MANUAL Merge branch 'develop' into beta - so we can release 0.9.7.2

Some tests on TravisCI are still failing, but tests pass locally except
for known SVD errors during gauge opt.  We're in the process of getting
the TravisCI builds & tests working again.

Author: Erik Nielsen

packages/pygsti/_version.py

@@ -4,4 +4,4 @@
 #    in the file "license.txt" in the top-level pyGSTi directory
 #*****************************************************************
 """ PyGSTi version number """
-__version__ = "0.9.7.1"
+__version__ = "0.9.7.2"

packages/pygsti/baseobjs/label.py

@@ -639,7 +639,8 @@ def __new__(cls,name,tupOfTups,stateSpaceLabels,reps=1): # timestamp??
             The item data - a tuple of (string, state-space-labels) tuples
             which labels a parallel layer/level of a circuit.
         """
-        assert(isinstance(reps, _numbers.Integral) and isstr(name))
+        #if name is None: name = '' # backward compatibility (temporary - TODO REMOVE)
+        assert(isinstance(reps, _numbers.Integral) and isstr(name)), "Invalid name or reps: %s %s" % (str(name),str(reps))
         tupOfLabels = tuple((Label(tup) for tup in tupOfTups)) # Note: tup can also be a Label obj
         return tuple.__new__(cls, (name,stateSpaceLabels,reps) + tupOfLabels) # creates a CircuitLabel object using tuple's __new__
 

packages/pygsti/extras/drift/core.py

@@ -14,6 +14,7 @@
 
 from ... import objects as _obj
 from ...tools import hypothesis as _hyp
+from ...tools import compattools as _compat
 
 import numpy as _np
 import warnings as _warnings
@@ -68,7 +69,7 @@ def do_drift_characterization(ds, significance=0.05, marginalize='auto', transfo
                             spectrafrequencies='auto', testFreqInds=None,
                             groupoutcomes=None, enforceConstNumTimes='auto',
                             whichTests=(('avg','avg','avg'), ('per','avg','avg'), ('per','per','avg')), 
-                            betweenClassCorrection=True, inClassCorrection=('FWER','FWER','FDR','FDR'), 
+                            betweenClassCorrection=True, inClassCorrection=('FWER','FWER','FWER','FWER'), 
                             modelSelectionMethod=(('per','per','avg'),'detection'), estimator='FF-UAR', 
                             verbosity=1, name=None):
     """
@@ -256,7 +257,7 @@ def format_data(ds, marginalize='auto', groupoutcomes=None, enforceConstNumTimes
         # We do this, because this gets recorded in the results as whether we *have* enforced this.
         enforceConstNumTimes = False
 
-    if isinstance(marginalize,str):
+    if _compat.isstr(marginalize):
         assert(marginalize == 'auto')
         if len(list(ds.get_outcome_labels())) > 4:
             marginalize = True
@@ -816,4 +817,4 @@ def estimate_probability_trajectories(results, modelSelector=(('per','per','avg'
             #params, recon, uncert, aux = _est.estimate_probability_trace(timeseries, timestamps, results.transform, estimator,
             #                                                             hyperparameters, modes=modes, estimatorSettings)
 
-    return None
+    return None

packages/pygsti/extras/idletomography/idtcore.py

@@ -1092,7 +1092,6 @@ def do_idle_tomography(nQubits, dataset, maxLengths, pauliBasisDicts, maxweight=
         else:
             line_labels = (0,)
         GiStr = _objs.Circuit( idle_string, line_labels=line_labels )
-        print("Dataset has ",dataset)
     else:
         GiStr = _objs.Circuit( idle_string, num_lines=nQubits )
 

packages/pygsti/extras/rb/simulate.py

@@ -142,7 +142,7 @@ def oneshot_circuit_simulator_for_tensored_independent_pauli_errors(circuit, psp
 
     for l in range(depth):
 
