Fix a few warnings, rename add_to_tallies_file (#3639)

docs/source/usersguide/random_ray.rst

@@ -765,7 +765,7 @@ energy decomposition::
 
   # Create a "tallies.xml" file for the MGXS Library
   tallies = openmc.Tallies()
-  mgxs_lib.add_to_tallies_file(tallies, merge=True)
+  mgxs_lib.add_to_tallies(tallies, merge=True)
 
   # Export
   tallies.export_to_xml()

openmc/deplete/chain.py

@@ -630,7 +630,7 @@ class Chain:
 
         n = len(self)
 
-        # we accumulate indices and value entries for everything and create the matrix 
+        # we accumulate indices and value entries for everything and create the matrix
         # in one step at the end to avoid expensive index checks scipy otherwise does.
         rows, cols, vals = [], [], []
         def setval(i, j, val):
@@ -716,14 +716,17 @@ class Chain:
         return sp.csc_matrix((vals, (rows, cols)), shape=(n, n))
 
     def add_redox_term(self, matrix, buffer, oxidation_states):
-        """Adds a redox term to the depletion matrix from data contained in
+        r"""Adds a redox term to the depletion matrix from data contained in
         the matrix itself and a few user-inputs.
 
         The redox term to add to the buffer nuclide :math:`N_j` can be written
-        as: :math:`\frac{dN_j(t)}{dt} =
-                \cdots - \frac{1}{OS_j}\sum_i N_i a_{ij} \cdot OS_i `
+        as:
 
-        where :math:`OS` is the oxidation states vector and `a_{ij}` the
+        .. math::
+            \frac{dN_j(t)}{dt} = \cdots - \frac{1}{OS_j}\sum_i N_i a_{ij}
+            \cdot OS_i
+
+        where :math:`OS` is the oxidation states vector and :math:`a_{ij}` the
         corresponding term in the Bateman matrix.
 
         Parameters

openmc/mgxs/library.py

@@ -556,14 +556,14 @@ class Library:
 
                 self.all_mgxs[domain.id][mgxs_type] = mgxs
 
-    def add_to_tallies_file(self, tallies_file, merge=True):
-        """Add all tallies from all MGXS objects to a tallies file.
+    def add_to_tallies(self, tallies, merge=True):
+        """Add tallies from all MGXS objects to a tallies object.
 
         NOTE: This assumes that :meth:`Library.build_library` has been called
 
         Parameters
         ----------
-        tallies_file : openmc.Tallies
+        tallies : openmc.Tallies
             A Tallies collection to add each MGXS' tallies to generate a
             'tallies.xml' input file for OpenMC
         merge : bool
@@ -572,7 +572,7 @@ class Library:
 
         """
 
-        cv.check_type('tallies_file', tallies_file, openmc.Tallies)
+        cv.check_type('tallies', tallies, openmc.Tallies)
 
         # Add tallies from each MGXS for each domain and mgxs type
         for domain in self.domains:
@@ -587,7 +587,15 @@ class Library:
                             = list(range(1, self.num_delayed_groups + 1))
 
                 for tally in mgxs.tallies.values():
-                    tallies_file.append(tally, merge=merge)
+                    tallies.append(tally, merge=merge)
+
+    def add_to_tallies_file(self, tallies_file, merge=True):
+        warn(
+            "The Library.add_to_tallies_file(...) method has been renamed to"
+            "add_to_tallies(...) and will be removed in a future version of "
+            "OpenMC.", FutureWarning
+        )
+        self.add_to_tallies(tallies_file, merge=merge)
 
     def load_from_statepoint(self, statepoint):
         """Extracts tallies in an OpenMC StatePoint with the data needed to

openmc/mgxs/mgxs.py

@@ -2127,8 +2127,8 @@ class MGXS:
             df['std. dev.'] /= np.tile(densities, tile_factor)
 
             # Replace NaNs by zeros (happens if nuclide density is zero)
-            df['mean'].replace(np.nan, 0.0, inplace=True)
-            df['std. dev.'].replace(np.nan, 0.0, inplace=True)
+            df['mean'] = df['mean'].replace(np.nan, 0.0)
+            df['std. dev.'] = df['std. dev.'].replace(np.nan, 0.0)
 
         # Sort the dataframe by domain type id (e.g., distribcell id) and
         # energy groups such that data is from fast to thermal

openmc/model/model.py

@@ -1791,7 +1791,7 @@ class Model:
             mgxs_lib.build_library()
 
             # Create a "tallies.xml" file for the MGXS Library
-            mgxs_lib.add_to_tallies_file(model.tallies, merge=True)
+            mgxs_lib.add_to_tallies(model.tallies, merge=True)
 
