Merge branch 'master' of https://git.ipr.univ-rennes1.fr/epsi/msspec_python3

src/install.sh

@@ -60,7 +60,12 @@ 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
@@ -68,6 +73,23 @@ 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}]? "
@@ -77,9 +99,15 @@ 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
@@ -93,13 +121,66 @@ 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
@@ -110,6 +191,26 @@ 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."
@@ -139,7 +240,7 @@ 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."
@@ -159,7 +260,8 @@ 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"
@@ -183,10 +285,17 @@ 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 () {
@@ -196,6 +305,7 @@ 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"
 
@@ -205,6 +315,82 @@ 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
@@ -216,7 +402,7 @@ local_install () {
 	if [ x"${ANSWER}" = xn ]; then
 		rm -f "${LOGFILE}"
 	fi
-	
+
 	# self-explanatory
 	success_message
 }