codegraphcontext 0.4.12__py3-none-any.whl → 0.4.13__py3-none-any.whl

codegraphcontext/api/router.py

@@ -87,7 +87,7 @@ async def execute_query(
     server: MCPServer = Depends(get_server)
 ):
     result = await server.handle_tool_call("execute_cypher_query", {
-        "query": request.query,
+        "cypher_query": request.query,
         "params": request.params
     })
     

codegraphcontext/cli/config_manager.py

@@ -31,6 +31,7 @@ DEFAULT_CONFIG = {
     "FALKORDB_PATH": str(CONFIG_DIR / "global" / "db" / "falkordb"),
     "FALKORDB_SOCKET_PATH": str(CONFIG_DIR / "global" / "db" / "falkordb.sock"),
     "LADYBUGDB_PATH": str(CONFIG_DIR / "global" / "db" / "ladybugdb"),
+    "KUZUDB_PATH": str(CONFIG_DIR / "global" / "db" / "kuzudb"),
     "INDEX_VARIABLES": "true",
     "ALLOW_DB_DELETION": "false",
     "DEBUG_LOGS": "false",
@@ -72,6 +73,7 @@ CONFIG_DESCRIPTIONS = {
     "FALKORDB_PATH": "Path to FalkorDB database file",
     "FALKORDB_SOCKET_PATH": "Path to FalkorDB Unix socket",
     "LADYBUGDB_PATH": "Path to LadybugDB database directory",
+    "KUZUDB_PATH": "Path to KuzuDB database directory",
     "INDEX_VARIABLES": "Index variable nodes in the graph (lighter graph if false)",
     "ALLOW_DB_DELETION": "Allow full database deletion commands",
     "DEBUG_LOGS": "Enable debug logging (for development/troubleshooting)",
@@ -454,7 +456,7 @@ def validate_config_value(key: str, value: str) -> tuple[bool, Optional[str]]:
         except Exception as e:
             return False, f"Cannot create log directory: {e}"
     
-    if key in ("FALKORDB_PATH", "FALKORDB_SOCKET_PATH", "LADYBUGDB_PATH"):
+    if key in ("FALKORDB_PATH", "FALKORDB_SOCKET_PATH", "LADYBUGDB_PATH", "KUZUDB_PATH"):
         # Validate path is writable
         db_path = Path(normalize_config_path(value, absolute=True))
         try:

codegraphcontext/cli/main.py

@@ -250,7 +250,7 @@ def context_list():
 @context_app.command("create")
 def context_create(
     name: str = typer.Argument(..., help="Name of the new context"),
-    database: str = typer.Option(None, "--database", "-d", help="Database backend (falkordb, kuzudb, neo4j). Defaults to DEFAULT_DATABASE from config."),
+    database: str = typer.Option(None, "--database", "--db", "-db", "-d", help="Database backend (falkordb, kuzudb, neo4j). Defaults to DEFAULT_DATABASE from config."),
     db_path: str = typer.Option(None, "--db-path", help="Explicit path for the DB (defaults to ~/.codegraphcontext/contexts/<name>/db)"),
 ):
     """Create a new logical context."""
@@ -291,17 +291,14 @@ def _load_credentials(cli_context_flag: Optional[str] = None):
     Uses per-variable precedence - each variable is loaded from the highest priority source.
     Priority order (highest to lowest):
     1. Runtime environment variables (shell/CI)
-    2. Local `.env` in project directory (project-specific overrides)
+    2. Local `.codegraphcontext/.env` and `.env` in the current project directory (project-specific overrides)
     3. Global `~/.codegraphcontext/.env` (user defaults, including `cgc config set`)
     4. Local `mcp.json` env vars (project defaults)
-    1. Local `mcp.json` env vars (highest - explicit MCP server config)
-    2. ``<cwd>/.codegraphcontext/.env`` only (no parent-directory walk)
-    3. Global `~/.codegraphcontext/.env` (lowest - user defaults)
 
