Index: sm/trunk-jpl/jenkins/pine_island-mac-binaries
===================================================================
--- /issm/trunk-jpl/jenkins/pine_island-mac-binaries	(revision 25743)
+++ 	(revision )
@@ -1,72 +1,0 @@
-#--------------------#
-# ISSM Configuration #
-#--------------------#
-
-MATLAB_PATH="/Applications/MATLAB_R2018a.app"
-
-# NOTE:
-# - We can disable dependency tracking in the Autotools because the binaries
-#	should always be a one-time build.
-#
-ISSM_CONFIG='\
-	--prefix=${ISSM_DIR} \
-	--enable-standalone-executables \
-	--enable-standalone-modules \
-	--enable-standalone-libraries \
-	--disable-dependency-tracking \
-	--with-matlab-dir=${MATLAB_PATH} \
-	--with-fortran-lib="/usr/local/Cellar/gcc/10.2.0/lib/gcc/10/libgfortran.a /usr/local/Cellar/gcc/10.2.0/lib/gcc/10/libquadmath.a /usr/local/Cellar/gcc/10.2.0/lib/gcc/10/gcc/x86_64-apple-darwin15/10.2.0/libgcc.a" \
-	--with-mpi-include=${ISSM_DIR}/externalpackages/petsc/install/include \
-	--with-mpi-libflags="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lmpi -lmpicxx -lmpifort" \
-	--with-blas-lapack-dir=${ISSM_DIR}/externalpackages/petsc/install \
-	--with-metis-dir=${ISSM_DIR}/externalpackages/petsc/install \
-	--with-scalapack-dir=${ISSM_DIR}/externalpackages/petsc/install \
-	--with-mumps-dir=${ISSM_DIR}/externalpackages/petsc/install \
-	--with-petsc-dir=${ISSM_DIR}/externalpackages/petsc/install \
-	--with-triangle-dir=${ISSM_DIR}/externalpackages/triangle/install \
-	--with-chaco-dir=${ISSM_DIR}/externalpackages/chaco/install \
-	--with-m1qn3-dir=${ISSM_DIR}/externalpackages/m1qn3/install \
-	--with-semic-dir=${ISSM_DIR}/externalpackages/semic/install \
-'
-
-# Test suites
-MATLAB_TEST=0
-PYTHON_TEST=0
-JAVASCRIPT_TEST=0
-EXAMPLES_TEST=0
-
-#-------------------#
-# External Packages #
-#-------------------#
-
-EXTERNALPACKAGES="
-	autotools	install.sh
-	cmake		install.sh
-	petsc		install-3.14-mac-static.sh
-	triangle	install-mac-static.sh
-	chaco		install.sh
-	m1qn3		install.sh
-	semic		install.sh
-	shell2junit	install.sh
-"
-
-#---------#
-# Testing #
-#---------#
-
-# Number of CPUs used in ISSM compilation
-#
-# NOTE: One is usually safer as some packages are very sensitive to parallel
-# 		compilation
-#
-NUMCPUS_INSTALL=1
-
-# Number of CPUs used in the nightly runs
-NUMCPUS_RUN=1
-
-# Nightly run options
-#
-# See documentation in test/NightlyRun/runme.* for more information.
-#
-PYTHON_NROPTIONS=""
-MATLAB_NROPTIONS=""
Index: /issm/trunk-jpl/jenkins/pine_island-mac-binaries-matlab
===================================================================
--- /issm/trunk-jpl/jenkins/pine_island-mac-binaries-matlab	(revision 25744)
+++ /issm/trunk-jpl/jenkins/pine_island-mac-binaries-matlab	(revision 25744)
@@ -0,0 +1,86 @@
+#--------------------#
+# ISSM Configuration #
+#--------------------#
+
+MATLAB_PATH="/Applications/MATLAB_R2018a.app"
+
+# NOTE:
+# - We can disable dependency tracking in the Autotools because the binaries
+#	should always be a one-time build.
+#
+
+ISSM_CONFIG='\
+	--prefix=${ISSM_DIR} \
+	--enable-standalone-executables \
+	--enable-standalone-modules \
+	--enable-standalone-libraries \
+	--disable-dependency-tracking \
+	--with-matlab-dir=${MATLAB_PATH} \
+	--with-fortran-lib="/usr/local/Cellar/gcc/10.2.0/lib/gcc/10/libgfortran.a /usr/local/Cellar/gcc/10.2.0/lib/gcc/10/libquadmath.a /usr/local/Cellar/gcc/10.2.0/lib/gcc/10/gcc/x86_64-apple-darwin19/10.2.0/libgcc.a" \
+	--with-mpi-include=${ISSM_DIR}/externalpackages/petsc/install/include \
+	--with-mpi-libflags="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lmpi -lmpicxx -lmpifort" \
+	--with-blas-lapack-dir=${ISSM_DIR}/externalpackages/petsc/install \
+	--with-metis-dir=${ISSM_DIR}/externalpackages/petsc/install \
+	--with-scalapack-dir=${ISSM_DIR}/externalpackages/petsc/install \
+	--with-mumps-dir=${ISSM_DIR}/externalpackages/petsc/install \
+	--with-hdf5-dir=${ISSM_DIR}/externalpackages/petsc/install \
+	--with-petsc-dir=${ISSM_DIR}/externalpackages/petsc/install \
+	--with-gsl-dir=${ISSM_DIR}/externalpackages/gsl/install \
+	--with-boost-dir=${ISSM_DIR}/externalpackages/boost/install \
+	--with-dakota-dir=${ISSM_DIR}/externalpackages/dakota/install \
+	--with-triangle-dir=${ISSM_DIR}/externalpackages/triangle/install \
+	--with-chaco-dir=${ISSM_DIR}/externalpackages/chaco/install \
+	--with-m1qn3-dir=${ISSM_DIR}/externalpackages/m1qn3/install \
+	--with-semic-dir=${ISSM_DIR}/externalpackages/semic/install \
+'
+
+# Test suites
+MATLAB_TEST=0
+PYTHON_TEST=0
+JAVASCRIPT_TEST=0
+EXAMPLES_TEST=0
+
+#-------------------#
+# External Packages #
+#-------------------#
+
+EXTERNALPACKAGES="
+	autotools	install.sh
+	cmake		install.sh
+	petsc		install-3.12-mac-static.sh
+	gsl			install-static.sh
+	boost		install-1.7-mac-static.sh
+	dakota		install-6.2-mac-static.sh
+	netcdf		install-4.7-mac-parallel-static.sh
+	proj		install-6.2-static.sh
+	gdal		install-3-netcdf-static.sh
+	gshhg		install.sh
+	gmt			install-6-mac-static.sh
+	gmsh		install-4-mac-static.sh
+	triangle	install-mac-static.sh
+	chaco		install.sh
+	m1qn3		install.sh
+	semic		install.sh
+	shell2junit	install.sh
+"
+
+#---------#
+# Testing #
+#---------#
+
+# Number of CPUs used in ISSM compilation
+#
+# NOTE: One is usually safer as some packages are very sensitive to parallel
+# 		compilation
+#
+NUMCPUS_INSTALL=4
+
+# Number of CPUs used in the nightly runs
+NUMCPUS_RUN=1
+
+# Nightly run options
+#
+# See documentation in test/NightlyRun/runme.* for more information.
+#
+PYTHON_NROPTIONS=""
+MATLAB_NROPTIONS=""
Index: sm/trunk-jpl/jenkins/pine_island-mac-binaries-solid_earth
===================================================================
--- /issm/trunk-jpl/jenkins/pine_island-mac-binaries-solid_earth	(revision 25743)
+++ 	(revision )
@@ -1,82 +1,0 @@
-#--------------------#
-# ISSM Configuration #
-#--------------------#
-
-MATLAB_PATH="/Applications/MATLAB_R2018a.app"
-
-# NOTE:
-# - We can disable dependency tracking in the Autotools because the binaries
-#	should always be a one-time build.
