configure

#!/bin/bash

check_pkgconfig(){
	if [ "$CHECKED_PKGCONFIG" ]; then return; fi
	echo "Looking for pkg-config..."
	PKG_CONFIG_PATH=$(which pkg-config 2>&1)
	if [ "$?" -ne 0 ]; then
		echo "Error: pkg-config not found; you will need to specify library locations manually" 1>&2
		exit 1
	fi
	echo " Found $PKG_CONFIG_PATH"
	CHECKED_PKGCONFIG=1
}

find_package(){
	PKG=$1
	VAR_PREFIX=`echo $PKG | tr [:lower:] [:upper:]`
	TMP_FOUND=`eval echo "$"${VAR_PREFIX}_FOUND`
	if [ "$TMP_FOUND" ]; then return; fi
	check_pkgconfig
	echo "Looking for $PKG..."

	pkg-config --exists $PKG
	if [ "$?" -ne 0 ]; then
		echo " $PKG not found with pkg-config"
		return
	fi
	if [ $# -ge 2 ]; then
		MIN_VERSION=$2
		pkg-config --atleast-version $MIN_VERSION $PKG
		if [ "$?" -ne 0 ]; then
			echo "Error: installed $PKG version ("`pkg-config --modversion $PKG`") is too old; version >=$MIN_VERSION is required" 1>&2
			exit 1
		fi
	fi
	echo " Found $PKG version `pkg-config --modversion $PKG`"
	eval ${VAR_PREFIX}_FOUND=1
	eval ${VAR_PREFIX}_VERSION=\"`pkg-config --modversion $PKG`\"
	eval ${VAR_PREFIX}_CFLAGS=\"`pkg-config --cflags $PKG`\"
	eval ${VAR_PREFIX}_LDFLAGS=\"`pkg-config --libs $PKG`\"
	eval ${VAR_PREFIX}_INCDIR=\"`pkg-config --variable=includedir $PKG`\"
	eval ${VAR_PREFIX}_LIBDIR=\"`pkg-config --variable=libdir $PKG`\"
}

find_hdf5(){
	PKG=hdf5
	echo "Looking for $PKG..."
	VAR_PREFIX=`echo $PKG | tr [:lower:] [:upper:]`
	TMP_FOUND=`eval echo "$"${VAR_PREFIX}_FOUND`
	if [ "$TMP_FOUND" ]; then return; fi

	which h5cc 2>&1 > /dev/null
	if [ "$?" -ne 0 ]; then return; fi

	which h5ls 2>&1 > /dev/null
	if [ "$?" -eq 0 ]; then
		HDF5_VERSION=`h5ls --version | sed 's/.* \([0-9.]*\)/\1/'`
		echo " Found $PKG version $HDF5_VERSION via executables in \$PATH"
		if [ $# -ge 1 ]; then
			MIN_VERSION=$1
			#TODO: actually check version
		fi
	else
		echo " h5ls not found; cannot check $PKG version"
		echo " Proceeding with unknown version and hoping for the best"
	fi
	HDF5_COMPILE_COMMAND=`h5cc -show`
	for item in $HDF5_COMPILE_COMMAND; do
		item=`echo "$item" | sed 's| |\n|g' | sed -n 's/.*-L\([^ ]*\).*/\1/p'`
		if [ -n "$item" ]; then
			POSSIBLE_HDF5_LIBDIRS="$POSSIBLE_HDF5_LIBDIRS
				$item"
		fi
	done
	for HDF5_LIBDIR in $POSSIBLE_HDF5_LIBDIRS; do
		if [ -d $HDF5_LIBDIR -a \( -e $HDF5_LIBDIR/libhdf5.a -o -e $HDF5_LIBDIR/libhdf5.so \) ]; then
			break
		fi
	done
	if [ ! -d $HDF5_LIBDIR -o ! \( -e $HDF5_LIBDIR/libhdf5.a -o -e $HDF5_LIBDIR/libhdf5.so \) ]; then
		echo " Unable to guess $PKG library directory"
		return
	fi
	POSSIBLE_HDF5_INCDIRS=`echo "$HDF5_COMPILE_COMMAND" | sed 's| |\n|g' | sed -n 's/.*-I\([^ ]*\).*/\1/p'`
	POSSIBLE_HDF5_INCDIRS="$POSSIBLE_HDF5_INCDIRS ${HDF5_LIBDIR}/../include"
	for HDF5_INCDIR in $POSSIBLE_HDF5_INCDIRS; do
		if [ -d $HDF5_INCDIR -a -e $HDF5_INCDIR/H5version.h ]; then
			break
		fi
	done
	if [ ! -d $HDF5_INCDIR -o ! $HDF5_INCDIR/H5version.h ]; then
		echo " Unable to guess $PKG include directory"
		return
	fi

	HDF5_CFLAGS="-I${HDF5_INCDIR}"
	HDF5_LDFLAGS=`echo "$HDF5_COMPILE_COMMAND" | \
	sed 's/ /\\
	/g' | \
	sed -n -E \
	-e '/^[[:space:]]*-l/p' \
	-e '/^[[:space:]]*-L/p' \
	-e '/^[[:space:]]*-Wl,/p' \
	-e 's/^[[:space:]]*.*lib([^.]*)\.a/-l\1/p' \
	-e 's/^[[:space:]]*.*lib([^.]*)\.so/-l\1/p' \
	-e 's/^[[:space:]]*.*lib([^.]*)\.dylib/-l\1/p' `
	HDF5_LDFLAGS=`echo $HDF5_LDFLAGS` # collapse to single line

	HDF5_FOUND=1
}

# less searching for python than verfying that the given executable works and extracting relevant paths
try_find_python(){
	echo "Looking for python"

	if which ${PYTHON_EXE} > /dev/null 2>&1; then
		PYTHON_EXE=$(which ${PYTHON_EXE} 2>/dev/null)
		echo " Using python executable ${PYTHON_EXE}"
	else
		echo " ${PYTHON_EXE} is not a valid python executable"
		return
	fi

