@seqyuan/annodex 0.1.24 → 0.1.25

package/.next/static/css/eaefa02f8638a351.css

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auto!important}.topbar-chat-tools::-webkit-scrollbar{display:none}.topbar-system-button{flex:none}.topbar-session-stats{scrollbar-width:none;-webkit-overflow-scrolling:touch;flex:1 1 0;order:4;min-width:0;max-width:none;overflow-x:auto}.topbar-update-status{order:4;min-width:0;max-width:none;overflow:hidden;flex:1 1 0!important}.topbar-update-status span{text-overflow:ellipsis;min-width:0;overflow:hidden}.topbar-system-button{justify-content:center;width:30px;gap:0!important;padding:0!important}.topbar-system-label{display:none!important}.topbar-session-stats::-webkit-scrollbar{display:none}.chat-input-toolbar{flex-wrap:wrap;align-items:stretch!important;gap:4px 6px!important}.chat-input-toolbar-left,.chat-input-toolbar-right{scrollbar-width:none;-webkit-overflow-scrolling:touch;min-width:0;overflow:auto hidden}.chat-input-toolbar-left{flex:100%!important}.chat-input-toolbar-right{flex:100%!important;margin-left:0!important}.chat-input-toolbar-left::-webkit-scrollbar,.chat-input-toolbar-right::-webkit-scrollbar{display:none}.chat-input-toolbar-left>*,.chat-input-toolbar-right>*{flex-shrink:0}.chat-input-toolbar-spacer{display:none!important}.settings-dialog-backdrop{justify-content:stretch;align-items:stretch;padding:0}.settings-dialog-shell{border:none;border-radius:0;width:100%;height:100dvh;min-height:0}.settings-dialog-body{flex-direction:column}.settings-dialog-tabs{border-right:none;border-bottom:1px solid var(--border);gap:6px;width:100%;padding:7px;display:flex;overflow:auto hidden}.settings-dialog-tab{flex:0 0 132px;width:132px;margin:0;padding:8px}.settings-dialog-panel{flex:1}.chat-stats-center,.resize-handle{display:none!important}.sidebar-container{max-width:85vw;transition:transform .25s,box-shadow .25s;top:0;bottom:0;left:0;width:min(280px,85vw)!important;min-width:0!important;position:fixed!important}.sidebar-container.sidebar-open{transform:translate(0);box-shadow:4px 0 20px #00000026}.sidebar-container.sidebar-closed{box-shadow:none;pointer-events:none;transform:translate(-100%)}.right-panel-container{flex-shrink:0;transition:width .2s,min-width .2s;overflow:hidden}.right-panel-back-button{display:flex!important}.right-panel-container.right-panel-open{width:100%!important;min-width:0!important}.right-panel-container.right-panel-closed{border-left:none!important;width:0!important;min-width:0!important;display:none!important}}.docx-preview-container .docx-preview{color:#333;padding:40px 48px;font-family:-apple-system,BlinkMacSystemFont,Segoe UI,Roboto,sans-serif;line-height:1.6}.docx-preview-container .docx-preview h1,.docx-preview-container .docx-preview h2,.docx-preview-container .docx-preview h3{color:#1a1a1a;margin-top:1em;margin-bottom:.5em}.docx-preview-container .docx-preview p{margin-bottom:.5em}.docx-preview-container .docx-preview table{border-collapse:collapse;width:100%;margin:8px 0}.docx-preview-container .docx-preview td,.docx-preview-container .docx-preview th{text-align:left;border:1px solid #ddd;padding:6px 10px}.docx-preview-container .docx-preview img{max-width:100%;height:auto}.xlsx-preview table{border-collapse:collapse;font-size:12px;font-family:var(--font-mono);background:#fff}.xlsx-preview td,.xlsx-preview th{border:1px solid var(--border);white-space:nowrap;text-overflow:ellipsis;max-width:300px;padding:4px 8px;overflow:hidden}.xlsx-preview th{background:var(--bg-panel);color:var(--text);font-weight:600;position:sticky;top:0}@property --tw-rotate-x{syntax:"*";inherits:false}@property --tw-rotate-y{syntax:"*";inherits:false}@property --tw-rotate-z{syntax:"*";inherits:false}@property --tw-skew-x{syntax:"*";inherits:false}@property --tw-skew-y{syntax:"*";inherits:false}@property --tw-border-style{syntax:"*";inherits:false;initial-value:solid}@property --tw-leading{syntax:"*";inherits:false}@property --tw-ordinal{syntax:"*";inherits:false}@property --tw-slashed-zero{syntax:"*";inherits:false}@property --tw-numeric-figure{syntax:"*";inherits:false}@property --tw-numeric-spacing{syntax:"*";inherits:false}@property --tw-numeric-fraction{syntax:"*";inherits:false}@property --tw-outline-style{syntax:"*";inherits:false;initial-value:solid}@property --tw-blur{syntax:"*";inherits:false}@property --tw-brightness{syntax:"*";inherits:false}@property --tw-contrast{syntax:"*";inherits:false}@property --tw-grayscale{syntax:"*";inherits:false}@property --tw-hue-rotate{syntax:"*";inherits:false}@property --tw-invert{syntax:"*";inherits:false}@property --tw-opacity{syntax:"*";inherits:false}@property --tw-saturate{syntax:"*";inherits:false}@property --tw-sepia{syntax:"*";inherits:false}@property --tw-drop-shadow{syntax:"*";inherits:false}@property --tw-drop-shadow-color{syntax:"*";inherits:false}@property --tw-drop-shadow-alpha{syntax:"<percentage>";inherits:false;initial-value:100%}@property --tw-drop-shadow-size{syntax:"*";inherits:false}@property --tw-backdrop-blur{syntax:"*";inherits:false}@property --tw-backdrop-brightness{syntax:"*";inherits:false}@property --tw-backdrop-contrast{syntax:"*";inherits:false}@property --tw-backdrop-grayscale{syntax:"*";inherits:false}@property --tw-backdrop-hue-rotate{syntax:"*";inherits:false}@property --tw-backdrop-invert{syntax:"*";inherits:false}@property --tw-backdrop-opacity{syntax:"*";inherits:false}@property --tw-backdrop-saturate{syntax:"*";inherits:false}@property --tw-backdrop-sepia{syntax:"*";inherits:false}@property --tw-ease{syntax:"*";inherits:false}