-#
-ISSM_CONFIG='\
-	--prefix=${ISSM_DIR} \
-	--enable-standalone-executables \
-	--enable-standalone-modules \
-	--enable-standalone-libraries \
-	--disable-dependency-tracking \
-	--with-matlab-dir=${MATLAB_PATH} \
-	--with-python-dir=/System/Library/Frameworks/Python.framework/Versions/2.7 \
-	--with-python-numpy-dir=/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy \
-	--with-fortran-lib="/usr/local/Cellar/gcc/10.2.0/lib/gcc/10/libgfortran.a /usr/local/Cellar/gcc/10.2.0/lib/gcc/10/libquadmath.a /usr/local/Cellar/gcc/10.2.0/lib/gcc/10/gcc/x86_64-apple-darwin15/10.2.0/libgcc.a" \
-	--with-mpi-include=${ISSM_DIR}/externalpackages/petsc/install/include \
-	--with-mpi-libflags="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lmpi -lmpicxx -lmpifort" \
-	--with-blas-lapack-dir=${ISSM_DIR}/externalpackages/petsc/install \
-	--with-metis-dir=${ISSM_DIR}/externalpackages/petsc/install \
-	--with-scalapack-dir=${ISSM_DIR}/externalpackages/petsc/install \
-	--with-mumps-dir=${ISSM_DIR}/externalpackages/petsc/install \
-	--with-hdf5-dir=${ISSM_DIR}/externalpackages/petsc/install \
-	--with-petsc-dir=${ISSM_DIR}/externalpackages/petsc/install \
-	--with-triangle-dir=${ISSM_DIR}/externalpackages/triangle/install \
-	--with-boost-dir=${ISSM_DIR}/externalpackages/boost/install
-'
-
-#-------------------#
-# External Packages #
-#-------------------#
-
-#List of external pakages to be installed and their installation scripts
-EXTERNALPACKAGES="
-	autotools		install.sh
-	cmake			install.sh
-	petsc			install-3.14-mac-static.sh
-	boost			install-1.7-mac-static.sh
-	triangle		install-mac-static.sh
-	chaco			install.sh
-	m1qn3			install.sh
-	semic			install.sh
-	curl			install-7.67-static.sh
-	netcdf			install-4.7-mac-parallel-static.sh
-	proj			install-6.2-static.sh
-	gdal			install-3-python-netcdf-static.sh
-	gshhg			install.sh
-	gmt				install-6.0-mac-static.sh
-	gmsh			install-4-static.sh
-	shell2junit		install.sh
-"
-
-#---------#
-# Testing #
-#---------#
-
-# Test suites
-MATLAB_TEST=0
-PYTHON_TEST=0
-JAVASCRIPT_TEST=0
-EXAMPLES_TEST=0
-
-# Number of CPUs used in ISSM compilation
-#
-# NOTE: One is usually safer as some packages are very sensitive to parallel
-# 		compilation
-#
-NUMCPUS_INSTALL=4
-
-# Number of CPUs used in the nightly runs
-NUMCPUS_RUN=1
-
-# Nightly run options
-#
-# See documentation in test/NightlyRun/runme.* for more information.
-#
-MATLAB_NROPTIONS=""
-PYTHON_NROPTIONS=""
Index: sm/trunk-jpl/jenkins/pine_island-mac-binaries-with_dakota
===================================================================
--- /issm/trunk-jpl/jenkins/pine_island-mac-binaries-with_dakota	(revision 25743)
+++ 	(revision )
@@ -1,80 +1,0 @@
-#--------------------#
-# ISSM Configuration #
-#--------------------#
-
-MATLAB_PATH="/Applications/MATLAB_R2018a.app"
-
-# NOTE:
-# - We can disable dependency tracking in the Autotools because the binaries
-#	should always be a one-time build.
-#
-ISSM_CONFIG='\
-	--prefix=${ISSM_DIR} \
-	--enable-standalone-executables \
-	--enable-standalone-modules \
-	--enable-standalone-libraries \
-	--disable-dependency-tracking \
-	--with-matlab-dir=${MATLAB_PATH} \
-	--with-python-dir=/System/Library/Frameworks/Python.framework/Versions/2.7 \
-	--with-python-numpy-dir=/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy \
-	--with-fortran-lib="/usr/local/Cellar/gcc/10.2.0/lib/gcc/10/libgfortran.a /usr/local/Cellar/gcc/10.2.0/lib/gcc/10/libquadmath.a /usr/local/Cellar/gcc/10.2.0/lib/gcc/10/gcc/x86_64-apple-darwin15/10.2.0/libgcc.a" \
-	--with-mpi-include=${ISSM_DIR}/externalpackages/petsc/install/include \
-	--with-mpi-libflags="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lmpi -lmpicxx -lmpifort" \
-	--with-blas-lapack-dir=${ISSM_DIR}/externalpackages/petsc/install \
-	--with-metis-dir=${ISSM_DIR}/externalpackages/petsc/install \
-	--with-scalapack-dir=${ISSM_DIR}/externalpackages/petsc/install \
-	--with-mumps-dir=${ISSM_DIR}/externalpackages/petsc/install \
-	--with-petsc-dir=${ISSM_DIR}/externalpackages/petsc/install \
-	--with-gsl-dir=${ISSM_DIR}/externalpackages/gsl/install \
-	--with-boost-dir=${ISSM_DIR}/externalpackages/boost/install \
-	--with-dakota-dir=${ISSM_DIR}/externalpackages/dakota/install \
-	--with-triangle-dir=${ISSM_DIR}/externalpackages/triangle/install \
-	--with-chaco-dir=${ISSM_DIR}/externalpackages/chaco/install \
-	--with-m1qn3-dir=${ISSM_DIR}/externalpackages/m1qn3/install \
-	--with-semic-dir=${ISSM_DIR}/externalpackages/semic/install \
-'
-
-# Test suites
-MATLAB_TEST=0
-PYTHON_TEST=0
-JAVASCRIPT_TEST=0
-EXAMPLES_TEST=0
-
-#-------------------#
-# External Packages #
-#-------------------#
-
-EXTERNALPACKAGES="
-	autotools	install.sh
-	cmake		install.sh
-	petsc		install-3.14-mac-static.sh
-	gsl			install-static.sh
-	boost		install-1.7-mac-static.sh
-	dakota		install-6.2-mac-static.sh
-	triangle	install-mac-static.sh
-	chaco		install.sh
-	m1qn3		install.sh
-	semic		install.sh
-	shell2junit	install.sh
-"
-
-#---------#
-# Testing #
-#---------#
-
-# Number of CPUs used in ISSM compilation
-#
-# NOTE: One is usually safer as some packages are very sensitive to parallel
-# 		compilation
-#
-NUMCPUS_INSTALL=1
-
-# Number of CPUs used in the nightly runs
-NUMCPUS_RUN=1
-
-# Nightly run options
-#
-# See documentation in test/NightlyRun/runme.* for more information.
-#
-PYTHON_NROPTIONS=""
-MATLAB_NROPTIONS=""
Index: /issm/trunk-jpl/packagers/mac/package-issm-mac-binaries-matlab.sh
===================================================================
--- /issm/trunk-jpl/packagers/mac/package-issm-mac-binaries-matlab.sh	(revision 25744)
+++ /issm/trunk-jpl/packagers/mac/package-issm-mac-binaries-matlab.sh	(revision 25744)
@@ -0,0 +1,303 @@
+#!/bin/bash
+
+################################################################################
+# To be used after running,
+#
+#	${ISSM_DIR}/jenkins/jenkins.sh ${ISSM_DIR}/jenkins/pine_island-mac-binaries-matlab
+#
+# in the context of a Jenkins project.
+#
+# When no runtime errors occur, performs the following:
+# - Checks resulting executables and libraries against test suite.
+# - Packages and compresses executables and libraries.
+# - Commits compressed package to SVN repository to be signed by JPL 
+#	Cybersecurity.
+# - Retrieves signed package and transmits it to ISSM Web site for 
+#	distribution.
+#
+# To skip tests, run with -s/--skiptests option.
+#
+# Debugging:
+# - Relies on a very tight handshake with project on remote JPL Cybersecurity 
+#	Jenkins server. Debugging may be perfomed locally by running,
+#
+#		packagers/mac/sign-issm-mac-binaries-matlab.sh
+#
+#	with Apple Developer credentials.
+# - Removing stdout/stderr redirections to null device (> /dev/null 2>&1) can 
+#	help debug potential SVN issues.
+#
+# NOTE:
+# - Assumes that 'issm-binaries-user' and 'issm-binaries-pass' are set up in 
+#	the 'Bindings' section under a 'Username and password (separated)' binding 
+#	(requires 'Credentials Binding Plugin').
+# - For local debugging, the aformentioned credentials can be hardcoded into 
+#	the 'USERNAME' and 'PASSWORD' constants below.
+################################################################################
+
+# From https://developer.apple.com/documentation/macos-release-notes/macos-catalina-10_15-release-notes,
+#
+#	Command line tool support for Subversion — including svn, git-svn, and 
+#	related commands — is no longer provided by Xcode. (50266910)
+#
+# which results in,
+#
+#	svn: error: The subversion command line tools are no longer provided by 
+#	Xcode.
+#
+# when calling svn, even when subversion is installed via Homebrew and its path 
+# is available in PATH.
