; an explicit version must match exactly.\n */\nexport function resolveCmdStan(requested: string = INSTALLED_CMDSTAN_CHANNEL): CmdStanInstall {\n  const installs = listCmdStanInstalls();\n  if (requested === INSTALLED_CMDSTAN_CHANNEL) {\n    const newest = installs[0];\n    if (newest) return newest;\n    throw new Error(\n      \"CmdStan not found. Run `mcmc setup --engine stan`, or point MCMCJS_CMDSTAN at a CmdStan directory.\",\n    );\n  }\n  const match = installs.find((i) => i.version === requested);\n  if (match) return match;\n  throw new Error(\n    `CmdStan ${requested} not found. Run \\`mcmc setup --engine stan --stan-version ${requested}\\`, or point MCMCJS_CMDSTAN at a CmdStan directory.`,\n  );\n}\n\nasync function detect(\n  command: string,\n  args: string[],\n  parseVersion: (stdout: string) => string | undefined,\n  runner: CommandRunner,\n): Promise<ToolInfo> {\n  try {\n    const version = parseVersion(await runner(command, args));\n    if (version) return { found: true, version, path: command };\n  } catch {\n    // not available; fall through\n  }\n  return { found: false };\n}\n\nconst versionNumber = (stdout: string): string | undefined =>\n  stdout.match(/(\\d+\\.\\d+(?:\\.\\d+)?)/)?.[1];\n\n/** Detects GNU Make. */\nexport function detectMake(runner: CommandRunner = defaultRunner): Promise<ToolInfo> {\n  return detect(\"make\", [\"--version\"], versionNumber, runner);\n}\n\n/** Detects a C++ compiler (g++ first, then clang++). */\nexport async function detectCxx(runner: CommandRunner = defaultRunner): Promise<ToolInfo> {\n  for (const command of [\"g++\", \"clang++\"]) {\n    const info = await detect(command, [\"--version\"], versionNumber, runner);\n    if (info.found) return info;\n  }\n  return { found: false };\n}\n\n/** Probes `bin/stanc --version` of an install. */\nexport async function detectStanc(\n  install: CmdStanInstall | undefined,\n  runner: CommandRunner = defaultRunner,\n): Promise<ToolInfo> {\n  if (!install) return { found: false };\n  const stanc = join(install.home, \"bin\", \"stanc\");\n  return detect(stanc, [\"--version\"], versionNumber, runner);\n}\n","import { closeSync, openSync, readSync } from \"node:fs\";\nimport { fromStanName } from \"@mcmcjs/core\";\nimport type { DrawBatch } from \"@mcmcjs/engine\";\n\n// Mirrors the sampler-column renames applied by @mcmcjs/core's Stan CSV parser\n// (packages/core/src/parsers/stan.ts) so streamed leaves match the samples file.\nconst STAT_RENAME: Record<string, string> = {\n  lp__: \"lp\",\n  energy__: \"energy\",\n  divergent__: \"diverging\",\n  treedepth__: \"tree_depth\",\n  n_leapfrog__: \"n_steps\",\n  accept_stat__: \"acceptance_rate\",\n  stepsize__: \"step_size\",\n};\n\n/** Stan CSV column -> streamed leaf name; null for dropped diagnostic columns. */\nexport function columnToLeaf(column: string): string | null {\n  if (column.endsWith(\"__\")) return STAT_RENAME[column] ?? null;\n  return fromStanName(column);\n}\n\n/** CmdStan prints C++ formatting for non-finite doubles: inf, -inf, nan. */\nfunction parseStanNumber(field: string): number {\n  const value = Number(field);\n  if (!Number.isNaN(value) || field === \"nan\") return value;\n  if (field === \"inf\" || field === \"+inf\") return Number.POSITIVE_INFINITY;\n  if (field === \"-inf\") return Number.NEGATIVE_INFINITY;\n  return value;\n}\n\nexport interface StanCsvTail {\n  /** Reads newly appended rows and emits any full batches. */\n  poll(): void;\n  /** Final poll plus a flush of the remaining partial batch. */\n  finish(): void;\n}\n\n/**\n * Incrementally tails one growing CmdStan CSV, batching completed draws into\n * DrawBatch messages. Comment lines (the config echo, adaptation block, and\n * timing footer) are skipped; the first non-comment line is the header. A\n * trailing line without its newline is left buffered until it completes, and a\n * row is only accepted when its field count matches the header.\n */\nexport function createStanCsvTail(\n  filePath: string,\n  opts: {\n    /** 0-based chain index reported in batches. */\n    chain: number;\n    /** Draws per batch. */\n    batchSize: number;\n    onBatch: (batch: DrawBatch) => void;\n  },\n): StanCsvTail {\n  let position = 0;\n  let pending = \"\";\n  let leaves: (string | null)[] | undefined;\n  let seq = 0;\n  const rows: number[][] = [];\n\n  const emit = (count: number) => {\n    if (count === 0 || !leaves) return;\n    const draws: Record<string, number[]> = {};\n    for (let c = 0; c < leaves.length; c++) {\n      const leaf = leaves[c];\n      if (!leaf) continue;\n      const values = new Array<number>(count);\n      for (let r = 0; r < count; r++) values[r] = rows[r]?.[c] ?? Number.NaN;\n      draws[leaf] = values;\n    }\n    rows.splice(0, count);\n    opts.onBatch({ chain: opts.chain, seq, iteration: null, draws });\n    seq += 1;\n  };\n\n  const consume = (line: string) => {\n    const trimmed = line.trim();\n    if (trimmed.length === 0 || trimmed.startsWith(\"#\")) return;\n    if (!leaves) {\n      leaves = trimmed.split(\",\").map(columnToLeaf);\n      return;\n    }\n    const fields = trimmed.split(\",\");\n    if (fields.length !