add from_project parameter

start implementing support for running methods outside of the scportrait project structure

src/scportrait/pipeline/_base.py

@@ -177,13 +177,30 @@ class ProcessingStep(Logable):
     DEFAULT_SELECTION_DIR_NAME = "selection"
 
     def __init__(
-        self, config, directory, project_location, debug=False, overwrite=False, project=None, filehandler=None
+        self,
+        config,
+        directory = None,
+        project_location = None,
+        debug=False,
+        overwrite=False,
+        project=None,
+        filehandler=None,
+        from_project:bool = False,
     ):
         super().__init__(directory=directory)
 
         self.debug = debug
         self.overwrite = overwrite
-        self.project_location = project_location
+        if from_project:
+            self.project_run = True
+            self.project_location = project_location
+            self.project = project
+            self.filehandler = filehandler
+        else:
+            self.project_run = False
+            self.project_location = None
+            self.project = None
+            self.filehandler = None
 
         if isinstance(config, str):
             config = read_config(config)
@@ -195,9 +212,6 @@ def __init__(
             self.config = config
         self.overwrite = overwrite
 
-        self.project = project
-        self.filehandler = filehandler
-
         self.get_context()
 
         self.deep_debug = False

src/scportrait/pipeline/project.py

@@ -253,6 +253,7 @@ def _setup_segmentation_f(self, segmentation_f):
                 overwrite=self.overwrite,
                 project=None,
                 filehandler=self.filehandler,
+                from_project=True,
             )
 
     def _setup_extraction_f(self, extraction_f):
@@ -281,6 +282,7 @@ def _setup_extraction_f(self, extraction_f):
                 overwrite=self.overwrite,
                 project=self,
                 filehandler=self.filehandler,
+                from_project=True,
             )
 
     def _setup_featurization_f(self, featurization_f):
@@ -308,6 +310,7 @@ def _setup_featurization_f(self, featurization_f):
                 overwrite=False,  #this needs to be set to false as the featurization step should not remove previously created features
                 project=self,
                 filehandler=self.filehandler,
+                from_project=True,
             )
 
     def _setup_selection(self, selection_f):
@@ -335,6 +338,7 @@ def _setup_selection(self, selection_f):
                 overwrite=self.overwrite,
                 project=self,
                 filehandler=self.filehandler,
+                from_project=True,
             )
 
     def update_featurization_f(self, featurization_f):