	PYTHON_VERSION=`${PYTHON_EXE} -c 'import sys; print(str(sys.version_info.major)+"."+str(sys.version_info.minor))'`
	if [ "$?" -ne 0 ]; then
		echo "Unable to use python executable ${PYTHON_EXE} (version check failed)"
		return
	fi
	PYTHONVERSIONSIMPLE=`${PYTHON_EXE} -c 'import sys; print(str(sys.version_info.major)+str(sys.version_info.minor))'`
	
	PYTHON_INCDIR=`${PYTHON_EXE} -c 'from distutils import sysconfig; print(sysconfig.get_python_inc())'`
	if [ -d "$PYTHON_INCDIR" ]; then
		echo " Found python include dir $PYTHON_INCDIR"
	else
		echo " Unable to locate the python include dir"
		return
	fi

	# This is the directory to which libraries should be installed for python to find them
	PYTHON_MODULEDIR=`${PYTHON_EXE} -c 'from distutils.sysconfig import get_python_lib; print(get_python_lib(plat_specific=True, standard_lib=False))'`
	if [ "$PYTHON_MODULEDIR" ]; then
		echo " Python module install dir is $PYTHON_MODULEDIR"
	else
		echo " Unable to locate the python module dir"
		return
	fi
	
	# This is the directory that python claims contains its standard library, 
	# which may or may not include the actual libpython
	PYTHON_STDLIBDIR=`${PYTHON_EXE} -c 'from distutils import sysconfig; print(sysconfig.get_python_lib(plat_specific=True,standard_lib=True))'`
	# This may contain a suffix which appears after the version like in 'libpython3.6m'
	# See https://www.python.org/dev/peps/pep-3149/#proposal
	PYTHONLIBSUFFIX=`${PYTHON_EXE} -c 'from distutils import sysconfig; print(sysconfig.build_flags)' 2>/dev/null`

	# Here we just try to guess every location anyone has ever seen a libpython in the wild
	POSSIBLE_PYTHON_LIBDIRS="/lib /lib64 /usr/lib /usr/lib64 /usr/local/lib /usr/local/lib64 ${PYTHON_STDLIBDIR} ${PYTHON_STDLIBDIR}/lib"
	# sometimes Apple puts a symlink in ${PYTHONSTDLIBDIR}/lib, sometimes it doesn't
	TMP=`echo "$PYTHON_STDLIBDIR" | sed -n s'|\(.*/lib\)/python'"${PYTHON_VERSION}"'|\1|p'`
	if [ "$TMP" ]; then POSSIBLE_PYTHON_LIBDIRS="${POSSIBLE_PYTHON_LIBDIRS} ${TMP}"; fi
	# Ubuntu is special, of course
	if uname -a | grep -i 'ubuntu' > /dev/null; then
		POSSIBLE_PYTHON_LIBDIRS="${POSSIBLE_PYTHON_LIBDIRS} /usr/lib/$(uname -i)-linux-gnu"
	fi

	for PYTHON_LIBDIR in $POSSIBLE_PYTHON_LIBDIRS; do
		for PV in $PYTHON_VERSION $PYTHONVERSIONSIMPLE; do
			#echo "  Looking for ${PYTHON_LIBDIR}/libpython${PV}${PYTHONLIBSUFFIX}.(a|so|dylib)"
			if [ -d $PYTHON_LIBDIR ]; then
				if [ -e ${PYTHON_LIBDIR}/libpython${PV}${PYTHONLIBSUFFIX}.a ]; then
					PYTHON_LIBRARY=${PYTHON_LIBDIR}/libpython${PV}${PYTHONLIBSUFFIX}.a
					break
				elif [ -e ${PYTHON_LIBDIR}/libpython${PV}${PYTHONLIBSUFFIX}.so ];then
					PYTHON_LIBRARY=${PYTHON_LIBDIR}/libpython${PV}${PYTHONLIBSUFFIX}.so
					break
				elif [ -e ${PYTHON_LIBDIR}/libpython${PV}${PYTHONLIBSUFFIX}.dylib ]; then
					PYTHON_LIBRARY=${PYTHON_LIBDIR}/libpython${PV}${PYTHONLIBSUFFIX}.dylib
					break
				fi
			fi
		done
	done
	if [ -e "$PYTHON_LIBRARY" ]; then
		echo " Found python library $PYTHON_LIBRARY"
	else
		echo " Unable to locate the python library"
		return
	fi

	PYTHON_CFLAGS="-I${PYTHON_INCDIR}"
	PYTHON_LDFLAGS="-L${PYTHON_LIBDIR} -l$(echo "$PYTHON_LIBRARY" | sed 's|.*lib\(python.*\)\.[a-z]*|\1|')"
	PYTHON_FOUND=1
}

try_find_boost(){
	PKG=boost
	VAR_PREFIX=`echo $PKG | tr [:lower:] [:upper:]`
	TMP_FOUND=`eval echo "$"${VAR_PREFIX}_FOUND`
	if [ "$TMP_FOUND" ]; then return; fi
	if [ "$PYTHON_FOUND" ]; then
		PYV=`${PYTHON_EXE} -c 'import sys; print(str(sys.version_info.major)+str(sys.version_info.minor))'`
		PYVM=`${PYTHON_EXE} -c 'import sys; print(sys.version_info.major)'`
		echo "Looking for $PKG built for python ${PYV} in $GUESS_DIR..."
	else
		echo "Looking for $PKG in $GUESS_DIR..."
	fi
	