== leaves.length) return;\n    rows.push(fields.map(parseStanNumber));\n    if (rows.length >= opts.batchSize) emit(opts.batchSize);\n  };\n\n  const poll = () => {\n    let fd: number;\n    try {\n      fd = openSync(filePath, \"r\");\n    } catch {\n      return; // not created yet\n    }\n    try {\n      const chunk = Buffer.alloc(1 << 16);\n      for (;;) {\n        const read = readSync(fd, chunk, 0, chunk.length, position);\n        if (read <= 0) break;\n        position += read;\n        pending += chunk.toString(\"utf8\", 0, read);\n        for (;;) {\n          const nl = pending.indexOf(\"\\n\");\n          if (nl < 0) break;\n          consume(pending.slice(0, nl));\n          pending = pending.slice(nl + 1);\n        }\n      }\n    } finally {\n      closeSync(fd);\n    }\n  };\n\n  return {\n    poll,\n    finish() {\n      poll();\n      emit(rows.length);\n    },\n  };\n}\n","import type { CommandRunner, ToolInfo } from \"@mcmcjs/engine\";\nimport {\n  type CmdStanInstall,\n  detectCxx,\n  detectMake,\n  detectStanc,\n  listCmdStanInstalls,\n} from \"./environment\";\n\n/** A summary of the Stan toolchain available for inference. */\nexport interface StanDoctorReport {\n  cmdstan: ToolInfo;\n  stanc: ToolInfo;\n  make: ToolInfo;\n  cxx: ToolInfo;\n  /** The install a fit would use, when one exists. */\n  install?: CmdStanInstall;\n  /** True when a fit can compile and sample: CmdStan plus the build toolchain. */\n  ready: boolean;\n}\n\n/** Detects the installed Stan toolchain and reports whether inference can run. */\nexport async function runDoctor(runner?: CommandRunner): Promise<StanDoctorReport> {\n  const install = listCmdStanInstalls()[0];\n  const cmdstan: ToolInfo = install\n    ? { found: true, version: install.version, path: install.home }\n    : { found: false };\n  const [stanc, make, cxx] = await Promise.all([\n    detectStanc(install, runner),\n    detectMake(runner),\n    detectCxx(runner),\n  ]);\n  return {\n    cmdstan,\n    stanc,\n    make,\n    cxx,\n    install,\n    ready: cmdstan.found && make.found && cxx.found,\n  };\n}\n","import type { Engine, EngineContext, HealthReport } from \"@mcmcjs/engine\";\nimport { runDoctor } from \"./doctor\";\n\nexport const stanEngine: Engine = {\n  id: \"stan\",\n  displayName: \"Stan (CmdStan)\",\n  capabilities: { setup: true, versions: true, fit: true, predict: true },\n  async doctor(ctx: EngineContext): Promise<HealthReport> {\n    const report = await runDoctor(ctx.run);\n    const missingToolchain = !report.make.found || !report.cxx.found;\n    return {\n      engineId: \"stan\",\n      ready: report.ready,\n      tools: [\n        { name: \"cmdstan\", ...report.cmdstan },\n        { name: \"stanc\", ...report.stanc },\n        { name: \"make\", ...report.make },\n        { name: \"c++\", ...report.cxx },\n      ],\n      hint: report.ready\n        ? undefined\n        : missingToolchain\n          ? \"Stan models compile with the system toolchain; install make and a C++ compiler (g++ or clang++), then run `mcmc setup --engine stan`.\"\n          : \"CmdStan not found. Run `mcmc setup --engine stan`.\",\n    };\n  },\n};\n","import { createHash } from \"node:crypto\";\nimport {\n  existsSync,\n  mkdirSync,\n  mkdtempSync,\n  readFileSync,\n  renameSync,\n  rmSync,\n  writeFileSync,\n} from \"node:fs\";\nimport { tmpdir } from \"node:os\";\nimport { join } from \"node:path\";\nimport {\n  canonicalJson,\n  fromStanCSVFiles,\n  parseSamples,\n  type ResolvedSpec,\n  RUN_RECORD_SCHEMA_VERSION,\n  type RunRecord,\n  toMCMCChainsJson,\n} from \"@mcmcjs/core\";\nimport type { DrawBatch, FitProgress, FitResult } from \"@mcmcjs/engine\";\nimport { type CompileOptions, compileModel } from \"./compile\";\nimport { createStanCsvTail } from \"./csv\";\nimport type { CmdStanInstall } from \"./environment\";\nimport { createStanSpawn, parseIterationLine, type StanSpawn } from \"./runner\";\n\nexport interface StanFitIo {\n  /** Spawns CmdStan processes; injectable so runFit is testable without CmdStan. */\n  spawn?: StanSpawn;\n  /** Where the samples file is written. */\n  outPath: string;\n  /** Where the run record is written; defaults to `<outPath>.run.json`. */\n  recordPath?: string;\n  /** Streamed per-chain sampling progress. */\n  onProgress?: (progress: FitProgress) => void;\n  /** Streamed draw batches as sampling proceeds. */\n  onDraws?: (batch: DrawBatch) => void;\n  /** Draws per streamed batch (default 25). */\n  drawBatchSize?: number;\n  /** Aborts an in-progress fit; the run then ends with a \"cancelled\" status. */\n  signal?: AbortSignal;\n  /** Source path when the data came from a referenced file; recorded, not copied. */\n  dataFile?: string;\n  /** Overrides the recorded data hash (e.g. the data file's bytes hash). */\n  dataSha256?: string;\n  /** Model compile pass-through, injectable for tests. */\n  compile?: CompileOptions;\n  tmpDir?: string;\n}\n\nfunction sha256(text: string): string {\n  return createHash(\"sha256\").update(text).digest(\"hex\");\n}\n\nfunction tmpParent(): string {\n  const uid = typeof process.getuid === \"function\" ? `-${process.getuid()}` : \"\";\n  return join(tmpdir(), `mcmcjs${uid}`);\n}\n\n/** The per-chain CmdStan invocation. Chains share one seed; `id` varies the stream. */\nexport function chainArgs(\n  spec: ResolvedSpec,\n  chain1: number,\n  dataPath: string,\n  csvPath: string,\n): string[] {\n  const s = spec.sampler;\n  const total = s.draws + s.warmup;\n  // Progress at roughly 1% granularity without flooding stdout on long runs.