fix: improve gitignore and Jupyter notebook support

- Add nbconvert dependency for .ipynb file support
- Replace manual gitignore parsing with gitignore-parser library
- Proper recursive .gitignore handling (all subdirectories)
- Fix compliance with Git gitignore behavior
- Simplify code and improve reliability

🤖 Generated with [Claude Code](https://claude.ai/code)

Co-Authored-By: Claude <noreply@anthropic.com>

README.md

@@ -6,6 +6,7 @@
   <img src="https://img.shields.io/badge/Python-3.9%2B-blue.svg" alt="Python 3.9+">
   <img src="https://img.shields.io/badge/License-MIT-green.svg" alt="MIT License">
   <img src="https://img.shields.io/badge/Platform-Linux%20%7C%20macOS-lightgrey" alt="Platform">
+  <img src="https://img.shields.io/badge/MCP-Native%20Integration-blue?style=flat-square" alt="MCP Integration">
 </p>
 
 <h2 align="center" tabindex="-1" class="heading-element" dir="auto">
@@ -16,9 +17,10 @@ LEANN is an innovative vector database that democratizes personal AI. Transform
 
 LEANN achieves this through *graph-based selective recomputation* with *high-degree preserving pruning*, computing embeddings on-demand instead of storing them all. [Illustration Fig →](#️-architecture--how-it-works) | [Paper →](https://arxiv.org/abs/2506.08276)
 
-**Ready to RAG Everything?** Transform your laptop into a personal AI assistant that can search your **[file system](#-personal-data-manager-process-any-documents-pdf-txt-md)**, **[emails](#-your-personal-email-secretary-rag-on-apple-mail)**, **[browser history](#-time-machine-for-the-web-rag-your-entire-browser-history)**, **[chat history](#-wechat-detective-unlock-your-golden-memories)**, or external knowledge bases (i.e., 60M documents) - all on your laptop, with zero cloud costs and complete privacy.
+**Ready to RAG Everything?** Transform your laptop into a personal AI assistant that can semantic search your **[file system](#-personal-data-manager-process-any-documents-pdf-txt-md)**, **[emails](#-your-personal-email-secretary-rag-on-apple-mail)**, **[browser history](#-time-machine-for-the-web-rag-your-entire-browser-history)**, **[chat history](#-wechat-detective-unlock-your-golden-memories)**, **[codebase](#-claude-code-integration-transform-your-development-workflow)**\* , or external knowledge bases (i.e., 60M documents) - all on your laptop, with zero cloud costs and complete privacy.
 
-> **🚀 NEW: Claude Code Integration!** LEANN now provides native MCP integration for Claude Code users. Index your codebase and get intelligent code assistance directly in Claude Code. [Setup Guide →](packages/leann-mcp/README.md)
+
+\* Claude Code only supports basic `grep`-style keyword search. **LEANN** is a drop-in **semantic search MCP service fully compatible with Claude Code**, unlocking intelligent retrieval without changing your workflow. 🔥 Check out [the easy setup →](packages/leann-mcp/README.md)
 
 
 
@@ -28,7 +30,7 @@ LEANN achieves this through *graph-based selective recomputation* with *high-deg
   <img src="assets/effects.png" alt="LEANN vs Traditional Vector DB Storage Comparison" width="70%">
 </p>
 
-> **The numbers speak for themselves:** Index 60 million Wikipedia chunks in just 6GB instead of 201GB. From emails to browser history, everything fits on your laptop. [See detailed benchmarks for different applications below ↓](#storage-comparison)
+> **The numbers speak for themselves:** Index 60 million text chunks in just 6GB instead of 201GB. From emails to browser history, everything fits on your laptop. [See detailed benchmarks for different applications below ↓](#storage-comparison)
 
 
 🔒 **Privacy:** Your data never leaves your laptop. No OpenAI, no cloud, no "terms of service".
@@ -187,8 +189,8 @@ All RAG examples share these common parameters. **Interactive mode** is availabl
 --force-rebuild         # Force rebuild index even if it exists
 
 # Embedding Parameters
---embedding-model MODEL  # e.g., facebook/contriever, text-embedding-3-small or mlx-community/multilingual-e5-base-mlx
---embedding-mode MODE    # sentence-transformers, openai, or mlx
+--embedding-model MODEL  # e.g., facebook/contriever, text-embedding-3-small, nomic-embed-text, mlx-community/Qwen3-Embedding-0.6B-8bit or nomic-embed-text
+--embedding-mode MODE    # sentence-transformers, openai, mlx, or ollama
 
 # LLM Parameters (Text generation models)
 --llm TYPE              # LLM backend: openai, ollama, or hf (default: openai)
@@ -221,7 +223,7 @@ Ask questions directly about your personal PDFs, documents, and any directory co
   <img src="videos/paper_clear.gif" alt="LEANN Document Search Demo" width="600">
 </p>
 
-The example below asks a question about summarizing our paper (uses default data in `data/`, which is a directory with diverse data sources: two papers, Pride and Prejudice, and a README in Chinese) and this is the **easiest example** to run here:
+The example below asks a question about summarizing our paper (uses default data in `data/`, which is a directory with diverse data sources: two papers, Pride and Prejudice, and a Technical report about LLM in Huawei in Chinese), and this is the **easiest example** to run here:
 
 ```bash
 source .venv/bin/activate # Don't forget to activate the virtual environment
@@ -416,7 +418,26 @@ Once the index is built, you can ask questions like:
 
 </details>
 
+### 🚀 Claude Code Integration: Transform Your Development Workflow!
 
+**The future of code assistance is here.** Transform your development workflow with LEANN's native MCP integration for Claude Code. Index your entire codebase and get intelligent code assistance directly in your IDE.
+
+**Key features:**
+- 🔍 **Semantic code search** across your entire project
+- 📚 **Context-aware assistance** for debugging and development
+- 🚀 **Zero-config setup** with automatic language detection
+
+```bash
+# Install LEANN globally for MCP integration
+uv tool install leann-core
+
+# Setup is automatic - just start using Claude Code!
+```
+Try our fully agentic pipeline with auto query rewriting, semantic search planning, and more:
+
+![LEANN MCP Integration](assets/mcp_leann.png)
+
+**Ready to supercharge your coding?** [Complete Setup Guide →](packages/leann-mcp/README.md)
 
 ## 🖥️ Command Line Interface
 
@@ -446,11 +467,8 @@ leann --help
 ### Usage Examples
 
