Address PR review feedback

- Add new DGP functions to CLAUDE.md Module Structure section
- Restore trailing newlines to modified notebook files
- Add RuntimeWarnings investigation items to TODO.md

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

Author: igerber

CLAUDE.md

@@ -195,7 +195,12 @@ pytest tests/test_rust_backend.py -v
   - Integrates with HonestDiD for comprehensive sensitivity analysis
 
 - **`diff_diff/prep.py`** - Data preparation utilities:
-  - `generate_did_data` - Create synthetic data with known treatment effect
+  - `generate_did_data` - Create synthetic data with known treatment effect (basic 2x2 DiD)
+  - `generate_staggered_data` - Staggered adoption data for CallawaySantAnna/SunAbraham
+  - `generate_factor_data` - Factor model data for TROP/SyntheticDiD
+  - `generate_ddd_data` - Triple Difference (DDD) design data
+  - `generate_panel_data` - Panel data with optional parallel trends violations
+  - `generate_event_study_data` - Event study data with simultaneous treatment
   - `make_treatment_indicator`, `make_post_indicator` - Create binary indicators
   - `wide_to_long`, `balance_panel` - Panel data reshaping
   - `validate_did_data`, `summarize_did_data` - Data validation and summary

TODO.md

@@ -92,6 +92,21 @@ Enhancements for `honest_did.py`:
 
 ---
 
+## RuntimeWarnings in Linear Algebra Operations
+
+Pre-existing RuntimeWarnings in matrix operations that should be investigated:
+
+- [ ] `linalg.py:162` - "divide by zero", "overflow", "invalid value" in fitted value computation
+  - Occurs during `X @ coefficients` when coefficients contain extreme values
+  - Seen in test_prep.py during treatment effect recovery tests
+- [ ] `triple_diff.py:307,323` - Similar warnings in propensity score computation
+  - Occurs in IPW and DR estimation methods with covariates
+  - Related to logistic regression overflow in edge cases
+
+**Note**: These warnings do not affect correctness of results but should be handled gracefully (e.g., with `np.errstate` context managers or input validation).
+
+---
+
 ## Rust Backend Optimizations
 
 Deferred from PR #58 code review (completed in v2.0.3):

docs/tutorials/02_staggered_did.ipynb

@@ -912,4 +912,4 @@
  },
  "nbformat": 4,
  "nbformat_minor": 4
-}
+}

docs/tutorials/04_parallel_trends.ipynb

@@ -798,4 +798,4 @@
  },
  "nbformat": 4,
  "nbformat_minor": 4
-}
+}

docs/tutorials/07_pretrends_power.ipynb

@@ -768,4 +768,4 @@
  },
  "nbformat": 4,
  "nbformat_minor": 5
-}
+}

docs/tutorials/08_triple_diff.ipynb

@@ -470,4 +470,4 @@
  },
  "nbformat": 4,
  "nbformat_minor": 4
-}
+}

docs/tutorials/10_trop.ipynb

@@ -616,4 +616,4 @@
  },
  "nbformat": 4,
  "nbformat_minor": 4
-}
+}