@bgicli/bgicli 2.4.6 → 2.4.7

package/dist/bgi.js

@@ -13602,7 +13602,6 @@ var DEFAULT_PROVIDER = "bailian";
 
 // src/config.ts
 var BGI_DIR = (0, import_path2.join)((0, import_os.homedir)(), ".bgicli");
-var WORKFLOWS_DIR = (0, import_path2.join)(BGI_DIR, "workflows");
 var TOOLS_DIR = (0, import_path2.join)(BGI_DIR, "tools");
 var SKILLS_DIR = (0, import_path2.join)(BGI_DIR, "skills");
 var USER_SKILLS_DIR = (0, import_path2.join)(BGI_DIR, "user-skills");
@@ -13610,7 +13609,7 @@ var DATABASES_FILE = (0, import_path2.join)(BGI_DIR, "databases.json");
 var DATA_VERSION_FILE = (0, import_path2.join)(BGI_DIR, ".data-version");
 var CONFIG_FILE = (0, import_path2.join)(BGI_DIR, "config.json");
 function ensureDirs() {
-  for (const dir of [BGI_DIR, WORKFLOWS_DIR, TOOLS_DIR, SKILLS_DIR, USER_SKILLS_DIR]) {
+  for (const dir of [BGI_DIR, TOOLS_DIR, SKILLS_DIR, USER_SKILLS_DIR]) {
     if (!(0, import_fs2.existsSync)(dir)) (0, import_fs2.mkdirSync)(dir, { recursive: true });
   }
 }
@@ -14634,7 +14633,7 @@ You have access to these tools:
 > \u662F\u5426\u6FC0\u6D3B\u8FD9\u4E9B\u6280\u80FD\u5F00\u59CB\u5206\u6790\uFF1F
 
 **\u7B2C\u4E09\u6B65 \u2014 \u6FC0\u6D3B\u6280\u80FD\uFF0C\u8BFB\u53D6 SKILL.md**
-\u7528\u6237\u786E\u8BA4\u540E\u7ACB\u5373\u6267\u884C\uFF1A\`cat ${WORKFLOWS_DIR}/<skill-id>/SKILL.md\`
+\u7528\u6237\u786E\u8BA4\u540E\u7ACB\u5373\u6267\u884C\uFF1A\`cat ${SKILLS_DIR}/<skill-id>/SKILL.md\`
 \u4E25\u683C\u6309\u7167 SKILL.md \u7684\u6BCF\u4E00\u6B65\u6267\u884C\uFF0C\u4E0D\u8DF3\u8FC7\u3001\u4E0D\u81EA\u884C\u53D1\u6325\u3002
 
 **\u7B2C\u56DB\u6B65 \u2014 \u53EA\u95EE\u771F\u6B63\u5FC5\u8981\u7684\u6570\u636E\u95EE\u9898**
@@ -14651,13 +14650,13 @@ SKILL.md \u8BFB\u5B8C\u540E\uFF0C\u53EA\u8BE2\u95EE\u6267\u884C\u6240\u9700\u768
 
 ---
 
-## Skill Library (22 Bioinformatics Skills)
+## Skill Library
 
-All skills are at: **${WORKFLOWS_DIR}**
+All skills are at: **${SKILLS_DIR}**
 
 For any skill, read its guide first:
 \`\`\`bash
-cat ${WORKFLOWS_DIR}/<skill-id>/SKILL.md
+cat ${SKILLS_DIR}/<skill-id>/SKILL.md
 \`\`\`
 
 ### \u{1F9EC} Transcriptomics
@@ -14737,16 +14736,9 @@ ${dbSection ?? "\uFF08\u6682\u672A\u6CE8\u518C\u4EFB\u4F55\u6570\u636E\u5E93\u30
 
