@styx-api/cli 0.3.0 → 0.5.0

package/dist/bin.cjs

@@ -1,5 +1,5 @@
 #!/usr/bin/env node
-const require_write = require('./write-CpqGjb9N.cjs');
+const require_write = require('./write-B8IfXD3y.cjs');
 let cac = require("cac");
 
 //#region src/command.ts

package/dist/bin.mjs

@@ -1,5 +1,5 @@
 #!/usr/bin/env node
-import { i as build, n as knownBackends, r as resolveBackends, t as writeFiles } from "./write-BSYxLVtX.mjs";
+import { i as build, n as knownBackends, r as resolveBackends, t as writeFiles } from "./write-DydpQpbm.mjs";
 import { cac } from "cac";
 
 //#region src/command.ts

package/dist/index.cjs

@@ -1,4 +1,4 @@
-const require_write = require('./write-CpqGjb9N.cjs');
+const require_write = require('./write-B8IfXD3y.cjs');
 
 exports.build = require_write.build;
 exports.detectLevel = require_write.detectLevel;

package/dist/index.d.cts.map

@@ -1 +1 @@
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+{"version":3,"file":"index.d.cts","names":[],"sources":["../src/build.ts","../src/catalog.ts","../src/backends.ts","../src/write.ts"],"mappings":";;;KAoBY,SAAA;AAAA,UAUK,YAAA;EAVL;EAYV,KAAA;;EAEA,OAAA;EAdmB;EAgBnB,GAAA;EAN2B;EAQ3B,QAAA,EAAU,OAAA;EAEK;EAAf,IAAA,EAAM,SAAA;AAAA;;UAIS,SAAA;EANL;EAQV,IAAA;EACA,OAAA;AAAA;;UAIe,UAAA;EACf,YAAA;EACA,UAAA;EACA,WAAA;AAAA;AAAA,UAGe,WAAA;EACf,KAAA,EAAO,SAAA;EACP,MAAA;EACA,QAAA;EARA;EAUA,KAAA,GAAQ,UAAA;AAAA;;;AALV;;;iBAkBgB,KAAA,CAAM,OAAA,EAAS,YAAA,GAAe,WAAA;;;;;AAvD9C;;;UCViB,cAAA;EACf,IAAA,EAAM,WAAA;EACN,QAAA,EAAU,cAAA;EDkBiB;EChB3B,QAAA;AAAA;AAAA,UAGe,cAAA;EACf,IAAA,EAAM,WAAA;EACN,IAAA,EAAM,UAAA;AAAA;AAAA,UAGS,UAAA;EDkBf;EChBA,IAAA;EDgBe;ECdf,UAAA;EACA,YAAA;AAAA;;;;ADwBF;;KC2CY,YAAA;AAAA,iBAEI,WAAA,CAAY,GAAA,WAAc,YAAA;;;;;;iBAmH1B,WAAA,CAAY,IAAA,WAAe,cAAA;;;cC1L9B,aAAA;AAAA,iBAEG,eAAA,CAAgB,KAAA;EAAoB,QAAA,EAAU,OAAA;EAAW,OAAA;AAAA;;;iBCtBzD,UAAA,CAAW,KAAA,EAAO,SAAA"}

package/dist/index.d.mts.map

@@ -1 +1 @@
-{"version":3,"file":"index.d.mts","names":[],"sources":["../src/build.ts","../src/catalog.ts","../src/backends.ts","../src/write.ts"],"mappings":";;;KAoBY,SAAA;AAAA,UAUK,YAAA;EAVL;EAYV,KAAA;;EAEA,OAAA;EAdmB;EAgBnB,GAAA;EAN2B;EAQ3B,QAAA,EAAU,OAAA;EAEK;EAAf,IAAA,EAAM,SAAA;AAAA;;UAIS,SAAA;EANL;EAQV,IAAA;EACA,OAAA;AAAA;;UAIe,UAAA;EACf,YAAA;EACA,UAAA;EACA,WAAA;AAAA;AAAA,UAGe,WAAA;EACf,KAAA,EAAO,SAAA;EACP,MAAA;EACA,QAAA;EARA;EAUA,KAAA,GAAQ,UAAA;AAAA;;;AALV;;;iBAkBgB,KAAA,CAAM,OAAA,EAAS,YAAA,GAAe,WAAA;;;;;AAvD9C;;;UCViB,cAAA;EACf,IAAA,EAAM,WAAA;EACN,QAAA,EAAU,cAAA;EDkBiB;EChB3B,QAAA;AAAA;AAAA,UAGe,cAAA;EACf,IAAA,EAAM,WAAA;EACN,IAAA,EAAM,UAAA;AAAA;AAAA,UAGS,UAAA;EDkBf;EChBA,IAAA;EDgBe;ECdf,UAAA;EACA,YAAA;AAAA;;;;ADwBF;;KC2CY,YAAA;AAAA,iBAEI,WAAA,CAAY,GAAA,WAAc,YAAA;;;;;;iBAmH1B,WAAA,CAAY,IAAA,WAAe,cAAA;;;cC9L9B,aAAA;AAAA,iBAEG,eAAA,CAAgB,KAAA;EAAoB,QAAA,EAAU,OAAA;EAAW,OAAA;AAAA;;;iBClBzD,UAAA,CAAW,KAAA,EAAO,SAAA"}
+{"version":3,"file":"index.d.mts","names":[],"sources":["../src/build.ts","../src/catalog.ts","../src/backends.ts","../src/write.ts"],"mappings":";;;KAoBY,SAAA;AAAA,UAUK,YAAA;EAVL;EAYV,KAAA;;EAEA,OAAA;EAdmB;EAgBnB,GAAA;EAN2B;EAQ3B,QAAA,EAAU,OAAA;EAEK;EAAf,IAAA,EAAM,SAAA;AAAA;;UAIS,SAAA;EANL;EAQV,IAAA;EACA,OAAA;AAAA;;UAIe,UAAA;EACf,YAAA;EACA,UAAA;EACA,WAAA;AAAA;AAAA,UAGe,WAAA;EACf,KAAA,EAAO,SAAA;EACP,MAAA;EACA,QAAA;EARA;EAUA,KAAA,GAAQ,UAAA;AAAA;;;AALV;;;iBAkBgB,KAAA,CAAM,OAAA,EAAS,YAAA,GAAe,WAAA;;;;;AAvD9C;;;UCViB,cAAA;EACf,IAAA,EAAM,WAAA;EACN,QAAA,EAAU,cAAA;EDkBiB;EChB3B,QAAA;AAAA;AAAA,UAGe,cAAA;EACf,IAAA,EAAM,WAAA;EACN,IAAA,EAAM,UAAA;AAAA;AAAA,UAGS,UAAA;EDkBf;EChBA,IAAA;EDgBe;ECdf,UAAA;EACA,YAAA;AAAA;;;;ADwBF;;KC2CY,YAAA;AAAA,iBAEI,WAAA,CAAY,GAAA,WAAc,YAAA;;;;;;iBAmH1B,WAAA,CAAY,IAAA,WAAe,cAAA;;;cC1L9B,aAAA;AAAA,iBAEG,eAAA,CAAgB,KAAA;EAAoB,QAAA,EAAU,OAAA;EAAW,OAAA;AAAA;;;iBCtBzD,UAAA,CAAW,KAAA,EAAO,SAAA"}

