Merge 25ad8c9 into 827d223

armi/__init__.py

@@ -121,6 +121,7 @@ def init(choice=None, fName=None, cs=None):
     .. impl:: Settings are used to define an ARMI run.
         :id: I_ARMI_SETTING1
         :implements: R_ARMI_SETTING
+        :qualified_code: Nala
 
         This method initializes an ARMI run, and if successful returns an Operator.
         That operator is designed to drive the reactor simulation through time steps to

armi/apps.py

@@ -48,6 +48,7 @@ class App:
     .. impl:: An App has a plugin manager.
         :id: I_ARMI_APP_PLUGINS
         :implements: R_ARMI_APP_PLUGINS
+        :qualified_code: Nala
 
         The App class is intended to be subclassed in order to customize the functionality
         and look-and-feel of the ARMI Framework for a specific use case. An App contains a
@@ -131,6 +132,7 @@ def getSettings(self) -> Dict[str, Setting]:
         .. impl:: Applications will not allow duplicate settings.
             :id: I_ARMI_SETTINGS_UNIQUE
             :implements: R_ARMI_SETTINGS_UNIQUE
+            :qualified_code: Nala
 
             Each ARMI application includes a collection of Plugins. Among other
             things, these plugins can register new settings in addition to

armi/bookkeeping/db/database3.py

@@ -112,6 +112,7 @@ class Database3:
     .. impl:: The database files are H5, and thus language agnostic.
         :id: I_ARMI_DB_H51
         :implements: R_ARMI_DB_H5
+        :qualified_code: Nala
 
         This class implements a light wrapper around H5 files, so they can be used to
         store ARMI outputs. H5 files are commonly used in scientific applications in
@@ -234,6 +235,7 @@ def writeSystemAttributes(h5db):
         .. impl:: Add system attributes to the database.
             :id: I_ARMI_DB_QA
             :implements: R_ARMI_DB_QA
+            :qualified_code: Nala
 
             This method writes some basic system information to the H5 file. This is
             designed as a starting point, so users can see information about the system
@@ -470,6 +472,7 @@ def writeInputsToDB(self, cs, csString=None, geomString=None, bpString=None):
         .. impl:: The run settings are saved the settings file.
             :id: I_ARMI_DB_CS
             :implements: R_ARMI_DB_CS
+            :qualified_code: Nala
 
             A ``Settings`` object is passed into this method, and then the settings are
             converted into a YAML string stream. That stream is then written to the H5
@@ -479,6 +482,7 @@ def writeInputsToDB(self, cs, csString=None, geomString=None, bpString=None):
         .. impl:: The reactor blueprints are saved the settings file.
             :id: I_ARMI_DB_BP
             :implements: R_ARMI_DB_BP
+            :qualified_code: Nala
 
             A ``Blueprints`` string is optionally passed into this method, and then
             written to the H5 file. If it is not passed in, this method will attempt to
@@ -710,6 +714,7 @@ def load(
         .. impl:: Users can load a reactor from a DB.
             :id: I_ARMI_DB_R_LOAD
             :implements: R_ARMI_DB_R_LOAD
+            :qualified_code: Nala
 
             This method creates a ``Reactor`` object by reading the reactor state out
             of an ARMI database file. This is done by passing in mandatory arguements

armi/bookkeeping/db/databaseInterface.py

@@ -225,6 +225,7 @@ def prepRestartRun(self):
         .. impl:: Runs at a particular timenode can be re-instantiated for a snapshot.
             :id: I_ARMI_SNAPSHOT_RESTART
             :implements: R_ARMI_SNAPSHOT_RESTART
+            :qualified_code: Nala
 
             This method loads the state of a reactor from a particular point in time
             from a standard ARMI

armi/bookkeeping/db/layout.py

@@ -386,6 +386,7 @@ def writeToDB(self, h5group):
         .. impl:: Write data to the DB for a given time step.
             :id: I_ARMI_DB_TIME
             :implements: R_ARMI_DB_TIME
+            :qualified_code: Nala
 