-    Step 2 skips duplicate loading when that file is the same path as the global file.
-    Arbitrary repo-root `.env` files are not loaded—only CodeGraphContext config paths.
+    Duplicate loading is skipped when the local file resolves to the same path as the global file.
+    Arbitrary parent directory `.env` files are not loaded—ensuring isolation.
     """
-    from dotenv import dotenv_values, find_dotenv
+    from dotenv import dotenv_values
     from codegraphcontext.cli.config_manager import (
         ensure_config_dir,
         codegraphcontext_dotenv_at_cwd,
@@ -360,12 +357,12 @@ def _load_credentials(cli_context_flag: Optional[str] = None):
         except Exception as e:
             console.print(f"[yellow]Warning: Could not load global .env: {e}[/yellow]")
     
-    # 2. Local project .env (project-specific overrides)
+    # 2. Local project .env (project-specific overrides - restricted to CWD only, no parent walk)
     try:
-        dotenv_path = find_dotenv(usecwd=True, raise_error_if_not_found=False)
-        if dotenv_path:
-            with open(dotenv_path, "r", encoding="utf-8", errors="replace") as f:
-                _append_source(str(dotenv_path), dotenv_values(stream=f))
+        local_dot_env = Path.cwd() / ".env"
+        if local_dot_env.exists() and local_dot_env.resolve() != global_env_path.resolve():
+            with open(local_dot_env, "r", encoding="utf-8", errors="replace") as f:
+                _append_source(str(local_dot_env), dotenv_values(stream=f))
     except Exception as e:
         console.print(f"[yellow]Warning: Could not load .env from current directory: {e}[/yellow]")
 
@@ -637,7 +634,7 @@ def bundle_export(
         if repo_path:
             console.print(f"[dim]Repository: {repo_path}[/dim]")
         else:
-            console.print(f"[dim]Exporting all repositories[/dim]")
+            console.print("[dim]Exporting all repositories[/dim]")
         
         bundle = CGCBundle(db_manager)
         success, message = bundle.export_to_bundle(
@@ -748,7 +745,7 @@ def bundle_load(
     
     # Try to download from registry
     console.print(f"[yellow]Bundle '{bundle_name}' not found locally.[/yellow]")
-    console.print(f"[cyan]Attempting to download from registry...[/cyan]")
+    console.print("[cyan]Attempting to download from registry...[/cyan]")
     
     try:
         from .registry_commands import download_bundle
@@ -768,7 +765,7 @@ def bundle_load(
     
     except Exception as e:
         console.print(f"[bold red]Error: {e}[/bold red]")
-        console.print(f"[dim]Use 'cgc registry list' to see available bundles[/dim]")
+        console.print("[dim]Use 'cgc registry list' to see available bundles[/dim]")
         raise typer.Exit(code=1)
 
 # Shortcut commands at root level
@@ -888,7 +885,7 @@ def registry_download(
     bundle_path = download_bundle(name, output_dir, auto_load=load)
     
     if load and bundle_path:
-        console.print(f"\n[cyan]Loading bundle...[/cyan]")
+        console.print("\n[cyan]Loading bundle...[/cyan]")
         bundle_import(bundle_path, clear=False)
 
 @registry_app.command("request")
@@ -941,13 +938,13 @@ def doctor():
         if config_manager.CONFIG_FILE.exists():
             console.print(f"   [green]✓[/green] Config loaded from {config_manager.CONFIG_FILE}")
         else:
-            console.print(f"   [yellow]ℹ[/yellow] No .env config found, using defaults")
+            console.print("   [yellow]ℹ[/yellow] No .env config found, using defaults")
             console.print(f"   [dim]Config will be created at: {config_manager.CONFIG_FILE}[/dim]")
             
         if config_manager.CONTEXT_CONFIG_FILE.exists():
             console.print(f"   [green]✓[/green] Context config loaded from {config_manager.CONTEXT_CONFIG_FILE}")
         else:
-            console.print(f"   [yellow]ℹ[/yellow] No Context config found")
+            console.print("   [yellow]ℹ[/yellow] No Context config found")
             console.print(f"   [dim]Context config will be auto-generated at: {config_manager.CONTEXT_CONFIG_FILE}[/dim]")
         