package/dist/index.mjs

@@ -1,3 +1,3 @@
-import { a as detectLevel, i as build, n as knownBackends, o as loadCatalog, r as resolveBackends, t as writeFiles } from "./write-BSYxLVtX.mjs";
+import { a as detectLevel, i as build, n as knownBackends, o as loadCatalog, r as resolveBackends, t as writeFiles } from "./write-DydpQpbm.mjs";
 
 export { build, detectLevel, knownBackends, loadCatalog, resolveBackends, writeFiles };

package/dist/{write-CpqGjb9N.cjs → write-B8IfXD3y.cjs}

@@ -406,7 +406,9 @@ const registry = {
 	ts: () => new _styx_api_core.TypeScriptBackend(),
 	schema: () => new _styx_api_core.JsonSchemaBackend(),
 	"json-schema": () => new _styx_api_core.JsonSchemaBackend(),
-	boutiques: () => new _styx_api_core.BoutiquesBackend()
+	boutiques: () => new _styx_api_core.BoutiquesBackend(),
+	nipype: () => new _styx_api_core.NipypeBackend(),
+	pydra: () => new _styx_api_core.PydraBackend()
 };
 const knownBackends = Object.keys(registry);
 function resolveBackends(names) {

package/dist/{write-BSYxLVtX.mjs → write-DydpQpbm.mjs}

@@ -1,6 +1,6 @@
 import { mkdirSync, readFileSync, readdirSync, statSync, writeFileSync } from "node:fs";
 import * as path from "node:path";
-import { BoutiquesBackend, JsonSchemaBackend, PythonBackend, TypeScriptBackend, compile, createContext, defaultPipeline, resolveOutputs, solve } from "@styx-api/core";
+import { BoutiquesBackend, JsonSchemaBackend, NipypeBackend, PydraBackend, PythonBackend, TypeScriptBackend, compile, createContext, defaultPipeline, resolveOutputs, solve } from "@styx-api/core";
 
 //#region src/catalog.ts
 function readJson(file) {
@@ -378,7 +378,9 @@ const registry = {
 	ts: () => new TypeScriptBackend(),
 	schema: () => new JsonSchemaBackend(),
 	"json-schema": () => new JsonSchemaBackend(),
-	boutiques: () => new BoutiquesBackend()
+	boutiques: () => new BoutiquesBackend(),
+	nipype: () => new NipypeBackend(),
+	pydra: () => new PydraBackend()
 };
 const knownBackends = Object.keys(registry);
 function resolveBackends(names) {
@@ -413,4 +415,4 @@ function writeFiles(files) {
 
 //#endregion
 export { detectLevel as a, build as i, knownBackends as n, loadCatalog as o, resolveBackends as r, writeFiles as t };
-//# sourceMappingURL=write-BSYxLVtX.mjs.map
+//# sourceMappingURL=write-DydpQpbm.mjs.map

