feat: Enhance CLI with improved list and smart remove commands

- **Better UX**: Current project shown first with clear separation
- **Visual improvements**: Icons (🏠/📂), better formatting, size info
- **Smart guidance**: Context-aware usage examples and getting started tips

- **Safety first**: Always shows ALL matching indexes across projects
- **Intelligent handling**:
  - Single match: Clear location display with cross-project warnings
  - Multiple matches: Interactive selection with final confirmation
- **Prevents accidents**: No more deleting wrong indexes due to name conflicts
- **User-friendly**: 'c' to cancel, clear visual hierarchy, detailed info

- **Clean logging**: Hide debug messages for better CLI experience
- **Comprehensive search**: Always scan all projects for transparency
- **Error handling**: Graceful handling of edge cases and user input

- **Safer**: Eliminates risk of accidental index deletion
- **Clearer**: Users always know what they're operating on
- **Smarter**: Automatic detection and handling of common scenarios

.gitattributes

@@ -0,0 +1 @@
+paper_plot/data/big_graph_degree_data.npz filter=lfs diff=lfs merge=lfs -text

.github/workflows/build-reusable.yml

@@ -87,7 +87,7 @@ jobs:
     runs-on: ${{ matrix.os }}
 
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v4
         with:
           ref: ${{ inputs.ref }}
           submodules: recursive
@@ -98,23 +98,21 @@ jobs:
           python-version: ${{ matrix.python }}
 
       - name: Install uv
-        uses: astral-sh/setup-uv@v6
+        uses: astral-sh/setup-uv@v4
 
       - name: Install system dependencies (Ubuntu)
         if: runner.os == 'Linux'
         run: |
           sudo apt-get update
           sudo apt-get install -y libomp-dev libboost-all-dev protobuf-compiler libzmq3-dev \
-            pkg-config libabsl-dev libaio-dev libprotobuf-dev \
-            patchelf
+            pkg-config libopenblas-dev patchelf libabsl-dev libaio-dev libprotobuf-dev
 
           # Install Intel MKL for DiskANN
           wget -q https://registrationcenter-download.intel.com/akdlm/IRC_NAS/79153e0f-74d7-45af-b8c2-258941adf58a/intel-onemkl-2025.0.0.940.sh
           sudo sh intel-onemkl-2025.0.0.940.sh -a --components intel.oneapi.lin.mkl.devel --action install --eula accept -s
           source /opt/intel/oneapi/setvars.sh
           echo "MKLROOT=/opt/intel/oneapi/mkl/latest" >> $GITHUB_ENV
-          echo "LD_LIBRARY_PATH=/opt/intel/oneapi/compiler/latest/linux/compiler/lib/intel64_lin" >> $GITHUB_ENV
-          echo "LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/intel/oneapi/mkl/latest/lib/intel64" >> $GITHUB_ENV
+          echo "LD_LIBRARY_PATH=/opt/intel/oneapi/mkl/latest/lib/intel64:$LD_LIBRARY_PATH" >> $GITHUB_ENV
 
       - name: Install system dependencies (macOS)
         if: runner.os == 'macOS'
@@ -306,53 +304,3 @@ jobs:
         with:
           name: packages-${{ matrix.os }}-py${{ matrix.python }}
           path: packages/*/dist/
-
-
-  arch-smoke:
-    name: Arch Linux smoke test (install & import)
-    needs: build
-    runs-on: ubuntu-latest
-    container:
-      image: archlinux:latest
-
-    steps:
-      - name: Prepare system
-        run: |
-          pacman -Syu --noconfirm
-          pacman -S --noconfirm python python-pip gcc git zlib openssl
-
-      - name: Download ALL wheel artifacts from this run
-        uses: actions/download-artifact@v5
-        with:
-          # Don't specify name, download all artifacts
-          path: ./wheels
-
-      - name: Install uv
-        uses: astral-sh/setup-uv@v6
-
-      - name: Create virtual environment and install wheels
-        run: |
-          uv venv
-          source .venv/bin/activate || source .venv/Scripts/activate
-          uv pip install --find-links wheels leann-core
-          uv pip install --find-links wheels leann-backend-hnsw
-          uv pip install --find-links wheels leann-backend-diskann
-          uv pip install --find-links wheels leann
-
-      - name: Import & tiny runtime check
-        env:
-          OMP_NUM_THREADS: 1
-          MKL_NUM_THREADS: 1
-        run: |
-          source .venv/bin/activate || source .venv/Scripts/activate
-          python - <<'PY'
-          import leann
-          import leann_backend_hnsw as h
-          import leann_backend_diskann as d
-          from leann import LeannBuilder, LeannSearcher
-          b = LeannBuilder(backend_name="hnsw")
-          b.add_text("hello arch")
-          b.build_index("arch_demo.leann")
-          s = LeannSearcher("arch_demo.leann")
-          print("search:", s.search("hello", top_k=1))
-          PY

