From 09dbbc4de89b8affba431ef02e86bfd987fb9296 Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <edo.paskino@gmail.com>
Date: Fri, 25 Jun 2021 08:16:56 +0100
Subject: [PATCH] Build full cil (#195)

closes #192
closes #181
---
 scripts/UPDATE.sh                |  4 ++--
 scripts/update_VM_to_full_CIL.sh | 14 ++++++++++----
 vagrant/Vagrantfile              |  2 +-
 3 files changed, 13 insertions(+), 7 deletions(-)
 mode change 100755 => 100644 scripts/UPDATE.sh

diff --git a/scripts/UPDATE.sh b/scripts/UPDATE.sh
old mode 100755
new mode 100644
index b4a2eef0..b28878e5
--- a/scripts/UPDATE.sh
+++ b/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
diff --git a/scripts/update_VM_to_full_CIL.sh b/scripts/update_VM_to_full_CIL.sh
index bdc6a152..151a0194 100755
--- a/scripts/update_VM_to_full_CIL.sh
+++ b/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"
diff --git a/vagrant/Vagrantfile b/vagrant/Vagrantfile
index 17671622..6ea975fa 100644
--- a/vagrant/Vagrantfile
+++ b/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"]