@seqyuan/annodex 0.1.12 → 0.1.14

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@seqyuan/annodex",
-  "version": "0.1.12",
+  "version": "0.1.14",
   "description": "AI-native bioinformatics workspace by Annoroad",
   "license": "MIT",
   "bin": {
@@ -8,16 +8,17 @@
   },
   "files": [
     "bin",
-    "app",
-    "components",
-    "hooks",
-    "lib",
+    ".next",
+    "!.next/cache",
+    "!.next/dev",
+    "!.next/types",
+    "!.next/**/*.js.map",
+    "!.next/trace",
+    "!.next/trace-build",
+    "lib/default-SOUL.md",
+    "lib/default-HARNESS.md",
     "public",
-    "scripts/postinstall.cjs",
-    "proxy.ts",
     "next.config.ts",
-    "postcss.config.mjs",
-    "tsconfig.json",
     "package.json"
   ],
   "scripts": {
@@ -28,8 +29,7 @@
     "test:compat": "node --test tests/compat-proxy.test.mjs",
     "pack:check": "node scripts/check-npm-pack.mjs",
     "prepublishOnly": "node scripts/check-npm-pack.mjs",
-    "release": "npm version patch --no-git-tag-version && npm publish --access public",
-    "postinstall": "node scripts/postinstall.cjs"
+    "release": "npm version patch --no-git-tag-version && npm run build && npm run pack:check && npm publish --access public"
   },
   "dependencies": {
     "@codemirror/autocomplete": "^6.20.2",
@@ -50,13 +50,7 @@
     "@codemirror/theme-one-dark": "^6.1.3",
     "@codemirror/view": "^6.43.0",
     "@openai/codex": "^0.118.0",
-    "@tailwindcss/postcss": "^4.2.2",
-    "@types/bcryptjs": "^2.4.6",
-    "@types/node": "^25",
-    "@types/react": "^19",
-    "@types/react-dom": "^19",
     "@types/react-syntax-highlighter": "^15.5.13",
-    "@types/ws": "^8.18.1",
     "bcryptjs": "^3.0.3",
     "codemirror": "^6.0.2",
     "docx-preview": "^0.3.7",
@@ -64,20 +58,26 @@
     "mermaid": "^11.15.0",
     "next": "16.2.1",
     "pdfjs-dist": "^5.7.284",
-    "postcss": "^8",
     "react": "^19.2.4",
     "react-dom": "^19.2.4",
     "react-markdown": "^10.1.0",
     "react-syntax-highlighter": "^16.1.1",
     "remark-gfm": "^4.0.1",
     "smol-toml": "^1.6.1",
-    "tailwindcss": "^4.2.2",
-    "typescript": "^5",
     "ws": "^8.18.0",
     "xlsx": "^0.18.5"
   },
   "devDependencies": {
+    "@tailwindcss/postcss": "^4.2.2",
+    "@types/bcryptjs": "^2.4.6",
+    "@types/node": "^25",
+    "@types/react": "^19",
+    "@types/react-dom": "^19",
+    "@types/ws": "^8.18.1",
     "eslint": "^9",
-    "eslint-config-next": "16.2.1"
+    "eslint-config-next": "16.2.1",
+    "postcss": "^8",
+    "tailwindcss": "^4.2.2",
+    "typescript": "^5"
   }
 }

package/app/api/agent/[id]/events/route.ts

@@ -1,94 +0,0 @@
-import { resolveSessionPath } from "@/lib/session-reader";
-import { getRpcSession, startRpcSession } from "@/lib/rpc-manager";
-import { statSync } from "fs";
-
-export const dynamic = "force-dynamic";
-
-function directoryExists(path: string): boolean {
-  try {
-    return statSync(path).isDirectory();
-  } catch {
-    return false;
-  }
-}
-
-// GET /api/agent/[id]/events - SSE stream of agent events
-export async function GET(
-  req: Request,
-  { params }: { params: Promise<{ id: string }> }
-) {
-  const { id } = await params;
-
-  let realSessionId = id;
-
-  // Fast path: already-running session
-  let session = getRpcSession(id);
-  if (!session || !session.isAlive()) {
-    const cwd = await resolveSessionPath(id);
-    if (!cwd) {
-      return new Response("Session not found", { status: 404 });
-    }
-    if (!directoryExists(cwd)) {
-      return new Response(`Project directory no longer exists: ${cwd}`, { status: 400 });
-    }
-    try {
-      const started = await startRpcSession(id, id, cwd);
-      session = started.session;
-      realSessionId = started.realSessionId;
-    } catch (error) {
-      return new Response(`Failed to start agent: ${error}`, { status: 500 });
-    }
-  } else {
-    realSessionId = session.sessionId;
-  }
-
-  const stream = new ReadableStream({
-    start(controller) {
-      let closed = false;
-      const encode = (data: unknown) => {
-        if (closed) return;
-        const text = `data: ${JSON.stringify(data)}\n\n`;
-        try {
-          controller.enqueue(new TextEncoder().encode(text));
-        } catch {
-          closed = true;
-        }
-      };
-
-      // Send initial connected event
-      encode({ type: "connected", sessionId: realSessionId });
-
-      const unsubscribe = session!.onEvent((event) => {
-        encode(event);
-      });
-
-      // Heartbeat every 30s to prevent server/proxy timeout
-      const heartbeat = setInterval(() => {
-        try {
-          controller.enqueue(new TextEncoder().encode(":\n\n"));
-        } catch {
-          // controller already closed
-        }
-      }, 30_000);
-
-      // Cleanup when client disconnects
-      const cleanup = () => {
-        if (closed) return;
-        closed = true;
-        clearInterval(heartbeat);
-        unsubscribe();
-        try { controller.close(); } catch { /* already closed */ }
-      };
-
-      req.signal?.addEventListener("abort", cleanup);
-    },
-  });
-
-  return new Response(stream, {
-    headers: {
-      "Content-Type": "text/event-stream",
-      "Cache-Control": "no-cache",
-      Connection: "keep-alive",
-    },
-  });
-}

