Fix save with multifile=True not saving separate subconfigs for items in a list

CHANGELOG.rst

@@ -35,6 +35,8 @@ Fixed
   (`#772 <https://github.com/omni-us/jsonargparse/pull/772>`__).
 - ``omegaconf+`` parser mode failing when there are ``inf``, ``-inf`` or ``nan``
   values (`#773 <https://github.com/omni-us/jsonargparse/pull/773>`__).
+- ``save`` with ``multifile=True`` not saving separate subconfigs for items in a
+  list (`#779 <https://github.com/omni-us/jsonargparse/pull/779>`__).
 
 
 v4.41.0 (2025-09-04)

jsonargparse/_core.py

@@ -930,25 +930,36 @@ def check_overwrite(path):
 
             ActionLink.strip_link_target_keys(self, cfg)
 
+            def is_path_action(key):
+                action = _find_action(self, key)
+                return isinstance(action, (ActionJsonSchema, ActionJsonnet, ActionTypeHint, _ActionConfigLoad))
+
+            def save_path(val):
+                val_path = Path(os.path.basename(val["__path__"].absolute), mode="fc")
+                check_overwrite(val_path)
+                val_out = strip_meta(val)
+                if isinstance(val, Namespace):
+                    val_out = val_out.as_dict()
+                if "__orig__" in val:
+                    val_str = val["__orig__"]
+                else:
+                    is_json = str(val_path).lower().endswith(".json")
+                    val_str = dump_using_format(self, val_out, "json_indented" if is_json else format)
+                with open(val_path.absolute, "w") as f:
+                    f.write(val_str)
+                return os.path.basename(val_path)
+
             def save_paths(cfg):
                 for key in cfg.get_sorted_keys():
                     val = cfg[key]
                     if isinstance(val, (Namespace, dict)) and "__path__" in val:
-                        action = _find_action(self, key)
-                        if isinstance(action, (ActionJsonSchema, ActionJsonnet, ActionTypeHint, _ActionConfigLoad)):
-                            val_path = Path(os.path.basename(val["__path__"].absolute), mode="fc")
-                            check_overwrite(val_path)
-                            val_out = strip_meta(val)
-                            if isinstance(val, Namespace):
-                                val_out = val_out.as_dict()
-                            if "__orig__" in val:
-                                val_str = val["__orig__"]
-                            else:
-                                is_json = str(val_path).lower().endswith(".json")
-                                val_str = dump_using_format(self, val_out, "json_indented" if is_json else format)
-                            with open(val_path.absolute, "w") as f:
-                                f.write(val_str)
-                            cfg[key] = os.path.basename(val_path.absolute)
+                        if is_path_action(key):
+                            cfg[key] = save_path(val)
+                    elif isinstance(val, list):
+                        if is_path_action(key):
+                            for num, item in enumerate(val):
+                                if isinstance(item, (Namespace, dict)) and "__path__" in item:
+                                    val[num] = save_path(item)
                     elif isinstance(val, Path) and key in self.save_path_content and "r" in val.mode:
                         val_path = Path(os.path.basename(val.absolute), mode="fc")
                         check_overwrite(val_path)
@@ -1356,9 +1367,9 @@ def _apply_actions(
             cfg_branch = cfg
             cfg = Namespace()
             cfg[parent_key] = cfg_branch
-            keys = [parent_key + "." + k for k in cfg_branch.__dict__]
+            keys = [parent_key + "." + k for k in cfg_branch.keys(branches=True, nested=False)]
         else:
-            keys = list(cfg.__dict__)
+            keys = list(cfg.keys(branches=True, nested=False))
 
         if prev_cfg:
             prev_cfg = prev_cfg.clone()
@@ -1385,7 +1396,7 @@ def _apply_actions(
                 if isinstance(value, dict):
                     value = Namespace(value)
                 if isinstance(value, Namespace):
-                    new_keys = value.__dict__.keys()
+                    new_keys = value.keys(branches=True, nested=False)
                     keys += [key + "." + k for k in new_keys if key + "." + k not in keys]
                 cfg[key] = value
                 continue

jsonargparse/_namespace.py

@@ -233,21 +233,23 @@ def as_flat(self) -> argparse.Namespace:
             setattr(flat, key, val)
         return flat
 
-    def items(self, branches: bool = False) -> Iterator[Tuple[str, Any]]:
+    def items(self, branches: bool = False, nested: bool = True) -> Iterator[Tuple[str, Any]]:
         """Returns a generator of all leaf (key, value) items, optionally including branches."""
         for key, val in vars(self).items():
             key = del_clash_mark(key)
             if isinstance(val, Namespace):
                 if branches:
                     yield key, val
+                if not nested:
+                    continue
                 for subkey, subval in val.items(branches):
                     yield key + "." + del_clash_mark(subkey), subval
             else:
                 yield key, val
 