 ---
 
-## Extended Skills (979\u4E2A)
-
-\u66F4\u591A\u5185\u7F6E\u6280\u80FD\u4F4D\u4E8E: **${SKILLS_DIR}**
-
-\u6BCF\u4E2A\u6280\u80FD\u76EE\u5F55\u5305\u542B\u4E00\u4E2A \`SKILL.md\` \u6587\u4EF6\uFF0C\u8BFB\u53D6\u65B9\u5F0F:
-\`\`\`bash
-cat ${SKILLS_DIR}/<skill-id>/SKILL.md
-\`\`\`
+## More Skills
 
-**\u6DB5\u76D6\u9886\u57DF**\uFF08\u7528\u6237\u901A\u8FC7 /sk \u547D\u4EE4\u52A0\u8F7D\u540E\u81EA\u52A8\u6CE8\u5165\u4E0A\u4E0B\u6587\uFF09:
+\u6240\u6709\u5185\u7F6E\u6280\u80FD\u5747\u4F4D\u4E8E **${SKILLS_DIR}**\uFF0C\u6DB5\u76D6\u9886\u57DF\uFF08\u7528\u6237\u901A\u8FC7 /sk \u547D\u4EE4\u52A0\u8F7D\u540E\u81EA\u52A8\u6CE8\u5165\u4E0A\u4E0B\u6587\uFF09:
 - \u6587\u732E\u68C0\u7D22: pubmed-search, arxiv-search, bgpt-paper-search
 - \u7ED3\u6784\u751F\u7269\u5B66: alphafold, alphafold-database, bindcraft, binder-design
 - \u5355\u7EC6\u80DE: anndata, cellagent-annotation, scvi-tools
@@ -17297,11 +17289,24 @@ function installBundledData() {
   const bundledData = (0, import_path6.join)(__dirname, "..", "data");
   if (!(0, import_fs6.existsSync)(bundledData)) return;
   ensureDirs();
+  const legacyWorkflowsDir = (0, import_path6.join)(BGI_DIR, "workflows");
+  if ((0, import_fs6.existsSync)(legacyWorkflowsDir)) {
+    try {
+      for (const entry of (0, import_fs6.readdirSync)(legacyWorkflowsDir)) {
+        const src = (0, import_path6.join)(legacyWorkflowsDir, entry);
+        const dest = (0, import_path6.join)(SKILLS_DIR, entry);
+        if ((0, import_fs6.statSync)(src).isDirectory() && !(0, import_fs6.existsSync)(dest)) {
+          (0, import_fs6.cpSync)(src, dest, { recursive: true });
+        }
+      }
+      (0, import_fs6.rmSync)(legacyWorkflowsDir, { recursive: true, force: true });
+    } catch {
+    }
+  }
   const installedDataVersion = (0, import_fs6.existsSync)(DATA_VERSION_FILE) ? (0, import_fs6.readFileSync)(DATA_VERSION_FILE, "utf8").trim() : "";
   const needsUpdate = installedDataVersion !== VERSION2;
   const targets = [
-    { src: (0, import_path6.join)(bundledData, "workflows"), dest: WORKFLOWS_DIR, name: "Skills (\u5206\u6790\u7C7B)" },
-    { src: (0, import_path6.join)(bundledData, "skills"), dest: SKILLS_DIR, name: "Skills (\u6269\u5C55\u7C7B)" },
+    { src: (0, import_path6.join)(bundledData, "skills"), dest: SKILLS_DIR, name: "Skills" },
     { src: (0, import_path6.join)(bundledData, "tools"), dest: TOOLS_DIR, name: "\u5DE5\u5177" }
   ];
   let installed = false;
@@ -17505,7 +17510,6 @@ function collectAllSkills() {
     });
   };
   addFrom(SKILLS_DIR, "skill");
-  addFrom(WORKFLOWS_DIR, "skill");
   addFrom(USER_SKILLS_DIR, "user");
   return entries;
 }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@bgicli/bgicli",
-  "version": "2.4.6",
+  "version": "2.4.7",
   "description": "BGI CLI — Bioinformatics AI terminal for Chinese researchers (百炼/DeepSeek/Kimi/Qwen)",
   "bin": {
     "bgi": "dist/bgi.js"