Reorganizing Math Utilities (#584)

CONTRIBUTING.md

@@ -1,6 +1,6 @@
 # How to contribute
 
-The ARMI framework project strongly encourages developers to help contribute to and build the code.
+The ARMI framework project strongly encourages developers to help contribute to the codebase.
 
 The ARMI framework code is open source, and your contributions will become open source.
 Although fewer laws apply to open source materials because they are publicly-available, you still
@@ -13,16 +13,16 @@ There are a lot of things we need help with right off the bat, to get your feet
 * Many more type annotations are desired. Type issues cause lots of bugs.
 * Fewer Pylint warnings
 * Better documentation
-* Additional relevance to thermal reactors
 * Better test coverage
 * Targeted speedups (e.g. informed by a profiler)
+* Additional relevance to thermal reactors
 
 Naturally, we encourage other kinds of contributions as well.
 
 ## Testing
 
 Any contribution must pass all included unit tests. The tests are built and run with the
-pytest system. Please add new tests if you add new functionality. You can generally just run
+`pytest` system. Please add new tests if you add new functionality. You can generally just run
 `tox` to build the testing environment and execute all the tests and pylint checks.
 
 ## Submitting changes

armi/apps.py

@@ -32,9 +32,9 @@
 import collections
 
 from armi import plugins, pluginManager, meta, settings
+from armi.reactor import parameters
 from armi.settings import Setting
 from armi.settings import fwSettings
-from armi.reactor import parameters
 
 
 class App:

armi/bookkeeping/report/reportingUtils.py

@@ -30,11 +30,12 @@
 
 import armi
 from armi import runLog
-from armi import utils
+from armi.utils import getFileSHA1Hash
 from armi.utils import iterables
 from armi.utils import units
 from armi.utils import textProcessors
 from armi.utils import plotting
+from armi.utils.mathematics import findClosest
 from armi import interfaces
 from armi.bookkeeping import report
 from armi.reactor.flags import Flags
@@ -131,7 +132,7 @@ def _listInputFiles(cs):
             shaHash = (
                 "MISSING"
                 if (not fName or not os.path.exists(fName))
-                else utils.getFileSHA1Hash(fName, digits=10)
+                else getFileSHA1Hash(fName, digits=10)
             )
             inputInfo.append((label, fName, shaHash))
 
@@ -649,9 +650,8 @@ def summarizeZones(core, cs):
     peakAssem = highPow[peakIndex]
 
     avgPFrac = sum(pFracList) / len(pFracList)  # true mean power fraction
-    _avgAssemPFrac, avgIndex = utils.findClosest(
-        pFracList, avgPFrac, indx=True
-    )  # the closest-to-average pfrac in the list
+    # the closest-to-average pfrac in the list
+    _avgAssemPFrac, avgIndex = findClosest(pFracList, avgPFrac, indx=True)
     avgAssem = highPow[avgIndex]  # the actual average assembly
 
     # ok, now need counts, and peak and avg. flow and power in high power region.

armi/conftest.py

@@ -34,7 +34,6 @@
 
 
 def pytest_sessionstart(session):
-
     print("Initializing generic ARMI Framework application")
     configure(apps.App())
     bootstrapArmiTestEnv()

armi/materials/lithium.py

@@ -20,9 +20,9 @@
 """
 
 from armi import runLog
-from armi import utils
 from armi.materials import material
 from armi.nucDirectory import nuclideBases as nb
+from armi.utils.mathematics import getFloat
 
 
 class Lithium(material.Fluid):
@@ -46,7 +46,7 @@ def applyInputParams(self, LI_wt_frac=None, LI6_wt_frac=None, *args, **kwargs):
 
         LI6_wt_frac = LI6_wt_frac or LI_wt_frac
 
-        enrich = utils.getFloat(LI6_wt_frac)
+        enrich = getFloat(LI6_wt_frac)
         # allow 0.0 to pass in!
         if enrich is not None:
             self.adjustMassEnrichment(LI6_wt_frac)

armi/materials/sulfur.py

@@ -17,7 +17,7 @@
 """
 
 from armi import runLog
-from armi import utils
+from armi.utils.mathematics import linearInterpolation
 from armi.utils.units import getTk
 from armi.materials import material
 