package/bin/annodex.js

@@ -25,6 +25,8 @@ const bcrypt = require("bcryptjs");
 const https = require("https");
 // eslint-disable-next-line @typescript-eslint/no-require-imports
 const { randomBytes } = require("crypto");
+// eslint-disable-next-line @typescript-eslint/no-require-imports
+const { readAppSettings, ensureAppSettings } = require("../lib/app-settings.js");
 
 const pkgDir = path.join(__dirname, "..");
 const nextDir = path.join(pkgDir, ".next");
@@ -55,7 +57,6 @@ const STOP_TERM_TIMEOUT_MS = 6000;
 const STOP_KILL_TIMEOUT_MS = 2000;
 const PROCESS_TITLE = "annodex";
 const NEXT_PROCESS_TITLE = "annodex-next";
-const AUTO_RESTART_ENABLED = !/^(0|false|no)$/i.test(envFirst("ANNODEX_AUTO_RESTART", "ANNOVIBE_AUTO_RESTART") ?? "1");
 const AUTO_RESTART_POLL_MS = parsePositiveInt(envFirst("ANNODEX_AUTO_RESTART_POLL_MS", "ANNOVIBE_AUTO_RESTART_POLL_MS"), 60_000);
 const AUTO_RESTART_IDLE_GRACE_MS = parsePositiveInt(envFirst("ANNODEX_AUTO_RESTART_IDLE_GRACE_MS", "ANNOVIBE_AUTO_RESTART_IDLE_GRACE_MS"), 10_000);
 const AUTO_RESTART_MAX_WAIT_MS = parsePositiveInt(envFirst("ANNODEX_AUTO_RESTART_MAX_WAIT_MS", "ANNOVIBE_AUTO_RESTART_MAX_WAIT_MS"), 30 * 60_000);
@@ -272,6 +273,14 @@ function writeState(state) {
   fs.writeFileSync(stateFile, JSON.stringify({ ...state, updatedAt: nowIso() }, null, 2));
 }
 
+function autoRestartEnabled() {
+  const envValue = envFirst("ANNODEX_AUTO_RESTART", "ANNOVIBE_AUTO_RESTART");
+  if (envValue !== undefined) return !/^(0|false|no)$/i.test(envValue);
+  const settings = readAppSettings();
+  if (typeof settings.autoRestart === "boolean") return settings.autoRestart;
+  return true;
+}
+
 function findListeningPids(listenPort) {
   if (process.platform === "win32") return [];
   const pids = new Set();
@@ -572,6 +581,7 @@ async function startManagedServerWithPort(overridePort, overrideHost) {
 
 async function startManagedServer({ quiet = false, effectivePort: optPort, effectiveHost: optHost } = {}) {
   seedDefaults();
+  ensureAppSettings({ autoRestart: true });
   await maybeSetupAuth();
   if (!fs.existsSync(nextDir)) {
     console.error("Build artifacts not found. Please report this issue.");
@@ -668,18 +678,12 @@ Usage:
   annodex update          Update to the latest version
 