 ```bash
-# Build an index from current directory (default)
-leann build my-docs
-
-# Or from specific directory
-leann build my-docs --docs ./documents
+# build from a specific directory, and my_docs is the index name
+leann build my-docs --docs ./your_documents
 
 # Search your documents
 leann search my-docs "machine learning concepts"

apps/base_rag_example.py

@@ -75,7 +75,7 @@ class BaseRAGExample(ABC):
             "--embedding-mode",
             type=str,
             default="sentence-transformers",
-            choices=["sentence-transformers", "openai", "mlx"],
+            choices=["sentence-transformers", "openai", "mlx", "ollama"],
             help="Embedding backend mode (default: sentence-transformers)",
         )
 
@@ -85,7 +85,7 @@ class BaseRAGExample(ABC):
             "--llm",
             type=str,
             default="openai",
-            choices=["openai", "ollama", "hf"],
+            choices=["openai", "ollama", "hf", "simulated"],
             help="LLM backend to use (default: openai)",
         )
         llm_group.add_argument(

docs/claude-code-integration.md

@@ -1,150 +0,0 @@
-# Claude Code x LEANN 集成指南
-
-## ✅ 现状：已经可以工作！
-
-好消息：LEANN CLI已经完全可以在Claude Code中使用，无需任何修改！
-
-## 🚀 立即开始
-
-### 1. 激活环境
-```bash
-# 在LEANN项目目录下
-source .venv/bin/activate.fish  # fish shell
-# 或
-source .venv/bin/activate       # bash shell
-```
-
-### 2. 基本命令
-
-#### 查看现有索引
-```bash
-leann list
-```
-
-#### 搜索文档
-```bash
-leann search my-docs "machine learning" --recompute-embeddings
-```
-
-#### 问答对话
-```bash
-echo "What is machine learning?" | leann ask my-docs --llm ollama --model qwen3:8b --recompute-embeddings
-```
-
-#### 构建新索引
-```bash
-leann build project-docs --docs ./src --recompute-embeddings
-```
-
-## 💡 Claude Code 使用技巧
-
-### 在Claude Code中直接使用
-
-1. **激活环境**：
-   ```bash
-   cd /Users/andyl/Projects/LEANN-RAG
-   source .venv/bin/activate.fish
-   ```
-
-2. **搜索代码库**：
-   ```bash
-   leann search my-docs "authentication patterns" --recompute-embeddings --top-k 10
-   ```
-
-3. **智能问答**：
-   ```bash
-   echo "How does the authentication system work?" | leann ask my-docs --llm ollama --model qwen3:8b --recompute-embeddings
-   ```
-
-### 批量操作示例
-
-```bash
-# 构建项目文档索引
-leann build project-docs --docs ./docs --force
-
-# 搜索多个关键词
-leann search project-docs "API authentication" --recompute-embeddings
-leann search project-docs "database schema" --recompute-embeddings
-leann search project-docs "deployment guide" --recompute-embeddings
-
-# 问答模式
-echo "What are the API endpoints?" | leann ask project-docs --recompute-embeddings
-```
-
-## 🎯 Claude 可以立即执行的工作流
-
-### 代码分析工作流
-```bash
-# 1. 构建代码库索引
-leann build codebase --docs ./src --backend hnsw --recompute-embeddings
-
-# 2. 分析架构
-echo "What is the overall architecture?" | leann ask codebase --recompute-embeddings
-
-# 3. 查找特定功能
-leann search codebase "user authentication" --recompute-embeddings --top-k 5
-
-# 4. 理解实现细节
-echo "How is user authentication implemented?" | leann ask codebase --recompute-embeddings
-```
-
-### 文档理解工作流
-```bash
-# 1. 索引项目文档
-leann build docs --docs ./docs --recompute-embeddings
-
-# 2. 快速查找信息
-leann search docs "installation requirements" --recompute-embeddings
-
-# 3. 获取详细说明
-echo "What are the system requirements?" | leann ask docs --recompute-embeddings
-```
-
-## ⚠️ 重要提示
-
-1. **必须使用 `--recompute-embeddings`** - 这是关键参数，不加会报错
-2. **需要先激活虚拟环境** - 确保有LEANN的Python环境
-3. **Ollama需要预先安装** - ask功能需要本地LLM
-
-## 🔥 立即可用的Claude提示词
-
-```
-Help me analyze this codebase using LEANN:
-
-1. First, activate the environment:
-   cd /Users/andyl/Projects/LEANN-RAG && source .venv/bin/activate.fish
-
-2. Build an index of the source code:
-   leann build codebase --docs ./src --recompute-embeddings
-
-3. Search for authentication patterns:
-   leann search codebase "authentication middleware" --recompute-embeddings --top-k 10
-
-4. Ask about the authentication system:
-   echo "How does user authentication work in this codebase?" | leann ask codebase --recompute-embeddings
-
-Please execute these commands and help me understand the code structure.
-```
-
-## 📈 下一步改进计划
-
-虽然现在已经可以用，但还可以进一步优化：
-
-1. **简化命令** - 默认启用recompute-embeddings
-2. **配置文件** - 避免重复输入参数
-3. **状态管理** - 自动检测环境和索引
-4. **输出格式** - 更适合Claude解析的格式
-
-但这些都是锦上添花，现在就能用起来！
-
-## 🎉 总结
-
-**LEANN现在就可以在Claude Code中完美工作！**
-
-- ✅ 搜索功能正常
-- ✅ RAG问答功能正常
-- ✅ 索引构建功能正常
-- ✅ 支持多种数据源
-- ✅ 支持本地LLM
-
-只需要记住加上 `--recompute-embeddings` 参数就行！

docs/configuration-guide.md

@@ -49,14 +49,25 @@ Based on our experience developing LEANN, embedding models fall into three categ
 - **Cons**: Slower inference, longer index build times
 - **Use when**: Quality is paramount and you have sufficient compute resources. **Highly recommended** for production use
 