@@ -67,6 +67,4 @@ def volumetricExpansion(self, Tk=None, Tc=None):
         Tk = getTk(Tc, Tk)
 
         self.checkTempRange(334, 430, Tk, "volumetric expansion")
-        return utils.linearInterpolation(
-            x0=334, y0=5.28e-4, x1=430, y1=5.56e-4, targetX=Tk
-        )
+        return linearInterpolation(x0=334, y0=5.28e-4, x1=430, y1=5.56e-4, targetX=Tk)

armi/nucDirectory/nuclideBases.py

@@ -309,6 +309,7 @@ def __readMc2Nuclides():
     """
     with open(os.path.join(armi.context.RES, "mc2Nuclides.yaml"), "r") as mc2Nucs:
         mc2Nuclides = yaml.load(mc2Nucs, Loader=yaml.FullLoader)
+
     # now add the mc2 specific nuclideBases, and correct the mc2Ids when a > 0 and state = 0
     for name, data in mc2Nuclides.items():
         z = data["z"]

armi/operators/operator.py

@@ -31,7 +31,7 @@
 from armi import context
 from armi import runLog
 from armi.bookkeeping import memoryProfiler
-from armi import utils
+from armi.utils.mathematics import expandRepeatedFloats
 from armi.utils import codeTiming
 from armi.utils import pathTools
 from armi import settings
@@ -142,19 +142,19 @@ def _initFastPath():
 
     def _getCycleLengths(self):
         """Return the cycle length for each cycle of the system as a list."""
-        return utils.expandRepeatedFloats(self.cs["cycleLengths"]) or (
+        return expandRepeatedFloats(self.cs["cycleLengths"]) or (
             [self.cs["cycleLength"]] * self.cs["nCycles"]
         )
 
     def _getAvailabilityFactors(self):
         """Return the availability factors (capacity factor) for each cycle of the system as a list."""
-        return utils.expandRepeatedFloats(self.cs["availabilityFactors"]) or (
+        return expandRepeatedFloats(self.cs["availabilityFactors"]) or (
             [self.cs["availabilityFactor"]] * self.cs["nCycles"]
         )
 
     def _getPowerFractions(self):
         """Return the power fractions for each cycle of the system as a list."""
-        return utils.expandRepeatedFloats(self.cs["powerFractions"]) or (
+        return expandRepeatedFloats(self.cs["powerFractions"]) or (
             [1.0 for _cl in self.cycleLengths]
         )
 
@@ -919,7 +919,7 @@ def snapshotRequest(self, cycle, node):
         newFolder = "snapShot{0}_{1}".format(cycle, node)
         if os.path.exists(newFolder):
             runLog.important("Deleting existing snapshot data in {0}".format(newFolder))
-            utils.pathTools.cleanPath(newFolder)  # careful with cleanPath!
+            pathTools.cleanPath(newFolder)  # careful with cleanPath!
             # give it a minute.
             time.sleep(1)
 

armi/operators/settingsValidation.py

@@ -26,6 +26,7 @@
 import armi
 from armi import runLog, settings, utils
 from armi.utils import pathTools
+from armi.utils.mathematics import expandRepeatedFloats
 from armi.reactor import geometry
 from armi.reactor import systemLayoutInput
 from armi.physics import neutronics
@@ -463,7 +464,7 @@ def _willBeCopiedFrom(fName):
 
         def _factorsAreValid(factors, maxVal=1.0):
             try:
-                expandedList = utils.expandRepeatedFloats(factors)
+                expandedList = expandRepeatedFloats(factors)
             except (ValueError, IndexError):
                 return False
             return (
@@ -527,8 +528,8 @@ def _correctCycles():
         def decayCyclesHaveInputThatWillBeIgnored():
             """Check if there is any decay-related input that will be ignored."""
             try:
-                powerFracs = utils.expandRepeatedFloats(self.cs["powerFractions"])
-                availabilities = utils.expandRepeatedFloats(
+                powerFracs = expandRepeatedFloats(self.cs["powerFractions"])
+                availabilities = expandRepeatedFloats(
                     self.cs["availabilityFactors"]
                 ) or ([self.cs["availabilityFactor"]] * self.cs["nCycles"])
             except:  # pylint: disable=bare-except

armi/physics/fuelCycle/fuelHandlers.py

@@ -38,9 +38,8 @@
 from armi.reactor.flags import Flags
 from armi.operators import RunTypes
 from armi.utils import directoryChangers, pathTools
-from armi import utils
 from armi.utils import plotting
-from armi.utils.mathematics import resampleStepwise
+from armi.utils.mathematics import findClosest, resampleStepwise
 
 runLog = logging.getLogger(__name__)
 
@@ -1249,17 +1248,16 @@ def buildRingSchedule(
         # build widths
         widths = []
         for i, ring in enumerate(baseRings[:-1]):
-            widths.append(
-                abs(baseRings[i + 1] - ring) - 1
-            )  # 0 is the most restrictive, meaning don't even look in other rings.
+            # 0 is the most restrictive, meaning don't even look in other rings.
+            widths.append(abs(baseRings[i + 1] - ring) - 1)
         widths.append(0)  # add the last ring with width 0.
 
