@evomap/evolver 1.78.9 → 1.79.0

package/README.ja-JP.md

@@ -4,6 +4,7 @@
 [![License: GPL-3.0](https://img.shields.io/badge/License-GPL--3.0-blue.svg)](https://opensource.org/licenses/GPL-3.0)
 [![Node.js >= 18](https://img.shields.io/badge/Node.js-%3E%3D%2018-green.svg)](https://nodejs.org/)
 [![GitHub last commit](https://img.shields.io/github/last-commit/EvoMap/evolver)](https://github.com/EvoMap/evolver/commits/main)
+[![npm downloads](https://img.shields.io/npm/dm/@evomap/evolver.svg)](https://www.npmjs.com/package/@evomap/evolver)
 [![GitHub issues](https://img.shields.io/github/issues/EvoMap/evolver)](https://github.com/EvoMap/evolver/issues)
 [![arXiv](https://img.shields.io/badge/arXiv-2604.15097-b31b1b.svg)](https://arxiv.org/abs/2604.15097)
 

package/README.ko-KR.md

@@ -4,6 +4,7 @@
 [![License: GPL-3.0](https://img.shields.io/badge/License-GPL--3.0-blue.svg)](https://opensource.org/licenses/GPL-3.0)
 [![Node.js >= 18](https://img.shields.io/badge/Node.js-%3E%3D%2018-green.svg)](https://nodejs.org/)
 [![GitHub last commit](https://img.shields.io/github/last-commit/EvoMap/evolver)](https://github.com/EvoMap/evolver/commits/main)
+[![npm downloads](https://img.shields.io/npm/dm/@evomap/evolver.svg)](https://www.npmjs.com/package/@evomap/evolver)
 [![GitHub issues](https://img.shields.io/github/issues/EvoMap/evolver)](https://github.com/EvoMap/evolver/issues)
 [![arXiv](https://img.shields.io/badge/arXiv-2604.15097-b31b1b.svg)](https://arxiv.org/abs/2604.15097)
 

package/README.md

@@ -4,6 +4,7 @@
 [![License: GPL-3.0](https://img.shields.io/badge/License-GPL--3.0-blue.svg)](https://opensource.org/licenses/GPL-3.0)
 [![Node.js >= 18](https://img.shields.io/badge/Node.js-%3E%3D%2018-green.svg)](https://nodejs.org/)
 [![GitHub last commit](https://img.shields.io/github/last-commit/EvoMap/evolver)](https://github.com/EvoMap/evolver/commits/main)
+[![npm downloads](https://img.shields.io/npm/dm/@evomap/evolver.svg)](https://www.npmjs.com/package/@evomap/evolver)
 [![GitHub issues](https://img.shields.io/github/issues/EvoMap/evolver)](https://github.com/EvoMap/evolver/issues)
 [![arXiv](https://img.shields.io/badge/arXiv-2604.15097-b31b1b.svg)](https://arxiv.org/abs/2604.15097)
 

package/README.zh-CN.md

@@ -4,6 +4,7 @@
 [![License: GPL-3.0](https://img.shields.io/badge/License-GPL--3.0-blue.svg)](https://opensource.org/licenses/GPL-3.0)
 [![Node.js >= 18](https://img.shields.io/badge/Node.js-%3E%3D%2018-green.svg)](https://nodejs.org/)
 [![GitHub last commit](https://img.shields.io/github/last-commit/EvoMap/evolver)](https://github.com/EvoMap/evolver/commits/main)
+[![npm downloads](https://img.shields.io/npm/dm/@evomap/evolver.svg)](https://www.npmjs.com/package/@evomap/evolver)
 [![GitHub issues](https://img.shields.io/github/issues/EvoMap/evolver)](https://github.com/EvoMap/evolver/issues)
 [![arXiv](https://img.shields.io/badge/arXiv-2604.15097-b31b1b.svg)](https://arxiv.org/abs/2604.15097)
 

