mcp-code-indexer 3.0.0__tar.gz → 3.0.3__tar.gz

{mcp_code_indexer-3.0.0 → mcp_code_indexer-3.0.3}/MANIFEST.in

@@ -3,7 +3,7 @@ include LICENSE
 include pyproject.toml
 include requirements.txt
 recursive-include src/mcp_code_indexer/tiktoken_cache *
-recursive-include migrations *.sql
+recursive-include src/mcp_code_indexer/migrations *.sql
 recursive-include docs *.md
 recursive-exclude tests *
 recursive-exclude venv *

{mcp_code_indexer-3.0.0/src/mcp_code_indexer.egg-info → mcp_code_indexer-3.0.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: mcp-code-indexer
-Version: 3.0.0
+Version: 3.0.3
 Summary: MCP server that tracks file descriptions across codebases, enabling AI agents to efficiently navigate and understand code through searchable summaries and token-aware overviews.
 Author: MCP Code Indexer Contributors
 Maintainer: MCP Code Indexer Contributors
@@ -59,8 +59,8 @@ Dynamic: requires-python
 
 # MCP Code Indexer 🚀
 
-[![PyPI version](https://badge.fury.io/py/mcp-code-indexer.svg?19)](https://badge.fury.io/py/mcp-code-indexer)
-[![Python](https://img.shields.io/pypi/pyversions/mcp-code-indexer.svg?19)](https://pypi.org/project/mcp-code-indexer/)
+[![PyPI version](https://badge.fury.io/py/mcp-code-indexer.svg?21)](https://badge.fury.io/py/mcp-code-indexer)
+[![Python](https://img.shields.io/pypi/pyversions/mcp-code-indexer.svg?21)](https://pypi.org/project/mcp-code-indexer/)
 [![License](https://img.shields.io/badge/License-MIT-blue.svg)](https://opensource.org/licenses/MIT)
 
 A production-ready **Model Context Protocol (MCP) server** that revolutionizes how AI agents navigate and understand codebases. Built for high-concurrency environments with advanced database resilience, the server provides instant access to intelligent descriptions, semantic search, and context-aware recommendations while maintaining 800+ writes/sec throughput.

{mcp_code_indexer-3.0.0 → mcp_code_indexer-3.0.3}/README.md

@@ -1,7 +1,7 @@
 # MCP Code Indexer 🚀
 
-[![PyPI version](https://badge.fury.io/py/mcp-code-indexer.svg?19)](https://badge.fury.io/py/mcp-code-indexer)
-[![Python](https://img.shields.io/pypi/pyversions/mcp-code-indexer.svg?19)](https://pypi.org/project/mcp-code-indexer/)
+[![PyPI version](https://badge.fury.io/py/mcp-code-indexer.svg?21)](https://badge.fury.io/py/mcp-code-indexer)
+[![Python](https://img.shields.io/pypi/pyversions/mcp-code-indexer.svg?21)](https://pypi.org/project/mcp-code-indexer/)
 [![License](https://img.shields.io/badge/License-MIT-blue.svg)](https://opensource.org/licenses/MIT)
 
 A production-ready **Model Context Protocol (MCP) server** that revolutionizes how AI agents navigate and understand codebases. Built for high-concurrency environments with advanced database resilience, the server provides instant access to intelligent descriptions, semantic search, and context-aware recommendations while maintaining 800+ writes/sec throughput.

{mcp_code_indexer-3.0.0 → mcp_code_indexer-3.0.3}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "mcp-code-indexer"
-version = "3.0.0"
+version = "3.0.3"
 description = "MCP server that tracks file descriptions across codebases, enabling AI agents to efficiently navigate and understand code through searchable summaries and token-aware overviews."
 readme = "README.md"
 license = {text = "MIT"}

{mcp_code_indexer-3.0.0 → mcp_code_indexer-3.0.3}/src/mcp_code_indexer/database/database.py

@@ -110,7 +110,10 @@ class DatabaseManager:
         # Database initialization now uses the modern retry executor directly
         