\n  const refresh = Math.max(1, Math.floor(total / 100));\n  return [\n    \"sample\",\n    `num_samples=${s.draws}`,\n    `num_warmup=${s.warmup}`,\n    \"adapt\",\n    `delta=${s.adapt_delta}`,\n    \"data\",\n    `file=${dataPath}`,\n    \"random\",\n    `seed=${spec.seed}`,\n    `id=${chain1}`,\n    \"output\",\n    `file=${csvPath}`,\n    `refresh=${refresh}`,\n  ];\n}\n\nfunction errorTail(stderr: string): string | undefined {\n  const lines = stderr\n    .trim()\n    .split(\"\\n\")\n    .map((l) => l.trim())\n    .filter(Boolean);\n  return lines.at(-1);\n}\n\n/** Runs one Stan inference on a resolved CmdStan install. */\nexport async function runFit(\n  spec: ResolvedSpec,\n  install: CmdStanInstall,\n  io: StanFitIo,\n): Promise<FitResult> {\n  const startedAt = new Date().toISOString();\n  const start = performance.now();\n  const runtimeRequested = spec.backend.version;\n  const fail = (stage: FitResult[\"stage\"], error: string): FitResult => ({\n    status: \"error\",\n    runtimeRequested,\n    elapsedMs: Math.round(performance.now() - start),\n    stage,\n    error,\n  });\n\n  if (io.signal?.aborted) {\n    return { status: \"cancelled\", runtimeRequested, elapsedMs: 0 };\n  }\n\n  let binaryPath: string;\n  try {\n    ({ binaryPath } = await compileModel(install, spec.modelPath, io.compile));\n  } catch (error) {\n    return fail(\"compile\", (error as Error).message);\n  }\n  if (io.signal?.aborted) {\n    return {\n      status: \"cancelled\",\n      runtimeRequested,\n      elapsedMs: Math.round(performance.now() - start),\n    };\n  }\n\n  const ownTmp = io.tmpDir === undefined;\n  let tmp: string;\n  if (io.tmpDir === undefined) {\n    mkdirSync(tmpParent(), { recursive: true });\n    tmp = mkdtempSync(join(tmpParent(), \"stan-fit-\"));\n  } else {\n    tmp = io.tmpDir;\n  }\n\n  try {\n    const dataPath = join(tmp, \"data.json\");\n    writeFileSync(dataPath, JSON.stringify(spec.data));\n\n    const chains = spec.sampler.chains;\n    const spawn = io.spawn ?? createStanSpawn();\n    const csvPaths = Array.from({ length: chains }, (_, i) => join(tmp, `chain_${i + 1}.csv`));\n\n    const tails = io.onDraws\n      ? csvPaths.map((path, i) =>\n          createStanCsvTail(path, {\n            chain: i,\n            batchSize: io.drawBatchSize ?? 25,\n            onBatch: io.onDraws as (batch: DrawBatch) => void,\n          }),\n        )\n      : [];\n    const pollTimer =\n      tails.length > 0\n        ? setInterval(() => {\n            for (const tail of tails) tail.poll();\n          }, 150)\n        : undefined;\n    pollTimer?.unref?.();\n\n    let results: { code: number; stderr: string; cancelled?: boolean }[];\n    try {\n      results = await Promise.all(\n        csvPaths.map((csvPath, i) => {\n          const onProgress = io.onProgress;\n          return spawn(binaryPath, chainArgs(spec, i + 1, dataPath, csvPath), {\n            signal: io.signal,\n            onStdoutLine: onProgress\n              ? (line) => {\n                  const p = parseIterationLine(line);\n                  if (!p) return;\n                  onProgress({\n                    chain: i + 1,\n                    of: chains,\n                    fraction: p.total > 0 ? p.iteration / p.total : 0,\n                    done: p.iteration === p.total,\n                  });\n                }\n              : undefined,\n          });\n        }),\n      );\n    } finally {\n      if (pollTimer) clearInterval(pollTimer);\n    }\n    for (const tail of tails) tail.finish();\n\n    const elapsedMs = Math.round(performance.now() - start);\n    if (io.signal?.aborted || results.some((r) => r.cancelled)) {\n      return { status: \"cancelled\", runtimeRequested, elapsedMs };\n    }\n    const failed = results.findIndex((r) => r.code !== 0);\n    if (failed >= 0) {\n      const r = results[failed];\n      return fail(\n        \"sample\",\n        `chain ${failed + 1} exited with code ${r?.code}${\n          r && errorTail(r.stderr) ? `: ${errorTail(r.stderr)}` : \"\"\n        }`,\n      );\n    }\n\n    let samplesJson: string;\n    try {\n      const texts = csvPaths.map((path) => readFileSync(path, \"utf8\"));\n      samplesJson = JSON.stringify(toMCMCChainsJson(fromStanCSVFiles(texts)));\n      parseSamples(samplesJson);\n    } catch (error) {\n      return fail(\"load_samples\", `could not read CmdStan output: ${(error as Error).message}`);\n    }\n\n    try {\n      const partial = `${io.outPath}.tmp`;\n      writeFileSync(partial, samplesJson);\n      renameSync(partial, io.outPath);\n    } catch (error) {\n      return fail(\"write\", (error as Error).message);\n    }\n\n    const record: RunRecord = {\n      schema_version: RUN_RECORD_SCHEMA_VERSION,\n      spec_hash: spec.specHash,\n      seed: spec.seed,\n      backend: { id: spec.backend.id, runtime: spec.backend.runtime },\n      runtime: { requested: runtimeRequested, actual: install.version, path: install.home },\n      model_sha256: existsSync(spec.modelPath)\n        ? sha256(readFileSync(spec.modelPath, \"utf8\"))\n        : undefined,\n      data_sha256: io.dataSha256 ?? sha256(canonicalJson(spec.data)),\n      ...