Merge pull request #1096 from paulromano/pyapi-reaction-fix

Support IncidentNeutron.from_hdf5() for files without 'redundant'

examples/jupyter/mgxs-part-ii.ipynb

@@ -2048,8 +2048,8 @@
     "o16 = df[df['nuclide'] == 'O16']['mean']\n",
     "\n",
     "# Cast DataFrames as NumPy arrays\n",
-    "h1 = h1.as_matrix()\n",
-    "o16 = o16.as_matrix()\n",
+    "h1 = h1.values\n",
+    "o16 = o16.values\n",
     "\n",
     "# Reshape arrays to 2D matrix for plotting\n",
     "h1.shape = (fine_groups.num_groups, fine_groups.num_groups)\n",

openmc/arithmetic.py

@@ -1,6 +1,6 @@
 import sys
 import copy
-from collections import Iterable
+from collections.abc import Iterable
 
 import numpy as np
 import pandas as pd

openmc/data/photon.py

@@ -1,4 +1,5 @@
-from collections import OrderedDict, Mapping, Callable
+from collections import OrderedDict
+from collections.abc import Mapping, Callable
 from copy import deepcopy
 from io import StringIO
 from numbers import Integral, Real
@@ -740,7 +741,7 @@ class IncidentPhoton(EqualityMixin):
                         shell_values.insert(0, None)
                         df = relax.transitions[shell].replace(
                             shell_values, range(len(shell_values)))
-                        sub_group.create_dataset('transitions', data=df.as_matrix())
+                        sub_group.create_dataset('transitions', data=df.values)
 
                 # Determine threshold
                 threshold = rx.xs.x[0]

openmc/data/reaction.py

@@ -924,7 +924,7 @@ class Reaction(EqualityMixin):
         rx = cls(mt)
         rx.q_value = group.attrs['Q_value']
         rx.center_of_mass = bool(group.attrs['center_of_mass'])
-        rx.redundant = bool(group.attrs['redundant'])
+        rx.redundant = bool(group.attrs.get('redundant', False))
 
         # Read cross section at each temperature
         for T, Tgroup in group.items():

openmc/data/resonance_covariance.py

@@ -1,4 +1,4 @@
-from collections import MutableSequence
+from collections.abc import MutableSequence
 import warnings
 import io
 import copy

openmc/filter.py

@@ -1,5 +1,6 @@
 from abc import ABCMeta
-from collections import Iterable, OrderedDict
+from collections import OrderedDict
+from collections.abc import Iterable
 import copy
 import hashlib
 from itertools import product

openmc/mesh.py

@@ -1,4 +1,4 @@
-from collections import Iterable
+from collections.abc import Iterable
 from numbers import Real, Integral
 from xml.etree import ElementTree as ET
 import sys

openmc/mgxs/groups.py

@@ -1,4 +1,4 @@
-from collections import Iterable
+from collections.abc import Iterable
 from numbers import Real
 import copy
 import sys

openmc/universe.py

@@ -1,4 +1,5 @@
-from collections import OrderedDict, Iterable
+from collections import OrderedDict
+from collections.abc import Iterable
 from copy import copy, deepcopy
 from numbers import Integral, Real
 import random

tests/unit_tests/test_data_decay.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 
-from collections import Mapping
+from collections.abc import Mapping
 import os
 from math import log
 

tests/unit_tests/test_data_misc.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 
-from collections import Mapping
+from collections.abc import Mapping
 import os
 
 import numpy as np

tests/unit_tests/test_data_neutron.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 
-from collections import Mapping, Callable
+from collections.abc import Mapping, Callable
 import os
 
 import numpy as np

tests/unit_tests/test_data_photon.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 
-from collections import Mapping, Callable
+from collections.abc import Mapping, Callable
 import os
 
 import numpy as np

tests/unit_tests/test_data_thermal.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 
-from collections import Callable
+from collections.abc import Callable
 import os
 
 import numpy as np