 	if [ "$#" -eq 1 ]; then
 		GUESS_DIR=$1
 		POSSIBLE_BOOST_LIBDIRS="${GUESS_DIR}/lib ${GUESS_DIR}/lib64 ${GUESS_DIR}/lib/x86_64-linux-gnu"
		POSSIBLE_BOOST_INCDIRS="${GUESS_DIR}/include"
	elif [ "$#" -eq 2 ]; then
		GUESS_DIR="$1 and $2"
		POSSIBLE_BOOST_LIBDIRS="$2"
		POSSIBLE_BOOST_INCDIRS="$1"
	else
		echo "Wrong number of arguments to try_find_boost"
		return
 	fi
	if [ "$PYTHON_FOUND" ]; then
		for PYV_SUFFIX in $PYV $PYVM ''; do
			for BOOST_LIBDIR in $POSSIBLE_BOOST_LIBDIRS; do
				if [ -d $BOOST_LIBDIR -a \( -e $BOOST_LIBDIR/libboost_python${PYV_SUFFIX}.a -o -e $BOOST_LIBDIR/libboost_python${PYV_SUFFIX}.so -o -e $BOOST_LIBDIR/libboost_python${PYV_SUFFIX}.dylib \) ]; then
					if [ ! "$PYV_SUFFIX" ]; then
						echo " Found boost_python with no python version tag; hoping it is compatible"
					fi
					BOOST_PYTHON_FOUND=1
					BOOST_PYTHON_LDFLAGS="-lboost_python${PYV_SUFFIX}"
					break
				fi
			done
			if [ "$BOOST_PYTHON_FOUND" ]; then break; fi
		done
		if [ ! "$BOOST_PYTHON_FOUND" ]; then
			echo " Unable to locate the boost_python library in $GUESS_DIR"
		fi
	fi
	for BOOST_INCDIR in $POSSIBLE_BOOST_INCDIRS; do
		if [ -d $BOOST_INCDIR -a -e $BOOST_INCDIR/boost/version.hpp ]; then
			break
		fi
	done
	if [ ! -d "$BOOST_INCDIR" -o ! -e "$BOOST_INCDIR/boost/version.hpp" ]; then
		echo " Unable to locate boost/version.hpp in $GUESS_DIR"
		return
	fi
	BOOST_CFLAGS="-I${BOOST_INCDIR}"
	BOOST_LDFLAGS="-Wl,-rpath -Wl,${BOOST_LIBDIR} -L${BOOST_LIBDIR}"
	BOOST_FOUND=1
	echo " Found boost in $GUESS_DIR"
	echo " Boost include directory is ${BOOST_INCDIR}"
	if [ "$BOOST_LIBDIR" ]; then
		echo " Boost library directory is ${BOOST_LIBDIR}"
	fi
}

find_numpy(){
	echo "Looking for numpy..."
	NUMPY_INCDIR=$(${PYTHON_EXE} -c 'import numpy; print(numpy.get_include())')
	if [ "$?" -ne 0 ]; then
		echo "Unable to import numpy using ${PYTHON_EXE}"
		return
	fi
	NUMPY_CFLAGS="-I${NUMPY_INCDIR}"
	NUMPY_FOUND=1
	echo " Found numpy"
	echo " Numpy include directory is ${NUMPY_INCDIR}"
}

ensure_found(){
	PKG=$1
	VAR_PREFIX=`echo $PKG | tr [:lower:] [:upper:]`
	TMP_FOUND=`eval echo "$"${VAR_PREFIX}_FOUND`
	if [ "$TMP_FOUND" ]; then return; fi
	#not found
	lowername=`echo $PKG | tr [A-Z] [a-z]`

	TMP_INCDIR=`eval echo "$"${VAR_PREFIX}_INCDIR`
	TMP_LIBDIR=`eval echo "$"${VAR_PREFIX}_LIBDIR`
	if [ "$TMP_INCDIR" -a "$TMP_LIBDIR" ]; then
		echo "Error: $PKG not found in $TMP_INCDIR and $TMP_LIBDIR or with pkg-config" 1>&2
		echo "Please verify that the path given to --with-${lowername} is correct" 1>&2
	else
		echo "Error: $PKG not installed or not registered with pkg-config" 1>&2
		echo "Please specify location using the --with-${lowername} flag" 1>&2
	fi
	unset TMP_INCDIR
	unset TMP_LIBDIR
	exit 1
}

PREFIX=/usr/local
INSTALL_LIBDIR=lib

VERSION_NUM=101100
VERSION=`echo $VERSION_NUM | awk '{
	major = int($1/100000);
	minor = int($1/100)%1000;
	patch = $1%100;
	print major"."minor"."patch;
}'`

OS_NAME=`uname -s`

GUESS_CC=gcc
GUESS_CXX=g++
GUESS_AR=ar
GUESS_LD=ld
if [ "$OS_NAME" = Linux ]; then
	DYN_SUFFIX=.so
	DYN_OPT='-shared -Wl,-soname,$(shell basename $(DYN_PRODUCT))'
	DYN_OPT_PY='-shared -Wl,-soname,$(shell basename $(PYTHON_LIB))'
fi
if [ "$OS_NAME" = Darwin ]; then
	GUESS_CC=clang
	GUESS_CXX=clang++
	GUESS_LD=clang++
	DYN_SUFFIX=.dylib
	DYN_OPT='-dynamiclib -compatibility_version $(VERSION) -current_version $(VERSION)'
	DYN_OPT_PY='-dynamiclib -compatibility_version $(VERSION) -current_version $(VERSION)'
fi

CC=${CC-$GUESS_CC}
CXX=${CXX-$GUESS_CXX}
AR=${AR-$GUESS_AR}
LD=${LD-$GUESS_LD}

PYTHON_EXE="python"
if which "$PYTHON_EXE" > /dev/null 2>&1; then
	: # good, keep our initial guess
elif which "python3" > /dev/null 2>&1; then
	PYTHON_EXE="python3"
fi

HELP="Usage: ./configure [OPTION]... 