             This method writes a snapshot of the current state of the reactor to the
             database. It takes a pointer to an existing HDF5 file as input, and it

armi/bookkeeping/historyTracker.py

@@ -99,6 +99,7 @@ class HistoryTrackerInterface(interfaces.Interface):
         than the database.
         :id: I_ARMI_HIST_TRACK
         :implements: R_ARMI_HIST_TRACK
+        :qualified_code: Nala
 
         This is a special :py:class:`Interface <armi.interfaces.Interface>` that is
         designed to store assembly and cross section data throughout time. This is done

armi/bookkeeping/snapshotInterface.py

@@ -48,6 +48,7 @@ class SnapshotInterface(interfaces.Interface):
     .. impl:: Save extra data to be saved from a run, at specified time nodes.
         :id: I_ARMI_SNAPSHOT0
         :implements: R_ARMI_SNAPSHOT
+        :qualified_code: Nala
 
         This is a special :py:class:`Interface <armi.interfaces.Interface>` that is
         designed to run along all the other Interfaces during a simulation, to save off

armi/cases/case.py

@@ -335,6 +335,7 @@ def run(self):
         .. impl:: The case class allows for a generic ARMI simulation.
             :id: I_ARMI_CASE
             :implements: R_ARMI_CASE
+            :qualified_code: Nala
 
             This method is responsible for "running" the ARMI simulation
             instigated by the inputted settings. This initializes an
@@ -568,6 +569,7 @@ def checkInputs(self):
         .. impl:: Perform validity checks on case inputs.
             :id: I_ARMI_CASE_CHECK
             :implements: R_ARMI_CASE_CHECK
+            :qualified_code: Nala
 
             This method checks the validity of the current settings. It relies
             on an :py:class:`~armi.operators.settingsValidation.Inspector`

armi/cases/inputModifiers/inputModifiers.py

@@ -21,6 +21,7 @@ class InputModifier:
     .. impl:: A generic tool to modify user inputs on multiple cases.
         :id: I_ARMI_CASE_MOD1
         :implements: R_ARMI_CASE_MOD
+        :qualified_code: Nala
 
         This class serves as an abstract base class for modifying the inputs of
         a case, typically case settings. Child classes must implement a

armi/cases/suite.py

@@ -47,6 +47,7 @@ class CaseSuite:
     .. impl:: CaseSuite allows for one case to start after another completes.
         :id: I_ARMI_CASE_SUITE
         :implements: R_ARMI_CASE_SUITE
+        :qualified_code: Nala
 
         The CaseSuite object allows multiple, often related,
         :py:class:`~armi.cases.case.Case` objects to be run sequentially. A CaseSuite

armi/cases/suiteBuilder.py

@@ -48,6 +48,7 @@ class SuiteBuilder:
     .. impl:: A generic tool to modify user inputs on multiple cases.
         :id: I_ARMI_CASE_MOD0
         :implements: R_ARMI_CASE_MOD
+        :qualified_code: Nala
 
         This class provides the capability to create a
         :py:class:`~armi.cases.suite.CaseSuite` based on programmatic

armi/cli/__init__.py

@@ -107,6 +107,7 @@ class ArmiCLI:
     .. impl:: The basic ARMI CLI, for running a simulation.
         :id: I_ARMI_CLI_CS
         :implements: R_ARMI_CLI_CS
+        :qualified_code: Nala
 
         Provides a basic command-line interface (CLI) for running an ARMI simulation. Available
         commands can be listed with ``-l``. Information on individual commands can be obtained by

armi/cli/entryPoint.py

@@ -57,6 +57,7 @@ class EntryPoint:
     .. impl:: Generic CLI base class for developers to use.
         :id: I_ARMI_CLI_GEN
         :implements: R_ARMI_CLI_GEN
+        :qualified_code: Nala
 
         Provides a base class for plugin developers to use in creating application-specific CLIs.
         Valid subclasses must at least provide a ``name`` class attribute.

armi/interfaces.py

@@ -48,6 +48,7 @@ class STACK_ORDER:  # noqa: invalid-class-name
     .. impl:: Define an ordered list of interfaces.
         :id: I_ARMI_OPERATOR_INTERFACES0
         :implements: R_ARMI_OPERATOR_INTERFACES
+        :qualified_code: Nala
 
