Merge branch 'devel' into wangc/update_submodule_ID

idaholab · May 15, 2023 · 13bf9b3 · 13bf9b3
2 parents 66421a1 + b605d47
commit 13bf9b3
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diff --git a/.gitignore b/.gitignore
@@ -1,79 +1,40 @@
+.failed_tests
 .libs
+.ravenrc
+*-dbg
+*-devel
+*-oprof
+*-opt
+*.a
+*.csv
+*.ctf
+*.d
 *.dylib
+*.e
 *.la
 *.lo
-*.d
 *.o
-*.a
-*-opt
-*-dbg
-*-oprof
-*-devel
-*.e
-*.csv
+*.ravencntr
+*.ravenStatus
 *.so
 *~
-*.ctf
-tests/core_example/PWR_CoreChannel_controlled_var_restart_test_out_restart_0020.ravenaux
-tests/core_example/PWR_CoreChannel_controlled_var_test_out_restart_0020.ravenaux
-*.ravencntr
-control_modules/distribution1D.py
-control_modules/distribution1D_wrap.cxx
-control_modules/raventools.py
-control_modules/raventools_wrap.cxx
-control_modules/libdistribution1D.so*
-control_modules/libdistribution1D.so*
-control_modules/libraventools.so*
-control_modules/libraventools.so*
-libRAVEN*.so*
-RAVEN-devel
-tests/framework/DataBaseStorage/
-tests/framework/GridTestBison/CustomSampler/
-tests/framework/GridTestRaven/FirstMRun/
-tests/framework/LHStestBison/myLHS/
-tests/framework/LHStestRaven/FirstMRun/
-tests/framework/MCTestBison/CustomSampler/
-tests/framework/MCTestBison/CustomSampler_noalias/
-tests/framework/branch/DETrunTest/
-tests/framework/SBO_DET/DET/
-tests/framework/mode_test/FirstMRun/
-tests/framework/output_check/*.png
-tests/framework/output_check/FirstMRun/
-tests/framework/revirD_tset/FirstMRun/
-tests/framework/test_extract_data_s_from_hdf5/MonteCarlo/
-tests/framework/test_rom_trainer/MC_for_rom_trainer/
-tests/framework/mpi_driver_test/FirstMRun/
-tests/framework/CodeInterfaceTests/MelcorInterface/testMelcor/*
-tests/framework/CodeInterfaceTests/RELAP5interfaceTestSingleRun/*
-work_in_progress/remote_tools/remote_tools
-work_in_progress/remote_tools/remote_tools.py
-work_in_progress/remote_tools/remote_tools_wrap.cxx
-work_in_progress/remote_tools/time
-framework/DatabaseStorage/
-tests/framework/LHStestFerret/myLHS/
-tests/framework/PreconditionedDynamicEventTree/PreconditionedDETrunTest/
-tests/framework/CUBIT_MOOSE_test/grid_run/
-tests/framework/BISON_and_MESH_test/grid_run/
-tests/framework/RedundantInputs/sim_py_MC/
-tests/framework/RedundantInputs/sim_py_grid/
-tests/plugins
-plugins/ExamplePlugin/doc/version.tex
+build_out*
 build/
-.failed_tests
-.ravenrc
-*.ravenStatus
 install/
-src/crow_modules/distribution1D.py
+libRAVEN*.so*
+plugins/ExamplePlugin/doc/version.tex
+raven_cxx.egg-info/
+raven_framework.egg-info/
+raven_framework*.whl
+src/contrib/amsc.egg-info/
 src/crow_modules/distribution1D_wrap.cpp
-src/crow_modules/interpolationND.py
+src/crow_modules/distribution1D.py
 src/crow_modules/interpolationND_wrap.cpp
-src/crow_modules/randomENG.py
+src/crow_modules/interpolationND.py
 src/crow_modules/randomENG_wrap.cpp
-build_out*
+src/crow_modules/randomENG.py
 test_out*
-framework/contrib/PythonFMU/pythonfmu.egg-info/
-raven_framework.egg-info/
-raven_framework*.whl
+dist/
 
