@seqyuan/annodex 0.1.1

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

@@ -0,0 +1,106 @@
+// This file is generated automatically by Next.js
+// 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/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"
+type PageRoutes = never
+type LayoutRoutes = "/"
+type RedirectRoutes = never
+type RewriteRoutes = never
+type Routes = AppRoutes | PageRoutes | LayoutRoutes | RedirectRoutes | RewriteRoutes | AppRouteHandlerRoutes
+
+
+interface ParamMap {
+  "/": {}
+  "/api/agent/[id]": { "id": string; }
+  "/api/agent/[id]/events": { "id": string; }
+  "/api/agent/new": {}
+  "/api/auth/all-providers": {}
+  "/api/auth/api-key/[provider]": { "provider": string; }
+  "/api/auth/login": {}
+  "/api/auth/login/[provider]": { "provider": string; }
+  "/api/auth/logout/[provider]": { "provider": string; }
+  "/api/auth/providers": {}
+  "/api/auth/status": {}
+  "/api/default-cwd": {}
+  "/api/files/[...path]": { "path": string[]; }
+  "/api/harness": {}
+  "/api/home": {}
+  "/api/internal/runtime": {}
+  "/api/models": {}
+  "/api/models-config": {}
+  "/api/models-config/discover": {}
+  "/api/models-config/test": {}
+  "/api/projects": {}
+  "/api/projects/browse": {}
+  "/api/reports/[id]": { "id": string; }
+  "/api/search": {}
+  "/api/sessions": {}
+  "/api/sessions/[id]": { "id": string; }
+  "/api/sessions/[id]/context": { "id": string; }
+  "/api/sessions/new": {}
+  "/api/settings": {}
+  "/api/skills": {}
+  "/api/skills/install": {}
+  "/api/skills/search": {}
+  "/api/soul": {}
+  "/api/version": {}
+  "/login": {}
+}
+
+
+export type ParamsOf<Route extends Routes> = ParamMap[Route]
+
+interface LayoutSlotMap {
+  "/": never
+}
+
+
+export type { AppRoutes, PageRoutes, LayoutRoutes, RedirectRoutes, RewriteRoutes, ParamMap, AppRouteHandlerRoutes }
+
+declare global {
+  /**
+   * Props for Next.js App Router page components
+   * @example
+   * ```tsx
+   * export default function Page(props: PageProps<'/blog/[slug]'>) {
+   *   const { slug } = await props.params
+   *   return <div>Blog post: {slug}</div>
+   * }
+   * ```
+   */
+  interface PageProps<AppRoute extends AppRoutes> {
+    params: Promise<ParamMap[AppRoute]>
+    searchParams: Promise<Record<string, string | string[] | undefined>>
+  }
+
+  /**
+   * Props for Next.js App Router layout components
+   * @example
+   * ```tsx
+   * export default function Layout(props: LayoutProps<'/dashboard'>) {
+   *   return <div>{props.children}</div>
+   * }
+   * ```
+   */
+  type LayoutProps<LayoutRoute extends LayoutRoutes> = {
+    params: Promise<ParamMap[LayoutRoute]>
+    children: React.ReactNode
+  } & {
+    [K in LayoutSlotMap[LayoutRoute]]: React.ReactNode
+  }
+
+  /**
+   * Context for Next.js App Router route handlers
+   * @example
+   * ```tsx
+   * export async function GET(request: NextRequest, context: RouteContext<'/api/users/[id]'>) {
+   *   const { id } = await context.params
+   *   return Response.json({ id })
+   * }
+   * ```
+   */
+  interface RouteContext<AppRouteHandlerRoute extends AppRouteHandlerRoutes> {
+    params: Promise<ParamMap[AppRouteHandlerRoute]>
+  }
+}

package/.next/types/validator.ts

@@ -0,0 +1,376 @@
+// This file is generated automatically by Next.js
+// Do not edit this file manually
+// This file validates that all pages and layouts export the correct types
+
+import type { AppRoutes, LayoutRoutes, ParamMap, AppRouteHandlerRoutes } from "./routes.js"
+import type { ResolvingMetadata, ResolvingViewport } from "next/types.js"
+import type { NextRequest } from 'next/server.js'
+
+type AppPageConfig<Route extends AppRoutes = AppRoutes> = {
+  default: React.ComponentType<{ params: Promise<ParamMap[Route]> } & any> | ((props: { params: Promise<ParamMap[Route]> } & any) => React.ReactNode | Promise<React.ReactNode> | never | void | Promise<void>)
