Redesign Skill system: unified skill package with ZIP download

.github/workflows/generate-skills.yml

@@ -8,7 +8,7 @@ on:
     branches: [main, master]
     paths:
       - '**.qmd'
-      - 'skill.md'
+      - 'skill-spec.md'
       - '.github/scripts/generate_skills.py'
   workflow_dispatch:
     inputs:
@@ -119,19 +119,28 @@ jobs:
             git status --short
           fi
 
+      - name: Check for changes (including unified skill.md)
+        id: git-check-unified
+        run: |
+          if git diff --quiet skill.md && git diff --quiet -- skills/; then
+            echo "No unified skill or skills directory changes."
+          else
+            echo "unified_changed=true" >> "$GITHUB_OUTPUT"
+          fi
+
       - name: Commit and push skill documents
-        if: steps.git-check.outputs.committed == 'true'
+        if: steps.git-check.outputs.committed == 'true' || steps.git-check-unified.outputs.unified_changed == 'true'
         run: |
           git config user.email "github-actions[bot]@users.noreply.github.com"
           git config user.name  "github-actions[bot]"
-          git add skills/
+          git add skills/ skill.md
           git commit -m "chore: regenerate AI skill documents" \
             -m "Auto-generated skill documents from QMD tutorials."
           BRANCH="${PR_BRANCH:-${{ github.ref_name }}}"
           git push origin "${BRANCH}"
 
       - name: Post PR comment
-        if: steps.git-check.outputs.committed == 'true' && inputs.pr_number != ''
+        if: (steps.git-check.outputs.committed == 'true' || steps.git-check-unified.outputs.unified_changed == 'true') && inputs.pr_number != ''
         uses: actions/github-script@v7
         with:
           script: |

.github/workflows/quarto-publish.yml

@@ -373,6 +373,19 @@ jobs:
           QUARTO_JULIA_PROJECT: ${{ env.QUARTO_JULIA_PROJECT }}
         run: Rscript -e 'babelquarto::render_website()'
 
+      - name: Generate unified skill ZIP package
+        run: |
+          mkdir -p _site/
+          # Stage files with correct names for the zip
+          SKILL_TMP=$(mktemp -d)
+          cp skill.md "${SKILL_TMP}/skill.md"
+          cp files/gallery_data.csv "${SKILL_TMP}/gallery_data.csv"
+          cp files/gallery_data_zh.csv "${SKILL_TMP}/gallery_data_zh.csv"
+          cp files/bizard-skill-readme.md "${SKILL_TMP}/README.md"
+          (cd "${SKILL_TMP}" && zip -r - skill.md gallery_data.csv gallery_data_zh.csv README.md) > _site/bizard-skill.zip
+          rm -rf "${SKILL_TMP}"
+          echo "✅ Created _site/bizard-skill.zip ($(du -h _site/bizard-skill.zip | cut -f1))"
+
       # ── Save freeze cache (ALWAYS – even on failure) ─────────
       # This is the key to reducing wasted work across consecutive
       # failed builds. Even if the render fails on file #400,

Skills.qmd

@@ -8,27 +8,64 @@ from: markdown+emoji
 
 ## What are Bizard Skills? :brain:
 
-**Bizard Skills** convert every tutorial in this atlas into a compact, structured **AI skill document** — a plain-text summary of what a chart is, when to use it, what packages it needs (R, Python, or Julia), and the minimal reproducible code to produce it. Skills can be:
+**Bizard Skills** is an AI skill package that turns your AI assistant into a biomedical visualization expert. When you load this skill, your AI can:
 
-- Copied directly into AI assistant context windows (ChatGPT, Copilot, Claude, etc.)
-- Used by local LLM tools like [LM Studio](https://lmstudio.ai/) or [Ollama](https://ollama.ai/)
-- Downloaded as a ZIP for offline use in custom AI pipelines
-- Referenced by automated bioinformatics workflows
+- **Recommend** the best visualization type for your data and research question
+- **Generate** reproducible R / Python / Julia plotting code adapted from Bizard tutorials
+- **Search** across 793 curated figure examples using the included gallery data
+- **Link** you to the full tutorial for detailed customization
+
+The skill package works with any AI tool that supports custom instructions or knowledge files:
+
+- **ChatGPT / GPT-4**: Load as custom instructions + knowledge file
+- **Claude**: Upload as project files
+- **GitHub Copilot Chat**: Reference with `#file:skill.md`
+- **Local LLMs** (Ollama, LM Studio): Load as system prompt context
 