 # eclipse
 .project
@@ -106,3 +67,7 @@ framework/states.txt
 
 # plugin installation paths
 plugins/plugin_directory.xml
+
+# vscode
+.vscode
+*.code-workspace
diff --git a/MANIFEST.in b/MANIFEST.in
@@ -0,0 +1,6 @@
+include crow/include/distributions/*.h
+include crow/include/utilities/*.h
+recursive-include crow/contrib/include/Eigen *
+recursive-include crow/contrib/include/boost *
+include include/contrib/AMSC/*.h
+include include/contrib/ngl/*.h*
diff --git a/build_raven b/build_raven
@@ -16,6 +16,7 @@ echo Making RAVEN ...
 # defaults
 MAKE_ARGS=" "
 LIBS_MODE=0 # 0 is "create", 1 is "load"
+EDITABLE=0 # 0 is install regular, 1 is install editable
 #### FUTURE WORK:
 ####   combine "make" and "establish_conda_env.sh" into one installation command
 ECE_ARGS=" "
@@ -39,7 +40,9 @@ do
        ;;
      --jobs) MAKE_ARGS="-j $1 ${MAKE_ARGS}"; ;;
      --skip-conda)
-      LIBS_MODE=2
+         LIBS_MODE=2 ;;
+     --editable)
+         EDITABLE=1
 #    --help)     ECE_ARGS="${ECE_ARGS} --help"; ;;
 #    --optional) ECE_ARGS="${ECE_ARGS} --optional"; ;;
 #    --no-clean) ECE_ARGS="${ECE_ARGS} --no-clean"; ;;
@@ -104,14 +107,18 @@ if test `uname` = Darwin; then
     export MACOSX_DEPLOYMENT_TARGET;
 fi
 
-PIP_COMMAND=pip3
-(cd $RAVEN_BUILD_DIR && ${PIP_COMMAND} --verbose install . --upgrade --target ./install)
-
-#pip install will add a duplicate ravenframework directory, so delete so there isn't
-# confusion over which of the two copies to use.
-(cd $RAVEN_BUILD_DIR && rm -Rf install/ravenframework)
+(cd $PYTHON_FMU_DIR && ./build_pythonfmu || echo PythonFMU not built)
 
-(cd $PYTHON_FMU_DIR && ./build_pythonfmu || echo PythonFMU build failed)
+PIP_COMMAND=pip3
+if [[ $EDITABLE == 0 ]]
+then # Don't install editable
+    (cd $RAVEN_BUILD_DIR && ${PIP_COMMAND} --verbose install . --upgrade --target ./install)
+    #pip install will add a duplicate ravenframework directory, so delete so there isn't
+    # confusion over which of the two copies to use.
+    (cd $RAVEN_BUILD_DIR && rm -Rf install/ravenframework)
+else #do install editable
+    $PIP_COMMAND --verbose install --editable . --upgrade --target ./install
+fi
 
 if [ ! -z "$RAVEN_SIGNATURE" ];
 then

diff --git a/clean_raven b/clean_raven
@@ -11,9 +11,19 @@ rm -f ${RAVEN_DIR}/ravenframework/contrib/AMSC/_amsc*.so \
     ${RAVEN_DIR}/src/contrib/amsc_wrap.cpp \
     ${RAVEN_DIR}/src/contrib/amsc.py \
     ${RAVEN_DIR}/src/contrib/amsc.pyc
+rm -f ${RAVEN_DIR}/src/AMSC/_amsc*.so \
+    ${RAVEN_DIR}/src/AMSC/amsc*egg-info \
+    ${RAVEN_DIR}/src/AMSC/amsc.py \
+    ${RAVEN_DIR}/src/AMSC/amsc.pyc \
+    ${RAVEN_DIR}/src/AMSC/amsc_wrap.cxx \
+    ${RAVEN_DIR}/src/AMSC/amsc_wrap.cpp
 rm -Rf ${RAVEN_DIR}/build  \
    ${RAVEN_DIR}/crow/install/ \
-   ${RAVEN_DIR}/install/
+   ${RAVEN_DIR}/install/ \
+   ${RAVEN_DIR}/setup.cfg
+rm -f ${RAVEN_DIR}/src/crow_modules/*.so \
+   ${RAVEN_DIR}/src/crow_modules/[dir]*.py \
+   ${RAVEN_DIR}/src/crow_modules/*.cpp
 find ${RAVEN_DIR}/ravenframework  -name '*.pyc' -exec rm '{}' \;
 find ${RAVEN_DIR}/scripts  -name '*.pyc' -exec rm '{}' \;
 find ${RAVEN_DIR}/rook  -name '*.pyc' -exec rm '{}' \;
@@ -29,6 +39,7 @@ find ${RAVEN_DIR}/scripts  -name '__pycache__' -exec rm -Rf '{}' \;
 find ${RAVEN_DIR}/rook  -name '__pycache__' -exec rm -Rf '{}' \;
 find ${RAVEN_DIR}/tests  -name '__pycache__' -exec rm -Rf '{}' \;
 find ${RAVEN_DIR}/plugins  -name '__pycache__' -exec rm -Rf '{}' \;
+find ${RAVEN_DIR}/src  -name '__pycache__' -exec rm -Rf '{}' \;
 
 rm -f ${CROW_DIR}/control_modules/_distribution1D.so \
    ${CROW_DIR}/control_modules/_crowtools.so \
@@ -59,4 +70,5 @@ rm -Rf ${CROW_DIR}/src/distributions/*.lo \
 rm -Rf ${CROW_DIR}/src/distributions/*.d \
  ${CROW_DIR}/src/tools/*.d \
  ${CROW_DIR}/src/utilities/*.d
+rm -Rf raven_framework.egg-info/
 
diff --git a/dependencies.xml b/dependencies.xml
@@ -35,18 +35,22 @@ Note all install methods after "main" take
 -->
 <dependencies>
   <main>
-    <h5py>2.10</h5py>
-    <numpy>1.18</numpy>
-    <scipy>1.2</scipy>
-    <scikit-learn>0.21</scikit-learn>
-    <pandas>1.1</pandas>
-    <xarray>0.16</xarray>
+    <h5py/>
+    <numpy>1.22</numpy>
+    <scipy>1.7</scipy>
+    <scikit-learn>1.0</scikit-learn>
+    <pandas>1.3</pandas>
+    <!-- Note most versions of xarray work, but some (such as 0.20) don't -->
+    <xarray>2023</xarray>
     <netcdf4>1.5</netcdf4>
-    <matplotlib>3.2</matplotlib>
-    <statsmodels/>
-    <cloudpickle>1.6</cloudpickle>
-    <tensorflow>2.0</tensorflow>
-    <python skip_check='True'>3</python>
+    <matplotlib>3.5</matplotlib>
+    <statsmodels>0.13</statsmodels>
+    <cloudpickle>2.2</cloudpickle>
+    <tensorflow os='mac,linux'>2.10</tensorflow>
+    <tensorflow source="pip" os='windows'>2.10</tensorflow>
+    <!-- conda is really slow on windows if the version is not specified.-->
+    <python skip_check='True' os='windows'>3.8</python>
+    <python skip_check='True' os='mac,linux'>3</python>
     <hdf5 skip_check='True'/>
     <swig skip_check='True'/>
     <pylint/>
@@ -55,17 +59,26 @@ Note all install methods after "main" take
     <psutil/>
     <pip/>
     <importlib_metadata/>
-    <pyside2/>
+    <pyside2 optional='True'/>
     <nomkl os='linux' skip_check='True'/>
     <numexpr os='linux'/>
     <cmake skip_check='True' optional='True'/>
-    <ray os="mac,linux" source="pip" pip_extra="[default]">1.9</ray>
-    <imageio>2.9</imageio>
+    <ray source="pip" pip_extra="[default]" os='mac,linux'>2.2</ray>
+    <ray source="pip" pip_extra="[default]" os='windows'>1.13</ray>
+    <!-- redis is needed by ray, but on windows, this seems to need to be explicitly stated -->
+    <redis source="pip" os='windows'/>
+    <imageio>2.22</imageio>
     <line_profiler optional='True'/>
     <!-- <ete3 optional='True'/> -->
     <pywavelets optional='True'>1.1</pywavelets>
+    <numdifftools source="pip">0.9</numdifftools>
     <fmpy optional='True'/>
     <xmlschema source="pip"/>
+    <pyomo optional='True'>6.4</pyomo>
+    <glpk skip_check='True' optional='True'/>
+    <ipopt skip_check='True' optional='True'/>
+    <cyipopt optional='True'/>
+    <pyomo-extensions source="pyomo" skip_check='True' optional='True'/>
     <setuptools/>
   </main>
   <alternate name="pip">
@@ -76,4 +89,12 @@ Note all install methods after "main" take
     <nomkl>remove</nomkl>
     <numexpr>remove</numexpr>
   </alternate>
+  <alternate name="none">
+    <hdf5>remove</hdf5>
+    <swig>remove</swig>
+    <pip>remove</pip>
+    <python>remove</python>
+    <nomkl>remove</nomkl>
+    <numexpr>remove</numexpr>
+  </alternate>
 </dependencies>
diff --git a/developer_tools/XSDSchemas/Optimizers.xsd b/developer_tools/XSDSchemas/Optimizers.xsd
@@ -87,7 +87,16 @@
         <xsd:element name="persistence"        type="xsd:integer" minOccurs="0"/>
         <xsd:element name="objective"          type="xsd:float" minOccurs="0"/>
         <xsd:element name="temperature"        type="xsd:float" minOccurs="0"/>
+      </xsd:all>
+    </xsd:complexType>
+
+    <xsd:complexType name="GAConvergenceType">
+      <xsd:all>
+        <xsd:element name="persistence"        type="xsd:integer" minOccurs="0"/>
+        <xsd:element name="objective"          type="xsd:float" minOccurs="0"/>
         <xsd:element name="AHDp"               type="xsd:float" minOccurs="0"/>
+        <xsd:element name="AHD"                type="xsd:float" minOccurs="0"/>
+        <xsd:element name="HDSM"               type="xsd:float" minOccurs="0"/>
       </xsd:all>
     </xsd:complexType>
 
