linting

cstar/base/additional_code.py

@@ -50,13 +50,14 @@ class AdditionalCode:
        Verify whether the files associated with this AdditionalCode instance can be found at `local_dir`
     """
 
-    def __init__(self,
-                 base_model: BaseModel,
-                 location: str,
-                 subdir: str = "",
-                 checkout_target: Optional[str] = None,
-                 source_mods: Optional[List[str]] = None,
-                 namelists: Optional[List[str]] = None,
+    def __init__(
+        self,
+        base_model: BaseModel,
+        location: str,
+        subdir: str = "",
+        checkout_target: Optional[str] = None,
+        source_mods: Optional[List[str]] = None,
+        namelists: Optional[List[str]] = None,
     ):
         """
         Initialize an AdditionalCode object from a DataSource  and a list of code files
@@ -177,7 +178,7 @@ def get(self, local_dir: str | Path) -> None:
                 (self.source.source_type == "directory")
                 or (self.source.source_type == "repository")
             ):
-                source_dir = Path(self.source.location)/self.subdir
+                source_dir = Path(self.source.location) / self.subdir
 
             else:
                 raise ValueError(
@@ -195,11 +196,11 @@ def get(self, local_dir: str | Path) -> None:
 
                 if file_list is None:
                     continue
-                (local_dir/file_type).mkdir(parents=True, exist_ok=True)
+                (local_dir / file_type).mkdir(parents=True, exist_ok=True)
 
                 for f in file_list:
                     src_file_path = source_dir / f
-                    tgt_file_path = local_dir / file_type/ Path(f).name
+                    tgt_file_path = local_dir / file_type / Path(f).name
                     print(f"copying {src_file_path} to {tgt_file_path}")
                     if src_file_path.exists():
                         shutil.copy(src_file_path, tgt_file_path)

cstar/case.py

@@ -660,7 +660,9 @@ def setup(self) -> None:
 
             # Get AdditionalCode
             if component.additional_code is not None:
-                component.additional_code.get(self.caseroot/"additional_code"/component.base_model.name)
+                component.additional_code.get(
+                    self.caseroot / "additional_code" / component.base_model.name
+                )
 
             # Get InputDatasets
             # tgt_dir=self.caseroot+'/input_datasets/'+component.base_model.name

cstar/roms/component.py

@@ -232,7 +232,7 @@ def run(
         self,
         n_time_steps: Optional[int] = None,
         account_key: Optional[str] = None,
-        output_dir: Optional[str] = None,
+        output_dir: Optional[str | Path] = None,
         walltime: Optional[str] = _CSTAR_SYSTEM_MAX_WALLTIME,
         job_name: str = "my_roms_run",
     ) -> None:
@@ -264,6 +264,10 @@ def run(
             )
         if output_dir is None:
             output_dir = self.exe_path.parent
+        output_dir = Path(output_dir)
+
+        # Set run path to output dir for clarity: we are running in the output dir but
+        # these are conceptually different:
         run_path = output_dir
 
         if self.additional_code is None: