Replace raw SQL with ORM

[jb3rndt]

This replaces the table DDLs and insert statements with sqlalchemy.

The ability to set the table name through the config makes handling the models a bit cumbersome, raising the question whether we really need this?

(Does not include migrations using Alembic yet)

[lisehr]

The original thought was that other people (external researchers) might store the dq results in their own table with customized names. For now, it should work thought but the goal of Metis is to keep it generic and reusable in different settings.

sqlalchemy: great move, thanks. only one suggestion: could you rename the models.py to something more specific? Models in Metis could be anything (ML models, data models, etc.) - please make clear that these are the models required by sqlalchemy.

[Copilot]

Pull Request Overview

This PR migrates database operations from raw SQL to SQLAlchemy ORM, eliminating manual DDL statements and parameterized queries in favor of declarative models and ORM sessions. The refactor consolidates common database logic into a base DatabaseWriter class while maintaining database-specific implementations for SQLite and PostgreSQL.

• Replaces raw SQL CREATE TABLE and INSERT statements with SQLAlchemy declarative models
• Introduces a new DatabaseWriter base class to centralize ORM operations
• Implements dynamic table name configuration through a model registration pattern

Reviewed Changes

Copilot reviewed 4 out of 7 changed files in this pull request and generated 2 comments.

File	Description
metis/writer/sqlite_writer.py	Refactored to extend DatabaseWriter, implements SQLite-specific engine creation
metis/writer/postgres_writer.py	Refactored to extend DatabaseWriter, implements PostgreSQL-specific engine creation
metis/writer/database_writer.py	New base class implementing shared ORM logic for database writers
metis/database_models.py	New file defining SQLAlchemy declarative models with dynamic table name support

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[jb3rndt]

Thank you, good point. I've changed the file from models.py -> database_models.py.