 ::: callout-tip
-**How to use a skill**: Click any card below to view the skill document, then copy its content into your AI assistant prompt. You can also use the **📋 Get AI Skill** button on any tutorial page!
+**Quick start**: Download the ZIP below → Load `skill.md` as your AI's instructions → Upload `gallery_data.csv` as a knowledge file → Ask: *"Help me create a volcano plot for my differential expression results"*
 :::
 
-::: callout-note
-## Skill Generation Specification
-Skills are generated following the professional specification in [`skill.md`](https://github.com/openbiox/Bizard/blob/main/skill.md). The specification guides both LLM-based and rule-based skill generation to ensure consistent, high-quality output.
-:::
+---
+
+## Download the Skill Package {#download}
+
+The ZIP contains:
+
+- **`skill.md`** — AI skill instructions: teaches your AI assistant how to use Bizard for visualization recommendations and code generation
+- **`gallery_data.csv`** — 793 visualization examples with image URLs, tutorial links, descriptions, and categories
+- **`gallery_data_zh.csv`** — Chinese version of the gallery data
+- **`README.md`** — Installation guide for different AI tools
+
+```{=html}
+<div style="text-align:center;margin:2rem 0;">
+  <a class="bizard-skill-dl" href="bizard-skill.zip" download
+    style="display:inline-flex;align-items:center;gap:0.5rem;background:linear-gradient(135deg,#3a86ff,#2563eb);color:#fff;border:none;padding:1rem 2.5rem;border-radius:10px;cursor:pointer;font-size:1.1rem;font-weight:700;text-decoration:none;box-shadow:0 4px 14px rgba(58,134,255,.3);transition:transform .15s,box-shadow .15s;"
+    onmouseover="this.style.transform='translateY(-2px)';this.style.boxShadow='0 6px 20px rgba(58,134,255,.4)'"
+    onmouseout="this.style.transform='none';this.style.boxShadow='0 4px 14px rgba(58,134,255,.3)'">
+    ⬇️ Download Bizard Skill ZIP
+  </a>
+</div>
+<script>
+// Fix download link paths for pages served under subdirectories (e.g. zh/)
+(function() {
+  var parts = window.location.pathname.replace(/\/+$/, '').split('/');
+  var segmentsAfterRoot = parts.length - 2;
+  var prefix = '';
+  for (var i = 0; i < segmentsAfterRoot; i++) prefix += '../';
+  if (!prefix) prefix = './';
+  document.querySelectorAll('a.bizard-skill-dl, a[href="bizard-skill.zip"], a[href$="/bizard-skill.zip"]').forEach(function(a) {
+    a.href = prefix + 'bizard-skill.zip';
+  });
+})();
+</script>
+```
 
 ---
 
 ## Browse Skills by Category {#browse}
 
-Use the search box, language filter, or click a category to filter skills.
+Use the search box, language filter, or click a category to browse all available visualization skills.
 
 ```{=html}
 <div id="skills-browser" style="margin-bottom:2rem;">
@@ -179,34 +216,24 @@ function copySkill() {
 
 ---
 
-## Download All Skills
-
-The full skill database is available as JSON:
+## Download Resources
 
-- **[`skills/index.json`](skills/index.json)** — Lightweight index (names, categories, packages, URLs)
-- **[`skills/bizard_skills.json`](skills/bizard_skills.json)** — Full skill documents with code
+- **[Download Skill ZIP](bizard-skill.zip)** — Complete unified skill package
+- **[`skills/index.json`](skills/index.json)** — Lightweight JSON index (names, categories, packages, URLs)
+- **[`skills/bizard_skills.json`](skills/bizard_skills.json)** — Full skill documents with embedded code
 
 ## Regenerating Skills
 
-Skills can be regenerated using the generation script, which supports both LLM-powered and offline modes:
+Skills are **automatically regenerated** when tutorials are updated on the main branch. To regenerate manually:
 
 ```bash
 # LLM mode (requires API key in environment)
 python .github/scripts/generate_skills.py --format both --verbose
 