package/dist/{write-BSYxLVtX.mjs.map → write-DydpQpbm.mjs.map}

@@ -1 +1 @@
-{"version":3,"file":"write-BSYxLVtX.mjs","names":[],"sources":["../src/catalog.ts","../src/build.ts","../src/backends.ts","../src/write.ts"],"sourcesContent":["import { readFileSync, readdirSync, statSync } from \"node:fs\";\nimport * as path from \"node:path\";\n\nimport type { Documentation, PackageMeta, ProjectMeta } from \"@styx-api/core\";\n\n/**\n * Loaded catalog: a project containing packages, each holding one or more\n * apps. We always normalize to project > package > app even when the catalog\n * root only describes a subset of the hierarchy (e.g. a single version dir).\n */\nexport interface CatalogProject {\n  meta: ProjectMeta;\n  packages: CatalogPackage[];\n  /** Non-fatal issues found while walking the catalog (e.g. skipped stub apps). */\n  warnings: string[];\n}\n\nexport interface CatalogPackage {\n  meta: PackageMeta;\n  apps: CatalogApp[];\n}\n\nexport interface CatalogApp {\n  /** Stable identifier from `app.json#name`, used for the emitted module slug. */\n  name: string;\n  /** Absolute path to the descriptor file referenced by `app.json#source`. */\n  sourcePath: string;\n  sourceFormat?: string;\n}\n\ninterface ProjectJson {\n  name?: string;\n  version?: string;\n  license?: string;\n  packages?: string[];\n  docs?: Documentation;\n}\n\ninterface PackageJson {\n  name?: string;\n  versions?: string[];\n  default?: string;\n  docs?: Documentation;\n}\n\ninterface VersionJson {\n  name?: string;\n  container?: string;\n  apps?: string[];\n  executables?: { required?: string[]; ignored?: string[] };\n}\n\ninterface AppJson {\n  name?: string;\n  source?: { type?: string; path?: string };\n  docs?: Documentation;\n}\n\nfunction readJson<T>(file: string): T {\n  let raw: string;\n  try {\n    raw = readFileSync(file, \"utf8\");\n  } catch (e) {\n    throw new Error(`${file}: ${e instanceof Error ? e.message : String(e)}`);\n  }\n  try {\n    return JSON.parse(raw) as T;\n  } catch (e) {\n    throw new Error(`${file}: invalid JSON: ${e instanceof Error ? e.message : String(e)}`);\n  }\n}\n\nfunction exists(p: string): boolean {\n  try {\n    statSync(p);\n    return true;\n  } catch {\n    return false;\n  }\n}\n\nfunction isDir(p: string): boolean {\n  try {\n    return statSync(p).isDirectory();\n  } catch {\n    return false;\n  }\n}\n\n/**\n * Detect what level of the niwrap catalog a directory describes.\n * Project dirs contain `project.json`, package dirs contain `package.json`,\n * version dirs contain `version.json`, app dirs contain `app.json`.\n */\nexport type CatalogLevel = \"project\" | \"package\" | \"version\" | \"app\";\n\nexport function detectLevel(dir: string): CatalogLevel | null {\n  if (exists(path.join(dir, \"project.json\"))) return \"project\";\n  if (exists(path.join(dir, \"package.json\"))) return \"package\";\n  if (exists(path.join(dir, \"version.json\"))) return \"version\";\n  if (exists(path.join(dir, \"app.json\"))) return \"app\";\n  return null;\n}\n\n/**\n * Load one app descriptor. When `warnings` is supplied (catalog-walk mode), a\n * stub app (`app.json` present but no `source.path`) is skipped with a warning\n * instead of aborting the whole build - real catalogs list not-yet-wrapped tools\n * alongside wrapped ones. Without `warnings` (a direct single-app target) the\n * missing source is a hard error, since the user pointed straight at it.\n */\nfunction loadApp(appDir: string, warnings?: string[]): CatalogApp | null {\n  const appJsonPath = path.join(appDir, \"app.json\");\n  if (!exists(appJsonPath)) return null;\n  const app = readJson<AppJson>(appJsonPath);\n  const name = app.name ?? path.basename(appDir);\n  const sourceRel = app.source?.path;\n  if (!sourceRel) {\n    if (warnings) {\n      warnings.push(`${appJsonPath}: skipped (no source.path - not yet wrapped)`);\n      return null;\n    }\n    throw new Error(`${appJsonPath}: missing source.path`);\n  }\n  return {\n    name,\n    sourcePath: path.resolve(appDir, sourceRel),\n    sourceFormat: app.source?.type,\n  };\n}\n\nfunction loadVersion(versionDir: string, warnings?: string[]): CatalogPackage | null {\n  const versionPath = path.join(versionDir, \"version.json\");\n  if (!exists(versionPath)) return null;\n  const version = readJson<VersionJson>(versionPath);\n\n  // Sort the directory fallback so app order (and thus any shared-scope name\n  // dodging) is deterministic regardless of filesystem iteration order.\n  const appNames = version.apps ?? listSubdirs(versionDir).sort();\n  const apps: CatalogApp[] = [];\n  for (const appName of appNames) {\n    const appDir = path.join(versionDir, appName);\n    if (!isDir(appDir)) continue;\n    const app = loadApp(appDir, warnings);\n    if (app) apps.push(app);\n  }\n\n  // Try to enrich with the parent package.json if there is one (package > version layout).\n  const parentPkg = path.join(versionDir, \"..\", \"package.json\");\n  let pkgName: string | undefined;\n  let pkgDoc: Documentation | undefined;\n  if (exists(parentPkg)) {\n    const pkg = readJson<PackageJson>(parentPkg);\n    pkgName = pkg.name;\n    pkgDoc = pkg.docs;\n  }\n  pkgName ??= path.basename(path.dirname(versionDir));\n\n  return {\n    meta: {\n      name: pkgName,\n      version: version.name,\n      docker: version.container,\n      doc: pkgDoc,\n    },\n    apps,\n  };\n}\n\nfunction loadPackage(pkgDir: string, warnings?: string[]): CatalogPackage | null {\n  const pkgPath = path.join(pkgDir, \"package.json\");\n  if (!exists(pkgPath)) return null;\n  const pkg = readJson<PackageJson>(pkgPath);\n\n  const versionName = pkg.default ?? pkg.versions?.