         # Validate each config value
@@ -958,12 +955,12 @@ def doctor():
                 invalid_configs.append(f"{key}: {error_msg}")
         
         if invalid_configs:
-            console.print(f"   [red]✗[/red] Invalid configuration values found:")
+            console.print("   [red]✗[/red] Invalid configuration values found:")
             for err in invalid_configs:
                 console.print(f"     - {err}")
             all_checks_passed = False
         else:
-            console.print(f"   [green]✓[/green] All configuration values are valid")
+            console.print("   [green]✓[/green] All configuration values are valid")
     except Exception as e:
         console.print(f"   [red]✗[/red] Configuration error: {e}")
         all_checks_passed = False
@@ -1003,10 +1000,10 @@ def doctor():
                     console.print("       Start Neo4j Desktop or run: docker run -d -p 7687:7687 -p 7474:7474 neo4j")
                     all_checks_passed = False
 
-                console.print(f"   [cyan]Testing Neo4j authentication/query...[/cyan]")
+                console.print("   [cyan]Testing Neo4j authentication/query...[/cyan]")
                 is_connected, error_msg = DatabaseManager.test_connection(uri, username, password, database=database_name)
                 if is_connected:
-                    console.print(f"   [green]✓[/green] Neo4j connection successful")
+                    console.print("   [green]✓[/green] Neo4j connection successful")
                 else:
                     console.print(f"   [red]✗[/red] Neo4j connection failed (source: {db_source})")
                     console.print(f"       Reason: {error_msg}")
@@ -1015,28 +1012,28 @@ def doctor():
             from importlib.util import find_spec
 
             if find_spec("kuzu") is not None:
-                console.print(f"   [green]✓[/green] KuzuDB is installed")
+                console.print("   [green]✓[/green] KuzuDB is installed")
             else:
-                console.print(f"   [red]✗[/red] KuzuDB is not installed")
-                console.print(f"       Run: pip install kuzu")
+                console.print("   [red]✗[/red] KuzuDB is not installed")
+                console.print("       Run: pip install kuzu")
                 all_checks_passed = False
         elif default_db == "ladybugdb":
             from importlib.util import find_spec
 
             if find_spec("ladybug") is not None:
-                console.print(f"   [green]✓[/green] LadybugDB core (ladybug) is installed")
+                console.print("   [green]✓[/green] LadybugDB core (ladybug) is installed")
             else:
-                console.print(f"   [red]✗[/red] LadybugDB core (ladybug) is not installed")
-                console.print(f"       Run: pip install ladybug")
+                console.print("   [red]✗[/red] LadybugDB core (ladybug) is not installed")
+                console.print("       Run: pip install ladybug")
                 all_checks_passed = False
         else:
             # FalkorDB
             try:
                 import falkordb
-                console.print(f"   [green]✓[/green] FalkorDB Lite is installed")
+                console.print("   [green]✓[/green] FalkorDB Lite is installed")
             except ImportError:
-                console.print(f"   [yellow]⚠[/yellow] FalkorDB Lite not installed (Python 3.12+ only)")
-                console.print(f"       Run: pip install falkordblite")
+                console.print("   [yellow]⚠[/yellow] FalkorDB Lite not installed (Python 3.12+ only)")
+                console.print("       Run: pip install falkordblite")
     except Exception as e:
         console.print(f"   [red]✗[/red] Database check error: {e}")
         all_checks_passed = False
@@ -1045,11 +1042,11 @@ def doctor():
     console.print("\n[bold]3. Checking Tree-Sitter Installation...[/bold]")
     try:
         from tree_sitter import Language, Parser
-        console.print(f"   [green]✓[/green] tree-sitter is installed")
+        console.print("   [green]✓[/green] tree-sitter is installed")
         
