@seqyuan/annovibe 0.8.21 → 0.8.22

package/.next/types/app/api/subagents/status/route.ts

@@ -0,0 +1,351 @@
+// File: /home/runner/work/annovibe/annovibe/app/api/subagents/status/route.ts
+import * as entry from '../../../../../../app/api/subagents/status/route.js'
+import type { NextRequest } from 'next/server.js'
+
+import type { InstantConfigForTypeCheckInternal } from 'next/dist/build/segment-config/app/app-segment-config.js'
+
+type TEntry = typeof import('../../../../../../app/api/subagents/status/route.js')
+
+type SegmentParams<T extends Object = any> = T extends Record<string, any>
+  ? { [K in keyof T]: T[K] extends string ? string | string[] | undefined : never }
+  : T
+
+// Check that the entry is a valid entry
+checkFields<Diff<{
+  GET?: Function
+  HEAD?: Function
+  OPTIONS?: Function
+  POST?: Function
+  PUT?: Function
+  DELETE?: Function
+  PATCH?: Function
+  config?: {}
+  generateStaticParams?: Function
+  unstable_instant?: InstantConfigForTypeCheckInternal
+  unstable_dynamicStaleTime?: number
+  revalidate?: RevalidateRange<TEntry> | false
+  dynamic?: 'auto' | 'force-dynamic' | 'error' | 'force-static'
+  dynamicParams?: boolean
+  fetchCache?: 'auto' | 'force-no-store' | 'only-no-store' | 'default-no-store' | 'default-cache' | 'only-cache' | 'force-cache'
+  preferredRegion?: 'auto' | 'global' | 'home' | string | string[]
+  runtime?: 'nodejs' | 'experimental-edge' | 'edge'
+  maxDuration?: number
+  
+}, TEntry, ''>>()
+
+type RouteContext = { params: Promise<SegmentParams> }
+// Check the prop type of the entry function
+if ('GET' in entry) {
+  checkFields<
+    Diff<
+      ParamCheck<Request | NextRequest>,
+      {
+        __tag__: 'GET'
+        __param_position__: 'first'
+        __param_type__: FirstArg<MaybeField<TEntry, 'GET'>>
+      },
+      'GET'
+    >
+  >()
+  checkFields<
+    Diff<
+      ParamCheck<RouteContext>,
+      {
+        __tag__: 'GET'
+        __param_position__: 'second'
+        __param_type__: SecondArg<MaybeField<TEntry, 'GET'>>
+      },
+      'GET'
+    >
+  >()
+  
+  checkFields<
+    Diff<
+      {
+        __tag__: 'GET',
+        __return_type__: Response | void | never | Promise<Response | void | never>
+      },
+      {
+        __tag__: 'GET',
+        __return_type__: ReturnType<MaybeField<TEntry, 'GET'>>
+      },
+      'GET'
+    >
+  >()
+}
+// Check the prop type of the entry function
+if ('HEAD' in entry) {
+  checkFields<
+    Diff<
+      ParamCheck<Request | NextRequest>,
+      {
+        __tag__: 'HEAD'
+        __param_position__: 'first'
+        __param_type__: FirstArg<MaybeField<TEntry, 'HEAD'>>
+      },
+      'HEAD'
+    >
+  >()
+  checkFields<
+    Diff<
+      ParamCheck<RouteContext>,
+      {
+        __tag__: 'HEAD'
+        __param_position__: 'second'
+        __param_type__: SecondArg<MaybeField<TEntry, 'HEAD'>>
+      },
+      'HEAD'
+    >
+  >()
+  
+  checkFields<
+    Diff<
+      {
+        __tag__: 'HEAD',
+        __return_type__: Response | void | never | Promise<Response | void | never>
+      },
+      {
+        __tag__: 'HEAD',
+        __return_type__: ReturnType<MaybeField<TEntry, 'HEAD'>>
+      },
+      'HEAD'
+    >
+  >()
+}
+// Check the prop type of the entry function
+if ('OPTIONS' in entry) {
+  checkFields<
+    Diff<
+      ParamCheck<Request | NextRequest>,
+      {
+        __tag__: 'OPTIONS'
+        __param_position__: 'first'
+        __param_type__: FirstArg<MaybeField<TEntry, 'OPTIONS'>>
+      },
+      'OPTIONS'
+    >
+  >()
+  checkFields<
+    Diff<
+      ParamCheck<RouteContext>,
+      {
+        __tag__: 'OPTIONS'
+        __param_position__: 'second'
+        __param_type__: SecondArg<MaybeField<TEntry, 'OPTIONS'>>
+      },
+      'OPTIONS'
+    >
+  >()
+  
+  checkFields<
+    Diff<
+      {
+        __tag__: 'OPTIONS',
+        __return_type__: Response | void | never | Promise<Response | void | never>
+      },
+      {
+        __tag__: 'OPTIONS',
+        __return_type__: ReturnType<MaybeField<TEntry, 'OPTIONS'>>
+      },
+      'OPTIONS'
+    >
+  >()
+}
+// Check the prop type of the entry function
+if ('POST' in entry) {
+  checkFields<
+    Diff<
+      ParamCheck<Request | NextRequest>,
+      {
+        __tag__: 'POST'
+        __param_position__: 'first'
+        __param_type__: FirstArg<MaybeField<TEntry, 'POST'>>
+      },
+      'POST'
+    >
+  >()
+  checkFields<
+    Diff<
+      ParamCheck<RouteContext>,
+      {
+        __tag__: 'POST'
+        __param_position__: 'second'
+        __param_type__: SecondArg<MaybeField<TEntry, 'POST'>>
+      },
+      'POST'
+    >
+  >()
+  
+  checkFields<
+    Diff<
+      {
+        __tag__: 'POST',