.github/workflows/link-check.yml

@@ -14,6 +14,6 @@ jobs:
       - uses: actions/checkout@v4
       - uses: lycheeverse/lychee-action@v2
         with:
-          args: --no-progress --insecure --user-agent 'curl/7.68.0' README.md docs/ apps/ examples/ benchmarks/
+          args: --no-progress --insecure README.md docs/ apps/ examples/ benchmarks/
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.gitignore

@@ -18,7 +18,6 @@ demo/experiment_results/**/*.json
 *.eml
 *.emlx
 *.json
-!.vscode/*.json
 *.sh
 *.txt
 !CMakeLists.txt

.vscode/extensions.json

@@ -1,5 +0,0 @@
-{
-    "recommendations": [
-        "charliermarsh.ruff",
-    ]
-}

.vscode/settings.json

@@ -1,22 +0,0 @@
-{
-  "python.defaultInterpreterPath": ".venv/bin/python",
-  "python.terminal.activateEnvironment": true,
-  "[python]": {
-    "editor.defaultFormatter": "charliermarsh.ruff",
-    "editor.formatOnSave": true,
-    "editor.codeActionsOnSave": {
-      "source.organizeImports": "explicit",
-      "source.fixAll": "explicit"
-    },
-    "editor.insertSpaces": true,
-    "editor.tabSize": 4
-  },
-  "ruff.enable": true,
-  "files.watcherExclude": {
-    "**/.venv/**": true,
-    "**/__pycache__/**": true,
-    "**/*.egg-info/**": true,
-    "**/build/**": true,
-    "**/dist/**": true
-  }
-}

README.md

@@ -87,60 +87,17 @@ git submodule update --init --recursive
 ```
 
 **macOS:**
-
-Note: DiskANN requires MacOS 13.3 or later.
-
 ```bash
-brew install libomp boost protobuf zeromq pkgconf
-uv sync --extra diskann
+brew install llvm libomp boost protobuf zeromq pkgconf
+CC=$(brew --prefix llvm)/bin/clang CXX=$(brew --prefix llvm)/bin/clang++ uv sync
 ```
 
-**Linux (Ubuntu/Debian):**
-
-Note: On Ubuntu 20.04, you may need to build a newer Abseil and pin Protobuf (e.g., v3.20.x) for building DiskANN. See [Issue #30](https://github.com/yichuan-w/LEANN/issues/30) for a step-by-step note.
-
-You can manually install [Intel oneAPI MKL](https://www.intel.com/content/www/us/en/developer/tools/oneapi/onemkl.html) instead of `libmkl-full-dev` for DiskANN. You can also use `libopenblas-dev` for building HNSW only, by removing `--extra diskann` in the command below.
-
+**Linux:**
 ```bash
-sudo apt-get update && sudo apt-get install -y \
-  libomp-dev libboost-all-dev protobuf-compiler libzmq3-dev \
-  pkg-config libabsl-dev libaio-dev libprotobuf-dev \
-  libmkl-full-dev
+# Ubuntu/Debian (For Arch Linux: sudo pacman -S blas lapack openblas libaio boost protobuf abseil-cpp zeromq)
+sudo apt-get update && sudo apt-get install -y libomp-dev libboost-all-dev protobuf-compiler libabsl-dev libmkl-full-dev libaio-dev libzmq3-dev
 