[0] ?? firstVersionDir(pkgDir);\n  if (!versionName) return null;\n  const versionDir = path.join(pkgDir, versionName);\n  if (!isDir(versionDir)) return null;\n\n  const loaded = loadVersion(versionDir, warnings);\n  if (!loaded) return null;\n\n  return {\n    meta: {\n      name: pkg.name ?? path.basename(pkgDir),\n      version: versionName,\n      docker: loaded.meta.docker,\n      doc: pkg.docs ?? loaded.meta.doc,\n    },\n    apps: loaded.apps,\n  };\n}\n\nfunction listSubdirs(dir: string): string[] {\n  return readdirSync(dir, { withFileTypes: true })\n    .filter((e) => e.isDirectory())\n    .map((e) => e.name);\n}\n\nfunction firstVersionDir(pkgDir: string): string | null {\n  for (const name of listSubdirs(pkgDir)) {\n    if (exists(path.join(pkgDir, name, \"version.json\"))) return name;\n  }\n  return null;\n}\n\n/**\n * Load a catalog from any niwrap layout level. The level is auto-detected from\n * which `*.json` index file is present in `root`. Always returns a normalized\n * `project > package > app` shape, synthesizing missing layers as needed.\n */\nexport function loadCatalog(root: string): CatalogProject {\n  const level = detectLevel(root);\n  if (!level) {\n    throw new Error(\n      `${root}: no project.json / package.json / version.json / app.json found - not a catalog root`,\n    );\n  }\n\n  const warnings: string[] = [];\n\n  if (level === \"project\") {\n    const project = readJson<ProjectJson>(path.join(root, \"project.json\"));\n    const packageNames = project.packages ?? listSubdirs(root);\n    const packages: CatalogPackage[] = [];\n    for (const name of packageNames) {\n      const pkgDir = path.join(root, name);\n      const pkg = loadPackage(pkgDir, warnings);\n      if (pkg) packages.push(pkg);\n    }\n    return {\n      meta: {\n        name: project.name,\n        version: project.version,\n        doc: project.docs,\n        license: project.license ? { description: project.license } : undefined,\n      },\n      packages,\n      warnings,\n    };\n  }\n\n  if (level === \"package\") {\n    const pkg = loadPackage(root, warnings);\n    if (!pkg) throw new Error(`${root}: package.json present but no resolvable version`);\n    return { meta: { name: pkg.meta.name }, packages: [pkg], warnings };\n  }\n\n  if (level === \"version\") {\n    const pkg = loadVersion(root, warnings);\n    if (!pkg) throw new Error(`${root}: version.json present but failed to load`);\n    return { meta: { name: pkg.meta.name }, packages: [pkg], warnings };\n  }\n\n  // level === \"app\": a direct single-app target, so a missing source is fatal.\n  const app = loadApp(root);\n  if (!app) throw new Error(`${root}: app.json present but missing source.path`);\n  return {\n    meta: {},\n    packages: [\n      {\n        meta: { name: path.basename(path.dirname(root)) },\n        apps: [app],\n      },\n    ],\n    warnings,\n  };\n}\n","import { readFileSync } from \"node:fs\";\nimport * as path from \"node:path\";\n\nimport {\n  compile,\n  createContext,\n  defaultPipeline,\n  resolveOutputs,\n  solve,\n  type Backend,\n  type EmitResult,\n  type EmittedApp,\n  type EmittedPackage,\n  type FormatName,\n  type PackageMeta,\n  type ProjectMeta,\n} from \"@styx-api/core\";\n\nimport { loadCatalog, type CatalogProject } from \"./catalog.js\";\n\nexport type BuildMode = \"scripts\" | \"single\" | \"multi\";\n\n/** Frontend formats the compiler can parse; others are skipped with a warning. */\nconst SUPPORTED_FORMATS: ReadonlySet<string> = new Set<FormatName>([\n  \"boutiques\",\n  \"argdump\",\n  \"workbench\",\n  \"mrtrix\",\n]);\n\nexport interface BuildOptions {\n  /** Single-descriptor input file (mutually exclusive with `catalog`). */\n  input?: string;\n  /** Catalog directory (mutually exclusive with `input`). */\n  catalog?: string;\n  /** Output directory; per-backend files end up under `<out>/<backend.target>/...`. */\n  out: string;\n  /** Backends to run (instances pre-resolved by the caller). */\n  backends: Backend[];\n  /** Which emit tiers to run. */\n  mode: BuildMode;\n}\n\n/** A single file from a backend run, keyed by destination path. */\nexport interface BuiltFile {\n  /** Absolute destination path. */\n  path: string;\n  content: string;\n}\n\n/** Per-tool tallies for a catalog build (undefined for single-descriptor builds). */\nexport interface BuildStats {\n  appsCompiled: number;\n  appsFailed: number;\n  appsSkipped: number;\n}\n\nexport interface BuildResult {\n  files: BuiltFile[];\n  errors: string[];\n  warnings: string[];\n  /** Catalog-build tallies; set only by `--catalog` builds. */\n  stats?: BuildStats;\n}\n\n/** Render an unknown thrown value as a message string. */\nfunction errMsg(e: unknown): string {\n  return e instanceof Error ? e.message : String(e);\n}\n\n/**\n * Run the build. Returns the assembled file map and diagnostics; the caller\n * is responsible for actually writing to disk (so tests can introspect the\n * map directly).\n */\nexport function build(options: BuildOptions): BuildResult {\n  if (options.input && options.catalog) {\n    return { files: [], errors: [\"--input and --catalog are mutually exclusive\"], warnings: [] };\n  }\n  if (!options.input && !options.catalog) {\n    return {\n      files: [],\n      errors: [\"missing input: pass a descriptor path or --catalog\"],\n      warnings: [],\n    };\n  }\n\n  if (options.input) return buildSingle(options.input, options);\n  return buildCatalog(options.catalog!, options);\n}\n\nfunction buildSingle(inputPath: string, options: BuildOptions): BuildResult {\n  const result: BuildResult = { files: [], errors: [], warnings: [] };\n\n  const ctx = readAndCompile(inputPath, undefined, undefined, undefined, result);\n  if (!ctx) return result;\n\n  for (const backend of options.backends) {\n    let emitted;\n    try {\n      emitted = backend.emitApp(ctx);\n    } catch (e) {\n      result.errors.push(`[${backend.name}] ${errMsg(e)}`);\n      continue;\n    }\n    appendEmitMessages(result, emitted, backend);\n    for (const [name, content] of emitted.files) {\n      result.files.push({\n        path: path.resolve(options.out, backend.target, name),\n        content,\n      });\n    }\n  }\n  return result;\n}\n\nfunction buildCatalog(catalogPath: string, options: BuildOptions): BuildResult {\n  const result: BuildResult = {\n    files: [],\n    errors: [],\n    warnings: [],\n    stats: { appsCompiled: 0, appsFailed: 0, appsSkipped: 0 },\n  };\n  let catalog: CatalogProject;\n  try {\n    catalog = loadCatalog(catalogPath);\n  } catch (e) {\n    result.errors.push(e instanceof Error ? e.message : String(e));\n    return result;\n  }\n  result.warnings.push(...catalog.warnings);\n\n  // Skip/empty warnings are backend-independent, so only the first backend pass\n  // records them - otherwise they'd be duplicated once per backend.