Resolve install.sh confict with previous commit

src/install.sh

@@ -60,12 +60,7 @@ error_exit () {
 	printf "      for more informations.\n"
 	printf "      Below is an excerpt of the last 10 lines:\n"
 	printf "\n"
-<<<<<<< HEAD
 	tail "${LOGFILE}"
-=======
-#	tail -v -n 10 "${LOGFILE}"
-	tail -n 10 "${LOGFILE}"
->>>>>>> 1e676167338c9fe5ee07a649dea05da2a18eebbd
 
 	# uninstall if needed
 	pip uninstall -y msspec
@@ -73,23 +68,6 @@ error_exit () {
 	cleanup && exit 1
 }
 
-<<<<<<< HEAD
-=======
-
-
-get_os () {
-	for os in "ubuntu" "mageia" "archlinux"; do
-		cat /etc/*release /etc/*version /etc/*issue 2>/dev/null | grep -i "$os" 2>/dev/null 1>/dev/null
-		if test $? -eq 0; then
-			LINUX_OS="$os"
-			break
-		fi
-	done
-
-}
-
-
->>>>>>> 1e676167338c9fe5ee07a649dea05da2a18eebbd
 read_yes_no () {
     DEFAULT="$2"
     PROMPT="$1 (y/n) [${DEFAULT}]? "
@@ -99,15 +77,9 @@ read_yes_no () {
 
     VALID=1
     while test $VALID -ne 0; do
-<<<<<<< HEAD
 		printf "%s" "${PROMPT}"
         if [ x"$BYPASS" = xn ]; then 
 			read -r "INPUT"
-=======
-		printf "${PROMPT}"
-        if [ x"$BYPASS" = "xn" ]; then
-			read "RESPONSE"
->>>>>>> 1e676167338c9fe5ee07a649dea05da2a18eebbd
 		else
 			printf "\n"
 		fi
@@ -121,66 +93,13 @@ read_yes_no () {
 	log_message "ANSWER  : $ANSWER"
 }
 
-<<<<<<< HEAD
-=======
-
-read_folder () {
-    DEFAULT="$2"
-    PROMPT="$1 [${DEFAULT}]: "
-
-	ANSWER=""
-	unset FOLDER
-	printf "${PROMPT}"
-	if [ x"$BYPASS" = "xn" ]; then
-		read "ANSWER"
-	else
-		printf "\n"
-	fi
-	export FOLDER="${ANSWER:-$DEFAULT}"
-	log_message "QUESTION: $PROMPT"
-	log_message "ANSWER  : $FOLDER"
-}
-
-
-
-create_folder () {
-    FOLDER="$1"
-
-    ERR_MKDIR=1
-    ERR_ABORT=2
-    ERR_PERMS=3
-
-    if ! test -d "${FOLDER}" ; then
-        read_yes_no "The folder \"${FOLDER}\" does not exist. Should I create it" "y" #"$BYPASS"
-
-        case "${ANSWER}" in
-            y) mkdir -p "${FOLDER}" 2>>${LOGFILE} 1>>${LOGFILE} || return $ERR_MKDIR;;
-            n) log_message2 "Installation aborted by the user"  && return $ERR_ABORT ;;
-        esac
-    fi
-
-    if ! test -w "${FOLDER}" ; then
-        log_message2 "You do not have permission to write into \"${FOLDER}\"."
-        return $ERR_PERMS
-    fi
-}
-
-
->>>>>>> 1e676167338c9fe5ee07a649dea05da2a18eebbd
 wrap () {
 	log_message "================================================================================"
 	log_message "$2"
 	log_message "================================================================================"
-<<<<<<< HEAD
 	if [ "$DEBUG" = y ]; then
 		printf "%s...\n" "$2"
 		(eval "$1" || echo $? >"${GETOUTFILE}") | tee -a "${LOGFILE}"
-=======
-	if [ "$DEBUG" = "y" ]; then
-		eval "($1) 2>&1" | tee -a ${LOGFILE}
-		echo ${PIPESTATUS[0]} >${GETOUTFILE}
-
->>>>>>> 1e676167338c9fe5ee07a649dea05da2a18eebbd
 		rc=$(cat $GETOUTFILE)
 		if [ $rc != 0 ]; then
 			error_exit
@@ -191,26 +110,6 @@ wrap () {
 	fi
 }
 
-<<<<<<< HEAD
-=======
-update_path () {
-	# check if the shell path contains $BIN_FOLDER
-	SHELLRC="$HOME/.$(basename $SHELL)rc"
-	${ECHO} "$PATH" | grep "${BIN_FOLDER}" 2>/dev/null 1>/dev/null
-	if test $? -ne 0; then
-		${ECHO} "" >> $SHELLRC
-		${ECHO} "# Add the user's local binary folder" >> $SHELLRC
-		${ECHO} "export PATH=${BIN_FOLDER}:\$PATH" >> $SHELLRC
-		${ECHO} "Your PATH variable has been updated, the folder"
-		${ECHO} "${BIN_FOLDER} has been added to it."
-		${ECHO} ""
-		${ECHO} "Please source again your shell configuration file by typing:"
-		${ECHO} "source $SHELLRC"
-	fi
-}
-
-
->>>>>>> 1e676167338c9fe5ee07a649dea05da2a18eebbd
 success_message () {
 	log_message "========================================================"
 	log_message "MsSpec was successfully installed."
@@ -240,7 +139,7 @@ patience () {
     printf "\b\b Done.\n"
 }
 