Installation directories:
  --prefix=PREFIX         install files in PREFIX
                          [$PREFIX]

By default, \`make install' will install all the files in
\`$PREFIX/bin', \`$PREFIX/lib' etc.  You can specify
an installation prefix other than \`$PREFIX' using \`--prefix',
for instance \`--prefix=\$HOME'.

Fine tuning of the installation directories:

  --libdir=DIR            object code libraries [lib]

The following options can be used to maunally specify the 
locations of dependencies:
  --with-gsl=DIR                 use the copy of GSL in DIR
                                 assuming headers are in DIR/include
                                 and libraries in DIR/lib
  --with-gsl-incdir=DIR          use the copy of GSL in DIR
  --with-gsl-libdir=DIR          use the copy of GSL in DIR
  --with-hdf5=DIR                use the copy of HDF5 in DIR
                                 assuming headers are in DIR/include
                                 and libraries in DIR/lib
  --with-hdf5-incdir=DIR         use the copy of HDF5 in DIR
  --with-hdf5-libdir=DIR         use the copy of HDF5 in DIR
  --with-squids=DIR              use the copy of SQuIDS in DIR
                                 assuming headers are in DIR/include
                                 and libraries in DIR/lib
  --with-squids-incdir=DIR       use the copy of SQuIDS in DIR
  --with-squids-libdir=DIR       use the copy of SQuIDS in DIR
For the python bindings the following flags are used:
  --with-python-bindings         enable python binding compilation
  --with-boost-incdir=DIR        use the copy of Boost in DIR
  --with-boost-libdir=DIR        use the copy of Boost in DIR
  --with-boost=DIR               use the copy of Boost in DIR
                                 assuming headers are in DIR/include
                                 and libraries in DIR/lib
  --python-bin=PYTHON_EXECUTABLE use this python executable
                                 (default is 'python')
  --python-module-dir=DIR        install python module to this directory, rather
                                 than the default system location. The special 
                                 value site.USER_SITE will be automatically
                                 expanded using the python interpreter

Some influential environment variables:
CC          C compiler command
CXX         C++ compiler command
AR          Static linker command
LD          Dynamic linker command
" #`

for var in "$@"
do
	if [ "$var" = "--help" -o "$var" = "-h" ]; then
		echo "$HELP"
		exit 0
	fi

	TMP=`echo "$var" | sed -n 's/^--prefix=\(.*\)$/\1/p'`
	if [ "$TMP" ]; then PREFIX="$TMP"; continue; fi

	TMP=`echo "$var" | sed -n 's/^--libdir=\(.*\)$/\1/p'`
	if [ "$TMP" ]; then INSTALL_LIBDIR="$TMP"; continue; fi

	TMP=`echo "$var" | sed -n 's/^--with-gsl=\(.*\)$/\1/p'`
	if [ "$TMP" ]; then
		GSL_INCDIR="${TMP}/include";
		GSL_LIBDIR="${TMP}/lib";
	continue; fi

	TMP=`echo "$var" | sed -n 's/^--with-gsl-incdir=\(.*\)$/\1/p'`
	if [ "$TMP" ]; then GSL_INCDIR="$TMP"; continue; fi

	TMP=`echo "$var" | sed -n 's/^--with-gsl-libdir=\(.*\)$/\1/p'`
	if [ "$TMP" ]; then GSL_LIBDIR="$TMP"; continue; fi

	TMP=`echo "$var" | sed -n 's/^--with-hdf5=\(.*\)$/\1/p'`
	if [ "$TMP" ]; then
		HDF5_INCDIR="${TMP}/include";
		HDF5_LIBDIR="${TMP}/lib";
	continue; fi

	TMP=`echo "$var" | sed -n 's/^--with-hdf5-incdir=\(.*\)$/\1/p'`
	if [ "$TMP" ]; then HDF5_INCDIR="$TMP"; continue; fi

	TMP=`echo "$var" | sed -n 's/^--with-hdf5-libdir=\(.*\)$/\1/p'`
	if [ "$TMP" ]; then HDF5_LIBDIR="$TMP"; continue; fi

	TMP=`echo "$var" | sed -n 's/^--with-squids=\(.*\)$/\1/p'`
	if [ "$TMP" ]; then
		SQUIDS_INCDIR="${TMP}/include";
		SQUIDS_LIBDIR="${TMP}/lib";
	continue; fi

	TMP=`echo "$var" | sed -n 's/^--with-squids-incdir=\(.*\)$/\1/p'`
	if [ "$TMP" ]; then SQUIDS_INCDIR="$TMP"; continue; fi

	TMP=`echo "$var" | sed -n 's/^--with-squids-libdir=\(.*\)$/\1/p'`
	if [ "$TMP" ]; then SQUIDS_LIBDIR="$TMP"; continue; fi

	TMP=`echo "$var" | sed -n 's/^--with-python-bindings/true/p'`
	if [ "$TMP" ]; then PYTHON_BINDINGS=true; continue; fi

	TMP=`echo "$var" | sed -n 's/^--with-boost=\(.*\)$/\1/p'`
	if [ "$TMP" ]; then
		BOOST_INCDIR="${TMP}/include";
		BOOST_LIBDIR="${TMP}/lib";
	continue; fi

	TMP=`echo "$var" | sed -n 's/^--with-boost-libdir=\(.*\)$/\1/p'`
	if [ "$TMP" ]; then BOOST_LIBDIR="$TMP"; continue; fi
	TMP=`echo "$var" | sed -n 's/^--with-boost-incdir=\(.*\)$/\1/p'`
	if [ "$TMP" ]; then BOOST_INCDIR="$TMP"; continue; fi