             # Run
             statepoint_filename = model.run(cwd=directory)
@@ -1980,7 +1980,7 @@ class Model:
         mgxs_lib.build_library()
 
         # Create a "tallies.xml" file for the MGXS Library
-        mgxs_lib.add_to_tallies_file(model.tallies, merge=True)
+        mgxs_lib.add_to_tallies(model.tallies, merge=True)
 
         # Run
         statepoint_filename = model.run(cwd=directory)
@@ -2075,7 +2075,7 @@ class Model:
         mgxs_lib.build_library()
 
         # Create a "tallies.xml" file for the MGXS Library
-        mgxs_lib.add_to_tallies_file(model.tallies, merge=True)
+        mgxs_lib.add_to_tallies(model.tallies, merge=True)
 
         # Run
         statepoint_filename = model.run(cwd=directory)

openmc/tallies.py

@@ -738,13 +738,9 @@ class Tally(IDManagerMixin):
 
         Notes
         -----
-        This test is based on D'Agostino and Pearson's test [1]_. The test
-        requires at least 8 realizations to produce valid results.
-
-        References
-        ----------
-        .. [1] D'Agostino, R. B. (1971), "An omnibus test of normality for
-               moderate and large sample size", Biometrika, 58, 341-348
+        This test is based on `D'Agostino and Pearson's test
+        <https://doi.org/10.1093/biomet/60.3.613>`_. The test requires at least
+        8 realizations to produce valid results.
 
         """
         n = self.num_realizations
@@ -788,8 +784,8 @@ class Tally(IDManagerMixin):
         Parameters
         ----------
         alternative : {'two-sided', 'less', 'greater'}, optional
-            Defines the alternative hypothesis. Default is 'two-sided'.
-            The following options are available:
+            Defines the alternative hypothesis. Default is 'two-sided'. The
+            following options are available:
 
             * 'two-sided': the kurtosis of the distribution is different from
               that of the normal distribution
@@ -813,14 +809,9 @@ class Tally(IDManagerMixin):
 
         Notes
         -----
-        This test is based on D'Agostino and Pearson's test [1]_. The test
-        is typically recommended for at least 20 realizations to produce
-        valid results.
-
-        References
-        ----------
-        .. [1] D'Agostino, R. B. (1971), "An omnibus test of normality for
-               moderate and large sample size", Biometrika, 58, 341-348
+        This test is based on `D'Agostino and Pearson's test
+        <https://doi.org/10.1093/biomet/60.3.613>`_. The test is typically
+        recommended for at least 20 realizations to produce valid results.
 
         """
         n = self.num_realizations
@@ -855,9 +846,9 @@ class Tally(IDManagerMixin):
     def normaltest(self, alternative: str = "two-sided"):
         """Perform D'Agostino and Pearson's omnibus test for normality.
 
-        This method tests the null hypothesis that a sample comes from a
-        normal distribution. It combines skewness and kurtosis to produce an
-        omnibus test of normality.
+        This method tests the null hypothesis that a sample comes from a normal
+        distribution. It combines skewness and kurtosis to produce an omnibus
+        test of normality.
 
         Parameters
         ----------
@@ -886,23 +877,19 @@ class Tally(IDManagerMixin):
         Notes
         -----
         This test combines a test for skewness and a test for kurtosis to
-        produce an omnibus test [1]_. The test statistic is:
+        produce an `omnibus test <https://doi.org/10.1093/biomet/60.3.613>`_.
+        The test statistic is:
 
         .. math::
 
             K^2 = Z_1^2 + Z_2^2
 
-        where :math:`Z_1` is the z-score from the skewness test and
-        :math:`Z_2` is the z-score from the kurtosis test. This statistic
-        follows a chi-square distribution with 2 degrees of freedom.
+        where :math:`Z_1` is the z-score from the skewness test and :math:`Z_2`
+        is the z-score from the kurtosis test. This statistic follows a
+        chi-square distribution with 2 degrees of freedom.
 
         The test requires at least 20 realizations to produce valid results.
 
-        References
-        ----------
-        .. [1] D'Agostino, R. B. and Pearson, E. S. (1973), "Tests for
-               departure from normality", Biometrika, 60, 613-622
-
         """
         n = self.num_realizations
         if n < 20:

tests/regression_tests/mgxs_library_ce_to_mg/test.py

@@ -28,7 +28,7 @@ class MGXSTestHarness(PyAPITestHarness):
         self.mgxs_lib.build_library()
 
         # Initialize a tallies file
-        self.mgxs_lib.add_to_tallies_file(self._model.tallies, merge=False)
+        self.mgxs_lib.add_to_tallies(self._model.tallies, merge=False)
 
     def _run_openmc(self):
         # Initial run

tests/regression_tests/mgxs_library_ce_to_mg_nuclides/test.py

@@ -28,7 +28,7 @@ class MGXSTestHarness(PyAPITestHarness):
         self.mgxs_lib.build_library()
 