-show_help () {
+show_help () {        
     echo "Usage: $SCRIPT_NAME [OPTIONS]"
     echo "List of possible options:"
     echo "    -y          Accept all default choices."
@@ -260,8 +159,7 @@ check_dependencies () {
     gcc_ver_min=7
 	log_message "Checking if gfortran >= $gcc_ver_min is installed..."
 	command -V gfortran || return 1
-#	gcc_ver=$(gcc -dumpversion)
+	gcc_ver=$(gcc -dumpversion)
-	gcc_ver=$(echo $(gcc -dumpversion)| cut -d. -f1)
 	echo "You have gfortran version $gcc_ver installed"
     test "$gcc_ver" -ge "$gcc_ver_min" || return 1
 	log_message "Ok\n"
@@ -285,17 +183,10 @@ check_dependencies () {
 	log_message "Ok\n"
 
 	# we need virtualenv
-<<<<<<< HEAD
 	#log_message "Checking if virtualenv is installed..."
 	#command -V virtualenv || return 1
 	#log_message "Ok\n"
 	
-=======
-	log_message "Checking if virtualenv is installed..."
-	#command -V virtualenv || return 1
-	log_message "Ok\n"
-
->>>>>>> 1e676167338c9fe5ee07a649dea05da2a18eebbd
 }
 
 local_install () {
@@ -305,7 +196,6 @@ local_install () {
 	# check dependencies
 	wrap "check_dependencies" "Checking dependencies"
 
-<<<<<<< HEAD
 	# build the Fortran code
 	wrap "make pybinding VERBOSE=1" "Building Phagen and Spec Python dynamic library"
 
@@ -315,82 +205,6 @@ local_install () {
 	# install the package
 	wrap "make install VERBOSE=1" "Installing the msspec package"
 
-=======
-	# ask for a place to put the binary
-	#read_folder "Please, type in the folder where to place the binary" "${DEFAULT_BIN}"
-	#BIN_FOLDER=${FOLDER}
-	#create_folder "${BIN_FOLDER}" || error_exit
-	#export BIN_FOLDER
-
-	# If in a virtualenv, ask if we should install inside
-	if [ x"$VIRTUAL_ENV" != x ]; then
-		read_yes_no "You are running a Python virtual environment. Do you wish to install msspec inside ?" "y"
-		case ${ANSWER} in
-			y)	# get the python version of this venv...
-				v=$(python -V 2>&1 | cut -d" " -f2 | cut -d. -f1)
-				# and stops if < 3
-				if [ $v -lt 3 ]; then
-					log_message "The Python version of this venv is < 3"
-					error_exit
-				fi
-				;;
-		   	n)	# The user decided to stop there
-				log_message "Please deactivate your virtual environment and restart the setup program."
-				error_exit
-				;;
-		esac
-	# Else, we are not in a virtualenv
-	else
-		pip_opt=""
-		# so ask if we should create one
-		read_yes_no "Do you wish to create a virtual environment to install MsSpec inside" "y"
-		case ${ANSWER} in
-			y) 	# Create the destination folder
-				read_folder "Please, type in the base installation folder" "${DEFAULT_DEST}"
-				DEST_FOLDER=${FOLDER}/MsSpec-${VERSION}
-				if [ -d $DEST_FOLDER ]; then
-					export DEST_ALREADY_EXISTS="y" # to avoid cleaning the existing DEST_FOLDER in case of any problem
-					read_yes_no "The folder $DEST_FOLDER already exists. Overwrite" "y"
-					case ${ANSWER} in
-						y) 	# overwrite
-							create_folder "${DEST_FOLDER}" || error_exit
-							;;
-						n)	# stop here otherwise
-							error_exit
-							;;
-					esac
-				fi
-				export DEST_FOLDER
-				wrap "virtualenv -vvv --python=${PYTHON} --system-site-packages --prompt=\"(msspec-${VERSION}) \" ${DEST_FOLDER}/venv" \
-					"Create a Python virtual environment"
-				. ${DEST_FOLDER}/venv/bin/activate
-				;;
-			n) 	# install in the user $HOME
-				pip_opt="--user"
-				;;
-		esac
-	fi
-
-	# build and run setuptools to create a source distribution
-	wrap "make sdist" \
-	     "Building MsSpec python package"
-
-	# install the package with pip
-	wrap "pip install $pip_opt dist/msspec-*.tar.gz" \
-	     "Installing pymsspec python package and its dependencies"
-
-#
-## move the frontend to the binary folder
-##wrap "mkdir -p ${LOCALBIN} && \
-##      cp ./msspec ${LOCALBIN} && chmod u+x ${LOCALBIN}/msspec && \
-##	  ${ECHO} \"msspec installed in ${LOCALBIN}\"" \
-##	 "Installing the msspec frontend"
-# "cp ./msspec ${BIN_FOLDER} && chmod ugo+rx ${BIN_FOLDER}/msspec" "Installing the msspec frontend"
-#
-## move the uninstal script
-#wrap "cp ./uninstall.sh ${DEST}" "Moving the uninstall script"
-#
->>>>>>> 1e676167338c9fe5ee07a649dea05da2a18eebbd
 	# Run unit tests ?
 	read_yes_no "Do you wish to run unit tests" "y"
 	if [ x"${ANSWER}" = xy ]; then
@@ -402,7 +216,7 @@ local_install () {
 	if [ x"${ANSWER}" = xn ]; then
 		rm -f "${LOGFILE}"
 	fi
-
+	
 	# self-explanatory
 	success_message
 }