feat: add overwrite

src/wic/api/pythonapi.py

@@ -281,9 +281,13 @@ def _yml(self) -> dict:
         }
         return d
 
-    def _save_cwl(self, path: Path) -> None:
+    def _save_cwl(self, path: Path, overwrite: bool) -> None:
         cwl_adapters = path.joinpath("cwl_adapters")
         cwl_adapters.mkdir(exist_ok=True, parents=True)
+        if not overwrite:
+            if cwl_adapters.joinpath(f"{self.clt_name}.cwl").exists():
+                return
+        # does not exist:
         with open(
             cwl_adapters.joinpath(f"{self.clt_name}.cwl"),
             "w",
@@ -299,7 +303,8 @@ def _save_cwl(self, path: Path) -> None:
 class Workflow:
     steps: list[Step]
     name: str
-    yml_path: Optional[Path] = field(default=None, init=False, repr=False)
+    path: Path = field(default=Path.cwd())
+    yml_path: Optional[Path] = field(default=None, init=False, repr=False)  # pylint: disable=E3701
 
     def __post_init__(self) -> None:
         for s in self.steps:
@@ -309,6 +314,7 @@ def __post_init__(self) -> None:
                 raise InvalidStepError(
                     f"{s.clt_name} is missing required inputs"
                 ) from exc
+        self.path.joinpath(self.name).mkdir(parents=True, exist_ok=True)
 
     def append(self, step_: Step) -> None:
         """Append step to Workflow."""
@@ -328,25 +334,36 @@ def _save_yaml(self) -> None:
         with open(self.yml_path, "w", encoding="utf-8") as file:
             file.write(yaml.dump(self.yaml))
 
-    def _save_all_cwl(self) -> None:
+       # copy to wf path, only informational, not used by WIC
+        with open(self.path.joinpath(self.name, f"{self.name}.yml"), "w", encoding="utf-8") as file:
+            file.write(yaml.dump(self.yaml))
+
+    def _save_all_cwl(self, overwrite: bool) -> None:
         """Save CWL files to cwl_adapters.
 
         This is necessary for WIC to compile the workflow.
         """
         _WIC_PATH.mkdir(parents=True, exist_ok=True)
         for s in self.steps:
             try:
-                s._save_cwl(_WIC_PATH)  # pylint: disable=W0212
+                s._save_cwl(_WIC_PATH, overwrite)  # pylint: disable=W0212
+            except BaseException as exc:
+                raise exc
+
+       # copy to wf path, only informational, not used by WIC
+        for s in self.steps:
+            try:
+                s._save_cwl(self.path.joinpath(self.name), overwrite)  # pylint: disable=W0212
             except BaseException as exc:
                 raise exc
 
-    def compile(self, run_local: bool = False) -> Path:
+    def compile(self, run_local: bool = False, overwrite: bool = False) -> Path:
         """Compile Workflow using WIC.
 
         Returns path to compiled CWL Workflow.
         """
 
-        self._save_all_cwl()
+        self._save_all_cwl(overwrite)
         self._save_yaml()
         logger.info(f"Compiling {self.name}")
         args = ["wic", "--yaml", f"{self.name}.yml"]
@@ -366,9 +383,12 @@ def compile(self, run_local: bool = False) -> Path:
             logger.info(exc.stdout)
             raise exc
         logger.info(proc.stdout)
-        return _WIC_PATH.joinpath("autogenerated", f"{self.name}.cwl")
+        # copy files to wf path
+        compiled_cwl_path = _WIC_PATH.joinpath("autogenerated", f"{self.name}.cwl")
+        self.path.joinpath(self.name, f"{self.name}.cwl").symlink_to(compiled_cwl_path)
+        return compiled_cwl_path
 
-    def run(self) -> None:
+    def run(self, overwrite: bool = False) -> None:
         """Run compiled workflow."""
         logger.info(f"Running {self.name}")
-        self.compile(run_local=True)
+        self.compile(run_local=True, overwrite=overwrite)