finish removing double-run guard

Author: e-kenneally

CPAC/surface/globals.py

@@ -22,7 +22,6 @@
 from warnings import warn
 import pkg_resources as p
 import yaml
-from CPAC.surface.globals import DOUBLERUN_GUARD_MESSAGE
 from CPAC.utils.utils import load_preconfig
 from .diff import dct_diff
 

CPAC/utils/configuration/configuration.py

@@ -20,7 +20,7 @@
 from datetime import datetime
 from hashlib import sha1
 import yaml
-from CPAC.surface.globals import DOUBLERUN_GUARD_MESSAGE
+
 from CPAC.utils.configuration import Configuration, Preconfiguration, \
                                      preconfig_yaml
 from CPAC.utils.utils import set_nested_value, update_config_dict, \
@@ -87,18 +87,7 @@ def dump(self, new_dict, parents=None):
         -------
         str
         """
-        # Initialize variable for automatically updated value
-        if parents == ['surface_analysis', 'freesurfer'] or parents is None:
-            freesurfer_extraction = False
-            try:
-                brain_extractions = self.get_nested(
-                    new_dict, ['anatomical_preproc', 'brain_extraction',
-                               'using'])
-            except KeyError:
-                brain_extractions = []
-            if (brain_extractions is not None and
-                    'FreeSurfer-ABCD' in brain_extractions):
-                freesurfer_extraction = True
+    
         # SSOT FSLDIR
         try:  # Get from current config
             fsldir = self.get_nested(new_dict,
@@ -117,17 +106,6 @@ def dump(self, new_dict, parents=None):
             _dump = ['%YAML 1.1', '---']
             if 'pipeline_setup' not in new_dict:
                 new_dict['pipeline_setup'] = None
-            # Insert automatically-changed value in original dict
-            # if freesurfer_extraction:
-            #     new_dict = set_nested_value(
-            #         new_dict, ['surface_analysis', 'freesurfer',
-            #         'run_reconall'], False)
-            ingress_keys = ['surface_analysis', 'freesurfer', 'ingress_reconall']
-            try:
-                self.get_nested(new_dict, ingress_keys)
-            except KeyError:
-                new_dict = set_nested_value(new_dict, ingress_keys,
-                                            self.get_nested(self._dict, ingress_keys))
         else:
             _dump = []
         # Prepare for indentation
@@ -150,7 +128,7 @@ def dump(self, new_dict, parents=None):
                 value = self.get_nested(new_dict, keys)
             except KeyError:  # exclude unincluded keys
                 continue
-            
+
             # Print comment if there's one above this key in the template
             if comment:
                 if key != 'pipeline_setup':