Merge branch 'main' of https://github.com/terrapower/armi into entryp…

…oint

.coveragerc

@@ -6,6 +6,9 @@ omit =
     armi/utils/tests/test_gridGui.py
     venv/
 source = armi
+# change default .coverage file to something that doesn't have a dot
+# because our Windows file server can't handle dots. :s
+data_file = coverage_results.cov
 
 [coverage:run]
 parallel = true

armi/cases/case.py

@@ -29,8 +29,10 @@
 import glob
 import os
 import pathlib
+import platform
 import pstats
 import re
+import shutil
 import sys
 import textwrap
 import time
@@ -380,7 +382,7 @@ def _startCoverage(self):
         cov = None
         if self.cs["coverage"]:
             cov = coverage.Coverage(
-                config_file=os.path.join(context.RES, "coveragerc"), debug=["dataio"]
+                config_file=Case._getCoverageRcFile(makeCopy=True), debug=["dataio"]
             )
             if context.MPI_SIZE > 1:
                 # interestingly, you cannot set the parallel flag in the constructor
@@ -415,8 +417,7 @@ def _endCoverage(cov=None):
             # combine all the parallel coverage data files into one and make
             # the XML and HTML reports for the whole run.
             combinedCoverage = coverage.Coverage(
-                config_file=os.path.join(context.RES, "coveragerc"),
-                debug=["dataio"],
+                config_file=Case._getCoverageRcFile(), debug=["dataio"]
             )
             combinedCoverage.config.parallel = True
             # combine does delete the files it merges
@@ -425,6 +426,30 @@ def _endCoverage(cov=None):
             combinedCoverage.html_report()
             combinedCoverage.xml_report()
 
+    @staticmethod
+    def _getCoverageRcFile(makeCopy=False):
+        """Helper to provide the coverage configuration file according to the OS.
+
+        Parameters
+        ----------
+        makeCopy : bool (optional)
+            Whether or not to copy the coverage config file to an alternate file path
+
+        Returns
+        -------
+        covFile : str
+            path of coveragerc file
+        """
+        covRcDir = os.path.abspath(context.PROJECT_ROOT)
+        covFile = os.path.join(covRcDir, ".coveragerc")
+        if platform.system() == "Windows":
+            covFileWin = os.path.join(covRcDir, "coveragerc")
+            if makeCopy == True:
+                # Make a copy of the file without the dot in the name
+                shutil.copy(covFile, covFileWin)
+            return covFileWin
+        return covFile
+
     def _startProfiling(self):
         """Helper to the Case.run(): start the Python profiling,
         if the CaseSettings file says to.

armi/cases/tests/test_cases.py

@@ -19,11 +19,8 @@
 import logging
 import os
 import platform
-import sys
 import unittest
 
-import coverage
-
 from armi import cases
 from armi import context
 from armi import getApp
@@ -124,6 +121,16 @@ def test_independentVariables(self):
             for name, val in vals.items():
                 self.assertEqual(newCase.independentVariables[name], val)
 
+    def test_getCoverageRcFile(self):
+        case = cases.Case(settings.Settings())
+        covRcDir = os.path.abspath(context.PROJECT_ROOT)
+        # Don't actually copy the file, just check the file paths match
+        covRcFile = case._getCoverageRcFile(makeCopy=False)
+        if platform.system() == "Windows":
+            self.assertEqual(covRcFile, os.path.join(covRcDir, "coveragerc"))
+        else:
+            self.assertEqual(covRcFile, os.path.join(covRcDir, ".coveragerc"))
+
     def test_startCoverage(self):
         with directoryChangers.TemporaryDirectoryChanger():
             cs = settings.Settings(ARMI_RUN_PATH)

armi/cli/modify.py

@@ -61,6 +61,13 @@ def addOptions(self):
             default=".",
             help="A root directory in which to search for settings files, e.g., armi/tests.",
         )
+        self.parser.add_argument(
+            "--settingsWriteStyle",
+            type=str,
+            default="short",
+            help="Writing style for which settings get written back to the settings files.",
+            choices=["short", "medium", "full"],
+        )
         self.parser.add_argument(
             "patterns",
             type=str,
@@ -102,7 +109,7 @@ def invoke(self):
                 inspector.run()
 
             if not self.args.list_setting_files:
-                cs.writeToYamlFile(cs.path)
+                cs.writeToYamlFile(cs.path, style=self.args.settingsWriteStyle)
 
         runLog.important(
             "Finished {} {} settings files.".format(messages[1], len(csInstances))

armi/cli/tests/test_runEntryPoint.py

@@ -100,6 +100,7 @@ def test_cloneArmiRunCommandBatchBasics(self):
 
         self.assertEqual(ca.name, "clone-batch")
         self.assertEqual(ca.settingsArgument, "required")
+        self.assertEqual(ca.args.additional_files, ["test"])
 
 
 class TestCloneSuiteCommand(unittest.TestCase):
@@ -109,6 +110,7 @@ def test_cloneSuiteCommandBasics(self):
         cs.parse_args(["-d", "test"])
 
         self.assertEqual(cs.name, "clone-suite")
+        self.assertEqual(cs.args.directory, "test")
 
 
 class TestCompareCases(unittest.TestCase):
@@ -213,10 +215,13 @@ class TestModifyCaseSettingsCommand(unittest.TestCase):
     def test_modifyCaseSettingsCommandBasics(self):
         mcs = ModifyCaseSettingsCommand()
         mcs.addOptions()
-        mcs.parse_args(["--rootDir", "/path/to/", "fake.yaml"])
+        mcs.parse_args(
+            ["--rootDir", "/path/to/", "--settingsWriteStyle", "medium", "fake.yaml"]
+        )
 
         self.assertEqual(mcs.name, "modify")
         self.assertEqual(mcs.args.rootDir, "/path/to/")
+        self.assertEqual(mcs.args.settingsWriteStyle, "medium")
         self.assertEqual(mcs.args.patterns, ["fake.yaml"])
 
     def test_modifyCaseSettingsCommandInvoke(self):

armi/context.py

@@ -87,8 +87,9 @@ def setMode(cls, mode):
 
 
 ROOT = os.path.abspath(os.path.dirname(__file__))
+PROJECT_ROOT = os.path.join(ROOT, "..")
 RES = os.path.join(ROOT, "resources")
-DOC = os.path.abspath(os.path.join(ROOT, "..", "doc"))
+DOC = os.path.abspath(os.path.join(PROJECT_ROOT, "doc"))
 USER = getpass.getuser()
 START_TIME = time.ctime()
 

armi/nuclearDataIO/__init__.py

@@ -97,8 +97,6 @@ def _getNeutronKeywords(cycle, suffix, xsID):
             keywords = [xsID]
             if suffix not in [None, ""]:
                 keywords.append("-" + suffix)
-        else:
-            raise ValueError("The cycle or XS ID must be specified.")
     return keywords
 
 

armi/operators/operator.py

@@ -904,25 +904,6 @@ def _attachInterfaces(self):
         for i in self.interfaces:
             i.attachReactor(self, self.r)
 
-    def dumpRestartData(self, cycle, time_, factorList):
-        """
-        Write some information about the cycle and shuffling to a auxiliary file for potential restarting.
-
-        Notes
-        -----
-        This is old and can be deprecated now that the database contains
-        the entire state. This was historically needed to have complete information regarding
-        shuffling when figuring out ideal fuel management operations.
-        """
-        if cycle >= len(self.restartData):
-            self.restartData.append((cycle, time_, factorList))
-        else:
-            # try to preserve loaded restartdata so we don't lose it in restarts.
-            self.restartData[cycle] = (cycle, time_, factorList)
-        with open(self.cs.caseTitle + ".restart.dat", "w") as restart:
-            for info in self.restartData:
-                restart.write("cycle=%d   time=%10.6E   factorList=%s\n" % info)
-
     def _loadRestartData(self):
         """
         Read a restart.dat file which contains all the fuel management factorLists and cycle lengths.

