Resolve install.sh confict with previous commit
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parent
ad52398853
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9d76465b11
188
src/install.sh
188
src/install.sh
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@ -60,12 +60,7 @@ error_exit () {
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printf " for more informations.\n"
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printf " Below is an excerpt of the last 10 lines:\n"
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printf "\n"
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<<<<<<< HEAD
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tail "${LOGFILE}"
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=======
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# tail -v -n 10 "${LOGFILE}"
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tail -n 10 "${LOGFILE}"
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>>>>>>> 1e676167338c9fe5ee07a649dea05da2a18eebbd
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# uninstall if needed
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pip uninstall -y msspec
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@ -73,23 +68,6 @@ error_exit () {
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cleanup && exit 1
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}
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<<<<<<< HEAD
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=======
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get_os () {
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for os in "ubuntu" "mageia" "archlinux"; do
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cat /etc/*release /etc/*version /etc/*issue 2>/dev/null | grep -i "$os" 2>/dev/null 1>/dev/null
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if test $? -eq 0; then
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LINUX_OS="$os"
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break
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fi
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done
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}
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>>>>>>> 1e676167338c9fe5ee07a649dea05da2a18eebbd
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read_yes_no () {
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DEFAULT="$2"
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PROMPT="$1 (y/n) [${DEFAULT}]? "
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@ -99,15 +77,9 @@ read_yes_no () {
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VALID=1
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while test $VALID -ne 0; do
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<<<<<<< HEAD
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printf "%s" "${PROMPT}"
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if [ x"$BYPASS" = xn ]; then
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read -r "INPUT"
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=======
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printf "${PROMPT}"
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if [ x"$BYPASS" = "xn" ]; then
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read "RESPONSE"
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>>>>>>> 1e676167338c9fe5ee07a649dea05da2a18eebbd
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else
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printf "\n"
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fi
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@ -121,66 +93,13 @@ read_yes_no () {
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log_message "ANSWER : $ANSWER"
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}
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<<<<<<< HEAD
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=======
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read_folder () {
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DEFAULT="$2"
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PROMPT="$1 [${DEFAULT}]: "
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ANSWER=""
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unset FOLDER
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printf "${PROMPT}"
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if [ x"$BYPASS" = "xn" ]; then
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read "ANSWER"
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else
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printf "\n"
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fi
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export FOLDER="${ANSWER:-$DEFAULT}"
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log_message "QUESTION: $PROMPT"
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log_message "ANSWER : $FOLDER"
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}
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create_folder () {
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FOLDER="$1"
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ERR_MKDIR=1
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ERR_ABORT=2
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ERR_PERMS=3
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if ! test -d "${FOLDER}" ; then
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read_yes_no "The folder \"${FOLDER}\" does not exist. Should I create it" "y" #"$BYPASS"
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case "${ANSWER}" in
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y) mkdir -p "${FOLDER}" 2>>${LOGFILE} 1>>${LOGFILE} || return $ERR_MKDIR;;
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n) log_message2 "Installation aborted by the user" && return $ERR_ABORT ;;
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esac
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fi
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if ! test -w "${FOLDER}" ; then
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log_message2 "You do not have permission to write into \"${FOLDER}\"."
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return $ERR_PERMS
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fi
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}
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>>>>>>> 1e676167338c9fe5ee07a649dea05da2a18eebbd
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wrap () {
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log_message "================================================================================"
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log_message "$2"
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log_message "================================================================================"
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<<<<<<< HEAD
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if [ "$DEBUG" = y ]; then
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printf "%s...\n" "$2"
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(eval "$1" || echo $? >"${GETOUTFILE}") | tee -a "${LOGFILE}"
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=======
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if [ "$DEBUG" = "y" ]; then
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eval "($1) 2>&1" | tee -a ${LOGFILE}
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echo ${PIPESTATUS[0]} >${GETOUTFILE}
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>>>>>>> 1e676167338c9fe5ee07a649dea05da2a18eebbd
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rc=$(cat $GETOUTFILE)
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if [ $rc != 0 ]; then
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error_exit
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@ -191,26 +110,6 @@ wrap () {
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fi
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}
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<<<<<<< HEAD
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=======
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update_path () {
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# check if the shell path contains $BIN_FOLDER
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SHELLRC="$HOME/.$(basename $SHELL)rc"
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${ECHO} "$PATH" | grep "${BIN_FOLDER}" 2>/dev/null 1>/dev/null
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if test $? -ne 0; then
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${ECHO} "" >> $SHELLRC
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${ECHO} "# Add the user's local binary folder" >> $SHELLRC
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${ECHO} "export PATH=${BIN_FOLDER}:\$PATH" >> $SHELLRC
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${ECHO} "Your PATH variable has been updated, the folder"
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${ECHO} "${BIN_FOLDER} has been added to it."
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${ECHO} ""
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${ECHO} "Please source again your shell configuration file by typing:"
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${ECHO} "source $SHELLRC"
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fi
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}
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>>>>>>> 1e676167338c9fe5ee07a649dea05da2a18eebbd
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success_message () {
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log_message "========================================================"
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log_message "MsSpec was successfully installed."
