@seqyuan/annodex 0.1.66 → 0.1.67

package/README.md

@@ -2,7 +2,7 @@
 
 AI-native bioinformatics workspace by Annoroad, backed by Codex app-server. Browser workspace for project-scoped agent chat, file preview, extensions, and multi-provider models.
 
-Version: `0.1.66`  
+Version: `0.1.67`  
 Repository: [seqyuan/annodex](https://github.com/seqyuan/annodex)  
 Docs site: see [`site/`](site/) (Fumadocs)
 

package/bin/annodex-im-gateway.js

@@ -454,11 +454,16 @@ class ProjectWeComBridge {
         chatId: inbound.chatId,
       });
 
+      if (result.ok === false) {
+        console.error(`[im] turn failed for ${this.project.cwd} user ${inbound.userId}: ${result.error || result.reply || "unknown error"}`);
+      }
+
       const text = typeof result.reply === "string" && result.reply.trim()
         ? result.reply.trim()
         : (result.error ? String(result.error) : "No reply from annodex.");
       await reply.finish(text);
     } catch (error) {
+      console.error(`[im] turn request failed for ${this.project.cwd} user ${inbound.userId}: ${String(error)}`);
       await reply.fail(`annodex IM error: ${String(error)}`);
     } finally {
       if (refreshTimer) clearInterval(refreshTimer);

package/bin/annodex.js

@@ -535,12 +535,28 @@ function waitForPidExit(pid, timeoutMs) {
 
 async function terminatePid(pid, termTimeoutMs = STOP_TERM_TIMEOUT_MS, killTimeoutMs = STOP_KILL_TIMEOUT_MS) {
   if (!isPidAlive(pid)) return true;
+  if (process.platform === "linux") {
+    try {
+      process.kill(-pid, "SIGTERM");
+      if (await waitForPidExit(pid, termTimeoutMs)) return true;
+    } catch {
+      // Process may not be a group leader; fall back to single-pid termination.
+    }
+  }
   try {
     process.kill(pid, "SIGTERM");
   } catch {
     return !isPidAlive(pid);
   }
   if (await waitForPidExit(pid, termTimeoutMs)) return true;
+  if (process.platform === "linux") {
+    try {
+      process.kill(-pid, "SIGKILL");
+      if (await waitForPidExit(pid, killTimeoutMs)) return true;
+    } catch {
+      // ignore
+    }
+  }
   try {
     process.kill(pid, "SIGKILL");
   } catch {
@@ -549,6 +565,81 @@ async function terminatePid(pid, termTimeoutMs = STOP_TERM_TIMEOUT_MS, killTimeo
   return waitForPidExit(pid, killTimeoutMs);
 }
 
