Fix broadcast list unwrapping and mixed positional list handling

src/experiment_generator/perturbation_experiment.py

@@ -340,6 +340,27 @@ def _select_from_list(row: list):
                         if isinstance(inner, list) and len(inner) == 0:
                             continue
 
+                        # handle mixed positional inventories, such as [PRESERVE, {input: ...}]
+                        if any(isinstance(d, Mapping) for d in inner):
+                            slots = []
+                            for i in inner:
+                                # keep markers as is
+                                if _is_removed_str(i) or _is_preserved_str(i):
+                                    slots.append(i)
+                                    continue
+
+                                # recurse into dicts
+                                if isinstance(i, Mapping):
+                                    keep_v, cleaned = _filter_value(
+                                        self._extract_run_specific_params(i, indx, total_exps)
+                                    )
+                                    slots.append(cleaned if keep_v else {})
+                                    continue
+
+                                # scalar slots
+                                slots.append(i)
+
+                        # inner is all dicts
                         if all(isinstance(d, Mapping) for d in inner):
                             # recurse for each dict
                             items = []

src/experiment_generator/utils.py

@@ -262,6 +262,11 @@ def update_config_entries(
         if not should_apply:
             continue  # no change for this key; keep existing value
 
+        # if the incoming value is a single value list but the base value is scalar,
+        # then treat it as a scalar.
+        if isinstance(v, list) and len(v) == 1 and not isinstance(base.get(k), list):
+            v = v[0]
+
         key_path = _path_join(path, str(k))
 
         if isinstance(v, Mapping) and isinstance(base.get(k), Mapping):

tests/test_perturbation_experiment.py

@@ -322,6 +322,19 @@ def test_manage_perturb_expt_creat_branches_applies_updates_and_commits(
         # sequence branch: inner list is [PRESERVE]
         ({"queue3": [["PRESERVE"]]}, 0, 2, {"queue3": ["PRESERVE"]}),
         ({"queue3": [["PRESERVE"]]}, 1, 2, {"queue3": ["PRESERVE"]}),
+        # mixed positional list of lists with markers and mappings and scalars
+        (
+            {"submodels": [["PRESERVE", {}, "foo"]]},
+            0,
+            2,
+            {"submodels": ["PRESERVE", None, "foo"]},
+        ),
+        (
+            {"submodels": [["REMOVE", {}, "foo"]]},
+            1,
+            2,
+            {"submodels": ["REMOVE", None, "foo"]},
+        ),
     ],
 )
 def test_extract_run_specific_params_rules(tmp_repo_dir, indata, param_dict, indx, total, expected):

tests/test_utils.py

@@ -426,6 +426,16 @@ def test_merge_lists_positional_mapping_branch_uses_current_mapping_slot():
     assert out == [{"a": 1, "keep": 0, "b": 2}]
 
 
+def test_update_config_entries_unwraps_single_item_list_to_scalar_when_base_is_scalar():
+    base = {"ncpus": 4}
+
+    changes = {"ncpus": [8]}  # single-item list
+
+    update_config_entries(base, changes, pop_key=True)
+
+    assert base == {"ncpus": 8}
+
+
 # def test_empty_mapping_in_change_keeps_existing_slot():
 #     base = {"lst": [{"a": 1}, {"b": 2}]}
 #     # empty mapping also means PRESERVE