package/app/api/agent/[id]/route.ts

@@ -1,83 +0,0 @@
-import { NextResponse } from "next/server";
-import { statSync } from "fs";
-import { resolveSessionPath } from "@/lib/session-reader";
-import { startRpcSession, getRpcSession } from "@/lib/rpc-manager";
-
-function directoryExists(path: string): boolean {
-  try {
-    return statSync(path).isDirectory();
-  } catch {
-    return false;
-  }
-}
-
-// POST /api/agent/[id] - Send a command to an existing session
-export async function POST(
-  req: Request,
-  { params }: { params: Promise<{ id: string }> }
-) {
-  const { id } = await params;
-
-  try {
-    const body = await req.json() as { type: string; [key: string]: unknown };
-
-    // Fast path: already-running session
-    const existing = getRpcSession(id);
-    if (existing?.isAlive()) {
-      const result = await existing.send(body);
-      return NextResponse.json({
-        success: true,
-        data: result,
-        ...(existing.sessionId !== id ? { sessionId: existing.sessionId } : {}),
-      });
-    }
-
-    if (body.type === "abort") {
-      return NextResponse.json({ success: true, data: { running: false } });
-    }
-
-    // Resolve session cwd from registry
-    const cwd = await resolveSessionPath(id);
-    if (!cwd) {
-      return NextResponse.json({ error: "Session not found" }, { status: 404 });
-    }
-    if (!directoryExists(cwd)) {
-      return NextResponse.json(
-        { error: `Project directory no longer exists: ${cwd}` },
-        { status: 400 },
-      );
-    }
-
-    // Start/resume the session via codex
-    const { session, realSessionId } = await startRpcSession(id, id, cwd);
-    const result = await session.send(body);
-
-    return NextResponse.json({
-      success: true,
-      data: result,
-      ...(realSessionId !== id ? { sessionId: realSessionId } : {}),
-    });
-  } catch (error) {
-    return NextResponse.json({ error: String(error) }, { status: 500 });
-  }
-}
-
-// GET /api/agent/[id] - Get current agent state
-export async function GET(
-  _req: Request,
-  { params }: { params: Promise<{ id: string }> }
-) {
-  const { id } = await params;
-
-  try {
-    const session = getRpcSession(id);
-    if (!session || !session.isAlive()) {
-      return NextResponse.json({ running: false });
-    }
-
-    const state = await session.send({ type: "get_state" });
-    return NextResponse.json({ running: session.isBusy(), state });
-  } catch (error) {
-    return NextResponse.json({ error: String(error) }, { status: 500 });
-  }
-}

package/app/api/agent/new/route.ts

@@ -1,53 +0,0 @@
-import { NextResponse } from "next/server";
-import { existsSync } from "fs";
-import { startRpcSession } from "@/lib/rpc-manager";
-
-// POST /api/agent/new  body: { cwd, provider?, modelId?, toolNames?, thinkingLevel?, sendImmediately? }
-// Creates a new codex thread. By default, the caller should connect SSE first,
-// then send the first prompt via POST /api/agent/[id].
-export async function POST(req: Request) {
-  try {
-    const body = await req.json() as { cwd?: string; [key: string]: unknown };
-    const { cwd, ...command } = body;
-
-    if (!cwd || typeof cwd !== "string") {
-      return NextResponse.json({ error: "cwd is required" }, { status: 400 });
-    }
-    if (!existsSync(cwd)) {
-      return NextResponse.json({ error: `Directory does not exist: ${cwd}` }, { status: 400 });
-    }
-
-    const { provider, modelId, toolNames, thinkingLevel, sendImmediately, ...promptCommand } = command as {
-      provider?: string;
-      modelId?: string;
-      toolNames?: string[];
-      thinkingLevel?: string;
-      sendImmediately?: boolean;
-      [key: string]: unknown;
-    };
-
-    // Create a new session with a unique temp key
-    const tempKey = `__new__${Date.now()}`;
-    const { session, realSessionId } = await startRpcSession(
-      tempKey, "", cwd, toolNames,
-      provider && modelId ? { provider, modelId } : undefined,
-      thinkingLevel,
-    );
-
-    // Keep files-route cache in sync
-    globalThis.__annodexAllowedRootsCache?.roots.add(cwd);
-
-    // Apply pre-selected model before sending the prompt
-    if (provider && modelId) {
-      await session.send({ type: "set_model", provider, modelId });
-    }
-
-    const result = sendImmediately
-      ? await session.send(promptCommand)
-      : null;
-
-    return NextResponse.json({ success: true, sessionId: realSessionId, data: result });
-  } catch (error) {
-    return NextResponse.json({ error: String(error) }, { status: 500 });
-  }
-}

