Fixes Python2 compatibility issues in new workspace/reports. Cleans u…

…p factory.py.

Adds a new "compattools.py" file with "isstr" and "isint" function to
properly check if something is an integer or string in Python2 or Python3
(the issues involved are that Python2 has a 'long' type that Python3
doesn't, and in Python3 the default string type is unicode).  These new
functions have been added throughout pyGSTi to replace isinstance(x, int)
and isinstance(x, str) and variants thereof to give better Python2
compatibility across the board.  Such comparisons are especially relevant
to the reporting code.

Fixes a bug with using the 'exec' statement within Python2 -- (you can't
use 'exec' in a function which contains nested functions unless you specify
the locals).

Consolidates code within factory.py, adding some internal subroutines and
making _merge_template do more processing (e.g. inlining CSS files).
Additional linlogPercentage and errgen_type parameters added to factory
functions, so start moving away from having "display options" contained
in a Results object.

Adds precision argument to WorkspaceTable's render() function, which
 should later get plumbed up to an argument of the factory functions.

All of the recently added tutorials now run using a python2 kernel,
which is the closest thing we have to a python2 test at this point.

packages/pygsti/construction/gatestringconstruction.py

@@ -11,6 +11,7 @@
 import numpy.random as _rndm
 
 from ..tools import listtools as _lt
+from ..tools import compattools as _compat
 from ..objects import gatestring as _gs
 from .spamspecconstruction import get_spam_strs as _get_spam_strs
 
@@ -91,7 +92,7 @@ def create_gatestring_list(*args,**kwargs):
                 gateStr = result
             elif isinstance(result,list) or isinstance(result,tuple):
                 gateStr = _gs.GateString(result)
-            elif isinstance(result,str):
+            elif _compat.isstr(result):
                 gateStr = _gs.GateString(None, result)
             lst.append(gateStr)
 
@@ -514,7 +515,7 @@ def gatestring_list( listOfGateLabelTuplesOrStrings ):
             ret.append(x)
         elif isinstance(x,tuple) or isinstance(x,list):
             ret.append( _gs.GateString(x) )
-        elif isinstance(x,str):
+        elif _compat.isstr(x):
             ret.append( _gs.GateString(None, x) )
         else:
             raise ValueError("Cannot convert type %s into a GateString" % str(type(x)))

packages/pygsti/drivers/longsequence.py

@@ -18,6 +18,7 @@
 from .. import construction as _construction
 from .. import objects as _objs
 from .. import io as _io
+from ..tools import compattools as _compat
 
 def do_long_sequence_gst(dataFilenameOrSet, targetGateFilenameOrSet,
                          prepStrsListOrFilename, effectStrsListOrFilename,
@@ -189,24 +190,24 @@ def do_long_sequence_gst(dataFilenameOrSet, targetGateFilenameOrSet,
     if advancedOptions is None: advancedOptions = {}
 
     #Get/load fiducials
-    if isinstance(prepStrsListOrFilename, str):
+    if _compat.isstr(prepStrsListOrFilename):
         prepStrs = _io.load_gatestring_list(prepStrsListOrFilename)
     else: prepStrs = prepStrsListOrFilename
 
     if effectStrsListOrFilename is None:
         effectStrs = prepStrs #use same strings for effectStrs if effectStrsListOrFilename is None
     else:
-        if isinstance(effectStrsListOrFilename, str):
+        if _compat.isstr(effectStrsListOrFilename):
             effectStrs = _io.load_gatestring_list(effectStrsListOrFilename)
         else: effectStrs = effectStrsListOrFilename
 
     #Get/load germs
-    if isinstance(germsListOrFilename, str):
+    if _compat.isstr(germsListOrFilename):
         germs = _io.load_gatestring_list(germsListOrFilename)
     else: germs = germsListOrFilename
 
     #Get/load target gateset
-    if isinstance(targetGateFilenameOrSet, str):
+    if _compat.isstr(targetGateFilenameOrSet):
         gs_target = _io.load_gateset(targetGateFilenameOrSet)
     else:
         gs_target = targetGateFilenameOrSet #assume a GateSet object
@@ -340,13 +341,13 @@ def do_long_sequence_gst_base(dataFilenameOrSet, targetGateFilenameOrSet,
     printer = _objs.VerbosityPrinter.build_printer(verbosity, comm)
 
     #Get/load target gateset
-    if isinstance(targetGateFilenameOrSet, str):
+    if _compat.isstr(targetGateFilenameOrSet):
         gs_target = _io.load_gateset(targetGateFilenameOrSet)
     else:
         gs_target = targetGateFilenameOrSet #assume a GateSet object
 