-### Quick Start: OpenAI Embeddings (Fastest Setup)
+### Quick Start: Cloud and Local Embedding Options
 
+**OpenAI Embeddings (Fastest Setup)**
 For immediate testing without local model downloads:
 ```bash
 # Set OpenAI embeddings (requires OPENAI_API_KEY)
 --embedding-mode openai --embedding-model text-embedding-3-small
 ```
 
+**Ollama Embeddings (Privacy-Focused)**
+For local embeddings with complete privacy:
+```bash
+# First, pull an embedding model
+ollama pull nomic-embed-text
+
+# Use Ollama embeddings
+--embedding-mode ollama --embedding-model nomic-embed-text
+```
+
 <details>
 <summary><strong>Cloud vs Local Trade-offs</strong></summary>
 
@@ -211,9 +222,15 @@ python apps/document_rag.py --query "What are the main techniques LEANN explores
 
 3. **Use MLX on Apple Silicon** (optional optimization):
    ```bash
-   --embedding-mode mlx --embedding-model mlx-community/multilingual-e5-base-mlx
+   --embedding-mode mlx --embedding-model mlx-community/Qwen3-Embedding-0.6B-8bit
    ```
+    MLX might not be the best choice, as we tested and found that it only offers 1.3x acceleration compared to HF, so maybe using ollama is a better choice for embedding generation
 
+4. **Use Ollama**
+   ```bash
+   --embedding-mode ollama --embedding-model nomic-embed-text
+   ```
+   To discover additional embedding models in ollama, check out https://ollama.com/search?c=embedding or read more about embedding models at https://ollama.com/blog/embedding-models, please do check the model size that works best for you
 ### If Search Quality is Poor
 
 1. **Increase retrieval count**:

packages/leann-backend-diskann/leann_backend_diskann/diskann_embedding_server.py

@@ -261,7 +261,7 @@ if __name__ == "__main__":
         "--embedding-mode",
         type=str,
         default="sentence-transformers",
-        choices=["sentence-transformers", "openai", "mlx"],
+        choices=["sentence-transformers", "openai", "mlx", "ollama"],
         help="Embedding backend mode",
     )
     parser.add_argument(

packages/leann-backend-diskann/pyproject.toml

@@ -4,8 +4,8 @@ build-backend = "scikit_build_core.build"
 
 [project]
 name = "leann-backend-diskann"
-version = "0.2.2"
-dependencies = ["leann-core==0.2.2", "numpy", "protobuf>=3.19.0"]
+version = "0.2.6"
+dependencies = ["leann-core==0.2.6", "numpy", "protobuf>=3.19.0"]
 
 [tool.scikit-build]
 # Key: simplified CMake path

packages/leann-backend-hnsw/leann_backend_hnsw/hnsw_embedding_server.py

@@ -295,7 +295,7 @@ if __name__ == "__main__":
         "--embedding-mode",
         type=str,
         default="sentence-transformers",
-        choices=["sentence-transformers", "openai", "mlx"],
+        choices=["sentence-transformers", "openai", "mlx", "ollama"],
         help="Embedding backend mode",
     )
 

packages/leann-backend-hnsw/pyproject.toml

@@ -6,10 +6,10 @@ build-backend = "scikit_build_core.build"
 
 [project]
 name = "leann-backend-hnsw"
-version = "0.2.2"
+version = "0.2.6"
 description = "Custom-built HNSW (Faiss) backend for the Leann toolkit."
 dependencies = [
-    "leann-core==0.2.2",
+    "leann-core==0.2.6",
     "numpy",
     "pyzmq>=23.0.0",
     "msgpack>=1.0.0",

packages/leann-core/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "leann-core"
-version = "0.2.2"
+version = "0.2.6"
 description = "Core API and plugin system for LEANN"
 readme = "README.md"
 requires-python = ">=3.9"
@@ -31,6 +31,8 @@ dependencies = [
     "PyPDF2>=3.0.0",
     "pymupdf>=1.23.0",
     "pdfplumber>=0.10.0",
+    "nbconvert>=7.0.0",  # For .ipynb file support
+    "gitignore-parser>=0.1.12",  # For proper .gitignore handling
     "mlx>=0.26.3; sys_platform == 'darwin'",
     "mlx-lm>=0.26.0; sys_platform == 'darwin'",
 ]

packages/leann-core/src/leann/chat.py

@@ -17,12 +17,12 @@ logging.basicConfig(level=logging.INFO)
 logger = logging.getLogger(__name__)
 
 
-def check_ollama_models() -> list[str]:
+def check_ollama_models(host: str) -> list[str]:
     """Check available Ollama models and return a list"""
     try:
         import requests
 
-        response = requests.get("http://localhost:11434/api/tags", timeout=5)
+        response = requests.get(f"{host}/api/tags", timeout=5)
         if response.status_code == 200:
             data = response.json()
             return [model["name"] for model in data.get("models", [])]
@@ -309,10 +309,12 @@ def search_hf_models(query: str, limit: int = 10) -> list[str]:
     return search_hf_models_fuzzy(query, limit)
 
 
-def validate_model_and_suggest(model_name: str, llm_type: str) -> str | None:
+def validate_model_and_suggest(
+    model_name: str, llm_type: str, host: str = "http://localhost:11434"
+) -> str | None:
     """Validate model name and provide suggestions if invalid"""
     if llm_type == "ollama":
-        available_models = check_ollama_models()
+        available_models = check_ollama_models(host)
         if available_models and model_name not in available_models:
             error_msg = f"Model '{model_name}' not found in your local Ollama installation."
 