+  generateStaticParams?: (props: { params: ParamMap[Route] }) => Promise<any[]> | any[]
+  generateMetadata?: (
+    props: { params: Promise<ParamMap[Route]> } & any,
+    parent: ResolvingMetadata
+  ) => Promise<any> | any
+  generateViewport?: (
+    props: { params: Promise<ParamMap[Route]> } & any,
+    parent: ResolvingViewport
+  ) => Promise<any> | any
+  metadata?: any
+  viewport?: any
+}
+
+type LayoutConfig<Route extends LayoutRoutes = LayoutRoutes> = {
+  default: React.ComponentType<LayoutProps<Route>> | ((props: LayoutProps<Route>) => React.ReactNode | Promise<React.ReactNode> | never | void | Promise<void>)
+  generateStaticParams?: (props: { params: ParamMap[Route] }) => Promise<any[]> | any[]
+  generateMetadata?: (
+    props: { params: Promise<ParamMap[Route]> } & any,
+    parent: ResolvingMetadata
+  ) => Promise<any> | any
+  generateViewport?: (
+    props: { params: Promise<ParamMap[Route]> } & any,
+    parent: ResolvingViewport
+  ) => Promise<any> | any
+  metadata?: any
+  viewport?: any
+}
+
+type RouteHandlerConfig<Route extends AppRouteHandlerRoutes = AppRouteHandlerRoutes> = {
+  GET?: (request: NextRequest, context: { params: Promise<ParamMap[Route]> }) => Promise<Response | void> | Response | void
+  POST?: (request: NextRequest, context: { params: Promise<ParamMap[Route]> }) => Promise<Response | void> | Response | void
+  PUT?: (request: NextRequest, context: { params: Promise<ParamMap[Route]> }) => Promise<Response | void> | Response | void
+  PATCH?: (request: NextRequest, context: { params: Promise<ParamMap[Route]> }) => Promise<Response | void> | Response | void
+  DELETE?: (request: NextRequest, context: { params: Promise<ParamMap[Route]> }) => Promise<Response | void> | Response | void
+  HEAD?: (request: NextRequest, context: { params: Promise<ParamMap[Route]> }) => Promise<Response | void> | Response | void
+  OPTIONS?: (request: NextRequest, context: { params: Promise<ParamMap[Route]> }) => Promise<Response | void> | Response | void
+}
+
+
+// Validate ../../app/login/page.tsx
+{
+  type __IsExpected<Specific extends AppPageConfig<"/login">> = Specific
+  const handler = {} as typeof import("../../app/login/page.js")
+  type __Check = __IsExpected<typeof handler>
+  // @ts-ignore
+  type __Unused = __Check
+}
+
+// Validate ../../app/page.tsx
+{
+  type __IsExpected<Specific extends AppPageConfig<"/">> = Specific
+  const handler = {} as typeof import("../../app/page.js")
+  type __Check = __IsExpected<typeof handler>
+  // @ts-ignore
+  type __Unused = __Check
+}
+
+// Validate ../../app/api/agent/[id]/events/route.ts
+{
+  type __IsExpected<Specific extends RouteHandlerConfig<"/api/agent/[id]/events">> = Specific
+  const handler = {} as typeof import("../../app/api/agent/[id]/events/route.js")
+  type __Check = __IsExpected<typeof handler>
+  // @ts-ignore
+  type __Unused = __Check
+}
+
+// Validate ../../app/api/agent/[id]/route.ts
+{
+  type __IsExpected<Specific extends RouteHandlerConfig<"/api/agent/[id]">> = Specific
+  const handler = {} as typeof import("../../app/api/agent/[id]/route.js")
+  type __Check = __IsExpected<typeof handler>
+  // @ts-ignore
+  type __Unused = __Check
+}
+
+// Validate ../../app/api/agent/new/route.ts
+{
+  type __IsExpected<Specific extends RouteHandlerConfig<"/api/agent/new">> = Specific
+  const handler = {} as typeof import("../../app/api/agent/new/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
+  const handler = {} as typeof import("../../app/api/auth/all-providers/route.js")
+  type __Check = __IsExpected<typeof handler>
+  // @ts-ignore
+  type __Unused = __Check
+}
+
+// Validate ../../app/api/auth/api-key/[provider]/route.ts
+{
+  type __IsExpected<Specific extends RouteHandlerConfig<"/api/auth/api-key/[provider]">> = Specific
