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Author: DiogoRibeiro7

fix_recommendations.md

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+# Fixing gen_surv Repository Issues
+
+## Priority 1: Critical Fixes
+
+### 1. Fix `__init__.py` Import Issues
+
+Update `gen_surv/__init__.py` to include missing imports:
+
+```python
+# Add these imports
+from .aft import gen_aft_log_logistic
+from .competing_risks import gen_competing_risks, gen_competing_risks_weibull
+from .mixture import gen_mixture_cure, cure_fraction_estimate
+from .piecewise import gen_piecewise_exponential
+
+# Update __all__ to include:
+__all__ = [
+    # ... existing exports ...
+    "gen_aft_log_logistic",
+    "gen_competing_risks", 
+    "gen_competing_risks_weibull",
+    "gen_mixture_cure",
+    "cure_fraction_estimate", 
+    "gen_piecewise_exponential",
+]
+```
+
+### 2. Add Missing Validators
+
+Create validation functions in `validate.py`:
+
+```python
+def validate_gen_aft_weibull_inputs(n, beta, shape, scale, model_cens, cens_par):
+    # Add validation logic
+    
+def validate_gen_aft_log_logistic_inputs(n, beta, shape, scale, model_cens, cens_par):
+    # Add validation logic
+    
+def validate_competing_risks_inputs(n, n_risks, baseline_hazards, betas, model_cens, cens_par):
+    # Add validation logic
+```
+
+### 3. Update CLI Integration
+
+Modify `cli.py` to handle all available models:
+
+```python
+# Add support for competing_risks, mixture, and piecewise models
+# Update parameter handling for each model type
+```
+
+## Priority 2: Version Consistency
+
+### Update Version Numbers
+
+1. **CITATION.cff**: Change version from "1.0.3" to "1.0.8"
+2. **docs/source/conf.py**: Change release from '1.0.3' to '1.0.8'
+
+## Priority 3: Testing and Documentation
+
+### Add Missing Tests
+
+Create test files:
+- `tests/test_censoring.py`
+- `tests/test_mixture.py` 
+- `tests/test_piecewise.py`
+- `tests/test_summary.py`
+- `tests/test_visualization.py`
+
+### Update Documentation
+
+1. Add competing risks, mixture, and piecewise models to `theory.md`
+2. Update examples in documentation to include new models
+
+## Priority 4: Code Quality Improvements
+
+### Standardize Parameter Naming
+
+- Consistently use `covariate_cols` instead of mixing `covar` and `covariate_cols`
+- Standardize return column names across all models
+
+### Add Type Hints
+
+Complete type hints for all public functions, especially in:
+- `mixture.py`
+- `piecewise.py` 
+- `summary.py`
+
+## Verification Steps
+
+After implementing fixes:
+
+1. **Test imports**: `python -c "from gen_surv import gen_aft_log_logistic, gen_competing_risks"`
+2. **Test CLI**: `python -m gen_surv dataset competing_risks --n 10`
+3. **Run full test suite**: `poetry run pytest`
+4. **Check version consistency**: `python scripts/check_version_match.py`
+5. **Build docs**: `poetry run sphinx-build docs/source docs/build`
+
+## Impact Assessment
+
+These fixes will:
+- ✅ Eliminate ImportError exceptions for users
+- ✅ Make all models accessible via public API
+- ✅ Ensure CLI works for all supported models
+- ✅ Improve user experience and API consistency
+- ✅ Maintain backward compatibility