Resolve install.sh confict with previous commit
This commit is contained in:
parent
ad52398853
commit
9d76465b11
188
src/install.sh
188
src/install.sh
|
|
@ -60,12 +60,7 @@ error_exit () {
|
||||||
printf " for more informations.\n"
|
printf " for more informations.\n"
|
||||||
printf " Below is an excerpt of the last 10 lines:\n"
|
printf " Below is an excerpt of the last 10 lines:\n"
|
||||||
printf "\n"
|
printf "\n"
|
||||||
<<<<<<< HEAD
|
|
||||||
tail "${LOGFILE}"
|
tail "${LOGFILE}"
|
||||||
=======
|
|
||||||
# tail -v -n 10 "${LOGFILE}"
|
|
||||||
tail -n 10 "${LOGFILE}"
|
|
||||||
>>>>>>> 1e676167338c9fe5ee07a649dea05da2a18eebbd
|
|
||||||
|
|
||||||
# uninstall if needed
|
# uninstall if needed
|
||||||
pip uninstall -y msspec
|
pip uninstall -y msspec
|
||||||
|
|
@ -73,23 +68,6 @@ error_exit () {
|
||||||
cleanup && exit 1
|
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 () {
|
read_yes_no () {
|
||||||
DEFAULT="$2"
|
DEFAULT="$2"
|
||||||
PROMPT="$1 (y/n) [${DEFAULT}]? "
|
PROMPT="$1 (y/n) [${DEFAULT}]? "
|
||||||
|
|
@ -99,15 +77,9 @@ read_yes_no () {
|
||||||
|
|
||||||
VALID=1
|
VALID=1
|
||||||
while test $VALID -ne 0; do
|
while test $VALID -ne 0; do
|
||||||
<<<<<<< HEAD
|
|
||||||
printf "%s" "${PROMPT}"
|
printf "%s" "${PROMPT}"
|
||||||
if [ x"$BYPASS" = xn ]; then
|
if [ x"$BYPASS" = xn ]; then
|
||||||
read -r "INPUT"
|
read -r "INPUT"
|
||||||
=======
|
|
||||||
printf "${PROMPT}"
|
|
||||||
if [ x"$BYPASS" = "xn" ]; then
|
|
||||||
read "RESPONSE"
|
|
||||||
>>>>>>> 1e676167338c9fe5ee07a649dea05da2a18eebbd
|
|
||||||
else
|
else
|
||||||
printf "\n"
|
printf "\n"
|
||||||
fi
|
fi
|
||||||
|
|
@ -121,66 +93,13 @@ read_yes_no () {
|
||||||
log_message "ANSWER : $ANSWER"
|
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 () {
|
wrap () {
|
||||||
log_message "================================================================================"
|
log_message "================================================================================"
|
||||||
log_message "$2"
|
log_message "$2"
|
||||||
log_message "================================================================================"
|
log_message "================================================================================"
|
||||||
<<<<<<< HEAD
|
|
||||||
if [ "$DEBUG" = y ]; then
|
if [ "$DEBUG" = y ]; then
|
||||||
printf "%s...\n" "$2"
|
printf "%s...\n" "$2"
|
||||||
(eval "$1" || echo $? >"${GETOUTFILE}") | tee -a "${LOGFILE}"
|
(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 $GETOUTFILE)
|
rc=$(cat $GETOUTFILE)
|
||||||
if [ $rc != 0 ]; then
|
if [ $rc != 0 ]; then
|
||||||
error_exit
|
error_exit
|
||||||
|
|
@ -191,26 +110,6 @@ wrap () {
|
||||||
fi
|
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 () {
|
success_message () {
|
||||||
log_message "========================================================"
|
log_message "========================================================"
|
||||||
log_message "MsSpec was successfully installed."
|
log_message "MsSpec was successfully installed."
|
||||||
|
|
@ -260,8 +159,7 @@ check_dependencies () {
|
||||||
gcc_ver_min=7
|
gcc_ver_min=7
|
||||||
log_message "Checking if gfortran >= $gcc_ver_min is installed..."
|
log_message "Checking if gfortran >= $gcc_ver_min is installed..."
|
||||||
command -V gfortran || return 1
|
command -V gfortran || return 1
|
||||||
# gcc_ver=$(gcc -dumpversion)
|
gcc_ver=$(gcc -dumpversion)
|
||||||
gcc_ver=$(echo $(gcc -dumpversion)| cut -d. -f1)
|
|
||||||
echo "You have gfortran version $gcc_ver installed"
|
echo "You have gfortran version $gcc_ver installed"
|
||||||
test "$gcc_ver" -ge "$gcc_ver_min" || return 1
|
test "$gcc_ver" -ge "$gcc_ver_min" || return 1
|
||||||
log_message "Ok\n"
|
log_message "Ok\n"
|
||||||
|
|
@ -285,17 +183,10 @@ check_dependencies () {
|
||||||
log_message "Ok\n"
|
log_message "Ok\n"
|
||||||
|
|
||||||
# we need virtualenv
|
# we need virtualenv
|
||||||
<<<<<<< HEAD
|
|
||||||
#log_message "Checking if virtualenv is installed..."
|
#log_message "Checking if virtualenv is installed..."
|
||||||
#command -V virtualenv || return 1
|
#command -V virtualenv || return 1
|
||||||
#log_message "Ok\n"
|
#log_message "Ok\n"
|
||||||
|
|
||||||
=======
|
|
||||||
log_message "Checking if virtualenv is installed..."
|
|
||||||
#command -V virtualenv || return 1
|
|
||||||
log_message "Ok\n"
|
|
||||||
|
|
||||||
>>>>>>> 1e676167338c9fe5ee07a649dea05da2a18eebbd
|
|
||||||
}
|
}
|
||||||
|
|
||||||
local_install () {
|
local_install () {
|
||||||
|
|
@ -305,7 +196,6 @@ local_install () {
|
||||||
# check dependencies
|
# check dependencies
|
||||||
wrap "check_dependencies" "Checking dependencies"
|
wrap "check_dependencies" "Checking dependencies"
|
||||||
|
|
||||||
<<<<<<< HEAD
|
|
||||||
# build the Fortran code
|
# build the Fortran code
|
||||||
wrap "make pybinding VERBOSE=1" "Building Phagen and Spec Python dynamic library"
|
wrap "make pybinding VERBOSE=1" "Building Phagen and Spec Python dynamic library"
|
||||||
|
|
||||||
|
|
@ -315,82 +205,6 @@ local_install () {
|
||||||
# install the package
|
# install the package
|
||||||
wrap "make install VERBOSE=1" "Installing the msspec package"
|
wrap "make install VERBOSE=1" "Installing the msspec package"
|
||||||
|
|
||||||
=======
|
|
||||||
# ask for a place to put the binary
|
|
||||||
#read_folder "Please, type in the folder where to place the binary" "${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 ${DEST}" "Moving the uninstall script"
|
|
||||||
#
|
|
||||||
>>>>>>> 1e676167338c9fe5ee07a649dea05da2a18eebbd
|
|
||||||
# Run unit tests ?
|
# Run unit tests ?
|
||||||
read_yes_no "Do you wish to run unit tests" "y"
|
read_yes_no "Do you wish to run unit tests" "y"
|
||||||
if [ x"${ANSWER}" = xy ]; then
|
if [ x"${ANSWER}" = xy ]; then
|
||||||
|
|
|
||||||
Loading…
Reference in New Issue