Feat/update review

[DiogoRibeiro7]

Pull Request Overview

This PR adds comprehensive testing infrastructure and visualization capabilities to the gen_surv package. It introduces new features like survival data visualization with Kaplan-Meier curves, data quality checking tools, and comprehensive test coverage across all modules.

Key changes include:

• New visualization module with plotting functions for survival curves and hazard comparisons
• Comprehensive test coverage across all existing modules with property-based testing
• Data quality checking and summarization utilities

[codecov]

Codecov Report

❌ Patch coverage is 96.21849% with 45 lines in your changes missing coverage. Please review.

Files with missing lines	Patch %	Lines
gen_surv/summary.py	94.80%	8 Missing ⚠️
gen_surv/_covariates.py	90.14%	7 Missing ⚠️
gen_surv/validation.py	95.83%	7 Missing ⚠️
gen_surv/visualization.py	92.20%	6 Missing ⚠️
gen_surv/integration.py	80.00%	5 Missing ⚠️
gen_surv/__init__.py	85.18%	4 Missing ⚠️
gen_surv/competing_risks.py	97.80%	4 Missing ⚠️
gen_surv/mixture.py	97.33%	2 Missing ⚠️
gen_surv/piecewise.py	98.88%	1 Missing ⚠️
gen_surv/sklearn_adapter.py	95.65%	1 Missing ⚠️

📢 Thoughts on this report? Let us know!

[Copilot]

Pull Request Overview

This PR adds comprehensive testing infrastructure and visualization capabilities to the gen_surv package. It introduces new features like survival data visualization with Kaplan-Meier curves, data quality checking tools, and comprehensive test coverage across all modules.

Key changes include:

• New visualization module with plotting functions for survival curves and hazard comparisons
• Comprehensive test coverage across all existing modules with property-based testing
• Data quality checking and summarization utilities

Reviewed Changes

Copilot reviewed 109 out of 111 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
tests/test_visualization.py	Tests for new visualization functionality including survival curves and summary statistics
tests/test_version.py	Enhanced version testing with better error handling
tests/test_validate.py	Comprehensive validation testing with proper imports and error handling
tests/test_thmm.py	Cleaned up THMM tests with proper parameter naming
tests/test_tdcm.py	Improved TDCM tests with better formatting
tests/test_summary_*.py	New tests for data summarization and quality checking functionality
tests/test_sklearn_adapter.py	Tests for scikit-learn compatibility wrapper
tests/test_piecewise*.py	Tests for piecewise exponential survival models
tests/test_mixture.py	Tests for mixture cure fraction models
tests/test_interface.py	Enhanced interface tests with better error handling
tests/test_integration_*.py	Integration tests for various export formats and external library compatibility
tests/test_generate_*.py	Comprehensive generation tests including regression and deterministic testing
tests/test_export.py	Tests for data export functionality in multiple formats
tests/test_cphm.py	Enhanced CPHM tests with comprehensive coverage
tests/test_competing_risks.py	Extensive tests for competing risks models with property-based testing
tests/test_cmm.py	Improved CMM tests with reproducibility checks
tests/test_cli_*.py	Comprehensive CLI testing including integration and visualization commands
tests/test_censoring.py	Tests for various censoring mechanisms
tests/test_bivariate.py	Enhanced bivariate distribution tests with proper error types
tests/test_api_contract.py	API contract testing for signature stability
tests/test_aft*.py	Comprehensive AFT model tests with property-based testing
tests/conftest.py	New pytest configuration with baseline testing infrastructure
tasks.py	Updated build tasks with better formatting
pyproject.toml	Updated dependencies and project configuration
gen_surv/visualization.py	New visualization module with survival plotting capabilities
gen_surv/validation.py	Comprehensive validation framework with custom exception types
gen_surv/validate.py	Compatibility wrapper for validation utilities
gen_surv/thmm.py	Enhanced with proper type hints and documentation
gen_surv/tdcm.py	Improved implementation with vectorized operations
gen_surv/summary.py	New data summarization and quality checking utilities
gen_surv/sklearn_adapter.py	Scikit-learn compatibility wrapper
gen_surv/piecewise.py	New piecewise exponential survival models

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