(io.dataFile ? { data_file: io.dataFile } : {}),\n      samples_file: io.outPath,\n      started_at: startedAt,\n      elapsed_ms: Math.round(performance.now() - start),\n    };\n    try {\n      writeFileSync(\n        io.recordPath ?? `${io.outPath}.run.json`,\n        `${JSON.stringify(record, null, 2)}\\n`,\n      );\n    } catch (error) {\n      return fail(\"write\", `could not write the run record: ${(error as Error).message}`);\n    }\n\n    return {\n      status: \"ok\",\n      samplesFile: io.outPath,\n      runtimeRequested,\n      runtimeActual: install.version,\n      elapsedMs: Math.round(performance.now() - start),\n    };\n  } finally {\n    if (ownTmp) rmSync(tmp, { recursive: true, force: true });\n  }\n}\n","import { type ChildProcess, spawn } from \"node:child_process\";\nimport { killTree } from \"@mcmcjs/engine\";\n\nconst DETACHED = process.platform !== \"win32\";\n\nexport interface StanSpawnResult {\n  code: number;\n  stderr: string;\n  cancelled?: boolean;\n}\n\nexport interface StanSpawnOptions {\n  /** Called once per complete stdout line (CmdStan prints progress there). */\n  onStdoutLine?: (line: string) => void;\n  signal?: AbortSignal;\n  timeoutMs?: number;\n}\n\n/** Spawns one CmdStan process, streaming stdout lines to the caller. */\nexport type StanSpawn = (\n  command: string,\n  args: string[],\n  opts?: StanSpawnOptions,\n) => Promise<StanSpawnResult>;\n\nconst STDERR_LIMIT = 1 << 22;\n\n/**\n * The production StanSpawn: detached on POSIX so cancellation kills the whole\n * process group, stdout parsed line-by-line for progress, stderr captured for\n * error reporting.\n */\nexport function createStanSpawn(defaultTimeoutMs = 30 * 60_000): StanSpawn {\n  return (command, args, opts = {}) =>\n    new Promise((resolve) => {\n      const child: ChildProcess = spawn(command, args, {\n        stdio: [\"ignore\", \"pipe\", \"pipe\"],\n        detached: DETACHED,\n      });\n\n      let stderr = \"\";\n      let stdoutPending = \"\";\n      let cancelled = false;\n      let settled = false;\n\n      const timeoutMs = opts.timeoutMs ?? defaultTimeoutMs;\n      const timer = setTimeout(() => {\n        stderr += \"process timed out and was killed\\n\";\n        killTree(child);\n      }, timeoutMs);\n      timer.unref?.();\n\n      const onAbort = () => {\n        cancelled = true;\n        killTree(child);\n      };\n      if (opts.signal) {\n        if (opts.signal.aborted) onAbort();\n        else opts.signal.addEventListener(\"abort\", onAbort, { once: true });\n      }\n\n      child.stdout?.on(\"data\", (data: Buffer) => {\n        stdoutPending += data.toString(\"utf8\");\n        for (;;) {\n          const nl = stdoutPending.indexOf(\"\\n\");\n          if (nl < 0) break;\n          opts.onStdoutLine?.(stdoutPending.slice(0, nl));\n          stdoutPending = stdoutPending.slice(nl + 1);\n        }\n      });\n      child.stderr?.on(\"data\", (data: Buffer) => {\n        if (stderr.length < STDERR_LIMIT) stderr += data.toString(\"utf8\");\n      });\n\n      const settle = (code: number) => {\n        if (settled) return;\n        settled = true;\n        clearTimeout(timer);\n        opts.signal?.removeEventListener(\"abort\", onAbort);\n        if (stdoutPending.length > 0) opts.onStdoutLine?.(stdoutPending);\n        resolve({ code, stderr, cancelled: cancelled || undefined });\n      };\n\n      child.on(\"error\", (error) => {\n        stderr = stderr || error.message;\n        settle(1);\n      });\n      child.on(\"close\", (code) => settle(code ?? 1));\n    });\n}\n\n/** Parses one CmdStan progress line; null when the line is not progress. */\nexport function parseIterationLine(\n  line: string,\n): { iteration: number; total: number; warmup: boolean } | null {\n  const match = line.match(/Iteration:\\s*(\\d+)\\s*\\/\\s*(\\d+)\\s*\\[\\s*\\d+%\\]\\s*\\((Warmup|Sampling)\\)/);\n  if (!match) return null;\n  return {\n    iteration: Number.parseInt(match[1] ?? \"0\", 10),\n    total: Number.parseInt(match[2] ?? \"0\", 10),\n    warmup: match[3] === \"Warmup\",\n  };\n}\n","import { join } from \"node:path\";\nimport type { ResolvedSpec } from \"@mcmcjs/core\";\nimport type { FitResult } from \"@mcmcjs/engine\";\nimport { resolveCmdStan } from \"./environment\";\nimport { runFit, type StanFitIo } from \"./fit\";\n\n// Structurally identical to the Julia engine's matrix shapes, so the CLI's\n// matrix rendering works with either engine's result.