\n  options.backends.forEach((backend, i) => {\n    runBackendOverCatalog(backend, catalog, options.mode, options.out, result, i === 0);\n  });\n  return result;\n}\n\n/**\n * Parse a descriptor, run the default optimization pipeline, solve to\n * bindings, and build a `CodegenContext` wired up with the supplied\n * package/project meta. Returns null on read failure (with the error already\n * appended to `result`). Parse-level errors/warnings are also appended.\n */\nfunction readAndCompile(\n  sourcePath: string,\n  format: string | undefined,\n  pkg: PackageMeta | undefined,\n  proj: ProjectMeta | undefined,\n  result: BuildResult,\n): ReturnType<typeof createContext> | null {\n  let source: string;\n  try {\n    source = readFileSync(sourcePath, \"utf8\");\n  } catch (e) {\n    result.errors.push(`${sourcePath}: ${errMsg(e)}`);\n    return null;\n  }\n\n  // Isolate the compile pipeline: a single descriptor that makes the solver or\n  // a downstream pass throw is recorded as an error and skipped, so one bad tool\n  // can't crash a whole-catalog build.\n  try {\n    // Honor the catalog's declared format when it's one we support, so we don't\n    // fall back to content sniffing (and get a clearer error if it mis-parses).\n    const parsed = compile(\n      source,\n      format && SUPPORTED_FORMATS.has(format)\n        ? { filename: sourcePath, format: format as FormatName }\n        : sourcePath,\n    );\n    for (const e of parsed.errors) result.errors.push(`${sourcePath}: ${e.message}`);\n    for (const w of parsed.warnings) result.warnings.push(`${sourcePath}: ${w.message}`);\n\n    const piped = defaultPipeline.apply(parsed.expr);\n    if (piped.warnings) {\n      for (const w of piped.warnings) result.warnings.push(`${sourcePath}: ${w}`);\n    }\n\n    const solveResult = solve(piped.expr);\n    const outputs = resolveOutputs(piped.expr, solveResult);\n    return createContext(piped.expr, solveResult, outputs, {\n      app: parsed.meta,\n      package: pkg,\n      project: proj,\n    });\n  } catch (e) {\n    result.errors.push(`${sourcePath}: ${errMsg(e)}`);\n    return null;\n  }\n}\n\nfunction runBackendOverCatalog(\n  backend: Backend,\n  catalog: CatalogProject,\n  mode: BuildMode,\n  outRoot: string,\n  result: BuildResult,\n  recordWarnings: boolean,\n): void {\n  const backendRoot = path.resolve(outRoot, backend.target);\n  const packagesEmitted: EmittedPackage[] = [];\n\n  for (const pkg of catalog.packages) {\n    const pkgDir = pkg.meta.name ?? 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We always normalize to project > package > app even when the catalog\n * root only describes a subset of the hierarchy (e.g. a single version dir).\n */\nexport interface CatalogProject {\n  meta: ProjectMeta;\n  packages: CatalogPackage[];\n  /** Non-fatal issues found while walking the catalog (e.g. skipped stub apps). */\n  warnings: string[];\n}\n\nexport interface CatalogPackage {\n  meta: PackageMeta;\n  apps: CatalogApp[];\n}\n\nexport interface CatalogApp {\n  /** Stable identifier from `app.json#name`, used for the emitted module slug. */\n  name: string;\n  /** Absolute path to the descriptor file referenced by `app.json#source`. */\n  sourcePath: string;\n  sourceFormat?: string;\n}\n\ninterface ProjectJson {\n  name?: string;\n  version?: string;\n  license?: string;\n  packages?: string[];\n  docs?: Documentation;\n}\n\ninterface PackageJson {\n  name?: string;\n  versions?: string[];\n  default?: string;\n  docs?: Documentation;\n}\n\ninterface VersionJson {\n  name?: string;\n  container?: string;\n  apps?: string[];\n  executables?: { required?: string[]; ignored?: string[] };\n}\n\ninterface AppJson {\n  name?: string;\n  source?: { type?: string; path?: string };\n  docs?: Documentation;\n}\n\nfunction readJson<T>(file: string): T {\n  let raw: string;\n  try {\n    raw = readFileSync(file, \"utf8\");\n  } catch (e) {\n    throw new Error(`${file}: ${e instanceof Error ? e.message : String(e)}`);\n  }\n  try {\n    return JSON.parse(raw) as T;\n  } catch (e) {\n    throw new Error(`${file}: invalid JSON: ${e instanceof Error ? e.message : String(e)}`);\n  }\n}\n\nfunction exists(p: string): boolean {\n  try {\n    statSync(p);\n    return true;\n  } catch {\n    return false;\n  }\n}\n\nfunction isDir(p: string): boolean {\n  try {\n    return statSync(p).isDirectory();\n  } catch {\n    return false;\n  }\n}\n\n/**\n * Detect what level of the niwrap catalog a directory describes.\n * Project dirs contain `project.json`, package dirs contain `package.json`,\n * version dirs contain `version.json`, app dirs contain `app.json`.\n */\nexport type CatalogLevel = \"project\" | \"package\" | \"version\" | \"app\";\n\nexport function detectLevel(dir: string): CatalogLevel | null {\n  if (exists(path.join(dir, \"project.json\"))) return \"project\";\n  if (exists(path.join(dir, \"package.json\"))) return \"package\";\n  if (exists(path.join(dir, \"version.json\"))) return \"version\";\n  if (exists(path.join(dir, \"app.json\"))) return \"app\";\n  return null;\n}\n\n/**\n * Load one app descriptor. When `warnings` is supplied (catalog-walk mode), a\n * stub app (`app.json` present but no `source.path`) is skipped with a warning\n * instead of aborting the whole build - real catalogs list not-yet-wrapped tools\n * alongside wrapped ones. Without `warnings` (a direct single-app target) the\n * missing source is a hard error, since the user pointed straight at it.