	TMP=`echo "$var" | sed -n 's/^--python-bin=\(.*\)$/\1/p'`
	if [ "$TMP" ]; then PYTHON_EXE=$TMP; continue; fi
	TMP=`echo "$var" | sed -n 's/^--python-module-dir=\(.*\)$/\1/p'`
	if [ "$TMP" ]; then USER_PYTHON_MODULE_DIR="${TMP}"; continue; fi

	echo "config.sh: Unknown or malformed option '$var'" 1>&2
	exit 1
done

if [ "$GSL_INCDIR" -a "$GSL_LIBDIR" ]; then
	echo "Checking manually specified GSL..."
	if [ -d "$GSL_INCDIR/gsl" \
         -a -e "$GSL_INCDIR/gsl/gsl_version.h" \
         -a -d "$GSL_LIBDIR" \
         -a -e "$GSL_LIBDIR/libgsl.a" ]; then
		GSL_FOUND=1
		GSL_CFLAGS="-I$GSL_INCDIR"
		GSL_LDFLAGS="-L$GSL_LIBDIR -lgsl -lgslcblas -lm"
	else
		echo "Warning: manually specifed GSL not found; will attempt auto detection"
	fi
fi

find_package gsl 1.15

if [ "$HDF5_INCDIR" -a "$HDF5_LIBDIR" ]; then
	echo "Checking manually specified HDF5..."
	if [ -d "$HDF5_INCDIR" \
         -a -e "$HDF5_INCDIR/H5version.h" \
         -a -d "$HDF5_LIBDIR" \
         -a -e "$HDF5_LIBDIR/libhdf5.a" \
         -a -e "$HDF5_LIBDIR/libhdf5_hl.a" ]; then
		HDF5_FOUND=1
		HDF5_CFLAGS="-I$HDF5_INCDIR"
		HDF5_LDFLAGS="-L$HDF5_LIBDIR -lhdf5 -lhdf5_hl"
	else
		echo "Warning: manually specifed HDF5 not found; will attempt auto detection"
	fi
fi

#Do not use this due to broken Ubuntu package
#find_package hdf5 1.8
find_hdf5

if [ "$SQUIDS_INCDIR" -a "$SQUIDS_LIBDIR" ]; then
	echo "Checking manually specified SQUIDS..."
	if [ -d "$SQUIDS_INCDIR" \
         -a -d "$SQUIDS_LIBDIR" \
         -a -e "$SQUIDS_LIBDIR/libSQuIDS.a" ]; then
		SQUIDS_FOUND=1
		SQUIDS_CFLAGS="-I$SQUIDS_INCDIR"
		SQUIDS_LDFLAGS="-L$SQUIDS_LIBDIR -lSQuIDS"
		if $CXX --version | grep -q "Free Software Foundation"; then
			SQUIDS_CFLAGS="$SQUIDS_CFLAGS -Wno-abi"
		fi
	else
		echo "Warning: manually specifed SQUIDS not found; will attempt auto detection"
	fi
fi

find_package squids 1.2

if [ $PYTHON_BINDINGS ]; then
	try_find_python
	if [ "$PYTHON_FOUND" != 1 ]; then
		echo "*** Failed to find python; python bindings will not be built ***"
		unset PYTHON_BINDINGS
	else
		if [ "$USER_PYTHON_MODULE_DIR" ]; then
			if [ "$USER_PYTHON_MODULE_DIR" == "site.USER_SITE" ]; then
				PYTHON_MODULEDIR=`${PYTHON_EXE} -c 'import site; print(site.USER_SITE)'`
			else
				PYTHON_MODULEDIR="$USER_PYTHON_MODULE_DIR"
			fi
		fi
	fi

	if [ "$BOOST_INCDIR" -a "$BOOST_LIBDIR" ]; then
		echo "Checking manually specified boost..."
		try_find_boost "$BOOST_INCDIR" "$BOOST_LIBDIR"
		if [ ! "$BOOST_FOUND" ]; then
			echo "Warning: manually specifed boost not found; will attempt auto detection"
		fi
	fi
	try_find_boost /usr
	try_find_boost /usr/local
	if [ "$BOOST_PYTHON_FOUND" != 1 ]; then
		echo "*** Failed to find boost python; python bindings will not be built ***"
		unset PYTHON_BINDINGS
	fi
	find_numpy
	if [ "$NUMPY_FOUND" != 1 ]; then
		echo "*** Failed to find numpy; python bindings will not be built ***"
		unset PYTHON_BINDINGS
	fi
fi

ensure_found gsl
ensure_found hdf5
ensure_found squids

# Resolve PREFIX absolutely
OLDPWD=`pwd`
cd "$PREFIX"
PREFIX=`pwd`
cd "$OLDPWD"

SOURCE_PATH=`pwd`

if [ ! -d ./build/ ]; then
    mkdir build;
fi
if [ ! -d ./lib/ ]; then
    mkdir lib;
fi

echo "Generating config file..."

# Somewhat evil: HDF5 does not register with pkg-config, which causes the latter
# to error out because it cannot find nuSQuIDS dependencies.
# Solution: Since we found HDF5 (hopefully correctly), register it ourselves.
echo "# WARNING: This configuration file was heutristically generated by nuSQuIDS
# and may not be complete or correct
libdir=${HDF5_LIBDIR}
includedir=${HDF5_INCDIR}" > lib/hdf5.pc
echo '
Name: HDF5
Description: "A data model, library, and file format for storing and managing data."
URL: https://www.hdfgroup.org/HDF5/' >> lib/hdf5.pc
echo "Version: ${HDF5_VERSION}" >> lib/hdf5.pc
echo "Cflags: ${HDF5_CFLAGS}
Libs: ${HDF5_LDFLAGS}
" >> lib/hdf5.pc

echo "prefix=$PREFIX" > lib/nusquids.pc
echo '
libdir=${prefix}/'"$INSTALL_LIBDIR"'
includedir=${prefix}/include