armi/physics/neutronics/parameters.py

@@ -725,6 +725,7 @@ def linPowByPinGamma(self, value):
             units="1/cm^2/s",
             description="Neutron flux above 100keV",
             location=ParamLocation.AVERAGE,
+            categories=["detailedAxialExpansion"],
         )
 
         pb.defParam(

armi/reactor/converters/tests/test_uniformMesh.py

@@ -274,7 +274,8 @@ def test_applyStateToOriginal(self):
         for b in self.converter.convReactor.core.getBlocks():
             b.p.mgFlux = range(33)
             b.p.adjMgFlux = range(33)
-            b.p.flux = 5
+            b.p.fastFlux = 2.0
+            b.p.flux = 5.0
             b.p.power = 5.0
             b.p.pdens = 0.5
 
@@ -292,6 +293,7 @@ def test_applyStateToOriginal(self):
         self.converter.applyStateToOriginal()
 
         for b in self.r.core.getBlocks():
+            self.assertAlmostEqual(b.p.fastFlux, 2.0)
             self.assertAlmostEqual(b.p.flux, 5.0)
             self.assertAlmostEqual(b.p.pdens, 0.5)
 

armi/settings/caseSettings.py

@@ -29,6 +29,7 @@
 import logging
 import os
 from copy import copy, deepcopy
+from ruamel.yaml import YAML
 
 from armi import context
 from armi import runLog
@@ -357,24 +358,70 @@ def writeToYamlFile(self, fName, style="short"):
 
         Notes
         -----
-        This resets the current CS's path to the newly written path.
+        This resets the current CS's path to the newly written absolute path.
 
         Parameters
         ----------
         fName : str
             the file to write to
-        style : str
-            the method of output to be used when creating the file for
-            the current state of settings
+        style : str (optional)
+            the method of output to be used when creating the file for the current
+            state of settings
         """
         self.path = pathTools.armiAbsPath(fName)
+        if style == "medium":
+            settingsSetByUser = self.getSettingsSetByUser(self.path)
+        else:
+            settingsSetByUser = []
         with open(self.path, "w") as stream:
-            writer = self.writeToYamlStream(stream, style)
+            writer = self.writeToYamlStream(stream, style, settingsSetByUser)
         return writer
 
-    def writeToYamlStream(self, stream, style="short"):
-        """Write settings in yaml format to an arbitrary stream."""
-        writer = settingsIO.SettingsWriter(self, style=style)
+    def getSettingsSetByUser(self, fPath):
+        """
+        Grabs the list of settings in the user-defined input file so that the settings
+        can be tracked outside of a Settings Object
+
+        Parameters
+        ----------
+        fPath : str
+            The absolute file path of the settings file
+
+        Returns
+        -------
+        userSettingsNames : list
+            The settings names read in from a yaml settings file
+        """
+
+        # We do not want to load these as settings, but just grab the dictionary straight
+        # from the settings file to know which settings are user-defined
+        with open(fPath, "r") as stream:
+            yaml = YAML()
+            tree = yaml.load(stream)
+            userSettings = tree[settingsIO.Roots.CUSTOM]
+        userSettingsNames = list(userSettings.keys())
+        return userSettingsNames
+
+    def writeToYamlStream(self, stream, style="short", settingsSetByUser=[]):
+        """
+        Write settings in yaml format to an arbitrary stream.
+
+        Parameters
+        ----------
+        stream : file object
+            Writable file stream
+        style : str (optional)
+            Writing style for settings file. Can be short, medium, or full.
+        settingsSetByUser : list
+            List of settings names in user-defined settings file
+
+        Returns
+        -------
+        writer : SettingsWriter object
+        """
+        writer = settingsIO.SettingsWriter(
+            self, style=style, settingsSetByUser=settingsSetByUser
+        )
         writer.writeYaml(stream)
         return writer