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>

.github/workflows/build-reusable.yml

@@ -54,26 +54,16 @@ jobs:
             python: '3.12'
           - os: ubuntu-22.04
             python: '3.13'
-          - os: macos-14
+          - os: macos-latest
             python: '3.9'
-          - os: macos-14
+          - os: macos-latest
             python: '3.10'
-          - os: macos-14
+          - os: macos-latest
             python: '3.11'
-          - os: macos-14
+          - os: macos-latest
             python: '3.12'
-          - os: macos-14
+          - os: macos-latest
             python: '3.13'
-          - os: macos-13
-            python: '3.9'
-          - os: macos-13
-            python: '3.10'
-          - os: macos-13
-            python: '3.11'
-          - os: macos-13
-            python: '3.12'
-          # Note: macos-13 + Python 3.13 excluded due to PyTorch compatibility
-          # (PyTorch 2.5+ supports Python 3.13 but not Intel Mac x86_64)
     runs-on: ${{ matrix.os }}
 
     steps:
@@ -119,59 +109,48 @@ jobs:
             uv pip install --system delocate
           fi
 
-      - name: Set macOS environment variables
-        if: runner.os == 'macOS'
-        run: |
-          # Use brew --prefix to automatically detect Homebrew installation path
-          HOMEBREW_PREFIX=$(brew --prefix)
-          echo "HOMEBREW_PREFIX=${HOMEBREW_PREFIX}" >> $GITHUB_ENV
-          echo "OpenMP_ROOT=${HOMEBREW_PREFIX}/opt/libomp" >> $GITHUB_ENV
-
-          # Set CMAKE_PREFIX_PATH to let CMake find all packages automatically
-          echo "CMAKE_PREFIX_PATH=${HOMEBREW_PREFIX}" >> $GITHUB_ENV
-
-          # Set compiler flags for OpenMP (required for both backends)
-          echo "LDFLAGS=-L${HOMEBREW_PREFIX}/opt/libomp/lib" >> $GITHUB_ENV
-          echo "CPPFLAGS=-I${HOMEBREW_PREFIX}/opt/libomp/include" >> $GITHUB_ENV
-
       - name: Build packages
         run: |
           # Build core (platform independent)
-          cd packages/leann-core
+          if [[ "${{ matrix.os }}" == ubuntu-* ]]; then
-          uv build
+            cd packages/leann-core
-          cd ../..
+            uv build
+            cd ../..
+          fi
 
           # Build HNSW backend
           cd packages/leann-backend-hnsw
-          if [[ "${{ matrix.os }}" == macos-* ]]; then
+          if [ "${{ matrix.os }}" == "macos-latest" ]; then
-            # Use system clang for better compatibility
+            # Use system clang instead of homebrew LLVM for better compatibility
             export CC=clang
             export CXX=clang++
             export MACOSX_DEPLOYMENT_TARGET=11.0
-            uv build --wheel --python ${{ matrix.python }} --find-links ${GITHUB_WORKSPACE}/packages/leann-core/dist
+            uv build --wheel --python python
           else
-            uv build --wheel --python ${{ matrix.python }} --find-links ${GITHUB_WORKSPACE}/packages/leann-core/dist
+            uv build --wheel --python python
           fi
           cd ../..
 
           # Build DiskANN backend
           cd packages/leann-backend-diskann
-          if [[ "${{ matrix.os }}" == macos-* ]]; then
+          if [ "${{ matrix.os }}" == "macos-latest" ]; then
-            # Use system clang for better compatibility
+            # Use system clang instead of homebrew LLVM for better compatibility
             export CC=clang
             export CXX=clang++
             # DiskANN requires macOS 13.3+ for sgesdd_ LAPACK function
             export MACOSX_DEPLOYMENT_TARGET=13.3
-            uv build --wheel --python ${{ matrix.python }} --find-links ${GITHUB_WORKSPACE}/packages/leann-core/dist
+            uv build --wheel --python python
           else
-            uv build --wheel --python ${{ matrix.python }} --find-links ${GITHUB_WORKSPACE}/packages/leann-core/dist
+            uv build --wheel --python python
           fi
           cd ../..
 
