🐛 fix choices

src/snk_cli/dynamic_typer.py

@@ -149,15 +149,13 @@ def _create_cli_parameter(self, option: Option):
         """
         annotation_type = option.type
         default = option.default
-        if option.type is Enum or option.choices:
-            if not option.choices:
-                raise ValueError(f"Enum type {option.name} requires choices to be defined.")
-            annotation_type = Enum(f'{option.name}', {str(e): str(e) for e in option.choices})
+        if option.choices:
+            annotation_type = Enum(f'{option.name}', {str(e): annotation_type(e) for e in option.choices})
             if default:
               try:
                 default = annotation_type(default)
               except ValueError:
-                raise ValueError(f"Default value {default} for option {option.name} is not a valid choice.")
+                raise ValueError(f"Default value '{default}' for option '{option.name}' is not a valid choice.")
         return Parameter(
             option.name,
             kind=Parameter.POSITIONAL_OR_KEYWORD,

src/snk_cli/options/utils.py

@@ -63,7 +63,10 @@ def create_option_from_annotation(
     updated = False
     if config_default is None or default != config_default:
         updated = True
-    annotation_type = annotation_values.get(f"{annotation_key}:type", get_default_type(default)).lower()
+    annotation_type = annotation_values.get(f"{annotation_key}:type", None) 
+    if annotation_type is not None: 
+        assert annotation_type in types, f"Type '{annotation_type}' not supported."
+    annotation_type = annotation_type or get_default_type(default)
     annotation_type = types.get(
         annotation_type, List[str] if "list" in annotation_type else str
     )
@@ -75,6 +78,9 @@ def create_option_from_annotation(
     default=annotation_values.get(f"{annotation_key}:default", default)
     if default and get_origin(annotation_type) is tuple:
         assert len(default) == 2, f"Default value ({default}) for '{annotation_key}' should be a list of length 2."
+    choices = annotation_values.get(f"{annotation_key}:choices", None)
+    if choices:
+        assert isinstance(choices, list), f"Choices should be a list for '{annotation_key}'."
     return Option(
         name=name,
         original_key=annotation_key,

src/snk_cli/utils.py

@@ -98,6 +98,10 @@ def serialise(d):
     if isinstance(d, Path) or isinstance(d, datetime):
         return str(d)
 
+    # check enum type
+    if hasattr(d, "value"):
+        return d.value
+
     if isinstance(d, tuple):
         return list(d) 
 

tests/test_cli/test_snk_config.py

@@ -44,7 +44,7 @@ def test_non_standard_configfile(tmp_path):
     assert "config2" in res.stdout, res.stderr
 
 def test_snk_config_with_enums(tmp_path):
-    runner = dynamic_runner({}, SnkConfig(cli={"test": {"choices": ["enum1", "enum2"], "type": "enum"}}), tmp_path=tmp_path)
+    runner = dynamic_runner({}, SnkConfig(cli={"test": {"choices": ["enum1", "enum2"], "type": "str"}}), tmp_path=tmp_path)
     res = runner.invoke(["run", "--help"])
     assert res.exit_code == 0, res.stderr
     assert "enum1" in res.stdout, res.stderr

tests/test_types.py

@@ -140,3 +140,19 @@ def test_pair(snakemake_config, annotations, cli_args, expected):
     res = runner.invoke(["run"] + cli_args)
     assert res.exit_code == 0, res.stderr
     assert expected in res.stdout, res.stderr
+
+@pytest.mark.parametrize("snakemake_config,annotations,cli_args,expected", [
+    # choices
+    (
+        {"example": 1},
+        {"example": {"type": "int", "choices": [1, 2, 3]}},
+        ["--example", 1],
+        "{'example': 1}"
+    ) 
+    ])
+def test_choices(snakemake_config, annotations, cli_args, expected):
+    snk_config = SnkConfig(cli=annotations)
+    runner = dynamic_runner(snakemake_config, snk_config)
+    res = runner.invoke(["run"] + cli_args)
+    assert res.exit_code == 0, res.stderr
+    assert expected in res.stdout, res.stderr