         # Apply migrations in order
-        migrations_dir = Path(__file__).parent.parent.parent.parent / "migrations"
+        # Migrations are now bundled with the package
+        migrations_dir = Path(__file__).parent.parent / "migrations"
+        if not migrations_dir.exists():
+            raise RuntimeError(f"Could not find migrations directory at {migrations_dir}")
         migration_files = sorted(migrations_dir.glob("*.sql"))
         
         async with aiosqlite.connect(self.db_path) as db:
@@ -120,16 +123,48 @@ class DatabaseManager:
             # Configure WAL mode and optimizations for concurrent access
             await self._configure_database_optimizations(db, include_wal_mode=self.enable_wal_mode)
             
-            # Apply each migration
+            # Create migrations tracking table
+            await db.execute('''
+                CREATE TABLE IF NOT EXISTS migrations (
+                    id INTEGER PRIMARY KEY AUTOINCREMENT,
+                    filename TEXT UNIQUE NOT NULL,
+                    applied_at TIMESTAMP DEFAULT CURRENT_TIMESTAMP
+                )
+            ''')
+            await db.commit()
+            
+            # Get list of already applied migrations
+            cursor = await db.execute('SELECT filename FROM migrations')
+            applied_migrations = {row[0] for row in await cursor.fetchall()}
+            
+            # Apply each migration that hasn't been applied yet
             for migration_file in migration_files:
-                logger.info(f"Applying migration: {migration_file.name}")
-                with open(migration_file, 'r') as f:
-                    migration_sql = f.read()
+                migration_name = migration_file.name
+                if migration_name in applied_migrations:
+                    logger.info(f"Skipping already applied migration: {migration_name}")
+                    continue
+                    
+                logger.info(f"Applying migration: {migration_name}")
+                try:
+                    migration_sql = migration_file.read_text(encoding='utf-8')
+                except AttributeError:
+                    # Fallback for regular file objects
+                    with open(migration_file, 'r', encoding='utf-8') as f:
+                        migration_sql = f.read()
                 
-                await db.executescript(migration_sql)
-                await db.commit()
+                try:
+                    await db.executescript(migration_sql)
+                    
+                    # Record that migration was applied
+                    await db.execute('INSERT INTO migrations (filename) VALUES (?)', (migration_name,))
+                    await db.commit()
+                    logger.info(f"Successfully applied migration: {migration_name}")
+                except Exception as e:
+                    logger.error(f"Failed to apply migration {migration_name}: {e}")
+                    await db.rollback()
+                    raise
             
-        logger.info(f"Database initialized at {self.db_path} with {len(migration_files)} migrations")
+        logger.info(f"Database initialized at {self.db_path} with {len(migration_files)} total migrations")
     
     async def _configure_database_optimizations(self, db: aiosqlite.Connection, include_wal_mode: bool = True) -> None:
         """

{mcp_code_indexer-3.0.0 → mcp_code_indexer-3.0.3}/src/mcp_code_indexer/error_handler.py

@@ -254,6 +254,7 @@ class StructuredFormatter(logging.Formatter):
     def format(self, record: logging.LogRecord) -> str:
         """Format log record as structured JSON."""
         import json
+        from . import __version__
         
         log_data = {
             "timestamp": datetime.utcnow().isoformat(),
@@ -262,7 +263,8 @@ class StructuredFormatter(logging.Formatter):
             "message": record.getMessage(),
             "module": record.module,
             "function": record.funcName,
-            "line": record.lineno
+            "line": record.lineno,
+            "version": __version__
         }
         
         # Add structured data if present

{mcp_code_indexer-3.0.0 → mcp_code_indexer-3.0.3/src/mcp_code_indexer}/migrations/004_remove_branch_dependency.sql

@@ -5,8 +5,8 @@
 -- Ensure WAL mode is enabled for safe migrations
 PRAGMA journal_mode=WAL;
 
--- Enable foreign key support
-PRAGMA foreign_keys=ON;
+-- Temporarily disable foreign key constraints for migration
+PRAGMA foreign_keys=OFF;
 
 -- Start transaction for atomic migration
 BEGIN TRANSACTION;
@@ -33,6 +33,17 @@ CREATE INDEX idx_file_descriptions_new_file_hash ON file_descriptions_new(file_h
 CREATE INDEX idx_file_descriptions_new_last_modified ON file_descriptions_new(last_modified);
 CREATE INDEX idx_file_descriptions_new_to_be_cleaned ON file_descriptions_new(to_be_cleaned);
 