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@ -260,8 +159,7 @@ check_dependencies () {
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gcc_ver_min=7
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log_message "Checking if gfortran >= $gcc_ver_min is installed..."
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command -V gfortran || return 1
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# gcc_ver=$(gcc -dumpversion)
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gcc_ver=$(echo $(gcc -dumpversion)| cut -d. -f1)
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gcc_ver=$(gcc -dumpversion)
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echo "You have gfortran version $gcc_ver installed"
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test "$gcc_ver" -ge "$gcc_ver_min" || return 1
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log_message "Ok\n"
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@ -285,17 +183,10 @@ check_dependencies () {
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log_message "Ok\n"
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# we need virtualenv
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<<<<<<< HEAD
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#log_message "Checking if virtualenv is installed..."
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#command -V virtualenv || return 1
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#log_message "Ok\n"
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=======
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log_message "Checking if virtualenv is installed..."
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#command -V virtualenv || return 1
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log_message "Ok\n"
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>>>>>>> 1e676167338c9fe5ee07a649dea05da2a18eebbd
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}
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local_install () {
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@ -305,7 +196,6 @@ local_install () {
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# check dependencies
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wrap "check_dependencies" "Checking dependencies"
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<<<<<<< HEAD
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# build the Fortran code
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wrap "make pybinding VERBOSE=1" "Building Phagen and Spec Python dynamic library"
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@ -315,82 +205,6 @@ local_install () {
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# install the package
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wrap "make install VERBOSE=1" "Installing the msspec package"
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=======
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# ask for a place to put the binary
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#read_folder "Please, type in the folder where to place the binary" "${DEFAULT_BIN}"
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#BIN_FOLDER=${FOLDER}
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#create_folder "${BIN_FOLDER}" || error_exit
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#export BIN_FOLDER
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# If in a virtualenv, ask if we should install inside
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if [ x"$VIRTUAL_ENV" != x ]; then
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read_yes_no "You are running a Python virtual environment. Do you wish to install msspec inside ?" "y"
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case ${ANSWER} in
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y) # get the python version of this venv...
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v=$(python -V 2>&1 | cut -d" " -f2 | cut -d. -f1)
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# and stops if < 3
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if [ $v -lt 3 ]; then
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log_message "The Python version of this venv is < 3"
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error_exit
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fi
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;;
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n) # The user decided to stop there
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log_message "Please deactivate your virtual environment and restart the setup program."
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error_exit
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;;
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esac
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# Else, we are not in a virtualenv
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else
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pip_opt=""
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# so ask if we should create one
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read_yes_no "Do you wish to create a virtual environment to install MsSpec inside" "y"
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case ${ANSWER} in
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y) # Create the destination folder
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read_folder "Please, type in the base installation folder" "${DEFAULT_DEST}"
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DEST_FOLDER=${FOLDER}/MsSpec-${VERSION}
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if [ -d $DEST_FOLDER ]; then
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export DEST_ALREADY_EXISTS="y" # to avoid cleaning the existing DEST_FOLDER in case of any problem
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read_yes_no "The folder $DEST_FOLDER already exists. Overwrite" "y"
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case ${ANSWER} in
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y) # overwrite
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create_folder "${DEST_FOLDER}" || error_exit
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;;
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n) # stop here otherwise
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error_exit
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;;
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esac
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fi
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export DEST_FOLDER
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wrap "virtualenv -vvv --python=${PYTHON} --system-site-packages --prompt=\"(msspec-${VERSION}) \" ${DEST_FOLDER}/venv" \
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"Create a Python virtual environment"
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. ${DEST_FOLDER}/venv/bin/activate
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;;
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n) # install in the user $HOME
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pip_opt="--user"
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;;
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esac
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fi
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# build and run setuptools to create a source distribution
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wrap "make sdist" \
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"Building MsSpec python package"
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# install the package with pip
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wrap "pip install $pip_opt dist/msspec-*.tar.gz" \
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"Installing pymsspec python package and its dependencies"
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#
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## move the frontend to the binary folder
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##wrap "mkdir -p ${LOCALBIN} && \
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## cp ./msspec ${LOCALBIN} && chmod u+x ${LOCALBIN}/msspec && \
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## ${ECHO} \"msspec installed in ${LOCALBIN}\"" \
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## "Installing the msspec frontend"
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# "cp ./msspec ${BIN_FOLDER} && chmod ugo+rx ${BIN_FOLDER}/msspec" "Installing the msspec frontend"
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#
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## move the uninstal script
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#wrap "cp ./uninstall.sh ${DEST}" "Moving the uninstall script"
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#
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>>>>>>> 1e676167338c9fe5ee07a649dea05da2a18eebbd
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# Run unit tests ?
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read_yes_no "Do you wish to run unit tests" "y"
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if [ x"${ANSWER}" = xy ]; then
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