Merge branch 'master' of https://github.com/keckler/armi into unshape…

…dComponent

.github/workflows/docs.yaml

@@ -24,6 +24,8 @@ jobs:
         run: sudo apt-get -y install pandoc
       - name: Install Tox and any other packages
         run: pip install tox
+      - name: Setup Graphviz
+        uses: ts-graphviz/setup-graphviz@v1
       - name: Make HTML Docs
         run: tox -e doc
       - name: deploy

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

README.rst

@@ -434,6 +434,6 @@ only use third-party Python libraries that have MIT or BSD licenses.
 .. |Build Status| image:: https://github.com/terrapower/armi/actions/workflows/unittests.yaml/badge.svg?branch=master
     :target: https://github.com/terrapower/armi/actions/workflows/unittests.yaml
 
-.. |Code Coverage| image:: https://coveralls.io/repos/github/terrapower/armi/badge.svg?branch=master&kill_cache=1
+.. |Code Coverage| image:: https://coveralls.io/repos/github/terrapower/armi/badge.svg?branch=master&kill_cache=2
     :target: https://coveralls.io/github/terrapower/armi?branch=master
 

armi/__init__.py

@@ -306,7 +306,7 @@ def configure(app: Optional[apps.App] = None, permissive=False):
     app = app or apps.App()
 
     if _app is not None:
-        if permissive and type(_app) is type(app):
+        if permissive and isinstance(app, apps.App):
             return
         else:
             raise RuntimeError(

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/db/database3.py

@@ -1480,15 +1480,7 @@ def getHistoriesByLocation(
             )
 
             lLocation = layout.location
-            # filter for objects that live under the desired ancestor and at a desired
-            # location
-            # TODO: There might be a numpy way of doing this faster, were we to treat
-            # the locations as a numpy array. The elements are tuple of int, tuple of
-            # float, or sometimes even None, as determined by the pack/unpackLocations
-            # implementations, so it might not be possible, let alone trivial to do
-            # this. One approach could be to go back to the locations in their raw
-            # HDF5 form, then list index into that, along with locationType, and
-            # re-unpack them. 🤔
+            # filter for objects that live under the desired ancestor and at a desired location
             objectIndicesInLayout = numpy.array(
                 [
                     i

armi/bookkeeping/historyTracker.py

@@ -279,133 +279,6 @@ def filterTimeIndices(self, timeIndices, boc=False, moc=False, eoc=False):
 
         return filtered
 
-    def getTimeIndices(self, a=None, boc=False, moc=False, eoc=False):
-        r"""
-        Generate a list of timestep indices where valid history data exist for the given criteria.
-
-        Parameters
-        ----------
-        a : Assembly, optional
-            If given, only generate time indices where the assembly `a` is in the core. Default: All assemblies.
-
-        boc, moc, eoc : bool, optional
-            Will return boc/moc/eoc timenodes in every cycle. If any of these are true, allNodes becomes False
-
-        Returns
-        -------
-        timeIndices : list
-            A list of integers where history data exists.
-
-        Examples
-        --------
-        If there are 5 nodes per cycle (burnSteps = 4),
-        0 1 2 3 4 | 5 6 7 8 9 | 10 11 12 13 14 | ...:
-
-        >>> getTimeIndices(moc=True):
-        [2, 7, 12, ...]
-
-        Warning
-        -------
-        This is no longer functional, as much of the old history tracking was based on
-        implementation details of the Database, version 2. We now directly support
-        history tracking through the Database, version 3. At some point this code should
-        be removed.
-
-        See Also
-        --------
-        getTimeSteps : gets time in years where the assembly is in the core
-
-        """
-        timeIndices = []
-        coreGrid = self.r.core.spatialGrid
-        for globalNode in range(
-            utils.getTimeStepNum(self.r.p.cycle, self.r.p.timeNode, self.cs) + 1
-        ):
-            if a is None:
-                timeIndices.append(globalNode)
-            else:
-                fBlock = a.getFirstBlock(Flags.FUEL)
-                if fBlock is None:
-                    blockLocationLabel = None
-                else:
-                    blockLocationLabel = self._blockLocationAtTimenode(
-                        fBlock, globalNode
-                    )
-                    runLog.info(
-                        "Location label of {} at timestep {} is {}".format(
-                            fBlock, globalNode, blockLocationLabel
-                        )
-                    )
-                # only add this timestep if it's around for this assembly.
-                if blockLocationLabel is not None:
-                    # this label doesn't actually properly correspond to the block
-                    # location label determined by _blockLocationAtTimenode.
-                    # blockLocationLabel is supposed to be coming from a previous time
-                    # state in the database.
-                    if a.spatialLocator.grid is coreGrid:
-                        timeIndices.append(globalNode)
-
-        return self.filterTimeIndices(timeIndices, boc, moc, eoc)
-
-    def getBOCEOCTimeIndices(self, assem=None):
-        r"""returns a list of time step indices that only include BOC and EOC, no intermediate ones."""
-        tIndices = self.getTimeIndices(assem)  # list of times in years
-        counter = 0
-        filtered = []
-        for tIndex in tIndices:
-            if counter == 0:
-                # boc. add it.
-                filtered.append(tIndex)
-                counter += 1
-            elif counter == self.cs["burnSteps"]:
-                # eoc. add it.
-                filtered.append(tIndex)
-                counter = 0
-            else:
-                # not boc or eoc. Just increment counter. tick, tick, tick
-                counter += 1
-
-        return filtered
-
-    def getAssemParamHistory(self, a, neededParams):
-        """Gets the history typically used for the Alchemy Writer
-
-        Returns
-        -------
-        assemHistory : dict, nested with 3 levels,
-            e.g. assemHistory[block][time_step][parameter] = value of parameter at time step on block
-
-
-        Raises
-        ------
-        RuntimeError
-            When the assembly has no history.
-        """
-        timeSteps = self.getTimeIndices(a)
-        if not timeSteps:
-            raise RuntimeError(
-                "Time steps empty. Cannot get assembly history for {}".format(a)
-            )
-
-        # assemHistory[block][time_step][parameter] = value of parameter at time step on block
-        assemHistory = OrderedDict([(block, None) for block in a.getBlocks(Flags.FUEL)])
-        for block in assemHistory:
-            assemHistory[block] = OrderedDict([(ts, None) for ts in timeSteps])
-
-            for ts in assemHistory[block]:
-                assemHistory[block][ts] = OrderedDict(
-                    [(param, None) for param in neededParams]
-                )
-
-                for param in assemHistory[block][ts]:
-                    val = self.getBlockHistoryVal(block.getName(), param, ts)
-                    assemHistory[block][ts][param] = val
-                assemHistory[block][ts]["location"] = self.getBlockHistoryVal(
-                    block.getName(), "loc", ts
-                )
-
-        return assemHistory
-
     def writeAssemHistory(self, a, fName=""):
         """Write the assembly history report to a text file."""
         fName = fName or self._getAssemHistoryFileName(a)

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))
 
@@ -382,7 +383,7 @@ def writeCycleSummary(core):
     core:  armi.reactor.reactors.Core
     cs: armi.settings.caseSettings.Settings
     """
-    ## would io be worth considering for this?
+    # would io be worth considering for this?
     cycle = core.r.p.cycle
     str_ = []
     runLog.important("Cycle {0} Summary:".format(cycle))
@@ -582,7 +583,7 @@ def summarizePower(core):
 
     # calculate total power
     tot = sum(sums.values()) or float("inf")
-    ## NOTE: if tot is 0.0, set to infinity to prevent ZeroDivisionError
+    # NOTE: if tot is 0.0, set to infinity to prevent ZeroDivisionError
 
     runLog.important("Power summary")
     for atype, val in sums.items():
@@ -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.
@@ -870,7 +870,6 @@ def _setGeneralSimulationData(core, cs, coreDesignTable):
     )
 
 
-## Block Design Report
 def makeBlockDesignReport(r):
     r"""Summarize the block designs from the loading file
 

armi/bookkeeping/report/tests/test_report.py

@@ -61,10 +61,7 @@ def test_setData(self):
         self.assertEqual(filled_instance["banana_3"], ["sundae", "chocolate"])
 
     def test_printReports(self):
-        """testing testing
-
-        :ref:`REQ86d884bb-6133-4078-8804-5a334c935338`
-        """
+        """testing printReports method"""
         repInt = reportInterface.ReportInterface(None, None)
         rep = repInt.printReports()
 

armi/cases/inputModifiers/tests/test_inputModifiers.py

@@ -15,7 +15,7 @@
 import unittest
 import os
 import io
-import yaml
+from ruamel import yaml
 
 from armi.utils import directoryChangers
 from armi import cases
@@ -201,7 +201,7 @@ def SuiteNaming(index, _case, _mods):
                 f"case-suite-testBPBM/000{case_nbr}/armi-000{case_nbr}-blueprints.yaml",
                 "r",
             )
-            bp_dict = yaml.safe_load(yamlfile)
+            bp_dict = yaml.load(yamlfile)
             yamlfile.close()
 
             self.assertEqual(bp_dict["blocks"]["fuel 1"]["clad"]["od"], 3.14)

armi/cases/tests/test_suiteBuilder.py

@@ -15,13 +15,23 @@
 """
 Unit tests for the SuiteBuilder
 """
+import os
 import unittest
-from armi.cases.inputModifiers.inputModifiers import SamplingInputModifier
+
 from armi import cases, settings
+from armi.cases.inputModifiers.inputModifiers import SamplingInputModifier
 from armi.cases.suiteBuilder import LatinHyperCubeSuiteBuilder
 
-
-cs = settings.Settings("armi/tests/tutorials/anl-afci-177.yaml")
+cs = settings.Settings(
+    os.path.join(
+        os.path.dirname(os.path.abspath(__file__)),
+        "..",
+        "..",
+        "tests",
+        "tutorials",
+        "anl-afci-177.yaml",
+    )
+)
 case = cases.Case(cs)
 
 

armi/cli/__init__.py

@@ -156,18 +156,18 @@ def listCommands(self):
 
         sub = re.compile(r"\s+").sub
 
-        ## given a string, condense white space into a single space
+        # given a string, condense white space into a single space
         condense = lambda s: sub(" ", s.strip())
 
         commands = self._entryPoints.values()
 
         formatter = "{name:<{width}}{desc}".format
         print("\ncommands:")
         for cmd in sorted(commands, key=lambda cmd: cmd.name):
-            ## Each command can optionally define a class attribute `description`
-            ## as documentation. If description is not defined (default=None since
-            ## it should inherit from EntryPoint), then the docstring is used.
-            ## If the docstring is also None, then fall back to an empty string.
+            """Each command can optionally define a class attribute `description`
+            as documentation. If description is not defined (default=None since
+            it should inherit from EntryPoint), then the docstring is used.
+            If the docstring is also None, then fall back to an empty string."""
             desc = condense(cmd.description or cmd.__doc__ or "")
             print(wrapper.fill(formatter(width=indent, name=cmd.name, desc=desc)))