Moving from shutil.copy to safeCopy (#2024)

armi/bookkeeping/db/database.py

@@ -77,8 +77,7 @@
 from armi.reactor.reactorParameters import makeParametersReadOnly
 from armi.reactor.reactors import Core, Reactor
 from armi.settings.fwSettings.globalSettings import CONF_SORT_REACTOR
-from armi.utils import getNodesPerCycle
-from armi.utils import safeMove
+from armi.utils import getNodesPerCycle, safeCopy, safeMove
 from armi.utils.textProcessors import resolveMarkupInclusions
 
 # CONSTANTS
@@ -700,7 +699,7 @@ def syncToSharedFolder(self):
         # Close the h5 file so it can be copied
         self.h5db.close()
         self.h5db = None
-        shutil.copy(self._fullPath, self._fileName)
+        safeCopy(self._fullPath, self._fileName)
 
         # Garbage collect so we don't have multiple databases hanging around in memory
         gc.collect()

armi/bookkeeping/db/tests/test_database3.py

@@ -12,31 +12,27 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 """Tests for the Database class."""
-from glob import glob
 import io
 import os
 import shutil
 import subprocess
 import unittest
+from glob import glob
 
 import h5py
 import numpy as np
 
-from armi.bookkeeping.db import _getH5File
-from armi.bookkeeping.db import database
-from armi.bookkeeping.db import loadOperator
+from armi.bookkeeping.db import _getH5File, database, loadOperator
 from armi.bookkeeping.db.databaseInterface import DatabaseInterface
 from armi.bookkeeping.db.jaggedArray import JaggedArray
 from armi.reactor import parameters
 from armi.reactor.excoreStructure import ExcoreCollection, ExcoreStructure
-from armi.reactor.reactors import Core
-from armi.reactor.reactors import Reactor
+from armi.reactor.reactors import Core, Reactor
 from armi.reactor.spentFuelPool import SpentFuelPool
 from armi.reactor.tests.test_reactors import loadTestReactor, reduceTestReactorRings
 from armi.settings.fwSettings.globalSettings import CONF_SORT_REACTOR
-from armi.tests import mockRunLogs
-from armi.tests import TEST_ROOT
-from armi.utils import getPreviousTimeNode
+from armi.tests import TEST_ROOT, mockRunLogs
+from armi.utils import getPreviousTimeNode, safeCopy
 from armi.utils.directoryChangers import TemporaryDirectoryChanger
 
 # determine if this is a parallel run, and git is installed
@@ -783,7 +779,7 @@ def setUp(self):
         thisDir = self.td.destination
         yamls = glob(os.path.join(TEST_ROOT, "smallestTestReactor", "*.yaml"))
         for yam in yamls:
-            shutil.copy(os.path.join(TEST_ROOT, "smallestTestReactor", yam), thisDir)
+            safeCopy(os.path.join(TEST_ROOT, "smallestTestReactor", yam), thisDir)
 
         # Add an EVST to this reactor
         with open("refSmallestReactor.yaml", "w") as f:

armi/bookkeeping/report/newReports.py

@@ -12,22 +12,20 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from abc import ABC, abstractmethod
-from enum import Enum
-from enum import auto
-from operator import itemgetter
-from typing import Union, Dict
 import base64
 import collections
 import copy
 import os
-import shutil
+from abc import ABC, abstractmethod
+from enum import Enum, auto
+from operator import itemgetter
+from typing import Dict, Union
 
 import htmltree
 import matplotlib.pyplot as plt
 
-from armi import context
-from armi import runLog
+from armi import context, runLog
+from armi.utils import safeCopy
 
 
 class ReportContent:
@@ -86,14 +84,14 @@ def writeReports(self):
         doc = htmltree.Html(head, body)
 
         # Copy css file to the correct folder containing the reportContent.html
-        shutil.copy(
+        safeCopy(
             os.path.abspath(
                 os.path.join(os.path.abspath(__file__), os.pardir, "styles.css")
             ),
             "styles.css",
         )
 
-        shutil.copy(
+        safeCopy(
             os.path.abspath(
                 os.path.join(os.path.abspath(__file__), os.pardir, "report.js")
             ),

armi/operators/operator.py

@@ -25,13 +25,10 @@
 import collections
 import os
 import re
-import shutil
 import time
 from typing import Tuple
 
-from armi import context
-from armi import interfaces
-from armi import runLog
+from armi import context, interfaces, runLog
 from armi.bookkeeping import memoryProfiler
 from armi.bookkeeping.report import reportingUtils
 from armi.operators.runTypes import RunTypes
@@ -41,22 +38,22 @@
 )
 from armi.settings import settingsValidation
 from armi.settings.fwSettings.globalSettings import (
-    CONF_TIGHT_COUPLING,
-    CONF_TIGHT_COUPLING_MAX_ITERS,
     CONF_CYCLES_SKIP_TIGHT_COUPLING_INTERACTION,
     CONF_DEFERRED_INTERFACE_NAMES,
     CONF_DEFERRED_INTERFACES_CYCLE,
+    CONF_TIGHT_COUPLING,
+    CONF_TIGHT_COUPLING_MAX_ITERS,
 )
-from armi.utils import codeTiming
 from armi.utils import (
-    pathTools,
-    getPowerFractions,
+    codeTiming,
     getAvailabilityFactors,
-    getStepLengths,
-    getCycleLengths,
     getBurnSteps,
-    getMaxBurnSteps,
+    getCycleLengths,
     getCycleNames,
+    getMaxBurnSteps,
+    getPowerFractions,
+    getStepLengths,
+    pathTools,
 )
 
 
@@ -1219,16 +1216,15 @@ def snapshotRequest(self, cycle, node, iteration=None):
                     )
                 else:
                     newFile = "{0}_{1:03d}_{2:d}{3}".format(base, cycle, node, ext)
-                # add the cycle and timenode to the XS input file names so that a rx-coeff case that runs
-                # in here won't overwrite them.
-                shutil.copy(fileName, os.path.join(newFolder, newFile))
+                # add the cycle and timenode to the XS input file names so that a rx-coeff case that
+                # runs in here won't overwrite them.
+                pathTools.copyOrWarn(
+                    fileName, fileName, os.path.join(newFolder, newFile)
+                )
             if "rzmflx" in fileName:
                 pathTools.copyOrWarn("rzmflx for snapshot", fileName, newFolder)
 
-        fileNamePossibilities = [
-            f"ISOTXS-c{cycle}n{node}",
-            f"ISOTXS-c{cycle}",
-        ]
+        fileNamePossibilities = [f"ISOTXS-c{cycle}n{node}", f"ISOTXS-c{cycle}"]
         if iteration is not None:
             fileNamePossibilities = [
                 f"ISOTXS-c{cycle}n{node}i{iteration}"

armi/physics/neutronics/crossSectionGroupManager.py

@@ -54,7 +54,6 @@
 import collections
 import copy
 import os
-import shutil
 import string
 
 import numpy as np
@@ -66,7 +65,8 @@
 from armi.reactor.components import basicShapes
 from armi.reactor.converters.blockConverters import stripComponents
 from armi.reactor.flags import Flags
-from armi.utils.units import TRACE_NUMBER_DENSITY, C_TO_K
+from armi.utils import safeCopy
+from armi.utils.units import C_TO_K, TRACE_NUMBER_DENSITY
 
 ORDER = interfaces.STACK_ORDER.BEFORE + interfaces.STACK_ORDER.CROSS_SECTIONS
 
@@ -1195,7 +1195,7 @@ def _copyPregeneratedXSFile(self, xsID):
             )
             # Prevent copy error if the path and destination are the same.
             if xsFileLocation != dest:
-                shutil.copy(xsFileLocation, dest)
+                safeCopy(xsFileLocation, dest)
 
     def _copyPregeneratedFluxSolutionFile(self, xsID):
         # stop a race condition to copy files between all processors
@@ -1211,7 +1211,7 @@ def _copyPregeneratedFluxSolutionFile(self, xsID):
         )
         # Prevent copy error if the path and destination are the same.
         if fluxFileLocation != dest:
-            shutil.copy(fluxFileLocation, dest)
+            safeCopy(fluxFileLocation, dest)
 
     def _getPregeneratedXsFileLocationData(self, xsID):
         """

armi/physics/neutronics/latticePhysics/latticePhysicsInterface.py

@@ -18,22 +18,19 @@
 Parent classes for codes responsible for generating broad-group cross sections
 """
 import os
-import shutil
 
-from armi import interfaces
-from armi import nuclearDataIO
-from armi import runLog
+from armi import interfaces, nuclearDataIO, runLog
 from armi.physics import neutronics
+from armi.physics.neutronics import LatticePhysicsFrequency
 from armi.physics.neutronics.const import CONF_CROSS_SECTION
 from armi.physics.neutronics.settings import (
-    CONF_GEN_XS,
     CONF_CLEAR_XS,
+    CONF_GEN_XS,
+    CONF_LATTICE_PHYSICS_FREQUENCY,
     CONF_TOLERATE_BURNUP_CHANGE,
     CONF_XS_KERNEL,
-    CONF_LATTICE_PHYSICS_FREQUENCY,
 )
-from armi.physics.neutronics import LatticePhysicsFrequency
-from armi.utils import codeTiming
+from armi.utils import codeTiming, safeCopy
 
 LATTICE_PHYSICS = "latticePhysics"
 
@@ -149,17 +146,17 @@ def updateXSLibrary(self, cycle, node=None):
 
     def _renameExistingLibrariesForStatepoint(self, cycle, node):
         """Copy the existing neutron and/or gamma libraries into cycle-dependent files."""
-        shutil.copy(
+        safeCopy(
             neutronics.ISOTXS, nuclearDataIO.getExpectedISOTXSFileName(cycle, node)
         )
         if self.includeGammaXS:
-            shutil.copy(
+            safeCopy(
                 neutronics.GAMISO,
                 nuclearDataIO.getExpectedGAMISOFileName(
                     cycle=cycle, node=node, suffix=self._getSuffix(cycle)
                 ),
             )
-            shutil.copy(
+            safeCopy(
                 neutronics.PMATRX,
                 nuclearDataIO.getExpectedPMATRXFileName(
                     cycle=cycle, node=node, suffix=self._getSuffix(cycle)
@@ -195,7 +192,7 @@ def _copyLibraryFilesForCycle(cycle, libFiles):
             else:
                 runLog.info("Using {} as an active library".format(baseName))
                 if cycleName != baseName:
-                    shutil.copy(cycleName, baseName)
+                    safeCopy(cycleName, baseName)
 
     def _readGammaBinaries(self, lib, gamisoFileName, pmatrxFileName):
         raise NotImplementedError(

armi/settings/settingsValidation.py

@@ -24,21 +24,16 @@
 import itertools
 import os
 import re
-import shutil
 
-from armi import context
-from armi import getPluginManagerOrFail
-from armi import runLog
+from armi import context, getPluginManagerOrFail, runLog
 from armi.physics import neutronics
-from armi.reactor import geometry
-from armi.reactor import systemLayoutInput
+from armi.reactor import geometry, systemLayoutInput
 from armi.settings.settingsIO import (
-    prompt,
     RunLogPromptCancel,
     RunLogPromptUnresolvable,
+    prompt,
 )
-from armi.utils import directoryChangers
-from armi.utils import pathTools
+from armi.utils import directoryChangers, pathTools, safeCopy
 from armi.utils.mathematics import expandRepeatedFloats
 
 
@@ -245,7 +240,7 @@ def run(self, cs=None):
             runLog.important(
                 f"Preserving original settings file by renaming `{renamePath}`"
             )
-            shutil.copy(self.cs.path, renamePath)
+            safeCopy(self.cs.path, renamePath)
             # save settings file
             self.cs.writeToYamlFile(self.cs.path)
 

armi/utils/directoryChangers.py

@@ -22,7 +22,7 @@
 from armi import context
 from armi import runLog
 from armi.utils import pathTools
-from armi.utils import safeMove
+from armi.utils import safeCopy, safeMove
 
 
 def _changeDirectory(destination):
@@ -187,8 +187,7 @@ def _transferFiles(initialPath, destinationPath, fileList, moveFiles=False):
         Transfer files into or out of the directory.
 
         This is used in ``moveFiles`` and ``retrieveFiles`` to shuffle files about when creating a
-        target directory or when coming back, respectively. Beware that this uses ``shutil.copy()``
-        under the hood, which doesn't play nicely with directories.
+        target directory or when coming back, respectively.
 
         Parameters
         ----------
@@ -239,7 +238,7 @@ def _transferFiles(initialPath, destinationPath, fileList, moveFiles=False):
                     safeMove(fromPath, toPath)
                 else:
                     runLog.extra("Copying {} to {}".format(fromPath, toPath))
-                    shutil.copy(fromPath, toPath)
+                    safeCopy(fromPath, toPath)
 
 
 class TemporaryDirectoryChanger(DirectoryChanger):

armi/utils/outputCache.py

@@ -36,17 +36,16 @@
 
 Notes
 -----
-Could probably be, like, a decorate on subprocess but we call subprocess a bunch of
-different ways.
+Could probably be, like, a decorate on subprocess but we call subprocess a bunch of different ways.
 """
 
 import hashlib
 import json
 import os
-import shutil
 import subprocess
 
 from armi import runLog
+from armi.utils import safeCopy
 from armi.utils.pathTools import cleanPath
 
 MANIFEST_NAME = "CRC-manifest.json"
@@ -106,7 +105,7 @@ def _copyOutputs(cachedFolder, locToRetrieveTo):
 
     for copy in copies:
         storedOutputPath, copyPath = copy
-        shutil.copy(storedOutputPath, copyPath)
+        safeCopy(storedOutputPath, copyPath)
 
     return True
 
@@ -166,7 +165,7 @@ def store(exePath, inputPaths, outputFiles, cacheDir):
     for outputFile in outputsThatExist:
         baseName = os.path.basename(outputFile)
         cachedLoc = os.path.join(folderLoc, baseName)
-        shutil.copy(outputFile, cachedLoc)
+        safeCopy(outputFile, cachedLoc)
 
     runLog.info("Added outputs for {} to the cache.".format(exePath))