Build full cil (SyneRBI#195)

closes SyneRBI#192 
closes SyneRBI#181

scripts/UPDATE.sh

@@ -203,8 +203,8 @@ SuperBuild(){
         -DBUILD_CIL_LITE=ON\
         -DCYTHON_EXECUTABLE="$CYTHON_EXECUTABLE"\
         -DPYTHON_EXECUTABLE="$PYTHON_EXECUTABLE"\
-	-DBUILD_pet_rd_tools=ON
-  make -j${num_parallel}
+        -DBUILD_pet_rd_tools=ON
+  cmake --build . -j${num_parallel}
 
   if [ ! -f ${SIRF_INSTALL_PATH}/share/gadgetron/config/gadgetron.xml ]
   then

scripts/update_VM_to_full_CIL.sh

@@ -4,7 +4,7 @@
 #   the CCPi Regularisation Toolkit and TomoPhantom.
 #   
 #
-# Author: Kris Thielemans
+# Author: Kris Thielemans, Edoardo Pasca
 
 echo "This script assumes you have run update_VM.sh already."
 echo "Things will go horribly wrong otherwise."
@@ -15,10 +15,15 @@ if [ -z "$SIRF_PATH" -o ! -d $SIRF_PATH -o ! -d $SIRF_PATH/../STIR ]; then
    exit 1
 fi
 
-# change build files to also build the STIR executables
+APT_GET_INSTALL="sudo apt-get install -y --no-install-recommends"
+# install CIL prerequisites
+${APT_GET_INSTALL} cython3 python3-h5py python3-wget
+# install ASTRA prerequisites
+${APT_GET_INSTALL} autotools-dev automake autogen autoconf libtool
+# change build files to also build the CIL and ASTRA executables
 cd $SIRF_PATH/../..
 cmake -DBUILD_CIL:BOOL=ON .
-make -j2 
+cmake --build . -j2 
 
 # update/get CIL demos
 cd $SIRF_SRC_PATH
@@ -30,7 +35,8 @@ else
    cd ./CIL-Demos
 fi
 
-python -m pip install --user nbstripout
+#make sure nbstripout is installed and apply filter to CIL-Demos repo
+python3 -m pip install --user nbstripout
 nbstripout --install
 
 echo "All done"

vagrant/Vagrantfile

@@ -74,7 +74,7 @@ Vagrant.configure("2") do |config|
        "--medium", "emptydrive"
        ]
 
-	vb.name = "SIRF 3.1.0-rc.1"
+	vb.name = "SIRF 3.1.0-rc.2"
     vb.customize ["modifyvm", :id, 
 	              "--clipboard", "bidirectional",
                   "--vram", "32"]