preparing for paper release

[cmatKhan]

No description provided.

[codecov]

Codecov Report

❌ Patch coverage is 69.35484% with 228 lines in your changes missing coverage. Please review.
✅ Project coverage is 71.79%. Comparing base (2e3ce86) to head (1c5d8bd).
⚠️ Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
tfbpmodeling/interface.py	50.90%	67 Missing and 14 partials ⚠️
tfbpmodeling/bootstrap_model_results.py	47.25%	44 Missing and 4 partials ⚠️
tfbpmodeling/modeling_input_data.py	71.97%	23 Missing and 21 partials ⚠️
tfbpmodeling/bootstrapped_input_data.py	83.21%	19 Missing and 5 partials ⚠️
tfbpmodeling/bootstrap_stratified_cv.py	69.38%	9 Missing and 6 partials ⚠️
tfbpmodeling/stratified_cv.py	53.33%	7 Missing and 7 partials ⚠️
...odeling/evaluate_interactor_significance_linear.py	92.30%	1 Missing and 1 partial ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #77      +/-   ##
==========================================
- Coverage   72.59%   71.79%   -0.81%     
==========================================
  Files           5       13       +8     
  Lines         697      826     +129     
  Branches      116      116              
==========================================
+ Hits          506      593      +87     
- Misses        125      174      +49     
+ Partials       66       59       -7     

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[Copilot]

Pull Request Overview

This PR prepares the tfbpmodeling package for paper release by restructuring the codebase through significant refactoring. The changes break down a large monolithic file into smaller, focused modules and update imports accordingly.

• Modularizes the codebase by extracting classes and functions from lasso_modeling.py into separate files
• Updates all test files to use the new module structure with corrected imports
• Removes deprecated files including SigmoidModel.py and related sigmoid modeling tests
• Adds new utility functions and consolidates the interface layer

Reviewed Changes

Copilot reviewed 31 out of 31 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
tfbpmodeling/utils/exclude_predictor_variables.py	New utility function for filtering predictor variables with exclusion logic
tfbpmodeling/tests/test_utils.py	Tests for the new exclude_predictor_variables utility function
tfbpmodeling/tests/test_*.py	Updated test files with corrected imports and removed sigmoid-related tests
tfbpmodeling/modeling_input_data.py	Extracted ModelingInputData class with improved scaling functionality
tfbpmodeling/bootstrap_*.py	Modularized bootstrap-related classes and functions
tfbpmodeling/interface.py	New consolidated interface module for command-line functionality
tfbpmodeling/stratification_classification.py	Simplified to remove perturbation-based binning
tfbpmodeling/__main__.py	Significantly reduced by moving functionality to interface module

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[Copilot]

There is a spelling error in the comment on line 362: 'indicies' should be 'indices'.

[Copilot]

The backslash line continuation is unnecessary here since the expression is already within parentheses on line 221. Consider removing the backslash and properly indenting the second line.

Suggested change

	formula = f"{random_sample_data_no_signal.perturbed_tf} + \
	{' + '.join(interaction_terms)} - 1"
	formula = (
	f"{random_sample_data_no_signal.perturbed_tf} + {' + '.join(interaction_terms)} - 1"
	)