\nexport interface StanMatrixEntry {\n  version: string;\n  status: \"ok\" | \"error\" | \"cancelled\";\n  samplesFile?: string;\n  runtimeActual?: string;\n  elapsedMs: number;\n  stage?: FitResult[\"stage\"];\n  error?: string;\n}\n\nexport interface StanMatrixResult {\n  entries: StanMatrixEntry[];\n  /** True only when every requested version ran and succeeded. */\n  ok: boolean;\n}\n\nexport interface StanMatrixIo {\n  /** Directory the per-version samples files are written into. */\n  outDir: string;\n  dataFile?: string;\n  dataSha256?: string;\n  /** Continue after a version fails instead of stopping. */\n  keepGoing?: boolean;\n  signal?: AbortSignal;\n  /** Fit pass-through, injectable for tests. */\n  fit?: Pick<StanFitIo, \"spawn\" | \"compile\">;\n}\n\n/** Runs one spec across several installed CmdStan versions. */\nexport async function runMatrix(\n  spec: ResolvedSpec,\n  versions: string[],\n  io: StanMatrixIo,\n): Promise<StanMatrixResult> {\n  const entries: StanMatrixEntry[] = [];\n  for (const version of versions) {\n    let entry: StanMatrixEntry;\n    try {\n      const install = resolveCmdStan(version);\n      const result = await runFit({ ...spec, backend: { ...spec.backend, version } }, install, {\n        ...io.fit,\n        outPath: join(io.outDir, `${version}.samples.json`),\n        dataFile: io.dataFile,\n        dataSha256: io.dataSha256,\n        signal: io.signal,\n      });\n      entry = {\n        version,\n        status: result.status,\n        samplesFile: result.samplesFile,\n        runtimeActual: result.runtimeActual,\n        elapsedMs: result.elapsedMs,\n        stage: result.stage,\n        error: result.error,\n      };\n    } catch (error) {\n      entry = { version, status: \"error\", elapsedMs: 0, error: (error as Error).message };\n    }\n    entries.push(entry);\n    if (entry.status === \"cancelled\") break;\n    if (entry.status === \"error\" && !io.keepGoing) break;\n  }\n  return {\n    entries,\n    ok: entries.length === versions.length && entries.every((e) => e.status === \"ok\"),\n  };\n}\n","import { createHash } from \"node:crypto\";\nimport {\n  existsSync,\n  mkdirSync,\n  mkdtempSync,\n  readFileSync,\n  renameSync,\n  rmSync,\n  writeFileSync,\n} from \"node:fs\";\nimport { tmpdir } from \"node:os\";\nimport { join } from \"node:path\";\nimport {\n  canonicalJson,\n  fromStanCSVFiles,\n  parseSamples,\n  type ResolvedSpec,\n  RUN_RECORD_SCHEMA_VERSION,\n  type RunRecord,\n  type Samples,\n  toMCMCChainsJson,\n  toStanName,\n} from \"@mcmcjs/core\";\nimport type { FitResult } from \"@mcmcjs/engine\";\nimport { type CompileOptions, compileModel } from \"./compile\";\nimport type { CmdStanInstall } from \"./environment\";\nimport { createStanSpawn, type StanSpawn } from \"./runner\";\n\nexport interface StanPredictIo {\n  /** Where the posterior-predictive samples file is written. */\n  outPath: string;\n  /** The posterior samples file fed to prediction. */\n  samplesPath: string;\n  /** Spawns CmdStan processes; injectable so runPredict is testable without CmdStan. */\n  spawn?: StanSpawn;\n  /** Model compile pass-through, injectable for tests. */\n  compile?: CompileOptions;\n  signal?: AbortSignal;\n  tmpDir?: string;\n}\n\n/**\n * The prediction data: [data] with [predict].data overrides. Unlike the Julia\n * engines, targets are not blanked; Stan predictions come from the model's own\n * generated quantities block, which reads the data as-is.\n */\nexport function predictData(spec: ResolvedSpec): Record<string, unknown> {\n  if (!spec.predict) throw new Error(\"spec has no [predict] block\");\n  return { ...spec.data, ...(spec.predict.data ?? {}) };\n}\n\n/**\n * One Stan-CSV of fitted parameters per chain, rebuilt from the samples file.\n * CmdStan's generate_quantities reads parameters by header name and ignores\n * extra columns, so a header plus the parameter draws is sufficient.\n */\nexport function fittedParamsCsv(samples: Samples, chain: number): string {\n  const names = samples.variables;\n  const header = names.map(toStanName).join(\",\");\n  const columns = names.map((name) => samples.draws.get(name) as Float64Array);\n  const start = chain * samples.nDraws;\n  const rows: string[] = [header];\n  for (let i = 0; i < samples.nDraws; i++) {\n    rows.push(columns.map((col) => stanCell(col[start + i] ?? Number.NaN)).join(\",\"));\n  }\n  return `${rows.join(\"\\n\")}\\n`;\n}\n\nfunction stanCell(value: number): string {\n  if (Number.isFinite(value)) return String(value);\n  if (Number.isNaN(value)) return \"nan\";\n  return value > 0 ? \"inf\" : \"-inf\";\n}\n\n/** Whether a scalarized variable name belongs to a predict target base name. */\nexport function matchesTarget(name: string, targets: readonly string[]): boolean {\n  return targets.some((t) => name === t || name.startsWith(`${t}[`));\n}\n\nfunction filterToTargets(all: Samples, targets: readonly string[]): Samples {\n  const draws = new Map<string, Float64Array>();\n  for (const name of all.variables) {\n    if (matchesTarget(name, targets)) {\n      draws.set(name, all.draws.get(name) as Float64Array);\n    }\n  }\n  return {\n    variables: [...draws.keys()],\n    nChains: all.nChains,\n    nDraws: all.nDraws,\n    draws,\n    sampleStats: new Map(),\n  };\n}\n\nfunction baseNames(variables: readonly string[]): string[] {\n  return [...new Set(variables.map((v) => v.replace(/\\[.