@@ -469,7 +471,7 @@ class OllamaChat(LLMInterface):
                 requests.get(host)
 
             # Pre-check model availability with helpful suggestions
-            model_error = validate_model_and_suggest(model, "ollama")
+            model_error = validate_model_and_suggest(model, "ollama", host)
             if model_error:
                 raise ValueError(model_error)
 

packages/leann-core/src/leann/cli.py

@@ -86,7 +86,9 @@ Examples:
 
         # Build command
         build_parser = subparsers.add_parser("build", help="Build document index")
-        build_parser.add_argument("index_name", help="Index name")
+        build_parser.add_argument(
+            "index_name", nargs="?", help="Index name (default: current directory name)"
+        )
         build_parser.add_argument(
             "--docs", type=str, default=".", help="Documents directory (default: current directory)"
         )
@@ -94,6 +96,13 @@ Examples:
             "--backend", type=str, default="hnsw", choices=["hnsw", "diskann"]
         )
         build_parser.add_argument("--embedding-model", type=str, default="facebook/contriever")
+        build_parser.add_argument(
+            "--embedding-mode",
+            type=str,
+            default="sentence-transformers",
+            choices=["sentence-transformers", "openai", "mlx", "ollama"],
+            help="Embedding backend mode (default: sentence-transformers)",
+        )
         build_parser.add_argument("--force", "-f", action="store_true", help="Force rebuild")
         build_parser.add_argument("--graph-degree", type=int, default=32)
         build_parser.add_argument("--complexity", type=int, default=64)
@@ -194,6 +203,37 @@ Examples:
         with open(global_registry, "w") as f:
             json.dump(projects, f, indent=2)
 
+    def _build_gitignore_parser(self, docs_dir: str):
+        """Build gitignore parser using gitignore-parser library."""
+        from gitignore_parser import parse_gitignore
+
+        # Try to parse the root .gitignore
+        gitignore_path = Path(docs_dir) / ".gitignore"
+
+        if gitignore_path.exists():
+            try:
+                # gitignore-parser automatically handles all subdirectory .gitignore files!
+                matches = parse_gitignore(str(gitignore_path))
+                print(f"📋 Loaded .gitignore from {docs_dir} (includes all subdirectories)")
+                return matches
+            except Exception as e:
+                print(f"Warning: Could not parse .gitignore: {e}")
+        else:
+            print("📋 No .gitignore found")
+
+        # Fallback: basic pattern matching for essential files
+        essential_patterns = {".git", ".DS_Store", "__pycache__", "node_modules", ".venv", "venv"}
+
+        def basic_matches(file_path):
+            path_parts = Path(file_path).parts
+            return any(part in essential_patterns for part in path_parts)
+
+        return basic_matches
+
+    def _should_exclude_file(self, relative_path: Path, gitignore_matches) -> bool:
+        """Check if a file should be excluded using gitignore parser."""
+        return gitignore_matches(str(relative_path))
+
     def list_indexes(self):
         print("Stored LEANN indexes:")
 
@@ -275,34 +315,49 @@ Examples:
         if custom_file_types:
             print(f"Using custom file types: {custom_file_types}")
 
-        # Try to use better PDF parsers first
+        # Build gitignore parser
+        gitignore_matches = self._build_gitignore_parser(docs_dir)
+
+        # Try to use better PDF parsers first, but only if PDFs are requested
         documents = []
         docs_path = Path(docs_dir)
 
-        for file_path in docs_path.rglob("*.pdf"):
-            print(f"Processing PDF: {file_path}")
+        # Check if we should process PDFs
+        should_process_pdfs = custom_file_types is None or ".pdf" in custom_file_types
 
-            # Try PyMuPDF first (best quality)
-            text = extract_pdf_text_with_pymupdf(str(file_path))
-            if text is None:
-                # Try pdfplumber
-                text = extract_pdf_text_with_pdfplumber(str(file_path))
+        if should_process_pdfs:
+            for file_path in docs_path.rglob("*.pdf"):
+                # Check if file matches any exclude pattern
+                relative_path = file_path.relative_to(docs_path)
+                if self._should_exclude_file(relative_path, gitignore_matches):
+                    continue
 
-            if text:
-                # Create a simple document structure
-                from llama_index.core import Document
+                print(f"Processing PDF: {file_path}")
 
-                doc = Document(text=text, metadata={"source": str(file_path)})
-                documents.append(doc)
-            else:
-                # Fallback to default reader
-                print(f"Using default reader for {file_path}")
-                default_docs = SimpleDirectoryReader(
-                    str(file_path.parent),
-                    filename_as_id=True,
-                    required_exts=[file_path.suffix],
-                ).load_data()
-                documents.extend(default_docs)
+                # Try PyMuPDF first (best quality)
+                text = extract_pdf_text_with_pymupdf(str(file_path))
+                if text is None:
+                    # Try pdfplumber
+                    text = extract_pdf_text_with_pdfplumber(str(file_path))
+
+                if text:
+                    # Create a simple document structure
+                    from llama_index.core import Document
+
+                    doc = Document(text=text, metadata={"source": str(file_path)})
+                    documents.append(doc)
+                else:
+                    # Fallback to default reader
+                    print(f"Using default reader for {file_path}")
+                    try:
+                        default_docs = SimpleDirectoryReader(
+                            str(file_path.parent),
+                            filename_as_id=True,
+                            required_exts=[file_path.suffix],
+                        ).load_data()
+                        documents.extend(default_docs)
+                    except Exception as e:
+                        print(f"Warning: Could not process {file_path}: {e}")
 
