Fix: SQLite duplicate study (load_if_exists), sampling crash with n<11, add --clean flag

projects/hydrotech-beam/studies/01_doe_landscape/run_doe.py

@@ -418,6 +418,10 @@ def run_study(args: argparse.Namespace) -> None:
     db_path = results_dir / "optuna_study.db"
     storage = f"sqlite:///{db_path}"
 
+    if args.clean and db_path.exists():
+        logger.info("--clean flag: deleting existing DB at %s", db_path)
+        db_path.unlink()
+
     if args.resume:
         logger.info("Resuming existing study: %s", args.study_name)
         study = optuna.load_study(
@@ -430,7 +434,7 @@ def run_study(args: argparse.Namespace) -> None:
             study_name=args.study_name,
             storage=storage,
             direction="minimize",  # minimize mass
-            load_if_exists=False,
+            load_if_exists=True,  # safe re-run: reuse if exists
             sampler=optuna.samplers.TPESampler(seed=args.seed),
         )
         logger.info("Created new study: %s (storage: %s)", args.study_name, db_path)
@@ -622,6 +626,11 @@ def parse_args() -> argparse.Namespace:
         action="store_true",
         help="Resume an existing study instead of creating a new one",
     )
+    parser.add_argument(
+        "--clean",
+        action="store_true",
+        help="Delete existing results DB before starting (fresh run)",
+    )
     parser.add_argument(
         "--verbose", "-v",
         action="store_true",

projects/hydrotech-beam/studies/01_doe_landscape/sampling.py

@@ -173,6 +173,16 @@ def _ensure_integer_coverage(
         logger.info("All 11 hole_count levels represented ✓")
         return samples
 
+    # Skip patching when sample size is too small to cover all levels
+    n_samples = len(samples)
+    if n_samples < len(all_levels):
+        logger.info(
+            "Only %d samples — too few to cover all 11 hole_count levels "
+            "(need ≥11). Skipping stratified patching.",
+            n_samples,
+        )
+        return samples
+
     logger.warning(
         "Missing hole_count levels: %s — patching with replacements",
         sorted(missing_levels),