-uv sync --extra diskann
-```
-
-**Linux (Arch Linux):**
-
-```bash
-sudo pacman -Syu && sudo pacman -S --needed base-devel cmake pkgconf git gcc \
-  boost boost-libs protobuf abseil-cpp libaio zeromq
-
-# For MKL in DiskANN
-sudo pacman -S --needed base-devel git
-git clone https://aur.archlinux.org/paru-bin.git
-cd paru-bin && makepkg -si
-paru -S intel-oneapi-mkl intel-oneapi-compiler
-source /opt/intel/oneapi/setvars.sh
-
-uv sync --extra diskann
-```
-
-**Linux (RHEL / CentOS Stream / Oracle / Rocky / AlmaLinux):**
-
-See [Issue #50](https://github.com/yichuan-w/LEANN/issues/50) for more details.
-
-```bash
-sudo dnf groupinstall -y "Development Tools"
-sudo dnf install -y libomp-devel boost-devel protobuf-compiler protobuf-devel \
-  abseil-cpp-devel libaio-devel zeromq-devel pkgconf-pkg-config
-
-# For MKL in DiskANN
-sudo dnf install -y intel-oneapi-mkl intel-oneapi-mkl-devel \
-  intel-oneapi-openmp || sudo dnf install -y intel-oneapi-compiler
-source /opt/intel/oneapi/setvars.sh
-
-uv sync --extra diskann
+uv sync
 ```
 
 </details>
@@ -585,10 +542,8 @@ Options:
 leann list
 
 # Lists all indexes across all projects with status indicators:
-# ✅ - Index is complete and ready to use
-# ❌ - Index is incomplete or corrupted
-# 📁 - CLI-created index (in .leann/indexes/)
-# 📄 - App-created index (*.leann.meta.json files)
+# ✓ - Index is complete and ready to use
+# ✗ - Index is incomplete or corrupted
 ```
 