 # Offline mode (rule-based extraction)
 python .github/scripts/generate_skills.py --offline --format both --verbose
-
-# Process specific files only
-python .github/scripts/generate_skills.py --files Omics/VolcanoPlot.qmd --verbose
 ```
 
-Skills are also **automatically regenerated** when tutorials are updated on the main branch, and can be triggered manually via a PR comment:
-
-```
-/skill                          → regenerate skills for changed files
-/skill Omics/VolcanoPlot.qmd    → regenerate for a specific file
-/skill --offline                → use offline mode
-```
+The unified `skill.md` is automatically rebuilt from the skills index every time skills are generated.
 
-See the [Skill Generation Guide](https://github.com/openbiox/Bizard/blob/main/skill.md) for the full specification.
+See the [Skill Generation Specification](https://github.com/openbiox/Bizard/blob/main/skill-spec.md) for the full technical specification.

Skills.zh.qmd

@@ -8,27 +8,64 @@ from: markdown+emoji
 
 ## 什么是 Bizard 技能？ :brain:
 
-**Bizard 技能** 将本图集中的每个教程转换为紧凑、结构化的 **AI 技能文档** — 纯文本摘要，包含图表用途、使用时机、所需包（R、Python 或 Julia）以及最小可复现代码。技能可以：
+**Bizard 技能** 是一个 AI 技能包，可以让你的 AI 助手成为生物医学可视化专家。加载此技能后，你的 AI 可以：
 
-- 直接复制到 AI 助手的上下文窗口中（ChatGPT、Copilot、Claude 等）
-- 与本地 LLM 工具配合使用，如 [LM Studio](https://lmstudio.ai/) 或 [Ollama](https://ollama.ai/)
-- 作为 ZIP 包下载，用于离线 AI 管道
-- 在自动化生物信息学工作流中引用
+- **推荐** 最适合你数据和研究问题的可视化类型
+- **生成** 基于 Bizard 教程的可复现 R / Python / Julia 绑图代码
+- **搜索** 793 个精选图形示例（使用附带的画廊数据）
+- **链接** 到完整教程以获取详细的自定义选项
+
+技能包适用于任何支持自定义指令或知识文件的 AI 工具：
+
+- **ChatGPT / GPT-4**：作为自定义指令 + 知识文件加载
+- **Claude**：作为项目文件上传
+- **GitHub Copilot Chat**：使用 `#file:skill.md` 引用
+- **本地 LLM**（Ollama、LM Studio）：作为系统提示上下文加载
 
 ::: callout-tip
-**如何使用技能**：点击下方任意卡片查看技能文档，然后将内容复制到 AI 助手提示中。您也可以在任何教程页面使用 **📋 获取 AI 技能** 按钮！
+**快速开始**：下载下方 ZIP 包 → 将 `skill.md` 加载为 AI 指令 → 上传 `gallery_data.csv` 作为知识文件 → 提问：*"帮我为差异表达结果创建一个火山图"*
 :::
 
-::: callout-note
-## 技能生成规范
-技能根据 [`skill.md`](https://github.com/openbiox/Bizard/blob/main/skill.md) 中的专业规范生成。该规范指导 LLM 和规则引擎生成一致、高质量的技能文档。
-:::
+---
+
+## 下载技能包 {#download}
+
+ZIP 包含：
+
+- **`skill.md`** — AI 技能指令：教会你的 AI 助手如何使用 Bizard 进行可视化推荐和代码生成
+- **`gallery_data.csv`** — 793 个可视化示例，包含图片 URL、教程链接、描述和分类
+- **`gallery_data_zh.csv`** — 画廊数据的中文版本
+- **`README.md`** — 不同 AI 工具的安装指南
+
+```{=html}
+<div style="text-align:center;margin:2rem 0;">
+  <a class="bizard-skill-dl" href="bizard-skill.zip" download
+    style="display:inline-flex;align-items:center;gap:0.5rem;background:linear-gradient(135deg,#3a86ff,#2563eb);color:#fff;border:none;padding:1rem 2.5rem;border-radius:10px;cursor:pointer;font-size:1.1rem;font-weight:700;text-decoration:none;box-shadow:0 4px 14px rgba(58,134,255,.3);transition:transform .15s,box-shadow .15s;"
+    onmouseover="this.style.transform='translateY(-2px)';this.style.boxShadow='0 6px 20px rgba(58,134,255,.4)'"
+    onmouseout="this.style.transform='none';this.style.boxShadow='0 4px 14px rgba(58,134,255,.3)'">
+    ⬇️ 下载 Bizard 技能 ZIP
+  </a>
+</div>
+<script>
+// Fix download link paths for pages served under subdirectories (e.g. zh/)
+(function() {
+  var parts = window.location.pathname.replace(/\/+$/, '').split('/');
+  var segmentsAfterRoot = parts.length - 2;
+  var prefix = '';
+  for (var i = 0; i < segmentsAfterRoot; i++) prefix += '../';
+  if (!prefix) prefix = './';
+  document.querySelectorAll('a.bizard-skill-dl, a[href="bizard-skill.zip"], a[href$="/bizard-skill.zip"]').forEach(function(a) {
+    a.href = prefix + 'bizard-skill.zip';
+  });
+})();
+</script>
+```
 
 ---
 
 ## 按分类浏览技能 {#browse}
 
-使用搜索框、语言筛选或点击分类来筛选技能。
+使用搜索框、语言筛选或点击分类来浏览所有可用的可视化技能。
 