*$/, \"\")))];\n}\n\nfunction sha256(text: string): string {\n  return createHash(\"sha256\").update(text).digest(\"hex\");\n}\n\nfunction tmpParent(): string {\n  const uid = typeof process.getuid === \"function\" ? `-${process.getuid()}` : \"\";\n  return join(tmpdir(), `mcmcjs${uid}`);\n}\n\n/**\n * Draws posterior-predictive samples through CmdStan's generate_quantities:\n * the model's generated quantities block re-runs once per posterior draw, and\n * the columns matching [predict].targets become the predictive samples file.\n */\nexport async function runPredict(\n  spec: ResolvedSpec,\n  install: CmdStanInstall,\n  io: StanPredictIo,\n): Promise<FitResult> {\n  const startedAt = new Date().toISOString();\n  const start = performance.now();\n  const runtimeRequested = spec.backend.version;\n  const elapsed = () => Math.round(performance.now() - start);\n  const fail = (stage: FitResult[\"stage\"], error: string): FitResult => ({\n    status: \"error\",\n    runtimeRequested,\n    elapsedMs: elapsed(),\n    stage,\n    error,\n  });\n\n  const targets = spec.predict?.targets;\n  if (!targets || targets.length === 0) {\n    return fail(\"predict\", \"spec has no [predict] block\");\n  }\n  if (io.signal?.aborted) {\n    return { status: \"cancelled\", runtimeRequested, elapsedMs: 0 };\n  }\n\n  let posterior: Samples;\n  try {\n    posterior = parseSamples(readFileSync(io.samplesPath, \"utf8\"));\n  } catch (error) {\n    return fail(\"load_samples\", `posterior samples did not parse: ${(error as Error).message}`);\n  }\n\n  let binaryPath: string;\n  try {\n    ({ binaryPath } = await compileModel(install, spec.modelPath, io.compile));\n  } catch (error) {\n    return fail(\"compile\", (error as Error).message);\n  }\n\n  const ownTmp = io.tmpDir === undefined;\n  let tmp: string;\n  if (io.tmpDir === undefined) {\n    mkdirSync(tmpParent(), { recursive: true });\n    tmp = mkdtempSync(join(tmpParent(), \"stan-predict-\"));\n  } else {\n    tmp = io.tmpDir;\n  }\n\n  try {\n    const data = predictData(spec);\n    const dataPath = join(tmp, \"data.json\");\n    writeFileSync(dataPath, JSON.stringify(data));\n\n    const spawn = io.spawn ?? createStanSpawn();\n    const chains = posterior.nChains;\n    // CmdStan rejects a fitted_params name that is a substring of the output\n    // name, so the two use unrelated stems.\n    const results = await Promise.all(\n      Array.from({ length: chains }, (_, i) => {\n        const fittedPath = join(tmp, `fitted_${i + 1}.csv`);\n        writeFileSync(fittedPath, fittedParamsCsv(posterior, i));\n        return spawn(\n          binaryPath,\n          [\n            \"generate_quantities\",\n            `fitted_params=${fittedPath}`,\n            \"data\",\n            `file=${dataPath}`,\n            \"random\",\n            `seed=${spec.seed}`,\n            `id=${i + 1}`,\n            \"output\",\n            `file=${join(tmp, `gq_${i + 1}.csv`)}`,\n          ],\n          { signal: io.signal },\n        );\n      }),\n    );\n\n    if (io.signal?.aborted || results.some((r) => r.cancelled)) {\n      return { status: \"cancelled\", runtimeRequested, elapsedMs: elapsed() };\n    }\n    const failed = results.findIndex((r) => r.code !== 0);\n    if (failed >= 0) {\n      const stderr = results[failed]?.stderr ?? \"\";\n      if (/doesn't generate any quantities/i.test(stderr)) {\n        return fail(\n          \"predict\",\n          `the Stan model has no generated quantities block; add one that computes ${targets.join(\", \")}`,\n        );\n      }\n      const tail = stderr.trim().split(\"\\n\").filter(Boolean).at(-1);\n      return fail(\n        \"predict\",\n        `generate_quantities failed for chain ${failed + 1}${tail ? `: ${tail}` : \"\"}`,\n      );\n    }\n\n    let predictive: Samples;\n    try {\n      const texts = Array.from({ length: chains }, (_, i) =>\n        readFileSync(join(tmp, `gq_${i + 1}.csv`), \"utf8\"),\n      );\n      predictive = filterToTargets(fromStanCSVFiles(texts), targets);\n    } catch (error) {\n      return fail(\n        \"load_samples\",\n        `could not read generate_quantities output: ${(error as Error).message}`,\n      );\n    }\n    if (predictive.variables.length === 0) {\n      const available = baseNames(fromStanCSVFilesNames(tmp, chains));\n      return fail(\n        \"predict\",\n        `no generated quantity matches targets ${targets.join(\", \")}; the model generates: ${\n          available.length > 0 ? available.join(\", \") : \"(nothing)\"\n        }`,\n      );\n    }\n\n    try {\n      const json = JSON.stringify(toMCMCChainsJson(predictive));\n      parseSamples(json);\n      const partial = `${io.outPath}.tmp`;\n      writeFileSync(partial, json);\n      renameSync(partial, io.outPath);\n    } catch (error) {\n      return fail(\"write\", (error as Error).message);\n    }\n\n    const record: RunRecord = {\n      schema_version: RUN_RECORD_SCHEMA_VERSION,\n      spec_hash: spec.specHash,\n      seed: spec.seed,\n      backend: { id: spec.backend.id, runtime: spec.backend.runtime },\n      runtime: { requested: runtimeRequested, actual: install.version, path: install.home },\n      model_sha256: existsSync(spec.modelPath)\n        ? sha256(readFileSync(spec.modelPath, \"utf8\"))\n        : undefined,\n      data_sha256: sha256(canonicalJson(data)),\n      posterior_samples: io.samplesPath,\n      posterior_samples_sha256: sha256(readFileSync(io.samplesPath, \"utf8\")),\n      samples_file: io.outPath,\n      started_at: startedAt,\n      elapsed_ms: elapsed(),\n    };\n    try {\n      writeFileSync(`${io.outPath}.run.json`, `${JSON.stringify(record, null, 2)}\\n`);\n    } catch (error) {\n      return fail(\"write\", `could not write the run record: ${(error as Error).message}`);\n    }\n\n    return {\n      status: \"ok\",\n      samplesFile: io.outPath,\n      runtimeRequested,\n      runtimeActual: install.version,\n      elapsedMs: elapsed(),\n    };\n  } finally {\n    if (ownTmp) rmSync(tmp, { recursive: true, force: true });\n  }\n}\n\nfunction fromStanCSVFilesNames(tmp: string, chains: number): string[] {\n  try {\n    const texts = Array.from({ length: chains }, (_, i) =>\n      readFileSync(join(tmp, `gq_${i + 1}.csv`), \"utf8\"),\n    );\n    return [...fromStanCSVFiles(texts).variables];\n  } catch {\n    return [];\n  }\n}\n","import { existsSync } from \"node:fs\";\nimport { cpus } from \"node:os\";\nimport { join } from \"node:path\";\nimport type { CommandRunner, ToolInfo } from \"@mcmcjs/engine\";\nimport { createRunner } from \"@mcmcjs/engine\";\nimport { runDoctor, type StanDoctorReport } from \"./doctor\";\nimport { managedStanRoot, PINNED_CMDSTAN_VERSION } from \"./environment\";\n\n/** An executable and its arguments, run directly (no shell word-splitting). */\nexport interface InstallCommand {\n  command: string;\n  args: string[];\n}\n\n/** A single provisioning step needed to make the toolchain ready. */\nexport interface SetupStep {\n  tool: \"toolchain\" | \"cmdstan\" | \"build\";\n  label: string;\n  /** The command to run, or null when the step cannot be performed automatically. */\n  command: InstallCommand | null;\n}\n\nfunction releaseUrl(version: string): string {\n  return `https://github.com/stan-dev/cmdstan/releases/download/v${version}/cmdstan-${version}.tar.gz`;\n}\n\n/** POSIX single-quoting: safe against $, backticks, spaces, and quotes. */\nfunction shq(value: string): string {\n  return `'${value.replaceAll(\"'\", `'\\\\''`)}'`;\n}\n\n/** The managed home a given CmdStan version installs into. */\nexport function managedCmdStanHome(version: string): string {\n  return join(managedStanRoot(), `cmdstan-${version}`);\n}\n\n/** The ordered steps needed to reach a ready toolchain, given the current state. */\nexport function planSetup(\n  report: StanDoctorReport,\n  platform: NodeJS.Platform,\n  version: string = PINNED_CMDSTAN_VERSION,\n): SetupStep[] {\n  const steps: SetupStep[] = [];\n\n  if (!report.make.found || !report.cxx.found) {\n    const missing = [\n      ...(report.make.found ? [] : [\"make\"]),\n      ...(report.cxx.found ? [] : [\"a C++ compiler (g++ or clang++)\"]),\n    ].join(\" and \");\n    // System package managers vary too much to script; report what is missing.\n    steps.push({\n      tool: \"toolchain\",\n      label: `install ${missing} with your system package manager`,\n      command: null,\n    });\n  }\n\n  if (report.cmdstan.found && report.cmdstan.version === version) return steps;\n\n  const home = managedCmdStanHome(version);\n  const posix = platform !== \"win32\";\n  // The tarball extracts into a staging dir and moves into place atomically, so\n  // a partial download is never mistaken for an install on the next run.\n  if (!existsSync(join(home, \"makefile\"))) {\n    const root = shq(managedStanRoot());\n    const staging = shq(join(managedStanRoot(), `.download-${version}`));\n    const finalHome = shq(home);\n    const extracted = shq(join(managedStanRoot(), `.download-${version}`, `cmdstan-${version}`));\n    steps.push({\n      tool: \"cmdstan\",\n      label: `download CmdStan ${version}`,\n      command: posix\n        ? {\n            command: \"sh\",\n            args: [\n              \"-c\",\n              `rm -rf ${staging} && mkdir -p ${staging} && curl -fsSL ${shq(releaseUrl(version))} | tar -xz -C ${staging} && rm -rf ${finalHome} && mv ${extracted} ${finalHome} && rm -rf ${staging} && mkdir -p ${root}`,\n            ],\n          }\n        : null,\n    });\n  }\n  // `make build` compiles stanc/main.o/precompiled headers; it is idempotent,\n  // so a partially built install just resumes. stansummary is one of the last\n  // artifacts, so its presence marks a completed build.\n  if (!existsSync(join(home, \"bin\", \"stansummary\"))) {\n    steps.push({\n      tool: \"build\",\n      label: `build CmdStan ${version} (one-time, a few minutes)`,\n      command: posix\n        ? { command: \"make\", args: [\"-C\", home, \"build\", `-j${cpus().length}`] }\n        : null,\n    });\n  }\n  return steps;\n}\n\nexport type StepStatus = \"ran\" | \"skipped\" | \"failed\" | \"unsupported\";\n\nexport interface SetupStepResult extends SetupStep {\n  status: StepStatus;\n  /** Error detail when the step failed. */\n  detail?: string;\n}\n\nexport interface StanSetupResult {\n  cmdstan: ToolInfo;\n  stanc: ToolInfo;\n  make: ToolInfo;\n  cxx: ToolInfo;\n  /** True when a Stan fit can run after setup. */\n  ready: boolean;\n  steps: SetupStepResult[];\n}\n\nexport interface StanSetupOptions {\n  /** Runs detection commands. Injectable for tests. */\n  runner?: CommandRunner;\n  /** Runs install steps, which may take several minutes. Injectable for tests. */\n  installer?: CommandRunner;\n  /** Target platform; defaults to the current process platform. */\n  platform?: NodeJS.Platform;\n  /** Plan the steps but do not run them. */\n  dryRun?: boolean;\n  /** CmdStan version to provision; defaults to the pinned version. */\n  version?: string;\n}\n\nfunction validateVersion(version: string): void {\n  if (!