package/index.js

@@ -104,6 +104,42 @@ function parseMs(v, fallback) {
   return fallback;
 }
 
+function parseBoolEnv(v, fallback) {
+  if (v == null) return fallback;
+  const s = String(v).toLowerCase().trim();
+  if (s === '' ) return fallback;
+  if (s === 'false' || s === '0' || s === 'off' || s === 'no') return false;
+  if (s === 'true' || s === '1' || s === 'on' || s === 'yes') return true;
+  return fallback;
+}
+
+class CycleTimeoutError extends Error {
+  constructor(timeoutMs, phase, cycleNum) {
+    super('Cycle hard-timeout exceeded after ' + timeoutMs + 'ms (cycle=' + cycleNum + ', phase=' + phase + ')');
+    this.name = 'CycleTimeoutError';
+    this.code = 'CYCLE_TIMEOUT';
+    this.timeoutMs = timeoutMs;
+    this.phase = phase;
+    this.cycleNum = cycleNum;
+  }
+}
+
+// Atomic write of the cycle_progress.json file. Wrapper polls this file every
+// 60s; if updated_at goes stale beyond EVOLVE_INNER_STUCK_TIMEOUT_SEC the
+// wrapper treats the inner core as zombie and SIGKILLs it. See Issue #19 (the
+// 22-day stuck-cycle incident) and the cross-repo timeout plan for context.
+function writeCycleProgressAtomic(progressPath, fields) {
+  try {
+    const data = Object.assign({}, fields, { updated_at: Date.now() });
+    const tmp = progressPath + '.tmp.' + process.pid;
+    fs.writeFileSync(tmp, JSON.stringify(data, null, 2) + '\n', 'utf8');
+    fs.renameSync(tmp, progressPath);
+    return true;
+  } catch (e) {
+    return false;
+  }
+}
+
 function getLastSignals(statePath) {
   try {
     const st = readJsonSafe(statePath);
@@ -255,6 +291,7 @@ async function main() {
 
         const { getEvolutionDir, getEvolverLogPath } = require('./src/gep/paths');
         const solidifyStatePath = path.join(getEvolutionDir(), 'evolution_solidify_state.json');
+        const cycleProgressPath = path.join(getEvolutionDir(), 'cycle_progress.json');
 
         const minSleepMs = parseMs(process.env.EVOLVER_MIN_SLEEP_MS, 2000);
         const maxSleepMs = parseMs(process.env.EVOLVER_MAX_SLEEP_MS, 300000);
@@ -270,6 +307,15 @@ async function main() {
         const maxRssMb = parseMs(process.env.EVOLVER_MAX_RSS_MB, 500) || 500;
         const suicideEnabled = String(process.env.EVOLVER_SUICIDE || '').toLowerCase() !== 'false';
 
+        // Issue #19: hard timeout around evolve.run() to break out of zombie
+        // cycles (e.g. unclosed socket / stuck LLM call). On timeout we throw
+        // CycleTimeoutError, log diagnostic stderr, and force suicide-respawn
+        // so the wrapper sees a fresh PID + cycle. Also write cycle_progress
+        // every progressUpdateMs so the wrapper has a true heartbeat to poll.
+        const cycleTimeoutEnabled = parseBoolEnv(process.env.EVOLVER_CYCLE_TIMEOUT_ENABLED, true);
+        const cycleTimeoutMs = parseMs(process.env.EVOLVER_CYCLE_TIMEOUT_MS, 2700000); // 45 min default
+        const progressUpdateMs = parseMs(process.env.EVOLVER_PROGRESS_UPDATE_MS, 60000); // 1 min default
+
         // Start hub heartbeat (keeps node alive independently of evolution cycles)
         try {
           if (process.env.EVOMAP_PROXY === '1' || process.env.A2A_TRANSPORT === 'mailbox') {
@@ -388,8 +434,46 @@ async function main() {
 
           const t0 = Date.now();
           let ok = false;
+          // Issue #19: write progress at cycle start, refresh it every
+          // progressUpdateMs (default 60s) while evolve.run() is active, and
+          // wrap evolve.run() with Promise.race(timeout) so a hung internal
+          // call cannot freeze the daemon for days.
+          writeCycleProgressAtomic(cycleProgressPath, {
+            pid: process.pid,
+            outer_cycle: cycleCount,
+            inner_cycle: cycleCount,
+            started_at: t0,
+            phase: 'evolve.run',
+          });
+          let progressTicker = null;
+          if (progressUpdateMs > 0) {
+            progressTicker = setInterval(function () {
+              writeCycleProgressAtomic(cycleProgressPath, {
+                pid: process.pid,
+                outer_cycle: cycleCount,
+                inner_cycle: cycleCount,
+                started_at: t0,
+                phase: 'evolve.run',
+              });
+            }, progressUpdateMs);
+            if (typeof progressTicker.unref === 'function') progressTicker.unref();
+          }
+          let cycleTimeoutHandle = null;
+          let cycleTimedOut = false;
           try {
-            await evolve.run();
+            const evolvePromise = evolve.run();
+            if (cycleTimeoutEnabled && cycleTimeoutMs > 0) {
+              const timeoutPromise = new Promise(function (_, reject) {
+                cycleTimeoutHandle = setTimeout(function () {
+                  cycleTimedOut = true;
+                  reject(new CycleTimeoutError(cycleTimeoutMs, 'evolve.run', cycleCount));
+                }, cycleTimeoutMs);
+                if (cycleTimeoutHandle && typeof cycleTimeoutHandle.unref === 'function') cycleTimeoutHandle.unref();
+              });
+              await Promise.race([evolvePromise, timeoutPromise]);
+            } else {
+              await evolvePromise;
+            }
             ok = true;
 