+#
+shopt -s expand_aliases
+alias svn='/usr/local/bin/svn'
+
+## Override certain other aliases
+#
+alias grep=$(which grep)
+
+## Constants
+#
+
+MATLAB_NROPTIONS="'benchmark','all','exclude',[125,126,234,235,418,420,435,444,445,701,702,703,1101,1102,1103,1104,1105,1106,1107,1108,1109,1110,1201,1202,1203,1204,1205,1206,1207,1208,1301,1302,1303,1304,1401,1402,1601,1602,2006,2020,2021,2051,2052,2053,3001:3200,3201,3202,3300,3480,3481,4001,4002,4003]" # NOTE: Combination of test suites from basic, Dakota, and Solid Earth builds, with tests that require a restart and those that require the JVM excluded
+MATLAB_PATH="/Applications/MATLAB_R2018a.app"
+NOTARIZATION_LOGFILE="notarization.log"
+PASSWORD=$env:issm-binaries-pass
+PKG="ISSM-macOS-MATLAB" # Name of directory to copy distributable files to
+SIGNED_REPO_COPY="./signed"
+SIGNED_REPO_URL="https://issm.ess.uci.edu/svn/issm-binaries/mac/matlab/signed"
+SIGNING_CHECK_PERIOD=60 # seconds
+SIGNING_LOCK_FILE="signing.lock"
+UNSIGNED_REPO_COPY="./unsigned"
+UNSIGNED_REPO_URL="https://issm.ess.uci.edu/svn/issm-binaries/mac/matlab/unsigned"
+USERNAME=$env:issm-binaries-user
+
+COMPRESSED_PKG="${PKG}.zip"
+
+## Environment
+#
+export PATH="${ISSM_DIR}/bin:$(getconf PATH)" # Ensure that we pick up binaries from 'bin' directory rather than 'externalpackages'
+
+## Parse options
+#
+skip_tests=0
+transfer_only=0
+while [[ "$#" -gt 0 ]]; do
+    case $1 in
+        -s|--skiptests) skip_tests=1; shift ;;
+        -t|--transferonly) transfer_only=1; shift ;;
+        *) echo "Unknown parameter passed: $1"; exit 1 ;;
+    esac
+    shift
+done
+
+if [ ${transfer_only} -eq 0 ]; then
+	# Check if MATLAB exists
+	if ! [ -d ${MATLAB_PATH} ]; then
+		echo "${MATLAB_PATH} does not point to a MATLAB installation! Please modify MATLAB_PATH variable in $(basename $0) and try again."
+		exit 1
+	fi
+
+	# Clean up from previous packaging (not necessary for single builds on Jenkins, 
+	# but useful when testing packaging locally)
+	echo "Cleaning up existing assets"
+	cd ${ISSM_DIR}
+	rm -rf ${PKG} ${COMPRESSED_PKG} ${SIGNED_REPO_COPY} ${UNSIGNED_REPO_COPY}
+	mkdir ${PKG}
+
+	# Check out copy of SVN repository for signed macOS packages
+	#
+	# NOTE: Get empty copy because we do not want to have to check out package from 
+	#		previous signing.
+	#
+	echo "Checking out copy of repository for signed packages"
+	svn co \
+		--username ${USERNAME} \
+		--password ${PASSWORD} \
+		--depth empty \
+		${SIGNED_REPO_URL} \
+		${SIGNED_REPO_COPY} > /dev/null 2>&1
+
+	# If lock file exists, a signing build is still in process by JPL Cybersecurity
+	svn up ${SIGNED_REPO_COPY}/${SIGNING_LOCK_FILE} > /dev/null 2>&1
+	if [[ -f ${SIGNED_REPO_COPY}/${SIGNING_LOCK_FILE} ]]; then
+		echo "Previous signing job still in process by JPL Cybersecurity. Please try again later."
+		exit 1
+	fi
+
+	# Add required binaries and libraries to package and modify them where needed
+	cd ${ISSM_DIR}/bin
+
+	echo "Modify generic"
+	cat generic_static.m | sed -e "s/generic_static/generic/g" > generic.m
+
+	echo "Moving MPICH binaries to bin/"
+	if [ -f ${ISSM_DIR}/externalpackages/petsc/install/bin/mpiexec ]; then
+		cp ${ISSM_DIR}/externalpackages/petsc/install/bin/mpiexec .
+		cp ${ISSM_DIR}/externalpackages/petsc/install/bin/hydra_pmi_proxy .
+	elif [ -f ${ISSM_DIR}/externalpackages/mpich/install/bin/mpiexec ]; then
+		cp ${ISSM_DIR}/externalpackages/mpich/install/bin/mpiexec .
+		cp ${ISSM_DIR}/externalpackages/mpich/install/bin/hydra_pmi_proxy .
+	else
+		echo "MPICH not found"
+		exit 1
+	fi
+
+	echo "Moving GDAL binaries to bin/"
+	if [ -f ${ISSM_DIR}/externalpackages/gdal/install/bin/gdal-config ]; then
+		cp ${ISSM_DIR}/externalpackages/gdal/install/bin/gdalsrsinfo .
+		cp ${ISSM_DIR}/externalpackages/gdal/install/bin/gdaltransform .
+	else
+		echo "GDAL not found"
+		exit 1
+	fi
+
+	echo "Moving GMT binaries to bin/"
+	if [ -f ${ISSM_DIR}/externalpackages/gmt/install/bin/gmt-config ]; then
+		cp ${ISSM_DIR}/externalpackages/gmt/install/bin/gmt .
+		cp ${ISSM_DIR}/externalpackages/gmt/install/bin/gmtselect .
+	else
+		echo "GMT not found"
+		exit 1
+	fi
+
+	echo "Moving Gmsh binaries to bin/"
+	if [ -f ${ISSM_DIR}/externalpackages/gmsh/install/bin/gmsh ]; then
+		cp ${ISSM_DIR}/externalpackages/gmsh/install/bin/gmsh .
+	else
+		echo "Gmsh not found"
+		exit 1
+	fi
+
+	# Run tests
+	if [ ${skip_tests} -eq 0 ]; then
+		echo "Running tests"
+		cd ${ISSM_DIR}/test/NightlyRun
+		rm matlab.log 2> /dev/null
+
+		# Run tests, redirecting output to logfile and suppressing output to console
+		${MATLAB_PATH}/bin/matlab -nojvm -nosplash -r "try, addpath ${ISSM_DIR}/bin ${ISSM_DIR}/lib; runme(${MATLAB_NROPTIONS}); exit; catch me,fprintf('%s',getReport(me)); exit; end" -logfile matlab.log &> /dev/null
+
+		# Check that MATLAB did not exit in error
+		matlabExitCode=`echo $?`
+		matlabExitedInError=`grep -E "Activation cannot proceed|license|Error" matlab.log | wc -l`
+
+		if [[ ${matlabExitCode} -ne 0 || ${matlabExitedInError} -ne 0 ]]; then
+			echo "----------MATLAB exited in error!----------"
+			cat matlab.log
+			echo "-----------End of matlab.log-----------"
+
+			# Clean up execution directory
+			rm -rf ${ISSM_DIR}/execution/*
+
+			exit 1
+		fi
+
+		# Check that all tests passed
+		numTestsFailed=`cat matlab.log | grep -c -e "FAILED|ERROR"`
+
+		if [[ ${numTestsFailed} -ne 0 ]]; then
+			echo "One or more tests FAILED"
+			exit 1
+		else
+			echo "All tests PASSED"
+		fi
+	else
+		echo "Skipping tests"
+	fi
+
+	# Create package
+	cd ${ISSM_DIR}
+	svn cleanup --remove-ignored --remove-unversioned test # Clean up test directory (before copying to package)
+	echo "Copying assets to package: ${PKG}"
+	cp -rf bin examples lib scripts test ${PKG}/
+	echo "Cleaning up unneeded/unwanted files"
+	rm -f ${PKG}/bin/generic_static.* # Remove static versions of generic cluster classes
+	rm -f ${PKG}/lib/*.a # Remove static libraries from package
+	rm -f ${PKG}/lib/*.la # Remove libtool libraries from package
+	rm -rf ${PKG}/test/SandBox # Remove testing sandbox from package
+
+	# Compress package
+	echo "Compressing package"
+	ditto -ck --sequesterRsrc --keepParent ${PKG} ${COMPRESSED_PKG}
+
+	# Commit lock file to repository for signed packages
+	echo "Committing lock file to repository for signed packages"
+	touch ${SIGNED_REPO_COPY}/${SIGNING_LOCK_FILE}
+	svn add ${SIGNED_REPO_COPY}/${SIGNING_LOCK_FILE} > /dev/null 2>&1
+	svn commit --message "ADD: New lock file" ${SIGNED_REPO_COPY} > /dev/null 2>&1
+
+	# Save current working copy revision number
+	svn up ${SIGNED_REPO_COPY} > /dev/null 2>&1
+	CURRENT_REV=$(svn info --show-item last-changed-revision ${SIGNED_REPO_COPY})
+
+	# Check out copy of SVN repository for unsigned macOS packages
+	echo "Checking out copy of repository for unsigned packages"
+	svn co \
+		--username ${USERNAME} \
+		--password ${PASSWORD} \
+		${UNSIGNED_REPO_URL} \
+		${UNSIGNED_REPO_COPY} > /dev/null 2>&1
+
+	# Commit new compressed package to repository for unsigned binaries
+	#
+	# NOTE: This will not work if, for any reason, the checksum on the compressed 
+	#		package is unchanged.