-        layer = circuit.get_layer_with_idles(l,idleGateName=idle1Q_placeholder)
+        layer = circuit.get_layer_with_idles(l, idleGateName=idle1Q_placeholder)
         s, p = _symp.symplectic_rep_of_clifford_layer(layer,n,Qlabels=circuit.line_labels,srep_dict=srep)        
         # Apply the perfect layer to the current state.
         sout, pout = _symp.apply_clifford_to_stabilizer_state(s, p, sout, pout)
@@ -183,7 +183,7 @@ def oneshot_circuit_simulator_for_tensored_independent_pauli_errors(circuit, psp
     return outputasstring
 
 def rb_with_pauli_errors(pspec, errormodel, lengths, k, counts, subsetQs=None, filename=None, rbtype='DRB', 
-                         rbspec =[], returndata=True, appenddata=False, verbosity=0):
+                         rbspec =[], returndata=True, appenddata=False, verbosity=0, idle1Q_placeholder='I'):
     """
     Simulates RB with Pauli errors. Can be used to simulated Clifford RB, direct RB and mirror RB. This
     function:
@@ -293,7 +293,7 @@ def rb_with_pauli_errors(pspec, errormodel, lengths, k, counts, subsetQs=None, f
             #    print(" - Simulating circuit...",end='')
 
             outcome = circuit_simulator_for_tensored_independent_pauli_errors(
-                c, pspec, errormodel, counts, alloutcomes=False,idle1Q_placeholder='I')
+                c, pspec, errormodel, counts, alloutcomes=False, idle1Q_placeholder=idle1Q_placeholder)
               #EGN: Hardcoded 'I' here. Could make this into an arg, but there's really
               #  no need for the user to modify this unless they use 'I' as a gate label.
             if verbosity > 0: print(lind+1,end=',')
@@ -498,7 +498,9 @@ def error_row(er): return _np.array([1-er,0.,0.,er])
 
     return errormodel
 
-
+#
+# TODO : DOES THIS NEED AND IDLE PLACEHOLDER?
+#
 def create_local_pauli_error_model(pspec, oneQgate_errorrate_dict, twoQgate_errorrate_dict,
                                   measurement_errorrate_dict={}, ptype='uniform'):
     """

packages/pygsti/objects/dataset.py

@@ -1771,7 +1771,18 @@ def load(self, fileOrFilename):
         else:
             f = fileOrFilename
 
-        state_dict = _pickle.load(f)
+        try:
+            state_dict = _pickle.load(f)
+        except AttributeError:
+            # HACK TO ALLOW UUIDs saved on python3.7 work with earlier python versions that don't have uuid.SafeUUID
+            # HACK - maybe move this to leagacyio to deal with Python 3 versions < 3.7 not having SafeUUID?
+            class dummy_SafeUUID(object): 
+                def __new__(self,*args):  
+                    return _uuid.UUID.__new__(uuid.UUID,*args)
+            _sys.modules['uuid'].SafeUUID = dummy_SafeUUID
+            state_dict = _pickle.load(f)
+            del _sys.modules['uuid'].SafeUUID
+            
 
         if "gsIndexKeys" in state_dict:
             _warnings.warn("Loading a deprecated-format DataSet.  Please re-save asap.")

packages/pygsti/report/plotly_plot_ex.py

@@ -7,6 +7,7 @@
 #*****************************************************************
 
 import os as _os
+from plotly import __version__ as _plotly_version
 from plotly import tools as _plotlytools
 from plotly.offline.offline import _plot_html
 #from plotly.offline.offline import get_plotlyjs
@@ -99,12 +100,17 @@ def plot_ex(figure_or_data, show_link=True, link_text='Export to plot.ly',
     config['showLink'] = show_link
     config['linkText'] = link_text
 