 **Remove Command:**
@@ -602,7 +557,6 @@ Options:
 # - Shows all matching indexes across projects
 # - Requires confirmation for cross-project removal
 # - Interactive selection when multiple matches found
-# - Supports both CLI and app-created indexes
 ```
 
 </details>

apps/base_rag_example.py

@@ -10,7 +10,6 @@ from typing import Any
 
 import dotenv
 from leann.api import LeannBuilder, LeannChat
-from leann.registry import register_project_directory
 from llama_index.core.node_parser import SentenceSplitter
 
 dotenv.load_dotenv()
@@ -215,11 +214,6 @@ class BaseRAGExample(ABC):
         builder.build_index(index_path)
         print(f"Index saved to: {index_path}")
 
-        # Register project directory so leann list can discover this index
-        # The index is saved as args.index_dir/index_name.leann
-        # We want to register the current working directory where the app is run
-        register_project_directory(Path.cwd())
-
         return index_path
 
     async def run_interactive_chat(self, args, index_path: str):

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

@@ -614,7 +614,7 @@ class LeannSearcher:
             zmq_port=zmq_port,
         )
         # logger.info(f"  Generated embedding shape: {query_embedding.shape}")
-        # time.time() - start_time
+        time.time() - start_time
         # logger.info(f"  Embedding time: {embedding_time} seconds")
 
         start_time = time.time()
@@ -680,9 +680,8 @@ class LeannSearcher:
         This method should be called after you're done using the searcher,
         especially in test environments or batch processing scenarios.
         """
-        backend = getattr(self.backend_impl, "embedding_server_manager", None)
-        if backend is not None:
-            backend.stop_server()
+        if hasattr(self.backend_impl, "embedding_server_manager"):
+            self.backend_impl.embedding_server_manager.stop_server()
 
     # Enable automatic cleanup patterns
     def __enter__(self):

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

@@ -707,28 +707,20 @@ class GeminiChat(LLMInterface):
         logger.info(f"Sending request to Gemini with model {self.model}")
 
         try:
-            from google.genai.types import GenerateContentConfig
-
-            generation_config = GenerateContentConfig(
-                temperature=kwargs.get("temperature", 0.7),
-                max_output_tokens=kwargs.get("max_tokens", 1000),
-            )
+            # 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"]
+                generation_config["top_p"] = kwargs["top_p"]
 
             response = self.client.models.generate_content(
-                model=self.model,
-                contents=prompt,
-                config=generation_config,
+                model=self.model, contents=prompt, config=generation_config
             )
-            # Handle potential None response text
-            response_text = response.text
-            if response_text is None:
-                logger.warning("Gemini returned None response text")
-                return ""
-            return response_text.strip()
+            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}"

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

@@ -1,14 +1,13 @@
 import argparse
 import asyncio
 from pathlib import Path
-from typing import Optional, Union
+from typing import Union
 
 from llama_index.core import SimpleDirectoryReader
 from llama_index.core.node_parser import SentenceSplitter
 from tqdm import tqdm
 
 from .api import LeannBuilder, LeannChat, LeannSearcher
-from .registry import register_project_directory
 
 
 def extract_pdf_text_with_pymupdf(file_path: str) -> str:
@@ -264,7 +263,31 @@ Examples:
 
     def register_project_dir(self):
         """Register current project directory in global registry"""
-        register_project_directory()
+        global_registry = Path.home() / ".leann" / "projects.json"
+        global_registry.parent.mkdir(exist_ok=True)
+
+        current_dir = str(Path.cwd())
+
+        # Load existing registry
+        projects = []
+        if global_registry.exists():
+            try:
+                import json
+
+                with open(global_registry) as f:
+                    projects = json.load(f)
+            except Exception:
+                projects = []
+
+        # Add current directory if not already present
+        if current_dir not in projects:
+            projects.append(current_dir)
+
+        # Save registry
+        import json
+
+        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."""
@@ -350,10 +373,13 @@ Examples:
             valid_projects.append(current_path)
 
         # Separate current and other projects
+        current_project = None
         other_projects = []
 
         for project_path in valid_projects:
-            if project_path != current_path:
+            if project_path == current_path:
+                current_project = project_path
+            else:
                 other_projects.append(project_path)
 
         print("📚 LEANN Indexes")
@@ -363,20 +389,35 @@ Examples:
         current_indexes_count = 0
 
         # Show current project first (most important)
-        print("\n🏠 Current Project")