         # Initialize a tallies file
-        self.mgxs_lib.add_to_tallies_file(self._model.tallies, merge=False)
+        self.mgxs_lib.add_to_tallies(self._model.tallies, merge=False)
 
     def _run_openmc(self):
         # Initial run

tests/regression_tests/mgxs_library_condense/test.py

@@ -36,7 +36,7 @@ class MGXSTestHarness(PyAPITestHarness):
         self.mgxs_lib.build_library()
 
         # Add tallies
-        self.mgxs_lib.add_to_tallies_file(self._model.tallies, merge=False)
+        self.mgxs_lib.add_to_tallies(self._model.tallies, merge=False)
 
     def _get_results(self, hash_output=False):
         """Digest info in the statepoint and return as a string."""

tests/regression_tests/mgxs_library_correction/test.py

@@ -29,7 +29,7 @@ class MGXSTestHarness(PyAPITestHarness):
         self.mgxs_lib.build_library()
 
         # Add tallies
-        self.mgxs_lib.add_to_tallies_file(self._model.tallies, merge=False)
+        self.mgxs_lib.add_to_tallies(self._model.tallies, merge=False)
 
     def _get_results(self, hash_output=False):
         """Digest info in the statepoint and return as a string."""

tests/regression_tests/mgxs_library_distribcell/test.py

@@ -36,7 +36,7 @@ class MGXSTestHarness(PyAPITestHarness):
         self.mgxs_lib.build_library()
 
         # Add tallies
-        self.mgxs_lib.add_to_tallies_file(self._model.tallies, merge=False)
+        self.mgxs_lib.add_to_tallies(self._model.tallies, merge=False)
         self._model.tallies.export_to_xml()
 
     def _get_results(self, hash_output=False):

tests/regression_tests/mgxs_library_hdf5/test.py

@@ -40,7 +40,7 @@ class MGXSTestHarness(PyAPITestHarness):
         self.mgxs_lib.build_library()
 
         # Add tallies
-        self.mgxs_lib.add_to_tallies_file(self._model.tallies, merge=False)
+        self.mgxs_lib.add_to_tallies(self._model.tallies, merge=False)
 
     def _get_results(self, hash_output=False):
         """Digest info in the statepoint and return as a string."""

tests/regression_tests/mgxs_library_histogram/test.py

@@ -30,7 +30,7 @@ class MGXSTestHarness(PyAPITestHarness):
         self.mgxs_lib.build_library()
 
         # Add tallies
-        self.mgxs_lib.add_to_tallies_file(self._model.tallies, merge=False)
+        self.mgxs_lib.add_to_tallies(self._model.tallies, merge=False)
 
     def _get_results(self, hash_output=False):
         """Digest info in the statepoint and return as a string."""

tests/regression_tests/mgxs_library_mesh/test.py

@@ -57,7 +57,7 @@ def model():
     model.mgxs_lib.build_library()
 
     # Add tallies
-    model.mgxs_lib.add_to_tallies_file(model.tallies, merge=False)
+    model.mgxs_lib.add_to_tallies(model.tallies, merge=False)
 
     return model
 

tests/regression_tests/mgxs_library_no_nuclides/test.py

@@ -39,7 +39,7 @@ class MGXSTestHarness(PyAPITestHarness):
         self.mgxs_lib.build_library()
 
         # Add tallies
-        self.mgxs_lib.add_to_tallies_file(self._model.tallies, merge=False)
+        self.mgxs_lib.add_to_tallies(self._model.tallies, merge=False)
 
     def _get_results(self, hash_output=False):
         """Digest info in the statepoint and return as a string."""

tests/regression_tests/mgxs_library_nuclides/test.py

@@ -36,7 +36,7 @@ class MGXSTestHarness(PyAPITestHarness):
         self.mgxs_lib.build_library()
 
         # Add tallies
-        self.mgxs_lib.add_to_tallies_file(self._model.tallies, merge=False)
+        self.mgxs_lib.add_to_tallies(self._model.tallies, merge=False)
 
     def _get_results(self, hash_output=True):
         """Digest info in the statepoint and return as a string."""

tests/regression_tests/mgxs_library_specific_nuclides/test.py

@@ -37,7 +37,7 @@ class MGXSTestHarness(PyAPITestHarness):
         self.mgxs_lib.build_library()
 
         # Add tallies
-        self.mgxs_lib.add_to_tallies_file(self._model.tallies, merge=True)
+        self.mgxs_lib.add_to_tallies(self._model.tallies, merge=True)
 
     def _get_results(self, hash_output=True):
         """Digest info in the statepoint and return as a string."""