+        __return_type__: Response | void | never | Promise<Response | void | never>
+      },
+      {
+        __tag__: 'POST',
+        __return_type__: ReturnType<MaybeField<TEntry, 'POST'>>
+      },
+      'POST'
+    >
+  >()
+}
+// Check the prop type of the entry function
+if ('PUT' in entry) {
+  checkFields<
+    Diff<
+      ParamCheck<Request | NextRequest>,
+      {
+        __tag__: 'PUT'
+        __param_position__: 'first'
+        __param_type__: FirstArg<MaybeField<TEntry, 'PUT'>>
+      },
+      'PUT'
+    >
+  >()
+  checkFields<
+    Diff<
+      ParamCheck<RouteContext>,
+      {
+        __tag__: 'PUT'
+        __param_position__: 'second'
+        __param_type__: SecondArg<MaybeField<TEntry, 'PUT'>>
+      },
+      'PUT'
+    >
+  >()
+  
+  checkFields<
+    Diff<
+      {
+        __tag__: 'PUT',
+        __return_type__: Response | void | never | Promise<Response | void | never>
+      },
+      {
+        __tag__: 'PUT',
+        __return_type__: ReturnType<MaybeField<TEntry, 'PUT'>>
+      },
+      'PUT'
+    >
+  >()
+}
+// Check the prop type of the entry function
+if ('DELETE' in entry) {
+  checkFields<
+    Diff<
+      ParamCheck<Request | NextRequest>,
+      {
+        __tag__: 'DELETE'
+        __param_position__: 'first'
+        __param_type__: FirstArg<MaybeField<TEntry, 'DELETE'>>
+      },
+      'DELETE'
+    >
+  >()
+  checkFields<
+    Diff<
+      ParamCheck<RouteContext>,
+      {
+        __tag__: 'DELETE'
+        __param_position__: 'second'
+        __param_type__: SecondArg<MaybeField<TEntry, 'DELETE'>>
+      },
+      'DELETE'
+    >
+  >()
+  
+  checkFields<
+    Diff<
+      {
+        __tag__: 'DELETE',
+        __return_type__: Response | void | never | Promise<Response | void | never>
+      },
+      {
+        __tag__: 'DELETE',
+        __return_type__: ReturnType<MaybeField<TEntry, 'DELETE'>>
+      },
+      'DELETE'
+    >
+  >()
+}
+// Check the prop type of the entry function
+if ('PATCH' in entry) {
+  checkFields<
+    Diff<
+      ParamCheck<Request | NextRequest>,
+      {
+        __tag__: 'PATCH'
+        __param_position__: 'first'
+        __param_type__: FirstArg<MaybeField<TEntry, 'PATCH'>>
+      },
+      'PATCH'
+    >
+  >()
+  checkFields<
+    Diff<
+      ParamCheck<RouteContext>,
+      {
+        __tag__: 'PATCH'
+        __param_position__: 'second'
+        __param_type__: SecondArg<MaybeField<TEntry, 'PATCH'>>
+      },
+      'PATCH'
+    >
+  >()
+  
+  checkFields<
+    Diff<
+      {
+        __tag__: 'PATCH',
+        __return_type__: Response | void | never | Promise<Response | void | never>
+      },
+      {
+        __tag__: 'PATCH',
+        __return_type__: ReturnType<MaybeField<TEntry, 'PATCH'>>
+      },
+      'PATCH'
+    >
+  >()
+}
+
+// Check the arguments and return type of the generateStaticParams function
+if ('generateStaticParams' in entry) {
+  checkFields<Diff<{ params: SegmentParams }, FirstArg<MaybeField<TEntry, 'generateStaticParams'>>, 'generateStaticParams'>>()
+  checkFields<Diff<{ __tag__: 'generateStaticParams', __return_type__: any[] | Promise<any[]> }, { __tag__: 'generateStaticParams', __return_type__: ReturnType<MaybeField<TEntry, 'generateStaticParams'>> }>>()
+}
+
+export interface PageProps {
+  params?: Promise<SegmentParams>
+  searchParams?: Promise<any>
+}
+export interface LayoutProps {
+  children?: React.ReactNode
+
+  params?: Promise<SegmentParams>
+}
+
+// =============
+// Utility types
+type RevalidateRange<T> = T extends { revalidate: any } ? NonNegative<T['revalidate']> : never
+
+// If T is unknown or any, it will be an empty {} type. Otherwise, it will be the same as Omit<T, keyof Base>.
+type OmitWithTag<T, K extends keyof any, _M> = Omit<T, K>
+type Diff<Base, T extends Base, Message extends string = ''> = 0 extends (1 & T) ? {} : OmitWithTag<T, keyof Base, Message>
+
+type FirstArg<T extends Function> = T extends (...args: [infer T, any]) => any ? unknown extends T ? any : T : never
+type SecondArg<T extends Function> = T extends (...args: [any, infer T]) => any ? unknown extends T ? any : T : never
+type MaybeField<T, K extends string> = T extends { [k in K]: infer G } ? G extends Function ? G : never : never
+
+type ParamCheck<T> = {
+  __tag__: string
+  __param_position__: string
+  __param_type__: T
+}
+
+function checkFields<_ extends { [k in keyof any]: never }>() {}
+
+// https://github.com/sindresorhus/type-fest
+type Numeric = number | bigint
+type Zero = 0 | 0n
+type Negative<T extends Numeric> = T extends Zero ? never : `${T}` extends `-${string}` ? T : never
+type NonNegative<T extends Numeric> = T extends Zero ? T : Negative<T> extends never ? T : '__invalid_negative_number__'