Name: nuSQuIDS
Description: Toolbox for neutrino oscillation experiments
URL: https://github.com/arguelles/nuSQuIDS' >> lib/nusquids.pc
echo "Version: $VERSION" >> lib/nusquids.pc
echo 'Requires: gsl >= 1.15 hdf5 >= 1.8 squids >= 1.2.0
Libs: -L${libdir} -lnuSQuIDS
Cflags: -I${includedir}
' >> lib/nusquids.pc

echo "Generating version header..."
sed -e "s|__NUSQUIDS_VERSION__|$VERSION_NUM|g" \
    -e "s|__NUSQUIDS_VERSION_STR__|$VERSION|g" \
    < resources/version.h.in > include/nuSQuIDS/version.h

INSTALL_FLAG_PREFIX="NUSQUIDS_DATA_PATH_INSTALL_FLAG_PREFIX_"
INSTALL_FLAG_SUFFIX="_NUSQUIDS_DATA_PATH_INSTALL_FLAG_SUFFIX"
INSTALL_FLAG_OFF="A"
INSTALL_FLAG_ON="B"
REPLACE_INSTALL_FLAG="s|${INSTALL_FLAG_PREFIX}${INSTALL_FLAG_OFF}${INSTALL_FLAG_SUFFIX}|${INSTALL_FLAG_PREFIX}${INSTALL_FLAG_ON}${INSTALL_FLAG_SUFFIX}|g"

echo "Generating data path header..."
echo "#include <cstring>
#define SOURCE_DATA_PATH \"${SOURCE_PATH}/data/\"
#define INSTALL_DATA_PATH \"${PREFIX}/share/nuSQuIDS/\"

namespace{

const char dataPathBitOffValue='$INSTALL_FLAG_OFF';
//This needs to be volatile so that the compiler can't optimize away reads from it,
//which is important since we plan to change the value of the constant between compile-time 
//and run-time
const volatile char dataPathBitContainer[] = \"${INSTALL_FLAG_PREFIX}${INSTALL_FLAG_OFF}${INSTALL_FLAG_SUFFIX}\";

bool getInstallBit(){
	static const std::size_t prefixLen = strlen(\"${INSTALL_FLAG_PREFIX}\");
	return dataPathBitContainer[prefixLen]!='${INSTALL_FLAG_OFF}';
}

}

" > build/resource_paths.h

echo "Generating makefile..."
echo "# Compiler
CC=$CC
CXX=$CXX
AR=$AR
LD=$LD

DYN_SUFFIX=$DYN_SUFFIX
DYN_OPT=$DYN_OPT
DYN_OPT_PY=$DYN_OPT_PY

VERSION=$VERSION
PREFIX=$PREFIX
INSTALL_LIBDIR:=$INSTALL_LIBDIR
" > ./Makefile

echo '
PATH_nuSQUIDS=$(shell pwd)
PATH_SQUIDS=$(SQUIDS_DIR)

SOURCES = $(wildcard src/*.cpp)
OBJECTS = $(patsubst src/%.cpp,build/%.o,$(SOURCES))

EXAMPLES := examples/Single_energy/single_energy \
            examples/Multiple_energy/multiple_energy \
            examples/Atm_default/atm_default \
            examples/Bodies/bodies \
            examples/Xsections/xsections \
            examples/NSI/nsi \
            examples/LV/lv \
            examples/Atm_BSM/atm_bsm\
            examples/HDF5_Write_Read/write \
            examples/HDF5_Write_Read/read \
            examples/Constant_density_layers/const_dens_layers \
            examples/Astrophysical_neutrino_flavor_ratio/astro_flv_ratio

CXXFLAGS= -std=c++11

# Directories
'  >> ./Makefile
echo "GSL_CFLAGS=$GSL_CFLAGS" >> ./Makefile
echo "GSL_LDFLAGS=$GSL_LDFLAGS" >> ./Makefile

echo "HDF5_CFLAGS=$HDF5_CFLAGS" >> ./Makefile
echo "HDF5_LDFLAGS=$HDF5_LDFLAGS" >> ./Makefile

echo "SQUIDS_CFLAGS=$SQUIDS_CFLAGS" >> ./Makefile
echo "SQUIDS_LDFLAGS=$SQUIDS_LDFLAGS" >> ./Makefile

if [ "$PYTHON_BINDINGS" ]; then
	echo "PYTHON_CFLAGS=$PYTHON_CFLAGS" >> ./Makefile
	echo "PYTHON_LDFLAGS=$PYTHON_LDFLAGS" >> ./Makefile
	echo "BOOST_PYTHON_LDFLAGS=$BOOST_PYTHON_LDFLAGS" >> ./Makefile
	echo "PYTHON_MODULEDIR=$PYTHON_MODULEDIR" >> ./Makefile
	echo "NUMPY_CFLAGS=$NUMPY_CFLAGS" >> ./Makefile
fi

echo '

INCnuSQUIDS=$(PATH_nuSQUIDS)/include
LIBnuSQUIDS=$(PATH_nuSQUIDS)/lib

# FLAGS
CFLAGS= -O3 -fPIC -Ibuild -I$(INCnuSQUIDS) $(SQUIDS_CFLAGS) $(GSL_CFLAGS) $(HDF5_CFLAGS)
LDFLAGS= -Wl,-rpath -Wl,$(LIBnuSQUIDS) -L$(LIBnuSQUIDS)
LDFLAGS+= $(SQUIDS_LDFLAGS) $(GSL_LDFLAGS) $(HDF5_LDFLAGS) -lpthread
EXAMPLES_FLAGS=-I$(INCnuSQUIDS) $(CXXFLAGS) $(CFLAGS)

# Project files
NAME=nuSQuIDS
STAT_PRODUCT=lib/lib$(NAME).a
DYN_PRODUCT=lib/lib$(NAME)$(DYN_SUFFIX)
PYTHON_LIB:=lib/$(NAME).so