+	#
+	echo "Committing package to repository for unsigned packages"
+	cp ${COMPRESSED_PKG} ${UNSIGNED_REPO_COPY}
+	svn add ${UNSIGNED_REPO_COPY}/${COMPRESSED_PKG} > /dev/null 2>&1
+	svn commit --message "CHG: New unsigned package" ${UNSIGNED_REPO_COPY} > /dev/null 2>&1
+
+	# Check status of signing
+	echo "Checking progress of signing..."
+	IN_PROCESS=1
+	SUCCESS=0
+
+	while [ ${IN_PROCESS} -eq 1 ]; do
+		echo "...in progress still; checking again in ${SIGNING_CHECK_PERIOD} seconds."
+		sleep ${SIGNING_CHECK_PERIOD}
+		svn up ${SIGNED_REPO_COPY} > /dev/null 2>&1
+		NEW_REV=$(svn info --show-item last-changed-revision ${SIGNED_REPO_COPY})
+
+		if [ ${NEW_REV} -ne ${CURRENT_REV} ]; then
+			IN_PROCESS=0
+
+			svn up ${SIGNED_REPO_COPY}/${NOTARIZATION_LOGFILE} > /dev/null 2>&1
+			svn up ${SIGNED_REPO_COPY}/${COMPRESSED_PKG} > /dev/null 2>&1
+
+			# No error, so check status
+			STATUS=$(grep 'Status:' ${SIGNED_REPO_COPY}/${NOTARIZATION_LOGFILE} | sed -e 's/[[:space:]]*Status: //')
+			if [[ "${STATUS}" == "success" ]]; then
+				echo 'Notarization successful!'
+
+				# Set flag indicating notarization was successful
+				SUCCESS=1
+			else
+				echo 'Notarization failed!'
+			fi
+		fi
+	done
+else # transfer_only == 1
+	# Assume that previous build resulted in successful signing of package but 
+	# that transfer to ISSM Web site failed and user built this project again 
+	# with -t/--transferonly option.
+	SUCCESS=1
+fi
+
+# Handle result of signing
+if [ ${SUCCESS} -eq 1 ]; then
+	# Transfer signed package to ISSM Web site
+	echo 'Transferring signed package to ISSM Web site'
+	scp -i ~/.ssh/pine_island_to_ross ${SIGNED_REPO_COPY}/${COMPRESSED_PKG} jenkins@ross.ics.uci.edu:/var/www/html/${COMPRESSED_PKG}
+
+	if [ $? -ne 0 ]; then
+		echo "Transfer failed! Verify connection then build this project again (with -t/--transferonly option to skip testing and signing)."
+		exit 1
+	fi
+else
+	echo '----------------------- Contents of notarization logfile -----------------------'
+	cat ${SIGNED_REPO_COPY}/${NOTARIZATION_LOGFILE}
+	echo '--------------------------------------------------------------------------------'
+
+	exit 1
+fi
Index: sm/trunk-jpl/packagers/mac/package-issm-mac-binaries-solid_earth.sh
===================================================================
--- /issm/trunk-jpl/packagers/mac/package-issm-mac-binaries-solid_earth.sh	(revision 25743)
+++ 	(revision )
@@ -1,175 +1,0 @@
-#!/bin/bash
-
-
-# Script to test, package, and transfer distributable to ISSM Web site.
-# Corresponds with build generated by configuration in 
-# $ISSM_DIR/jenkins/pine_island-mac-binaries-solid_earth.
-#
-
-## Constants
-#
-MATLAB_NROPTIONS="'benchmark','slr','exclude',[2020 2021]"
-MATLAB_PATH="/Applications/MATLAB_R2018a.app"
-PACKAGE="ISSM-Solid_Earth" # Name of directory to copy distributable files to
-PYTHON_NROPTIONS="--benchmark slr --exclude 2020 2021"
-TARBALL_NAME="issm-linux-solid_earth"
-TARBALL="${TARBALL_NAME}.tar.gz"
-
-## Environment
-#
-export PATH="${ISSM_DIR}/bin:$(getconf PATH)" # Ensure that we pick up binaries from 'bin' directory rather than 'externalpackages'
-
-# Check if MATLAB exists
-if ! [ -d ${MATLAB_PATH} ]; then
-	echo "${MATLAB_PATH} does not point to a MATLAB installation! Please modify MATLAB_PATH variable in $(basename $0) and try again."
-	exit 1
-fi
-
-# Clean up from previous packaging
-echo "Cleaning up existing assets"
-cd ${ISSM_DIR}
-rm -rf ${PACKAGE}
-mkdir ${PACKAGE}
-
-# Add/modify required binaries
-cd ${ISSM_DIR}/bin
-
-echo "Modifying generic"
-cat generic_static.m | sed -e "s/generic_static/generic/g" > generic.m
-cat generic_static.py | sed -e "s/generic_static/generic/g" > generic.py
-
-echo "Moving MPICH binaries to bin/"
-if [ -f ${ISSM_DIR}/externalpackages/petsc/install/bin/mpiexec ]; then
-	cp ${ISSM_DIR}/externalpackages/petsc/install/bin/mpiexec .
-	cp ${ISSM_DIR}/externalpackages/petsc/install/bin/hydra_pmi_proxy .
-elif [ -f ${ISSM_DIR}/externalpackages/mpich/install/bin/mpiexec ]; then
-	cp ${ISSM_DIR}/externalpackages/mpich/install/bin/mpiexec .
-	cp ${ISSM_DIR}/externalpackages/mpich/install/bin/hydra_pmi_proxy .
-else
-	echo "MPICH not found"
-	exit 1
-fi
-
-echo "Moving GDAL binaries to bin/"
-if [ -f ${ISSM_DIR}/externalpackages/gdal/install/bin/gdal-config ]; then
-	cp ${ISSM_DIR}/externalpackages/gdal/install/bin/gdalsrsinfo .
-	cp ${ISSM_DIR}/externalpackages/gdal/install/bin/gdaltransform .
-else
-	echo "GDAL not found"
-	exit 1
-fi
-
-echo "Moving GMT binaries to bin/"
-if [ -f ${ISSM_DIR}/externalpackages/gmt/install/bin/gmt-config ]; then
-	cp ${ISSM_DIR}/externalpackages/gmt/install/bin/gmt .
-	cp ${ISSM_DIR}/externalpackages/gmt/install/bin/gmtselect .
-else
-	echo "GMT not found"
-	exit 1
-fi
-
-echo "Moving Gmsh binaries to bin/"
-if [ -f ${ISSM_DIR}/externalpackages/gmsh/install/bin/gmsh ]; then
-	cp ${ISSM_DIR}/externalpackages/gmsh/install/bin/gmsh .
