Annotated function can be called directly

docs/test_docs.py

@@ -0,0 +1,12 @@
+from docs import GetRegistryLink
+
+
+def test_registry_link():
+    assert (
+        GetRegistryLink()('lir.config.substitution.parse_categorical')
+        == ':class:`lir.config.substitution.parse_categorical <lir.config.substitution.CategoricalHyperparameter>`'
+    )
+    assert (
+        GetRegistryLink()('hyperparameter_types.categorical')
+        == ':class:`hyperparameter_types.categorical <lir.config.substitution.CategoricalHyperparameter>`'
+    )

lir/config/base.py

@@ -1,4 +1,5 @@
 import inspect
+import warnings
 from abc import ABC, abstractmethod
 from collections.abc import Callable, Iterator, Mapping, Sequence
 from dataclasses import dataclass
@@ -627,6 +628,15 @@ def parse(
         ) -> Any:
             return func(config, output_dir)  # type: ignore
 
+        def __call__(self, config: ConfigValue | None = None, output_dir: Path | None = None) -> Any:
+            if config and output_dir:
+                return self.parse(config, output_dir)
+            else:
+                warnings.warn(
+                    DeprecationWarning('legacy invocation of annotated function (remove parentheses)'), stacklevel=2
+                )
+                return self
+
         def reference(self) -> str:
             # return the reference argument, if any
             if reference is not None:
@@ -643,7 +653,7 @@ def reference(self) -> str:
             # last resort: fallback to wrapped function name
             return get_full_name(func)
 
-    return ConfigParserFunction
+    return ConfigParserFunction()
 
 
 def pop_field(

lir/config/substitution.py

@@ -225,8 +225,8 @@ def _parse_categorical_option(spec: Any, path: str, option_index: int | None) ->
     return HyperparameterOption(name, {path: value})
 
 
-@config_parser(reference='lir.config.substitution.parse_categorical')
-def parse_categorical(spec: ConfigValue, output_path: Path) -> 'CategoricalHyperparameter':
+@config_parser
+def parse_categorical(spec: ConfigValue, output_path: Path) -> CategoricalHyperparameter:
     """
     Parse a categorical hyperparameter from configuration.
 
@@ -282,7 +282,7 @@ def _parse_clustered_option(spec: ConfigValue) -> HyperparameterOption:
     return HyperparameterOption(option_name, substitutions)
 
 
-@config_parser(reference='lir.config.substitution.parse_clustered')
+@config_parser
 def parse_clustered(spec: ConfigValue, output_path: Path) -> CategoricalHyperparameter:
     """
     Parse the configuration section of a clustered hyperparameter.
@@ -316,7 +316,7 @@ def parse_clustered(spec: ConfigValue, output_path: Path) -> CategoricalHyperpar
     return CategoricalHyperparameter(parameter_name, options)
 
 
-@config_parser(reference='lir.config.substitution.parse_constant')
+@config_parser
 def parse_constant(spec: ConfigValue, output_path: Path) -> CategoricalHyperparameter:
     """
     Parse the configuration section of a constant.
@@ -400,8 +400,8 @@ def options(self) -> list[HyperparameterOption]:
         return [HyperparameterOption(str(value), {self.path: value}) for value in values]
 
 
-@config_parser(reference='lir.config.substitution.parse_float')
-def parse_float(spec: ConfigValue, output_path: Path) -> 'FloatHyperparameter':
+@config_parser
+def parse_float(spec: ConfigValue, output_path: Path) -> FloatHyperparameter:
     """
     Parse a floating-point hyperparameter from configuration.
 
@@ -514,8 +514,8 @@ def options(self) -> list[HyperparameterOption]:
         return options
 
 
-@config_parser(reference='lir.config.substitution.parse_folder')
-def parse_folder(spec: ConfigValue, output_path: Path) -> 'FolderHyperparameter':
+@config_parser
+def parse_folder(spec: ConfigValue, output_path: Path) -> FolderHyperparameter:
     """
     Parse a folder hyperparameter from configuration.
 
@@ -564,13 +564,13 @@ def parse_parameter(
 
         parser = registry.get(parameter_type, search_path=['hyperparameter_types'])
     elif 'value' in spec:
-        parser = parse_constant()  # type: ignore
+        parser = parse_constant  # type: ignore
     elif 'options' in spec and 'path' in spec:
-        parser = parse_categorical()  # type: ignore
+        parser = parse_categorical  # type: ignore
     elif 'options' in spec and 'name' in spec:
-        parser = parse_clustered()  # type: ignore
+        parser = parse_clustered  # type: ignore
     elif 'high' in spec:
-        parser = parse_float()  # type: ignore
+        parser = parse_float  # type: ignore
     else:
         raise YamlParseError(
             spec.context,

pyproject.toml

@@ -119,15 +119,10 @@ lint.select = [
     "S",    # bandit
     "PIE",  # flake8-pie
 ]
-lint.per-file-ignores = {"tests/*" = [
-        "D",     # Ignore missing docstrings in tests.
-        "S101",  # Allow use of assert in tests.
-    ], "*_test.py" = [
-        "D",     # Ignore missing docstrings in tests.
-        "S101",  # Allow use of assert in tests.
-    ], "docs/snippets/*.py" = [
-        "D",     # Ignore missing  docstrings in snippets.
-    ]} 
+lint.per-file-ignores = {"!lir/*" = [
+    "D",     # Ignore missing docstrings in tests.
+    "S101",  # Allow use of assert in tests.
+]} 
 lint.pydocstyle.convention = "numpy"
 
 [tool.mypy]

tests/algorithms/test_bootstraps.py

@@ -125,4 +125,4 @@ def test_interval_extrapolation(sample_steps_and_data):
 )
 def test_bootstrap_config(config):
     config = ConfigValue.wrap([], config)
-    bootstrap().parse(config, Path('/'))
+    bootstrap(config, Path('/'))

tests/config/test_base.py

@@ -129,9 +129,11 @@ def my_config_parser(config: ConfigValue, output_path: Path) -> int:
     return pop_field(config, 'key', validate_type=int)
 
 
+@pytest.mark.filterwarnings('ignore:legacy')
 def test_config_parser():
     config = ConfigValue.wrap([], {'key': 42})
-    assert my_config_parser().parse(config, Path('/')) == 42
+    assert my_config_parser(config.clone(), Path('/')) == 42
+    assert my_config_parser().parse(config.clone(), Path('/')) == 42
 
 
 def test_generic_config_parser():

tests/datasets/test_csv_parser.py

@@ -156,7 +156,7 @@ def test_csv_parser(
     parser_args['file'] = str(csv_file)
     parser_args = ConfigValue.wrap([], parser_args)
     try:
-        parser = feature_data_csv_file_parser().parse(parser_args, tmp_path)
+        parser = feature_data_csv_file_parser(parser_args, tmp_path)
         actual_result = parser.get_instances()
         if expected_result is not None:
             assert actual_result == expected_result
@@ -173,7 +173,7 @@ def test_csv_parser_label_column_alias_warns(tmp_path: Path):
 
     parser_args = ConfigValue.wrap([], {'label_column': 'label', 'file': str(csv_file)})
     with pytest.warns(UserWarning, match='label_column'):
-        parser = feature_data_csv_file_parser().parse(parser_args, tmp_path)
+        parser = feature_data_csv_file_parser(parser_args, tmp_path)
     actual_result = parser.get_instances()
 
     assert actual_result == FeatureData(hypothesis=np.array([1]), features=np.ones((1, 2)))