+  const handler = {} as typeof import("../../app/api/auth/api-key/[provider]/route.js")
+  type __Check = __IsExpected<typeof handler>
+  // @ts-ignore
+  type __Unused = __Check
+}
+
+// Validate ../../app/api/auth/login/[provider]/route.ts
+{
+  type __IsExpected<Specific extends RouteHandlerConfig<"/api/auth/login/[provider]">> = Specific
+  const handler = {} as typeof import("../../app/api/auth/login/[provider]/route.js")
+  type __Check = __IsExpected<typeof handler>
+  // @ts-ignore
+  type __Unused = __Check
+}
+
+// Validate ../../app/api/auth/login/route.ts
+{
+  type __IsExpected<Specific extends RouteHandlerConfig<"/api/auth/login">> = Specific
+  const handler = {} as typeof import("../../app/api/auth/login/route.js")
+  type __Check = __IsExpected<typeof handler>
+  // @ts-ignore
+  type __Unused = __Check
+}
+
+// Validate ../../app/api/auth/logout/[provider]/route.ts
+{
+  type __IsExpected<Specific extends RouteHandlerConfig<"/api/auth/logout/[provider]">> = Specific
+  const handler = {} as typeof import("../../app/api/auth/logout/[provider]/route.js")
+  type __Check = __IsExpected<typeof handler>
+  // @ts-ignore
+  type __Unused = __Check
+}
+
+// Validate ../../app/api/auth/providers/route.ts
+{
+  type __IsExpected<Specific extends RouteHandlerConfig<"/api/auth/providers">> = Specific
+  const handler = {} as typeof import("../../app/api/auth/providers/route.js")
+  type __Check = __IsExpected<typeof handler>
+  // @ts-ignore
+  type __Unused = __Check
+}
+
+// Validate ../../app/api/auth/status/route.ts
+{
+  type __IsExpected<Specific extends RouteHandlerConfig<"/api/auth/status">> = Specific
+  const handler = {} as typeof import("../../app/api/auth/status/route.js")
+  type __Check = __IsExpected<typeof handler>
+  // @ts-ignore
+  type __Unused = __Check
+}
+
+// Validate ../../app/api/default-cwd/route.ts
+{
+  type __IsExpected<Specific extends RouteHandlerConfig<"/api/default-cwd">> = Specific
+  const handler = {} as typeof import("../../app/api/default-cwd/route.js")
+  type __Check = __IsExpected<typeof handler>
+  // @ts-ignore
+  type __Unused = __Check
+}
+
+// Validate ../../app/api/files/[...path]/route.ts
+{
+  type __IsExpected<Specific extends RouteHandlerConfig<"/api/files/[...path]">> = Specific
+  const handler = {} as typeof import("../../app/api/files/[...path]/route.js")
+  type __Check = __IsExpected<typeof handler>
+  // @ts-ignore
+  type __Unused = __Check
+}
+
+// Validate ../../app/api/harness/route.ts
+{
+  type __IsExpected<Specific extends RouteHandlerConfig<"/api/harness">> = Specific
+  const handler = {} as typeof import("../../app/api/harness/route.js")
+  type __Check = __IsExpected<typeof handler>
+  // @ts-ignore
+  type __Unused = __Check
+}
+
+// Validate ../../app/api/home/route.ts
+{
+  type __IsExpected<Specific extends RouteHandlerConfig<"/api/home">> = Specific
+  const handler = {} as typeof import("../../app/api/home/route.js")
+  type __Check = __IsExpected<typeof handler>
+  // @ts-ignore
+  type __Unused = __Check
+}
+
+// Validate ../../app/api/internal/runtime/route.ts
+{
+  type __IsExpected<Specific extends RouteHandlerConfig<"/api/internal/runtime">> = Specific
+  const handler = {} as typeof import("../../app/api/internal/runtime/route.js")
+  type __Check = __IsExpected<typeof handler>
+  // @ts-ignore
+  type __Unused = __Check
+}
+
+// Validate ../../app/api/models-config/discover/route.ts
+{
+  type __IsExpected<Specific extends RouteHandlerConfig<"/api/models-config/discover">> = Specific
+  const handler = {} as typeof import("../../app/api/models-config/discover/route.js")
+  type __Check = __IsExpected<typeof handler>
+  // @ts-ignore
+  type __Unused = __Check
+}
+
+// Validate ../../app/api/models-config/route.ts