-else
-	echo "Gmsh not found"
-	exit 1
-fi
-
-# Run tests
-echo "Running tests"
-cd ${ISSM_DIR}/test/NightlyRun
-
-# Check that MATLAB tests run
-echo "Running MATLAB tests"
-
-rm matlab.log 2> /dev/null
-
-# Run MATLAB tests redirecting output to logfile and suppressing output to console
-${MATLAB_PATH}/bin/matlab -nojvm -nosplash -r "try, addpath ${ISSM_DIR}/bin ${ISSM_DIR}/lib; runme(${MATLAB_NROPTIONS}); exit; catch me,fprintf('%s',getReport(me)); exit; end" -logfile matlab.log &> /dev/null
-
-# Check that MATLAB did not exit in error
-matlabExitCode=`echo $?`
-matlabExitedInError=`grep -E "Activation cannot proceed|license|Error" matlab.log | wc -l`
-
-if [[ ${matlabExitCode} -ne 0 || ${matlabExitedInError} -ne 0 ]]; then
-	echo "----------MATLAB exited in error!----------"
-	cat matlab.log
-	echo "-----------End of matlab.log-----------"
-
-	# Clean up execution directory
-	rm -rf ${ISSM_DIR}/execution/*
-
-	exit 1
-fi
-
-# Check that all MATLAB tests passed
-numMatlabTestsFailed=`cat matlab.log | grep -c -e "FAILED|ERROR"`
-
-if [[ ${numMatlabTestsFailed} -ne 0 ]]; then
-	echo "One or more MATLAB tests FAILED"
-	exit 1;
-else
-	echo "All MATLAB tests PASSED"
-fi
-
-# Check that Python tests run
-echo "Running Python tests"
-
-export PATH="${PATH}:${ISSM_DIR}/bin"
-export PYTHONPATH="${ISSM_DIR}/src/m/dev"
-export PYTHONSTARTUP="${PYTHONPATH}/devpath.py"
-export PYTHONUNBUFFERED=1 # We don't want Python to buffer output, otherwise issm.exe output is not captured
-
-rm python.log 2> /dev/null
-./runme.py ${PYTHON_NROPTIONS} &> python.log 2>&1
-
-# Check that Python did not exit in error
-pythonExitCode=`echo $?`
-pythonExitedInError=`grep -E "Error|Standard exception|Traceback|bad interpreter" python.log | wc -l`
-
-if [[ ${pythonExitCode} -ne 0 || ${pythonExitedInError} -ne 0 ]]; then
-	echo "----------Python exited in error!----------"
-	cat python.log
-	echo "-----------End of python.log-----------"
-
-	# Clean up execution directory
-	rm -rf ${ISSM_DIR}/execution/*
-
-	exit 1
-fi
-
-# Check that all Python tests passed
-numPythonTestsFailed=`cat python.log | grep -c -e "FAILED|ERROR"`
-
-if [[ ${numPythonTestsFailed} -ne 0 ]]; then
-	echo "One or more Python tests FAILED"
-	exit 1
-else
-	echo "All Python tests PASSED"
-fi
-
-# Create tarball
-cd ${ISSM_DIR}
-rm -f ${TARBALL}
-svn cleanup --remove-ignored --remove-unversioned test # Clean up test directory (before copying to package)
-echo "Copying assets to package: ${PACKAGE}"
-cp -rf bin examples lib scripts test ${PACKAGE}/
-echo "Cleaning up unneeded/unwanted files"
-python -m compileall ${PACKAGE}/bin # Precompile all Python scripts to bytecode
-rm -f ${PACKAGE}/bin/*.py # Remove all Python scripts
-rm -f ${PACKAGE}/bin/generic_static.* # Remove static versions of generic cluster classes
-rm -f ${PACKAGE}/lib/*.a # Remove static libraries from package
-rm -f ${PACKAGE}/lib/*.la # Remove libtool libraries from package
-rm -rf ${PACKAGE}/test/SandBox # Remove testing sandbox from package
-echo "Creating tarball: ${TARBALL_NAME}"
-tar -czf ${TARBALL} ${PACKAGE}
-ls -lah ${ISSM_DIR}/${TARBALL}
-
-echo "Transferring binaries to ISSM Web site"
-scp -i ~/.ssh/pine_island_to_ross ${TARBALL} jenkins@ross.ics.uci.edu:/var/www/html/${TARBALL}
-
-if [ $? -ne 0 ]; then
-	echo "FAILED: Manually check connection"
-	exit 1
-fi
Index: sm/trunk-jpl/packagers/mac/package-issm-mac-binaries-with_dakota.sh
===================================================================
--- /issm/trunk-jpl/packagers/mac/package-issm-mac-binaries-with_dakota.sh	(revision 25743)
+++ 	(revision )
@@ -1,149 +1,0 @@
-#!/bin/bash
-
-
-# Script to test, package, and transfer distributable to ISSM Web site.
-# Corresponds with build generated by configuration in 
-# $ISSM_DIR/jenkins/pine_island-mac-binaries-with_dakota.
-#
-
-## Constants
-#
-MATLAB_NROPTIONS="'id',[IdFromString('Dakota')],'exclude',[125,126,234,235,418,420,444,445]"
-MATLAB_PATH="/Applications/MATLAB_R2018a.app"
-PACKAGE="ISSM" # Name of directory to copy distributable files to
-PYTHON_NROPTIONS="--include_name 'Dakota' --exclude 125 126 234 417 418 420 444 445"
-TARBALL_NAME="issm-mac-with_dakota"
-TARBALL="${TARBALL_NAME}.tar.gz"
-
-## Environment
-#
-export PATH="${ISSM_DIR}/bin:$(getconf PATH)" # Ensure that we pick up binaries from 'bin' directory rather than 'externalpackages'
-
-# Check if MATLAB exists
-if ! [ -d ${MATLAB_PATH} ]; then
-	echo "${MATLAB_PATH} does not point to a MATLAB installation! Please modify MATLAB_PATH variable in $(basename $0) and try again."
-	exit 1
-fi
-
-# Clean up from previous packaging
-echo "Cleaning up existing assets"
-cd ${ISSM_DIR}
-rm -rf ${PACKAGE}
-mkdir ${PACKAGE}
-
-# Add/modify required binaries
-cd ${ISSM_DIR}/bin
-
-echo "Modifying generic"
-cat generic_static.m | sed -e "s/generic_static/generic/g" > generic.m
-cat generic_static.py | sed -e "s/generic_static/generic/g" > generic.py
-
-echo "Moving MPICH binaries to bin/"
-if [ -f ${ISSM_DIR}/externalpackages/petsc/install/bin/mpiexec ]; then
-	cp ${ISSM_DIR}/externalpackages/petsc/install/bin/mpiexec .
-	cp ${ISSM_DIR}/externalpackages/petsc/install/bin/hydra_pmi_proxy .
-elif [ -f ${ISSM_DIR}/externalpackages/mpich/install/bin/mpiexec ]; then
-	cp ${ISSM_DIR}/externalpackages/mpich/install/bin/mpiexec .
-	cp ${ISSM_DIR}/externalpackages/mpich/install/bin/hydra_pmi_proxy .
-else
-	echo "MPICH not found"
-	exit 1
-fi
-
-# Run tests
-echo "Running tests"
-cd ${ISSM_DIR}/test/NightlyRun
-
-# Check that MATLAB tests run
-echo "Running MATLAB tests"
-
-rm matlab.log 2> /dev/null
-
-# Run MATLAB tests redirecting output to logfile and suppressing output to console
-${MATLAB_PATH}/bin/matlab -nojvm -nosplash -r "try, addpath ${ISSM_DIR}/bin ${ISSM_DIR}/lib; runme(${MATLAB_NROPTIONS}); exit; catch me,fprintf('%s',getReport(me)); exit; end" -logfile matlab.log &> /dev/null
-
-# Check that MATLAB did not exit in error
-matlabExitCode=`echo $?`
-matlabExitedInError=`grep -E "Activation cannot proceed|license|Error" matlab.log | wc -l`
-
-if [[ ${matlabExitCode} -ne 0 || ${matlabExitedInError} -ne 0 ]]; then
-	echo "----------MATLAB exited in error!----------"
-	cat matlab.log
-	echo "-----------End of matlab.log-----------"
-
-	# Clean up execution directory
-	rm -rf ${ISSM_DIR}/execution/*
-
-	exit 1
-fi
-
-# Check that all MATLAB tests passed
-numMatlabTestsFailed=`cat matlab.log | grep -c -e "FAILED|ERROR"`
-
-if [[ ${numMatlabTestsFailed} -ne 0 ]]; then
-	echo "One or more MATLAB tests FAILED"
-	exit 1;
-else
-	echo "All MATLAB tests PASSED"
-fi
-
-# Check that Python tests run
-echo "Running Python tests"
-
-export PATH="${PATH}:${ISSM_DIR}/bin"
-export PYTHONPATH="${ISSM_DIR}/src/m/dev"
-export PYTHONSTARTUP="${PYTHONPATH}/devpath.py"
-export PYTHONUNBUFFERED=1 # We don't want Python to buffer output, otherwise issm.exe output is not captured
-
-rm python.log 2> /dev/null
-./runme.py ${PYTHON_NROPTIONS} &> python.log 2>&1
-
-# Check that Python did not exit in error
-pythonExitCode=`echo $?`
-pythonExitedInError=`grep -E "Error|Standard exception|Traceback|bad interpreter" python.log | wc -l`
-
-if [[ ${pythonExitCode} -ne 0 || ${pythonExitedInError} -ne 0 ]]; then
-	echo "----------Python exited in error!----------"
-	cat python.log
-	echo "-----------End of python.log-----------"
-
-	# Clean up execution directory
-	rm -rf ${ISSM_DIR}/execution/*
-
-	exit 1
-fi
-
-# Check that all Python tests passed
-numPythonTestsFailed=`cat python.log | grep -c -e "FAILED|ERROR"`
-
-if [[ ${numPythonTestsFailed} -ne 0 ]]; then
-	echo "One or more Python tests FAILED"
-	exit 1
-else
-	echo "All Python tests PASSED"
-fi
-
-# Create tarball
-cd ${ISSM_DIR}
-rm -f ${TARBALL}
-svn cleanup --remove-ignored --remove-unversioned test # Clean up test directory (before copying to package)
-echo "Copying assets to package: ${PACKAGE}"
-cp -rf bin examples lib scripts test ${PACKAGE}/
-echo "Cleaning up unneeded/unwanted files"
-python -m compileall ${PACKAGE}/bin # Precompile all Python scripts to bytecode
-rm -f ${PACKAGE}/bin/*.py # Remove all Python scripts
-rm -f ${PACKAGE}/bin/generic_static.* # Remove static versions of generic cluster classes
-rm -f ${PACKAGE}/lib/*.a # Remove static libraries from package
-rm -f ${PACKAGE}/lib/*.la # Remove libtool libraries from package
-rm -rf ${PACKAGE}/test/SandBox # Remove testing sandbox from package
-echo "Creating tarball: ${TARBALL_NAME}"
-tar -czf ${TARBALL} ${PACKAGE}
-ls -lah ${ISSM_DIR}/${TARBALL}
-
-echo "Transferring binaries to ISSM Web site"
-scp -i ~/.ssh/pine_island_to_ross ${TARBALL} jenkins@ross.ics.uci.edu:/var/www/html/${TARBALL}
-
-if [ $? -ne 0 ]; then
-	echo "FAILED: Manually check connection"
-	exit 1
-fi
Index: sm/trunk-jpl/packagers/mac/package-issm-mac-binaries.sh
===================================================================
--- /issm/trunk-jpl/packagers/mac/package-issm-mac-binaries.sh	(revision 25743)
+++ 	(revision )
@@ -1,109 +1,0 @@
-#!/bin/bash
-
-
-# Script to test, package, and transfer distributable to ISSM Web site.