+-- Clean up orphaned data before consolidation
+-- Remove file_descriptions that reference non-existent projects
+DELETE FROM file_descriptions 
+WHERE project_id NOT IN (SELECT id FROM projects);
+
+-- Remove file_descriptions with invalid source_project_id
+UPDATE file_descriptions 
+SET source_project_id = NULL 
+WHERE source_project_id IS NOT NULL 
+  AND source_project_id NOT IN (SELECT id FROM projects);
+
 -- Consolidate data from old table - keep most recent description per file
 -- This handles multi-branch scenarios by selecting the newest data
 INSERT INTO file_descriptions_new (
@@ -76,6 +87,10 @@ CREATE TABLE project_overviews_new (
 -- Create indexes for the new table
 CREATE INDEX idx_project_overviews_new_last_modified ON project_overviews_new(last_modified);
 
+-- Clean up orphaned project overviews
+DELETE FROM project_overviews 
+WHERE project_id NOT IN (SELECT id FROM projects);
+
 -- Consolidate project overviews - keep the one with most tokens (most comprehensive)
 INSERT INTO project_overviews_new (
     project_id, overview, last_modified, total_files, total_tokens
@@ -162,5 +177,8 @@ END;
 DROP INDEX IF EXISTS idx_merge_conflicts_project;
 CREATE INDEX idx_merge_conflicts_project ON merge_conflicts(project_id, created);
 
+-- Re-enable foreign key constraints
+PRAGMA foreign_keys=ON;
+
 -- Commit the migration
 COMMIT;

{mcp_code_indexer-3.0.0 → mcp_code_indexer-3.0.3/src/mcp_code_indexer.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: mcp-code-indexer
-Version: 3.0.0
+Version: 3.0.3
 Summary: MCP server that tracks file descriptions across codebases, enabling AI agents to efficiently navigate and understand code through searchable summaries and token-aware overviews.
 Author: MCP Code Indexer Contributors
 Maintainer: MCP Code Indexer Contributors
@@ -59,8 +59,8 @@ Dynamic: requires-python
 
 # MCP Code Indexer 🚀
 
-[![PyPI version](https://badge.fury.io/py/mcp-code-indexer.svg?19)](https://badge.fury.io/py/mcp-code-indexer)
-[![Python](https://img.shields.io/pypi/pyversions/mcp-code-indexer.svg?19)](https://pypi.org/project/mcp-code-indexer/)
+[![PyPI version](https://badge.fury.io/py/mcp-code-indexer.svg?21)](https://badge.fury.io/py/mcp-code-indexer)
+[![Python](https://img.shields.io/pypi/pyversions/mcp-code-indexer.svg?21)](https://pypi.org/project/mcp-code-indexer/)
 [![License](https://img.shields.io/badge/License-MIT-blue.svg)](https://opensource.org/licenses/MIT)
 
 A production-ready **Model Context Protocol (MCP) server** that revolutionizes how AI agents navigate and understand codebases. Built for high-concurrency environments with advanced database resilience, the server provides instant access to intelligent descriptions, semantic search, and context-aware recommendations while maintaining 800+ writes/sec throughput.

{mcp_code_indexer-3.0.0 → mcp_code_indexer-3.0.3}/src/mcp_code_indexer.egg-info/SOURCES.txt

@@ -12,10 +12,6 @@ docs/database-resilience.md
 docs/git-hook-setup.md
 docs/monitoring.md
 docs/performance-tuning.md
-migrations/001_initial.sql
-migrations/002_performance_indexes.sql
-migrations/003_project_overviews.sql
-migrations/004_remove_branch_dependency.sql
 src/mcp_code_indexer/__init__.py
 src/mcp_code_indexer/__main__.py
 src/mcp_code_indexer/ask_handler.py
@@ -45,6 +41,10 @@ src/mcp_code_indexer/database/models.py
 src/mcp_code_indexer/database/retry_executor.py
 src/mcp_code_indexer/middleware/__init__.py
 src/mcp_code_indexer/middleware/error_middleware.py
+src/mcp_code_indexer/migrations/001_initial.sql
+src/mcp_code_indexer/migrations/002_performance_indexes.sql
+src/mcp_code_indexer/migrations/003_project_overviews.sql
+src/mcp_code_indexer/migrations/004_remove_branch_dependency.sql
 src/mcp_code_indexer/server/__init__.py
 src/mcp_code_indexer/server/mcp_server.py
 src/mcp_code_indexer/tiktoken_cache/9b5ad71b2ce5302211f9c61530b329a4922fc6a4