         try:
             from tree_sitter_language_pack import get_language
-            console.print(f"   [green]✓[/green] tree-sitter-language-pack is installed")
+            console.print("   [green]✓[/green] tree-sitter-language-pack is installed")
             
             from codegraphcontext.utils.tree_sitter_manager import LANGUAGE_ALIASES, LANGUAGE_PACK_NAMES
             all_langs = sorted(set(LANGUAGE_ALIASES.values()))
@@ -1067,7 +1064,7 @@ def doctor():
             if unavailable:
                 console.print(f"   [yellow]⚠[/yellow] Unavailable: {', '.join(unavailable)}")
         except ImportError:
-            console.print(f"   [red]✗[/red] tree-sitter-language-pack not installed")
+            console.print("   [red]✗[/red] tree-sitter-language-pack not installed")
             all_checks_passed = False
     except ImportError as e:
         console.print(f"   [red]✗[/red] tree-sitter not installed: {e}")
@@ -1085,12 +1082,12 @@ def doctor():
             try:
                 test_file.touch()
                 test_file.unlink()
-                console.print(f"   [green]✓[/green] Config directory is writable")
+                console.print("   [green]✓[/green] Config directory is writable")
             except Exception as e:
                 console.print(f"   [red]✗[/red] Config directory not writable: {e}")
                 all_checks_passed = False
         else:
-            console.print(f"   [yellow]⚠[/yellow] Config directory doesn't exist, will be created on first use")
+            console.print("   [yellow]⚠[/yellow] Config directory doesn't exist, will be created on first use")
     except Exception as e:
         console.print(f"   [red]✗[/red] Permission check error: {e}")
         all_checks_passed = False
@@ -1102,7 +1099,7 @@ def doctor():
     if cgc_path:
         console.print(f"   [green]✓[/green] cgc command found at: {cgc_path}")
     else:
-        console.print(f"   [yellow]⚠[/yellow] cgc command not in PATH (using python -m cgc)")
+        console.print("   [yellow]⚠[/yellow] cgc command not in PATH (using python -m cgc)")
     
     # Final summary
     console.print("\n" + "=" * 60)
@@ -2393,7 +2390,7 @@ def analyze_dead_code(
                 location_str
             )
         
-        console.print(f"\n[bold yellow]⚠️  Potentially Unused Functions:[/bold yellow]")
+        console.print("\n[bold yellow]⚠️  Potentially Unused Functions:[/bold yellow]")
         console.print(table)
         console.print(f"\n[dim]Total: {len(unused_funcs)} function(s)[/dim]")
         console.print(f"[dim]Note: {results.get('note', '')}[/dim]")

codegraphcontext/cli/registry_commands.py

@@ -11,7 +11,6 @@ from rich.table import Table
 from rich.progress import Progress, SpinnerColumn, TextColumn
 from pathlib import Path
 from typing import Optional, List, Dict, Any
-import time
 
 console = Console()
 
@@ -20,7 +19,7 @@ GITHUB_REPO = "CodeGraphContext"
 
 
 def fetch_available_bundles() -> List[Dict[str, Any]]:
-    """Fetch all available bundles from GitHub Releases (delegates to core BundleRegistry)."""
+    """Fetch all available bundles from the Hugging Face registry (delegates to core BundleRegistry)."""
     from ..core.bundle_registry import BundleRegistry
     return BundleRegistry.fetch_available_bundles()
 
@@ -34,17 +33,27 @@ def _get_base_package_name(bundle_name: str) -> str:
         'flask-main-abc123' -> 'flask'
         'requests' -> 'requests'
     """
+    import re
     # Remove .cgc extension if present
     name = bundle_name.replace('.cgc', '')
     
