style: apply ruff format

README.md

@@ -426,21 +426,21 @@ Once the index is built, you can ask questions like:
 **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, fully local index and lightweight
+- 🔍 **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 --with leann
-claude mcp add --scope user leann-server -- leann_mcp
+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)
+**Ready to supercharge your coding?** [Complete Setup Guide →](packages/leann-mcp/README.md)
 
 ## 🖥️ Command Line Interface
 
@@ -457,8 +457,7 @@ leann --help
 **To make it globally available:**
 ```bash
 # Install the LEANN CLI globally using uv tool
-uv tool install leann-core --with leann
-
+uv tool install leann-core
 
 # Now you can use leann from anywhere without activating venv
 leann --help

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

@@ -46,7 +46,6 @@ def compute_embeddings(
             - "sentence-transformers": Use sentence-transformers library (default)
             - "mlx": Use MLX backend for Apple Silicon
             - "openai": Use OpenAI embedding API
-            - "gemini": Use Google Gemini embedding API
         use_server: Whether to use embedding server (True for search, False for build)
 
     Returns:

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

@@ -680,52 +680,6 @@ class HFChat(LLMInterface):
         return response.strip()
 
 
-class GeminiChat(LLMInterface):
-    """LLM interface for Google Gemini models."""
-
-    def __init__(self, model: str = "gemini-2.5-flash", api_key: Optional[str] = None):
-        self.model = model
-        self.api_key = api_key or os.getenv("GEMINI_API_KEY")
-
-        if not self.api_key:
-            raise ValueError(
-                "Gemini API key is required. Set GEMINI_API_KEY environment variable or pass api_key parameter."
-            )
-
-        logger.info(f"Initializing Gemini Chat with model='{model}'")
-
-        try:
-            import google.genai as genai
-
-            self.client = genai.Client(api_key=self.api_key)
-        except ImportError:
-            raise ImportError(
-                "The 'google-genai' library is required for Gemini models. Please install it with 'uv pip install google-genai'."
-            )
-
-    def ask(self, prompt: str, **kwargs) -> str:
-        logger.info(f"Sending request to Gemini with model {self.model}")
-
-        try:
-            # Set generation configuration
-            generation_config = {
-                "temperature": kwargs.get("temperature", 0.7),
-                "max_output_tokens": kwargs.get("max_tokens", 1000),
-            }
-
-            # Handle top_p parameter
-            if "top_p" in kwargs:
-                generation_config["top_p"] = kwargs["top_p"]
-
-            response = self.client.models.generate_content(
-                model=self.model, contents=prompt, config=generation_config
-            )
-            return response.text.strip()
-        except Exception as e:
-            logger.error(f"Error communicating with Gemini: {e}")
-            return f"Error: Could not get a response from Gemini. Details: {e}"
-
-
 class OpenAIChat(LLMInterface):
     """LLM interface for OpenAI models."""
 
@@ -839,8 +793,6 @@ def get_llm(llm_config: Optional[dict[str, Any]] = None) -> LLMInterface:
         return HFChat(model_name=model or "deepseek-ai/deepseek-llm-7b-chat")
     elif llm_type == "openai":
         return OpenAIChat(model=model or "gpt-4o", api_key=llm_config.get("api_key"))
-    elif llm_type == "gemini":
-        return GeminiChat(model=model or "gemini-2.5-flash", api_key=llm_config.get("api_key"))
     elif llm_type == "simulated":
         return SimulatedChat()
     else:

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

@@ -148,6 +148,12 @@ Examples:
             type=str,
             help="Comma-separated list of file extensions to include (e.g., '.txt,.pdf,.pptx'). If not specified, uses default supported types.",
         )
+        build_parser.add_argument(
+            "--include-hidden",
+            action=argparse.BooleanOptionalAction,
+            default=False,
+            help="Include hidden files and directories (paths starting with '.') during indexing (default: false)",
+        )
         build_parser.add_argument(
             "--doc-chunk-size",
             type=int,
@@ -411,7 +417,10 @@ Examples:
                     print(f"  leann ask {example_name} --interactive")
 
     def load_documents(
-        self, docs_paths: Union[str, list], custom_file_types: Union[str, None] = None
+        self,
+        docs_paths: Union[str, list],
+        custom_file_types: Union[str, None] = None,
+        include_hidden: bool = False,
     ):
         # Handle both single path (string) and multiple paths (list) for backward compatibility
         if isinstance(docs_paths, str):
@@ -455,6 +464,10 @@ Examples:
 
         all_documents = []
 
+        # Helper to detect hidden path components
+        def _path_has_hidden_segment(p: Path) -> bool:
+            return any(part.startswith(".") and part not in [".", ".."] for part in p.parts)
+
         # First, process individual files if any
         if files:
             print(f"\n🔄 Processing {len(files)} individual file{'s' if len(files) > 1 else ''}...")
@@ -467,8 +480,12 @@ Examples:
 
                 files_by_dir = defaultdict(list)
                 for file_path in files:
-                    parent_dir = str(Path(file_path).parent)
-                    files_by_dir[parent_dir].append(file_path)
+                    file_path_obj = Path(file_path)
+                    if not include_hidden and _path_has_hidden_segment(file_path_obj):
+                        print(f"  ⚠️  Skipping hidden file: {file_path}")
+                        continue
+                    parent_dir = str(file_path_obj.parent)