\n */\nfunction loadApp(appDir: string, warnings?: string[]): CatalogApp | null {\n  const appJsonPath = path.join(appDir, \"app.json\");\n  if (!exists(appJsonPath)) return null;\n  const app = readJson<AppJson>(appJsonPath);\n  const name = app.name ?? path.basename(appDir);\n  const sourceRel = app.source?.path;\n  if (!sourceRel) {\n    if (warnings) {\n      warnings.push(`${appJsonPath}: skipped (no source.path - not yet wrapped)`);\n      return null;\n    }\n    throw new Error(`${appJsonPath}: missing source.path`);\n  }\n  return {\n    name,\n    sourcePath: path.resolve(appDir, sourceRel),\n    sourceFormat: app.source?.type,\n  };\n}\n\nfunction loadVersion(versionDir: string, warnings?: string[]): CatalogPackage | null {\n  const versionPath = path.join(versionDir, \"version.json\");\n  if (!exists(versionPath)) return null;\n  const version = readJson<VersionJson>(versionPath);\n\n  // Sort the directory fallback so app order (and thus any shared-scope name\n  // dodging) is deterministic regardless of filesystem iteration order.\n  const appNames = version.apps ?? listSubdirs(versionDir).sort();\n  const apps: CatalogApp[] = [];\n  for (const appName of appNames) {\n    const appDir = path.join(versionDir, appName);\n    if (!isDir(appDir)) continue;\n    const app = loadApp(appDir, warnings);\n    if (app) apps.push(app);\n  }\n\n  // Try to enrich with the parent package.json if there is one (package > version layout).\n  const parentPkg = path.join(versionDir, \"..\", \"package.json\");\n  let pkgName: string | undefined;\n  let pkgDoc: Documentation | undefined;\n  if (exists(parentPkg)) {\n    const pkg = readJson<PackageJson>(parentPkg);\n    pkgName = pkg.name;\n    pkgDoc = pkg.docs;\n  }\n  pkgName ??= path.basename(path.dirname(versionDir));\n\n  return {\n    meta: {\n      name: pkgName,\n      version: version.name,\n      docker: version.container,\n      doc: pkgDoc,\n    },\n    apps,\n  };\n}\n\nfunction loadPackage(pkgDir: string, warnings?: string[]): CatalogPackage | null {\n  const pkgPath = path.join(pkgDir, \"package.json\");\n  if (!exists(pkgPath)) return null;\n  const pkg = readJson<PackageJson>(pkgPath);\n\n  const versionName = pkg.default ?? pkg.versions?.[0] ?? firstVersionDir(pkgDir);\n  if (!versionName) return null;\n  const versionDir = path.join(pkgDir, versionName);\n  if (!isDir(versionDir)) return null;\n\n  const loaded = loadVersion(versionDir, warnings);\n  if (!loaded) return null;\n\n  return {\n    meta: {\n      name: pkg.name ?? path.basename(pkgDir),\n      version: versionName,\n      docker: loaded.meta.docker,\n      doc: pkg.docs ?? loaded.meta.doc,\n    },\n    apps: loaded.apps,\n  };\n}\n\nfunction listSubdirs(dir: string): string[] {\n  return readdirSync(dir, { withFileTypes: true })\n    .filter((e) => e.isDirectory())\n    .map((e) => e.name);\n}\n\nfunction firstVersionDir(pkgDir: string): string | null {\n  for (const name of listSubdirs(pkgDir)) {\n    if (exists(path.join(pkgDir, name, \"version.json\"))) return name;\n  }\n  return null;\n}\n\n/**\n * Load a catalog from any niwrap layout level. The level is auto-detected from\n * which `*.json` index file is present in `root`. Always returns a normalized\n * `project > package > app` shape, synthesizing missing layers as needed.\n */\nexport function loadCatalog(root: string): CatalogProject {\n  const level = detectLevel(root);\n  if (!level) {\n    throw new Error(\n      `${root}: no project.json / package.json / version.json / app.json found - not a catalog root`,\n    );\n  }\n\n  const warnings: string[] = [];\n\n  if (level === \"project\") {\n    const project = readJson<ProjectJson>(path.join(root, \"project.json\"));\n    const packageNames = project.packages ?? listSubdirs(root);\n    const packages: CatalogPackage[] = [];\n    for (const name of packageNames) {\n      const pkgDir = path.join(root, name);\n      const pkg = loadPackage(pkgDir, warnings);\n      if (pkg) packages.push(pkg);\n    }\n    return {\n      meta: {\n        name: project.name,\n        version: project.version,\n        doc: project.docs,\n        license: project.license ? { description: project.license } : undefined,\n      },\n      packages,\n      warnings,\n    };\n  }\n\n  if (level === \"package\") {\n    const pkg = loadPackage(root, warnings);\n    if (!pkg) throw new Error(`${root}: package.json present but no resolvable version`);\n    return { meta: { name: pkg.meta.name }, packages: [pkg], warnings };\n  }\n\n  if (level === \"version\") {\n    const pkg = loadVersion(root, warnings);\n    if (!pkg) throw new Error(`${root}: version.json present but failed to load`);\n    return { meta: { name: pkg.meta.name }, packages: [pkg], warnings };\n  }\n\n  // level === \"app\": a direct single-app target, so a missing source is fatal.\n  const app = loadApp(root);\n  if (!app) throw new Error(`${root}: app.json present but missing source.path`);\n  return {\n    meta: {},\n    packages: [\n      {\n        meta: { name: path.basename(path.dirname(root)) },\n        apps: [app],\n      },\n    ],\n    warnings,\n  };\n}\n","import { readFileSync } from \"node:fs\";\nimport * as path from \"node:path\";\n\nimport {\n  compile,\n  createContext,\n  defaultPipeline,\n  resolveOutputs,\n  solve,\n  type Backend,\n  type EmitResult,\n  type EmittedApp,\n  type EmittedPackage,\n  type FormatName,\n  type PackageMeta,\n  type ProjectMeta,\n} from \"@styx-api/core\";\n\nimport { loadCatalog, type CatalogProject } from \"./catalog.js\";\n\nexport type BuildMode = \"scripts\" | \"single\" | \"multi\";\n\n/** Frontend formats the compiler can parse; others are skipped with a warning. */\nconst SUPPORTED_FORMATS: ReadonlySet<string> = new Set<FormatName>([\n  \"boutiques\",\n  \"argdump\",\n  \"workbench\",\n  \"mrtrix\",\n]);\n\nexport interface BuildOptions {\n  /** Single-descriptor input file (mutually exclusive with `catalog`). */\n  input?: string;\n  /** Catalog directory (mutually exclusive with `input`). */\n  catalog?: string;\n  /** Output directory; per-backend files end up under `<out>/<backend.target>/...