Migrate from simple-parsing to pydantic for argument parsing

### Describe the feature

We want better configuration management and argument parsing for CLI and the API. To support the development, drop support for simple-parsing in favor of pydantic.

### Potential Solutions

1. Use Pydantic for creating configuration classes.
2. Decouple API and CLI fields in data classes and configuration.
3. Migrate the CLI to use Pydantic and Pydantic Argparse.