Ensure cli types are yaml serializable

snakebids/cli.py

@@ -12,6 +12,7 @@
 from typing_extensions import override
 
 from snakebids.exceptions import ConfigError, MisspecifiedCliFilterError
+from snakebids.io.yaml import get_yaml_io
 from snakebids.types import InputsConfig, OptionalFilter
 from snakebids.utils.utils import to_resolved_path
 
@@ -204,7 +205,7 @@ def create_parser(include_snakemake: bool = False) -> argparse.ArgumentParser:
     return parser
 
 
-def _find_type(name: str) -> type[Any]:
+def _find_type(name: str, *, yamlsafe: bool = True) -> type[Any]:
     import importlib
 
     if name == "Path":
@@ -218,6 +219,9 @@ def _find_type(name: str) -> type[Any]:
     if not callable(type_):
         msg = f"{name} cannot be used as a type"
         raise ConfigError(msg)
+    if yamlsafe and type_ not in get_yaml_io().representer.yaml_representers:
+        msg = f"{name} cannot be serialized into yaml"
+        raise ConfigError(msg)
     return type_
 
 

snakebids/tests/test_cli.py

@@ -24,7 +24,6 @@
 from snakebids.tests import strategies as sb_st
 from snakebids.tests.helpers import allow_function_scoped
 from snakebids.types import InputsConfig, OptionalFilter
-from snakebids.utils.utils import BidsEntity
 
 from .mock.config import parse_args, pybids_inputs
 
@@ -224,25 +223,17 @@ def test_convert_arg_to_builtin(
         args = parser.parse_args()
         assert isinstance(args.new_param, int)
 
-    def test_convert_arg_to_resolved_object(
-        self, parser: ArgumentParser, mocker: MockerFixture
-    ):
+    def test_non_serialiable_type_raises_error(self, parser: ArgumentParser):
         new_args = {
             "--new-param": {
                 "help": "Generic Help Message",
                 "type": "snakebids.utils.utils.BidsEntity",
             }
         }
-        mocker.patch.object(
-            sys, "argv", [*self.mock_all_args, "--new-param", "subject"]
-        )
-        add_dynamic_args(parser, new_args, {})
-        args = parser.parse_args()
-        assert isinstance(args.new_param, BidsEntity)
+        with pytest.raises(ConfigError, match="cannot be serialized into yaml"):
+            add_dynamic_args(parser, new_args, {})
 
-    def test_using_module_as_type_gives_error(
-        self, parser: ArgumentParser, mocker: MockerFixture
-    ):
+    def test_using_module_as_type_gives_error(self, parser: ArgumentParser):
         new_args = {
             "--new-param": {
                 "help": "Generic Help Message",
@@ -252,9 +243,7 @@ def test_using_module_as_type_gives_error(
         with pytest.raises(ConfigError, match="cannot be used as a type"):
             add_dynamic_args(parser, new_args, {})
 
-    def test_using_class_method_as_type_gives_error(
-        self, parser: ArgumentParser, mocker: MockerFixture
-    ):
+    def test_using_class_method_as_type_gives_error(self, parser: ArgumentParser):
         new_args = {
             "--new-param": {
                 "help": "Generic Help Message",