fix(pythonapi): automatic WIC path in Workflow class

src/wic/api/pythonapi.py

@@ -1,3 +1,4 @@
+# pylint: disable=W1203
 """CLT utilities."""
 import logging
 import subprocess
@@ -17,12 +18,17 @@
 from wic.api._types import CWL_TYPES_DICT
 
 if PYDANTIC_V2:
-    from pydantic import ConfigDict, field_validator
+    from pydantic import (  # type: ignore # pylint: disable=E0611, C0412
+        ConfigDict,
+        field_validator,
+    )
 else:
     from pydantic import validator
 
 logger = logging.getLogger("WIC Python API")
 
+_WIC_PATH = Path(__file__).parent.parent.parent.parent  # WIC dir
+
 
 class InvalidInputValueError(Exception):
     pass
@@ -330,16 +336,18 @@ def _save_cwl(self, path: Path) -> None:
             file.write(yaml.dump(self.yaml))
 
 
-@pydantic_dataclass
+if PYDANTIC_V2:
+    DATACLASS_CONFIG = ConfigDict(validate_assignment=True)
+else:
+    # mypy marks this incorrect if Pydantic V2
+    DATACLASS_CONFIG = ConfigDict(validate_on_init=True, validate_assignment=True)  # type: ignore
+
+
+@pydantic_dataclass(config=DATACLASS_CONFIG)
 class Workflow:
     steps: list[Step]
     name: str
-    path: Path
-    if PYDANTIC_V2:
-        yml_path: Path = field(init=False, repr=False)  # pylint: disable=E3701
-    else:
-        # mypy incorrectly marks this as redef
-        yml_path: Optional[Path] = field(init=False, default=None, repr=False)  # type: ignore # pylint: disable=E3701
+    yml_path: Optional[Path] = field(default=None, init=False, repr=False)  # pylint: disable=E3701
 
     def __post_init__(self) -> None:
         for s in self.steps:
@@ -350,8 +358,10 @@ def __post_init__(self) -> None:
                     f"{s.clt_name} is missing required inputs"
                 ) from exc
 
-    def step(self, step_: Step) -> None:
+    def append(self, step_: Step) -> None:
         """Append step to Workflow."""
+        if not isinstance(step_, Step):
+            raise TypeError("step must be a Step")
         self.steps.append(step_)
 
     @property
@@ -361,8 +371,8 @@ def yaml(self) -> dict[str, Any]:
         return d
 
     def _save_yaml(self) -> None:
-        self.path.mkdir(parents=True, exist_ok=True)
-        self.yml_path = self.path.joinpath(f"{self.name}.yml")
+        _WIC_PATH.mkdir(parents=True, exist_ok=True)
+        self.yml_path = _WIC_PATH.joinpath(f"{self.name}.yml")
         with open(self.yml_path, "w", encoding="utf-8") as file:
             file.write(yaml.dump(self.yaml))
 
@@ -371,15 +381,19 @@ def _save_all_cwl(self) -> None:
 
         This is necessary for WIC to compile the workflow.
         """
-        self.path.mkdir(parents=True, exist_ok=True)
+        _WIC_PATH.mkdir(parents=True, exist_ok=True)
         for s in self.steps:
             try:
-                s._save_cwl(self.path)  # pylint: disable=W0212
+                s._save_cwl(_WIC_PATH)  # pylint: disable=W0212
             except BaseException as exc:
                 raise exc
 
     def compile(self, run_local: bool = False) -> Path:
-        """Compile Workflow using WIC."""
+        """Compile Workflow using WIC.
+
+        Returns path to compiled CWL Workflow.
+        """
+
         self._save_all_cwl()
         self._save_yaml()
         logger.info(f"Compiling {self.name}")
@@ -390,7 +404,7 @@ def compile(self, run_local: bool = False) -> Path:
             proc = subprocess.run(
                 args=args,
                 capture_output=True,
-                cwd=self.path,
+                cwd=_WIC_PATH,
                 check=True,
                 text=True,
                 universal_newlines=True,
@@ -400,7 +414,7 @@ def compile(self, run_local: bool = False) -> Path:
             logger.info(exc.stdout)
             raise exc
         logger.info(proc.stdout)
-        return self.path.joinpath("autogenerated", f"{self.name}.cwl")
+        return _WIC_PATH.joinpath("autogenerated", f"{self.name}.cwl")
 
     def run(self) -> None:
         """Run compiled workflow."""