diff --git a/gridded/da/baseclasses/optimizer.py b/gridded/da/baseclasses/optimizer.py
index bed60e04df8c83657bd771648a9f3d310de40055..da03898a3607eef303bb6b993f948813e91ea288 100755
--- a/gridded/da/baseclasses/optimizer.py
+++ b/gridded/da/baseclasses/optimizer.py
@@ -417,35 +417,4 @@ class Optimizer(object):
 
 
 if __name__ == "__main__":
-
-    sys.path.append('../../')
-
-    from da.tools.initexit import start_logger 
-    from da.tools.initexit import CycleControl 
-    from da.ct.obs import CtObservations
-
-    opts = ['-v']
-    args = {'rc':'../../da.rc', 'logfile':'da_initexit.log', 'jobrcfilename':'test.rc'}
-
-    start_logger()
-    DaCycle = CycleControl(opts, args)
-
-    DaCycle.initialize()
-    print DaCycle
-
-
-    samples = CtObservations(DaCycle.DaSystem, datetime.datetime(2005, 3, 5))
-    samples.add_observations()
-    samples.add_simulations('/Users/peters/tmp/test_da/output/20050305/samples.000.nc')
-
-
-    nobs = len(samples.datalist)
-    dims = (int(DaCycle['time.nlag']),
-                  int(DaCycle['da.optimizer.nmembers']),
-                  int(DaCycle.DaSystem['nparameters']),
-                  nobs,)
-
-#   opt = CtOptimizer(dims)
-#   opt.state_to_matrix(StateVector)
-#   opt.MinimumLeastSquares()
-#   opt.matrix_to_state(StateVector)
+    pass
diff --git a/gridded/da/baseclasses/statevector.py b/gridded/da/baseclasses/statevector.py
index fb0bf004adcbe415245c87900eaf350099b57015..86f63cc32cad9e02b495be62da0afe1c8fe7d758 100755
--- a/gridded/da/baseclasses/statevector.py
+++ b/gridded/da/baseclasses/statevector.py
@@ -594,44 +594,5 @@ class StateVector(object):
 ################### End Class StateVector ###################
 
 if __name__ == "__main__":
-
-    sys.path.append('../../')
-
-    from da.tools.initexit import start_logger 
-    from da.tools.initexit import CycleControl 
-
-
-    opts = ['-v']
-    args = {'rc':'../../da.rc', 'logfile':'da_initexit.log', 'jobrcfilename':'test.rc'}
-
-    start_logger()
-    DaCycle = CycleControl(opts, args)
-
-    dummy = EnsembleMember(0)
-    print dummy
-
-    DaCycle.initialize()
-    print DaCycle
-
-    dims = (int(DaCycle['time.nlag']),
-                  int(DaCycle['da.optimizer.nmembers']),
-                  int(DaCycle.DaSystem['nparameters']),
-                  )
-
-    StateVector = StateVector(dims)
-    StateVector.make_new_ensemble(lag=1)
-
-    members = StateVector.EnsembleMembers[0]
-    members[0].write_to_file(DaCycle['dir.input'])
-
-    StateVector.propagate()
-    savedir = DaCycle['dir.output']
-    filename = os.path.join(savedir, 'savestate.nc')
-
-    StateVector.write_to_file(filename)
-
-    savedir = DaCycle['dir.output']
-    filename = os.path.join(savedir, 'savestate.nc')
-
-    StateVector.read_from_file(filename)
+    pass
 
diff --git a/gridded/da/ct/obs.py b/gridded/da/ct/obs.py
index de0e13be57fb13026a21941c250bf995627b34ee..7095ad77da81bbf0f254c86c1ed4d68cbbed895d 100755
--- a/gridded/da/ct/obs.py
+++ b/gridded/da/ct/obs.py
@@ -465,34 +465,4 @@ class MixingRatioSample(object):
 
