Merge pull request #285 from pyGSTio/bugfix-numpy-deprecations

Bugfix numpy deprecations

pygsti/baseobjs/qubitgraph.py

@@ -188,12 +188,12 @@ def __init__(self, qubit_labels, initial_connectivity=None, initial_edges=None,
 
         #Determine whether we'll be using directions or not: set self.directions
         if initial_connectivity is not None:
-            if initial_connectivity.dtype == _np.bool:
+            if initial_connectivity.dtype == _np.bool_:
                 assert(direction_names is None), \
                     "`initial_connectivity` must hold *integer* direction-indices when `direction_names` is non-None"
             else:
                 #TODO: fix numpy integer-type test here
-                assert(initial_connectivity.dtype == _np.int or initial_connectivity.dtype == _np.int64), \
+                assert(initial_connectivity.dtype == _np.int_ or initial_connectivity.dtype == _np.int64), \
                     ("`initial_connectivity` can only have dtype == bool or "
                      "int (but has dtype=%s)") % str(initial_connectivity.dtype)
                 assert(direction_names is not None), \

pygsti/circuits/circuit.py

@@ -75,7 +75,7 @@ def _np_to_quil_def_str(name, input_array):
 def _num_to_rqc_str(num):
     """Convert float to string to be included in RQC quil DEFGATE block
     (as written by _np_to_quil_def_str)."""
-    num = _np.complex(_np.real_if_close(num))
+    num = _np.complex_(_np.real_if_close(num))
     if _np.imag(num) == 0:
         output = str(_np.real(num))
         return output

pygsti/circuits/circuitstructure.py

@@ -152,7 +152,7 @@ def elementvec_to_matrix(self, elementvec, layout, mergeop="sum"):
                 ret[i, j] = sum(elementvec[layout.indices(opstr)])
         elif '%' in mergeop:
             fmt = mergeop
-            ret = _np.nan * _np.ones((self.num_rows, self.num_cols), dtype=_np.object)
+            ret = _np.nan * _np.ones((self.num_rows, self.num_cols), dtype=_np.object_)
             for (i, j), opstr in self.elements.items():
                 ret[i, j] = ", ".join(["NaN" if _np.isnan(x) else
                                        (fmt % x) for x in elementvec[layout.indices(opstr)]])

pygsti/data/datacomparator.py

@@ -75,11 +75,11 @@ def _loglikelihood_ratio(n_list_list):
         The log-likehood ratio for this model comparison.
     """
     nListC = _np.sum(n_list_list, axis=0)
-    pListC = nListC / _np.float(_np.sum(nListC))
+    pListC = nListC / _np.float_(_np.sum(nListC))
     lC = _loglikelihood(pListC, nListC)
     li_list = []
     for nList in n_list_list:
-        pList = _np.array(nList) / _np.float(_np.sum(nList))
+        pList = _np.array(nList) / _np.float_(_np.sum(nList))
         li_list.append(_loglikelihood(pList, nList))
     lS = _np.sum(li_list)
     return -2 * (lC - lS)

pygsti/extras/crosstalk/core.py

@@ -937,7 +937,7 @@ def pairwise_indep_expts(q):
     for i in range(q):
         for a in range(q):
             for b in range(q):
-                vals[a*q+b,i] = _np.int(_np.mod(a*i+b,q))
+                vals[a*q+b,i] = _np.int_(_np.mod(a*i+b,q))
 
     length = _np.shape(vals)[0]
     return length, vals

pygsti/report/workspace.py

@@ -1426,7 +1426,7 @@ def __init__(self, parent_switchboard, name, dependencies):
         self.dependencies = dependencies
 
         shape = [len(self.parent.positionLabels[i]) for i in dependencies]
-        self.base = _np.empty(shape, dtype=_np.object)
+        self.base = _np.empty(shape, dtype=_np.object_)
         index_all = (slice(None, None),) * len(shape)
         self.base[index_all] = NotApplicable(self.ws)
 

pygsti/report/workspaceplots.py

@@ -1956,7 +1956,7 @@ def _outcome_to_str(x):  # same function as in writers.py
 
 
 def _addl_mx_fn_outcomes(plaq, x, y, layout):
-    slmx = _np.empty((plaq.num_rows, plaq.num_cols), dtype=_np.object)
+    slmx = _np.empty((plaq.num_rows, plaq.num_cols), dtype=_np.object_)
     for i, j, opstr in plaq:
         slmx[i, j] = ", ".join([_outcome_to_str(ol) for ol in layout.outcomes(opstr)])
     return slmx

pygsti/tools/group.py

@@ -29,7 +29,7 @@ def is_integer(x):
     bool
     """
     #TODO: combine with compattools.isint(x) ??
-    return bool(isinstance(x, int) or isinstance(x, _np.integer))
+    return bool(isinstance(x, int) or isinstance(x, _np.int_))
 
 
 def construct_1q_clifford_group():

test/unit/objects/test_qibo_evotype.py

@@ -8,16 +8,24 @@
 from pygsti.circuits import Circuit
 from pygsti.modelpacks import smq2Q_XYI as std
 from pygsti.modelpacks import smq1Q_XYI as std1Q
-from pygsti.evotypes import qibo as evo_qibo  # don't clobber qibo!
+
+#Deprecated numpy calls are currently breaking the qibo import
+#so add in a catch for this exception and skip this test if that happens.
+try:
+    from pygsti.evotypes import qibo as evo_qibo  # don't clobber qibo!
+except AttributeError:
+    _qibo = None
+
 from pygsti.evotypes.densitymx_slow.opreps import OpRepIdentityPlusErrorgen
 from pygsti.evotypes.densitymx.opreps import OpRepDenseSuperop
 from ..util import BaseCase
 
+#also catch the attribute error here
 try:
     import qibo as _qibo
     if version.parse(_qibo.__version__) < version.parse("0.1.7"):
         _qibo = None  # version too low - doesn't contain all the builtin gates, e.g. qibo.gates.S
-except ImportError:
+except (ImportError, AttributeError):
     _qibo = None