-        print(f"   {current_path}")
-        print("   " + "─" * 45)
+        if current_project:
+            current_indexes_dir = current_project / ".leann" / "indexes"
+            if current_indexes_dir.exists():
+                current_index_dirs = [d for d in current_indexes_dir.iterdir() if d.is_dir()]
 
-        current_indexes = self._discover_indexes_in_project(current_path)
-        if current_indexes:
-            for idx in current_indexes:
-                total_indexes += 1
-                current_indexes_count += 1
-                type_icon = "📁" if idx["type"] == "cli" else "📄"
-                print(f"   {current_indexes_count}. {type_icon} {idx['name']} {idx['status']}")
-                if idx["size_mb"] > 0:
-                    print(f"      📦 Size: {idx['size_mb']:.1f} MB")
+                print("\n🏠 Current Project")
+                print(f"   {current_project}")
+                print("   " + "─" * 45)
+
+                if current_index_dirs:
+                    for index_dir in current_index_dirs:
+                        total_indexes += 1
+                        current_indexes_count += 1
+                        index_name = index_dir.name
+                        meta_file = index_dir / "documents.leann.meta.json"
+                        status = "✅" if meta_file.exists() else "❌"
+
+                        print(f"   {current_indexes_count}. {index_name} {status}")
+                        if meta_file.exists():
+                            size_mb = sum(
+                                f.stat().st_size for f in index_dir.iterdir() if f.is_file()
+                            ) / (1024 * 1024)
+                            print(f"      📦 Size: {size_mb:.1f} MB")
+                else:
+                    print("   📭 No indexes in current project")
         else:
+            print("\n🏠 Current Project")
+            print(f"   {current_path}")
+            print("   " + "─" * 45)
             print("   📭 No indexes in current project")
 
         # Show other projects (reference information)
@@ -385,19 +426,29 @@ Examples:
             print("   " + "─" * 45)
 
             for project_path in other_projects:
-                project_indexes = self._discover_indexes_in_project(project_path)
-                if not project_indexes:
+                indexes_dir = project_path / ".leann" / "indexes"
+                if not indexes_dir.exists():
+                    continue
+
+                index_dirs = [d for d in indexes_dir.iterdir() if d.is_dir()]
+                if not index_dirs:
                     continue
 
                 print(f"\n   📂 {project_path.name}")
                 print(f"      {project_path}")
 
-                for idx in project_indexes:
+                for index_dir in index_dirs:
                     total_indexes += 1
-                    type_icon = "📁" if idx["type"] == "cli" else "📄"
-                    print(f"      • {type_icon} {idx['name']} {idx['status']}")
-                    if idx["size_mb"] > 0:
-                        print(f"        📦 {idx['size_mb']:.1f} MB")
+                    index_name = index_dir.name
+                    meta_file = index_dir / "documents.leann.meta.json"
+                    status = "✅" if meta_file.exists() else "❌"
+
+                    print(f"      • {index_name} {status}")
+                    if meta_file.exists():
+                        size_mb = sum(
+                            f.stat().st_size for f in index_dir.iterdir() if f.is_file()
+                        ) / (1024 * 1024)
+                        print(f"        📦 {size_mb:.1f} MB")
 
         # Summary and usage info
         print("\n" + "=" * 50)
@@ -429,67 +480,6 @@ Examples:
                 print("\n💡 Create your first index:")
                 print("   leann build my-docs --docs ./documents")
 
-    def _discover_indexes_in_project(self, project_path: Path):
-        """Discover all indexes in a project directory (both CLI and apps formats)"""
-        indexes = []
-
-        # 1. CLI format: .leann/indexes/index_name/
-        cli_indexes_dir = project_path / ".leann" / "indexes"
-        if cli_indexes_dir.exists():
-            for index_dir in cli_indexes_dir.iterdir():
-                if index_dir.is_dir():
-                    meta_file = index_dir / "documents.leann.meta.json"
-                    status = "✅" if meta_file.exists() else "❌"
-
-                    size_mb = 0
-                    if meta_file.exists():
-                        try:
-                            size_mb = sum(
-                                f.stat().st_size for f in index_dir.iterdir() if f.is_file()
-                            ) / (1024 * 1024)
-                        except (OSError, PermissionError):
-                            pass
-
-                    indexes.append(
-                        {
-                            "name": index_dir.name,
-                            "type": "cli",
-                            "status": status,
-                            "size_mb": size_mb,
-                            "path": index_dir,
-                        }
-                    )
-
-        # 2. Apps format: *.leann.meta.json files anywhere in the project
-        for meta_file in project_path.rglob("*.leann.meta.json"):