+{
+  type __IsExpected<Specific extends RouteHandlerConfig<"/api/models-config">> = Specific
+  const handler = {} as typeof import("../../app/api/models-config/route.js")
+  type __Check = __IsExpected<typeof handler>
+  // @ts-ignore
+  type __Unused = __Check
+}
+
+// Validate ../../app/api/models-config/test/route.ts
+{
+  type __IsExpected<Specific extends RouteHandlerConfig<"/api/models-config/test">> = Specific
+  const handler = {} as typeof import("../../app/api/models-config/test/route.js")
+  type __Check = __IsExpected<typeof handler>
+  // @ts-ignore
+  type __Unused = __Check
+}
+
+// Validate ../../app/api/models/route.ts
+{
+  type __IsExpected<Specific extends RouteHandlerConfig<"/api/models">> = Specific
+  const handler = {} as typeof import("../../app/api/models/route.js")
+  type __Check = __IsExpected<typeof handler>
+  // @ts-ignore
+  type __Unused = __Check
+}
+
+// Validate ../../app/api/projects/browse/route.ts
+{
+  type __IsExpected<Specific extends RouteHandlerConfig<"/api/projects/browse">> = Specific
+  const handler = {} as typeof import("../../app/api/projects/browse/route.js")
+  type __Check = __IsExpected<typeof handler>
+  // @ts-ignore
+  type __Unused = __Check
+}
+
+// Validate ../../app/api/projects/route.ts
+{
+  type __IsExpected<Specific extends RouteHandlerConfig<"/api/projects">> = Specific
+  const handler = {} as typeof import("../../app/api/projects/route.js")
+  type __Check = __IsExpected<typeof handler>
+  // @ts-ignore
+  type __Unused = __Check
+}
+
+// Validate ../../app/api/reports/[id]/route.ts
+{
+  type __IsExpected<Specific extends RouteHandlerConfig<"/api/reports/[id]">> = Specific
+  const handler = {} as typeof import("../../app/api/reports/[id]/route.js")
+  type __Check = __IsExpected<typeof handler>
+  // @ts-ignore
+  type __Unused = __Check
+}
+
+// Validate ../../app/api/search/route.ts
+{
+  type __IsExpected<Specific extends RouteHandlerConfig<"/api/search">> = Specific
+  const handler = {} as typeof import("../../app/api/search/route.js")
+  type __Check = __IsExpected<typeof handler>
+  // @ts-ignore
+  type __Unused = __Check
+}
+
+// Validate ../../app/api/sessions/[id]/context/route.ts
+{
+  type __IsExpected<Specific extends RouteHandlerConfig<"/api/sessions/[id]/context">> = Specific
+  const handler = {} as typeof import("../../app/api/sessions/[id]/context/route.js")
+  type __Check = __IsExpected<typeof handler>
+  // @ts-ignore
+  type __Unused = __Check
+}
+
+// Validate ../../app/api/sessions/[id]/route.ts
+{
+  type __IsExpected<Specific extends RouteHandlerConfig<"/api/sessions/[id]">> = Specific
+  const handler = {} as typeof import("../../app/api/sessions/[id]/route.js")
+  type __Check = __IsExpected<typeof handler>
+  // @ts-ignore
+  type __Unused = __Check
+}
+
+// Validate ../../app/api/sessions/new/route.ts
+{
+  type __IsExpected<Specific extends RouteHandlerConfig<"/api/sessions/new">> = Specific
+  const handler = {} as typeof import("../../app/api/sessions/new/route.js")
+  type __Check = __IsExpected<typeof handler>
+  // @ts-ignore
+  type __Unused = __Check
+}
+
+// Validate ../../app/api/sessions/route.ts
+{
+  type __IsExpected<Specific extends RouteHandlerConfig<"/api/sessions">> = Specific
+  const handler = {} as typeof import("../../app/api/sessions/route.js")
+  type __Check = __IsExpected<typeof handler>
+  // @ts-ignore
+  type __Unused = __Check
+}
+
+// Validate ../../app/api/settings/route.ts
+{
+  type __IsExpected<Specific extends RouteHandlerConfig<"/api/settings">> = Specific
+  const handler = {} as typeof import("../../app/api/settings/route.js")
+  type __Check = __IsExpected<typeof handler>
+  // @ts-ignore
+  type __Unused = __Check
+}
+
+// Validate ../../app/api/skills/install/route.ts
+{
