Applied suggested changes per @paulromano's code review

Co-authored-by: Paul Romano <paul.k.romano@gmail.com>

openmc/deplete/abc.py

@@ -22,7 +22,7 @@ from uncertainties import ufloat
 from openmc.data import DataLibrary
 from openmc.lib import MaterialFilter, Tally
 from openmc.checkvalue import check_type, check_greater_than
-from openmc import comm
+from openmc.mpi import comm
 from .results import Results
 from .chain import Chain
 from .results_list import ResultsList

openmc/deplete/helpers.py

@@ -10,7 +10,7 @@ import sys
 
 from numpy import dot, zeros, newaxis, asarray
 
-from openmc import comm
+from openmc.mpi import comm
 from openmc.checkvalue import check_type, check_greater_than
 from openmc.data import JOULE_PER_EV, REACTION_MT
 from openmc.lib import (

openmc/deplete/operator.py

@@ -20,7 +20,7 @@ from uncertainties import ufloat
 import openmc
 from openmc.checkvalue import check_value
 import openmc.lib
-from openmc import comm
+from openmc.mpi import comm
 from .abc import TransportOperator, OperatorResult
 from .atom_number import AtomNumber
 from .reaction_rates import ReactionRates

openmc/deplete/results.py

@@ -9,7 +9,7 @@ import copy
 import h5py
 import numpy as np
 
-from openmc import comm, MPI
+from openmc.mpi import comm, MPI
 from .reaction_rates import ReactionRates
 
 VERSION_RESULTS = (1, 1)

openmc/lib/core.py

@@ -363,6 +363,7 @@ def plot_geometry(output=True):
     """Plot geometry
 
     .. versionchanged:: 0.13.0
+       The *output* argument was added.
 
     Parameters
     ----------
@@ -388,6 +389,7 @@ def run(output=True):
     """Run simulation
 
     .. versionchanged:: 0.13.0
+       The *output* argument was added.
 
     Parameters
     ----------

openmc/model/model.py

@@ -109,15 +109,13 @@ class Model:
         self._cells_by_name = {}
         for cell in cells.values():
             if cell.name not in self._cells_by_name:
-                self._cells_by_name[cell.name] = [cell]
-            else:
-                self._cells_by_name[cell.name].append(cell)
+                self._cells_by_name[cell.name] = set()
+            self._cells_by_name[cell.name].add(cell)
         self._materials_by_name = {}
         for mat in mats:
             if mat.name not in self._materials_by_name:
-                self._materials_by_name[mat.name] = [mat]
-            else:
-                self._materials_by_name[mat.name].append(mat)
+                self._materials_by_name[mat.name] = set()
+            self._materials_by_name[mat.name].add(mat)
 
     @property
     def geometry(self):
@@ -196,8 +194,7 @@ class Model:
     def from_xml(cls, geometry='geometry.xml', materials='materials.xml',
                  settings='settings.xml'):
         """Create model from existing XML files
-        When initializing this way, the user must manually load plots, tallies,
-        the chain_file and fission_q attributes.
+        When initializing this way, the user must manually load plots and tallies.
 
         Parameters
         ----------
@@ -288,6 +285,8 @@ class Model:
         """Deplete model using specified timesteps/power
 
         .. versionchanged:: 0.13.0
+           The *final_step*, *operator_kwargs*, *directory*, and *output*
+           arguments were added.
 
         Parameters
         ----------
@@ -319,8 +318,7 @@ class Model:
         elif isinstance(operator_kwargs, dict):
             op_kwargs = operator_kwargs
         else:
-            msg = "operator_kwargs must be a dict or None"
-            raise ValueError(msg)
+            raise ValueError("operator_kwargs must be a dict or None")
 
         # Import openmc.deplete here so the Model can be used even if the
         # shared library is unavailable.

tests/unit_tests/test_deplete_chain.py

@@ -7,7 +7,7 @@ import os
 from pathlib import Path
 
 import numpy as np
-from openmc import comm
+from openmc.mpi import comm
 from openmc.deplete import Chain, reaction_rates, nuclide, cram, pool
 import pytest
 

tests/unit_tests/test_deplete_integrator.py

@@ -14,7 +14,7 @@ import numpy as np
 from uncertainties import ufloat
 import pytest
 
-from openmc import comm
+from openmc.mpi import comm
 from openmc.deplete import (
     ReactionRates, Results, ResultsList, OperatorResult, PredictorIntegrator,
     CECMIntegrator, CF4Integrator, CELIIntegrator, EPCRK4Integrator,