+function looksLikeAnnodexCodexAppServer(cmdline) {
+  if (!cmdline) return false;
+  const lower = cmdline.toLowerCase();
+  if (!lower.includes("app-server")) return false;
+  return (
+    lower.includes("annodex-router") ||
+    lower.includes("model_providers.annodex-router") ||
+    lower.includes("@seqyuan/annodex") ||
+    lower.includes("/annodex/") ||
+    lower.includes("\\annodex\\")
+  );
+}
+
+function looksLikeAnnodexImGateway(cmdline) {
+  return !!cmdline && cmdline.includes("annodex-im-gateway");
+}
+
+function listProcessPids() {
+  const pids = [];
+  if (process.platform === "linux") {
+    try {
+      for (const entry of fs.readdirSync("/proc")) {
+        if (/^\d+$/.test(entry)) {
+          const pid = Number(entry);
+          if (Number.isInteger(pid) && pid > 0) pids.push(pid);
+        }
+      }
+      return pids;
+    } catch {
+      // Fall through to ps.
+    }
+  }
+  try {
+    const result = spawnSync("ps", ["-eo", "pid="], { encoding: "utf8" });
+    if (result.status === 0) {
+      for (const line of result.stdout.split(/\r?\n/)) {
+        const pid = Number(line.trim());
+        if (Number.isInteger(pid) && pid > 0) pids.push(pid);
+      }
+    }
+  } catch {
+    // ignore
+  }
+  return pids;
+}
+
+function findMatchingProcessPids(matcher) {
+  const pids = new Set();
+  for (const pid of listProcessPids()) {
+    if (pid === process.pid) continue;
+    const cmdline = readProcessCmdline(pid);
+    if (matcher(cmdline)) pids.add(pid);
+  }
+  return [...pids];
+}
+
+async function stopMatchingProcesses(matcher, label, quiet = false) {
+  const pids = findMatchingProcessPids(matcher);
+  if (pids.length === 0) return { found: 0, stopped: true, pids: [] };
+
+  let stopped = true;
+  for (const pid of pids) {
+    stopped = (await terminatePid(pid)) && stopped;
+  }
+
+  if (!quiet) {
+    const pidList = pids.join(", ");
+    console.log(stopped
+      ? `annodex stop: stopped ${pids.length} ${label}${pids.length === 1 ? "" : "es"} (pid${pids.length === 1 ? "" : "s"} ${pidList})`
+      : `annodex stop: failed to stop some ${label} processes (pids ${pidList})`);
+  }
+
+  return { found: pids.length, stopped, pids };
+}
+
 function renderState(state, json = false) {
   const supervisorAlive = !!state && isPidAlive(state.supervisorPid);
   const nextAlive = !!state && isPidAlive(state.nextPid);
@@ -614,7 +705,9 @@ async function stopManagedServer(quiet = false) {
   const state = readState();
   if (!state) {
     const portStop = await stopVerifiedPortListeners(port, quiet);
-    if (portStop.found) return portStop.stopped ? 0 : 1;
+    const codexStop = await stopMatchingProcesses(looksLikeAnnodexCodexAppServer, "orphaned codex app-server process", quiet);
+    if (portStop.found) return portStop.stopped && codexStop.stopped ? 0 : 1;
+    if (codexStop.found > 0) return codexStop.stopped ? 0 : 1;
     if (!quiet) console.log("annodex stop: already stopped");
     return 0;
   }
@@ -630,9 +723,12 @@ async function stopManagedServer(quiet = false) {
   }
   if (stopped) {
     removeState();
+    const codexStop = await stopMatchingProcesses(looksLikeAnnodexCodexAppServer, "orphaned codex app-server process", quiet);
     if (!quiet) console.log(`annodex stop: stopped${supervisorPid ? ` pid ${supervisorPid}` : ""}`);
+    if (!codexStop.stopped) return 1;
     return 0;
   }
+  await stopMatchingProcesses(looksLikeAnnodexCodexAppServer, "orphaned codex app-server process", quiet);
   if (!quiet) console.error(`annodex stop: failed to stop pid ${supervisorPid}`);
   return 1;
 }
@@ -967,6 +1063,14 @@ function runDoctor(json = false, repair = false) {
   }
   if (report.codex.selected.exists === false) report.recommendations.push("ANNODEX_CODEX_PATH is set but does not exist. Fix or unset it.");
   if (versionProbe && !versionProbe.ok) report.recommendations.push("codex --version probe failed. Check the selected codex path and macOS security dialogs/logs.");
+  const orphanCodexPids = findMatchingProcessPids(looksLikeAnnodexCodexAppServer);
+  if (orphanCodexPids.length > 0) {
+    report.recommendations.push(`Found ${orphanCodexPids.length} orphaned codex app-server process${orphanCodexPids.length === 1 ? "" : "es"} (pids ${orphanCodexPids.join(", ")}). Run \`annodex stop\` to clean them up.`);
+  }
+  const orphanGatewayPids = findMatchingProcessPids(looksLikeAnnodexImGateway);
+  if (orphanGatewayPids.length > 0 && !isPidAlive(readState()?.supervisorPid)) {
+    report.recommendations.push(`annodex-im-gateway is running (pids ${orphanGatewayPids.join(", ")}) but annodex is stopped — IM replies need annodex running; the gateway can stay up.`);
+  }
 
   if (json) {
     console.log(JSON.stringify(report, null, 2));
@@ -1025,7 +1129,7 @@ Usage:
   annodex [options]
   annodex start          Start annodex in background
   annodex restart        Stop then start annodex in background
-  annodex stop           Stop background annodex
+  annodex stop           Stop background annodex (and orphaned codex app-server processes)
   annodex status [--json] Show background server status
   annodex logs [-f]      Show background server logs
   annodex doctor [--json] [--repair] Diagnose local codex/runtime setup

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@seqyuan/annodex",
-  "version": "0.1.66",
+  "version": "0.1.67",
   "description": "AI-native bioinformatics workspace by Annoroad",
   "license": "MIT",
   "bin": {