             if (String(process.env.EVOLVE_BRIDGE || '').toLowerCase() === 'false') {
@@ -403,7 +487,37 @@ async function main() {
             }
           } catch (error) {
             const msg = error && error.message ? String(error.message) : String(error);
+            if (error && error.code === 'CYCLE_TIMEOUT') {
+              console.error('[Daemon] ' + msg);
+              if (progressTicker) { clearInterval(progressTicker); progressTicker = null; }
+              if (cycleTimeoutHandle) { clearTimeout(cycleTimeoutHandle); cycleTimeoutHandle = null; }
+              writeCycleProgressAtomic(cycleProgressPath, {
+                pid: process.pid,
+                outer_cycle: cycleCount,
+                inner_cycle: cycleCount,
+                started_at: t0,
+                phase: 'cycle_timeout_respawn',
+              });
+              try {
+                const logFd = fs.openSync(getEvolverLogPath(), 'a');
+                const spawnOpts = {
+                  detached: true,
+                  stdio: ['ignore', logFd, logFd],
+                  env: process.env,
+                  windowsHide: true,
+                };
+                const child = spawn(process.execPath, [__filename, ...args], spawnOpts);
+                child.unref();
+              } catch (spawnErr) {
+                console.error('[Daemon] Force-restart spawn after cycle timeout failed: ' + (spawnErr && spawnErr.message || spawnErr));
+              }
+              releaseLock();
+              process.exit(1);
+            }
             console.error(`Evolution cycle failed: ${msg}`);
+          } finally {
+            if (progressTicker) { clearInterval(progressTicker); progressTicker = null; }
+            if (cycleTimeoutHandle) { clearTimeout(cycleTimeoutHandle); cycleTimeoutHandle = null; }
           }
           const dt = Date.now() - t0;
 
@@ -496,6 +610,13 @@ async function main() {
             const signals = getLastSignals(solidifyStatePath).join(',');
             console.log(`[Verbose] cycle=${cycleCount} ok=${ok} dt=${dt}ms sleep=${totalSleepMs}ms (base=${currentSleepMs} jitter=${jitter} sat=${saturationMultiplier}x) rss=${memMb}MB signals=[${signals}]`);
           }
+          writeCycleProgressAtomic(cycleProgressPath, {
+            pid: process.pid,
+            outer_cycle: cycleCount,
+            inner_cycle: cycleCount,
+            started_at: t0,
+            phase: 'sleep',
+          });
           await sleepMs(totalSleepMs);
 
           } catch (loopErr) {
@@ -1097,6 +1218,7 @@ async function main() {
       })();
       const dryRun = args.includes('--dry-run');
       const listUnpublished = !args.includes('--no-unpublished-list');
+      const force = args.includes('--force');
       const limitPerPage = 100;
 
       const validScopes = new Set(['all', 'purchased', 'published']);
@@ -1173,11 +1295,25 @@ async function main() {
 
       const existingGenes = loadGenes();
       const existingCapsules = loadCapsules();
+      // Dedup by Hub asset_id is the only safe key. Local-facing `id` (e.g.
+      // `gene_gep_repair_from_errors`) collides between bundled default seed
+      // genes and identically-named assets that the user later published, so
+      // dedup-by-id silently skips legitimate Hub copies on first sync. Track
+      // hub_asset_id (set by previous syncs / publishes) and only skip when
+      // we've already seen the same Hub-side identity.
+      const localHubAssetIds = new Set();
+      for (const g of existingGenes) {
+        if (g && g.hub_asset_id) localHubAssetIds.add(String(g.hub_asset_id));
+      }
+      for (const c of existingCapsules) {
+        if (c && c.hub_asset_id) localHubAssetIds.add(String(c.hub_asset_id));
+      }
       const localGeneIds = new Set(existingGenes.filter(function (g) { return g && g.id; }).map(function (g) { return g.id; }));
       const localCapsuleIds = new Set(existingCapsules.filter(function (c) { return c && c.id; }).map(function (c) { return c.id; }));
 