         At each time node during a simulation, an ordered colletion of Interfaces
         are run (referred to as the interface stack). But ARMI does not force the order upon the analyst.
@@ -90,6 +91,7 @@ class TightCoupler:
     .. impl:: The TightCoupler defines the convergence criteria for physics coupling.
         :id: I_ARMI_OPERATOR_PHYSICS0
         :implements: R_ARMI_OPERATOR_PHYSICS
+        :qualified_code: Nala
 
         During a simulation, the developers of an ARMI application frequently want to
         iterate on some physical calculation until that calculation has converged to
@@ -259,6 +261,7 @@ class Interface:
     .. impl:: The interface shall allow code execution at important operational points in time.
         :id: I_ARMI_INTERFACE
         :implements: R_ARMI_INTERFACE
+        :qualified_code: Nala
 
         The Interface class defines a number methods with names like ``interact***``.
         These methods are called in order at each time node. This allows for an

armi/materials/__init__.py

@@ -52,6 +52,7 @@ def setMaterialNamespaceOrder(order):
         of duplicates.
         :id: I_ARMI_MAT_ORDER
         :implements: R_ARMI_MAT_ORDER
+        :qualified_code: Nala
 
         An ARMI application will need materials. Materials can be imported from
         any code the application has access to, like plugin packages. This leads to
@@ -144,6 +145,7 @@ def resolveMaterialClassByName(name: str, namespaceOrder: List[str] = None):
     .. impl:: Materials can be searched across packages in a defined namespace.
         :id: I_ARMI_MAT_NAMESPACE
         :implements: R_ARMI_MAT_NAMESPACE
+        :qualified_code: Nala
 
         During the runtime of an ARMI application, but particularly during the
         construction of the reactor in memory, materials will be requested by name. At

armi/materials/material.py

@@ -39,6 +39,7 @@ class Material:
     .. impl:: The abstract material class.
         :id: I_ARMI_MAT_PROPERTIES
         :implements: R_ARMI_MAT_PROPERTIES
+        :qualified_code: Nala
 
         The ARMI Materials library is based on the Object-Oriented Programming design
         approach, and uses this generic ``Material`` base class. In this class we
@@ -49,6 +50,7 @@ class Material:
     .. impl:: Materials generate nuclide mass fractions at instantiation.
         :id: I_ARMI_MAT_FRACS
         :implements: R_ARMI_MAT_FRACS
+        :qualified_code: Nala
 
         An ARMI material is meant to be able to represent real world materials that
         might be used in the construction of a nuclear reactor. As such, they are
@@ -121,6 +123,7 @@ def name(self):
         .. impl:: The name of a material is accessible.
             :id: I_ARMI_MAT_NAME
             :implements: R_ARMI_MAT_NAME
+            :qualified_code: Nala
 
             Every instance of an ARMI material must have a simple, human-readable
             string name. And, if possible, we want this string to match the class
@@ -743,6 +746,7 @@ def linearExpansion(self, Tk=None, Tc=None):
         .. impl:: Fluid materials are not thermally expandable.
             :id: I_ARMI_MAT_FLUID
             :implements: R_ARMI_MAT_FLUID
+            :qualified_code: Nala
 
             ARMI does not model thermal expansion of fluids. The ``Fluid`` superclass
             therefore sets the thermal expansion coefficient to zero. All fluids

armi/materials/void.py

@@ -26,6 +26,7 @@ class Void(material.Fluid):
     .. impl:: Define a void material with zero density.
         :id: I_ARMI_MAT_VOID
         :implements: R_ARMI_MAT_VOID
+        :qualified_code: Nala
 
         To help with expansion, it is sometimes useful to put a small section of void
         material into the reactor model. This is not meant to represent a true void,

armi/nucDirectory/elements.py

@@ -19,6 +19,7 @@
 .. impl:: A tool for querying basic data for elements of the periodic table.
     :id: I_ARMI_ND_ELEMENTS0
     :implements: R_ARMI_ND_ELEMENTS
+    :qualified_code: Nala
 