/^\\d+\\.\\d+\\.\\d+(-rc\\d+)?$/.test(version)) {\n    throw new Error(\n      `invalid CmdStan version: \"${version}\" (expected e.g. ${PINNED_CMDSTAN_VERSION})`,\n    );\n  }\n}\n\n/** Installs the CmdStan toolchain needed for Stan inference. */\nexport async function runSetup(options: StanSetupOptions = {}): Promise<StanSetupResult> {\n  const {\n    runner,\n    installer = createRunner(30 * 60_000),\n    platform = process.platform,\n    dryRun = false,\n    version = PINNED_CMDSTAN_VERSION,\n  } = options;\n  validateVersion(version);\n\n  const before = await runDoctor(runner);\n  const plan = planSetup(before, platform, version);\n  const strip = ({ install: _install, ...report }: StanDoctorReport) => report;\n  if (plan.length === 0) return { ...strip(before), steps: [] };\n\n  if (dryRun) {\n    return {\n      ...strip(before),\n      steps: plan.map((step) => ({ ...step, status: step.command ? \"skipped\" : \"unsupported\" })),\n    };\n  }\n\n  const steps: SetupStepResult[] = [];\n  let failed = false;\n  for (const step of plan) {\n    if (!step.command) {\n      steps.push({ ...step, status: \"unsupported\" });\n      failed = failed || step.tool === \"toolchain\";\n      continue;\n    }\n    if (failed) {\n      steps.push({ ...step, status: \"skipped\" });\n      continue;\n    }\n    try {\n      await installer(step.command.command, step.command.args);\n      steps.push({ ...step, status: \"ran\" });\n    } catch (error) {\n      const detail = error instanceof Error ? error.message : String(error);\n      steps.push({ ...step, status: \"failed\", detail });\n      failed = true;\n    }\n  }\n\n  const after = await runDoctor(runner);\n  return { ...strip(after), steps };\n}\n","import { rmSync } from \"node:fs\";\nimport { join } from \"node:path\";\nimport type { RuntimeVersion } from \"@mcmcjs/engine\";\nimport { listCmdStanInstalls, managedStanRoot } from \"./environment\";\nimport { runSetup, type StanSetupOptions, type StanSetupResult } from \"./setup\";\n\n/**\n * Lists the installed CmdStan versions, newest first. The newest is the\n * default: the `installed` channel resolves to it.\n */\nexport function listVersions(): RuntimeVersion[] {\n  return listCmdStanInstalls().map((install, index) => ({\n    id: install.version,\n    version: install.version,\n    path: install.home,\n    isDefault: index === 0,\n  }));\n}\n\n/** Installs a CmdStan version into the managed root. */\nexport function addVersion(\n  version: string,\n  options: Omit<StanSetupOptions, \"version\"> = {},\n): Promise<StanSetupResult> {\n  return runSetup({ ...options, version });\n}\n\n/**\n * Removes a managed CmdStan install. Only versions under the managed root are\n * removable; `~/.cmdstan` installs and explicit env-var homes are never touched.\n */\nexport function removeVersion(version: string): void {\n  const install = listCmdStanInstalls().find((i) => i.version === version);\n  if (!install) {\n    throw new Error(`CmdStan ${version} is not installed`);\n  }\n  const managedHome = join(managedStanRoot(), `cmdstan-${version}`);\n  if (install.home !== managedHome) {\n    throw new Error(\n      `CmdStan ${version} at ${install.home} is not managed by mcmcjs; remove it yourself if intended`,\n    );\n  }\n  rmSync(managedHome, { recursive: true, force: true 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package/package.json

@@ -0,0 +1,56 @@
+{
+  "name": "@mcmcjs/stan",
+  "version": "0.1.0",
+  "description": "Stan runtime engine for MCMC.js: provisions CmdStan, compiles models, and runs NUTS with streamed progress and draws.",
+  "keywords": [
+    "mcmc",
+    "bayesian",
+    "inference",
+    "stan",
+    "cmdstan",
+    "nuts"
+  ],
+  "license": "MIT",
+  "author": {
+    "name": "Shravan Goswami",
+    "email": "contact@shravangoswami.com",
+    "url": "https://shravangoswami.com"
+  },
+  "homepage": "https://github.com/mcmcjs/mcmcjs/tree/main/packages/stan#readme",
+  "repository": {
+    "type": "git",
+    "url": "git+https://github.com/mcmcjs/mcmcjs.git",
+    "directory": "packages/stan"
+  },
+  "bugs": {
+    "url": "https://github.com/mcmcjs/mcmcjs/issues"
+  },
+  "type": "module",
+  "main": "./dist/index.cjs",
+  "module": "./dist/index.js",
+  "types": "./dist/index.d.ts",
+  "exports": {
+    ".": {
+      "types": "./dist/index.d.ts",
+      "import": "./dist/index.js",
+      "require": "./dist/index.cjs"
+    }
+  },
+  "files": [
+    "dist"
+  ],
+  "engines": {
+    "node": ">=22"
+  },
+  "publishConfig": {
+    "access": "public"
+  },
+  "scripts": {
+    "build": "tsup",
+    "typecheck": "tsc --noEmit"
+  },
+  "dependencies": {
+    "@mcmcjs/core": "workspace:*",
+    "@mcmcjs/engine": "workspace:*"
+  }
+}