         # Load other file types with default reader
         if custom_file_types:
@@ -368,13 +423,34 @@ Examples:
             ]
         # Try to load other file types, but don't fail if none are found
         try:
+            # Create a custom file filter function using our PathSpec
+            def file_filter(file_path: str) -> bool:
+                """Return True if file should be included (not excluded)"""
+                try:
+                    docs_path_obj = Path(docs_dir)
+                    file_path_obj = Path(file_path)
+                    relative_path = file_path_obj.relative_to(docs_path_obj)
+                    return not self._should_exclude_file(relative_path, gitignore_matches)
+                except (ValueError, OSError):
+                    return True  # Include files that can't be processed
+
             other_docs = SimpleDirectoryReader(
                 docs_dir,
                 recursive=True,
                 encoding="utf-8",
                 required_exts=code_extensions,
+                file_extractor={},  # Use default extractors
+                filename_as_id=True,
             ).load_data(show_progress=True)
-            documents.extend(other_docs)
+
+            # Filter documents after loading based on gitignore rules
+            filtered_docs = []
+            for doc in other_docs:
+                file_path = doc.metadata.get("file_path", "")
+                if file_filter(file_path):
+                    filtered_docs.append(doc)
+
+            documents.extend(filtered_docs)
         except ValueError as e:
             if "No files found" in str(e):
                 print("No additional files found for other supported types.")
@@ -447,7 +523,13 @@ Examples:
 
     async def build_index(self, args):
         docs_dir = args.docs
-        index_name = args.index_name
+        # Use current directory name if index_name not provided
+        if args.index_name:
+            index_name = args.index_name
+        else:
+            index_name = Path.cwd().name
+            print(f"Using current directory name as index: '{index_name}'")
+
         index_dir = self.indexes_dir / index_name
         index_path = self.get_index_path(index_name)
 
@@ -469,6 +551,7 @@ Examples:
         builder = LeannBuilder(
             backend_name=args.backend,
             embedding_model=args.embedding_model,
+            embedding_mode=args.embedding_mode,
             graph_degree=args.graph_degree,
             complexity=args.complexity,
             is_compact=args.compact,

packages/leann-core/src/leann/embedding_compute.py

@@ -6,6 +6,7 @@ Preserves all optimization parameters to ensure performance
 
 import logging
 import os
+from concurrent.futures import ThreadPoolExecutor, as_completed
 from typing import Any
 
 import numpy as np
@@ -35,7 +36,7 @@ def compute_embeddings(
     Args:
         texts: List of texts to compute embeddings for
         model_name: Model name
-        mode: Computation mode ('sentence-transformers', 'openai', 'mlx')
+        mode: Computation mode ('sentence-transformers', 'openai', 'mlx', 'ollama')
         is_build: Whether this is a build operation (shows progress bar)
         batch_size: Batch size for processing
         adaptive_optimization: Whether to use adaptive optimization based on batch size
@@ -55,6 +56,8 @@ def compute_embeddings(
         return compute_embeddings_openai(texts, model_name)
     elif mode == "mlx":
         return compute_embeddings_mlx(texts, model_name)
+    elif mode == "ollama":
+        return compute_embeddings_ollama(texts, model_name, is_build=is_build)
     else:
         raise ValueError(f"Unsupported embedding mode: {mode}")
 
@@ -365,3 +368,262 @@ def compute_embeddings_mlx(chunks: list[str], model_name: str, batch_size: int =
 