 
 if __name__ == "__main__":
-
-    from da.tools.initexit import start_logger
-    from datetime import datetime
-
-
-    sys.path.append(os.getcwd())
-
-    start_logger()
-
-    obs = CtObservations()
-
-    #DaCycle = JobStart(['-v'], {'rc':'da.rc'})
-    #DaCycle['time.sample.start'] = datetime(2000, 1, 1)
-    #DaCycle['time.sample.end'] = datetime(2000, 1, 2)
-    
-
-    #obs.initialize()
-    #obs.Validate()
-    #obs.add_observations()
-    #print(obs.Data.getvalues('obs'))
-    obs.Data = []
-    obs.Data.append(MixingRatioSample("10",datetime(2000,1,1)))
-    obs.Data.append(MixingRatioSample("20",datetime(2000,1,2)))
-    obs.Data.append(MixingRatioSample("30",datetime(2000,1,3)))
-    obs.Data.append(MixingRatioSample("40",datetime(2000,1,4)))
-    for d in obs.Data:
-        print d
-    new = obs.Data.unflagged()
-    print new
-    #new = obs.Data.selectsite("10")
-    #print new
+    pass
diff --git a/gridded/da/ct/obspack.py b/gridded/da/ct/obspack.py
index 49648c36724be6ea38c91ea33164f276b6b782ee..31783f0c52964feaa91805477b9314c46dc847ab 100755
--- a/gridded/da/ct/obspack.py
+++ b/gridded/da/ct/obspack.py
@@ -478,41 +478,4 @@ class MixingRatioSample(object):
 
 
 if __name__ == "__main__":
-
-    
-    from da.tools.initexit import CycleControl
-    from da.ct.dasystem import CtDaSystem 
-
-    sys.path.append('../../')
-
-    logging.root.setLevel(logging.DEBUG)
-
-    DaCycle = CycleControl(args={'rc':'../../dagriddedjet.rc'})
-    DaCycle.initialize()
-    DaCycle.parse_times()
-
-    DaSystem = CtDaSystem('../rc/carbontracker.rc')
-    DaSystem.initialize()
-
-    DaCycle.DaSystem = DaSystem
-
-    obs = ObsPackObservations()
-    obs.DaCycle = DaCycle
-
-    while DaCycle['time.start'] < DaCycle['time.finish']:
-
-        DaCycle['time.sample.start'] = DaCycle['time.start']
-        DaCycle['time.sample.end'] = DaCycle['time.end']
-
-        obs.initialize()
-        obs.validate()
-        obs.add_observations()
-        obs.add_model_data_mismatch()
-
-        print(obs.getvalues('obs'))
-        print(obs.getvalues('mdm'))
-
-        DaCycle.advance_cycle_times()
-
-
-
+    pass
\ No newline at end of file
diff --git a/gridded/da/ct/obspack_geocarbon.py b/gridded/da/ct/obspack_geocarbon.py
index efd799f80a0eda901953a239f54f40fef478d30b..6f413d62acb860325d18a8a9bcef85e9f7d329b9 100755
--- a/gridded/da/ct/obspack_geocarbon.py
+++ b/gridded/da/ct/obspack_geocarbon.py
@@ -507,37 +507,7 @@ class MixingRatioSample(object):
 
 
 if __name__ == "__main__":
-
-    from da.tools.initexit import CycleControl
-    from da.ct.dasystem import CtDaSystem 
-
-    sys.path.append('../../')
-
-    logging.root.setLevel(logging.DEBUG)
-
-    DaCycle = CycleControl(args={'rc':'../../ctdas-ei-gfed2-bcb-6x4-gridded.rc'})
-    DaCycle.parse_times()
-
-    DaSystem = CtDaSystem('../rc/carbontracker_geocarbon_gridded.rc')
-
-    DaCycle.DaSystem = DaSystem
-
-    obs = ObsPackObservations()
-    obs.DaCycle = DaCycle
-
-    while DaCycle['time.start'] < DaCycle['time.finish']:
-
-        DaCycle['time.sample.start'] = DaCycle['time.start']
-        DaCycle['time.sample.end'] = DaCycle['time.end']
-
-        obs.initialize()
-        obs.add_observations()
-        obs.add_model_data_mismatch()
-
-        print(obs.getvalues('obs'))
-        print(obs.getvalues('mdm'))
-
-        DaCycle.advance_cycle_times()
+    pass
 
 
 
diff --git a/gridded/da/ct/optimizer.py b/gridded/da/ct/optimizer.py
index 80c555107a4268cfa717f8a0aa2672a8f04f69e1..20a18d80fe580d06339530596766930032c54b3c 100755
--- a/gridded/da/ct/optimizer.py
+++ b/gridded/da/ct/optimizer.py
@@ -86,27 +86,4 @@ class CtOptimizer(Optimizer):
 ################### End Class CtOptimizer ###################
 
 if __name__ == "__main__":
-
-    from da.tools.initexit import start_logger 
-    from da.tools.pipeline import start_job 
-
-    sys.path.append(os.getcwd())
-
-    opts = ['-v']
-    args = {'rc':'da.rc', 'logfile':'da_initexit.log', 'jobrcfilename':'test.rc'}
-
-    start_logger()
-
-    DaCycle = start_job(opts, args)
-    DaCycle.initialize()
-
-    opt = CtOptimizer()
-
-    nobs = 100
-    dims = (int(DaCycle['time.nlag']),
-                  int(DaCycle['da.optimizer.nmembers']),
-                  int(DaCycle.DaSystem['nparameters']),
-                  nobs,)
-
-    opt.initialize(dims)
-    opt.set_localization(type='CT2007')
+    pass
diff --git a/gridded/da/ct/statevector.py b/gridded/da/ct/statevector.py
index fbaf06d2314d1d338450fe9a26b577f73c994c2f..58fb3dd5f359f7441cd79fa4d058e066502583d4 100755
--- a/gridded/da/ct/statevector.py
+++ b/gridded/da/ct/statevector.py
@@ -142,34 +142,4 @@ class CtStateVector(StateVector):
 
 
 if __name__ == "__main__":
-    from da.tools.initexit import start_logger 
-    from da.tools.pipeline import start_job
-
-    sys.path.append(os.getcwd())
-
-    opts = ['-v']
-    args = {'rc':'da.rc', 'logfile':'da_initexit.log', 'jobrcfilename':'test.rc'}
-
-    start_logger()
-
-    DaCycle = start_job(opts, args)
-
-    DaCycle.initialize()
-
-    StateVector = CtStateVector()
-
-    StateVector.initialize()
-
-    for n in range(dims[0]):
-        cov = StateVector.get_covariance()
-        dummy = StateVector.make_new_ensemble(n + 1, cov)
-
-    StateVector.propagate()
-
-    savedir = DaCycle['dir.output']
-    filename = os.path.join(savedir, 'savestate.nc')
-
-    dummy = StateVector.write_to_file()
-
-    StateVector.read_from_file(filename)
-
+    pass
diff --git a/gridded/da/ctgridded/statevector.py b/gridded/da/ctgridded/statevector.py
index c69abd52c92a1e8b85b0347747041e34f8d91995..6e2d35ad70703006cbe8fcd95c4e4764c9e027c0 100755
--- a/gridded/da/ctgridded/statevector.py
+++ b/gridded/da/ctgridded/statevector.py
@@ -200,62 +200,4 @@ class CtGriddedStateVector(StateVector):
 
 
 if __name__ == "__main__":
-
-
-    from da.tools.initexit import start_logger , parse_options
-    from da.tools.initexit import CycleControl
-    from da.ctgridded.dasystem import CtGriddedDaSystem 
-
-    sys.path.append(os.getcwd())
-    sys.path.append('../../')
-
-    opts = ['-v']
-    args = {'rc':'../../dagridded.rc'}
-
-    start_logger(level=logging.DEBUG)
-
-    DaCycle = CycleControl(opts, args)
-
-    DaSystem = CtGriddedDaSystem('../../da/rc/carbontrackergridded.rc')
-    StateVector = CtGriddedStateVector()
-
-    DaSystem.initialize()
-    DaSystem.validate()
-    DaCycle.DaSystem = DaSystem
-    DaCycle.initialize()
-    StateVector.DaCycle = DaCycle # also embed object in StateVector so it can access cycle information for I/O etc
-
-    dummy = StateVector.initialize()
-
-    for n in range(1):
-        cov = StateVector.get_covariance(DaCycle['time.start'])
-        dummy = StateVector.make_new_ensemble(n + 1, cov)
-
-    #StateVector.propagate()
-
-    #savedir         = './'
-    #filename        = os.path.join(savedir,'savestate.nc')
-    #dummy = StateVector.WriteToFile(filename)
-    #StateVector.ReadFromFile(filename)
-
-    StateVector.state2tc(fluxvector=np.ones(StateVector.nparams))
-
-    sys.exit(2)
-
-    members = StateVector.EnsembleMembers[-1]
-
-    
-
-    for mem in members[0:1]:
-
-        mem.ParameterValues = np.arange(StateVector.nparams) + 1.0
-        data = StateVector.vector2grid(vectordata=mem.ParameterValues)
-        params = StateVector.vector2grid(griddata=data, reverse=True, method="minval")
-
-        tcparams = StateVector.vector2tc(mem.ParameterValues)
-
-    print (StateVector.gridmap - data).min()
-    print (StateVector.gridmap - data).max()
-    print (mem.ParameterValues - params).min()
-    print (mem.ParameterValues - params).max()
-
+    pass
diff --git a/gridded/da/test/test_optimizer.py b/gridded/da/test/test_optimizer.py
index 98e85e4aecbec48fad46eb4ba203d3fa029807ca..dd7ae99c5044fed2bd7f23fd492b3b77a154b574 100755
--- a/gridded/da/test/test_optimizer.py
+++ b/gridded/da/test/test_optimizer.py
@@ -205,39 +205,4 @@ def serial_vs_bulk():
 
 
 if __name__ == "__main__":
-
-    import sys
-
-    sys.path.append('../../')
-
-    import os
-    from da.tools.general import start_logger 
-    from da.tools.initexit import CycleControl 
-    from da.ct.statevector import CtStateVector, CtMember
-    from da.ct.obs import CtObservations, MixingRatioSample
-    from da.ct.optimizer import CtOptimizer
-    import numpy as np
-    import da.tools.rc as rc
-    import datetime
-    import Nio
-    import matplotlib.pyplot as plt
-
-    opts = ['-v']
-    args = {'rc':'da.rc', 'logfile':'da_initexit.log', 'jobrcfilename':'test.rc'}
-
-    start_logger()
-    DaCycle = CycleControl(opts, args)
-
-    dummy = CtMember(0)
-    DaCycle.initialize()
-    StateVector = CtStateVector(DaCycle)
-    samples = CtObservations(DaCycle.DaSystem, datetime.datetime(2000, 1, 1))
-
-    # This is a test of the CarbonTracker release ct2009 fortran solution and the one implemented here
-
-    #serial_py_against_serial_fortran()
-    #sys.exit(0)
-
-    serial_vs_bulk()
-    sys.exit(0)
-
+    pass
diff --git a/gridded/da/tm5/observationoperator.py b/gridded/da/tm5/observationoperator.py
index 2a27ee5310d0ce9a25c15b2a7eb3dbbb4ec85b59..39ed8df32666ca2c6e3d6690011f6cbfa5a1a739 100755
--- a/gridded/da/tm5/observationoperator.py
+++ b/gridded/da/tm5/observationoperator.py
@@ -627,29 +627,7 @@ class TM5ObservationOperator(ObservationOperator):
                    
 
 if __name__ == "__main__":
-
-    sys.path.append('../../')
-
-    from da.tools.initexit import start_logger
-    from da.tools.pipeline import start_job
-    import datetime as dtm
-
-    sys.path.append(os.getcwd())
-
-    start_logger()
-
-    DaCycle = start_job([], {'rc':'da.rc'})
-    DaCycle.initialize()
-    DaCycle['time.sample.start'] = dtm.datetime(2000, 1, 1)
-    DaCycle['time.sample.end'] = dtm.datetime(2000, 1, 2)
-    DaCycle['time.sample.window'] = 0
-
-    tm = TM5ObservationOperator()
-    tm.Setup()
-    tm.initialize()
-    tm.run()
-    tm.save_data()
-
+    pass