fix: revision of output slurm file for cns refine.csh

aria/core/Cluster.py

@@ -107,7 +107,7 @@ class ClusteringXMLPickler(XMLBasePickler):
 
     def load_from_element(self, xml_elt):
         """
-        Load clustering settings from XMLElement
+        Instantiate clustering settings from XMLElement
 
         Parameters
         ----------

aria/core/JobManager.py

@@ -280,10 +280,15 @@ class Job(Thread, AriaBaseClass):
         checkscript = '_%s' % str(jobid) if jobid else ''
 
         if jobid:
+            # Update script output with job id
+            script = checkscript.join(os.path.splitext(d['script']))
+            self._up_script(d['script'], {'sge_job_id': jobid},
+                            script)
             # Create specific checkpoint file
             checkscript = checkscript.join(os.path.splitext(d['check_script']))
             self._up_script(d['check_script'], {'sge_job_id': jobid},
                             checkscript)
+            d['script'] = script
             d['check_script'] = checkscript
 
         checkcmd = self.checkcmd_template % d

aria/core/PeakAssigner.py

@@ -41,6 +41,8 @@ def peak_shape(deltas, errors):
 
 
 class PeakAssignerSettings(Settings):
+    order = ()
+
     def create(self):
         from .Settings import NonNegativeFloat
         from .Settings import YesNoChoice, FourLetterString, String
@@ -711,7 +713,7 @@ class PeakAssignerTextPickler(AriaBaseClass):
 class PeakAssignerXMLPickler(XMLBasePickler):
     def _xml_state(self, x):
         """
-        Define clustering xml tag from PeakAssignerSettings object
+        Instantiate Peak assigner xml tag from PeakAssignerSettings object
 
         Parameters
         ----------