remove superflous and dead code in Python API

src/sophios/api/_types.py

@@ -1,7 +1,5 @@
 """CWL Types."""
 from enum import Enum
-from pathlib import Path
-from typing import Any
 
 
 class CWLTypesEnum(str, Enum):

src/sophios/api/pythonapi.py

@@ -1,7 +1,6 @@
 # pylint: disable=W1203
 """CLT utilities."""
 import logging
-import subprocess as sub
 from pathlib import Path, PurePath
 from typing import Any, ClassVar, Optional, TypeVar, Union, Dict, List
 
@@ -39,9 +38,6 @@ def filter(self, record: logging.LogRecord) -> bool:
 logger_wicad.addFilter(DisableEverythingFilter())
 
 
-_WIC_PATH = Path(__file__).parent.parent.parent.parent  # WIC dir
-
-
 class InvalidInputValueError(Exception):
     pass
 
@@ -461,16 +457,6 @@ def _yml(self) -> dict:
             d["when"] = self.when
         return d
 
-    def _save_cwl(self, path: Path) -> None:
-        cwl_adapters = path.joinpath("cwl_adapters")
-        cwl_adapters.mkdir(exist_ok=True, parents=True)
-        with open(
-            cwl_adapters.joinpath(f"{self.process_name}.cwl"),
-            "w",
-            encoding="utf-8",
-        ) as file:
-            file.write(yaml.dump(self.yaml))
-
     def get_inp_attr(self, __name: str) -> Any:
         """Returns the input object of the given name"""
         return self.inputs[self._input_names.index(__name)]
@@ -647,10 +633,6 @@ def add_output(self, __name: str) -> Any:
         self.outputs.append(out)
         return out
 
-    # def __repr__(self) -> str:
-    #     repr_ = ...
-    #     return repr_
-
     def __setattr__(self, __name: str, __value: Any) -> Any:
         if __name in ["inputs", "outputs", "yaml", "cfg_yaml", "process_name", "_input_names", "_output_names",
                       "__private_attributes__", "__pydantic_private__"]:
@@ -682,25 +664,6 @@ def __getattr__(self, __name: str) -> Any:
         # The same goes for __setattr__ and __delattr__, see: https://github.com/pydantic/pydantic/issues/8643"
         return super().__getattr__(__name)  # type: ignore
 
-    def _save_yaml(self) -> None:
-        _WIC_PATH.mkdir(parents=True, exist_ok=True)
-        self.yml_path = _WIC_PATH.joinpath(f"{self.process_name}.wic")
-        with open(f"{self.process_name}.wic", "w", encoding="utf-8") as file:
-            file.write(yaml.dump(self.yaml))
-
-    def _save_all_cwl(self) -> 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:
-                if isinstance(s, Step):
-                    s._save_cwl(_WIC_PATH)  # pylint: disable=W0212
-            except BaseException as exc:
-                raise exc
-
     def flatten_steps(self) -> list[Step]:
         """Flattens all Steps into a linear list. This is similar, but different, from inlineing.
 
@@ -797,8 +760,6 @@ def get_cwl_workflow(self, args_dict: Dict[str, str] = {}) -> Json:
             "yaml_inputs": yaml_inputs,
             **cwl_ast
         }
-        # delete the skeletal and ephemeral autogenerated folder
-        _ = sub.run(['rm -rf autogenerated'], shell=True, check=False, executable="/bin/bash")
         return workflow_json
 
     def run(self, compile_args_dict: Dict[str, str] = {}, run_args_dict: Dict[str, str] = {}) -> None:

src/sophios/compiler.py

@@ -146,7 +146,7 @@ def compile_workflow_once(yaml_tree_ast: YamlTree,
     (yaml_path_orig, yaml_tree_orig) = copy.deepcopy(yaml_tree_ast)
 
     if not testing:
-        print(' starting', ('  ' * len(namespaces)) + yaml_path)
+        print(' starting compilation of', ('  ' * len(namespaces)) + yaml_path)
 
     # Check for top-level yml dsl args
     wic = {'wic': yaml_tree.get('wic', {})}
@@ -909,7 +909,7 @@ def populate_scalar_val(in_dict: dict) -> Any:
         yaml_inputs.update(new_keyval)
 
     if not testing:
-        print('finishing', ('  ' * len(namespaces)) + yaml_path)
+        print('finishing compilation of', ('  ' * len(namespaces)) + yaml_path)
     # Note: We do not necessarily need to return inputs_workflow.
     # 'Internal' inputs are encoded in yaml_tree. See Comment above.
     node_data = NodeData(namespaces, yaml_stem, yaml_tree_orig, yaml_tree, tool_i, yaml_inputs,