package/.next/types/routes.d.ts

@@ -2,7 +2,7 @@
 // Do not edit this file manually
 
 type AppRoutes = "/" | "/login"
-type AppRouteHandlerRoutes = "/api/agent/[id]" | "/api/agent/[id]/events" | "/api/agent/new" | "/api/auth/all-providers" | "/api/auth/api-key/[provider]" | "/api/auth/login" | "/api/auth/login/[provider]" | "/api/auth/logout/[provider]" | "/api/auth/providers" | "/api/auth/status" | "/api/default-cwd" | "/api/files/[...path]" | "/api/harness" | "/api/home" | "/api/internal/runtime" | "/api/models" | "/api/models-config" | "/api/models-config/discover" | "/api/models-config/test" | "/api/plot-kernels" | "/api/plot-kernels/status" | "/api/plot-kernels/stop" | "/api/projects" | "/api/projects/browse" | "/api/reports/[id]" | "/api/search" | "/api/sessions" | "/api/sessions/[id]" | "/api/sessions/[id]/context" | "/api/sessions/new" | "/api/settings" | "/api/skills" | "/api/skills/install" | "/api/skills/search" | "/api/soul" | "/api/version" | "/favicon.ico"
+type AppRouteHandlerRoutes = "/api/agent/[id]" | "/api/agent/[id]/events" | "/api/agent/new" | "/api/apps" | "/api/apps/[id]/[[...path]]" | "/api/auth/all-providers" | "/api/auth/api-key/[provider]" | "/api/auth/login" | "/api/auth/login/[provider]" | "/api/auth/logout/[provider]" | "/api/auth/providers" | "/api/auth/status" | "/api/default-cwd" | "/api/files/[...path]" | "/api/harness" | "/api/home" | "/api/internal/runtime" | "/api/models" | "/api/models-config" | "/api/models-config/discover" | "/api/models-config/test" | "/api/plot-kernels" | "/api/plot-kernels/status" | "/api/plot-kernels/stop" | "/api/projects" | "/api/projects/browse" | "/api/reports/[id]" | "/api/search" | "/api/sessions" | "/api/sessions/[id]" | "/api/sessions/[id]/context" | "/api/sessions/new" | "/api/settings" | "/api/skills" | "/api/skills/install" | "/api/skills/search" | "/api/soul" | "/api/subagents/status" | "/api/version" | "/favicon.ico"
 type PageRoutes = never
 type LayoutRoutes = "/"
 type RedirectRoutes = never
@@ -15,6 +15,8 @@ interface ParamMap {
   "/api/agent/[id]": { "id": string; }
   "/api/agent/[id]/events": { "id": string; }
   "/api/agent/new": {}
+  "/api/apps": {}
+  "/api/apps/[id]/[[...path]]": { "id": string; "path"?: string[]; }
   "/api/auth/all-providers": {}
   "/api/auth/api-key/[provider]": { "provider": string; }
   "/api/auth/login": {}
@@ -47,6 +49,7 @@ interface ParamMap {
   "/api/skills/install": {}
   "/api/skills/search": {}
   "/api/soul": {}
+  "/api/subagents/status": {}
   "/api/version": {}
   "/favicon.ico": {}
   "/login": {}