-            if meta_file.is_file():
-                # Extract index name from filename (remove .leann.meta.json extension)
-                index_name = meta_file.name.replace(".leann.meta.json", "")
-
-                # Apps indexes are considered complete if the .leann.meta.json file exists
-                status = "✅"
-
-                # Calculate total size of all related files
-                size_mb = 0
-                try:
-                    index_dir = meta_file.parent
-                    for related_file in index_dir.glob(f"{index_name}.leann*"):
-                        size_mb += related_file.stat().st_size / (1024 * 1024)
-                except (OSError, PermissionError):
-                    pass
-
-                indexes.append(
-                    {
-                        "name": index_name,
-                        "type": "app",
-                        "status": status,
-                        "size_mb": size_mb,
-                        "path": meta_file,
-                    }
-                )
-
-        return indexes
-
     def remove_index(self, index_name: str, force: bool = False):
         """Safely remove an index - always show all matches for transparency"""
 
@@ -647,7 +637,7 @@ Examples:
             return False
 
     def _delete_index_directory(
-        self, index_dir: Path, index_name: str, project_path: Optional[Path] = None
+        self, index_dir: Path, index_name: str, project_path: Path | None = None
     ):
         """Actually delete the index directory"""
         try:

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

@@ -2,10 +2,8 @@
 
 import importlib
 import importlib.metadata
-import json
 import logging
-from pathlib import Path
-from typing import TYPE_CHECKING, Optional, Union
+from typing import TYPE_CHECKING
 
 if TYPE_CHECKING:
     from leann.interface import LeannBackendFactoryInterface
@@ -45,54 +43,3 @@ def autodiscover_backends():
             # print(f"WARN: Could not import backend module '{backend_module_name}': {e}")
             pass
     # print("INFO: Backend auto-discovery finished.")
-
-
-def register_project_directory(project_dir: Optional[Union[str, Path]] = None):
-    """
-    Register a project directory in the global LEANN registry.
-
-    This allows `leann list` to discover indexes created by apps or other tools.
-
-    Args:
-        project_dir: Directory to register. If None, uses current working directory.
-    """
-    if project_dir is None:
-        project_dir = Path.cwd()
-    else:
-        project_dir = Path(project_dir)
-
-    # Only register directories that have some kind of LEANN content
-    # Either .leann/indexes/ (CLI format) or *.leann.meta.json files (apps format)
-    has_cli_indexes = (project_dir / ".leann" / "indexes").exists()
-    has_app_indexes = any(project_dir.rglob("*.leann.meta.json"))
-
-    if not (has_cli_indexes or has_app_indexes):
-        # Don't register if there are no LEANN indexes
-        return
-
-    global_registry = Path.home() / ".leann" / "projects.json"
-    global_registry.parent.mkdir(exist_ok=True)
-
-    project_str = str(project_dir.resolve())
-
-    # Load existing registry
-    projects = []
-    if global_registry.exists():
-        try:
-            with open(global_registry) as f:
-                projects = json.load(f)
-        except Exception:
-            logger.debug("Could not load existing project registry")
-            projects = []
-
-    # Add project if not already present
-    if project_str not in projects:
-        projects.append(project_str)
-
-        # Save updated registry
-        try:
-            with open(global_registry, "w") as f:
-                json.dump(projects, f, indent=2)
-            logger.debug(f"Registered project directory: {project_str}")
-        except Exception as e:
-            logger.warning(f"Could not save project registry: {e}")

pyproject.toml

@@ -14,6 +14,8 @@ dependencies = [
     "numpy>=1.26.0",
     "torch",
     "tqdm",
+    "flask",
+    "flask_compress",
     "datasets>=2.15.0",
     "evaluate",
     "colorama",
@@ -64,7 +66,9 @@ test = [
     "pytest>=7.0",
     "pytest-timeout>=2.0",
     "llama-index-core>=0.12.0",
+    "llama-index-readers-file>=0.4.0",
     "python-dotenv>=1.0.0",
+    "sentence-transformers>=2.2.0",
 ]
 
 diskann = [
@@ -96,8 +100,13 @@ leann-backend-hnsw = { path = "packages/leann-backend-hnsw", editable = true }
 [tool.ruff]
 target-version = "py39"
 line-length = 100
-extend-exclude = ["third_party"]
-
+extend-exclude = [
+    "third_party",
+    "*.egg-info",
+    "__pycache__",
+    ".git",
+    ".venv",
+]
 
 [tool.ruff.lint]
 select = [
@@ -120,12 +129,21 @@ ignore = [
     "RUF012", # mutable class attributes should be annotated with typing.ClassVar
 ]
 
+[tool.ruff.lint.per-file-ignores]
+"test/**/*.py" = ["E402"]      # module level import not at top of file (common in tests)
+"examples/**/*.py" = ["E402"]  # module level import not at top of file (common in examples)
+
 [tool.ruff.format]
 quote-style = "double"
 indent-style = "space"
 skip-magic-trailing-comma = false
 line-ending = "auto"
 
+[dependency-groups]
+dev = [
+    "ruff>=0.12.4",
+]
+
 [tool.lychee]
 accept = ["200", "403", "429", "503"]
 timeout = 20