Merge pull request #2 from plonerma/config_output_dir_field

Updated source code to comply with new ruff version

.github/workflows/docs.yml

@@ -10,7 +10,8 @@ on:
 permissions:
   contents: write
 jobs:
-  deploy:
+  deploy_documentation:
+    name: "Deploy documentation to github pages"
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4

.github/workflows/publish.yml

@@ -8,8 +8,8 @@ permissions:
   contents: read
 
 jobs:
-  deploy:
-
+  publish:
+    name: "Publish to PyPI"
     runs-on: ubuntu-latest
 
     environment: release

.github/workflows/tests.yml

@@ -13,7 +13,7 @@ on:
     - "mkdocs.yml"
 
 jobs:
-  run:
+  test:
     name: "Test & Coverage"
     runs-on: ubuntu-latest
     strategy:

pyproject.toml

@@ -76,19 +76,19 @@ python = ["3.8", "3.9", "3.10", "3.11"]
 [tool.hatch.envs.lint]
 detached = true
 dependencies = [
-  "black>=23.1.0",
-  "mypy>=1.0.0",
-  "ruff>=0.0.243",
+  "black>=24.8.0",
+  "mypy>=1.7.0",
+  "ruff>=0.7.0",
 ]
 [tool.hatch.envs.lint.scripts]
 typing = "mypy --install-types --non-interactive {args:src/cordage tests}"
 style = [
-  "ruff {args:.}",
+  "ruff check {args:.}",
   "black --check --diff {args:.}",
 ]
 fmt = [
   "black {args:.}",
-  "ruff --fix {args:.}",
+  "ruff check --fix {args:.}",
   "style",
 ]
 all = [
@@ -104,6 +104,8 @@ skip-string-normalization = true
 [tool.ruff]
 target-version = "py38"
 line-length = 120
+
+[tool.ruff.lint]
 select = [
   "A",
   "ARG",
@@ -148,13 +150,13 @@ unfixable = [
   "F401",
 ]
 
-[tool.ruff.isort]
+[tool.ruff.lint.isort]
 known-first-party = ["cordage"]
 
-[tool.ruff.flake8-tidy-imports]
+[tool.ruff.lint.flake8-tidy-imports]
 ban-relative-imports = "all"
 
-[tool.ruff.per-file-ignores]
+[tool.ruff.lint.per-file-ignores]
 # Tests can use magic values, assertions, and relative imports
 "tests/**/*" = ["PLR2004", "S101", "TID252"]
 

src/cordage/context.py

@@ -10,8 +10,8 @@
 
 from cordage.experiment import Experiment, Series, Trial
 from cordage.global_config import GlobalConfig
+from cordage.util import ConfigClass, logger, nest_items, nested_update, read_dict_from_file
 from cordage.util import from_dict as config_from_dict
-from cordage.util import logger, nest_items, nested_update, read_dict_from_file
 
 
 class MissingType:
@@ -105,7 +105,7 @@ def __init__(
         func: Callable,  # expects a dataclass
         global_config: GlobalConfig,
         description: Optional[str] = None,
-        config_cls: Optional[Type] = None,
+        config_cls: Optional[Type[ConfigClass]] = None,
     ):
         self.global_config = global_config
         self.set_function(func)
@@ -208,6 +208,7 @@ def construct_argument_parser(self):
     def _add_argument_to_parser(self, arg_name: str, arg_type: Any, help: str, **kw):  # noqa: A002
         # If the field is also a dataclass, recurse (nested config)
         if dataclasses.is_dataclass(arg_type):
+            assert isinstance(arg_type, type)
             self.arg_group_config.add_argument(
                 f"--{arg_name}", type=Path, default=MISSING, help=help, metavar="PATH", **kw
             )
@@ -230,7 +231,7 @@ def _add_argument_to_parser(self, arg_name: str, arg_type: Any, help: str, **kw)
             )
 
         elif get_origin(arg_type) is Union:
-            args = [arg for arg in get_args(arg_type) if arg != type(None)]
+            args = [arg for arg in get_args(arg_type) if arg is not type(None)]
 
             if len(args) == 1:
                 # optional
@@ -241,7 +242,7 @@ def _add_argument_to_parser(self, arg_name: str, arg_type: Any, help: str, **kw)
                 raise TypeError(msg)
 
