@bgicli/bgicli 2.2.3 → 2.2.5

package/dist/bgi.js

@@ -13762,21 +13762,35 @@ function executeTool(name, args) {
     return { output: "", error: String(err) };
   }
 }
+function decodeBuffer(buf) {
+  if (!buf) return "";
+  if (typeof buf === "string") return buf;
+  try {
+    return new TextDecoder("utf-8", { fatal: true }).decode(buf);
+  } catch {
+    try {
+      return new TextDecoder("gbk").decode(buf);
+    } catch {
+      return buf.toString("latin1");
+    }
+  }
+}
 function toolBash(command, workdir, timeoutMs = 3e4) {
   try {
-    const out = (0, import_child_process.execSync)(command, {
+    const buf = (0, import_child_process.execSync)(command, {
       cwd: workdir ?? process.cwd(),
       timeout: timeoutMs,
-      encoding: "utf8",
+      encoding: "buffer",
       stdio: ["pipe", "pipe", "pipe"],
-      maxBuffer: 10 * 1024 * 1024
-      // 10 MB
+      maxBuffer: 10 * 1024 * 1024,
+      env: { ...process.env, PYTHONIOENCODING: "utf-8" }
     });
-    return { output: out.trim() };
+    return { output: decodeBuffer(buf).trim() };
   } catch (err) {
     const e2 = err;
-    const out = ((e2.stdout ?? "") + "\n" + (e2.stderr ?? "")).trim();
-    return { output: out, error: e2.message ?? String(err) };
+    const out = (decodeBuffer(e2.stdout) + "\n" + decodeBuffer(e2.stderr)).trim();
+    const cmdLine = (e2.message ?? "Command failed").split("\n")[0];
+    return { output: out, error: cmdLine };
   }
 }
 function toolReadFile(path, maxLines, offset) {
@@ -14103,6 +14117,34 @@ cat ${SKILLS_DIR}/<skill-id>/SKILL.md
 
 ---
 
+## Environment Awareness
+
+**\u9996\u6B21\u8FD0\u884C\u4EFB\u4F55 R/Python/\u751F\u4FE1\u5DE5\u5177\u4E4B\u524D\uFF0C\u5148\u68C0\u67E5\u5B83\u662F\u5426\u5DF2\u5B89\u88C5\uFF1A**
+
+\`\`\`bash
+# \u68C0\u67E5 R
+R --version 2>&1 | head -1
+
+# \u68C0\u67E5 Python
+python --version 2>&1 || python3 --version 2>&1
+
+# \u68C0\u67E5\u5E38\u7528\u751F\u4FE1\u5DE5\u5177
+samtools --version 2>&1 | head -1
+\`\`\`
+
+**\u5DE5\u5177\u672A\u5B89\u88C5\u65F6\u7684\u5904\u7406\u89C4\u5219\uFF08\u6309\u4F18\u5148\u7EA7\uFF09\uFF1A**
+1. \u660E\u786E\u544A\u77E5\u7528\u6237\u8BE5\u5DE5\u5177\u672A\u5B89\u88C5\uFF08\u4E0D\u8981\u7EE7\u7EED\u5047\u8BBE\u53EF\u7528\uFF09
+2. \u7ED9\u51FA\u5BF9\u5E94\u7CFB\u7EDF\u7684\u5B89\u88C5\u547D\u4EE4\uFF1A
+   - R\uFF1Ahttps://cran.r-project.org/ \uFF0CWindows \u63A8\u8350 \`winget install RProject.R\`
+   - Python\uFF1A\`winget install Python.Python.3\` \u6216 https://www.python.org/downloads/
+   - Conda/Mamba\uFF1A\`winget install Anaconda.Miniconda3\`\uFF08\u751F\u4FE1\u5305\u7BA1\u7406\u9996\u9009\uFF09
+   - samtools/STAR \u7B49\uFF1A\u5728 Linux/macOS \u7528 \`conda install -c bioconda <tool>\`
+3. \u8BE2\u95EE\u7528\u6237\u662F\u5426\u9700\u8981\u5E2E\u52A9\u5B8C\u6210\u5B89\u88C5\uFF0C\u6216\u6539\u7528\u5176\u4ED6\u5DF2\u5B89\u88C5\u7684\u5DE5\u5177\u66FF\u4EE3
+
+**\u4E0D\u8981\u5728\u5DE5\u5177\u7F3A\u5931\u65F6\u7EE7\u7EED\u6267\u884C\u4F9D\u8D56\u8BE5\u5DE5\u5177\u7684\u6B65\u9AA4\u3002**
+
+---
+
 ## Script Execution Rules
 
 \u{1F6A8} **\u5173\u952E\u89C4\u5219\uFF1A**

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@bgicli/bgicli",
-  "version": "2.2.3",
+  "version": "2.2.5",
   "description": "BGI CLI — Bioinformatics AI terminal for Chinese researchers (百炼/DeepSeek/Kimi/Qwen)",
   "bin": {
     "bgi": "dist/bgi.js"