try making a package from the code

tools_da.py

@@ -222,7 +222,9 @@ def PrepareObs(CycleInfo,type='forecast'):
         the observations will depend on the specific application, the final result of this step is an output 
         file called "observations.nc" which carries the x,y,z,t, dt information of each observation """
 
-    if   CycleInfo.da_settings['da.system'] == 'CarbonTracker':  import ct_tools as da_system
+    if   CycleInfo.da_settings['da.system'] == 'CarbonTracker':  
+        import ct_tools as da_system
+        import ct_observation_tools as obs
 
     msg             = "Using %s as DA system" % da_system.identifier     ; logging.debug(msg)
 
@@ -234,7 +236,7 @@ def PrepareObs(CycleInfo,type='forecast'):
 
     CycleInfo.da_settings['da.system.info'] = rc_da_system
 
-    Samples                         = da_system.PrepareObs(CycleInfo,type=type)
+    Samples                         = obs.PrepareObs(CycleInfo,type=type)
 
     return Samples
 
@@ -247,7 +249,7 @@ def PrepareState(CycleInfo):
 
     """
 
-    if   CycleInfo.da_settings['da.system'] == 'CarbonTracker':  import ct_tools as da_system
+    if   CycleInfo.da_settings['da.system'] == 'CarbonTracker':  import ct_statevector_tools as da_system
 
     StateVector = da_system.PrepareState(CycleInfo )
 
@@ -334,11 +336,13 @@ def ReadModelSamples(StateVector):
 def Optimize(CycleInfo, StateVector ):
     """ Perform least-squares minimization"""
 
-    if CycleInfo.da_settings['da.system'] == 'CarbonTracker':  import ct_tools as da_system
+    if CycleInfo.da_settings['da.system'] == 'CarbonTracker':  
+        import ct_tools as da_system
+        import ct_optimizer_tools as opt
 
     DaSystem  = da_system.DaInfo(CycleInfo.da_settings['da.system.rc'])
 
-    optimizer = da_system.CtOptimizer(CycleInfo, DaSystem)
+    optimizer = opt.CtOptimizer(CycleInfo, DaSystem)
 
 def CleanUpCycle(CycleInfo):
     """