         # Boolean field
-        elif arg_type == bool:
+        elif arg_type is bool:
             # Create a true and a false flag -> the destination is identical
             self.arg_group_config.add_argument(
                 f"--{arg_name}", action="store_true", default=MISSING, help=help + " (set the value to True)", **kw

src/cordage/experiment.py

@@ -25,9 +25,9 @@
     Set,
     Tuple,
     Type,
+    TypedDict,
     TypeVar,
     Union,
-    cast,
     overload,
 )
 
@@ -38,26 +38,49 @@
 except ImportError:
     colorlog = None  # type: ignore
 
+import typing
+
 from cordage.global_config import GlobalConfig
-from cordage.util import config_output_dir_type, flattened_items, from_dict, logger, nest_items, nested_update, to_dict
+from cordage.util import (
+    config_output_dir_type,
+    flattened_items,
+    from_dict,
+    logger,
+    nest_items,
+    nested_update,
+    to_dict,
+)
+
+if typing.TYPE_CHECKING:
+    from _typeshed import DataclassInstance
+
+
+ConfigClass = TypeVar("ConfigClass", bound="DataclassInstance")
+
+
+class SeriesConfiguration(TypedDict):
+    base_config: "DataclassInstance"
+    series_spec: Union[List[Dict], Dict[str, List], None]
+    series_skip: Optional[int]
 
-T = TypeVar("T")
+
+Configuration = TypeVar("Configuration", SeriesConfiguration, "DataclassInstance")
 
 
 @dataclass
-class Metadata:
+class Metadata(Generic[Configuration]):
     function: str
 
     global_config: GlobalConfig
 
+    configuration: Union[Configuration, Dict[str, Any]]
+
     output_dir: Optional[Path] = None
     status: str = "pending"
 
     start_time: Optional[datetime] = None
     end_time: Optional[datetime] = None
 
-    configuration: Any = None
-
     result: Any = None
 
     parent_dir: Optional[Path] = None
@@ -85,10 +108,12 @@ def from_dict(cls, data: Mapping):
         return from_dict(cls, data)
 
 
-class MetadataStore:
+class MetadataStore(Generic[Configuration]):
     _warned_deprecated_nested_global_config: bool = False
 
-    def __init__(self, metadata: Optional[Metadata] = None, /, global_config: Optional[GlobalConfig] = None, **kw):
+    def __init__(
+        self, metadata: Optional[Metadata[Configuration]] = None, /, global_config: Optional[GlobalConfig] = None, **kw
+    ):
         self.metadata: Metadata
 
         if metadata is not None:
@@ -209,7 +234,7 @@ def load_metadata(cls, path: PathLike) -> Metadata:
         return metadata
 
 
-class Annotatable(MetadataStore):
+class Annotatable(MetadataStore[Configuration]):
     TAG_PATTERN = re.compile(r"\B#(\w*[a-zA-Z]+\w*)")
 
     def __init__(self, *args, **kw):
@@ -262,7 +287,7 @@ def load_annotations(self):
                 self.annotations = json.load(fp)
 
 
-class Experiment(Annotatable):
+class Experiment(Annotatable[Configuration]):
     def __init__(self, *args, **kwargs):
         super().__init__(*args, **kwargs)
 
@@ -359,7 +384,7 @@ def synchronize(self):
         return self
 
     @classmethod
-    def from_path(cls, path: PathLike, config_cls: Optional[Type] = None):
+    def from_path(cls, path: PathLike, config_cls: Optional[Type[ConfigClass]] = None):
         metadata: Metadata = cls.load_metadata(path)
 
         experiment: Experiment
@@ -448,12 +473,12 @@ def teardown_log(self):
             logger.removeHandler(handler)
 