-# Corresponds with build generated by configuration in 
-# $ISSM_DIR/jenkins/pine_island-mac-binaries.
-#
-
-## Constants
-#
-MATLAB_NROPTIONS="'exclude',[IdFromString('Dakota'),125,126,435,701,702,703]"
-MATLAB_PATH="/Applications/MATLAB_R2018a.app"
-PACKAGE="ISSM" # Name of directory to copy distributable files to
-TARBALL_NAME="issm-mac"
-TARBALL="${TARBALL_NAME}.tar.gz"
-
-## Environment
-#
-export PATH="${ISSM_DIR}/bin:$(getconf PATH)" # Ensure that we pick up binaries from 'bin' directory rather than 'externalpackages'
-
-# Check if MATLAB exists
-if ! [ -d ${MATLAB_PATH} ]; then
-	echo "${MATLAB_PATH} does not point to a MATLAB installation! Please modify MATLAB_PATH variable in $(basename $0) and try again."
-	exit 1
-fi
-
-# Clean up from previous packaging
-echo "Cleaning up existing assets"
-cd ${ISSM_DIR}
-rm -rf ${PACKAGE}
-mkdir ${PACKAGE}
-
-# Add/modify required binaries and libraries
-cd ${ISSM_DIR}/bin
-
-echo "Modify generic"
-cat generic_static.m | sed -e "s/generic_static/generic/g" > generic.m
-
-echo "Moving MPICH binaries to bin/"
-if [ -f ${ISSM_DIR}/externalpackages/petsc/install/bin/mpiexec ]; then
-	cp ${ISSM_DIR}/externalpackages/petsc/install/bin/mpiexec .
-	cp ${ISSM_DIR}/externalpackages/petsc/install/bin/hydra_pmi_proxy .
-elif [ -f ${ISSM_DIR}/externalpackages/mpich/install/bin/mpiexec ]; then
-	cp ${ISSM_DIR}/externalpackages/mpich/install/bin/mpiexec .
-	cp ${ISSM_DIR}/externalpackages/mpich/install/bin/hydra_pmi_proxy .
-else
-	echo "MPICH not found"
-	exit 1
-fi
-
-# Run tests
-echo "Running tests"
-cd ${ISSM_DIR}/test/NightlyRun
-
-# Check that MATLAB tests run
-echo "Running MATLAB tests"
-
-rm matlab.log 2> /dev/null
-
-# Run MATLAB tests redirecting output to logfile and suppressing output to console
-${MATLAB_PATH}/bin/matlab -nojvm -nosplash -r "try, addpath ${ISSM_DIR}/bin ${ISSM_DIR}/lib; runme(${MATLAB_NROPTIONS}); exit; catch me,fprintf('%s',getReport(me)); exit; end" -logfile matlab.log &> /dev/null
-
-# Check that MATLAB did not exit in error
-matlabExitCode=`echo $?`
-matlabExitedInError=`grep -E "Activation cannot proceed|license|Error" matlab.log | wc -l`
-
-if [[ ${matlabExitCode} -ne 0 || ${matlabExitedInError} -ne 0 ]]; then
-	echo "----------MATLAB exited in error!----------"
-	cat matlab.log
-	echo "-----------End of matlab.log-----------"
-
-	# Clean up execution directory
-	rm -rf ${ISSM_DIR}/execution/*
-
-	exit 1
-fi
-
-# Check that all MATLAB tests passed
-numMatlabTestsFailed=`cat matlab.log | grep -c -e "FAILED|ERROR"`
-
-if [[ ${numMatlabTestsFailed} -ne 0 ]]; then
-	echo "One or more MATLAB tests FAILED"
-	exit 1
-else
-	echo "All MATLAB tests PASSED"
-fi
-
-# Create tarball
-cd ${ISSM_DIR}
-rm -f ${TARBALL}
-svn cleanup --remove-ignored --remove-unversioned test # Clean up test directory (before copying to package)
-echo "Copying assets to package: ${PACKAGE}"
-cp -rf bin examples lib scripts test ${PACKAGE}/
-echo "Cleaning up unneeded/unwanted files"
-rm -f ${PACKAGE}/bin/generic_static.* # Remove static versions of generic cluster classes
-rm -f ${PACKAGE}/lib/*.a # Remove static libraries from package (we only need MEX-files)
-rm -f ${PACKAGE}/lib/*.la # Remove libtool libraries from package
-rm -rf ${PACKAGE}/test/SandBox # Remove testing sandbox from package
-echo "Creating tarball: ${TARBALL_NAME}"
-tar -czf ${TARBALL} ${PACKAGE}
-ls -lah ${ISSM_DIR}/${TARBALL}
-
-echo "Transferring binaries to ISSM Web site"
-scp -i ~/.ssh/pine_island_to_ross ${TARBALL} jenkins@ross.ics.uci.edu:/var/www/html/${TARBALL}
-
-if [ $? -ne 0 ]; then
-	echo "FAILED: Manually check connection"
-	exit 1
-fi
Index: /issm/trunk-jpl/packagers/mac/sign-issm-mac-binaries-matlab.sh
===================================================================
--- /issm/trunk-jpl/packagers/mac/sign-issm-mac-binaries-matlab.sh	(revision 25744)
+++ /issm/trunk-jpl/packagers/mac/sign-issm-mac-binaries-matlab.sh	(revision 25744)
@@ -0,0 +1,203 @@
+# From https://developer.apple.com/documentation/macos-release-notes/macos-catalina-10_15-release-notes,
+#
+#	Command line tool support for Subversion — including svn, git-svn, and 
+#	related commands — is no longer provided by Xcode. (50266910)
+#
+# which results in,
+#
+#	svn: error: The subversion command line tools are no longer provided by 
+#	Xcode.
+#
+# when calling svn, even when subversion is installed via Homebrew and its path 
+# is available in PATH.
+#
+shopt -s expand_aliases
+alias svn='/usr/local/bin/svn'
+
+## Override certain other aliases
+#
+alias cp=$(which cp)
+alias grep=$(which grep)
+
+AD_IDENTITY="**********"
+AD_USERNAME="**********"
+ALTOOL_PASSWORD="@keychain:**********"
+ASC_PROVIDER="**********"
+NOTARIZATION_CHECK_ATTEMPTS=60
+NOTARIZATION_CHECK_PERIOD=60
+NOTARIZATION_LOGFILE="notarization.log"
+NOTARIZATION_LOGFILE_PATH="."
+PKG="ISSM-macOS-MATLAB"
+PRIMARY_BUNDLE_ID="**********.issm.matlab"
+SIGNED_REPO_COPY="./signed"
+SIGNED_REPO_URL="https://issm.ess.uci.edu/svn/issm-binaries/mac/matlab/signed"
+SIGNING_LOCK_FILE="signing.lock"
+SUCCESS_LOGFILE="${SIGNED_REPO_COPY}/success.log"
+UNSIGNED_REPO_COPY="./unsigned"
+UNSIGNED_REPO_URL="https://issm.ess.uci.edu/svn/issm-binaries/mac/matlab/unsigned"
+
+COMPRESSED_PKG="${PKG}.zip"
+
+# Clean up from previous packaging (not necessary for single builds on Jenkins, 
+# but useful when testing packaging locally)
+echo 'Cleaning up existing assets'
+rm -rf ${PKG} ${COMPRESSED_PKG} ${NOTARIZATION_LOGFILE_PATH}/${NOTARIZATION_LOGFILE} ${SIGNED_REPO_COPY} ${UNSIGNED_REPO_COPY}
+mkdir ${PKG}
+
+# Check out copy of SVN repository for unsigned macOS packages
+echo 'Checking out copy of SVN respository for unsigned packages'
+svn co \
+	--username ${USERNAME} \
+	--password ${PASSWORD} \
+	${UNSIGNED_REPO_URL} \
+	${UNSIGNED_REPO_COPY}
+
+# Uncompress package
+echo 'Uncompressing package'
+ditto -xk ${UNSIGNED_REPO_COPY}/${COMPRESSED_PKG} .
