build/test for macos with install_name corrections.

.gitignore

@@ -5,3 +5,4 @@
 /build-win64/
 /.DS_Store
 /build-linux64/
+/build-macos/

VagrantBoxes/macos-test/.gitignore

@@ -0,0 +1 @@
+/.vagrant/

VagrantBoxes/macos-test/Vagrantfile

@@ -0,0 +1,77 @@
+# -*- mode: ruby -*-
+# vi: set ft=ruby :
+
+# All Vagrant configuration is done below. The "2" in Vagrant.configure
+# configures the configuration version (we support older styles for
+# backwards compatibility). Please don't change it unless you know what
+# you're doing.
+Vagrant.configure("2") do |config|
+  # The most common configuration options are documented and commented below.
+  # For a complete reference, please see the online documentation at
+  # https://docs.vagrantup.com.
+
+  # Every Vagrant development environment requires a box. You can search for
+  # boxes at https://atlas.hashicorp.com/search.
+  config.vm.box = "jhcook/macos-sierra"
+
+  # Disable automatic box update checking. If you disable this, then
+  # boxes will only be checked for updates when the user runs
+  # `vagrant box outdated`. This is not recommended.
+  # config.vm.box_check_update = false
+
+  # Create a forwarded port mapping which allows access to a specific port
+  # within the machine from a port on the host machine. In the example below,
+  # accessing "localhost:8080" will access port 80 on the guest machine.
+  # NOTE: This will enable public access to the opened port
+  # config.vm.network "forwarded_port", guest: 80, host: 8080
+
+  # Create a forwarded port mapping which allows access to a specific port
+  # within the machine from a port on the host machine and only allow access
+  # via 127.0.0.1 to disable public access
+  # config.vm.network "forwarded_port", guest: 80, host: 8080, host_ip: "127.0.0.1"
+
+  # Create a private network, which allows host-only access to the machine
+  # using a specific IP.
+  config.vm.network "private_network", ip: "192.168.33.10"
+
+  # Create a public network, which generally matched to bridged network.
+  # Bridged networks make the machine appear as another physical device on
+  # your network.
+  # config.vm.network "public_network"
+
+  # Share an additional folder to the guest VM. The first argument is
+  # the path on the host to the actual folder. The second argument is
+  # the path on the guest to mount the folder. And the optional third
+  # argument is a set of non-required options.
+  config.vm.synced_folder "../..", "/vagrant_numerics", type: "nfs"
+  config.vm.synced_folder ".", "/vagrant", type: "nfs"
+
+  # Provider-specific configuration so you can fine-tune various
+  # backing providers for Vagrant. These expose provider-specific options.
+  # Example for VirtualBox:
+  #
+  config.vm.provider "virtualbox" do |vb|
+  	vb.name = "vcell-numerics-macos-test"
+  #   # Display the VirtualBox GUI when booting the machine
+  #   vb.gui = true
+  #
+  #   # Customize the amount of memory on the VM:
+  #   vb.memory = "1024"
+  end
+  #
+  # View the documentation for the provider you are using for more
+  # information on available options.
+
+  # Define a Vagrant Push strategy for pushing to Atlas. Other push strategies
+  # such as FTP and Heroku are also available. See the documentation at
+  # https://docs.vagrantup.com/v2/push/atlas.html for more information.
+  # config.push.define "atlas" do |push|
+  #   push.app = "YOUR_ATLAS_USERNAME/YOUR_APPLICATION_NAME"
+  # end
+
+  # Enable provisioning with a shell script. Additional provisioners such as
+  # Puppet, Chef, Ansible, Salt, and Docker are also available. Please see the
+  # documentation for more information about their specific syntax and use.
+  config.vm.provision "shell", inline: <<-SHELL
+SHELL
+end

VagrantBoxes/macos-test/test.sh

@@ -0,0 +1,30 @@
+#!/usr/bin/env bash
+
+shopt -s -o nounset
+
+echo "testing solvers using binaries and libraries in build-linux64/bin and tests in testFiles"
+
+projectDir=/vagrant_numerics
+
+solverDir="${projectDir}/build-macos/bin"
+inputDir="${projectDir}/testFiles/input"
+workDir="${projectDir}/testFiles/working"
+archiveDir="${projectDir}/testFiles/archive/macos"
+
+mkdir -p $workDir
+mkdir -p $archiveDir
+
+cd $projectDir
+
+#
+# Test FiniteVolume_x64
+#
+mkdir -p ${workDir}/FiniteVolume
+rm ${workDir}/FiniteVolume/*
+cp ${inputDir}/FiniteVolume/SimID_11538992_0_* ${workDir}/FiniteVolume
+${solverDir}/FiniteVolume_x64 ${workDir}/FiniteVolume/SimID_11538992_0_.fvinput
+
+mkdir -p ${archiveDir}/FiniteVolume
+cp ${workDir}/FiniteVolume/SimID_11538992_0_*  ${archiveDir}/FiniteVolume
+rm ${workDir}/FiniteVolume/*
+

