Feat/update review #86
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* chore: tighten tooling and fix visualization * docs: document Python 3.10 requirement * ci: align workflow with review template
* Feat/remove ignore errors in mypy settings (#78) * feat: Add competing risks models and enhance data visualization * feat: Add competing risks models and enhance data visualization * chore: fixes * chore: fixes unit test * chore: solve issues with formatting * Add files via upload * docs: update fix reference (#37) * Add missing dependencies and configure quality tools (#39) * feat: add dataset export utility (#41) * Fix black formatting (#43) * Add extensive summary tests (#45) * Add visualization CLI tests (#47) * Expand validate tests (#49) * docs: rewrite README (#51) * Increase test coverage (#52) * Fix docs build and sort imports (#54) * Add scikit-survival integration (#56) * chore: finalize 1.0.9 release metadata (#58) * refactor: unify error handling (#60) * Feat/consolidate and optimize (#63) * chore: tighten tooling and fix visualization * docs: document Python 3.10 requirement * ci: align workflow with review template * feat: expose dev extras (#65) * test: broaden competing risks coverage (#67) * fix: ensure doc links and tag workflow (#69) * ci: streamline coverage and install flags (#71) * feat: share covariate utilities (#73) * ci: separate manual pypi publish (#76) * fix: tighten sequence checks and streamline competing-risk helpers * Revert "Feat/remove ignore errors in mypy settings (#78)" This reverts commit 3c799d0.
* Feat/remove ignore errors in mypy settings (#78) * feat: Add competing risks models and enhance data visualization * feat: Add competing risks models and enhance data visualization * chore: fixes * chore: fixes unit test * chore: solve issues with formatting * Add files via upload * docs: update fix reference (#37) * Add missing dependencies and configure quality tools (#39) * feat: add dataset export utility (#41) * Fix black formatting (#43) * Add extensive summary tests (#45) * Add visualization CLI tests (#47) * Expand validate tests (#49) * docs: rewrite README (#51) * Increase test coverage (#52) * Fix docs build and sort imports (#54) * Add scikit-survival integration (#56) * chore: finalize 1.0.9 release metadata (#58) * refactor: unify error handling (#60) * Feat/consolidate and optimize (#63) * chore: tighten tooling and fix visualization * docs: document Python 3.10 requirement * ci: align workflow with review template * feat: expose dev extras (#65) * test: broaden competing risks coverage (#67) * fix: ensure doc links and tag workflow (#69) * ci: streamline coverage and install flags (#71) * feat: share covariate utilities (#73) * ci: separate manual pypi publish (#76) * fix: tighten sequence checks and streamline competing-risk helpers * Revert "Feat/remove ignore errors in mypy settings (#78)" (#80) This reverts commit 3c799d0. * Update version to 1.0.9 --------- Co-authored-by: github-actions[bot] <github-actions[bot]@users.noreply.github.com>
* Feat/remove ignore errors in mypy settings (#78) * feat: Add competing risks models and enhance data visualization * feat: Add competing risks models and enhance data visualization * chore: fixes * chore: fixes unit test * chore: solve issues with formatting * Add files via upload * docs: update fix reference (#37) * Add missing dependencies and configure quality tools (#39) * feat: add dataset export utility (#41) * Fix black formatting (#43) * Add extensive summary tests (#45) * Add visualization CLI tests (#47) * Expand validate tests (#49) * docs: rewrite README (#51) * Increase test coverage (#52) * Fix docs build and sort imports (#54) * Add scikit-survival integration (#56) * chore: finalize 1.0.9 release metadata (#58) * refactor: unify error handling (#60) * Feat/consolidate and optimize (#63) * chore: tighten tooling and fix visualization * docs: document Python 3.10 requirement * ci: align workflow with review template * feat: expose dev extras (#65) * test: broaden competing risks coverage (#67) * fix: ensure doc links and tag workflow (#69) * ci: streamline coverage and install flags (#71) * feat: share covariate utilities (#73) * ci: separate manual pypi publish (#76) * fix: tighten sequence checks and streamline competing-risk helpers * Revert "Feat/remove ignore errors in mypy settings (#78)" (#80) This reverts commit 3c799d0. * Update version to 1.0.9 --------- Co-authored-by: github-actions[bot] <github-actions[bot]@users.noreply.github.com>
* tests: remove regression baselines * tests: add deterministic generation and visualize CLI integration
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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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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: