From 390607e2eef224a881b7a0349352ff3bfd7cb605 Mon Sep 17 00:00:00 2001
From: Congjian Wang - INL <congjian.wang@inl.gov>
Date: Thu, 19 Nov 2020 13:45:58 -0700
Subject: [PATCH] Debug (#1372)

* Adding ability to sign the .so files. (#1362)

Adding ability to sign the .so files.. This will be needed in future mac os releases.

* debug

* fix dymolainterface

* revert code interface changes

* update rounding error for time index

* fix index for duplicated values

Co-authored-by: Joshua J. Cogliati <joshua-cogliati-inl@users.noreply.github.com>
---
 build_raven                                        | 12 +++++++++++-
 doc/workshop/.gitignore                            |  1 +
 framework/CodeInterfaces/Dymola/DymolaInterface.py | 13 ++++++++++++-
 scripts/establish_conda_env.sh                     | 10 ++++++++++
 tests/framework/.gitignore                         | 12 ++++++++++++
 5 files changed, 46 insertions(+), 2 deletions(-)

diff --git a/build_raven b/build_raven
index f96661ca69..7e8dd9f2d6 100755
--- a/build_raven
+++ b/build_raven
@@ -107,5 +107,15 @@ fi
 
 (cd $RAVEN_BUILD_DIR && ${PYTHON_COMMAND} ./setup.py build_ext build install --install-platlib=./framework/contrib/AMSC)
 
-
+if [ ! -z "$RAVEN_SIGNATURE" ];
+then
+    #This is to allow the code to be signed on mac os computers.
+    # It requires a signature (possibly self signed) to be used.
+    # Creating a signature is discussed at:
+    # https://developer.apple.com/library/archive/documentation/Security/Conceptual/CodeSigningGuide/Procedures/Procedures.html
+    # RAVEN_SIGNATURE can be added to .ravenrc
+    echo "... Signing code with '$RAVEN_SIGNATURE' ..."
+    (cd $CROW_DIR/install/crow_modules && pwd && codesign -s "$RAVEN_SIGNATURE" -v *.so)
+    (cd $RAVEN_BUILD_DIR/framework/contrib/AMSC && pwd && codesign -s "$RAVEN_SIGNATURE" -v *.so)
+fi
 echo ... done!
diff --git a/doc/workshop/.gitignore b/doc/workshop/.gitignore
index 022fc33895..a0a3fa75ec 100644
--- a/doc/workshop/.gitignore
+++ b/doc/workshop/.gitignore
@@ -57,3 +57,4 @@ stochasticCollocation/inputs/run/training_data.xml
 timeDepDataMining/inputs/basicStatisticsTimeDependent/
 timeDepDataMining/inputs/resultsHierarchicalDTW/
 timeDepDataMining/inputs/timeSliceKMeans/
+forwardSampling/Inputs/test_*.xml
diff --git a/framework/CodeInterfaces/Dymola/DymolaInterface.py b/framework/CodeInterfaces/Dymola/DymolaInterface.py
index d8a8393455..9c651c4dd8 100644
--- a/framework/CodeInterfaces/Dymola/DymolaInterface.py
+++ b/framework/CodeInterfaces/Dymola/DymolaInterface.py
@@ -104,6 +104,7 @@
 import pandas as pd
 
 from CodeInterfaceBaseClass import CodeInterfaceBase
+from utils import mathUtils
 
 class Dymola(CodeInterfaceBase):
   """
@@ -449,9 +450,19 @@ def finalizeCodeOutput(self, command, output, workingDir):
       m = t.duplicated()
       if len(t[m]):
         # duplicated values
+        tIndex = None
+        iIndex = 1
         for i in range(len(t[m])):
           index = t[m].index[i]
-          t[index] = t[index] + numpy.finfo(float).eps
+          if tIndex is None:
+            tIndex = t[index]
+          else:
+            if mathUtils.compareFloats(tIndex, t[index], tol=1.0E-15):
+              iIndex += 1
+            else:
+              iIndex = 1
+              tIndex = t[index]
+          t[index] = t[index] + numpy.finfo(float).eps*t[index]*iIndex
         varTrajectories[:,0] = t.to_numpy()
       response = {var:varTrajectories[:,i] for (i, var) in enumerate(varNames[0])}
       # write CSV if the user requests it
diff --git a/scripts/establish_conda_env.sh b/scripts/establish_conda_env.sh
index 7308a15860..551f5d06f0 100755
--- a/scripts/establish_conda_env.sh
+++ b/scripts/establish_conda_env.sh
@@ -470,4 +470,14 @@ fi
 # activate environment and write settings if successful
 activate_env
 
+if [ -z "$RAVEN_SIGNATURE" ];
+then
+    RAVEN_SIGNATURE=$(read_ravenrc "RAVEN_SIGNATURE")
+fi
+if [ ! -z "$RAVEN_SIGNATURE" ];
+then
+    if [[ $ECE_VERBOSE == 0 ]]; then echo "... Using '$RAVEN_SIGNATURE' for signing ..."; fi
+    export RAVEN_SIGNATURE
+fi
+
 if [[ $ECE_VERBOSE == 0 ]]; then echo  ... done!; fi
diff --git a/tests/framework/.gitignore b/tests/framework/.gitignore
index 416d82575f..8539e3ce56 100644
--- a/tests/framework/.gitignore
+++ b/tests/framework/.gitignore
@@ -168,3 +168,15 @@ unit_tests/utils/parse/fromXmltoGetpot.i
 user_guide/EnsembleModel/run_basic/sample/
 ROM/TimeSeries/ARMA/ARMAreseed/
 ROM/TimeSeries/ARMA/Segmented/arma.pk
+ROM/TimeSeries/ARMA/Multicycle/arma.pk
+DataObjects/StringIO/sample/
+CodeInterfaceTests/RAVEN/Code/sample/
+CodeInterfaceTests/Neutrino/Neutrino_Base/sampleNeutrino/[1-3]
+CodeInterfaceTests/MOOSEBaseApps/MooseExample18WithGenericFile/myMC/[12]
+CodeInterfaceTests/MOOSEBaseApps/MooseExample18OnlyGenericFile/myMC/[12]
+CodeInterfaceTests/MOOSEBaseApps/MooseExample18OnlyGenericFile/myMC/ex18.i
+CodeInterfaceTests/MOOSEBaseApps/MooseExample18WithGenericFile/myMC/ex18.i
+CodeInterfaceTests/MOOSEBaseApps/InputParser/sample/[12]/formattest.i
+CodeInterfaceTests/MOOSEBaseApps/InputParser/sample/[12]/out~formattest
+CodeInterfaceTests/MOOSEBaseApps/InputParser/sample/formattest.i
+hybridModel/logicalCode/logicalModelCode/
\ No newline at end of file