     # Stack numpy arrays
     return np.stack(all_embeddings)
+
+
+def compute_embeddings_ollama(
+    texts: list[str], model_name: str, is_build: bool = False, host: str = "http://localhost:11434"
+) -> np.ndarray:
+    """
+    Compute embeddings using Ollama API.
+
+    Args:
+        texts: List of texts to compute embeddings for
+        model_name: Ollama model name (e.g., "nomic-embed-text", "mxbai-embed-large")
+        is_build: Whether this is a build operation (shows progress bar)
+        host: Ollama host URL (default: http://localhost:11434)
+
+    Returns:
+        Normalized embeddings array, shape: (len(texts), embedding_dim)
+    """
+    try:
+        import requests
+    except ImportError:
+        raise ImportError(
+            "The 'requests' library is required for Ollama embeddings. Install with: uv pip install requests"
+        )
+
+    if not texts:
+        raise ValueError("Cannot compute embeddings for empty text list")
+
+    logger.info(
+        f"Computing embeddings for {len(texts)} texts using Ollama API, model: '{model_name}'"
+    )
+
+    # Check if Ollama is running
+    try:
+        response = requests.get(f"{host}/api/version", timeout=5)
+        response.raise_for_status()
+    except requests.exceptions.ConnectionError:
+        error_msg = (
+            f"❌ Could not connect to Ollama at {host}.\n\n"
+            "Please ensure Ollama is running:\n"
+            "  • macOS/Linux: ollama serve\n"
+            "  • Windows: Make sure Ollama is running in the system tray\n\n"
+            "Installation: https://ollama.com/download"
+        )
+        raise RuntimeError(error_msg)
+    except Exception as e:
+        raise RuntimeError(f"Unexpected error connecting to Ollama: {e}")
+
+    # Check if model exists and provide helpful suggestions
+    try:
+        response = requests.get(f"{host}/api/tags", timeout=5)
+        response.raise_for_status()
+        models = response.json()
+        model_names = [model["name"] for model in models.get("models", [])]
+
+        # Filter for embedding models (models that support embeddings)
+        embedding_models = []
+        suggested_embedding_models = [
+            "nomic-embed-text",
+            "mxbai-embed-large",
+            "bge-m3",
+            "all-minilm",
+            "snowflake-arctic-embed",
+        ]
+
+        for model in model_names:
+            # Check if it's an embedding model (by name patterns or known models)
+            base_name = model.split(":")[0]
+            if any(emb in base_name for emb in ["embed", "bge", "minilm", "e5"]):
+                embedding_models.append(model)
+
+        # Check if model exists (handle versioned names)
+        model_found = any(
+            model_name == name.split(":")[0] or model_name == name for name in model_names
+        )
+
+        if not model_found:
+            error_msg = f"❌ Model '{model_name}' not found in local Ollama.\n\n"
+
+            # Suggest pulling the model
+            error_msg += "📦 To install this embedding model:\n"
+            error_msg += f"   ollama pull {model_name}\n\n"
+
+            # Show available embedding models
+            if embedding_models:
+                error_msg += "✅ Available embedding models:\n"
+                for model in embedding_models[:5]:
+                    error_msg += f"   • {model}\n"
+                if len(embedding_models) > 5:
+                    error_msg += f"   ... and {len(embedding_models) - 5} more\n"
+            else:
+                error_msg += "💡 Popular embedding models to install:\n"
+                for model in suggested_embedding_models[:3]:
+                    error_msg += f"   • ollama pull {model}\n"
+
+            error_msg += "\n📚 Browse more: https://ollama.com/library"
+            raise ValueError(error_msg)
+
+        # Verify the model supports embeddings by testing it
+        try:
+            test_response = requests.post(
+                f"{host}/api/embeddings", json={"model": model_name, "prompt": "test"}, timeout=10
+            )
+            if test_response.status_code != 200:
+                error_msg = (
+                    f"⚠️ Model '{model_name}' exists but may not support embeddings.\n\n"
+                    f"Please use an embedding model like:\n"
+                )
+                for model in suggested_embedding_models[:3]:
+                    error_msg += f"   • {model}\n"
+                raise ValueError(error_msg)
+        except requests.exceptions.RequestException:
+            # If test fails, continue anyway - model might still work
+            pass
+
+    except requests.exceptions.RequestException as e:
+        logger.warning(f"Could not verify model existence: {e}")
+
+    # Process embeddings with optimized concurrent processing
+    import requests
+
+    def get_single_embedding(text_idx_tuple):
+        """Helper function to get embedding for a single text."""
+        text, idx = text_idx_tuple
+        max_retries = 3
+        retry_count = 0
+
+        # Truncate very long texts to avoid API issues
+        truncated_text = text[:8000] if len(text) > 8000 else text
+
+        while retry_count < max_retries:
+            try:
+                response = requests.post(
+                    f"{host}/api/embeddings",
+                    json={"model": model_name, "prompt": truncated_text},
+                    timeout=30,
+                )
+                response.raise_for_status()
+
+                result = response.json()
+                embedding = result.get("embedding")
+
+                if embedding is None:
+                    raise ValueError(f"No embedding returned for text {idx}")
+
+                return idx, embedding
+
+            except requests.exceptions.Timeout:
+                retry_count += 1
+                if retry_count >= max_retries:
+                    logger.warning(f"Timeout for text {idx} after {max_retries} retries")
+                    return idx, None
+
+            except Exception as e:
+                if retry_count >= max_retries - 1:
+                    logger.error(f"Failed to get embedding for text {idx}: {e}")
+                    return idx, None
+                retry_count += 1
+
+        return idx, None
+
+    # Determine if we should use concurrent processing
+    use_concurrent = (
+        len(texts) > 5 and not is_build
+    )  # Don't use concurrent in build mode to avoid overwhelming
+    max_workers = min(4, len(texts))  # Limit concurrent requests to avoid overwhelming Ollama
+
+    all_embeddings = [None] * len(texts)  # Pre-allocate list to maintain order
+    failed_indices = []
+
+    if use_concurrent:
+        logger.info(
+            f"Using concurrent processing with {max_workers} workers for {len(texts)} texts"
+        )
+
+        with ThreadPoolExecutor(max_workers=max_workers) as executor:
+            # Submit all tasks
+            future_to_idx = {
+                executor.submit(get_single_embedding, (text, idx)): idx
+                for idx, text in enumerate(texts)
+            }
+
+            # Add progress bar for concurrent processing
+            try:
+                if is_build or len(texts) > 10:
+                    from tqdm import tqdm
+
+                    futures_iterator = tqdm(
+                        as_completed(future_to_idx),
+                        total=len(texts),
+                        desc="Computing Ollama embeddings",
+                    )
+                else:
+                    futures_iterator = as_completed(future_to_idx)
+            except ImportError:
+                futures_iterator = as_completed(future_to_idx)
+
+            # Collect results as they complete
+            for future in futures_iterator:
+                try:
+                    idx, embedding = future.result()
+                    if embedding is not None:
+                        all_embeddings[idx] = embedding
+                    else:
+                        failed_indices.append(idx)
+                except Exception as e:
+                    idx = future_to_idx[future]
+                    logger.error(f"Exception for text {idx}: {e}")
+                    failed_indices.append(idx)
+
+    else:
+        # Sequential processing with progress bar
+        show_progress = is_build or len(texts) > 10
+
+        try:
+            if show_progress:
+                from tqdm import tqdm
+
+                iterator = tqdm(
+                    enumerate(texts), total=len(texts), desc="Computing Ollama embeddings"
+                )
+            else:
+                iterator = enumerate(texts)
+        except ImportError:
+            iterator = enumerate(texts)
+
+        for idx, text in iterator:
+            result_idx, embedding = get_single_embedding((text, idx))
+            if embedding is not None:
+                all_embeddings[idx] = embedding
+            else:
+                failed_indices.append(idx)
+
+    # Handle failed embeddings
+    if failed_indices:
+        if len(failed_indices) == len(texts):
+            raise RuntimeError("Failed to compute any embeddings")
+
+        logger.warning(f"Failed to compute embeddings for {len(failed_indices)}/{len(texts)} texts")
+
+        # Use zero embeddings as fallback for failed ones
+        valid_embedding = next((e for e in all_embeddings if e is not None), None)
+        if valid_embedding:
+            embedding_dim = len(valid_embedding)
+            for idx in failed_indices:
+                all_embeddings[idx] = [0.0] * embedding_dim
+
+    # Remove None values and convert to numpy array
+    all_embeddings = [e for e in all_embeddings if e is not None]
+
+    # Convert to numpy array and normalize
+    embeddings = np.array(all_embeddings, dtype=np.float32)
+
+    # Normalize embeddings (L2 normalization)
+    norms = np.linalg.norm(embeddings, axis=1, keepdims=True)
+    embeddings = embeddings / (norms + 1e-8)  # Add small epsilon to avoid division by zero
+
+    logger.info(f"Generated {len(embeddings)} embeddings, dimension: {embeddings.shape[1]}")
+
+    return embeddings