     #Get/load dataset
-    if isinstance(dataFilenameOrSet, str):
+    if _compat.isstr(dataFilenameOrSet):
         ds = _io.load_dataset(dataFilenameOrSet, True, "aggregate", printer)
         default_dir = _os.path.dirname(dataFilenameOrSet) #default directory for reports, etc
         default_base = _os.path.splitext( _os.path.basename(dataFilenameOrSet) )[0]

packages/pygsti/objects/gatecalc.py

@@ -15,6 +15,7 @@
 from ..tools import gatetools as _gt
 from ..tools import mpitools as _mpit
 from ..tools import slicetools as _slct
+from ..tools import compattools as _compat
 from .profiler import DummyProfiler as _DummyProfiler
 _dummy_profiler = _DummyProfiler()
 
@@ -99,7 +100,7 @@ def _is_remainder_spamlabel(self, label):
         probabilities such that all SPAM label probabilities
         sum exactly to 1.0.
         """
-        if not isinstance(label,str): return False #b/c label could be a custom (rho,E) pair
+        if not _compat.isstr(label): return False #b/c label could be a custom (rho,E) pair
         return bool(self.spamdefs[label] == (self._remainderLabel, self._remainderLabel))
 
     def _get_remainder_row_index(self, spam_label_rows):

packages/pygsti/objects/gatemapcalc.py

@@ -15,6 +15,7 @@
 from ..tools import gatetools as _gt
 from ..tools import mpitools as _mpit
 from ..tools import slicetools as _slct
+from ..tools import compattools as _compat
 from .profiler import DummyProfiler as _DummyProfiler
 from .verbosityprinter import VerbosityPrinter as _VerbosityPrinter
 from .mapevaltree import MapEvalTree as _MapEvalTree
@@ -80,7 +81,7 @@ def __init__(self, dim, gates, preps, effects, povm_identity, spamdefs,
 
     #Same as GateMatrixCalc, but not general enough to be in base class
     def _rhoE_from_spamLabel(self, spamLabel):
-        if isinstance(spamLabel,str):
+        if _compat.isstr(spamLabel):
             (rholabel,elabel) = self.spamdefs[spamLabel]
             rho = self.preps[rholabel]
             E   = _np.conjugate(_np.transpose(self._get_evec(elabel)))

packages/pygsti/objects/gatematrixcalc.py

@@ -15,6 +15,7 @@
 from ..tools import gatetools as _gt
 from ..tools import mpitools as _mpit
 from ..tools import slicetools as _slct
+from ..tools import compattools as _compat
 from .profiler import DummyProfiler as _DummyProfiler
 from .verbosityprinter import VerbosityPrinter as _VerbosityPrinter
 from .matrixevaltree import MatrixEvalTree as _MatrixEvalTree
@@ -1561,7 +1562,7 @@ def _scaleExp(self, scaleExps):
 
 
     def _rhoE_from_spamLabel(self, spamLabel):
-        if isinstance(spamLabel,str):
+        if _compat.isstr(spamLabel):
             (rholabel,elabel) = self.spamdefs[spamLabel]
             rho = self.preps[rholabel]
             E   = _np.conjugate(_np.transpose(self._get_evec(elabel)))

packages/pygsti/objects/gateset.py

@@ -19,6 +19,7 @@
 from ..tools import gatetools as _gt
 from ..tools import likelihoodfns as _lf
 from ..tools import jamiolkowski as _jt
+from ..tools import compattools as _compat
 
 from . import evaltree as _evaltree
 from . import gate as _gate
@@ -2787,7 +2788,7 @@ def rotate(self, rotate=None, max_rotate=None, seed=None):
                 newGateset.gates[label].rotate(rot, myBasis)
 
         elif rotate is not None:
-            assert(isinstance(rotate,float) or isinstance(rotate,int) or len(rotate) == dim-1), "Invalid 'rotate' argument"
+            assert(isinstance(rotate,float) or _compat.isint(rotate) or len(rotate) == dim-1), "Invalid 'rotate' argument"
             for (i,label) in enumerate(self.gates):
                 newGateset.gates[label].rotate(rotate, myBasis)
 

packages/pygsti/objects/gatestring.py

@@ -7,6 +7,7 @@
 """ Defines the GateString class and derived classes which represent gate strings."""
 
 import numpy as _np
+from ..tools import compattools as _compat
 
 def _gateSeqToStr(seq):
     if len(seq) == 0: return "{}" #special case of empty gate string
@@ -161,7 +162,7 @@ def __add__(self,x):
         return GateString(self.tup + x.tup, s, bCheck=False)
 
     def __mul__(self,x):
-        assert( (isinstance(x,int) or _np.issubdtype(x,int)) and x >= 0)
+        assert( (_compat.isint(x) or _np.issubdtype(x,int)) and x >= 0)
         if x > 1: s = "(%s)^%d" % (self.str,x)
         elif x == 1: s = "(%s)" % self.str
         else: s = "{}"

packages/pygsti/objects/labeldicts.py

@@ -10,6 +10,7 @@
 
 from . import spamvec as _sv
 from . import gate as _gate
+from ..tools import compattools as _compat
 
 class PrefixOrderedDict(_collections.OrderedDict):
     def __init__(self, prefix, items=[]):
@@ -203,7 +204,7 @@ def __init__(self, remainderLabel, items=[]):
         super(OrderedSPAMLabelDict,self).__init__(items)
 
     def __setitem__(self, key, val):
-        if not isinstance(key, str):
+        if not _compat.isstr(key):
             key = str(key)
         if type(val) != tuple or len(val) != 2:
             raise KeyError("SPAM label values must be 2-tuples!")

