Remove PyYaml Dependency (#586)

* Removing PyYaml dependency
* Removing and Fixing old TODOs
* Fail Build if code coverage under 80%
* Improving code coverage

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/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/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/nucDirectory/nuclideBases.py

@@ -99,7 +99,7 @@ def getAttributes(nuc):
 import pathlib
 import glob
 
-import yaml
+from ruamel import yaml
 
 import armi
 from armi.nucDirectory import elements
@@ -308,7 +308,7 @@ def __readMc2Nuclides():
     that have already been added from RIPL.
     """
     with open(os.path.join(armi.context.RES, "mc2Nuclides.yaml"), "r") as mc2Nucs:
-        mc2Nuclides = yaml.load(mc2Nucs, Loader=yaml.FullLoader)
+        mc2Nuclides = yaml.load(mc2Nucs, yaml.RoundTripLoader)
 
     # now add the mc2 specific nuclideBases, and correct the mc2Ids when a > 0 and state = 0
     for name, data in mc2Nuclides.items():
@@ -400,7 +400,8 @@ def imposeBurnChain(burnChainStream):
         runLog.warning("Burn chain already imposed. Skipping reimposition.")
         return
     _burnChainImposed = True
-    burnData = yaml.load(burnChainStream, Loader=yaml.FullLoader)
+    burnData = yaml.load(burnChainStream, yaml.RoundTripLoader)
+
     for nucName, burnInfo in burnData.items():
         nuclide = byName[nucName]
         # think of this protected stuff as "module level protection" rather than class.

armi/physics/neutronics/fissionProductModel/lumpedFissionProduct.py

@@ -284,30 +284,20 @@ def getLumpedFissionProductNames(self):
         return self.keys()
 
     def getAllFissionProductNames(self):
-        """
-        Gets names of all fission products in this collection
-
-        TODO: This can use a set, continually updated from the keys() for each lfp, then converted
-        to a list. This will change the order of the fission products, though, so should be done
-        with care
-        """
-        fpNames = []
+        """Gets names of all fission products in this collection"""
+        fpNames = set()
         for lfp in self.values():
             for fp in lfp.keys():
-                if fp not in fpNames:
-                    fpNames.append(fp.name)
-        return fpNames
+                fpNames.add(fp.name)
+        return sorted(fpNames)
 
     def getAllFissionProductNuclideBases(self):
-        """
-        Gets names of all fission products in this collection
-        """
-        clideBases = []
+        """Gets names of all fission products in this collection"""
+        clideBases = set()
         for _lfpName, lfp in self.items():
             for fp in lfp.keys():
-                if fp not in clideBases:
-                    clideBases.append(fp)
-        return clideBases
+                clideBases.add(fp)
+        return sorted(clideBases)
 
     def getNumberDensities(self, objectWithParentDensities=None, densFunc=None):
         """

armi/reactor/blocks.py

@@ -113,6 +113,7 @@ def __init__(self, name, height=1.0, location=None):
         # TODO: what's causing these to have wrong values at BOL?
         for problemParam in ["THcornTemp", "THedgeTemp"]:
             self.p[problemParam] = []
+
         for problemParam in [
             "residence",
             "bondRemoved",

armi/reactor/reactors.py

@@ -887,7 +887,7 @@ def getAssembliesInCircularRing(
             )
 
         # determine if the circularRingList has been generated
-        ## TODO: make circularRingList a property that is generated on request
+        # TODO: make circularRingList a property that is generated on request
         if not self.circularRingList:
             self.circularRingList = self.buildCircularRingDictionary(
                 self._circularRingPitch
@@ -1230,9 +1230,8 @@ def regenAssemblyLists(self):
         self._getAssembliesByName()
         self._genBlocksByName()
         runLog.important("Regenerating Core Zones")
-        self.buildZones(
-            settings.getMasterCs()
-        )  # TODO: this call is questionable... the cs should correspond to analysis
+        # TODO: this call is questionable... the cs should correspond to analysis
+        self.buildZones(settings.getMasterCs())
         self._genChildByLocationLookupTable()
 
     def getAllXsSuffixes(self):
@@ -1571,7 +1570,6 @@ def findNeighbors(
             showBlanks = True.  This will have no effect if the model is full core since
             asymmetric models could find many duplicates in the other thirds
 
-
         Notes
         -----
         This only works for 1/3 or full core symmetry.
@@ -1580,7 +1578,6 @@ def findNeighbors(
         standard (ring, pos) map. because neighbors have consistent indices this way.  We
         then convert over to (ring, pos) using the lookup table that a reactor has.
 
-
         Returns
         -------
         neighbors : list of assembly objects
@@ -1597,7 +1594,6 @@ def findNeighbors(
             assembly. It will only return "None" for an assembly when that assembly is
             non-existing AND has no existing "symmetric identical".
 
-
         See Also
         --------
         grids.Grid.getSymmetricEquivalents
@@ -1607,19 +1603,20 @@ def findNeighbors(
             *a.spatialLocator.getCompleteIndices()
         )
 
-        ## TODO: where possible, move logic out of loops
+        dupReflectors = (
+            self.symmetry.domain == geometry.DomainType.THIRD_CORE
+            and self.symmetry.boundary == geometry.BoundaryType.PERIODIC
+            and duplicateAssembliesOnReflectiveBoundary
+        )
+
         neighbors = []
         for iN, jN, kN in neighborIndices:
             neighborLoc = self.spatialGrid[iN, jN, kN]
             neighbor = self.childrenByLocator.get(neighborLoc)
             if neighbor is not None:
                 neighbors.append(neighbor)
             elif showBlanks:
-                if (
-                    self.symmetry.domain == geometry.DomainType.THIRD_CORE
-                    and self.symmetry.boundary == geometry.BoundaryType.PERIODIC
-                    and duplicateAssembliesOnReflectiveBoundary
-                ):
+                if dupReflectors:
                     symmetricAssem = self._getReflectiveDuplicateAssembly(neighborLoc)
                     neighbors.append(symmetricAssem)
                 else:
@@ -2019,7 +2016,6 @@ def getMinimumPercentFluxInFuel(self, target=0.005):
         targetRing, fraction of flux : tuple
             targetRing is the ring with the fraction of flux that best meets the target.
         """
-
         # get the total number of assembly rings
         numRings = self.getNumRings()
 
@@ -2031,7 +2027,6 @@ def getMinimumPercentFluxInFuel(self, target=0.005):
 
         # loop there all of the rings
         for ringNumber in range(numRings, 0, -1):
-
             # compare to outer most ring
             # flatten list into one list of all blocks
             blocksInRing = list(
@@ -2089,7 +2084,7 @@ def getAvgTemp(self, typeSpec, blockList=None, flux2Weight=False):
         denom = 0.0
         if not blockList:
             blockList = list(self.getBlocks())
-            ## TODO: this doesn't need to be a list
+
         for b in blockList:
             if flux2Weight:
                 weight = b.p.flux ** 2.0
@@ -2290,13 +2285,12 @@ def processLoading(self, cs):
         for i, b in enumerate(refAssem):
             if b.hasFlags(Flags.GRID_PLATE):
                 stationaryBlocks.append(i)
+                # TODO: remove hard-coded assumption of grid plates (T3019)
                 runLog.extra(
                     "Detected a grid plate {}.  Adding to stationary blocks".format(b)
-                )  # TODO: remove hard-coded assumption of grid plates (T3019)
+                )
 
-        cs[
-            "stationaryBlocks"
-        ] = stationaryBlocks  # TODO: DeprecationWarning - changing settings
+        cs["stationaryBlocks"] = stationaryBlocks
 
         # Perform initial zoning task
         self.buildZones(cs)

armi/utils/tests/test_outputCache.py

@@ -0,0 +1,52 @@
+# Copyright 2022 TerraPower, LLC
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+""" tests of the propereties class """
+# pylint: disable=missing-function-docstring,missing-class-docstring,abstract-method,protected-access,invalid-name
+import os
+import time
+import unittest
+
+from armi.utils import directoryChangers
+from armi.utils import outputCache
+
+
+class TestOutputCache(unittest.TestCase):
+    def test_hashFiles(self):
+        with directoryChangers.TemporaryDirectoryChanger() as dc:
+            files = ["test_hashFiles1.txt", "test_hashFiles2.txt"]
+            for fileName in files:
+                with open(fileName, "w") as f:
+                    f.write("hi")
+
+            hashed = outputCache._hashFiles(files)
+
+            self.assertEqual(hashed, "e9f5713dec55d727bb35392cec6190ce")
+
+    def test_deleteCache(self):
+        with directoryChangers.TemporaryDirectoryChanger() as dc:
+            outDir = "snapshotOutput_Cache"
+            self.assertFalse(os.path.exists(outDir))
+
+            os.mkdir(outDir)
+            with open(os.path.join(outDir, "test_deleteCache2.txt"), "w") as f:
+                f.write("hi there")
+
+            self.assertTrue(os.path.exists(outDir))
+            time.sleep(2)
+            outputCache.deleteCache(outDir)
+            self.assertFalse(os.path.exists(outDir))
+
+
+if __name__ == "__main__":
+    unittest.main()

armi/utils/textProcessors.py

@@ -151,7 +151,7 @@ def resolveMarkupInclusions(
     -----
     While the use of ``!include`` appears as though it would invoke some sort of special
     custom YAML constructor code, this does not do that. Processing these inclusions as
-    part of the document parsing/composition that comes with pyyaml or ruamel.yaml could
+    part of the document parsing/composition that comes with ruamel.yaml could
     work, but has a number of prohibitive drawbacks (or at least reasons why it might
     not be worth doing). Using a custom constructor is more-or-less supported by
     ruamel.yaml (which we do use, as it is what underpins the yamlize package), but it

doc/release/0.2.rst

@@ -12,6 +12,7 @@ What's new in ARMI
 #. Added neutronics settings: ``inners`` and ``outers`` for downstream support.
 #. Removed unused Thermal Hydraulics settings.
 #. Minor code re-org, moving math utilities into their own module.
+#. Removed the ``PyYaml`` dependency.
 #. TBD
 
 Bug fixes

setup.py

@@ -66,7 +66,6 @@ def collectExtraFiles():
         "pluggy",
         "pyevtk",
         "pympler",
-        "pyyaml>=5.1",
         "scipy",
         "tabulate",
         "voluptuous",

tox.ini

@@ -34,7 +34,7 @@ deps=
     -r{toxinidir}/requirements.txt
     -r{toxinidir}/requirements-testing.txt
 commands =
-    pytest --cov-config=.coveragerc --cov=armi --ignore=armi/utils/tests/test_gridGui.py {posargs} armi
+    pytest --cov-config=.coveragerc --cov=armi --ignore=armi/utils/tests/test_gridGui.py --cov-fail-under=80 {posargs} armi
 
 # NOTE: This only runs the MPI unit tests.
 # NOTE: This will only work in POSIX/BASH Linux.
@@ -47,7 +47,7 @@ whitelist_externals =
 commands =
     pip install -r requirements.txt
     pip install -r requirements-testing.txt
-    mpiexec -n 2 pytest armi/tests/test_mpiFeatures.py
+    mpiexec -n 2 --use-hwthread-cpus pytest armi/tests/test_mpiFeatures.py
 
 [testenv:lint]
 ignore_errors = true