`. */\n  out: string;\n  /** Backends to run (instances pre-resolved by the caller). */\n  backends: Backend[];\n  /** Which emit tiers to run. */\n  mode: BuildMode;\n}\n\n/** A single file from a backend run, keyed by destination path. */\nexport interface BuiltFile {\n  /** Absolute destination path. */\n  path: string;\n  content: string;\n}\n\n/** Per-tool tallies for a catalog build (undefined for single-descriptor builds). */\nexport interface BuildStats {\n  appsCompiled: number;\n  appsFailed: number;\n  appsSkipped: number;\n}\n\nexport interface BuildResult {\n  files: BuiltFile[];\n  errors: string[];\n  warnings: string[];\n  /** Catalog-build tallies; set only by `--catalog` builds. */\n  stats?: BuildStats;\n}\n\n/** Render an unknown thrown value as a message string. */\nfunction errMsg(e: unknown): string {\n  return e instanceof Error ? e.message : String(e);\n}\n\n/**\n * Run the build. Returns the assembled file map and diagnostics; the caller\n * is responsible for actually writing to disk (so tests can introspect the\n * map directly).\n */\nexport function build(options: BuildOptions): BuildResult {\n  if (options.input && options.catalog) {\n    return { files: [], errors: [\"--input and --catalog are mutually exclusive\"], warnings: [] };\n  }\n  if (!options.input && !options.catalog) {\n    return {\n      files: [],\n      errors: [\"missing input: pass a descriptor path or --catalog\"],\n      warnings: [],\n    };\n  }\n\n  if (options.input) return buildSingle(options.input, options);\n  return buildCatalog(options.catalog!, options);\n}\n\nfunction buildSingle(inputPath: string, options: BuildOptions): BuildResult {\n  const result: BuildResult = { files: [], errors: [], warnings: [] };\n\n  const ctx = readAndCompile(inputPath, undefined, undefined, undefined, result);\n  if (!ctx) return result;\n\n  for (const backend of options.backends) {\n    let emitted;\n    try {\n      emitted = backend.emitApp(ctx);\n    } catch (e) {\n      result.errors.push(`[${backend.name}] ${errMsg(e)}`);\n      continue;\n    }\n    appendEmitMessages(result, emitted, backend);\n    for (const [name, content] of emitted.files) {\n      result.files.push({\n        path: path.resolve(options.out, backend.target, name),\n        content,\n      });\n    }\n  }\n  return result;\n}\n\nfunction buildCatalog(catalogPath: string, options: BuildOptions): BuildResult {\n  const result: BuildResult = {\n    files: [],\n    errors: [],\n    warnings: [],\n    stats: { appsCompiled: 0, appsFailed: 0, appsSkipped: 0 },\n  };\n  let catalog: CatalogProject;\n  try {\n    catalog = loadCatalog(catalogPath);\n  } catch (e) {\n    result.errors.push(e instanceof Error ? e.message : String(e));\n    return result;\n  }\n  result.warnings.push(...catalog.warnings);\n\n  // Skip/empty warnings are backend-independent, so only the first backend pass\n  // records them - otherwise they'd be duplicated once per backend.\n  options.backends.forEach((backend, i) => {\n    runBackendOverCatalog(backend, catalog, options.mode, options.out, result, i === 0);\n  });\n  return result;\n}\n\n/**\n * Parse a descriptor, run the default optimization pipeline, solve to\n * bindings, and build a `CodegenContext` wired up with the supplied\n * package/project meta. Returns null on read failure (with the error already\n * appended to `result`). Parse-level errors/warnings are also appended.\n */\nfunction readAndCompile(\n  sourcePath: string,\n  format: string | undefined,\n  pkg: PackageMeta | undefined,\n  proj: ProjectMeta | undefined,\n  result: BuildResult,\n): ReturnType<typeof createContext> | null {\n  let source: string;\n  try {\n    source = readFileSync(sourcePath, \"utf8\");\n  } catch (e) {\n    result.errors.push(`${sourcePath}: ${errMsg(e)}`);\n    return null;\n  }\n\n  // Isolate the compile pipeline: a single descriptor that makes the solver or\n  // a downstream pass throw is recorded as an error and skipped, so one bad tool\n  // can't crash a whole-catalog build.\n  try {\n    // Honor the catalog's declared format when it's one we support, so we don't\n    // fall back to content sniffing (and get a clearer error if it mis-parses).\n    const parsed = compile(\n      source,\n      format && SUPPORTED_FORMATS.has(format)\n        ? { filename: sourcePath, format: format as FormatName }\n        : sourcePath,\n    );\n    for (const e of parsed.errors) result.errors.push(`${sourcePath}: ${e.message}`);\n    for (const w of parsed.warnings) result.warnings.push(`${sourcePath}: ${w.message}`);\n\n    const piped = defaultPipeline.apply(parsed.expr);\n    if (piped.warnings) {\n      for (const w of piped.warnings) result.warnings.push(`${sourcePath}: ${w}`);\n    }\n\n    const solveResult = solve(piped.expr);\n    const outputs = resolveOutputs(piped.expr, solveResult);\n    return createContext(piped.expr, solveResult, outputs, {\n      app: parsed.meta,\n      package: pkg,\n      project: proj,\n    });\n  } catch (e) {\n    result.errors.push(`${sourcePath}: ${errMsg(e)}`);\n    return null;\n  }\n}\n\nfunction runBackendOverCatalog(\n  backend: Backend,\n  catalog: CatalogProject,\n  mode: BuildMode,\n  outRoot: string,\n  result: BuildResult,\n  recordWarnings: boolean,\n): void {\n  const backendRoot = path.resolve(outRoot, backend.target);\n  const packagesEmitted: EmittedPackage[] = [];\n\n  for (const pkg of catalog.packages) {\n    const pkgDir = pkg.meta.name ?? \"package\";\n    const appsEmitted: EmittedApp[] = [];\n    let skipped = 0;\n    // One scope shared across every tool in the suite so top-level names stay\n    // unique across the package's flat barrel re-exports.\n    const pkgScope = backend.newPackageScope?.();\n\n    for (const app of pkg.apps) {\n      // A tool can declare a format we have no frontend for yet (e.g. Workbench).