package/.next/types/validator.ts

@@ -92,6 +92,24 @@ type RouteHandlerConfig<Route extends AppRouteHandlerRoutes = AppRouteHandlerRou
   type __Unused = __Check
 }
 
+// Validate ../../app/api/apps/[id]/[[...path]]/route.ts
+{
+  type __IsExpected<Specific extends RouteHandlerConfig<"/api/apps/[id]/[[...path]]">> = Specific
+  const handler = {} as typeof import("../../app/api/apps/[id]/[[...path]]/route.js")
+  type __Check = __IsExpected<typeof handler>
+  // @ts-ignore
+  type __Unused = __Check
+}
+
+// Validate ../../app/api/apps/route.ts
+{
+  type __IsExpected<Specific extends RouteHandlerConfig<"/api/apps">> = Specific
+  const handler = {} as typeof import("../../app/api/apps/route.js")
+  type __Check = __IsExpected<typeof handler>
+  // @ts-ignore
+  type __Unused = __Check
+}
+
 // Validate ../../app/api/auth/all-providers/route.ts
 {
   type __IsExpected<Specific extends RouteHandlerConfig<"/api/auth/all-providers">> = Specific
@@ -380,6 +398,15 @@ type RouteHandlerConfig<Route extends AppRouteHandlerRoutes = AppRouteHandlerRou
   type __Unused = __Check
 }
 
+// Validate ../../app/api/subagents/status/route.ts
+{
+  type __IsExpected<Specific extends RouteHandlerConfig<"/api/subagents/status">> = Specific
+  const handler = {} as typeof import("../../app/api/subagents/status/route.js")
+  type __Check = __IsExpected<typeof handler>
+  // @ts-ignore
+  type __Unused = __Check
+}
+
 // Validate ../../app/api/version/route.ts
 {
   type __IsExpected<Specific extends RouteHandlerConfig<"/api/version">> = Specific

package/bin/pi-web.js

@@ -350,6 +350,14 @@ function getProcessSummary(pid) {
   };
 }
 
+function logSkippedProcess(info, listenPort = null) {
+  const label = info.cmdline || "unknown command";
+  const portText = listenPort ? `port ${listenPort} is used by ` : "";
+  console.error(`annovibe stop: ${portText}pid ${info.pid}, but it does not look like annovibe; not stopping it.`);
+  console.error(`command: ${label}`);
+  if (info.cwd) console.error(`cwd: ${info.cwd}`);
+}
+
 function looksLikeAnnoVibeProcess(info) {
   const cmdline = info.cmdline || "";
   const cwd = info.cwd || "";
@@ -390,10 +398,7 @@ async function stopVerifiedPortListeners(listenPort, quiet = false) {
 
   if (skipped.length > 0) {
     for (const info of skipped) {
-      const label = info.cmdline || "unknown command";
-      console.error(`annovibe stop: port ${listenPort} is used by pid ${info.pid}, but it does not look like annovibe; not stopping it.`);
-      console.error(`command: ${label}`);
-      if (info.cwd) console.error(`cwd: ${info.cwd}`);
+      logSkippedProcess(info, listenPort);
     }
   }
 