     The :py:mod:`elements <armi.nucDirectory.elements>` module defines the
     :py:class:`Element <armi.nucDirectory.elements.Element>` class which acts as
@@ -171,6 +172,7 @@ def __init__(self, z, symbol, name, phase="UNKNOWN", group="UNKNOWN"):
         .. impl:: An element of the periodic table.
             :id: I_ARMI_ND_ELEMENTS1
             :implements: R_ARMI_ND_ELEMENTS
+            :qualified_code: Nala
 
             The :py:class:`Element <armi.nucDirectory.elements.Element>` class
             acts as a data structure for organizing information about an

armi/nucDirectory/nuclideBases.py

@@ -18,6 +18,7 @@
 .. impl:: Isotopes and isomers can be queried by name, label, MC2-3 ID, MCNP ID, and AAAZZZS ID.
     :id: I_ARMI_ND_ISOTOPES0
     :implements: R_ARMI_ND_ISOTOPES
+    :qualified_code: Nala
 
     The :py:mod:`nuclideBases <armi.nucDirectory.nuclideBases>` module defines
     the :py:class:`NuclideBase <armi.nucDirectory.nuclideBases.NuclideBase>`
@@ -498,6 +499,7 @@ class NuclideBase(INuclide, IMcnpNuclide):
     .. impl:: Isotopes and isomers can be queried by name and label.
         :id: I_ARMI_ND_ISOTOPES1
         :implements: R_ARMI_ND_ISOTOPES
+        :qualified_code: Nala
 
         The :py:class:`NuclideBase <armi.nucDirectory.nuclideBases.NuclideBase>`
         class provides a data structure for information about a single nuclide,
@@ -582,6 +584,7 @@ def getMcc2Id(self):
         .. impl:: Isotopes and isomers can be queried by MC2-2 ID.
             :id: I_ARMI_ND_ISOTOPES2
             :implements: R_ARMI_ND_ISOTOPES
+            :qualified_code: Nala
 
             This method returns the ``mcc2id`` attribute of a
             :py:class:`NuclideBase <armi.nucDirectory.nuclideBases.NuclideBase>`
@@ -596,6 +599,7 @@ def getMcc3Id(self):
         .. impl:: Isotopes and isomers can be queried by MC2-3 ID.
             :id: I_ARMI_ND_ISOTOPES3
             :implements: R_ARMI_ND_ISOTOPES
+            :qualified_code: Nala
 
             This method returns the ``mcc3id`` attribute of a
             :py:class:`NuclideBase <armi.nucDirectory.nuclideBases.NuclideBase>`
@@ -611,6 +615,7 @@ def getMcnpId(self):
         .. impl:: Isotopes and isomers can be queried by MCNP ID.
             :id: I_ARMI_ND_ISOTOPES4
             :implements: R_ARMI_ND_ISOTOPES
+            :qualified_code: Nala
 
             This method generates the MCNP ID for an isotope using the standard
             MCNP format based on the atomic number A, number of protons Z, and
@@ -646,6 +651,7 @@ def getAAAZZZSId(self):
         .. impl:: Isotopes and isomers can be queried by AAAZZZS ID.
             :id: I_ARMI_ND_ISOTOPES5
             :implements: R_ARMI_ND_ISOTOPES
+            :qualified_code: Nala
 
             This method generates the AAAZZZS format ID for an isotope. Where
             AAA is the mass number, ZZZ is the atomic number, and S is the
@@ -1195,6 +1201,7 @@ def addNuclideBases():
     .. impl:: Separating natural abundance data from code.
         :id: I_ARMI_ND_DATA0
         :implements: R_ARMI_ND_DATA
+        :qualified_code: Nala
 
         This function reads the ``nuclides.dat`` file from the ARMI resources
         folder. This file contains metadata for 4,614 nuclides, including
@@ -1264,6 +1271,7 @@ def readMCCNuclideData():
     .. impl:: Separating MCC data from code.
         :id: I_ARMI_ND_DATA1
         :implements: R_ARMI_ND_DATA
+        :qualified_code: Nala
 