@@ -184,7 +193,7 @@
         <xsd:sequence>
             <xsd:element name="samplerInit"      type="optInitType"            minOccurs="0"/>
             <xsd:element name="GAparams"         type="GAoptInitType"          minOccurs="0" maxOccurs="1"/>
-            <xsd:element name="convergence"      type="SAConvergenceType"      minOccurs="0" maxOccurs="1"/>
+            <xsd:element name="convergence"      type="GAConvergenceType"      minOccurs="0" maxOccurs="1"/>
             <xsd:element name="coolingSchedule"  type="OptCoolingScheduleType" minOccurs="0" maxOccurs="1"/>
             <xsd:element name="variable"         type="optVarType"             minOccurs="1" maxOccurs='unbounded'/>
             <xsd:element name="objective"        type="xsd:string"             minOccurs="1" maxOccurs="1"/>

diff --git a/developer_tools/check_pip_packages.sh b/developer_tools/check_pip_packages.sh
@@ -0,0 +1,43 @@
+#!/bin/bash
+
+# This script tests that the 3.9 and 3.8 wheels built in directory dist
+# are installable. It will not work if there is more than one
+# version of the wheel for a python version (including for other os's)
+# It is designed to be run after (or similar):
+# rm -Rf dist; ./developer_tools/make_pip_packages.sh
+# It will install raven_framework in the python37_pip and python38_pip
+# conda environments
+# It requires that .ravenrc has a working CONDA_DEFS statement.
+# To run from the raven directory:
+# ./developer_tools/check_pip_packages.sh
+
+SCRIPT_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
+RAVEN_DIR=`dirname $SCRIPT_DIR`
+
+source $RAVEN_DIR/scripts/read_ravenrc.sh
+CONDA_DEFS=$(read_ravenrc "CONDA_DEFS")
+source ${CONDA_DEFS}
+
+cd $RAVEN_DIR
+
+ls -l dist
+
+#The following works to install from the dist directory, but also can install
+# from pypi so doesn't fail if wheels not created in dist, so can't be used
+# for automated testing
+#python -m pip install -f file://${RAVEN_DIR}/dist raven_framework || exit -1
+
+echo
+echo Checking Python 3.8
+
+conda activate python38_pip
+python -m pip uninstall -y raven_framework || echo not installed
+python -m pip install dist/raven_framework*cp38*.whl || exit -1
+
+
+echo
+echo Checking Python 3.9
+
+conda activate python39_pip
+python -m pip uninstall -y raven_framework || echo not installed
+python -m pip install dist/raven_framework*cp39*.whl || exit -1
diff --git a/developer_tools/createRegressionTestDocumentation.py b/developer_tools/createRegressionTestDocumentation.py
@@ -105,19 +105,18 @@ def noDescriptionTestsAndInformationOnTheOther(self):
     for testInfoFile in __testInfoList:
       if 'moose' in testInfoFile.split(os.sep) or not os.path.isfile(testInfoFile):
         continue
-      fileObject = open(testInfoFile,"r+")
-      fileLines = fileObject.readlines()
-      dirName = os.path.dirname(testInfoFile)