# Compilation rules
all: $(STAT_PRODUCT) $(DYN_PRODUCT)

examples : $(EXAMPLES)

$(DYN_PRODUCT) : $(OBJECTS)
	@echo Linking $(DYN_PRODUCT)
	@$(CXX) $(DYN_OPT) $(OBJECTS) $(LDFLAGS) -o $(DYN_PRODUCT)

$(STAT_PRODUCT) : $(OBJECTS)
	@echo Linking $(STAT_PRODUCT)
	@$(AR) -rcs $(STAT_PRODUCT) $(OBJECTS)

build/%.o : src/%.cpp
	@echo Compiling $< to $@
	@$(CXX) $(CXXFLAGS) -c $(CFLAGS) $< -o $@

examples/Single_energy/single_energy : $(DYN_PRODUCT) examples/Single_energy/main.cpp
	@echo Compiling single energy example
	@$(CXX) $(EXAMPLES_FLAGS) examples/Single_energy/main.cpp -lnuSQuIDS $(LDFLAGS) -o $@

examples/Astrophysical_neutrino_flavor_ratio/astro_flv_ratio : $(DYN_PRODUCT) examples/Astrophysical_neutrino_flavor_ratio/main.cpp
	@echo Compiling astrophysical neutrino flavor ratio example
	@$(CXX) $(EXAMPLES_FLAGS) examples/Astrophysical_neutrino_flavor_ratio/main.cpp -lnuSQuIDS $(LDFLAGS) -o $@

examples/Multiple_energy/multiple_energy : $(DYN_PRODUCT) examples/Multiple_energy/main.cpp
	@echo Compiling multiple energy example
	@$(CXX) $(EXAMPLES_FLAGS) examples/Multiple_energy/main.cpp -lnuSQuIDS $(LDFLAGS) -o $@

examples/HDF5_Write_Read/write : $(DYN_PRODUCT) examples/HDF5_Write_Read/write.cpp
	@echo Compiling HDF5 write
	@$(CXX) $(EXAMPLES_FLAGS) examples/HDF5_Write_Read/write.cpp -lnuSQuIDS $(LDFLAGS) -o $@

examples/HDF5_Write_Read/read : $(DYN_PRODUCT) examples/HDF5_Write_Read/read.cpp
	@echo Compiling HDF5 read
	@$(CXX) $(EXAMPLES_FLAGS) examples/HDF5_Write_Read/read.cpp -lnuSQuIDS $(LDFLAGS) -o $@

examples/Atm_default/atm_default : $(DYN_PRODUCT) examples/Atm_default/main.cpp
	@echo Compiling atmospheric example
	@$(CXX) $(EXAMPLES_FLAGS) examples/Atm_default/main.cpp -lnuSQuIDS $(LDFLAGS) -o $@

build/exBody.o : examples/Bodies/exBody.h examples/Bodies/exBody.cpp
	@$(CXX) $(EXAMPLES_FLAGS) -c examples/Bodies/exBody.cpp -o $@

build/ex_bodies_main.o : examples/Bodies/exBody.h examples/Bodies/main.cpp
	@$(CXX) $(EXAMPLES_FLAGS) -c examples/Bodies/main.cpp -o $@

examples/Bodies/bodies : $(DYN_PRODUCT) build/ex_bodies_main.o build/exBody.o
	@echo Compiling bodies example
	@$(CXX) $(EXAMPLES_FLAGS) build/ex_bodies_main.o build/exBody.o -lnuSQuIDS $(LDFLAGS) -o $@

build/exCross.o : examples/Xsections/exCross.h examples/Xsections/exCross.cpp
	@$(CXX) $(EXAMPLES_FLAGS) -c examples/Xsections/exCross.cpp -o $@

examples/Xsections/xsections : $(DYN_PRODUCT) examples/Xsections/main.cpp build/exCross.o
	@echo Compiling cross section example
	@$(CXX) $(EXAMPLES_FLAGS) examples/Xsections/main.cpp build/exCross.o -lnuSQuIDS $(LDFLAGS) -o $@

examples/NSI/nsi : $(DYN_PRODUCT) examples/NSI/main.cpp
	@echo Compiling non-standard interaction example
	@$(CXX) $(EXAMPLES_FLAGS) examples/NSI/main.cpp -lnuSQuIDS $(LDFLAGS) -o $@

examples/LV/lv : $(DYN_PRODUCT) examples/LV/main.cpp
	@echo Compiling Lorentz Violation example
	@$(CXX) $(EXAMPLES_FLAGS) examples/LV/main.cpp -lnuSQuIDS $(LDFLAGS) -o $@

examples/Atm_BSM/atm_bsm: $(DYN_PRODUCT) examples/Atm_BSM/main.cpp
	@echo Compiling atmospheric with beyond standard model physics example
	@$(CXX) $(EXAMPLES_FLAGS) examples/Atm_BSM/main.cpp -lnuSQuIDS $(LDFLAGS) -o $@

examples/Constant_density_layers/const_dens_layers : $(DYN_PRODUCT) examples/Constant_density_layers/main.cpp
	@echo Compiling constant density layer example
	@$(CXX) $(EXAMPLES_FLAGS) examples/Constant_density_layers/main.cpp -lnuSQuIDS $(LDFLAGS) -o $@

