Migrating to a Generalizable Scientist Agent Framework

[DomPTech]

Overview

This repo was initially built to work strictly on microscopy (specifically the Thermo Fisher Spectra 300 TEM). With asyncroscopy's migration to a more general hardware control framework, and my MCP server implementation, this agentic framework should follow the same changes. That means no more hardcoded prompts/instructions, no dependencies on specific libraries like PyTEMlib, no more hardcoded science tools (though we will retain general tools, like designing workflows).

Refactoring

• Remove requirements.txt and unneeded dependencies
• Refactor project structure (probably rename/remove app.py?)
• Remove UI
• Refactor core.py to be more general, remove microscopy.py, and rename workflow objects
• Rename project, update description and README