 Options:
-  -p, --port <port>     Port to listen on (default: 30121, env: PORT)
+  -p, --port <port>     Port to listen on (default: 30121)
   -H, --hostname <host> Hostname to bind to (default: localhost)
       --json            Print machine-readable status JSON
   -f, --follow          Follow logs
   -v, --version         Print version
   -h, --help            Show this help
-
-Environment:
-  PORT                  Server port
-  ANNODEX_PASSWORD     Set password on first start
-  ANNODEX_AUTO_RESTART Set 0/false/no to disable idle auto-restart after update
-  PI_CODING_AGENT_DIR   Custom pi agent data directory
 `);
   process.exit(0);
 }
@@ -903,8 +907,6 @@ function openBrowser(url) {
 }
 
 function startAutoRestartWatcher({ child, internalToken, writeCurrentState, markRestarting }) {
-  if (!AUTO_RESTART_ENABLED) return () => {};
-
   let pending = null;
   let idleSince = null;
   let restarting = false;
@@ -912,6 +914,14 @@ function startAutoRestartWatcher({ child, internalToken, writeCurrentState, mark
 
   const poll = async () => {
     if (restarting) return;
+    if (!autoRestartEnabled()) {
+      if (pending) {
+        pending = null;
+        idleSince = null;
+        writeCurrentState({ restartPending: false, installedVersion: null, restartDetectedAt: null, restartStartedAt: null });
+      }
+      return;
+    }
     const installedVersion = readInstalledVersion();
     if (!installedVersion || installedVersion === VERSION) {
       if (pending) {
@@ -1015,6 +1025,7 @@ function startAutoRestartWatcher({ child, internalToken, writeCurrentState, mark
 
 async function runServerProcess() {
   setStableProcessTitle(PROCESS_TITLE);
+  ensureAppSettings({ autoRestart: true });
   await maybeSetupAuth();
   if (!fs.existsSync(nextDir)) {
     console.error("Build artifacts not found. Please report this issue.");

package/lib/app-settings.js

@@ -0,0 +1,61 @@
+"use strict";
+/* eslint-disable @typescript-eslint/no-require-imports */
+
+const fs = require("fs");
+const path = require("path");
+const os = require("os");
+
+function getConfigDir() {
+  return process.env.ANNODEX_CONFIG_DIR
+    ?? process.env.ANNOVIBE_CONFIG_DIR
+    ?? path.join(os.homedir(), ".config", "annodex");
+}
+
+function getSettingsPath() {
+  return path.join(getConfigDir(), "settings.json");
+}
+
+function isRecord(value) {
+  return typeof value === "object" && value !== null && !Array.isArray(value);
+}
+
+function readRawSettings() {
+  const file = getSettingsPath();
+  if (!fs.existsSync(file)) return {};
+  try {
+    const parsed = JSON.parse(fs.readFileSync(file, "utf8"));
+    return isRecord(parsed) ? parsed : {};
+  } catch {
+    return {};
+  }
+}
+
+function readAppSettings() {
+  const raw = readRawSettings();
+  return {
+    autoRestart: typeof raw.autoRestart === "boolean" ? raw.autoRestart : undefined,
+  };
+}
+
+function writeAppSettings(patch) {
+  const dir = getConfigDir();
+  if (!fs.existsSync(dir)) fs.mkdirSync(dir, { recursive: true });
+  const next = {
+    ...readRawSettings(),
+    ...(typeof patch?.autoRestart === "boolean" ? { autoRestart: patch.autoRestart } : {}),
+  };
+  fs.writeFileSync(getSettingsPath(), JSON.stringify(next, null, 2), "utf8");
+  return readAppSettings();
+}
+
+function ensureAppSettings(defaults = { autoRestart: true }) {
+  const current = readRawSettings();
+  if (typeof current.autoRestart === "boolean") return readAppSettings();
+  return writeAppSettings(defaults);
+}
+
+module.exports = {
+  readAppSettings,
+  writeAppSettings,
+  ensureAppSettings,
+};

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@seqyuan/annodex",
-  "version": "0.1.24",
+  "version": "0.1.25",
   "description": "AI-native bioinformatics workspace by Annoroad",
   "license": "MIT",
   "bin": {
@@ -15,6 +15,7 @@
     "!.next/**/*.js.map",
     "!.next/trace",
     "!.next/trace-build",
+    "lib/app-settings.js",
     "lib/default-SOUL.md",
     "lib/default-HARNESS.md",
     "public",