 ```{=html}
 <div id="skills-browser" style="margin-bottom:2rem;">
@@ -175,34 +212,24 @@ function copySkill() {
 
 ---
 
-## 下载所有技能
-
-完整的技能数据库可通过 JSON 获取：
+## 下载资源
 
-- **[`skills/index.json`](skills/index.json)** — 轻量级索引
+- **[下载技能 ZIP 包](bizard-skill.zip)** — 完整的统一技能包
+- **[`skills/index.json`](skills/index.json)** — 轻量级 JSON 索引
 - **[`skills/bizard_skills.json`](skills/bizard_skills.json)** — 完整技能文档
 
 ## 重新生成技能
 
-技能支持 LLM 驱动和离线两种生成模式：
+技能在教程更新到主分支时**自动重新生成**。手动重新生成：
 
 ```bash
 # LLM 模式（需要配置 API 密钥）
 python .github/scripts/generate_skills.py --format both --verbose
 
 # 离线模式（基于规则提取）
 python .github/scripts/generate_skills.py --offline --format both --verbose
-
-# 仅处理特定文件
-python .github/scripts/generate_skills.py --files Omics/VolcanoPlot.qmd --verbose
 ```
 
-技能在教程更新到主分支时**自动重新生成**，也可以在 PR 中通过评论命令手动触发：
-
-```
-/skill                          → 重新生成已更改文件的技能
-/skill Omics/VolcanoPlot.qmd    → 重新生成特定文件的技能
-/skill --offline                → 使用离线模式
-```
+统一的 `skill.md` 在每次生成技能时从技能索引自动重建。
 
-查看完整规范：[技能生成指南](https://github.com/openbiox/Bizard/blob/main/skill.md)。
+查看完整技术规范：[技能生成规范](https://github.com/openbiox/Bizard/blob/main/skill-spec.md)。

files/bizard-skill-readme.md

@@ -0,0 +1,52 @@
+# Bizard AI Skill — Installation Guide
+
+## What's in this package?
+
+| File | Purpose |
+|------|---------|
+| `skill.md` | The AI skill instruction document — load this into your AI assistant |
+| `gallery_data.csv` | 793 visualization examples with image URLs, tutorial links, descriptions, and categories |
+| `gallery_data_zh.csv` | Chinese version of the gallery data |
+| `README.md` | This file |
+
+## Quick Start
+
+### ChatGPT / GPT-4
+
+1. Go to **Settings → Personalization → Custom Instructions** (or create a GPT)
+2. Paste the contents of `skill.md` into the system prompt / instructions
+3. Upload `gallery_data.csv` as a knowledge file
+4. Ask: *"I want to compare gene expression across cancer subtypes"*
+
+### Claude
+
+1. Start a new project or conversation
+2. Upload `skill.md` and `gallery_data.csv` as project files
+3. Ask: *"Help me create a volcano plot for my differential expression results"*
+
+### GitHub Copilot Chat
+
+1. Add `skill.md` and `gallery_data.csv` to your workspace
+2. Reference them with `#file:skill.md` in Copilot Chat
+3. Ask: *"Based on the Bizard skill, suggest a visualization for my survival data"*
+
+### Local LLMs (Ollama, LM Studio, etc.)
+
+1. Load `skill.md` as part of your system prompt
+2. Provide `gallery_data.csv` as context when asking visualization questions
+3. The skill will guide the model to recommend appropriate chart types and code
+
+## What can this skill do?
+
+Once installed, your AI assistant can:
+
+- **Recommend** the best visualization type for your biomedical data
+- **Generate** reproducible R / Python / Julia code based on Bizard tutorials
+- **Link** to the full tutorial at https://openbiox.github.io/Bizard/ for detailed customization
+- **Search** the gallery data to find specific figure examples
+
+## Learn More
+
+- **Website**: https://openbiox.github.io/Bizard/
+- **Repository**: https://github.com/openbiox/Bizard
+- **License**: CC-BY-NC — Bizard Collaboration Group, Luo Lab, and Wang Lab