 
-class Trial(Generic[T], Experiment):
+class Trial(Experiment["DataclassInstance"], Generic[ConfigClass]):
     def __init__(
         self,
-        metadata: Optional[Metadata] = None,
+        metadata: Optional[Metadata["DataclassInstance"]] = None,
         /,
-        config: Optional[T] = None,
+        config: Optional[ConfigClass] = None,
         **kw,
     ):
         if metadata is not None:
@@ -466,7 +491,13 @@ def __init__(
             super().__init__(configuration=config, **kw)
 
     @property
-    def config(self) -> T:
+    def config(self) -> ConfigClass:
+        if isinstance(self.metadata.configuration, dict):
+            msg = (
+                "`trial.config` is only available if the configuration was loaded with a configuration dataclass "
+                "(you could use `trial.metadata.configuration` instead)."
+            )
+            raise AttributeError(msg)
         return self.metadata.configuration
 
     def set_output_dir(self, path: Path):
@@ -479,12 +510,12 @@ def set_output_dir(self, path: Path):
         logging.info("Config: %s", self.metadata.configuration)
 
 
-class Series(Generic[T], Experiment):
+class Series(Generic[ConfigClass], Experiment[SeriesConfiguration]):
     def __init__(
         self,
         metadata: Optional[Metadata] = None,
         /,
-        base_config: Optional[T] = None,
+        base_config: Optional[ConfigClass] = None,
         series_spec: Union[List[Dict], Dict[str, List], None] = None,
         series_skip: Optional[int] = None,
         **kw,
@@ -502,7 +533,7 @@ def __init__(
 
         self.validate_series_spec()
 
-        self.trials: Optional[List[Trial[T]]] = None
+        self.trials: Optional[List[Trial[ConfigClass]]] = None
         self.make_all_trials()
 
     def set_output_dir(self, path: Path):
@@ -534,7 +565,7 @@ def only_list_nodes(d):
             assert series_spec is None
 
     @property
-    def base_config(self) -> T:
+    def base_config(self) -> ConfigClass:
         return self.metadata.configuration["base_config"]
 
     @property
@@ -565,12 +596,10 @@ def __exit__(self, *args):
         # else: do nothing
 
     @overload
-    def get_changing_fields(self, sep: Literal[None] = None) -> Set[Tuple[Any, ...]]:
-        ...
+    def get_changing_fields(self, sep: Literal[None] = None) -> Set[Tuple[Any, ...]]: ...
 
     @overload
-    def get_changing_fields(self, sep: str) -> Set[str]:
-        ...
+    def get_changing_fields(self, sep: str) -> Set[str]: ...
 
     def get_changing_fields(self, sep: Optional[str] = None) -> Union[Set[Tuple[Any, ...]], Set[str]]:
         keys: Set = set()
@@ -663,11 +692,11 @@ def make_all_trials(self):
 
                 nested_update(trial_config_data, trial_update)
 
-                trial_config: T
+                trial_config: ConfigClass
                 if isinstance(self.base_config, dict):
-                    trial_config = cast(T, trial_config_data)
+                    trial_config = trial_config_data
                 else:
-                    trial_config = cast(T, from_dict(type(self.base_config), trial_config_data))
+                    trial_config = from_dict(type(self.base_config), trial_config_data)
 
                 if i < self.series_skip:
                     status = "skipped"
@@ -680,7 +709,7 @@ def make_all_trials(self):
     def __iter__(self):
         return self.get_all_trials(include_skipped=False)
 
-    def get_all_trials(self, *, include_skipped: bool = False) -> Generator[Trial[T], None, None]:
+    def get_all_trials(self, *, include_skipped: bool = False) -> Generator[Trial[ConfigClass], None, None]:
         assert self.trials is not None
 
         if not self.is_singular: