Protocol Export from Protocol Developer

[Rohit-Kannachel]

Tried to implement a less complex protocol file export function to create an easier to read yaml file from protocol developer

[patrickcleeve2]

I don't agree with always removing these options from the dict, as others use the alignment/imaging settings. Instead of specifying method.name =="Waffle" (L1013), can you just add a flag here to remove the options for your use case. If it stays the way it is, it's gonna cause some silent issues later on

[Copilot]

Pull Request Overview

Adds a streamlined export path for protocols by introducing methods to generate and save a base (less verbose) YAML representation of an experiment.

• Introduces save_base_protocol to write out a simplified protocol file
• Implements to_dict_base_protocol and helper _reduced_milling_options_dict for pared-down dictionary output
• Retains full export via save and ensures backward compatibility

Comments suppressed due to low confidence (3)

autolamella/structures.py:1000

• [nitpick] The attribute tmp is ambiguous. Consider renaming it to something more descriptive (e.g., default_options or template_options).

options_dict = self.tmp

autolamella/structures.py:1007

• Add a docstring explaining the purpose, parameters, and return value of this helper to improve maintainability.

def _reduced_milling_options_dict(self,milling_dict):

autolamella/structures.py:985

• Consider adding unit tests for save_base_protocol and to_dict_base_protocol to verify the reduced YAML structure is generated correctly.

def save_base_protocol(self, path: Path, current_milling_dict: dict = None) -> None: