pyGSTi 0.9.12__cp39-cp39-win_amd64.whl → 0.9.13__cp39-cp39-win_amd64.whl

pygsti/protocols/gst.py

@@ -20,6 +20,7 @@ import pathlib as _pathlib
 
 import numpy as _np
 from scipy.stats import chi2 as _chi2
+from typing import Optional
 
 from pygsti.baseobjs.profiler import DummyProfiler as _DummyProfiler
 from pygsti.baseobjs.nicelyserializable import NicelySerializable as _NicelySerializable
@@ -37,6 +38,7 @@ from pygsti import baseobjs as _baseobjs
 from pygsti.processors import QuditProcessorSpec as _QuditProcessorSpec
 from pygsti.modelmembers import operations as _op
 from pygsti.models import Model as _Model
+from pygsti.models.explicitmodel import ExplicitOpModel as _ExplicitOpModel
 from pygsti.models.gaugegroup import GaugeGroup as _GaugeGroup, GaugeGroupElement as _GaugeGroupElement
 from pygsti.objectivefns import objectivefns as _objfns, wildcardbudget as _wild
 from pygsti.circuits.circuitlist import CircuitList as _CircuitList
@@ -44,6 +46,7 @@ from pygsti.baseobjs.resourceallocation import ResourceAllocation as _ResourceAl
 from pygsti.modelmembers import states as _states, povms as _povms
 from pygsti.tools.legacytools import deprecate as _deprecated_fn
 from pygsti.circuits import Circuit
+from pygsti.forwardsims import ForwardSimulator
 
 
 #For results object:
@@ -535,7 +538,7 @@ class GSTInitialModel(_NicelySerializable):
         if comm is None or comm.Get_rank() == 0:
             #Advanced Options can specify further manipulation of starting model
             if self.contract_start_to_cptp:
-                mdl_start = _alg.contract(mdl_start, "CPTP")
+                mdl_start = _alg.contract(mdl_start, "CPTPLND")
                 raise ValueError(
                     "'contractStartToCPTP' has been removed b/c it can change the parameterization of a model")
             if self.depolarize_start > 0:
@@ -593,7 +596,7 @@ class GSTBadFitOptions(_NicelySerializable):
         Actions to take when a GST fit is unsatisfactory. Allowed actions include:
         
         * 'wildcard': Find an admissable wildcard model.
-        * 'ddist_wildcard': Fits a single parameter wildcard model in which
+        * 'wildcard1d': Fits a single parameter wildcard model in which
           the amount of wildcard error added to an operation is proportional
           to the diamond distance between that operation and the target.
         * 'robust': scale data according out "robust statistics v1" algorithm,
@@ -637,10 +640,8 @@ class GSTBadFitOptions(_NicelySerializable):
 
     wildcard_methods: tuple, optional
         A list of the methods to use to optimize the wildcard error vector.  Default is `("neldermead",)`.
-        Options include `"neldermead"`, `"barrier"`, `"cvxopt"`, `"cvxopt_smoothed"`, `"cvxopt_small"`,
-        and `"cvxpy_noagg"`.  So many methods exist because different convex solvers behave differently
-        (unfortunately).  Leave as the default as a safe option, but `"barrier"` is pretty reliable and much
-        faster than `"neldermead"`, and is a good option so long as it runs.
+        Options include `"neldermead"`, `"barrier"`, and `"cvxpy_noagg"`.  Leave as the default as a safe option,
+        but `"barrier"` is pretty reliable and much faster than `"neldermead"`, and is a good option so long as it runs.
 
     wildcard_inadmissable_action: {"print", "raise"}, optional
         What to do when an inadmissable wildcard error vector is found.  The default just prints this
@@ -839,7 +840,9 @@ class GSTGaugeOptSuite(_NicelySerializable):
           - "varyValidSpamWt" : varies spam weight with SPAM penalty == 1.
           - "toggleValidSpam" : toggles spame penalty (0 or 1); fixed SPAM wt.
           - "unreliable2Q" : adds branch to a spam suite that weights 2Q gates less
-          - "none" : no gauge optimizations are performed.
+          - "none" : no gauge optimizations are performed. When passed individually
+             (not in a list with other suite names) then this results in an empty
+             GSTGaugeOptSuite object (w/gaugeopt_suite_names set to None).
 
     gaugeopt_argument_dicts : dict, optional
         A dictionary whose string-valued keys label different gauge optimizations (e.g. within a
@@ -870,8 +873,11 @@ class GSTGaugeOptSuite(_NicelySerializable):
     def __init__(self, gaugeopt_suite_names=None, gaugeopt_argument_dicts=None, gaugeopt_target=None):
         super().__init__()
         if gaugeopt_suite_names is not None:
-            self.gaugeopt_suite_names = (gaugeopt_suite_names,) \
-                if isinstance(gaugeopt_suite_names, str) else tuple(gaugeopt_suite_names)
+            if gaugeopt_suite_names == 'none':
+                self.gaugeopt_suite_names = None
+            else:
+                self.gaugeopt_suite_names = (gaugeopt_suite_names,) \
+                    if isinstance(gaugeopt_suite_names, str) else tuple(gaugeopt_suite_names)
         else:
             self.gaugeopt_suite_names = None
 
@@ -949,6 +955,8 @@ class GSTGaugeOptSuite(_NicelySerializable):
                 if hasattr(goparams, 'keys'):  # goparams is a simple dict
                     gaugeopt_suite_dict[lbl] = goparams.copy()
                     gaugeopt_suite_dict[lbl].update({'verbosity': printer})
+                elif goparams is None:
+                    gaugeopt_suite_dict[lbl] = None
                 else:  # assume goparams is an iterable
                     assert(isinstance(goparams, (list, tuple))), \
                         "If not a dictionary, gauge opt params should be a list or tuple of dicts!"
@@ -961,7 +969,13 @@ class GSTGaugeOptSuite(_NicelySerializable):
         if self.gaugeopt_target is not None:
             assert(isinstance(self.gaugeopt_target, _Model)), "`gaugeopt_target` must be None or a Model"
             for goparams in gaugeopt_suite_dict.values():
-                goparams_list = [goparams] if hasattr(goparams, 'keys') else goparams
+                if hasattr(goparams, 'keys'):
+                    goparams_list = [goparams] 
+                elif goparams is None: #edge case for 'none' suite
+                    continue
+                else:
+                    goparams_list = goparams
+
                 for goparams_dict in goparams_list:
                     if 'target_model' in goparams_dict:
                         _warnings.warn(("`gaugeOptTarget` argument is overriding"
@@ -1086,8 +1100,8 @@ class GSTGaugeOptSuite(_NicelySerializable):
         elif suite_name == "unreliable2Q":
             raise ValueError(("unreliable2Q is no longer a separate 'suite'.  You should precede it with the suite"
                               " name, e.g. 'stdgaugeopt-unreliable2Q' or 'varySpam-unreliable2Q'"))
-        elif suite_name == "none":
-            pass  # add nothing
+        elif suite_name == 'none':
+            gaugeopt_suite_dict[root_lbl] = None
         else:
             raise ValueError("Unknown gauge-optimization suite '%s'" % suite_name)
 
@@ -1120,6 +1134,9 @@ class GSTGaugeOptSuite(_NicelySerializable):
             for lbl, goparams in self.gaugeopt_argument_dicts.items():
                 goparams_list = [goparams] if hasattr(goparams, 'keys') else goparams
                 serialize_list = []
+                if lbl == 'trivial_gauge_opt':
+                    dicts_to_serialize[lbl] = None
+                    continue
                 for goparams_dict in goparams_list:
                     to_add = goparams_dict.copy()
                     if 'target_model' in to_add:
@@ -1151,6 +1168,9 @@ class GSTGaugeOptSuite(_NicelySerializable):
     def _from_nice_serialization(cls, state):  # memo holds already de-serialized objects
         gaugeopt_argument_dicts = {}
         for lbl, serialized_goparams_list in state['gaugeopt_argument_dicts'].items():
+            if lbl == 'trivial_gauge_opt':
+                gaugeopt_argument_dicts[lbl] = None
+                continue
             goparams_list = []
             for serialized_goparams in serialized_goparams_list:
                 to_add = serialized_goparams.copy()
@@ -1230,15 +1250,16 @@ class GateSetTomography(_proto.Protocol):
 
         if isinstance(optimizer, _opt.Optimizer):
             self.optimizer = optimizer
-            if isinstance(optimizer, _opt.CustomLMOptimizer) and optimizer.first_fditer is None:
-                #special behavior: can set optimizer's first_fditer to `None` to mean "fill with default"
+            if hasattr(optimizer,'first_fditer') and optimizer.first_fditer is None:
+                # special behavior: can set optimizer's first_fditer to `None` to mean "fill with default"
                 self.optimizer = _copy.deepcopy(optimizer)  # don't mess with caller's optimizer
                 self.optimizer.first_fditer = default_first_fditer
         else:
-            if optimizer is None: optimizer = {}
+            if optimizer is None:
+                optimizer = {}
             if 'first_fditer' not in optimizer:  # then add default first_fditer value
                 optimizer['first_fditer'] = default_first_fditer
-            self.optimizer = _opt.CustomLMOptimizer.cast(optimizer)
+            self.optimizer = _opt.SimplerLMOptimizer.cast(optimizer)
 
         self.objfn_builders = GSTObjFnBuilders.cast(objfn_builders)
 
@@ -1257,20 +1278,8 @@ class GateSetTomography(_proto.Protocol):
         self.circuit_weights = None
         self.unreliable_ops = ('Gcnot', 'Gcphase', 'Gms', 'Gcn', 'Gcx', 'Gcz')
 
-    #TODO: Maybe make methods like this separate functions??
-    #def run_using_germs_and_fiducials(self, dataset, target_model, prep_fiducials, meas_fiducials, germs, max_lengths):
-    #    design = StandardGSTDesign(target_model, prep_fiducials, meas_fiducials, germs, max_lengths)
-    #    return self.run(_proto.ProtocolData(design, dataset))
-    #
-    #def run_using_circuit_structures(self, target_model, circuit_structs, dataset):
-    #    design = StructuredGSTDesign(target_model, circuit_structs)
-    #    return self.run(_proto.ProtocolData(design, dataset))
-    #
-    #def run_using_circuit_lists(self, target_model, circuit_lists, dataset):
-    #    design = GateSetTomographyDesign(target_model, circuit_lists)
-    #    return self.run(_proto.ProtocolData(design, dataset))
-
-    def run(self, data, memlimit=None, comm=None, checkpoint=None, checkpoint_path=None, disable_checkpointing = False):
+    def run(self, data, memlimit=None, comm=None, checkpoint=None, checkpoint_path=None, disable_checkpointing=False,
+            simulator: Optional[ForwardSimulator.Castable]=None):
         """
         Run this protocol on `data`.
 
@@ -1303,6 +1312,11 @@ class GateSetTomography(_proto.Protocol):
             to disk during the course of this protocol. It is strongly recommended
             that this be kept set to False without good reason to disable the checkpoints.
 
+        simulator : ForwardSimulator.Castable or None
+            Ignored if None. If not None, then we call
+                fwdsim = ForwardSimulator.cast(simulator),
+            and we set the .sim attribute of every Model we encounter to fwdsim.
+
         Returns
         -------
         ModelEstimateResults
@@ -1337,54 +1351,56 @@ class GateSetTomography(_proto.Protocol):
         tnxt = _time.time(); profiler.add_time('GST: loading', tref); tref = tnxt
         mdl_start = self.initial_model.retrieve_model(data.edesign, self.gaugeopt_suite.gaugeopt_target,
                                                       data.dataset, comm)
-        
-        if not disable_checkpointing:
-            #Set the checkpoint_path variable if None
+        if simulator is not None:
+            mdl_start.sim = simulator
+
+        if disable_checkpointing:
+            seed_model = mdl_start.copy()
+            mdl_lsgst_list = []
+            starting_idx = 0
+        else:
+            # Set the checkpoint_path variable if None
             if checkpoint_path is None:
                 checkpoint_path = _pathlib.Path('./gst_checkpoints/' + self.name)
             else:
-                #cast this to a pathlib path with the file extension (suffix) dropped
+                # cast this to a pathlib path with the file extension (suffix) dropped
                 checkpoint_path = _pathlib.Path(checkpoint_path).with_suffix('')
-            
-            #create the parent directory of the checkpoint if needed:
+
+            # create the parent directory of the checkpoint if needed:
             checkpoint_path.parent.mkdir(parents=True, exist_ok=True)
-            
-            #If there is no checkpoint we should start from with the seed model,
-            #otherwise we should seed the next iteration with the last iteration's result.
-            #If there is no checkpoint initialize mdl_lsgst_list and final_objfn to be empty, 
-            #otherwise re-initialize their values from the checkpoint   
+
+            # If there is no checkpoint we should start from with the seed model,
+            # otherwise we should seed the next iteration with the last iteration's result.
+            # If there is no checkpoint initialize mdl_lsgst_list and final_objfn to be empty,
+            # otherwise re-initialize their values from the checkpoint
             if checkpoint is None:
                 seed_model = mdl_start.copy()
                 mdl_lsgst_list = []
                 checkpoint = GateSetTomographyCheckpoint()
             elif isinstance(checkpoint, GateSetTomographyCheckpoint):
-                #if the checkpoint's last completed iteration is non-negative
-                #(i.e. the checkpoint actually has data in it)
+                # if the checkpoint's last completed iteration is non-negative
+                # (i.e. the checkpoint actually has data in it)
                 if checkpoint.last_completed_iter >= 0:
                     seed_model = checkpoint.mdl_list[-1]
-                #otherwise seed with target
+                # otherwise seed with target
                 else:
                     seed_model = mdl_start.copy()
                 mdl_lsgst_list = checkpoint.mdl_list
                 final_objfn = checkpoint.final_objfn
-                #final_objfn initialized to None in the GateSetTomographyCheckpoint and will be overwritten
-                #during the loop below unless the last completed iteration is the final iteration
-                #in which case the loop should be skipped. If so I think it is ok that this gets
-                #left set to None. There looks to be some logic for handling this and it looks
-                #like the serialization routines effectively do this already, as the value
-                #of this is lost between writing and reading.
+                # final_objfn initialized to None in the GateSetTomographyCheckpoint and will be overwritten
+                # during the loop below unless the last completed iteration is the final iteration
+                # in which case the loop should be skipped. If so I think it is ok that this gets
+                # left set to None. There looks to be some logic for handling this and it looks
+                # like the serialization routines effectively do this already, as the value
+                # of this is lost between writing and reading.
             else:
-                NotImplementedError('The only currently valid checkpoint inputs are None and GateSetTomographyCheckpoint.')
-            
-            #note the last_completed_iter value is initialized to -1 so the below line 
+                NotImplementedError(
+                    'The only currently valid checkpoint inputs are None and GateSetTomographyCheckpoint.')
+
+            # note the last_completed_iter value is initialized to -1 so the below line
             # will have us correctly starting at 0 if this is a fresh checkpoint.
             starting_idx = checkpoint.last_completed_iter + 1
 
-        else:
-            seed_model = mdl_start.copy()
-            mdl_lsgst_list = []
-            starting_idx = 0
-
         tnxt = _time.time(); profiler.add_time('GST: Prep Initial seed', tref); tref = tnxt
         
         #Run Long-sequence GST on data
@@ -1404,18 +1420,18 @@ class GateSetTomography(_proto.Protocol):
             #then do the final iteration slightly differently since the generator should
             #give three return values.
             if i==len(bulk_circuit_lists)-1:
-                mdl_iter, opt_iter, final_objfn =  next(gst_iter_generator)
+                mdl_iter, opt_iter, final_objfn = next(gst_iter_generator)
             else:
                 mdl_iter, opt_iter =  next(gst_iter_generator)
             mdl_lsgst_list.append(mdl_iter)
             optima_list.append(opt_iter)
 
             if not disable_checkpointing:
-                #update the checkpoint along the way:
+                # update the checkpoint along the way:
                 checkpoint.mdl_list = mdl_lsgst_list
                 checkpoint.last_completed_iter += 1
                 checkpoint.last_completed_circuit_list = bulk_circuit_lists[i]
-                #write the updated checkpoint to disk:
+                # write the updated checkpoint to disk:
                 if resource_alloc.comm_rank == 0:
                     checkpoint.write(f'{checkpoint_path}_iteration_{i}.json')
 
@@ -1442,19 +1458,37 @@ class GateSetTomography(_proto.Protocol):
             target_model = self.gaugeopt_suite.gaugeopt_target
         elif self.initial_model.target_model is not None:
             target_model = self.initial_model.target_model.copy()
-        elif self.initial_model.model is not None and self.gaugeopt_suite.is_empty() is False:
+        elif self.initial_model.model is not None:
             # when we desparately need a target model but none have been specifically given: use initial model
             target_model = self.initial_model.model.copy()
         else:
+            msg = 'Could not identify a suitable target model, this may result'\
+                 +' in unexpected behavior or missing plots in reports.'
+            _warnings.warn(msg)
             target_model = None
 
+        if target_model is not None and simulator is not None:
+            target_model.sim = simulator
+
         estimate = _Estimate.create_gst_estimate(ret, target_model, mdl_start, mdl_lsgst_list, parameters)
         ret.add_estimate(estimate, estimate_key=self.name)
 
-        return _add_gaugeopt_and_badfit(ret, self.name, target_model,
-                                        self.gaugeopt_suite, self.unreliable_ops,
-                                        self.badfit_options, self.optimizer, resource_alloc, printer)
-
+        #Add some better handling for when gauge optimization is turned off (current code path isn't working.)
+        if not self.gaugeopt_suite.is_empty() or len(self.badfit_options.actions) > 0:  # maybe add flag to do this even when empty?
+            ret = _add_gaugeopt_and_badfit(ret, self.name, target_model,
+                                           self.gaugeopt_suite, self.unreliable_ops,
+                                           self.badfit_options, self.optimizer, 
+                                           resource_alloc, printer)
+        else:
+            #add a model to the estimate that we'll call the trivial gauge optimized model which
+            #will be set to be equal to the final iteration estimate.
+            ret.estimates[self.name].models['trivial_gauge_opt'] = mdl_lsgst_list[-1]
+            #and add a key for this to the goparameters dict (this is what the report
+            #generation looks at to determine the names of the gauge optimized models).
+            #Set the value to None as a placeholder.
+            ret.estimates[self.name].goparameters['trivial_gauge_opt'] = None
+        
+        return ret
 
 class LinearGateSetTomography(_proto.Protocol):
     """
@@ -1504,6 +1538,10 @@ class LinearGateSetTomography(_proto.Protocol):
         self.oplabel_aliases = None
         self.unreliable_ops = ('Gcnot', 'Gcphase', 'Gms', 'Gcn', 'Gcx', 'Gcz')
 
+        self.auxfile_types['target_model'] = 'serialized-object'
+        self.auxfile_types['gaugeopt_suite'] = 'serialized-object'
+        self.auxfile_types['badfit_options'] = 'serialized-object'
+
     def check_if_runnable(self, data):
         """
         Raises a ValueError if LGST cannot be run on data
@@ -1612,9 +1650,22 @@ class LinearGateSetTomography(_proto.Protocol):
                                    'final iteration estimate': mdl_lgst},
                              parameters)
         ret.add_estimate(estimate, estimate_key=self.name)
-        return _add_gaugeopt_and_badfit(ret, self.name, target_model, self.gaugeopt_suite,
+
+        #Add some better handling for when gauge optimization is turned off (current code path isn't working.)
+        if not self.gaugeopt_suite.is_empty():
+            ret = _add_gaugeopt_and_badfit(ret, self.name, target_model, self.gaugeopt_suite,
                                         self.unreliable_ops, self.badfit_options,
                                         None, resource_alloc, printer)
+        else:
+            #add a model to the estimate that we'll call the trivial gauge optimized model which
+            #will be set to be equal to the final iteration estimate.
+            ret.estimates[self.name].models['trivial_gauge_opt'] = mdl_lgst
+            #and add a key for this to the goparameters dict (this is what the report
+            #generation looks at to determine the names of the gauge optimized models).
+            #Set the value to None as a placeholder.
+            ret.estimates[self.name].goparameters['trivial_gauge_opt'] = None
+
+        return ret
 
 
 class StandardGST(_proto.Protocol):
@@ -1629,13 +1680,13 @@ class StandardGST(_proto.Protocol):
         parameterizations/constraints to apply to the estimated model.
         The default value is usually fine.  Allowed values are:
 
-        - "full" : full (completely unconstrained)
-        - "TP"   : TP-constrained
-        - "CPTP" : Lindbladian CPTP-constrained
-        - "H+S"  : Only Hamiltonian + Stochastic errors allowed (CPTP)
-        - "S"    : Only Stochastic errors allowed (CPTP)
-        - "Target" : use the target (ideal) gates as the estimate
-        - <model> : any key in the `models_to_test` argument
+        - "full"    : full (completely unconstrained)
+        - "TP"      : TP-constrained
+        - "CPTPLND" : Lindbladian CPTP-constrained
+        - "H+S"     : Only Hamiltonian + Stochastic errors allowed (CPTP)
+        - "S"       : Only Stochastic errors allowed (CPTP)
+        - "Target"  : use the target (ideal) gates as the estimate
+        - <model>   : any key in the `models_to_test` argument
 
     gaugeopt_suite : GSTGaugeOptSuite, optional
         Specifies which gauge optimizations to perform on each estimate.  Can also
@@ -1646,6 +1697,14 @@ class StandardGST(_proto.Protocol):
         optimization (only), and is useful when you want to gauge optimize toward
         something other than the *ideal* target gates.
 
+    target_model : Model, optional (default None)
+        If specified use this Model as the target model. Depending on other
+        specified keyword arguments this model may be used as the target for
+        the purposes of gauge optimization, report generation/analysis, and
+        initial seeding for optimization. (For almost all of these it may be the
+        case that other keyword argument values override this for certain
+        tasks).
+
     models_to_test : dict, optional
         A dictionary of Model objects representing (gate-set) models to
         test against the data.  These Models are essentially hypotheses for
@@ -1694,12 +1753,12 @@ class StandardGST(_proto.Protocol):
         self.target_model = target_model
         self.gaugeopt_suite = GSTGaugeOptSuite.cast(gaugeopt_suite)
         self.objfn_builders = GSTObjFnBuilders.cast(objfn_builders) if (objfn_builders is not None) else None
-        self.optimizer = _opt.CustomLMOptimizer.cast(optimizer)
+        self.optimizer = _opt.SimplerLMOptimizer.cast(optimizer)
         self.badfit_options = GSTBadFitOptions.cast(badfit_options)
         self.verbosity = verbosity
 
         if not isinstance(optimizer, _opt.Optimizer) and isinstance(optimizer, dict) \
-           and 'first_fditer' not in optimizer:  # then a dict was cast into a CustomLMOptimizer above.
+           and 'first_fditer' not in optimizer:  # then a dict was cast into an Optimizer above.
             # by default, set special "first_fditer=auto" behavior (see logic in GateSetTomography.__init__)
             self.optimizer.first_fditer = None
 
@@ -1713,12 +1772,8 @@ class StandardGST(_proto.Protocol):
         #Advanced options that could be changed by users who know what they're doing
         self.starting_point = {}  # a dict whose keys are modes
 
-    #def run_using_germs_and_fiducials(self, dataset, target_model, prep_fiducials, meas_fiducials, germs, max_lengths):
-    #    design = StandardGSTDesign(target_model, prep_fiducials, meas_fiducials, germs, max_lengths)
-    #    data = _proto.ProtocolData(design, dataset)
-    #    return self.run(data)
-
-    def run(self, data, memlimit=None, comm=None, checkpoint= None, checkpoint_path=None, disable_checkpointing = False):
+    def run(self, data, memlimit=None, comm=None, checkpoint=None, checkpoint_path=None,
+            disable_checkpointing=False, simulator: Optional[ForwardSimulator.Castable]=None):
         """
         Run this protocol on `data`.
 
@@ -1751,6 +1806,11 @@ class StandardGST(_proto.Protocol):
             to disk during the course of this protocol. It is strongly recommended
             that this be kept set to False without good reason to disable the checkpoints.
 
+        simulator : ForwardSimulator.Castable or None
+            Ignored if None. If not None, then we call
+                fwdsim = ForwardSimulator.cast(simulator),
+            and we set the .sim attribute of every Model we encounter to fwdsim.
+
         Returns
         -------
         ProtocolResults
@@ -1780,6 +1840,10 @@ class StandardGST(_proto.Protocol):
         else:
             target_model = None  # Usually this path leads to an error being raised below.
 
+        if target_model is not None:
+            if simulator is not None:
+                target_model.sim = simulator
+
         if not disable_checkpointing:
             #Set the checkpoint_path variable if None
             if checkpoint_path is None:
@@ -1813,8 +1877,12 @@ class StandardGST(_proto.Protocol):
         with printer.progress_logging(1):
             for i, mode in enumerate(modes):
                 printer.show_progress(i, len(modes), prefix='-- Std Practice: ', suffix=' (%s) --' % mode)
-                if not disable_checkpointing:
-                    #pre python 3.9 compatible version.
+                if disable_checkpointing:
+                    checkpoint_path = None
+                    child_checkpoint = None
+                else:
+                    child_checkpoint = checkpoint.children[mode]
+                    #The line below is for compatibility with Python 3.8 and lower.
                     checkpoint_path = checkpoint_path_base.with_name(f"{checkpoint_path_base.stem}_{mode.replace(' ', '_')}")
                     #The line below only works for python 3.9+
                     #checkpoint_path = checkpoint_path_base.with_stem(f"{checkpoint_path_base.stem}_{mode.replace(' ', '_')}")
@@ -1825,21 +1893,22 @@ class StandardGST(_proto.Protocol):
                     
                     mdltest = _ModelTest(target_model, target_model, self.gaugeopt_suite,
                                          mt_builder, self.badfit_options, verbosity=printer - 1, name=mode)
-                    if not disable_checkpointing:
-                        result = mdltest.run(data, memlimit, comm, checkpoint = checkpoint.children[mode],
-                                            checkpoint_path=checkpoint_path)
-                    else:
-                        result = mdltest.run(data, memlimit, comm, disable_checkpointing=True)
+                    result = mdltest.run(data, memlimit, comm,
+                                         disable_checkpointing=disable_checkpointing,
+                                         checkpoint=child_checkpoint,
+                                         checkpoint_path=checkpoint_path)
                     ret.add_estimates(result)
 
                 elif mode in models_to_test:
-                    mdltest = _ModelTest(models_to_test[mode], target_model, self.gaugeopt_suite,
+                    mdl = models_to_test[mode]
+                    if simulator is not None:
+                        mdl.sim = simulator
+                    mdltest = _ModelTest(mdl, target_model, self.gaugeopt_suite,
                                          None, self.badfit_options, verbosity=printer - 1, name=mode)
-                    if not disable_checkpointing:
-                        result = mdltest.run(data, memlimit, comm, checkpoint = checkpoint.children[mode],
-                                            checkpoint_path=checkpoint_path)
-                    else:
-                        result = mdltest.run(data, memlimit, comm, disable_checkpointing=True)
+                    result = mdltest.run(data, memlimit, comm,
+                                         disable_checkpointing=disable_checkpointing,
+                                         checkpoint=child_checkpoint,
+                                         checkpoint_path=checkpoint_path)
                     ret.add_estimates(result)
 
                 else:
@@ -1849,7 +1918,7 @@ class StandardGST(_proto.Protocol):
 
                     #Try to interpret `mode` as a parameterization
                     parameterization = mode  # for now, 1-1 correspondence
-                    initial_model = target_model
+                    initial_model = target_model.copy()
 
                     try:
                         initial_model.set_all_parameterizations(parameterization)
@@ -1858,13 +1927,14 @@ class StandardGST(_proto.Protocol):
                                          % (mode, str(e)))
 
                     initial_model = GSTInitialModel(initial_model, self.starting_point.get(mode, None))
+                    if simulator is not None:
+                        initial_model.sim = simulator
                     gst = GST(initial_model, self.gaugeopt_suite, self.objfn_builders,
                               self.optimizer, self.badfit_options, verbosity=printer - 1, name=mode)
-                    if not disable_checkpointing:
-                        result = gst.run(data, memlimit, comm, checkpoint = checkpoint.children[mode],
-                                        checkpoint_path=checkpoint_path)
-                    else:
-                        result = gst.run(data, memlimit, comm, disable_checkpointing=True)
+                    result = gst.run(data, memlimit, comm,
+                                     disable_checkpointing=disable_checkpointing,
+                                     checkpoint=child_checkpoint,
+                                     checkpoint_path=checkpoint_path)
                     ret.add_estimates(result)
 
         return ret
@@ -1945,7 +2015,7 @@ def _add_gaugeopt_and_badfit(results, estlbl, target_model, gaugeopt_suite,
     profiler = resource_alloc.profiler
 
     #Do final gauge optimization to *final* iteration result only
-    if gaugeopt_suite:
+    if gaugeopt_suite is not None and not gaugeopt_suite.is_empty():
         model_to_gaugeopt = results.estimates[estlbl].models['final iteration estimate']
         if gaugeopt_suite.gaugeopt_target is None:  # add a default target model to gauge opt if needed
             #TODO: maybe make these two lines into a method of GSTGaugeOptSuite for adding a target model?
@@ -1954,7 +2024,7 @@ def _add_gaugeopt_and_badfit(results, estlbl, target_model, gaugeopt_suite,
         _add_gauge_opt(results, estlbl, gaugeopt_suite,
                        model_to_gaugeopt, unreliable_ops, comm, printer - 1)
         profiler.add_time('%s: gauge optimization' % estlbl, tref); tref = _time.time()
-        
+
         _add_badfit_estimates(results, estlbl, badfit_options, optimizer, resource_alloc, printer, gaugeopt_suite= gaugeopt_suite)
         profiler.add_time('%s: add badfit estimates' % estlbl, tref); tref = _time.time()
     else:
@@ -2023,26 +2093,31 @@ def _add_gauge_opt(results, base_est_label, gaugeopt_suite, starting_model,
 
         printer.log("-- Performing '%s' gauge optimization on %s estimate --" % (go_label, base_est_label), 2)
 
-        #Get starting model
-        results.estimates[base_est_label].add_gaugeoptimized(goparams, None, go_label, comm, printer - 3)
+        #add logic for the case where no gauge optimization is performed.
+        if go_label == 'none':
+            results.estimates[base_est_label].add_gaugeoptimized(goparams, starting_model, go_label, comm, printer - 3)
+        else:
+            results.estimates[base_est_label].add_gaugeoptimized(goparams, None, go_label, comm, printer - 3)
+        
+        #Get starting model for next stage
         mdl_start = results.estimates[base_est_label].retrieve_start_model(goparams)
-
-        #Gauge optimize data-scaled estimate also
-        for suffix in ROBUST_SUFFIX_LIST:
-            robust_est_label = base_est_label + suffix
-            if robust_est_label in results.estimates:
-                mdl_start_robust = results.estimates[robust_est_label].retrieve_start_model(goparams)
-
-                if mdl_start_robust.frobeniusdist(mdl_start) < 1e-8:
-                    printer.log("-- Conveying '%s' gauge optimization from %s to %s estimate --" %
-                                (go_label, base_est_label, robust_est_label), 2)
-                    params = results.estimates[base_est_label].goparameters[go_label]  # no need to copy here
-                    gsopt = results.estimates[base_est_label].models[go_label].copy()
-                    results.estimates[robust_est_label].add_gaugeoptimized(params, gsopt, go_label, comm, printer - 3)
-                else:
-                    printer.log("-- Performing '%s' gauge optimization on %s estimate --" %
-                                (go_label, robust_est_label), 2)
-                    results.estimates[robust_est_label].add_gaugeoptimized(goparams, None, go_label, comm, printer - 3)
+        if mdl_start is not None:
+            #Gauge optimize data-scaled estimate also
+            for suffix in ROBUST_SUFFIX_LIST:
+                robust_est_label = base_est_label + suffix
+                if robust_est_label in results.estimates:
+                    mdl_start_robust = results.estimates[robust_est_label].retrieve_start_model(goparams)
+
+                    if mdl_start_robust.frobeniusdist(mdl_start) < 1e-8:
+                        printer.log("-- Conveying '%s' gauge optimization from %s to %s estimate --" %
+                                    (go_label, base_est_label, robust_est_label), 2)
+                        params = results.estimates[base_est_label].goparameters[go_label]  # no need to copy here
+                        gsopt = results.estimates[base_est_label].models[go_label].copy()
+                        results.estimates[robust_est_label].add_gaugeoptimized(params, gsopt, go_label, comm, printer - 3)
+                    else:
+                        printer.log("-- Performing '%s' gauge optimization on %s estimate --" %
+                                    (go_label, robust_est_label), 2)
+                        results.estimates[robust_est_label].add_gaugeoptimized(goparams, None, go_label, comm, printer - 3)
 
 
 def _add_badfit_estimates(results, base_estimate_label, badfit_options,
@@ -2285,9 +2360,16 @@ def _compute_wildcard_budget_1d_model(estimate, objfn_cache, mdc_objfn, paramete
     if gaugeopt_suite is None or gaugeopt_suite.gaugeopt_suite_names is None:
         gaugeopt_labels = None
         primitive_ops = list(ref.keys())
+        if sum([v**2 for v in ref.values()]) < 1e-4:
+            _warnings.warn("Reference values for 1D wildcard budget are all near-zero!"
+                           "This usually indicates an incorrect target model and will likely cause problems computing alpha.")
+
     else:
         gaugeopt_labels = gaugeopt_suite.gaugeopt_suite_names
         primitive_ops = list(ref[list(gaugeopt_labels)[0]].keys())
+        if sum([v**2 for v in ref[list(gaugeopt_labels)[0]].values()]) < 1e-4:
+            _warnings.warn("Reference values for 1D wildcard budget are all near-zero!"
+                           "This usually indicates an incorrect target model and will likely cause problems computing alpha.")
 