packages/leann-core/src/leann/mcp.py

@@ -1,7 +1,6 @@
 #!/usr/bin/env python3
 
 import json
-import os
 import subprocess
 import sys
 
@@ -26,32 +25,61 @@ def handle_request(request):
                 "tools": [
                     {
                         "name": "leann_search",
-                        "description": "Search LEANN index",
+                        "description": """🔍 Search code using natural language - like having a coding assistant who knows your entire codebase!
+
+🎯 **Perfect for**:
+- "How does authentication work?" → finds auth-related code
+- "Error handling patterns" → locates try-catch blocks and error logic
+- "Database connection setup" → finds DB initialization code
+- "API endpoint definitions" → locates route handlers
+- "Configuration management" → finds config files and usage
+
+💡 **Pro tip**: Use this before making any changes to understand existing patterns and conventions.""",
                         "inputSchema": {
                             "type": "object",
                             "properties": {
-                                "index_name": {"type": "string"},
-                                "query": {"type": "string"},
-                                "top_k": {"type": "integer", "default": 5},
+                                "index_name": {
+                                    "type": "string",
+                                    "description": "Name of the LEANN index to search. Use 'leann_list' first to see available indexes.",
+                                },
+                                "query": {
+                                    "type": "string",
+                                    "description": "Search query - can be natural language (e.g., 'how to handle errors') or technical terms (e.g., 'async function definition')",
+                                },
+                                "top_k": {
+                                    "type": "integer",
+                                    "default": 5,
+                                    "minimum": 1,
+                                    "maximum": 20,
+                                    "description": "Number of search results to return. Use 5-10 for focused results, 15-20 for comprehensive exploration.",
+                                },
+                                "complexity": {
+                                    "type": "integer",
+                                    "default": 32,
+                                    "minimum": 16,
+                                    "maximum": 128,
+                                    "description": "Search complexity level. Use 16-32 for fast searches (recommended), 64+ for higher precision when needed.",
+                                },
                             },
                             "required": ["index_name", "query"],
                         },
                     },
                     {
-                        "name": "leann_ask",
-                        "description": "Ask question using LEANN RAG",
+                        "name": "leann_status",
+                        "description": "📊 Check the health and stats of your code indexes - like a medical checkup for your codebase knowledge!",
                         "inputSchema": {
                             "type": "object",
                             "properties": {
-                                "index_name": {"type": "string"},
-                                "question": {"type": "string"},
+                                "index_name": {
+                                    "type": "string",
+                                    "description": "Optional: Name of specific index to check. If not provided, shows status of all indexes.",
+                                }
                             },
-                            "required": ["index_name", "question"],
                         },
                     },
                     {
                         "name": "leann_list",
-                        "description": "List all LEANN indexes",
+                        "description": "📋 Show all your indexed codebases - your personal code library! Use this to see what's available for search.",
                         "inputSchema": {"type": "object", "properties": {}},
                     },
                 ]
@@ -62,32 +90,46 @@ def handle_request(request):
         tool_name = request["params"]["name"]
         args = request["params"].get("arguments", {})
 
-        # Set working directory and environment
-        env = os.environ.copy()
-        cwd = "/Users/andyl/Projects/LEANN-RAG"
-
         try:
             if tool_name == "leann_search":
+                # Validate required parameters
+                if not args.get("index_name") or not args.get("query"):
+                    return {
+                        "jsonrpc": "2.0",
+                        "id": request.get("id"),
+                        "result": {
+                            "content": [
+                                {
+                                    "type": "text",
+                                    "text": "Error: Both index_name and query are required",
+                                }
+                            ]
+                        },
+                    }
+
+                # Build simplified command
                 cmd = [
                     "leann",
                     "search",
                     args["index_name"],
                     args["query"],
-                    "--recompute-embeddings",
                     f"--top-k={args.get('top_k', 5)}",
+                    f"--complexity={args.get('complexity', 32)}",
                 ]
-                result = subprocess.run(cmd, capture_output=True, text=True, cwd=cwd, env=env)
 