       let synced = 0;
-      let skipped = 0;
+      let skippedAlreadySynced = 0;
+      let skippedIdCollision = 0;
       let fetchErrors = 0;
 
       for (const asset of allAssets) {
@@ -1186,14 +1322,37 @@ async function main() {
         const localId = asset.local_id || assetId;
 
         if (assetType !== 'Gene' && assetType !== 'Capsule') {
-          skipped++;
+          skippedAlreadySynced++;
+          continue;
+        }
+
+        // Already-synced check: same Hub asset_id is already in our local
+        // store. Idempotent skip; safe to no-op even with --force because
+        // re-fetching the same payload would only rewrite identical bytes.
+        if (!force && localHubAssetIds.has(String(assetId))) {
+          skippedAlreadySynced++;
           continue;
         }
-        if (assetType === 'Gene' && localGeneIds.has(localId)) { skipped++; continue; }
-        if (assetType === 'Capsule' && localCapsuleIds.has(localId)) { skipped++; continue; }
+
+        // Local-id collision: a local entry with the same user-facing id
+        // already exists but has no hub_asset_id (e.g. bundled default seed
+        // gene, or a hand-edited entry). Without --force we keep the
+        // user-owned entry and warn so the user can decide.
+        if (!force) {
+          if (assetType === 'Gene' && localGeneIds.has(localId)) {
+            if (isVerbose) console.warn('  [sync] Skipping ' + localId + ' (local id collision; pass --force to overwrite with Hub copy)');
+            skippedIdCollision++;
+            continue;
+          }
+          if (assetType === 'Capsule' && localCapsuleIds.has(localId)) {
+            if (isVerbose) console.warn('  [sync] Skipping ' + localId + ' (local id collision; pass --force to overwrite with Hub copy)');
+            skippedIdCollision++;
+            continue;
+          }
+        }
 
         if (dryRun) {
-          console.log('  [dry-run] Would sync: ' + assetType + ' ' + assetId);
+          console.log('  [dry-run] Would sync: ' + assetType + ' ' + assetId + (force ? ' (force)' : ''));
           synced++;
           continue;
         }
@@ -1230,6 +1389,7 @@ async function main() {
             };
             upsertGene(geneObj);
             localGeneIds.add(geneObj.id);
+            localHubAssetIds.add(String(assetId));
           } else {
             const capsuleObj = {
               type: 'Capsule',
@@ -1244,6 +1404,7 @@ async function main() {
             };
             upsertCapsule(capsuleObj);
             localCapsuleIds.add(capsuleObj.id);
+            localHubAssetIds.add(String(assetId));
           }
           synced++;
         } catch (fetchErr) {
@@ -1252,7 +1413,12 @@ async function main() {
         }
       }
 
-      console.log('[sync] Done. scope=' + scopeArg + ' synced=' + synced + ' skipped=' + skipped + ' errors=' + fetchErrors);
+      const skippedTotal = skippedAlreadySynced + skippedIdCollision;
+      console.log('[sync] Done. scope=' + scopeArg + ' synced=' + synced + ' skipped=' + skippedTotal + ' (already_synced=' + skippedAlreadySynced + ', id_collision=' + skippedIdCollision + ') errors=' + fetchErrors);
+      if (skippedIdCollision > 0 && !force) {
+        console.log('[sync] ' + skippedIdCollision + ' Hub asset(s) share a local id with an existing local entry that has no hub_asset_id.');
+        console.log('[sync] Re-run with --force to overwrite those local entries with the Hub copies.');
+      }
       if (dryRun) console.log('[sync] (dry-run mode: no files were modified)');
 
       if (listUnpublished && doPublished) {
@@ -1467,6 +1633,7 @@ async function main() {
     - --status=draft,promoted,all       (only for published scope; default promoted+draft)
     - --export=<path.gepx>              (also bundle local assets into a .gepx archive)
     - --no-unpublished-list             (suppress local-only asset list)
+    - --force                           (overwrite local entries that share an id with a Hub asset; bypasses default-seed dedup)
     - --dry-run                         (preview without writing to local store)
   - solidify flags:
     - --dry-run
@@ -1535,4 +1702,7 @@ module.exports = {
   readJsonSafe,
   rejectPendingRun,
   isPendingSolidify,
+  parseBoolEnv,
+  CycleTimeoutError,
+  writeCycleProgressAtomic,
 };

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@evomap/evolver",
-  "version": "1.78.9",
+  "version": "1.79.0",
   "description": "A GEP-powered self-evolution engine for AI agents. Features automated log analysis and Genome Evolution Protocol (GEP) for auditable, reusable evolution assets.",
   "main": "index.js",
   "bin": {