Add alembic\env.py

alembic//env.py

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+# Romeo AI Research Assistant - Alembic Environment
+# Database migration environment configuration for SQLite (HF Storage)
+# Transitioned from Oracle to SQLite: 2026-03-15
+
+import asyncio
+from logging.config import fileConfig
+from sqlalchemy import pool
+from sqlalchemy.engine import Connection
+from sqlalchemy.ext.asyncio import async_engine_from_config
+from alembic import context
+
+# Import application modules
+import sys
+from pathlib import Path
+sys.path.append(str(Path(__file__).parent.parent))
+
+from app.core.config import settings
+from app.models.base import Base
+
+# Direct imports for each model to ensure Alembic detects them
+from app.models.user import User
+from app.models.paper import Paper
+from app.models.library import LibraryItem
+from app.models.seed import Seed
+from app.models.extraction import Extraction
+from app.models.proposal import Proposal
+from app.models.data import Dataset
+from app.models.writesage import Manuscript, ManuscriptSection
+
+# This is the Alembic Config object
+config = context.config
+
+# 🔥 Force Alembic to use the SQLite URL from your config.py
+# This ensures it looks at ./data/romeo_research.db
+config.set_main_option("sqlalchemy.url", settings.SQLALCHEMY_DATABASE_URI)
+
+if config.config_file_name is not None:
+    fileConfig(config.config_file_name)
+
+target_metadata = Base.metadata
+
+def run_migrations_offline() -> None:
+    """Run migrations in 'offline' mode."""
+    url = config.get_main_option("sqlalchemy.url")
+    context.configure(
+        url=url,
+        target_metadata=target_metadata,
+        literal_binds=True,
+        dialect_opts={"paramstyle": "named"},
+        # 🔥 REQUIRED FOR SQLITE: Allows table alterations by rebuilding tables
+        render_as_batch=True,
+    )
+
+    with context.begin_transaction():
+        context.run_migrations()
+
+def do_run_migrations(connection: Connection) -> None:
+    """Configure migration context for online mode."""
+    context.configure(
+        connection=connection, 
+        target_metadata=target_metadata,
+        # 🔥 REQUIRED FOR SQLITE: Allows table alterations by rebuilding tables
+        render_as_batch=True,
+    )
+
+    with context.begin_transaction():
+        context.run_migrations()
+
+async def run_async_migrations() -> None:
+    """In this scenario we need to create an Engine and associate a connection with the context."""
+    connectable = async_engine_from_config(
+        config.get_section(config.config_ini_section, {}),
+        prefix="sqlalchemy.",
+        poolclass=pool.NullPool,
+    )
+
+    async with connectable.connect() as connection:
+        await connection.run_sync(do_run_migrations)
+
+    await connectable.dispose()
+
+def run_migrations_online() -> None:
+    """Run migrations in 'online' mode."""
+    asyncio.run(run_async_migrations())
+
+if context.is_offline_mode():
+    run_migrations_offline()
+else:
+    run_migrations_online()