           # Build meta package (platform independent)
-          cd packages/leann
+          if [[ "${{ matrix.os }}" == ubuntu-* ]]; then
-          uv build
+            cd packages/leann
-          cd ../..
+            uv build
+            cd ../..
+          fi
 
       - name: Repair wheels (Linux)
         if: runner.os == 'Linux'
@@ -220,18 +199,20 @@ jobs:
           echo "📦 Built packages:"
           find packages/*/dist -name "*.whl" -o -name "*.tar.gz" | sort
 
-
       - name: Install built packages for testing
         run: |
-          # Create a virtual environment with the correct Python version
+          # Create a virtual environment
-          uv venv --python ${{ matrix.python }}
+          uv venv
           source .venv/bin/activate || source .venv/Scripts/activate
 
-          # Install packages using --find-links to prioritize local builds
+          # Install the built wheels
-          uv pip install --find-links packages/leann-core/dist --find-links packages/leann-backend-hnsw/dist --find-links packages/leann-backend-diskann/dist packages/leann-core/dist/*.whl || uv pip install --find-links packages/leann-core/dist packages/leann-core/dist/*.tar.gz
+          # Use --find-links to let uv choose the correct wheel for the platform
-          uv pip install --find-links packages/leann-core/dist packages/leann-backend-hnsw/dist/*.whl
+          if [[ "${{ matrix.os }}" == ubuntu-* ]]; then
-          uv pip install --find-links packages/leann-core/dist packages/leann-backend-diskann/dist/*.whl
+            uv pip install leann-core --find-links packages/leann-core/dist
-          uv pip install packages/leann/dist/*.whl || uv pip install packages/leann/dist/*.tar.gz
+            uv pip install leann --find-links packages/leann/dist
+          fi
+          uv pip install leann-backend-hnsw --find-links packages/leann-backend-hnsw/dist
+          uv pip install leann-backend-diskann --find-links packages/leann-backend-diskann/dist
 
           # Install test dependencies using extras
           uv pip install -e ".[test]"

README.md

@@ -3,11 +3,10 @@
 </p>
 
 <p align="center">
-  <img src="https://img.shields.io/badge/Python-3.9%20%7C%203.10%20%7C%203.11%20%7C%203.12%20%7C%203.13-blue.svg" alt="Python Versions">
+  <img src="https://img.shields.io/badge/Python-3.9%2B-blue.svg" alt="Python 3.9+">
-  <img src="https://github.com/yichuan-w/LEANN/actions/workflows/build-and-publish.yml/badge.svg" alt="CI Status">
-  <img src="https://img.shields.io/badge/Platform-Ubuntu%20%7C%20macOS%20(ARM64%2FIntel)-lightgrey" alt="Platform">
   <img src="https://img.shields.io/badge/License-MIT-green.svg" alt="MIT License">
-  <img src="https://img.shields.io/badge/MCP-Native%20Integration-blue" alt="MCP Integration">
+  <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">

packages/leann-backend-diskann/CMakeLists.txt

@@ -0,0 +1,8 @@
+# packages/leann-backend-diskann/CMakeLists.txt (simplified version)
+
+cmake_minimum_required(VERSION 3.20)
+project(leann_backend_diskann_wrapper)
+
+# Tell CMake to directly enter the DiskANN submodule and execute its own CMakeLists.txt
+# DiskANN will handle everything itself, including compiling Python bindings
+add_subdirectory(src/third_party/DiskANN)

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

@@ -4,7 +4,7 @@ import os
 import struct
 import sys
 from pathlib import Path
-from typing import Any, Literal, Optional
+from typing import Any, Literal
 
 import numpy as np
 import psutil
@@ -259,7 +259,7 @@ class DiskannSearcher(BaseSearcher):
         prune_ratio: float = 0.0,
         recompute_embeddings: bool = False,
         pruning_strategy: Literal["global", "local", "proportional"] = "global",
-        zmq_port: Optional[int] = None,
+        zmq_port: int | None = None,
         batch_recompute: bool = False,
         dedup_node_dis: bool = False,
         **kwargs,

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

@@ -10,7 +10,6 @@ import sys
 import threading
 import time
 from pathlib import Path
-from typing import Optional
 
 import numpy as np
 import zmq
@@ -33,7 +32,7 @@ if not logger.handlers:
 
 
 def create_diskann_embedding_server(
-    passages_file: Optional[str] = None,
+    passages_file: str | None = None,
     zmq_port: int = 5555,
     model_name: str = "sentence-transformers/all-mpnet-base-v2",
     embedding_mode: str = "sentence-transformers",

packages/leann-backend-diskann/pyproject.toml

@@ -4,8 +4,8 @@ build-backend = "scikit_build_core.build"
 
 [project]
 name = "leann-backend-diskann"
-version = "0.2.7"
+version = "0.2.6"
-dependencies = ["leann-core==0.2.7", "numpy", "protobuf>=3.19.0"]
+dependencies = ["leann-core==0.2.6", "numpy", "protobuf>=3.19.0"]
 
