feat: Add delete overlap option to pth2json and improve model saving …

[QG-phy]

This pull request introduces a new option to convert models to a "no overlap" (orthogonal) version during checkpoint conversion, and includes several improvements and bug fixes related to model configuration and checkpoint handling. The most important changes are grouped below.

New feature: No-overlap model conversion

• Added a --deleteoverlap flag to the pth2json CLI command in main.py, enabling users to convert models to a version without the "overlap" parameter.
• Implemented logic in pth2json.py to remove the "overlap" key from the model parameters, update related options, and ensure orthogonal conversion when the flag is set.

Model configuration bug fixes

• Improved handling of the push option in argcheck.py by adding a threshold check to ensure that push parameters are meaningful before requiring related data options.
• Fixed logic in pth2json.py to correctly update the freeze and push options when converting to the no-overlap version, preventing potential configuration errors.

Checkpoint management

• Cleaned up redundant code in the checkpoint deletion logic within the iteration method of saver.py, ensuring only one block handles checkpoint queue overflow.[Copilot is generating a summary...]…logic

[Copilot]

Pull Request Overview

This pull request introduces a new delete overlap option to the pth2json CLI command and includes several bug fixes for model configuration and checkpoint management. The main purpose is to enable conversion of models to an orthogonal (no-overlap) version during checkpoint conversion.

• Added --deleteoverlap flag to pth2json CLI for converting models to orthogonal versions
• Fixed push option validation logic to check threshold values before requiring data options
• Removed duplicate checkpoint deletion code in the saver module

Reviewed Changes

Copilot reviewed 4 out of 4 changed files in this pull request and generated 3 comments.

File	Description
dptb/entrypoints/main.py	Adds the new --deleteoverlap CLI argument to pth2json command
dptb/entrypoints/pth2json.py	Implements the core logic for converting models to orthogonal version when deleteoverlap flag is set
dptb/utils/argcheck.py	Improves push option validation by checking threshold values before requiring data options
dptb/plugins/saver.py	Removes duplicate checkpoint deletion logic in the iteration method

[Copilot]

The comparison == ['overlap'] will always be False when get('freeze', False) returns the default value False. This should check if the freeze value is a list containing 'overlap' more safely.

Suggested change

	if json_dict['model_options']['nnsk'].get('freeze',False) == ['overlap']:
	json_dict['model_options']['nnsk']['freeze'] = False
	elif isinstance(json_dict['model_options']['nnsk'].get('freeze',False), list):
	json_dict['model_options']['nnsk']['freeze'] = [x for x in json_dict['model_options']['nnsk']['freeze'] if x != 'overlap']
	freeze_val = json_dict['model_options']['nnsk'].get('freeze', False)
	if isinstance(freeze_val, list) and freeze_val == ['overlap']:
	json_dict['model_options']['nnsk']['freeze'] = False
	elif isinstance(freeze_val, list):
	json_dict['model_options']['nnsk']['freeze'] = [x for x in freeze_val if x != 'overlap']

[Copilot]

This condition will never be True because get('freeze', False) returns False as default, and isinstance(False, list) is always False. The default value should be None or an empty list to properly handle the case where freeze is not set.

Suggested change

	if json_dict['model_options']['nnsk'].get('freeze',False) == ['overlap']:
	json_dict['model_options']['nnsk']['freeze'] = False
	elif isinstance(json_dict['model_options']['nnsk'].get('freeze',False), list):
	if json_dict['model_options']['nnsk'].get('freeze',[]) == ['overlap']:
	json_dict['model_options']['nnsk']['freeze'] = False
	elif isinstance(json_dict['model_options']['nnsk'].get('freeze',[]), list):

[Copilot]

Similar to the freeze logic above, using False as the default value for get('push', False) means isinstance(False, dict) will always be False. The default should be None to properly detect when push is a dictionary.

Suggested change

	if isinstance(json_dict['model_options']['nnsk'].get('push',False), dict):
	if isinstance(json_dict['model_options']['nnsk'].get('push', None), dict):