+    #Add version-dependent kwargs to _plot_html call below
+    kwargs = {}
+    if tuple(map(int,_plotly_version.split('.'))) >= (3,7,0): # then auto_play arg exists
+        kwargs['auto_play'] = False
+    
     #Note: removing width and height from layout above causes default values to
-    # be used (the '100%'s hardcoded below) which subsequently trigger adding a resize script.
+    # be used (the '100%'s hardcoded below) which subsequently trigger adding a resize script.        
     plot_html, plotdivid, _, _ = _plot_html(
         fig, config, validate, '100%', '100%',
-        global_requirejs=False) #no need for global_requirejs here 
-                                #since we now extract js and remake full script.
+        global_requirejs=False, #no need for global_requirejs here 
+        **kwargs)               #since we now extract js and remake full script.
 
     if orig_width: fig['layout']['width'] = orig_width
     if orig_height: fig['layout']['height'] = orig_height

packages/pygsti/report/workspaceplots.py

@@ -1623,14 +1623,14 @@ def _create(self, plottypes, gss, dataset, model,
                 linlog_color = "yellow"
                 ytitle="chi<sup>2</sup>"
                 mx_fn = _mx_fn_directchi2 # use a *global* function so cache can tell it's the same
-                extra_arg = (dataset, directGSTmodels, minProbClipForWeighting)
+                extra_arg = (dataset, directGSTmodels, minProbClipForWeighting, gss)
 
             elif ptyp == "directlogl":
                 colormapType = "linlog"
                 linlog_color = "yellow"
                 ytitle="Direct 2 log(L ratio)"
                 mx_fn = _mx_fn_directlogl # use a *global* function so cache can tell it's the same
-                extra_arg = (dataset, directGSTmodels, minProbClipForWeighting)
+                extra_arg = (dataset, directGSTmodels, minProbClipForWeighting, gss)
 
             elif ptyp == "dscmp":
                 assert(dscomparator is not None), \
@@ -1818,13 +1818,13 @@ def _mx_fn_errorrate(plaq,x,y,directGSTmodels): #error rate as 1x1 matrix which
     return _np.array( [[ _ph.small_eigval_err_rate(plaq.base, directGSTmodels) ]] )
 
 def _mx_fn_directchi2(plaq,x,y,extra):
-    dataset, directGSTmodels, minProbClipForWeighting = extra
+    dataset, directGSTmodels, minProbClipForWeighting, gss = extra
     return _ph.direct_chi2_matrix(
         plaq, gss, dataset, directGSTmodels.get(plaq.base,None),
         minProbClipForWeighting)
 
 def _mx_fn_directlogl(plaq,x,y,extra):
-    dataset, directGSTmodels, minProbClipForWeighting = extra
+    dataset, directGSTmodels, minProbClipForWeighting, gss = extra
     return _ph.direct_logl_matrix(
         plaq, gss, dataset, directGSTmodels.get(plaq.base,None),
         minProbClipForWeighting)

scripts/upgrade2v0.9.7.py

@@ -442,6 +442,7 @@ def main(argv):
 "gateset" : "model",
 "GateMap" : "MapOperator",
 "GateRep" : "OpRep",
+"pyquil.gates" : "pyquil.gates",
 ".gates" : ".operations",
 "dgate" : "doperation",
 "hgate" : "hoperation",

test/test_packages/algorithms/testGaugeOpt.py

@@ -92,7 +92,7 @@ def test_gaugeopt_and_contract(self):
         mdl_lgst_tp         = self.runSilent(pygsti.gaugeopt_to_target, mdl_lgst, None,
                                             spam_penalty_factor=1.0, verbosity=10, checkJac=True)
 
-        mdl_lgst.basis = Basis("gm",2) #so CPTP optimizations can work on mdl_lgst
+        mdl_lgst.basis = Basis.cast("gm",2) #so CPTP optimizations can work on mdl_lgst
         mdl_lgst_cptp       = self.runSilent(pygsti.gaugeopt_to_target, mdl_lgst, None,
                                             cptp_penalty_factor=1.0, spam_penalty_factor=1.0, verbosity=10, checkJac=True)