\n      // Skip it with a warning rather than failing the whole catalog build.\n      if (app.sourceFormat && !SUPPORTED_FORMATS.has(app.sourceFormat)) {\n        skipped++;\n        if (recordWarnings) {\n          if (result.stats) result.stats.appsSkipped++;\n          result.warnings.push(\n            `${app.sourcePath}: skipped (unsupported source format \"${app.sourceFormat}\")`,\n          );\n        }\n        continue;\n      }\n\n      const ctx = readAndCompile(app.sourcePath, app.sourceFormat, pkg.meta, catalog.meta, result);\n      if (!ctx) {\n        if (recordWarnings && result.stats) result.stats.appsFailed++;\n        continue;\n      }\n\n      // Isolate emit so one tool that makes a backend throw doesn't crash the run.\n      let emitted: EmittedApp;\n      try {\n        emitted = backend.emitApp(ctx, pkgScope);\n      } catch (e) {\n        result.errors.push(`[${backend.name} ${pkg.meta.name}/${app.name}] ${errMsg(e)}`);\n        if (recordWarnings && result.stats) result.stats.appsFailed++;\n        continue;\n      }\n      appendEmitMessages(result, emitted, backend, `${pkg.meta.name}/${app.name}`);\n      appsEmitted.push(emitted);\n      if (recordWarnings && result.stats) result.stats.appsCompiled++;\n\n      for (const [name, content] of emitted.files) {\n        result.files.push({ path: path.join(backendRoot, pkgDir, name), content });\n      }\n    }\n\n    // A suite whose every tool was skipped (e.g. all-Workbench) emits nothing;\n    // don't synthesize an empty package or wire it into the project metadata.\n    // Only warn when emptiness is due to skips - genuine failures already errored.\n    if (appsEmitted.length === 0) {\n      if (recordWarnings && skipped > 0 && skipped === pkg.apps.length) {\n        result.warnings.push(`${pkgDir}: all ${skipped} tool(s) skipped, package omitted`);\n      }\n      continue;\n    }\n\n    if (mode !== \"scripts\" && backend.emitPackage) {\n      try {\n        const pkgEmit = backend.emitPackage(pkg.meta, appsEmitted);\n        appendEmitMessages(result, pkgEmit, backend, pkg.meta.name);\n        packagesEmitted.push(pkgEmit);\n        for (const [name, content] of pkgEmit.files) {\n          result.files.push({ path: path.join(backendRoot, pkgDir, name), content });\n        }\n      } catch (e) {\n        result.errors.push(`[${backend.name} ${pkgDir}] package emit failed: ${errMsg(e)}`);\n      }\n    }\n  }\n\n  if (mode === \"multi\" && backend.emitProject && packagesEmitted.length > 0) {\n    try {\n      const projEmit = backend.emitProject(catalog.meta, packagesEmitted);\n      appendEmitMessages(result, projEmit, backend, catalog.meta.name);\n      for (const [name, content] of projEmit.files) {\n        result.files.push({ path: path.join(backendRoot, name), content });\n      }\n    } catch (e) {\n      result.errors.push(`[${backend.name}] project emit failed: ${errMsg(e)}`);\n    }\n  }\n}\n\nfunction appendEmitMessages(\n  result: BuildResult,\n  emit: EmitResult,\n  backend: Backend,\n  scope?: string,\n): void {\n  const tag = scope ? `[${backend.name} ${scope}]` : `[${backend.name}]`;\n  for (const e of emit.errors) result.errors.push(`${tag} ${e.message}`);\n  for (const w of emit.warnings) result.warnings.push(`${tag} ${w.message}`);\n}\n","import {\n  BoutiquesBackend,\n  JsonSchemaBackend,\n  NipypeBackend,\n  PydraBackend,\n  PythonBackend,\n  TypeScriptBackend,\n  type Backend,\n} from \"@styx-api/core\";\n\n/**\n * Registry of backends keyed by CLI alias. The alias is what users pass to\n * `-b`; the backend's `name`/`target` is what we use for the output subdir.\n */\nconst registry: Record<string, () => Backend> = {\n  python: () => new PythonBackend(),\n  typescript: () => new TypeScriptBackend(),\n  ts: () => new TypeScriptBackend(),\n  schema: () => new JsonSchemaBackend(),\n  \"json-schema\": () => new JsonSchemaBackend(),\n  boutiques: () => new BoutiquesBackend(),\n  nipype: () => new NipypeBackend(),\n  pydra: () => new PydraBackend(),\n};\n\nexport const knownBackends = Object.keys(registry);\n\nexport function resolveBackends(names: string[]): { backends: Backend[]; unknown: string[] } {\n  const backends: Backend[] = [];\n  const seen = new Set<string>();\n  const unknown: string[] = [];\n  for (const name of names) {\n    const factory = registry[name];\n    if (!factory) {\n      unknown.push(name);\n      continue;\n    }\n    const backend = factory();\n    if (seen.has(backend.name)) continue;\n    seen.add(backend.name);\n    backends.push(backend);\n  }\n  return { backends, unknown };\n}\n","import { mkdirSync, writeFileSync } from \"node:fs\";\nimport * as path from \"node:path\";\n\nimport type { BuiltFile } from \"./build.js\";\n\nexport function writeFiles(files: BuiltFile[]): void {\n  for (const file of files) {\n    mkdirSync(path.dirname(file.path), { recursive: true });\n    writeFileSync(file.path, file.content, \"utf8\");\n  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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@styx-api/cli",
-  "version": "0.3.0",
+  "version": "0.5.0",
   "description": "Command-line interface for the Styx compiler (@styx-api/core): build typed wrappers from CLI tool descriptors and catalogs.",
   "keywords": [
     "styx",
@@ -49,7 +49,7 @@
     "prepublishOnly": "tsdown"
   },
   "dependencies": {
-    "@styx-api/core": "0.3.0",
+    "@styx-api/core": "0.5.0",
     "cac": "^6.7.14"
   },
   "devDependencies": {

package/src/backends.ts

@@ -1,6 +1,8 @@
 import {
   BoutiquesBackend,
   JsonSchemaBackend,
+  NipypeBackend,
+  PydraBackend,
   PythonBackend,
   TypeScriptBackend,
   type Backend,
@@ -17,6 +19,8 @@ const registry: Record<string, () => Backend> = {
   schema: () => new JsonSchemaBackend(),
   "json-schema": () => new JsonSchemaBackend(),
   boutiques: () => new BoutiquesBackend(),
+  nipype: () => new NipypeBackend(),
+  pydra: () => new PydraBackend(),
 };
 
 export const knownBackends = Object.keys(registry);