+  type __IsExpected<Specific extends RouteHandlerConfig<"/api/skills/install">> = Specific
+  const handler = {} as typeof import("../../app/api/skills/install/route.js")
+  type __Check = __IsExpected<typeof handler>
+  // @ts-ignore
+  type __Unused = __Check
+}
+
+// Validate ../../app/api/skills/route.ts
+{
+  type __IsExpected<Specific extends RouteHandlerConfig<"/api/skills">> = Specific
+  const handler = {} as typeof import("../../app/api/skills/route.js")
+  type __Check = __IsExpected<typeof handler>
+  // @ts-ignore
+  type __Unused = __Check
+}
+
+// Validate ../../app/api/skills/search/route.ts
+{
+  type __IsExpected<Specific extends RouteHandlerConfig<"/api/skills/search">> = Specific
+  const handler = {} as typeof import("../../app/api/skills/search/route.js")
+  type __Check = __IsExpected<typeof handler>
+  // @ts-ignore
+  type __Unused = __Check
+}
+
+// Validate ../../app/api/soul/route.ts
+{
+  type __IsExpected<Specific extends RouteHandlerConfig<"/api/soul">> = Specific
+  const handler = {} as typeof import("../../app/api/soul/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
+  const handler = {} as typeof import("../../app/api/version/route.js")
+  type __Check = __IsExpected<typeof handler>
+  // @ts-ignore
+  type __Unused = __Check
+}
+
+
+
+
+
+// Validate ../../app/layout.tsx
+{
+  type __IsExpected<Specific extends LayoutConfig<"/">> = Specific
+  const handler = {} as typeof import("../../app/layout.js")
+  type __Check = __IsExpected<typeof handler>
+  // @ts-ignore
+  type __Unused = __Check
+}

package/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2026 agegr
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

package/README.md

@@ -0,0 +1,59 @@
+# annodex
+
+AI-native bioinformatics workspace by Annoroad, backed by Codex app-server. It provides browser-based project/session browsing, streaming agent chat, branch navigation, reports, and file viewing/editing.
+
+Version: `0.1.1`
+Repository: [seqyuan/annodex](https://github.com/seqyuan/annodex)
+
+## Quick Start
+
+```bash
+npm install -g @seqyuan/annodex
+annodex
+```
+
+Open [http://localhost:30141](http://localhost:30141). On first start, annodex can optionally set a password, similar to Jupyter.
+
+## CLI
+
+```bash
+annodex                      # start managed background server
+annodex start                # start if not already running
+annodex restart              # stop then start
+annodex stop                 # stop background server
+annodex status               # show server status
+annodex logs                 # show recent logs
+annodex logs -f              # follow logs
+annodex --port 8080          # custom port
+annodex --hostname 127.0.0.1 # bind host
+annodex --version            # print version
+annodex --help               # print help
+annodex update               # update global package
+annodex passwd               # set/change password
+annodex passwd --reset       # remove password
+
+PORT=8080 annodex
+ANNODEX_PASSWORD=xxx annodex
+```
+
+Managed servers auto-restart after package updates once active agent sessions are idle. Set `ANNODEX_AUTO_RESTART=0` to disable. Legacy `ANNOVIBE_*` and `PIDEX_*` environment variables are still accepted for migration.
+
+## Data
+
+- Codex threads are read through `codex app-server` from Codex's own storage.
+- annodex settings live under `~/.config/annodex`.
+- Provider settings are stored in `~/.config/annodex/providers.json`.
+- Project registry is stored in `~/.config/annodex/annodex-projects.json`.
+- Password auth is stored in `~/.config/annodex/web-auth.json`.
+
+## Development
+
+```bash
+npm install
+npm run dev   # port 30141
+```
+
+Typecheck: `node_modules/.bin/tsc --noEmit`
+Lint: `npm run lint`
+
+Do not run `next build` during dev; it pollutes `.next/` and can break `npm run dev`.