 [tool.scikit-build]
 # Key: simplified CMake path
@@ -17,5 +17,3 @@ editable.mode = "redirect"
 cmake.build-type = "Release"
 build.verbose = true
 build.tool-args = ["-j8"]
-# Let CMake find packages via Homebrew prefix
-cmake.define = {CMAKE_PREFIX_PATH = {env = "CMAKE_PREFIX_PATH"}, OpenMP_ROOT = {env = "OpenMP_ROOT"}}

packages/leann-backend-hnsw/CMakeLists.txt

@@ -5,20 +5,11 @@ set(CMAKE_CXX_COMPILER_WORKS 1)
 
 # Set OpenMP path for macOS
 if(APPLE)
-    # Detect Homebrew installation path (Apple Silicon vs Intel)
+    set(OpenMP_C_FLAGS "-Xpreprocessor -fopenmp -I/opt/homebrew/opt/libomp/include")
-    if(EXISTS "/opt/homebrew/opt/libomp")
+    set(OpenMP_CXX_FLAGS "-Xpreprocessor -fopenmp -I/opt/homebrew/opt/libomp/include")
-        set(HOMEBREW_PREFIX "/opt/homebrew")
-    elseif(EXISTS "/usr/local/opt/libomp")
-        set(HOMEBREW_PREFIX "/usr/local")
-    else()
-        message(FATAL_ERROR "Could not find libomp installation. Please install with: brew install libomp")
-    endif()
-    
-    set(OpenMP_C_FLAGS "-Xpreprocessor -fopenmp -I${HOMEBREW_PREFIX}/opt/libomp/include")
-    set(OpenMP_CXX_FLAGS "-Xpreprocessor -fopenmp -I${HOMEBREW_PREFIX}/opt/libomp/include")
     set(OpenMP_C_LIB_NAMES "omp")
     set(OpenMP_CXX_LIB_NAMES "omp")
-    set(OpenMP_omp_LIBRARY "${HOMEBREW_PREFIX}/opt/libomp/lib/libomp.dylib")
+    set(OpenMP_omp_LIBRARY "/opt/homebrew/opt/libomp/lib/libomp.dylib")
 
     # Force use of system libc++ to avoid version mismatch
     set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -stdlib=libc++")

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

@@ -2,7 +2,7 @@ import logging
 import os
 import shutil
 from pathlib import Path
-from typing import Any, Literal, Optional
+from typing import Any, Literal
 
 import numpy as np
 from leann.interface import (
@@ -152,7 +152,7 @@ class HNSWSearcher(BaseSearcher):
         self,
         query: np.ndarray,
         top_k: int,
-        zmq_port: Optional[int] = None,
+        zmq_port: int | None = None,
         complexity: int = 64,
         beam_width: int = 1,
         prune_ratio: float = 0.0,

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

@@ -10,7 +10,6 @@ import sys
 import threading
 import time
 from pathlib import Path
-from typing import Union
 
 import msgpack
 import numpy as np
@@ -34,7 +33,7 @@ if not logger.handlers:
 
 
 def create_hnsw_embedding_server(
-    passages_file: Union[str, None] = None,
+    passages_file: str | None = None,
     zmq_port: int = 5555,
     model_name: str = "sentence-transformers/all-mpnet-base-v2",
     distance_metric: str = "mips",

packages/leann-backend-hnsw/pyproject.toml

@@ -6,10 +6,10 @@ build-backend = "scikit_build_core.build"
 
 [project]
 name = "leann-backend-hnsw"
-version = "0.2.7"
+version = "0.2.6"
 description = "Custom-built HNSW (Faiss) backend for the Leann toolkit."
 dependencies = [
-    "leann-core==0.2.7",
+    "leann-core==0.2.6",
     "numpy",
     "pyzmq>=23.0.0",
     "msgpack>=1.0.0",
@@ -22,8 +22,6 @@ cmake.build-type = "Release"
 build.verbose = true
 build.tool-args = ["-j8"]
 
-# CMake definitions to optimize compilation and find Homebrew packages
+# CMake definitions to optimize compilation
 [tool.scikit-build.cmake.define]
 CMAKE_BUILD_PARALLEL_LEVEL = "8"
-CMAKE_PREFIX_PATH = {env = "CMAKE_PREFIX_PATH"}
-OpenMP_ROOT = {env = "OpenMP_ROOT"}

packages/leann-core/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "leann-core"
-version = "0.2.7"
+version = "0.2.6"
 description = "Core API and plugin system for LEANN"
 readme = "README.md"
 requires-python = ">=3.9"
@@ -33,8 +33,8 @@ dependencies = [
     "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' and platform_machine == 'arm64'",
+    "mlx>=0.26.3; sys_platform == 'darwin'",
-    "mlx-lm>=0.26.0; sys_platform == 'darwin' and platform_machine == 'arm64'",
+    "mlx-lm>=0.26.0; sys_platform == 'darwin'",
 ]
 