+
+# Clear extended attributes on all files
+xattr -cr ${PKG}
+
+# Build list of executables
+EXECUTABLES=$(\
+	echo ${PKG}/bin/mpiexec; \
+	echo ${PKG}/bin/hydra_pmi_proxy; \
+	echo ${PKG}/bin/gdalsrsinfo; \
+	echo ${PKG}/bin/gdaltransform; \
+	echo ${PKG}/bin/gmt; \
+	echo ${PKG}/bin/gmtselect; \
+	echo ${PKG}/bin/gmsh; \
+	find ${PKG} -type f -name *.exe; \
+	find ${PKG} -type f -name *.mexmaci64; \
+)
+
+# Sign all executables in package
+echo 'Signing all executables in package'
+codesign -s ${AD_IDENTITY} --timestamp --options=runtime ${EXECUTABLES}
+
+# NOTE: Skipping signature validation because this is not a true package nor app
+
+# Compress signed package
+echo 'Compressing signed package'
+ditto -ck --sequesterRsrc --keepParent ${PKG} ${COMPRESSED_PKG}
+
+# Submit compressed package for notarization
+echo 'Submitting signed package for notarization'
+xcrun altool --notarize-app --primary-bundle-id ${PRIMARY_BUNDLE_ID} --username ${AD_USERNAME} --password ${ALTOOL_PASSWORD} --asc-provider ${ASC_PROVIDER} --file ${COMPRESSED_PKG} &> ${NOTARIZATION_LOGFILE_PATH}/${NOTARIZATION_LOGFILE}
+
+# Sleep until notarization request response is received
+echo 'Waiting for notarizaion request response'
+while [[ ! -f ${NOTARIZATION_LOGFILE_PATH}/${NOTARIZATION_LOGFILE} || ! -z $(find ${NOTARIZATION_LOGFILE_PATH} -empty -name ${NOTARIZATION_LOGFILE}) ]]; do
+	sleep 30
+done
+
+echo 'Notarizaion request response received'
+
+# Check if UUID exists in response
+HAS_UUID=$(grep 'RequestUUID = ' ${NOTARIZATION_LOGFILE_PATH}/${NOTARIZATION_LOGFILE}) # NOTE: Checking for "RequestUUID = " because "RequestUUID" shows up in some error messages
+if [[ -z "${HAS_UUID}" ]]; then
+	echo 'Notarization failed!'
+	echo '----------------------- Contents of notarization logfile -----------------------'
+	cat ${NOTARIZATION_LOGFILE_PATH}/${NOTARIZATION_LOGFILE}
+	echo '--------------------------------------------------------------------------------'
+
+	# Clean up
+	rm -rf ${PKG} ${COMPRESSED_PKG}
+
+	exit 1
+fi
+
+# Get UUID from notarization request response
+UUID=$(echo ${HAS_UUID} | sed 's/[[:space:]]*RequestUUID = //')
+echo "UUID: ${UUID}" 
+
+# Check notarization status
+#
+# NOTE: Currently, this checks if notarization was successful, but we are not 
+#		able to staple notarization as this is not a true package nor app and, 
+#		at the very least, MATLAB Mex files cannot be stapled. As such, clients 
+#		will not be able to clear Gatekeeper if they are offline.
+#
+echo 'Checking notarization status'
+SUCCESS=0
+for ATTEMPT in $(seq 1 ${NOTARIZATION_CHECK_ATTEMPTS}); do
+	echo "    Attempt #${ATTEMPT}..."
+	xcrun altool --notarization-info ${UUID} --username ${AD_USERNAME} --password ${ALTOOL_PASSWORD} &> ${NOTARIZATION_LOGFILE_PATH}/${NOTARIZATION_LOGFILE}
+	if [[ -f ${NOTARIZATION_LOGFILE_PATH}/${NOTARIZATION_LOGFILE} && -z $(find ${NOTARIZATION_LOGFILE_PATH} -empty -name ${NOTARIZATION_LOGFILE}) ]]; then
+
+		# First, check if there is an error
+		ERROR_CHECK=$(grep 'Error' ${NOTARIZATION_LOGFILE_PATH}/${NOTARIZATION_LOGFILE})
+		if [[ ! -z "${ERROR_CHECK}" ]]; then
+			break
+		fi
+
+		# No error, so check status
+		STATUS=$(grep 'Status:' ${NOTARIZATION_LOGFILE_PATH}/${NOTARIZATION_LOGFILE} | sed -e 's/[[:space:]]*Status: //')
+		if [[ "${STATUS}" == "success" ]]; then
+			# Staple notarization to all elements of package that were previously signed
+			#xcrun stapler staple ${EXECUTABLES} # NOTE: Fails with "Stapler is incapable of working with MATLAB Mex files."
+
+			# Validate stapling of notarization
+			#xcrun stapler validation ${EXECUTABLES} # NOTE: Skipping notarization stapling validation because this is not a true package nor app
+
+			# Compress signed and notarized package
+			ditto -ck --sequesterRsrc --keepParent ${PKG} ${COMPRESSED_PKG}
+
+			# Set flag indicating notarization was successful
+			SUCCESS=1
+
+			break
+		elif [[ "${STATUS}" == "in progress" ]]; then
+			echo "    ...in progress still; checking again in ${NOTARIZATION_CHECK_PERIOD} seconds."
+			sleep ${NOTARIZATION_CHECK_PERIOD}
+		elif [[ "${STATUS}" == "invalid" ]]; then
+			break
+		fi
+	else
+		if [ $ATTEMPT -lt ${NOTARIZATION_CHECK_ATTEMPTS} ]; then
+			echo "    ...not ready yet; checking again in ${NOTARIZATION_CHECK_PERIOD} seconds."
+			sleep ${NOTARIZATION_CHECK_PERIOD}
+		else
+			echo '    ...maximum attempts reached, but no response, or something else went wrong.'
+			echo '    If contents of notarization status check logfile appear to be valid, increase NOTARIZATION_CHECK_ATTEMPTS and run again.'
+			break
+		fi
+	fi
+done
+
+# Check out copy of SVN repository for signed macOS packages
+echo 'Checking out copy of SVN respository for signed packages'
+svn co \
+	--username ${USERNAME} \
+	--password ${PASSWORD} \
+	${SIGNED_REPO_URL} \
+	${SIGNED_REPO_COPY}
+
+# Copy notarization file to repository for signed binaries
+cp ${NOTARIZATION_LOGFILE_PATH}/${NOTARIZATION_LOGFILE} ${SIGNED_REPO_COPY}
+svn add ${SIGNED_REPO_COPY}/${NOTARIZATION_LOGFILE} > /dev/null 2>&1
+
+# Remove lock file from repository for signed binaries
+svn delete ${SIGNED_REPO_COPY}/${SIGNING_LOCK_FILE} > /dev/null 2>&1
+
+if [ ${SUCCESS} -eq 1 ]; then
+	echo 'Notarization successful!'
+
+	# Copy signed package to repository for signed binaries
+	cp ${COMPRESSED_PKG} ${SIGNED_REPO_COPY}
+	svn add ${SIGNED_REPO_COPY}/${COMPRESSED_PKG} > /dev/null 2>&1
+
+	# Commit changes
+	svn commit --message "CHG: New signed package (success)" ${SIGNED_REPO_COPY}
+else
+	echo 'Notarization failed!'
+	echo '----------------------- Contents of notarization logfile -----------------------'
+	cat ${NOTARIZATION_LOGFILE_PATH}/${NOTARIZATION_LOGFILE}
+	echo '--------------------------------------------------------------------------------'
+
+	# Commit changes
+	svn commit --message "CHG: New signed package (failure)" ${SIGNED_REPO_COPY}
+
+	exit 1
+fi
Index: /issm/trunk-jpl/packagers/mac/test-issm-mac-binaries-matlab.sh
===================================================================
--- /issm/trunk-jpl/packagers/mac/test-issm-mac-binaries-matlab.sh	(revision 25744)
+++ /issm/trunk-jpl/packagers/mac/test-issm-mac-binaries-matlab.sh	(revision 25744)
@@ -0,0 +1,51 @@
+#!/bin/bash
+
+# This script is intended to test ISSM macOS MATLAB binaries downloaded to a 
+# user-end machine.