-    # Split by hyphen and take the first part
-    # This assumes package names don't contain hyphens (may need refinement)
-    parts = name.split('-')
-    
-    # For multi-word package names like 'python-bitcoin-utils',
-    # we need smarter logic. For now, take first part.
-    # TODO: Improve this with a known package list or better heuristics
-    return parts[0]
+    # If the bundle name contains '-main-' or '-master-', split on that
+    for branch_indicator in ('-main-', '-master-'):
+        if branch_indicator in name:
+            return name.split(branch_indicator)[0]
+            
+    # Try matching standard trailing branch and commit hash pattern
+    # e.g., -[branch]-[commit_hash] where commit_hash is a hex string
+    match = re.search(r'-(?:main|master|dev|development|release)-[a-fA-F0-9]{7,40}$', name)
+    if match:
+        return name[:match.start()]
+        
+    # Try matching generic trailing branch and 7-8 char hex commit hash
+    match_generic = re.search(r'-([a-zA-Z0-9_]+)-([a-fA-F0-9]{7,8})$', name)
+    if match_generic:
+        return name[:match_generic.start()]
+        
+    return name
 
 
 def list_bundles(verbose: bool = False, unique: bool = False):
@@ -200,7 +209,7 @@ def download_bundle(name: str, output_dir: Optional[str] = None, auto_load: bool
             console.print(f"[cyan]  → {bundle.get('full_name')}[/cyan]")
             
             if len(matching_bundles) > 1:
-                console.print(f"\n[dim]Other available versions:[/dim]")
+                console.print("\n[dim]Other available versions:[/dim]")
                 for b in matching_bundles[1:4]:  # Show up to 3 alternatives
                     console.print(f"[dim]  • {b.get('full_name')}[/dim]")
                 if len(matching_bundles) > 4:
@@ -253,7 +262,7 @@ def download_bundle(name: str, output_dir: Optional[str] = None, auto_load: bool
         if not typer.confirm("Overwrite?", default=False):
             console.print("[yellow]Download cancelled[/yellow]")
             if auto_load:
-                console.print(f"[cyan]Using existing bundle for loading...[/cyan]")
+                console.print("[cyan]Using existing bundle for loading...[/cyan]")
                 return str(output_path)
             return
         output_path.unlink()
@@ -324,14 +333,14 @@ def request_bundle(repo_url: str, wait: bool = False):
     console.print("[cyan]Please use one of these methods:[/cyan]\n")
     
     console.print("1. [bold]Via Website (Recommended):[/bold]")
-    console.print(f"   Visit: https://codegraphcontext.vercel.app")
+    console.print("   Visit: https://codegraphcontext.vercel.app")
     console.print(f"   Enter: {repo_url}")
-    console.print(f"   Click 'Generate Bundle'\n")
+    console.print("   Click 'Generate Bundle'\n")
     
     console.print("2. [bold]Via GitHub Actions (Manual):[/bold]")
     console.print(f"   Go to: https://github.com/{GITHUB_ORG}/{GITHUB_REPO}/actions")
-    console.print(f"   Select: 'Generate Bundle On-Demand'")
-    console.print(f"   Click: 'Run workflow'")
+    console.print("   Select: 'Generate Bundle On-Demand'")
+    console.print("   Click: 'Run workflow'")
     console.print(f"   Enter: {repo_url}\n")
     
     console.print("[dim]Bundle generation typically takes 5-10 minutes.[/dim]")

codegraphcontext/cli/setup_wizard.py

@@ -92,8 +92,8 @@ def _generate_mcp_json(creds):
                     "disabledTools": [],
                     "disabled": False
                 },
-                "disabled": False,
-                "alwaysAllow": []
+                "disabled": False 
+        
             }
         }
     }

codegraphcontext/core/__init__.py

@@ -95,7 +95,7 @@ def get_database_manager(db_path: Optional[str] = None) -> Union['DatabaseManage
                 info_logger("FalkorDB Lite is not supported or not installed. Falling back to KùzuDB.")
                 if _is_kuzudb_available():
                     from .database_kuzu import KuzuDBManager
-                    return KuzuDBManager()
+                    return KuzuDBManager(db_path=db_path)
                 raise ValueError("Database set to 'falkordb' but FalkorDB Lite is not installed or not supported on this OS.\nRun 'pip install falkordblite'")
             
             from .database_falkordb import FalkorDBManager, FalkorDBUnavailableError
@@ -168,6 +168,12 @@ def get_database_manager(db_path: Optional[str] = None) -> Union['DatabaseManage
         info_logger(f"Using KùzuDB (default) at {db_path or 'default path'}")
         return KuzuDBManager(db_path=db_path)
 