 [project.optional-dependencies]

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

@@ -10,7 +10,7 @@ import time
 import warnings
 from dataclasses import dataclass, field
 from pathlib import Path
-from typing import Any, Literal, Optional
+from typing import Any, Literal
 
 import numpy as np
 
@@ -33,7 +33,7 @@ def compute_embeddings(
     model_name: str,
     mode: str = "sentence-transformers",
     use_server: bool = True,
-    port: Optional[int] = None,
+    port: int | None = None,
     is_build=False,
 ) -> np.ndarray:
     """
@@ -157,12 +157,12 @@ class LeannBuilder:
         self,
         backend_name: str,
         embedding_model: str = "facebook/contriever",
-        dimensions: Optional[int] = None,
+        dimensions: int | None = None,
         embedding_mode: str = "sentence-transformers",
         **backend_kwargs,
     ):
         self.backend_name = backend_name
-        backend_factory: Optional[LeannBackendFactoryInterface] = BACKEND_REGISTRY.get(backend_name)
+        backend_factory: LeannBackendFactoryInterface | None = BACKEND_REGISTRY.get(backend_name)
         if backend_factory is None:
             raise ValueError(f"Backend '{backend_name}' not found or not registered.")
         self.backend_factory = backend_factory
@@ -242,7 +242,7 @@ class LeannBuilder:
         self.backend_kwargs = backend_kwargs
         self.chunks: list[dict[str, Any]] = []
 
-    def add_text(self, text: str, metadata: Optional[dict[str, Any]] = None):
+    def add_text(self, text: str, metadata: dict[str, Any] | None = None):
         if metadata is None:
             metadata = {}
         passage_id = metadata.get("id", str(len(self.chunks)))
@@ -554,7 +554,7 @@ class LeannSearcher:
         if "labels" in results and "distances" in results:
             logger.info(f"  Processing {len(results['labels'][0])} passage IDs:")
             for i, (string_id, dist) in enumerate(
-                zip(results["labels"][0], results["distances"][0])
+                zip(results["labels"][0], results["distances"][0], strict=False)
             ):
                 try:
                     passage_data = self.passage_manager.get_passage(string_id)
@@ -592,7 +592,7 @@ class LeannChat:
     def __init__(
         self,
         index_path: str,
-        llm_config: Optional[dict[str, Any]] = None,
+        llm_config: dict[str, Any] | None = None,
         enable_warmup: bool = False,
         **kwargs,
     ):
@@ -608,7 +608,7 @@ class LeannChat:
         prune_ratio: float = 0.0,
         recompute_embeddings: bool = True,
         pruning_strategy: Literal["global", "local", "proportional"] = "global",
-        llm_kwargs: Optional[dict[str, Any]] = None,
+        llm_kwargs: dict[str, Any] | None = None,
         expected_zmq_port: int = 5557,
         **search_kwargs,
     ):

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

@@ -8,7 +8,7 @@ import difflib
 import logging
 import os
 from abc import ABC, abstractmethod
-from typing import Any, Optional
+from typing import Any
 
 import torch
 
@@ -311,7 +311,7 @@ def search_hf_models(query: str, limit: int = 10) -> list[str]:
 
 def validate_model_and_suggest(
     model_name: str, llm_type: str, host: str = "http://localhost:11434"
-) -> Optional[str]:
+) -> str | None:
     """Validate model name and provide suggestions if invalid"""
     if llm_type == "ollama":
         available_models = check_ollama_models(host)
@@ -685,7 +685,7 @@ class HFChat(LLMInterface):
 class OpenAIChat(LLMInterface):
     """LLM interface for OpenAI models."""
 
-    def __init__(self, model: str = "gpt-4o", api_key: Optional[str] = None):
+    def __init__(self, model: str = "gpt-4o", api_key: str | None = None):
         self.model = model
         self.api_key = api_key or os.getenv("OPENAI_API_KEY")
 
@@ -761,7 +761,7 @@ class SimulatedChat(LLMInterface):
         return "This is a simulated answer from the LLM based on the retrieved context."
 