@@ -532,21 +537,44 @@ async function stopManagedServer(quiet = false) {
     return 0;
   }
 
-  const supervisorPid = state.supervisorPid;
-  const nextPid = state.nextPid;
+  const supervisorPid = Number(state.supervisorPid);
+  const nextPid = Number(state.nextPid);
+  const statePort = state.port ?? port;
+  const candidatePids = [...new Set([supervisorPid, nextPid])]
+    .filter((pid) => Number.isInteger(pid) && pid > 0 && isPidAlive(pid));
+
   let stopped = true;
-  if (isPidAlive(supervisorPid)) {
-    stopped = await terminatePid(supervisorPid);
+  let verifiedCount = 0;
+  const stoppedPids = [];
+  for (const pid of candidatePids) {
+    const info = getProcessSummary(pid);
+    if (!looksLikeAnnoVibeProcess(info)) {
+      logSkippedProcess(info);
+      continue;
+    }
+    verifiedCount += 1;
+    const candidateStopped = await terminatePid(pid);
+    if (candidateStopped) stoppedPids.push(pid);
+    stopped = candidateStopped && stopped;
   }
-  if (nextPid && isPidAlive(nextPid)) {
-    stopped = (await terminatePid(nextPid)) && stopped;
+
+  const portStop = await stopVerifiedPortListeners(statePort, quiet);
+  if (portStop.found) {
+    stopped = portStop.stopped && stopped;
   }
+
   if (stopped) {
     removeState();
-    if (!quiet) console.log(`annovibe stop: stopped${supervisorPid ? ` pid ${supervisorPid}` : ""}`);
+    if (!quiet) {
+      if (verifiedCount > 0) {
+        console.log(`annovibe stop: stopped pid${stoppedPids.length === 1 ? "" : "s"} ${stoppedPids.join(", ")}`);
+      } else if (!portStop.found) {
+        console.log("annovibe stop: state was stale; cleaned up");
+      }
+    }
     return 0;
   }
-  if (!quiet) console.error(`annovibe stop: failed to stop pid ${supervisorPid}`);
+  if (!quiet) console.error(`annovibe stop: failed to stop annovibe process${verifiedCount === 1 ? "" : "es"}`);
   return 1;
 }
 
@@ -855,21 +883,21 @@ async function maybeSetupAuth() {
 
 function seedDefaults() {
   const defaultSoulSrc = path.join(pkgDir, "lib", "default-soul.md");
-  const soulDest = path.join(agentDir, "soul.md");
+  const soulDest = path.join(agentDir, "SOUL.md");
   if (!fs.existsSync(soulDest) && fs.existsSync(defaultSoulSrc)) {
     const dir = path.dirname(soulDest);
     if (!fs.existsSync(dir)) fs.mkdirSync(dir, { recursive: true });
     fs.copyFileSync(defaultSoulSrc, soulDest);
-    console.log("   🖖 Default soul.md seeded to ~/.pi/agent/soul.md");
+    console.log("   🖖 Default SOUL.md seeded to ~/.pi/agent/SOUL.md");
   }
 
   const defaultHarnessSrc = path.join(pkgDir, "lib", "visualization-harness.md");
-  const harnessDest = path.join(agentDir, "harness.md");
+  const harnessDest = path.join(agentDir, "HARNESS.md");
   if (!fs.existsSync(harnessDest) && fs.existsSync(defaultHarnessSrc)) {
     const dir = path.dirname(harnessDest);
     if (!fs.existsSync(dir)) fs.mkdirSync(dir, { recursive: true });
     fs.copyFileSync(defaultHarnessSrc, harnessDest);
-    console.log("   📊 Default harness.md seeded to ~/.pi/agent/harness.md");
+    console.log("   📊 Default HARNESS.md seeded to ~/.pi/agent/HARNESS.md");
   }
 }
 

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@seqyuan/annovibe",
-  "version": "0.8.21",
+  "version": "0.8.22",
   "description": "AI-native bioinformatics workspace by Annoroad",
   "license": "MIT",
   "bin": {

package/.next/static/cRtONXI0SmYC7X_hUWbB6/_buildManifest.js

@@ -1 +0,0 @@
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