+                    files_by_dir[parent_dir].append(str(file_path_obj))
 
                 # Load files from each parent directory
                 for parent_dir, file_list in files_by_dir.items():
@@ -479,6 +496,7 @@ Examples:
                         file_docs = SimpleDirectoryReader(
                             parent_dir,
                             input_files=file_list,
+                            # exclude_hidden only affects directory scans; input_files are explicit
                             filename_as_id=True,
                         ).load_data()
                         all_documents.extend(file_docs)
@@ -577,6 +595,8 @@ Examples:
                     # Check if file matches any exclude pattern
                     try:
                         relative_path = file_path.relative_to(docs_path)
+                        if not include_hidden and _path_has_hidden_segment(relative_path):
+                            continue
                         if self._should_exclude_file(relative_path, gitignore_matches):
                             continue
                     except ValueError:
@@ -604,6 +624,7 @@ Examples:
                         try:
                             default_docs = SimpleDirectoryReader(
                                 str(file_path.parent),
+                                exclude_hidden=not include_hidden,
                                 filename_as_id=True,
                                 required_exts=[file_path.suffix],
                             ).load_data()
@@ -632,6 +653,7 @@ Examples:
                     encoding="utf-8",
                     required_exts=code_extensions,
                     file_extractor={},  # Use default extractors
+                    exclude_hidden=not include_hidden,
                     filename_as_id=True,
                 ).load_data(show_progress=True)
 
@@ -781,7 +803,9 @@ Examples:
             paragraph_separator="\n\n",
         )
 
-        all_texts = self.load_documents(docs_paths, args.file_types)
+        all_texts = self.load_documents(
+            docs_paths, args.file_types, include_hidden=args.include_hidden
+        )
         if not all_texts:
             print("No documents found")
             return

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

@@ -57,8 +57,6 @@ def compute_embeddings(
         return compute_embeddings_mlx(texts, model_name)
     elif mode == "ollama":
         return compute_embeddings_ollama(texts, model_name, is_build=is_build)
-    elif mode == "gemini":
-        return compute_embeddings_gemini(texts, model_name, is_build=is_build)
     else:
         raise ValueError(f"Unsupported embedding mode: {mode}")
 
@@ -660,83 +658,3 @@ def compute_embeddings_ollama(
     logger.info(f"Generated {len(embeddings)} embeddings, dimension: {embeddings.shape[1]}")
 
     return embeddings
-
-
-def compute_embeddings_gemini(
-    texts: list[str], model_name: str = "text-embedding-004", is_build: bool = False
-) -> np.ndarray:
-    """
-    Compute embeddings using Google Gemini API.
-
-    Args:
-        texts: List of texts to compute embeddings for
-        model_name: Gemini model name (default: "text-embedding-004")
-        is_build: Whether this is a build operation (shows progress bar)
-
-    Returns:
-        Embeddings array, shape: (len(texts), embedding_dim)
-    """
-    try:
-        import os
-
-        import google.genai as genai
-    except ImportError as e:
-        raise ImportError(f"Google GenAI package not installed: {e}")
-
-    api_key = os.getenv("GEMINI_API_KEY")
-    if not api_key:
-        raise RuntimeError("GEMINI_API_KEY environment variable not set")
-
-    # Cache Gemini client
-    cache_key = "gemini_client"
-    if cache_key in _model_cache:
-        client = _model_cache[cache_key]
-    else:
-        client = genai.Client(api_key=api_key)
-        _model_cache[cache_key] = client
-        logger.info("Gemini client cached")
-
-    logger.info(
-        f"Computing embeddings for {len(texts)} texts using Gemini API, model: '{model_name}'"
-    )
-
-    # Gemini supports batch embedding
-    max_batch_size = 100  # Conservative batch size for Gemini
-    all_embeddings = []
-
-    try:
-        from tqdm import tqdm
-
-        total_batches = (len(texts) + max_batch_size - 1) // max_batch_size
-        batch_range = range(0, len(texts), max_batch_size)
-        batch_iterator = tqdm(
-            batch_range, desc="Computing embeddings", unit="batch", total=total_batches
-        )
-    except ImportError:
-        # Fallback when tqdm is not available
-        batch_iterator = range(0, len(texts), max_batch_size)
-
-    for i in batch_iterator:
-        batch_texts = texts[i : i + max_batch_size]
-
-        try:
-            # Use the embed_content method from the new Google GenAI SDK
-            response = client.models.embed_content(
-                model=model_name,
-                contents=batch_texts,
-                config=genai.types.EmbedContentConfig(
-                    task_type="RETRIEVAL_DOCUMENT"  # For document embedding
-                ),
-            )
-
-            # Extract embeddings from response
-            for embedding_data in response.embeddings:
-                all_embeddings.append(embedding_data.values)
-        except Exception as e:
-            logger.error(f"Batch {i} failed: {e}")
-            raise
-
-    embeddings = np.array(all_embeddings, dtype=np.float32)
-    logger.info(f"Generated {len(embeddings)} embeddings, dimension: {embeddings.shape[1]}")
-
-    return embeddings

packages/leann-mcp/README.md

@@ -92,7 +92,7 @@ leann build docs-and-configs --docs $(git ls-files "*.md" "*.yml" "*.yaml" "*.js
 ```
 
 
-## **Try this in Claude Code:**
+**Try this in Claude Code:**
 ```
 Help me understand this codebase. List available indexes and search for authentication patterns.
 ```