 
-def get_llm(llm_config: Optional[dict[str, Any]] = None) -> LLMInterface:
+def get_llm(llm_config: dict[str, Any] | None = None) -> LLMInterface:
     """
     Factory function to get an LLM interface based on configuration.
 

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

@@ -1,7 +1,6 @@
 import argparse
 import asyncio
 from pathlib import Path
-from typing import Union
 
 from llama_index.core import SimpleDirectoryReader
 from llama_index.core.node_parser import SentenceSplitter
@@ -311,7 +310,7 @@ Examples:
                     print(f'  leann search {example_name} "your query"')
                     print(f"  leann ask {example_name} --interactive")
 
-    def load_documents(self, docs_dir: str, custom_file_types: Union[str, None] = None):
+    def load_documents(self, docs_dir: str, custom_file_types: str | None = None):
         print(f"Loading documents from {docs_dir}...")
         if custom_file_types:
             print(f"Using custom file types: {custom_file_types}")

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

@@ -6,7 +6,6 @@ import subprocess
 import sys
 import time
 from pathlib import Path
-from typing import Optional
 
 import psutil
 
@@ -183,8 +182,8 @@ class EmbeddingServerManager:
                                        e.g., "leann_backend_diskann.embedding_server"
         """
         self.backend_module_name = backend_module_name
-        self.server_process: Optional[subprocess.Popen] = None
+        self.server_process: subprocess.Popen | None = None
-        self.server_port: Optional[int] = None
+        self.server_port: int | None = None
         self._atexit_registered = False
 
     def start_server(

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

@@ -1,5 +1,5 @@
 from abc import ABC, abstractmethod
-from typing import Any, Literal, Union
+from typing import Any, Literal
 
 import numpy as np
 
@@ -34,9 +34,7 @@ class LeannBackendSearcherInterface(ABC):
         pass
 
     @abstractmethod
-    def _ensure_server_running(
+    def _ensure_server_running(self, passages_source_file: str, port: int | None, **kwargs) -> int:
-        self, passages_source_file: str, port: Union[int, None], **kwargs
-    ) -> int:
         """Ensure server is running"""
         pass
 
@@ -50,7 +48,7 @@ class LeannBackendSearcherInterface(ABC):
         prune_ratio: float = 0.0,
         recompute_embeddings: bool = False,
         pruning_strategy: Literal["global", "local", "proportional"] = "global",
-        zmq_port: Union[int, None] = None,
+        zmq_port: int | None = None,
         **kwargs,
     ) -> dict[str, Any]:
         """Search for nearest neighbors
@@ -76,7 +74,7 @@ class LeannBackendSearcherInterface(ABC):
         self,
         query: str,
         use_server_if_available: bool = True,
-        zmq_port: Union[int, None] = None,
+        zmq_port: int | None = None,
     ) -> np.ndarray:
         """Compute embedding for a query string
 

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

@@ -1,7 +1,7 @@
 import json
 from abc import ABC, abstractmethod
 from pathlib import Path
-from typing import Any, Literal, Optional
+from typing import Any, Literal
 
 import numpy as np
 
@@ -169,7 +169,7 @@ class BaseSearcher(LeannBackendSearcherInterface, ABC):
         prune_ratio: float = 0.0,
         recompute_embeddings: bool = False,
         pruning_strategy: Literal["global", "local", "proportional"] = "global",
-        zmq_port: Optional[int] = None,
+        zmq_port: int | None = None,
         **kwargs,
     ) -> dict[str, Any]:
         """

packages/leann/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "leann"
-version = "0.2.7"
+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

@@ -40,8 +40,8 @@ dependencies = [
     # Other dependencies
     "ipykernel==6.29.5",
     "msgpack>=1.1.1",
-    "mlx>=0.26.3; sys_platform == 'darwin' and platform_machine == 'arm64'",
+    "mlx>=0.26.3; sys_platform == 'darwin'",
-    "mlx-lm>=0.26.0; sys_platform == 'darwin' and platform_machine == 'arm64'",
+    "mlx-lm>=0.26.0; sys_platform == 'darwin'",
     "psutil>=5.8.0",
     "pathspec>=0.12.1",
     "nbconvert>=7.16.6",
@@ -91,7 +91,7 @@ leann-backend-diskann = { path = "packages/leann-backend-diskann", editable = tr
 leann-backend-hnsw = { path = "packages/leann-backend-hnsw", editable = true }
 
 [tool.ruff]
-target-version = "py39"
+target-version = "py310"
 line-length = 100
 extend-exclude = [
     "third_party",