@bgicli/bgicli 2.3.5 → 2.3.7

package/dist/bgi.js

@@ -13855,7 +13855,7 @@ var TOOL_DEFINITIONS = [
           },
           timeout_ms: {
             type: "number",
-            description: "Timeout in milliseconds (default 300000 / 5 min, max 1800000 / 30 min for long jobs like STAR alignment)"
+            description: "Timeout in milliseconds (default 300000 / 5 min). For downloads (wget/curl/aria2c) or long computations (STAR, HISAT2, etc.) ALWAYS use at least 3600000 (60 min). Never set a short timeout for downloads \u2014 slow networks are normal, be patient."
           }
         },
         required: ["command"]
@@ -13959,13 +13959,14 @@ var TOOL_DEFINITIONS = [
 async function executeTool(name, args, onStream) {
   try {
     switch (name) {
-      case "bash":
-        return await toolBash(
-          args["command"],
-          args["workdir"],
-          args["timeout_ms"] ?? 3e5,
-          onStream
-        );
+      case "bash": {
+        const cmd = args["command"];
+        let timeoutMs = args["timeout_ms"] ?? 3e5;
+        if (/\b(wget|curl|aria2c|axel|rsync)\b/.test(cmd) && timeoutMs < 36e5) {
+          timeoutMs = 36e5;
+        }
+        return await toolBash(cmd, args["workdir"], timeoutMs, onStream);
+      }
       case "read_file":
         return toolReadFile(
           args["path"],
@@ -14297,6 +14298,7 @@ ${label} `);
         let streamedLines = 0;
         let lastLineWasEmpty = false;
         let spinnerCleared = false;
+        let partialLine = "";
         const MAX_STREAM_LINES = 200;
         let frame = 0;
         const spin = setInterval(() => {
@@ -14316,8 +14318,7 @@ ${label} `);
         let heartbeat = null;
         const onStream = isBash ? (chunk) => {
           lastChunkTime = Date.now();
-          if (streamedLines >= MAX_STREAM_LINES) return;
-          if (streamedLines === 0) {
+          if (streamedLines === 0 && partialLine.length === 0) {
             clearSpinner();
             process.stdout.write(`${label}
 `);
@@ -14329,22 +14330,36 @@ ${label} `);
               }
             }, 5e3);
           }
-          const lines = chunk.split("\n");
-          for (let i2 = 0; i2 < lines.length; i2++) {
-            const line = lines[i2];
-            if (line.trim() === "") {
-              if (lastLineWasEmpty) continue;
-              lastLineWasEmpty = true;
-            } else {
-              lastLineWasEmpty = false;
+          let i2 = 0;
+          while (i2 < chunk.length) {
+            const crPos = chunk.indexOf("\r", i2);
+            const nlPos = chunk.indexOf("\n", i2);
+            if (crPos === -1 && nlPos === -1) {
+              partialLine += chunk.slice(i2);
+              process.stdout.write("\r" + source_default.dim("  \u2502 ") + partialLine + "\x1B[K");
+              break;
             }
-            if (i2 < lines.length - 1 || line.length > 0) {
-              process.stdout.write(source_default.dim("  \u2502 ") + line + (i2 < lines.length - 1 ? "\n" : ""));
-              streamedLines++;
-              if (streamedLines >= MAX_STREAM_LINES) {
-                process.stdout.write(source_default.dim("\n  \u2502 ... (\u8F93\u51FA\u8FC7\u957F\uFF0C\u5DF2\u622A\u65AD)\n"));
-                break;
+            const nextPos = crPos === -1 ? nlPos : nlPos === -1 ? crPos : Math.min(crPos, nlPos);
+            const isCR = chunk[nextPos] === "\r";
+            partialLine += chunk.slice(i2, nextPos);
+            if (isCR) {
+              process.stdout.write("\r" + source_default.dim("  \u2502 ") + partialLine + "\x1B[K");
+              partialLine = "";
+              i2 = nextPos + 1;
+              if (i2 < chunk.length && chunk[i2] === "\n") i2++;
+            } else {
+              if (partialLine.trim() !== "" || !lastLineWasEmpty) {
+                if (streamedLines < MAX_STREAM_LINES) {
+                  process.stdout.write("\r" + source_default.dim("  \u2502 ") + partialLine + "\x1B[K\n");
+                  lastLineWasEmpty = partialLine.trim() === "";
+                  streamedLines++;
+                  if (streamedLines >= MAX_STREAM_LINES) {
+                    process.stdout.write(source_default.dim("  \u2502 ... (\u8F93\u51FA\u8FC7\u957F\uFF0C\u5DF2\u622A\u65AD)\n"));
+                  }
+                }
               }
+              partialLine = "";
+              i2 = nextPos + 1;
             }
           }
         } : void 0;
@@ -14353,6 +14368,12 @@ ${label} `);
           clearInterval(heartbeat);
           heartbeat = null;
         }
+        if (partialLine) {
+          if (streamedLines < MAX_STREAM_LINES) {
+            process.stdout.write("\r" + source_default.dim("  \u2502 ") + partialLine + "\x1B[K\n");
+          }
+          partialLine = "";
+        }
         if (stats) {
           if (result.error) stats.failCmds++;
           else stats.successCmds++;
@@ -15941,7 +15962,7 @@ function clearCheckpoints(sessionId) {
 
 // src/index.ts
 var import_fs7 = require("fs");
-var VERSION2 = "2.3.5";
+var VERSION2 = "2.3.7";
 var SKILLHUB_HUBS = {
   bgi: { label: "BGI\u5185\u7F51", apiBase: "https://clawhub.ai", backend: "clawhub" },
   clawhub: { label: "clawhub.ai", apiBase: "https://clawhub.ai", backend: "clawhub" },

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@bgicli/bgicli",
-  "version": "2.3.5",
+  "version": "2.3.7",
   "description": "BGI CLI — Bioinformatics AI terminal for Chinese researchers (百炼/DeepSeek/Kimi/Qwen)",
   "bin": {
     "bgi": "dist/bgi.js"