+    # Implicit: LadybugDB when available
+    if _is_ladybugdb_available():
+        from .database_ladybug import LadybugDBManager
+        info_logger(f"Using LadybugDB (default) at {db_path or 'default path'}")
+        return LadybugDBManager(db_path=db_path)
+
     # Implicit: Neo4j when configured
     if _is_neo4j_configured():
         from .database import DatabaseManager

codegraphcontext/core/bundle_registry.py

@@ -18,11 +18,9 @@ def _github_headers() -> dict:
 
 def _get_manifest_url() -> str:
     import os
-    hf_repo = os.environ.get("HF_REGISTRY_REPO") or "codegraphcontext/bundles"
+    hf_repo = os.environ.get("HF_REGISTRY_REPO") or "codegraphcontext/registry"
     return f"https://huggingface.co/datasets/{hf_repo}/raw/main/manifest.json"
 
-REGISTRY_API_URL = "https://api.github.com/repos/CodeGraphContext/CodeGraphContext/releases"
-
 class BundleRegistry:
     """
     Core logic for interacting with the CodeGraphContext bundle registry.
@@ -32,7 +30,7 @@ class BundleRegistry:
     @staticmethod
     def fetch_available_bundles() -> List[Dict[str, Any]]:
         """
-        Fetch all available bundles from GitHub Releases and the on-demand manifest.
+        Fetch all available bundles from the Hugging Face raw dataset registry manifest.
         Returns a list of bundle dictionaries with metadata.
         Preserves all versions - no deduplication.
         """
@@ -53,44 +51,6 @@ class BundleRegistry:
                         all_bundles.append(bundle)
         except Exception as e:
             logger.warning(f"Could not fetch on-demand bundles from manifest: {e}")
-        
-        # 2. Fetch weekly pre-indexed bundles
-        try:
-            response = requests.get(REGISTRY_API_URL, headers=_github_headers(), timeout=10)
-            if response.status_code == 200:
-                releases = response.json()
-                
-                # Find weekly releases (bundles-YYYYMMDD pattern)
-                weekly_releases = [r for r in releases if r['tag_name'].startswith('bundles-') and r['tag_name'] != 'bundles-latest']
-                
-                if weekly_releases:
-                    # Get the most recent weekly release
-                    latest_weekly = weekly_releases[0]
-                    
-                    for asset in latest_weekly.get('assets', []):
-                        if asset['name'].endswith('.cgc'):
-                            # Full bundle name without extension
-                            full_name = asset['name'].replace('.cgc', '')
-                            
-                            # Parse bundle name
-                            name_parts = full_name.split('-')
-                            bundle = {
-                                'name': name_parts[0],  # Base package name
-                                'full_name': full_name,  # Complete name with version
-                                'repo': f"{name_parts[0]}/{name_parts[0]}",  # Simplified
-                                'bundle_name': asset['name'],
-                                'version': name_parts[1] if len(name_parts) > 1 else 'latest',
-                                'commit': name_parts[2] if len(name_parts) > 2 else 'unknown',
-                                'size_bytes': asset.get('size', 0),
-                                'size': f"{asset['size'] / 1024 / 1024:.1f}MB",
-                                'download_url': asset['browser_download_url'],
-                                'generated_at': asset['updated_at'],
-                                'source': 'weekly'
-                            }
-                            all_bundles.append(bundle)
-        except Exception as e:
-            logger.warning(f"Could not fetch weekly bundles from GitHub API: {e}")
-        
         # Normalize all bundles to have required fields
         for bundle in all_bundles:
             # Ensure 'name' field exists (base package name)