-            elif tool_name == "leann_ask":
-                cmd = f'echo "{args["question"]}" | leann ask {args["index_name"]} --recompute-embeddings --llm ollama --model qwen3:8b'
-                result = subprocess.run(
-                    cmd, shell=True, capture_output=True, text=True, cwd=cwd, env=env
-                )
+                result = subprocess.run(cmd, capture_output=True, text=True)
+
+            elif tool_name == "leann_status":
+                if args.get("index_name"):
+                    # Check specific index status - for now, we'll use leann list and filter
+                    result = subprocess.run(["leann", "list"], capture_output=True, text=True)
+                    # We could enhance this to show more detailed status per index
+                else:
+                    # Show all indexes status
+                    result = subprocess.run(["leann", "list"], capture_output=True, text=True)
 
             elif tool_name == "leann_list":
-                result = subprocess.run(
-                    ["leann", "list"], capture_output=True, text=True, cwd=cwd, env=env
-                )
+                result = subprocess.run(["leann", "list"], capture_output=True, text=True)
 
             return {
                 "jsonrpc": "2.0",

packages/leann-mcp/README.md

@@ -1,18 +1,25 @@
-# LEANN Claude Code Integration
+# 🔥 LEANN Claude Code Integration
 
-Intelligent code assistance using LEANN's vector search directly in Claude Code.
+Transform your development workflow with intelligent code assistance using LEANN's semantic search directly in Claude Code.
 
 ## Prerequisites
 
-First, install LEANN CLI globally:
+**Step 1:** First, complete the basic LEANN installation following the [📦 Installation guide](../../README.md#installation) in the root README:
 
 ```bash
-uv tool install leann
+uv venv
+source .venv/bin/activate
+uv pip install leann
+```
+
+**Step 2:** Install LEANN globally for MCP integration:
+```bash
+uv tool install leann-core
 ```
 
 This makes the `leann` command available system-wide, which `leann_mcp` requires.
 
-## Quick Setup
+## 🚀 Quick Setup
 
 Add the LEANN MCP server to Claude Code:
 
@@ -20,23 +27,25 @@ Add the LEANN MCP server to Claude Code:
 claude mcp add leann-server -- leann_mcp
 ```
 
-## Available Tools
+## 🛠️ Available Tools
 
-- **`leann_list`** - List available indexes across all projects
-- **`leann_search`** - Search code and documents with semantic queries
-- **`leann_ask`** - Ask questions and get AI-powered answers from your codebase
+Once connected, you'll have access to these powerful semantic search tools in Claude Code:
 
-## Quick Start
+- **`leann_list`** - List all available indexes across your projects
+- **`leann_search`** - Perform semantic searches across code and documents
+- **`leann_ask`** - Ask natural language questions and get AI-powered answers from your codebase
+
+## 🎯 Quick Start Example
 
 ```bash
-# Build an index for your project
-leann build my-project
+# Build an index for your project (change to your actual path)
+leann build my-project --docs ./
 
 # Start Claude Code
 claude
 ```
 
-Then in Claude Code:
+**Try this in Claude Code:**
 ```
 Help me understand this codebase. List available indexes and search for authentication patterns.
 ```
@@ -46,24 +55,37 @@ Help me understand this codebase. List available indexes and search for authenti
 </p>
 
 
-## How It Works
+## 🧠 How It Works
 
-- **`leann`** - Core CLI tool for indexing and searching (installed globally)
+The integration consists of three key components working seamlessly together:
+
+- **`leann`** - Core CLI tool for indexing and searching (installed globally via `uv tool install`)
 - **`leann_mcp`** - MCP server that wraps `leann` commands for Claude Code integration
-- Claude Code calls `leann_mcp`, which executes `leann` commands and returns results
+- **Claude Code** - Calls `leann_mcp`, which executes `leann` commands and returns intelligent results
 
-## File Support
+## 📁 File Support
 
-Python, JavaScript, TypeScript, Java, Go, Rust, SQL, YAML, JSON, and 30+ more file types.
+LEANN understands **30+ file types** including:
+- **Programming**: Python, JavaScript, TypeScript, Java, Go, Rust, C++, C#
+- **Data**: SQL, YAML, JSON, CSV, XML
+- **Documentation**: Markdown, TXT, PDF
+- **And many more!**
 
-## Storage
+## 💾 Storage & Organization
 
-- Project indexes in `.leann/` directory (like `.git`)
-- Global project registry at `~/.leann/projects.json`
-- Multi-project support built-in
+- **Project indexes**: Stored in `.leann/` directory (just like `.git`)
+- **Global registry**: Project tracking at `~/.leann/projects.json`
+- **Multi-project support**: Switch between different codebases seamlessly
+- **Portable**: Transfer indexes between machines with minimal overhead
 
-## Removing
+## 🗑️ Uninstalling
+
+To remove the LEANN MCP server from Claude Code:
 
 ```bash
 claude mcp remove leann-server
 ```
+To remove LEANN
+```
+uv pip uninstall leann leann-backend-hnsw leann-core
+```

packages/leann/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "leann"
-version = "0.2.2"
+version = "0.2.6"
 description = "LEANN - The smallest vector index in the world. RAG Everything with LEANN!"
 readme = "README.md"
 requires-python = ">=3.9"

pyproject.toml

@@ -32,7 +32,7 @@ dependencies = [
     "pypdfium2>=4.30.0",
     # LlamaIndex core and readers - updated versions
     "llama-index>=0.12.44",
-    "llama-index-readers-file>=0.4.0",  # Essential for PDF parsing
+    "llama-index-readers-file>=0.4.0", # Essential for PDF parsing
     # "llama-index-readers-docling",  # Requires Python >= 3.10
     # "llama-index-node-parser-docling",  # Requires Python >= 3.10
     "llama-index-vector-stores-faiss>=0.4.0",
@@ -43,6 +43,9 @@ dependencies = [
     "mlx>=0.26.3; sys_platform == 'darwin'",
     "mlx-lm>=0.26.0; sys_platform == 'darwin'",
     "psutil>=5.8.0",
+    "pathspec>=0.12.1",
+    "nbconvert>=7.16.6",
+    "gitignore-parser>=0.1.12",
 ]
 
 [project.optional-dependencies]