VagrantBoxes/macos/build.sh

@@ -30,17 +30,3 @@ mkdir bin
 	..
 
 make
-
-#cp /usr/local/Cellar/[email protected]/1.8.19/lib/libhdf5_cpp.14.dylib bin
-#cp /usr/local/Cellar/[email protected]/1.8.19/lib/libhdf5.10.dylib bin
-#cp /usr/local/Cellar/[email protected]/1.8.19/lib/libhdf5_hl_cpp.11.dylib bin
-#cp /usr/local/Cellar/[email protected]/1.8.19/lib/libhdf5_hl.10.dylib bin
-#cp /usr/local/lib/libgfortran.4.dylib bin
-#cp /usr/local/lib/libquadmath.0.dylib bin
-#cp /usr/local/opt/szip/lib/libsz.2.dylib bin
-#cp /usr/local/lib/libgcc_s.1.dylib bin
-
-#cd /vagrant_numerics/${builddir}/bin
-#echo "fixing mac paths"
-#/vagrant/install_name_tool_macos.sh
-#cd /vagrant_numerics/${builddir}

VagrantBoxes/macos/install_name_tool_macos.sh

@@ -19,14 +19,10 @@ executables=(
 libraries=(
   "/usr/local/lib/libgfortran.4.dylib"
   "/usr/local/lib/libquadmath.0.dylib"
-  "/usr/local/Cellar/[email protected]/1.8.19/lib/libhdf5_cpp.14.dylib"
-  "/usr/local/Cellar/[email protected]/1.8.19/lib/libhdf5.10.dylib"
-  "/usr/local/Cellar/[email protected]/1.8.19/lib/libhdf5_hl_cpp.11.dylib"
-  "/usr/local/Cellar/[email protected]/1.8.19/lib/libhdf5_hl.10.dylib"
   "/usr/local/opt/[email protected]/lib/libhdf5_cpp.14.dylib"
   "/usr/local/opt/[email protected]/lib/libhdf5.10.dylib"
-  "/usr/local/opt/[email protected]/lib/libhdf5_hl_cpp.11.dylib"
-  "/usr/local/opt/[email protected]/lib/libhdf5_hl.10.dylib"
+  "/usr/local/Cellar/[email protected]/1.8.19/lib/libhdf5_cpp.14.dylib"
+  "/usr/local/Cellar/[email protected]/1.8.19/lib/libhdf5.10.dylib"
   "/usr/local/opt/szip/lib/libsz.2.dylib"
   "/usr/local/lib/libgcc_s.1.dylib"
   "/vagrant_numerics/build-macos/bin/libzip.3.0.dylib"

VagrantBoxes/macos/moveDependentLibraries.sh

@@ -0,0 +1,27 @@
+#!/usr/bin/env bash
+
+shopt -s -o nounset
+
+builddir="build-macos"
+cd /vagrant_numerics/${builddir}/bin
+
+cp /usr/local/opt/[email protected]/lib/libhdf5_cpp.14.dylib .
+cp /usr/local/opt/[email protected]/lib/libhdf5.10.dylib .
+cp /usr/local/opt/szip/lib/libsz.2.dylib .
+cp /usr/local/lib/libgfortran.4.dylib .
+cp /usr/local/lib/libgcc_s.1.dylib .
+cp /usr/local/lib/libquadmath.0.dylib .
+
+#cp /usr/local/Cellar/[email protected]/1.8.19/lib/libhdf5_cpp.14.dylib .
+#cp /usr/local/Cellar/[email protected]/1.8.19/lib/libhdf5.10.dylib .
+#cp /usr/local/Cellar/[email protected]/1.8.19/lib/libhdf5_hl_cpp.11.dylib .
+#cp /usr/local/Cellar/[email protected]/1.8.19/lib/libhdf5_hl.10.dylib .
+#cp /usr/local/lib/libgfortran.4.dylib .
+#cp /usr/local/lib/libquadmath.0.dylib .
+#cp /usr/local/opt/szip/lib/libsz.2.dylib .
+#cp /usr/local/lib/libgcc_s.1.dylib .
+
+cd /vagrant_numerics/${builddir}/bin
+chmod +w *
+echo "fixing mac paths"
+/vagrant/install_name_tool_macos.sh

libzip-1.2.0/lib/.gitignore

@@ -0,0 +1 @@
+/libzip.la