adding a routine to check runner's arguments and pipeline management argument don't collide

src/pypelines/__init__.py

-__version__ = "0.0.45"
+__version__ = "0.0.46"
 
 from . import loggs
 from .pipes import *

src/pypelines/celery_tasks.py

@@ -51,7 +51,6 @@ class CeleryAlyxTaskManager(BaseStepTaskManager):
                 try:
                     session = task.get_session()
                     application = task.get_application()
-                    arguments = task.arguments
 
                     with LogTask(task) as log_object:
                         logger = log_object.logger
@@ -63,13 +62,8 @@ class CeleryAlyxTaskManager(BaseStepTaskManager):
                             step: "BaseStep" = (
                                 application.pipelines[task.pipeline_name].pipes[task.pipe_name].steps[task.step_name]
                             )
-                            if arguments.get("refresh", False) or arguments.get("refresh_requirements", []):
-                                skip = False
-                            else:
-                                skip = True
-                            arguments.pop(skip)
 
-                            step.generate(session, extra=extra, skip=skip, check_requirements=True, **task.arguments)
+                            step.generate(session, extra=extra, **task.arguments, **task.management_arguments)
                             task.status_from_logs(log_object)
                         except Exception as e:
                             traceback_msg = format_traceback_exc()
@@ -157,8 +151,34 @@ class CeleryTaskRecord(dict):
 
     @property
     def arguments(self):
+        # once step arguments control will be done via file, these should take prio over the main step ran's file args
         args = self.get("arguments", {})
-        return args if args else {}
+        args = args if args else {}
+        management_args = self.management_arguments
+        filtered_args = {}
+        for key, value in args.items():
+            if key not in management_args.keys():
+                filtered_args[key] = value
+        return filtered_args
+
+    @property
+    def management_arguments(self):
+        default_management_args = {
+            "skip": True,
+            "refresh": False,
+            "refresh_requirements": False,
+            "check_requirements": True,
+            "save_output": True,
+        }
+        args = self.get("arguments", {})
+        management_args = {}
+        for key, default_value in default_management_args.items():
+            management_args[key] = args.get(key, default_value)
+
+        if management_args["refresh"] == True:
+            management_args["skip"] = False
+
+        return management_args
 
     @property
     def session_path(self) -> str:
@@ -310,12 +330,24 @@ def create_celery_app(conf_path, app_name="pypelines", v_host=None) -> "Celery |
                 files.append(file_loc)
         return files
 
-    def get_signature_string(signature):
+    def get_signature_as_string(signature):
         params = [
             param_value for param_name, param_value in signature.parameters.items() if param_name not in ["session"]
         ]
         return str(signature.replace(parameters=params))[1:-1].replace(" *,", "")
 
+    def get_signature_as_dict(signature_string):
+        from re import compile as re_compile
+        from ast import literal_eval
+
+        signature_pattern = re_compile(r" *(?P<key> *\w+) *= *(?P<value>.*?) *(?=(?:(?:, *\w+ *=)|(?:$)))")
+        patt = signature_pattern.findall(signature_string)
+        data = {}
+        for key, value in patt:
+            t_val = literal_eval(value)
+            data[key] = t_val
+        return data
+
     class Handshake(Task):
         name = f"{app_name}.handshake"
 
@@ -340,10 +372,12 @@ def create_celery_app(conf_path, app_name="pypelines", v_host=None) -> "Celery |
                 for pipe in pipeline.pipes.values():
                     for step in pipe.steps.values():
                         if step.complete_name in app.tasks.keys():
-                            sig = get_signature_string(step.generate.__signature__)
+                            str_sig = get_signature_as_string(step.generate.__signature__)
+                            dict_sig = get_signature_as_dict(str_sig)
                             doc = step.generate.__doc__
                             task_data = {
-                                "signature": sig,
+                                "signature": str_sig,
+                                "signature_dict": dict_sig,
                                 "docstring": doc,
                                 "step_name": step.step_name,
                                 "pipe_name": step.pipe_name,