#!/bin/sh

error() {
   echo "Configure failed due to the errors above!"
   exit 1
}

# Check for --no-updates in any position
updates="yes"
requested_help="no"
for var in "$@"; do
    case "$var" in
        --no-updates)
            echo "Skipping check for Amber updates"; updates="no";;
        -h|-H|--h|--he|--hel|--help|-help)
            updates="no"; requested_help="yes";;
        --full|--full-h|--full-he|--full-hel|--full-help) 
            updates="no"; requested_help="yes";;
    esac
done

# No arguments means we ask for help
if [ $# -eq 0 ]; then
    requested_help="yes"
    updates="no"
fi

if [ "$updates" = "yes" ]; then
   # Tell people we're checking for updates, since this could take a
   # couple seconds, especially if ambermd.org is down
   echo "Checking for updates..."

   # Check to see if there are any updates available. This will print a message
   # giving how many patches are available for Amber and AmberTools
   ./update_amber --check-updates

   # The return code of the above command tells us what happened. Return 1 for
   # an error, and return 2 if there are patches available
   ret_code=$?

   if [ $ret_code -eq 2 ]; then
      printf "There are patches available. Do you want to apply them now? [y/N]"
      echo " (Recommended Y) "
      read answer
      ans=`echo $answer | awk '{print substr($1,1,1)}'`

      if [ "$ans" = "y" -o "$ans" = "Y" ]; then
         # Since patch_amber may patch itself and quit before applying all patches,
         # continue to check for updates and update the tree until they have all
         # been applied.
         while [ $ret_code -eq 2 ]
         do
            ./update_amber --update
            if [ $? -ne 0 ]; then
               echo "Automatic patching failed! Check the errors before re-configuring"
               exit 1
            fi
            ./update_amber --check-updates 2>&1 > /dev/null
            ret_code=$?
         done
      else
         echo "NOT updating your tree and continuing anyway."
      fi
   elif [ $ret_code -eq 1 ]; then
      echo "Check for updates failed."
   fi
fi

# Simple redirection to carry out the configure script inside AmberTools/src

(cd AmberTools/src && ./configure2 $@) || error

# Bail out if we just got the usage statement
if [ "$requested_help" = "yes" ]; then
    exit 0
fi

ln -sf AmberTools/src/config.h .

# Make clean here

echo "Cleaning the src directories. This may take a few moments."
make clean > /dev/null 2>&1
echo "Configure complete."