-      # I do not want to use getpot!
-      for line in fileLines:
-        if line.strip().startswith("input"):
-          fileName = line.split("=")[-1].replace("'", "").replace('"', '').rstrip().strip()
-          fileName = os.path.join(dirName,fileName)
-          if os.path.split(fileName)[-1].lower().endswith('xml'):
-            __testList.append(os.path.abspath(fileName))
-          if os.path.split(fileName)[-1].lower().endswith('py'):
-            __testList.append(os.path.abspath(fileName))
-      fileObject.close()
+      with open(testInfoFile,"r+") as fileObject:
+        fileLines = fileObject.readlines()
+        dirName = os.path.dirname(testInfoFile)
+        # I do not want to use getpot!
+        for line in fileLines:
+          if line.strip().startswith("input"):
+            fileName = line.split("=")[-1].replace("'", "").replace('"', '').rstrip().strip()
+            fileName = os.path.join(dirName,fileName)
+            if os.path.split(fileName)[-1].lower().endswith('xml'):
+              __testList.append(os.path.abspath(fileName))
+            if os.path.split(fileName)[-1].lower().endswith('py'):
+              __testList.append(os.path.abspath(fileName))
     for testFile in __testList:
       if testFile.endswith('xml'):
         try: root = ET.parse(testFile).getroot()

diff --git a/developer_tools/createSQAtracebilityMatrix.py b/developer_tools/createSQAtracebilityMatrix.py
@@ -63,7 +63,7 @@ def createLatexFile(reqDictionary,reqDocument,outputLatex):
       # create table here
       fileObject.write("\\begin{tabularx}{\\textwidth}{|s|s|b|} \n")
       fileObject.write("\\hline \n")
-      fileObject.write("\\textbf{Requirment ID} & \\textbf{Requirment Description} & \\textbf{Test(s)}  \\\ \hline \n")
+      fileObject.write("\\textbf{Requirement ID} & \\textbf{Requirement Description} & \\textbf{Test(s)}  \\\ \hline \n")
       fileObject.write("\\hline \n")
       ravenPath =    os.path.realpath(os.path.join(os.path.realpath(__file__) ,"..","..",".."))
       for reqName,req in reqSet.items():
@@ -74,7 +74,7 @@ def createLatexFile(reqDictionary,reqDocument,outputLatex):
             requirementTests = source
         requirementTests = [] if requirementTests is None else requirementTests
         for i in range(len(requirementTests)):
-          requirementTests[i] = str(i+1) + ")" + requirementTests[i].replace(ravenPath,"").replace("_","\_").strip()
+          requirementTests[i] = str(i+1) + ")" + requirementTests[i].replace(ravenPath,"").replace("\\","/").replace("_","\_").strip()
         fileObject.write(" \\hspace{0pt}"+reqName.strip()+" & \\hspace{0pt}"+req['description']+" & \\hspace{0pt}"+ ' '.join(requirementTests)+" \\\ \hline \n")
         fileObject.write("\\hline \n")
       fileObject.write("\\caption*{"+reqSetName.strip()+"}\n")