-    def keys(self, branches: bool = False) -> Iterator[str]:
+    def keys(self, branches: bool = False, nested: bool = True) -> Iterator[str]:
         """Returns a generator of all leaf keys, optionally including branches."""
-        for key, _ in self.items(branches):
+        for key, _ in self.items(branches=branches, nested=nested):
             yield key
 
     def values(self, branches: bool = False) -> Iterator[Any]:

jsonargparse/_typehints.py

@@ -1396,7 +1396,7 @@ def discard_init_args_on_class_path_change(parser_or_action, prev_val, value):
             parser = ActionTypeHint.get_class_parser(value["class_path"], sub_add_kwargs)
         del_args = {}
         prev_val = subclass_spec_as_namespace(prev_val)
-        for key, val in list(prev_val.init_args.__dict__.items()):
+        for key, val in list(prev_val.init_args.items(branches=True, nested=False)):
             action = _find_action(parser, key)
             if action:
                 with parser_context(lenient_check=False, load_value_mode=parser.parser_mode):
@@ -1515,7 +1515,7 @@ def adapt_classes_any(val, serialize, instantiate_classes, sub_add_kwargs):
         val = subclass_spec_as_namespace(val)
         init_args = val.get("init_args")
         if init_args and not instantiate_classes:
-            for subkey, subval in init_args.__dict__.items():
+            for subkey, subval in init_args.items(branches=True, nested=False):
                 init_args[subkey] = adapt_classes_any(subval, serialize, instantiate_classes, sub_add_kwargs)
             val["init_args"] = init_args
         try:

jsonargparse_tests/test_core.py

@@ -699,6 +699,47 @@ def rm_out_files():
             assert json_or_yaml_load(schema_yaml_out.read_text()) == {"a": 1, "b": 2}
 
 
+class ListItem:
+    def __init__(self, a: int, b: str):
+        self.a = a
+        self.b = b
+
+
+def test_save_multifile_list(parser, tmp_cwd):
+    in_dir = tmp_cwd / "input"
+    out_dir = tmp_cwd / "output"
+    in_dir.mkdir()
+    out_dir.mkdir()
+    main_file_in = in_dir / "main.yaml"
+    main_file_out = out_dir / "main.yaml"
+    item_1_file_in = in_dir / "item1.yaml"
+    item_1_file_out = out_dir / "item1.yaml"
+    item_2_file_in = in_dir / "item2.yaml"
+    item_2_file_out = out_dir / "item2.yaml"
+
+    main_content = {"items": ["item1.yaml", "item2.yaml"]}
+    main_file_in.write_text(json_or_yaml_dump(main_content))
+    item_1_file_in.write_text(json_or_yaml_dump({"a": 1, "b": "x"}))
+    item_2_file_in.write_text(json_or_yaml_dump({"a": 2, "b": "y"}))
+
+    parser.add_argument("--config", action="config")
+    parser.add_argument(
+        "--items",
+        nargs="+",
+        type=ListItem,
+        required=True,
+        enable_path=True,
+    )
+
+    cfg = parser.parse_args([f"--config={main_file_in}"])
+    parser.save(cfg, main_file_out)
+    assert json_or_yaml_load(main_file_out.read_text()) == main_content
+    item_1_expected = {"class_path": f"{__name__}.ListItem", "init_args": {"a": 1, "b": "x"}}
+    assert json_or_yaml_load(item_1_file_out.read_text()) == item_1_expected
+    item_2_expected = {"class_path": f"{__name__}.ListItem", "init_args": {"a": 2, "b": "y"}}
+    assert json_or_yaml_load(item_2_file_out.read_text()) == item_2_expected
+
+
 def test_save_overwrite(example_parser, tmp_cwd):
     cfg = example_parser.parse_args(["--nums.val1=7"])
     example_parser.save(cfg, "config.yaml")

jsonargparse_tests/test_namespace.py

@@ -296,3 +296,35 @@ def test_add_argument_meta_key_error(meta_key, parser):
     with pytest.raises(ValueError) as ctx:
         parser.add_argument(meta_key)
     ctx.match(f'"{meta_key}" not allowed')
+
+
+def test_items_branches_nested():
+    ns = Namespace()
+    ns["a.b"] = 1
+    ns["a.c"] = 2
+    ns["d"] = 3
+
+    items = list(ns.items(branches=True))
+    assert items == [("a", Namespace(b=1, c=2)), ("a.b", 1), ("a.c", 2), ("d", 3)]
+
+    items = list(ns.items(branches=True, nested=False))
+    assert items == [("a", Namespace(b=1, c=2)), ("d", 3)]
+
+    items = list(ns.items(nested=False))
+    assert items == [("d", 3)]
+
+
+def test_keys_branches_nested():
+    ns = Namespace()
+    ns["a.b"] = 1
+    ns["a.c"] = 2
+    ns["d"] = 3
+
+    keys = list(ns.keys(branches=True))
+    assert keys == ["a", "a.b", "a.c", "d"]
+
+    keys = list(ns.keys(branches=True, nested=False))
+    assert keys == ["a", "d"]
+
+    keys = list(ns.keys(nested=False))
+    assert keys == ["d"]