packages/pygsti/objects/protectedarray.py

@@ -1,5 +1,6 @@
 from __future__ import division, print_function, absolute_import, unicode_literals
 import numpy as _np
+from ..tools import compattools as _compat
 
 class ProtectedArray(object):
     """
@@ -21,7 +22,7 @@ def __init__(self, input_array, indicesToProtect=None):
             for ky,L in zip(indicesToProtect,self.base.shape):
                 if isinstance( ky, slice ):
                     pindices = range(*ky.indices(L))
-                elif isinstance( ky, int ):
+                elif _compat.isint( ky ):
                     i = ky+L if ky<0 else ky
                     if i < 0 or i > L:
                         raise IndexError("index (%d) is out of range." % ky)
@@ -109,7 +110,7 @@ def __getitem__( self, key ) :
                     nTotalInDim = len(indices)
                     nUnprotectedInCurDim = (len(indices) - len(new_pindices))
 
-                elif isinstance( ky, int ):
+                elif _compat.isint( ky ):
                     i = ky+L if ky<0 else ky
                     if i > L:
                         raise IndexError("The index (%d) is out of range." % ky)
@@ -177,7 +178,7 @@ def __setitem__( self, key, val ) :
                         protectionViolation.append(True)
                     else: protectionViolation.append(False)
 
-                elif isinstance( ky, int ):
+                elif _compat.isint( ky ):
                     i = ky+L if ky<0 else ky
                     if i > L:
                         raise IndexError("The index (%d) is out of range." % ky)

packages/pygsti/objects/spamvec.py

@@ -13,6 +13,7 @@
 from ..      import optimize as _opt
 from ..tools import matrixtools as _mt
 from ..tools import gatetools as _gt
+from ..tools import compattools as _compat
 from .protectedarray import ProtectedArray as _ProtectedArray
 
 
@@ -537,7 +538,7 @@ def depolarize(self, amount):
         -------
         None
         """
-        if isinstance(amount,float) or isinstance(amount,int):
+        if isinstance(amount,float) or _compat.isint(amount):
             D = _np.diag( [1]+[1-amount]*(self.dim-1) )
         else:
             assert(len(amount) == self.dim-1)
@@ -748,7 +749,7 @@ def depolarize(self, amount):
         -------
         None
         """
-        if isinstance(amount,float) or isinstance(amount,int):
+        if isinstance(amount,float) or _compat.isint(amount):
             D = _np.diag( [1]+[1-amount]*(self.dim-1) )
         else:
             assert(len(amount) == self.dim-1)

packages/pygsti/objects/verbosityprinter.py

@@ -1,10 +1,11 @@
 from __future__ import division, print_function, absolute_import, unicode_literals
-import numbers as _numbers
 from contextlib import contextmanager as _contextmanager
 from copy       import deepcopy as _dc
 import sys         as _sys
 import math        as _math # used for digit formatting
 
+from ..tools import compattools as _compat
+
 def _num_digits(n):
     return int(_math.log10(n)) + 1 if n > 0 else 1
 
@@ -183,7 +184,7 @@ def build_printer(verbosity, comm=None):
           The printer object, constructed from either an integer or another printer
 
         '''
-        if isinstance(verbosity, _numbers.Integral):
+        if _compat.isint(verbosity):
             printer = VerbosityPrinter(verbosity, comm=comm)
         else:
             printer = verbosity.clone() # deepcopy the printer object if it has been passed as a verbosity

packages/pygsti/report/colormaps.py

@@ -175,7 +175,7 @@ def normalize(self, value):
         #vmin, vmax, midpoint = self.vmin, self.vmax, self.midpoint
         #
         #is_scalar = False
-        #if isinstance(value, float) or isinstance(value, int):
+        #if isinstance(value, float) or _compat.isint(value, int):
         #    is_scalar = True
         #result = _np.ma.array(value)
         #
@@ -223,7 +223,7 @@ def normalize(self, value):
         return value
 
         #is_scalar = False
-        #if isinstance(value, float) or isinstance(value, int):
+        #if isinstance(value, float) or _compat.isint(value, int):
         #    is_scalar = True
         #
         #result = _np.ma.array(value)