package/app/api/auth/all-providers/route.ts

@@ -1,21 +0,0 @@
-import { NextResponse } from "next/server";
-import { readMergedConfig } from "@/lib/annodex-config";
-
-export const dynamic = "force-dynamic";
-
-export async function GET() {
-  try {
-    const config = readMergedConfig();
-    return NextResponse.json({
-      providers: config.providers.map((provider) => ({
-        id: provider.id,
-        displayName: provider.name || provider.id,
-        configured: Boolean(provider.apiKey?.trim() || provider.baseUrl?.trim()),
-        source: "providers.json",
-        modelCount: provider.models.length,
-      })),
-    });
-  } catch {
-    return NextResponse.json({ providers: [] });
-  }
-}

package/app/api/auth/api-key/[provider]/route.ts

@@ -1,7 +0,0 @@
-import { NextResponse } from "next/server";
-
-export const dynamic = "force-dynamic";
-
-export async function PUT() {
-  return NextResponse.json({ success: true });
-}

package/app/api/auth/login/[provider]/route.ts

@@ -1,7 +0,0 @@
-import { NextResponse } from "next/server";
-
-export const dynamic = "force-dynamic";
-
-export async function POST() {
-  return NextResponse.json({ success: true });
-}

package/app/api/auth/login/route.ts

@@ -1,22 +0,0 @@
-import { NextResponse } from "next/server";
-import { verifyPassword, createAuthTokenFromConfig, getAuthCookieHeader } from "@/lib/auth";
-
-export async function POST(req: Request) {
-  try {
-    const { password } = await req.json() as { password?: string };
-    if (!password || typeof password !== "string") {
-      return NextResponse.json({ error: "Password required" }, { status: 400 });
-    }
-
-    if (!verifyPassword(password)) {
-      return NextResponse.json({ error: "Invalid password" }, { status: 401 });
-    }
-
-    const token = await createAuthTokenFromConfig();
-    const response = NextResponse.json({ success: true });
-    response.headers.set("Set-Cookie", getAuthCookieHeader(token));
-    return response;
-  } catch (error) {
-    return NextResponse.json({ error: String(error) }, { status: 500 });
-  }
-}

package/app/api/auth/logout/[provider]/route.ts

@@ -1,7 +0,0 @@
-import { NextResponse } from "next/server";
-
-export const dynamic = "force-dynamic";
-
-export async function POST() {
-  return NextResponse.json({ success: true });
-}

package/app/api/auth/providers/route.ts

@@ -1,15 +0,0 @@
-/**
- * Auth API — simplified for codex
- *
- * Codex handles authentication natively via `codex login`.
- * These endpoints return empty/success responses for backward compatibility
- * with the UI that expects them to exist.
- */
-
-import { NextResponse } from "next/server";
-
-export const dynamic = "force-dynamic";
-
-export async function GET() {
-  return NextResponse.json({ providers: [] });
-}

package/app/api/auth/status/route.ts

@@ -1,6 +0,0 @@
-import { NextResponse } from "next/server";
-import { isAuthEnabled } from "@/lib/auth";
-
-export async function GET() {
-  return NextResponse.json({ authEnabled: isAuthEnabled() });
-}

package/app/api/default-cwd/route.ts

@@ -1,22 +0,0 @@
-import { NextResponse } from "next/server";
-import { mkdirSync } from "fs";
-import { homedir } from "os";
-import { join } from "path";
-
-// POST /api/default-cwd
-// Creates ~/annodex/workspace/<YYYYMMDD> if it doesn't exist and returns the path.
-export async function POST() {
-  try {
-    const now = new Date();
-    const date = [
-      now.getFullYear(),
-      String(now.getMonth() + 1).padStart(2, "0"),
-      String(now.getDate()).padStart(2, "0"),
-    ].join("");
-    const dir = join(homedir(), "annodex", "workspace", date);
-    mkdirSync(dir, { recursive: true });
-    return NextResponse.json({ cwd: dir });
-  } catch (error) {
-    return NextResponse.json({ error: String(error) }, { status: 500 });
-  }
-}