         # step 2: locate which rings should be reversed to give the jump-ring effect.
         if jumpRingFrom is not None:
-            _closestRingFrom, jumpRingFromIndex = utils.findClosest(
+            _closestRingFrom, jumpRingFromIndex = findClosest(
                 baseRings, jumpRingFrom, indx=True
             )
-            _closestRingTo, jumpRingToIndex = utils.findClosest(
+            _closestRingTo, jumpRingToIndex = findClosest(
                 baseRings, jumpRingTo, indx=True
             )
         else:

armi/physics/neutronics/energyGroups.py

@@ -15,14 +15,15 @@
 Energy group structures for multigroup neutronics calculations.
 """
 
-import itertools
 import copy
+import itertools
 import math
 
 import numpy
 
 from armi import utils
 from armi import runLog
+from armi.utils.mathematics import findNearestValue
 from .const import (
     FAST_FLUX_THRESHOLD_EV,
     MAXIMUM_XS_LIBRARY_ENERGY,
@@ -32,10 +33,7 @@
 
 
 def getFastFluxGroupCutoff(eGrpStruc):
-    """
-    Given a constant "fast" energy threshold, return which ARMI energy group index contains this threshold.
-    """
-
+    """Given a constant "fast" energy threshold, return which ARMI energy group index contains this threshold."""
     gThres = -1
     for g, eV in enumerate(eGrpStruc):
         if eV < FAST_FLUX_THRESHOLD_EV:
@@ -302,9 +300,7 @@ def _create_multigroup_structures_on_finegroup_energies(
     modifiedEnergyBounds = set()
     modifiedEnergyBounds.add(max(finegroup_energy_bounds))
     for energyBound in multigroup_energy_bounds[1:]:
-        modifiedEnergyBounds.add(
-            utils.findNearestValue(finegroup_energy_bounds, energyBound)
-        )
+        modifiedEnergyBounds.add(findNearestValue(finegroup_energy_bounds, energyBound))
 
     return sorted(modifiedEnergyBounds, reverse=True)
 

armi/reactor/converters/uniformMesh.py

@@ -58,7 +58,7 @@
 import numpy
 
 from armi import runLog
-from armi import utils
+from armi.utils.mathematics import average1DWithinTolerance
 from armi.utils import iterables
 from armi.utils import plotting
 from armi.reactor import grids
@@ -124,7 +124,7 @@ def _computeAverageAxialMesh(self):
             aMesh = src.core.findAllAxialMeshPoints([a], applySubMesh=True)[1:]
             if len(aMesh) == refNumPoints:
                 allMeshes.append(aMesh)
-        self._uniformMesh = utils.average1DWithinTolerance(numpy.array(allMeshes))
+        self._uniformMesh = average1DWithinTolerance(numpy.array(allMeshes))
 
     @staticmethod
     def _createNewAssembly(sourceAssembly):

armi/reactor/reactors.py

@@ -32,7 +32,7 @@
 
 import numpy
 
-from armi import getPluginManagerOrFail, materials, nuclearDataIO, settings, utils
+from armi import getPluginManagerOrFail, materials, nuclearDataIO, settings
 from armi.reactor import assemblies
 from armi.reactor import assemblyLists
 from armi.reactor import composites
@@ -42,9 +42,10 @@
 from armi.reactor import parameters
 from armi.reactor import zones
 from armi.reactor import reactorParameters
-from armi.utils import units
+from armi.utils import createFormattedStrWithDelimiter, units
 from armi.utils.iterables import Sequence
 from armi.utils import directoryChangers
+from armi.utils.mathematics import average1DWithinTolerance
 from armi.reactor.flags import Flags
 from armi.settings.fwSettings.globalSettings import CONF_MATERIAL_NAMESPACE_ORDER
 from armi.nuclearDataIO import xsLibraries
@@ -1305,19 +1306,19 @@ def summarizeNuclideCategories(self):
                 [
                     (
                         "Fuel",
-                        utils.createFormattedStrWithDelimiter(
+                        createFormattedStrWithDelimiter(
                             self._nuclideCategories["fuel"]
                         ),
                     ),
                     (
                         "Coolant",
-                        utils.createFormattedStrWithDelimiter(
+                        createFormattedStrWithDelimiter(
                             self._nuclideCategories["coolant"]
                         ),
                     ),
                     (
                         "Structure",
-                        utils.createFormattedStrWithDelimiter(
+                        createFormattedStrWithDelimiter(
                             self._nuclideCategories["structure"]
                         ),
                     ),
@@ -1874,7 +1875,7 @@ def updateAxialMesh(self):
         # depending on what makes the most sense
         refAssem = self.refAssem
         refMesh = self.findAllAxialMeshPoints([refAssem])
-        avgHeight = utils.average1DWithinTolerance(
+        avgHeight = average1DWithinTolerance(
             numpy.array(
                 [
                     [