Merge pull request #58 from flaxandteal/fix/mypy-hook-errors-for-new-…

…devs

Mypy Errors Triggered in Local Development

.gitignore

@@ -129,6 +129,7 @@ ENV/
 env.bak/
 venv.bak/
 .pixi/
+.vscode/
 
 # Spyder project settings
 .spyderproject

.pre-commit-config.yaml

@@ -11,12 +11,17 @@ repos:
     hooks:
       # Run the linter.
       - id: ruff
-        args: [ --fix ]
+        args: [--fix]
       # Run the formatter.
       - id: ruff-format
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.9.0
+    rev: v1.8.0
     hooks:
       - id: mypy
-        args: [--strict, --install-types, --non-interactive]
-        additional_dependencies: [sympy, attrs, pytest, click, dask]
+        args: [
+          --strict,
+          --install-types,
+          --allow-subclassing-any,
+          --non-interactive,
+        ]
+        additional_dependencies: [sympy, attrs, pytest, click, dask]

src/dewret/__main__.py

@@ -133,7 +133,7 @@ def render(
     if output == "-":
 
         @contextmanager
-        def _opener(key: str, _: str) -> Generator[IO[Any], None, None]:
+        def _opener(key: str, mode: str) -> Generator[IO[Any], None, None]:
             print(" ------ ", key, " ------ ")
             yield sys.stdout
             print()

src/dewret/core.py

@@ -48,7 +48,8 @@
 BasicType = str | float | bool | bytes | int | None
 RawType = BasicType | list["RawType"] | dict[str, "RawType"]
 FirmType = RawType | list["FirmType"] | dict[str, "FirmType"] | tuple["FirmType", ...]
-ExprType = (FirmType | Basic | list["ExprType"] | dict[str, "ExprType"] | tuple["ExprType", ...]) # type: ignore
+# Basic is from Sympy, which does not have type annotations, so ExprType cannot pass mypy
+ExprType = (FirmType | Basic | list["ExprType"] | dict[str, "ExprType"] | tuple["ExprType", ...]) # type: ignore # fmt: skip
 
 U = TypeVar("U")
 T = TypeVar("T")

src/dewret/renderers/cwl.py

@@ -284,12 +284,15 @@ def from_step(cls, step: BaseStep) -> "StepDefinition":
         Args:
             step: step to convert.
         """
+        out: list[str] | dict[str, "CommandInputSchema"]
+        if attrs_has(step.return_type) or (is_dataclass(step.return_type) and isclass(step.return_type)):
+            out = to_output_schema("out", step.return_type)["fields"]
+        else:
+            out = ["out"]
         return cls(
             name=step.name,
             run=step.task.name,
-            out=(to_output_schema("out", step.return_type)["fields"])
-            if attrs_has(step.return_type) or is_dataclass(step.return_type)
-            else ["out"],
+            out=out,
             in_={
                 key: (
                     ReferenceDefinition.from_reference(param)
@@ -463,13 +466,14 @@ def to_output_schema(
             for field in attrs_fields(typ)
         }
     elif is_dataclass(typ):
-        fields = {
-            str(field.name): cast(
-                CommandInputSchema, to_output_schema(field.name, field.type)
-            )
-            for field in dataclass_fields(typ)
-        }
-
+        fields = {}
+        for field in dataclass_fields(typ):
+            if isinstance(field.type, type) and issubclass(field.type, RawType | AttrsInstance | DataclassProtocol):
+                fields[str(field.name)] = cast(
+                    CommandInputSchema, to_output_schema(field.name, field.type)
+                )
+            else:
+                raise TypeError("Types of fields in results must also be valid result-types themselves (string-defined types not currently allowed)")
     if fields:
         output = CommandOutputSchema(
             type="record",

src/dewret/workflow.py

@@ -928,7 +928,11 @@ def find_field(self: FieldableProtocol, field: str | int, fallback_type: type |
                     type_hints = get_type_hints(parent_type, localns={parent_type.__name__: parent_type}, include_extras=True)
                     field_type = type_hints.get(field)
                     if field_type is None:
-                        field_type = next(iter(filter(lambda fld: fld.name == field, dataclass_fields(parent_type)))).type
+                        dataclass_field_type = next(iter(filter(lambda fld: fld.name == field, dataclass_fields(parent_type)))).type
+                        if isinstance(dataclass_field_type, str):
+                            # TODO: we could ask Python to resolve the str expression for us
+                            raise TypeError("Dataclass fields must be provided as types directly, not str")
+                        field_type = dataclass_field_type
                 except StopIteration:
                     raise AttributeError(f"Dataclass {parent_type} does not have field {field}") from None
             elif attr_has(parent_type):