+#
+# NOTE: Tarball must already exist in INSTALL_DIR
+#
+
+INSTALL_DIR=~/Downloads
+MATLAB_NROPTIONS="'benchmark','all','exclude',[125,126,234,235,418,420,435,444,445,701,702,703,1101,1102,1103,1104,1105,1106,1107,1108,1109,1110,1201,1202,1203,1204,1205,1206,1207,1208,1301,1302,1303,1304,1401,1402,1601,1602,2006,2020,2021,2051,2052,2053,3001:3200,3201,3202,3300,3480,3481,4001,4002,4003]" # NOTE: Combination of test suites from basic, Dakota, and Solid Earth builds, with tests that require a restart and those that require the JVM excluded
+MATLAB_PATH="/Applications/MATLAB_R2018a.app"
+PKG="ISSM-macOS-MATLAB"
+
+COMPRESSED_PKG="${PKG}.zip"
+
+export ISSM_DIR="${INSTALL_DIR}/${PKG}"
+export PATH="${PATH}:${ISSM_DIR}/bin:${ISSM_DIR}/scripts"
+
+cd ${INSTALL_DIR}
+rm -rf ${PKG}
+tar -zxvf ${COMPRESSED_PKG}
+cd ${PKG}/test/NightlyRun
+
+# Check that MATLAB tests run
+echo "Running MATLAB tests"
+rm matlab.log 2> /dev/null
+
+# Run MATLAB tests redirecting output to logfile and suppressing output to console
+${MATLAB_PATH}/bin/matlab -nosplash -nodesktop -nojvm -r "try, addpath ../../bin; addpath ../../lib; runme(${MATLAB_NROPTIONS}); exit; catch me,fprintf('%s',getReport(me)); exit; end" -logfile matlab.log &> /dev/null
+
+# Check that MATLAB did not exit in error
+matlabExitCode=`echo $?`
+matlabExitedInError=`grep -E "Activation cannot proceed|license|Error|Warning: Name is nonexistent or not a directory" matlab.log | wc -l`
+
+if [[ ${matlabExitCode} -ne 0 || ${matlabExitedInError} -ne 0 ]]; then
+	echo "----------MATLAB exited in error!----------"
+	cat matlab.log
+	echo
+	echo "-----------End of matlab.log-----------"
+	exit 1
+fi
+
+# Check that all MATLAB tests passed
+numMatlabTestsFailed=`cat matlab.log | grep -c -e "FAILED|ERROR"`
+
+if [[ ${numMatlabTestsFailed} -ne 0 ]]; then
+	echo "One or more MATLAB tests FAILED"
+	exit 1
+else
+	echo "All MATLAB tests PASSED"
+fi
Index: sm/trunk-jpl/scripts/test-issm-mac-binaries-with_dakota.sh
===================================================================
--- /issm/trunk-jpl/scripts/test-issm-mac-binaries-with_dakota.sh	(revision 25743)
+++ 	(revision )
@@ -1,83 +1,0 @@
-#!/bin/bash
-
-# This script is intended to test binaries downloaded to a user-end machine.
-#
-# NOTE: Tarball must already exist in INSTALL_DIR
-#
-
-MATLAB_NROPTIONS="'id',[IdFromString('Dakota')],'exclude',[125,126,234,235,418,420,444,445]"
-MATLAB_PATH="/Applications/MATLAB_R2019b.app"
-INSTALL_DIR=~/Downloads
-PACKAGE_NAME="ISSM"
-PYTHON_NROPTIONS="--include_name 'Dakota' --exclude 125 126 234 417 418 420 444 445"
-TARBALL_NAME="issm-mac-with_dakota"
-TARBALL="${TARBALL_NAME}.tar.gz"
-
-export ISSM_DIR="${INSTALL_DIR}/${PACKAGE_NAME}"
-export PATH="${PATH}:${ISSM_DIR}/bin:${ISSM_DIR}/scripts"
-
-
-cd ${INSTALL_DIR}
-rm -rf ${PACKAGE_NAME}
-tar -zxvf ${TARBALL}
-cd ${PACKAGE_NAME}/test/NightlyRun
-
-# Check that MATLAB tests run
-echo "Running MATLAB tests"
-rm matlab.log 2> /dev/null
-
-# Run MATLAB tests redirecting output to logfile and suppressing output to console
-${MATLAB_PATH}/bin/matlab -nosplash -nodesktop -nojvm -r "try, addpath ../../bin; addpath ../../lib; runme(${MATLAB_NROPTIONS}); exit; catch me,fprintf('%s',getReport(me)); exit; end" -logfile matlab.log &> /dev/null
-
-# Check that MATLAB did not exit in error
-matlabExitCode=`echo $?`
-matlabExitedInError=`grep -E "Activation cannot proceed|license|Error" matlab.log | wc -l`
-
-if [[ ${matlabExitCode} -ne 0 || ${matlabExitedInError} -ne 0 ]]; then
-	echo "----------MATLAB exited in error!----------"
-	cat matlab.log
-	echo "-----------End of matlab.log-----------"
-	exit 1
-fi
-
-# Check that all MATLAB tests passed
-numMatlabTestsFailed=`cat matlab.log | grep -c -e "FAILED|ERROR"`
-
-if [[ ${numMatlabTestsFailed} -ne 0 ]]; then
-	echo "One or more MATLAB tests FAILED"
-	exit 1
-else
-	echo "All MATLAB tests PASSED"
-fi
-
-# Check that Python tests run
-echo "Running Python tests"
-
-export ISSM_DIR="${INSTALL_DIR}"
-export PYTHONPATH="${ISSM_DIR}/scripts"
-export PYTHONSTARTUP="${PYTHONPATH}/devpath.py"
-export PYTHONUNBUFFERED=1 # We don't want Python to buffer output, otherwise issm.exe output is not captured
-
-rm python.log 2> /dev/null
-./runme.py ${PYTHON_NROPTIONS} &> python.log 2>&1
-
-# Check that Python did not exit in error
-pythonExitCode=`echo $?`
-pythonExitedInError=`grep -E "runme.py: error" python.log | wc -l`
-
-if [[ ${pythonExitCode} -ne 0 || ${pythonExitedInError} -ne 0 ]]; then
-	echo "----------Python exited in error!----------"
-	cat python.log
-	echo "-----------End of python.log-----------"
-	exit 1
-fi
-
-# Check that all Python tests passed
-numPythonTestsFailed=`cat python.log | grep -c -e "FAILED|ERROR"`
-
-if [[ ${numPythonTestsFailed} -ne 0 ]]; then
-	echo "One or more Python tests FAILED"
-	exit 1
-else
-	echo "All Python tests PASSED"
-fi
Index: sm/trunk-jpl/scripts/test-issm-mac-binaries.sh
===================================================================
--- /issm/trunk-jpl/scripts/test-issm-mac-binaries.sh	(revision 25743)
+++ 	(revision )
@@ -1,49 +1,0 @@
-#!/bin/bash
-
-# This script is intended to test binaries downloaded to a user-end machine.
-#
-# NOTE: Tarball must already exist in INSTALL_DIR
-#
-
-export ISSM_DIR="${INSTALL_DIR}/${PACKAGE_NAME}"
-export PATH="${PATH}:${ISSM_DIR}/bin:${ISSM_DIR}/scripts"
-
-MATLAB_NROPTIONS="'exclude',[IdFromString('Dakota'),125,126,435,701,702,703]"
-MATLAB_PATH="/Applications/MATLAB_R2019b.app"
-INSTALL_DIR=~/Downloads
-PACKAGE_NAME="ISSM"
-TARBALL_NAME="issm-mac"
-TARBALL="${TARBALL_NAME}.tar.gz"
-
-cd ${INSTALL_DIR}
-rm -rf ${PACKAGE_NAME}
-tar -zxvf ${TARBALL}
-cd ${PACKAGE_NAME}/test/NightlyRun
-
-# Check that MATLAB tests run
-echo "Running MATLAB tests"
-rm matlab.log 2> /dev/null
-
-# Run MATLAB tests redirecting output to logfile and suppressing output to console
-${MATLAB_PATH}/bin/matlab -nosplash -nodesktop -nojvm -r "try, addpath ../../bin; addpath ../../lib; runme(${MATLAB_NROPTIONS}); exit; catch me,fprintf('%s',getReport(me)); exit; end" -logfile matlab.log &> /dev/null
-
-# Check that MATLAB did not exit in error
-matlabExitCode=`echo $?`
-matlabExitedInError=`grep -E "Activation cannot proceed|license|Error" matlab.log | wc -l`
-
-if [[ ${matlabExitCode} -ne 0 || ${matlabExitedInError} -ne 0 ]]; then
-	echo "----------MATLAB exited in error!----------"
-	cat matlab.log
-	echo "-----------End of matlab.log-----------"
-	exit 1
-fi
-
-# Check that all MATLAB tests passed
-numMatlabTestsFailed=`cat matlab.log | grep -c -e "FAILED|ERROR"`
-
-if [[ ${numMatlabTestsFailed} -ne 0 ]]; then
-	echo "One or more MATLAB tests FAILED"
-	exit 1
-else
-	echo "All MATLAB tests PASSED"
-fi