         This function reads the mcc-nuclides.yaml file from the ARMI resources
         folder. This file contains the MC\ :sup:`2`-2 ID (from ENDF/B-V.2) and MC\ :sup:`2`-3 ID
@@ -1297,6 +1305,7 @@ def updateNuclideBasesForSpecialCases():
     .. impl:: The special case name Am242g is supported.
         :id: I_ARMI_ND_ISOTOPES6
         :implements: R_ARMI_ND_ISOTOPES
+        :qualified_code: Nala
 
         This function updates the keys for the :py:class:`NuclideBase
         <armi.nucDirectory.nuclideBases.NuclideBase>` instances for Am-242m and

armi/nuclearDataIO/cccc/cccc.py

@@ -24,6 +24,7 @@
                  R_ARMI_NUCDATA_DIF3D,
                  R_ARMI_NUCDATA_PMATRX,
                  R_ARMI_NUCDATA_DLAYXS
+    :qualified_code: Nala
 
     This module provides a number of base classes that implement general
     capabilities for binary and ASCII file I/O. The :py:class:`IORecord` serves

armi/nuclearDataIO/cccc/dif3d.py

@@ -204,6 +204,7 @@ def readWrite(self):
         .. impl:: Tool to read and write DIF3D files.
             :id: I_ARMI_NUCDATA_DIF3D
             :implements: R_ARMI_NUCDATA_DIF3D
+            :qualified_code: Nala
 
             The reading and writing of the DIF3D binary file is performed using
             :py:class:`StreamWithDataContainer <.cccc.StreamWithDataContainer>`

armi/nuclearDataIO/cccc/dlayxs.py

@@ -229,6 +229,7 @@ def readWrite(self):
         .. impl:: Tool to read and write DLAYXS files.
             :id: I_ARMI_NUCDATA_DLAYXS
             :implements: R_ARMI_NUCDATA_DLAYXS
+            :qualified_code: Nala
 
             Reading and writing DLAYXS delayed neutron data files is performed
             using the general nuclear data I/O functionalities described in

armi/nuclearDataIO/cccc/gamiso.py

@@ -21,6 +21,7 @@
 .. impl:: Tool to read and write GAMISO files.
     :id: I_ARMI_NUCDATA_GAMISO
     :implements: R_ARMI_NUCDATA_GAMISO
+    :qualified_code: Nala
 
     The majority of the functionality in this module is inherited from the
     :py:mod:`~armi.nuclearDataIO.cccc.isotxs` module. See

armi/nuclearDataIO/cccc/geodst.py

@@ -136,6 +136,7 @@ def readWrite(self):
         .. impl:: Tool to read and write GEODST files.
             :id: I_ARMI_NUCDATA_GEODST
             :implements: R_ARMI_NUCDATA_GEODST
+            :qualified_code: Nala
 
             Reading and writing GEODST files is performed using the general
             nuclear data I/O functionalities described in

armi/nuclearDataIO/cccc/isotxs.py

@@ -268,6 +268,7 @@ def readWrite(self):
         .. impl:: Tool to read and write ISOTXS files.
             :id: I_ARMI_NUCDATA_ISOTXS
             :implements: R_ARMI_NUCDATA_ISOTXS
+            :qualified_code: Nala
 
             Reading and writing ISOTXS files is performed using the general
             nuclear data I/O functionalities described in

armi/nuclearDataIO/cccc/pmatrx.py

@@ -189,6 +189,7 @@ def readWrite(self):
         .. impl:: Tool to read and write PMATRX files.
             :id: I_ARMI_NUCDATA_PMATRX
             :implements: R_ARMI_NUCDATA_PMATRX
+            :qualified_code: Nala
 
             Reading and writing PMATRX files is performed using the general
             nuclear data I/O functionalities described in

armi/nuclearDataIO/xsCollections.py

@@ -790,6 +790,7 @@ def computeMacroscopicGroupConstants(
     .. impl:: Compute macroscopic cross sections from microscopic cross sections and number densities.
         :id: I_ARMI_NUCDATA_MACRO
         :implements: R_ARMI_NUCDATA_MACRO
+        :qualified_code: Nala
 
         This function computes the macroscopic cross sections of a specified
         reaction type from inputted microscopic cross sections and number