.PHONY: install uninstall clean test docs
clean:
	@echo Erasing generated files
	@rm -f $(PATH_nuSQUIDS)/build/*.o
	@rm -f $(PATH_nuSQUIDS)/$(STAT_PRODUCT) $(PATH_nuSQUIDS)/$(DYN_PRODUCT) $(PATH_nuSQUIDS)/$(PYTHON_LIB)

doxygen:
	@mkdir -p ./docs
	@doxygen src/doxyfile
docs:
	@mkdir -p ./docs
	@doxygen src/doxyfile

test: $(DYN_PRODUCT) $(STAT_PRODUCT)
	@cd ./test ; ./run_tests

install: $(DYN_PRODUCT) $(STAT_PRODUCT)
	@echo Installing headers in $(PREFIX)/include/nuSQuIDS
	@mkdir -p "$(PREFIX)/include/nuSQuIDS"
	@cp "$(INCnuSQUIDS)"/nuSQuIDS/*.h "$(PREFIX)/include/nuSQuIDS"
	@echo Installing libraries in $(PREFIX)/$(INSTALL_LIBDIR)
	@mkdir -p "$(PREFIX)/$(INSTALL_LIBDIR)"
	@LANG=C sed "'${REPLACE_INSTALL_FLAG}'" < $(DYN_PRODUCT) > "$(PREFIX)/$(INSTALL_LIBDIR)/lib$(NAME)$(DYN_SUFFIX)"
	@LANG=C sed "'${REPLACE_INSTALL_FLAG}'" < $(STAT_PRODUCT) > "$(PREFIX)/$(INSTALL_LIBDIR)/lib$(NAME).a"
	@chmod 755 "$(PREFIX)/$(INSTALL_LIBDIR)/lib$(NAME)$(DYN_SUFFIX)" "$(PREFIX)/$(INSTALL_LIBDIR)/lib$(NAME).a" 
	@echo Installing config information in $(PREFIX)/$(INSTALL_LIBDIR)/pkgconfig
	@mkdir -p "$(PREFIX)/$(INSTALL_LIBDIR)/pkgconfig"
	@cp lib/nusquids.pc "$(PREFIX)/$(INSTALL_LIBDIR)/pkgconfig"
	@echo Installing physics data in $(PREFIX)/share/nuSQuIDS
	@mkdir -p "$(PREFIX)/share/nuSQuIDS"
	@cp -r data/* "$(PREFIX)/share/nuSQuIDS/"
' >> ./Makefile

if `pkg-config hdf5`; then
:
else
	echo '	@cp lib/hdf5.pc "$(PREFIX)/$(INSTALL_LIBDIR)/pkgconfig"' >> ./Makefile
fi
echo '
uninstall:
	@echo Removing headers from $(PREFIX)/include/nuSQuIDS
	@rm -rf "$(PREFIX)/include/nuSQuIDS"
	@echo Removing libraries from $(PREFIX)/$(INSTALL_LIBDIR)
	@rm -f "$(PREFIX)/$(INSTALL_LIBDIR)/$(DYN_PRODUCT)"
	@rm -f "$(PREFIX)/$(INSTALL_LIBDIR)/$(STAT_PRODUCT)"
	@echo Removing config information from $(PREFIX)/$(INSTALL_LIBDIR)/pkgconfig
	@rm -f "$(PREFIX)/$(INSTALL_LIBDIR)/pkgconfig/nusquids.pc"
' >> ./Makefile

if [ "$PYTHON_BINDINGS" ]; then
	echo '

python : $(PYTHON_LIB)

$(PYTHON_LIB) : build/nuSQUIDSpy.o $(STAT_PRODUCT)
	@echo Linking python bindings
	@$(CXX) $(DYN_OPT_PY) build/nuSQUIDSpy.o -Llib -l$(NAME) $(LDFLAGS) $(BOOST_PYTHON_LDFLAGS) $(PYTHON_LDFLAGS) -o $(PYTHON_LIB)

build/nuSQUIDSpy.o : resources/python/src/nuSQUIDSpy.cpp
	@echo Compiling python bindings
	@$(CXX) $(CXXFLAGS) -c -Iresources/python/inc $(PYTHON_CFLAGS) $(NUMPY_CFLAGS) $(CFLAGS) $< -o $@

python-install : $(PYTHON_LIB)
	@echo Installing python module in $(PYTHON_MODULEDIR)
	@mkdir -p $(PYTHON_MODULEDIR)
	@cp $(PYTHON_LIB) $(PYTHON_MODULEDIR)

python-uninstall : $(PYTHON_LIB)
	@echo Removing python module from $(PYTHON_MODULEDIR)
	@rm $(PYTHON_MODULEDIR)/$(NAME).so

' >> ./Makefile
fi

echo "
export CXX=\"${CXX}\"
export CFLAGS=\"${CFLAGS} ${SQUIDS_CFLAGS} ${GSL_CFLAGS} ${HDF5_CFLAGS}\"
export CXXFLAGS=\"${CXXFLAGS} -std=c++11\"
export LDFLAGS=\"${LDFLAGS}  -lnuSQuIDS -lpthread ${SQUIDS_LDFLAGS} ${GSL_LDFLAGS} ${HDF5_LDFLAGS}\"
" > test/env_vars.sh
if uname | grep -q 'Darwin' ; then
	printf "export DYLD_LIBRARY_PATH=\"" >> test/env_vars.sh
	printf "${SOURCE_PATH}/lib:${SQUIDS_LIBDIR}:${GSL_LIBDIR}:${HDF5_LIBDIR}" >> test/env_vars.sh
	if [ "$DYLD_LIBRARY_PATH" ]; then
		printf ":${DYLD_LIBRARY_PATH}" >> test/env_vars.sh
	fi
else
	printf "export LD_LIBRARY_PATH=\"" >> test/env_vars.sh
	printf "${SOURCE_PATH}/lib:${SQUIDS_LIBDIR}:${GSL_LIBDIR}:${HDF5_LIBDIR}" >> test/env_vars.sh
	if [ "$LD_LIBRARY_PATH" ]; then
		printf ":${LD_LIBRARY_PATH}" >> test/env_vars.sh
	fi
fi
echo '"' >> test/env_vars.sh

echo "Done."
echo
echo "To build the library, run the following: make
After, to build examples: make examples"
if [ "$PYTHON_BINDINGS" ]; then
	echo "To build the python bindings run: make python"
	echo "To install the python bindings run: make python-install"
fi