     if gaugeopt_labels is None:
         wcm = _wild.PrimitiveOpsSingleScaleWildcardBudget(primitive_ops, [ref[k] for k in primitive_ops],
@@ -2312,21 +2394,38 @@ def _compute_1d_reference_values_and_name(estimate, badfit_options, gaugeopt_sui
         if gaugeopt_suite is None or gaugeopt_suite.gaugeopt_suite_names is None:
             final_model = estimate.models['final iteration estimate']
             target_model = estimate.models['target']
-            gaugeopt_model = _alg.gaugeopt_to_target(final_model, target_model)
+
+            if isinstance(final_model, _ExplicitOpModel):
+                gaugeopt_model = _alg.gaugeopt_to_target(final_model, target_model)
+                operations_dict = gaugeopt_model.operations
+                targetops_dict = target_model.operations
+                preps_dict = gaugeopt_model.preps
+                targetpreps_dict = target_model.preps
+                povmops_dict = gaugeopt_model.povms
+            else:
+                # Local/cloud noise models don't have default_gauge_group attribute and can't be gauge
+                #  optimized - at least not easily.
+                gaugeopt_model = final_model
+                operations_dict = gaugeopt_model.operation_blks['gates']
+                targetops_dict = target_model.operation_blks['gates']
+                preps_dict = gaugeopt_model.prep_blks['layers']
+                targetpreps_dict = target_model.prep_blks['layers']
+                povmops_dict = {}  # HACK - need to rewrite povm_diamonddist below to work
+
             dd = {}
-            for key, op in gaugeopt_model.operations.items():
-                dd[key] = 0.5 * _tools.diamonddist(op.to_dense(), target_model.operations[key].to_dense())
+            for key, op in operations_dict.items():
+                dd[key] = 0.5 * _tools.diamonddist(op.to_dense(), targetops_dict[key].to_dense())
                 if dd[key] < 0:  # indicates that diamonddist failed (cvxpy failure)
                     _warnings.warn(("Diamond distance failed to compute %s reference value for 1D wildcard budget!"
                                     " Falling back to trace distance.") % str(key))
-                    dd[key] = _tools.jtracedist(op.to_dense(), target_model.operations[key].to_dense())
+                    dd[key] = _tools.jtracedist(op.to_dense(), targetops_dict[key].to_dense())
 
             spamdd = {}
-            for key, op in gaugeopt_model.preps.items():
+            for key, op in preps_dict.items():
                 spamdd[key] = _tools.tracedist(_tools.vec_to_stdmx(op.to_dense(), 'pp'),
-                                               _tools.vec_to_stdmx(target_model.preps[key].to_dense(), 'pp'))
+                                               _tools.vec_to_stdmx(targetpreps_dict[key].to_dense(), 'pp'))
 
-            for key in gaugeopt_model.povms.keys():
+            for key in povmops_dict.keys():
                 spamdd[key] = 0.5 * _tools.optools.povm_diamonddist(gaugeopt_model, target_model, key)
 
             dd['SPAM'] = sum(spamdd.values())
@@ -2573,23 +2672,14 @@ def _compute_wildcard_budget(objfn_cache, mdc_objfn, parameters, badfit_options,
             elif method_name == "barrier":
                 _opt.optimize_wildcard_budget_barrier(budget, L1weights, mdc_objfn, two_dlogl_threshold,
                                                       redbox_threshold, printer, **method_options)
-            elif method_name == "cvxopt":
-                _opt.optimize_wildcard_budget_cvxopt(budget, L1weights, mdc_objfn, two_dlogl_threshold,
-                                                     redbox_threshold, printer, **method_options)
-            elif method_name == "cvxopt_smoothed":
-                _opt.optimize_wildcard_budget_cvxopt_smoothed(budget, L1weights, mdc_objfn,
-                                                              two_dlogl_threshold, redbox_threshold,
-                                                              printer, **method_options)
-            elif method_name == "cvxopt_small":
-                _opt.optimize_wildcard_budget_cvxopt_zeroreg(budget, L1weights, mdc_objfn,
-                                                             two_dlogl_threshold, redbox_threshold, printer,
-                                                             **method_options)
             elif method_name == "cvxpy_noagg":
                 _opt.optimize_wildcard_budget_percircuit_only_cvxpy(budget, L1weights, mdc_objfn,
                                                                     redbox_threshold, printer,
                                                                     **method_options)
             elif method_name == "none":
                 pass
+            elif method_name in ("cvxopt", "cvxopt_smoothed", "cvxopt_small"):
+                raise ValueError(f"Support for {method_name} was removed in pyGSTi release 0.9.13.")
             else:
                 raise ValueError("Invalid wildcard method name: %s" % method_name)
 
@@ -2983,7 +3073,8 @@ class ModelEstimateResults(_proto.ProtocolResults):
         self.estimates[estimate_key] = estimate
 
     def add_model_test(self, target_model, themodel,
-                       estimate_key='test', gaugeopt_keys="auto", verbosity=2):
+                       estimate_key='test', gaugeopt_keys="auto", verbosity=2,
+                       simulator: Optional[ForwardSimulator.Castable]=None):
         """
         Add a new model-test (i.e. non-optimized) estimate to this `Results` object.
 
@@ -3010,6 +3101,11 @@ class ModelEstimateResults(_proto.ProtocolResults):
         verbosity : int, optional
             Level of detail printed to stdout.
 
+        simulator : ForwardSimulator.Castable or None
+            Ignored if None. If not None, then we call
+                fwdsim = ForwardSimulator.cast(simulator),
+            and we set the .sim attribute of every Model we encounter to fwdsim.
+
         Returns
         -------
         None
@@ -3030,7 +3126,7 @@ class ModelEstimateResults(_proto.ProtocolResults):
         from .modeltest import ModelTest as _ModelTest
         mdltest = _ModelTest(themodel, target_model, gaugeopt_suite,
                              objfn_builder, badfit_options, name=estimate_key, verbosity=verbosity)
-        test_result = mdltest.run(self.data)
+        test_result = mdltest.run(self.data, simulator=simulator)
         self.add_estimates(test_result)
 
     def view(self, estimate_keys, gaugeopt_keys=None):