makeall.sh

# To set 

path_spock=$HOME # don't include the last '/' in the path

is_sift=0 # set this variable to 1 if you want to use SpOCK as part of
	  # SIFT. But if you want to use SpOCK independtly of SIFT,
	  # set it to 0

py_only=0 # if set to 1 and is_sift is 1 then doesnt compile SpOCK but
	  # just move the python scripts to ../ so that the demo can
	  # be run before installing SpOCK. cbv should st py_only to 1
	  # before distributing SIFT so that users alreay ahve all
	  # these python scripts in ../ and can run the demo without
	  # running this makeall.sh end of to set

arg_compiler=mpicc # $1
if [ "$arg_compiler" = "gcc" ]; then
    compiler="gcc"
    path_compiler=gcc
else
    compiler="mpicc"
    path_compiler=mpicc #/opt/local/bin/mpicc-openmpi-gcc7  #$2 don't include the last '/' in the path
fi 


if [ $is_sift -eq 1 ];then

    path_spice=./cspice # when distributing: ./cspice
    path_gsl=./gsl_installation # when distributing: ./gsl_installation

else

    #$3 don't include the last '/' in the
    path_spice=/Users/ridley/Software/Spice/cspice

    #path $4 you can put ./ for current directory but don't put ../
    #for one level up. in this case, put absolute path. also, don't
    #include the last '/' in the path
    # This is an installation with port on mac:
    path_gsl=/opt/local
    
fi

# to run SpOCK from python script with os.system(path_mpirun + " -np 4
# spock in.txt") -> looks like if cygwin then the system won't
# recognize mpirun so need to run orterun. But if linux.unix/other
# than cygwin, won't regcognize orterun so need to put mpirun

if [ $OSTYPE = "cygwin" ]; then
    path_mpirun="orterun"
else
    path_mpirun="mpirun"
fi

# if path to exectuable spock is not already in PATH then add
# it. Note: the user still needs to source the .bash_profile after
# running this makeall.sh file (not poassible to source it within this
# makeall.sh).
## create the varilable absolute path to executable spock
if [[ "${path_spock:0:1}" == "." ]]; then
    # if path_spock includes the current directory "." as first char
    # then repalce "." with absolute path of current directory to
    # create the absolute path to executable spock
    path_spock_after_pwd=$(cut -d "." -f 2 <<< "$path_spock") 
    path_spock_abso=$PWD$path_spock_after_pwd
elif [[ "${path_spock:0:1}" == "~" ]]; then
    # if path_spock includes the current directory "~" as first char
    # then repalce "~" with absolute path of home directory to create
    # the absolute path to executable spock
    path_spock_after_pwd=$(cut -d "." -f 0 <<< "$path_spock")
    # ignore warning with cut that is likely to be printed when
    # running this line
    path_spock_abso=$HOME$path_spock_after_pwd
else # otherwise that means that path_spock is already an absolute path
    path_spock_abso=$path_spock
fi
## now add path in .bash_profile if not already in PATH
if [[ ":$PATH:" == *"$path_spock_abso:"* ]]; then
    echo "already have path to SpOCK"
else
    echo "creating path to SpOCK"
    echo "" >> $HOME/.bash_profile
    echo "PATH=\$PATH:$path_spock_abso" >> $HOME/.bash_profile
fi

# add path to gsl lib and bin (suppsoed to prevent errors like "error
# while loading shared libraries"). Note: the user still needs to
# source the .bash_profile after running this makeall.sh file (not
# poassible to source it within this makeall.sh). !!! ALSO here for
# now only add ath to bin but mayeb need to add path to lib
## create the varilable absolute path to gsl
if [[ "${path_gsl:0:1}" == "." ]]; then
    # if path_gsl includes the current directory "." as first char
    # then repalce "." with absolute path of current directory to
    # create the absolute path to gsl
    path_gsl_after_pwd=$(cut -d "." -f 2 <<< "$path_gsl")
    path_gsl_abso=$PWD$path_gsl_after_pwd
else # otherwise that means that path_gsl is already an absolute path
    path_gsl_abso=$path_gsl
fi
## now add path in .bash_profile if not already in PATH
if [[ ":$PATH:" == *"$path_gsl_abso/bin:"* ]]; then
    echo "already have path to gsl lib and bin"
else
    echo "creating path to gsl lib and bin"
    echo "" >> $HOME/.bash_profile
    echo "PATH=\$PATH:$path_gsl_abso/bin" >> $HOME/.bash_profile
fi
# end end of add path to gsl lib and bin



## create the varilable absolute path to executable spice
if [[ "${path_spice:0:1}" == "." ]]; then
    # if path_spice includes the current directory "." as first char
    # then repalce "." with absolute path of current directory to
    # create the absolute path to executable spice
    path_spice_after_pwd=$(cut -d "." -f 2 <<< "$path_spice") 
    path_spice_abso=$PWD$path_spice_after_pwd
elif [[ "${path_spice:0:1}" == "~" ]]; then
    # if path_spice includes the current directory "~" as first char
    # then repalce "~" with absolute path of home directory to create
    # the absolute path to executable spice
    path_spice_after_pwd=$(cut -d "." -f 0 <<< "$path_spice")
    # ignore warning with cut that is likely to be printed when
    # running this line
    path_spice_abso=$HOME$path_spice_after_pwd
else # otherwise that means that path_spice is already an absolute path
    path_spice_abso=$path_spice   
fi
if [ $py_only -ne 1 ];then
    # cp SPICE files to SPICE directory if this has not already been
    # done. Same for gravitational spherical harmonincs and specular
    # points
    if [ ! -f "$path_spice_abso"/data/naif0012.tls ]; then
	cp ./inputs/naif0012.tls "$path_spice_abso"/data
	cp ./inputs/de432s.bsp "$path_spice_abso"/data
	cp ./inputs/earth_000101_210404_210111.bpc "$path_spice_abso"/data
	cp  ./inputs/pck00010.tpc "$path_spice_abso"/data
	cp ./inputs/egm96_to360_not_norm.txt "$path_spice_abso"/data
	cp ./inputs/{antenna.bin,antenna.info,sigma0_table.bin} "$path_spice_abso"/data
    fi
    if [ $is_sift -eq 1 ];then
	# if compiling SpOCK to use it as part of SIFT then copy files
	# for SIFT
	cp ./inputs/{cygnss_geometry_2016.txt,my_ground_stations.txt} ../../input_sift/
    fi

    # Compile SpOCK (and specular point codes)
    if [ $compiler = "gcc" ]; then
	# SpOCK
	make clean PATH_EXECUTABLE="$path_spock_abso"
	make all COMPILER=gcc PATH_COMPILER=$path_compiler PATH_SPICE="$path_spice_abso" PATH_GSL="$path_gsl_abso" PATH_EXECUTABLE="$path_spock_abso"
	# # Specular points binary files
	# $path_compiler -c -o ./src/mpi_fake/mpi.o ./src/mpi_fake/mpi.c 
	# ar r ./src/mpi_fake/libmpi.a ./src/mpi_fake/mpi.o 
	# ranlib ./src/mpi_fake/libmpi.a 
	# $path_compiler -c -o ./src/find_specular_points.o ./src/find_specular_points.c
	# $path_compiler -o "$path_spock_abso"/spec ./src/find_specular_points.o -L./src/mpi_fake -lmpi -lm  # change the path of the executable here
	# # Convert specular points binary files to txt files
	cd ./src/storm
	# make clean PATH_EXECUTABLE="$path_spock_abso"
	# make all COMPILER=gcc PATH_COMPILER=$path_compiler PATH_SPICE="$path_spice_abso" PATH_GSL="$path_gsl_abso" PATH_EXECUTABLE="$path_spock_abso"
	
    else
	# SpOCK
	make clean PATH_EXECUTABLE="$path_spock_abso"
	make all PATH_COMPILER=$path_compiler PATH_SPICE="$path_spice_abso" PATH_GSL="$path_gsl_abso" PATH_EXECUTABLE="$path_spock_abso"
	#echo sudo /usr/libexec/ApplicationFirewall/socketfilterfw -add "$path_spock_abso"/spock_dev
	#sudo /usr/libexec/ApplicationFirewall/socketfilterfw -add "$path_spock_abso"/spock_dev
	# # Specular points binary files
	#echo $path_compiler -o "$path_spock_abso"/spec ./src/find_specular_points_aspherical_dev.c -lm -w -I"$path_spice_abso" -I"$path_spice_abso"/include "$path_spice_abso"/lib/csupport.a "$path_spice_abso"/lib/cspice.a # change the path of the executable here
	echo $path_compiler -o "$path_spock_abso"/spec_gnss_rcg ./src/find_specular_points_aspherical_dev_gnss.c -lm -w -I"$path_spice_abso"/include "$path_spice_abso"/lib/csupport.a "$path_spice_abso"/lib/cspice.a # change the path of the executable here	# added on 2020-05-19
# 	sudo /usr/libexec/ApplicationFirewall/socketfilterfw -add "$path_spock_abso"/spec_gnss
# 	# Convert specular points binary files to txt files
	#cd ./src/storm
	#echo make all PATH_COMPILER=$path_compiler PATH_SPICE="$path_spice_abso" PATH_GSL="$path_gsl_abso" PATH_EXECUTABLE="$path_spock_abso"
	#make clean PATH_EXECUTABLE="$path_spock_abso"
	#make all PATH_COMPILER=$path_compiler PATH_SPICE="$path_spice_abso" PATH_GSL="$path_gsl_abso" PATH_EXECUTABLE="$path_spock_abso"
    fi
    #cd ../..

fi

exit

# Move python scripts to executable folders
if [ $is_sift -eq 1 ];then # if compiling SpOCK to run it within SIFT
    cp ./srcPython/{spock_cygnss_spec_parallel_for_sift.py,spock_main_input.py,cygnss_tle_for_sift.py,gps_tle_for_sift.py,report_coverage_ground_station_for_sift_parallel.py,nb_usable_proc.py,read_input_file.py,find_in_read_input_order_variables.py} ../ # moves these python scripts from srcPython (part of SpOCK) to the folder with the SIFT python scripts (the only diffence in spock_cygnss_spec_parallel_for_sift.py and spock_cygnss_spec_parallel.py is that spock_cygnss_spec_parallel_for_sift.py calls cygnss_tle.py snd gps_tle.py as python scripts not as executables
    i="spock_cygnss_spec_parallel_for_sift.py"
    echo "# PARAMETERS TO SET BEFORE RUNNING THIS SCRIPT">>  ../"$i"_python_path
    echo "path_mpirun = '$path_mpirun'">> ../"$i"_python_path
    echo "spice_path = '$path_spice_abso/data'">> ../"$i"_python_path
    echo "# end of PARAMETERS TO SET BEFORE RUNNING THIS SCRIPT">> ../"$i"_python_path
    cat ../"$i" >> ../"$i"_python_path
    mv ../"$i"_python_path ../"$i"
    #chmod +x /"$i"

else # if compiling SpOCK indepently of SIFT
    declare -a py_script=("spock_cygnss_spec_parallel.py" "spock_cygnss_spec_parallel_for_sift_sftp.py"
                "cygnss_tle.py" "gps_tle.py" "report_coverage_ground_station_for_sift_parallel_sftp.py"
                "spock_main_input.py" "read_input_file.py"
		"norad_id_to_cygnss_name.py" "cygnss_read_spock_spec.py" "cygnss_read_spock_spec_no_prn.py" "cygnss_read_spock_spec_bin.py"
		"read_output_file.py" 
		 "report_coverage_ground_station.py"
		"spock_animation.py" "download_tle.py" "spock_run_tle.py"
		"kalman_9state.py" "noise.py" "noise_drag.py" "nb_usable_proc.py"
		)

    ## now loop through the above array
    if [ ! -d "$path_spock_abso" ]; then
	mkdir "$path_spock_abso"
    fi


    PYTHONPATH='#!/Users/cbv/Library/Enthought/Canopy_64bit/User/bin/python'
    #'#!'"$(which python)" # Python path
    for i in "${py_script[@]}"
    do
	cp -p ./srcPython/"$i" "$path_spock_abso"/"$i"
	# need to add this line at top of each python executable (path of Python)
	echo "${PYTHONPATH}" > "$path_spock_abso"/"$i"_python_path
	if [ $i = "spock_cygnss_spec_parallel.py" ]; then # for certain Python scripts, need to tell the path to the program that runs the executables (mpirun for instance)
	    echo "# PARAMETERS TO SET BEFORE RUNNING THIS SCRIPT">> "$path_spock_abso"/"$i"_python_path
	    echo "path_mpirun = '$path_mpirun'">> "$path_spock_abso"/"$i"_python_path
	    echo "spice_path = '$path_spice_abso/data'">> "$path_spock_abso"/"$i"_python_path
	    echo "# end of PARAMETERS TO SET BEFORE RUNNING THIS SCRIPT">> "$path_spock_abso"/"$i"_python_path
	fi
	if [ $i = "spock_cygnss_spec_parallel_for_sift_sftp.py" ]; then # for certain Python scripts, need to tell the path to the program that runs the executables (mpirun for instance)
	    echo "# PARAMETERS TO SET BEFORE RUNNING THIS SCRIPT">> "$path_spock_abso"/"$i"_python_path
	    echo "path_mpirun = '$path_mpirun'">> "$path_spock_abso"/"$i"_python_path
	    echo "spice_path = '$path_spice_abso/data'">> "$path_spock_abso"/"$i"_python_path
	    echo "# end of PARAMETERS TO SET BEFORE RUNNING THIS SCRIPT">> "$path_spock_abso"/"$i"_python_path
	fi
	if [ $i = "spock_run_tle.py" ]; then # for certain Python scripts, need to tell the path to the program that runs the executables (mpirun for instance)
	    echo "# PARAMETERS TO SET BEFORE RUNNING THIS SCRIPT">> "$path_spock_abso"/"$i"_python_path
	    echo "path_mpirun = '$path_mpirun'">> "$path_spock_abso"/"$i"_python_path
	    echo "spice_path = '$path_spice_abso/data'">> "$path_spock_abso"/"$i"_python_path
	    echo "# end of PARAMETERS TO SET BEFORE RUNNING THIS SCRIPT">> "$path_spock_abso"/"$i"_python_path
	fi
	
	cat "$path_spock_abso"/"$i" >> "$path_spock_abso"/"$i"_python_path
	mv "$path_spock_abso"/"$i"_python_path "$path_spock_abso"/"$i"
	chmod +x "$path_spock_abso"/"$i"
    done

    #path_mpirun = 'mpirun-openmpi-gcc49'
fi