install

#!/bin/bash

function yes_or_no {
    while true; do
        read -p "$* [y/n]: " yn
        case $yn in
            [Yy]*) return 0  ;;
            [Nn]*) echo "Aborted" ; return  1 ;;
        esac
    done
}

echo "[0/4] Installing development limix 2.0.0 version"


if [ command -v python >/dev/null 2>&1 ]
then
    echo >&2 "python command has not been found. Aborting."
    exit 1
fi


if [ command -v pip >/dev/null 2>&1 ]
then
    echo >&2 "pip command has not been found. Aborting."
    exit 1
fi

USE_CONDA="no"

if ! [ command -v conda >/dev/null 2>&1 ]
then
    echo "Looks like you have conda package manager."
    msg="Shall we use it to install the C libraries? (Recommended.)"
    yes_or_no $msg && USE_CONDA="yes" || USE_CONDA="no"
fi

tmpdir=`mktemp -d 2>/dev/null || mktemp -d -t 'tmpdir'`
logfile="$tmpdir/limix.log"
exec 3>"$logfile"

function cleanup
{
    rm -rf "$tmpdir" >/dev/null 2>&1 || true
}

trap cleanup EXIT

if [[ $USE_CONDA == "no" ]]
then
    
    if [ command -v cmake >/dev/null 2>&1 ]
    then
        echo >&2 "cmake command has not been found. Aborting."
        exit 1
    fi
fi

function silent_run
{
    eval "$@ >&3 2>&1"
}

function silent_trun
{
    eval "$@ >&3 2>&1 || true"
}

function do_then_sudo
{
    eval "$@"
    if [ $? != 0 ]; then
        eval "sudo $@"
    fi
}

function failed
{
    echo "FAILED."
    echo "[_/_] LOG OUTPUT:"
    cat $logfile
    exit 1
}

GIT_URL=https://github.com/limix/limix.git
GIT_FOLDER="$tmpdir/limix"

silent_run pip uninstall limix --yes
silent_run pip uninstall limix --yes
silent_run pip uninstall limix --yes

echo -n "[1/4] Cloning repository... "
silent_run git clone -b 2.0.0 $GIT_URL $GIT_FOLDER
cd $GIT_FOLDER
[ $? == 0 ] && echo "done." || failed

function install_deps
{
    if [[ $USE_CONDA == "yes" ]]
    then
        conda install --yes -c conda-forge bgen liknorm
    else
        bash <(curl -fsSL https://raw.githubusercontent.com/limix/liknorm/master/install)
        bash <(curl -fsSL https://raw.githubusercontent.com/limix/bgen/master/install)
    fi
}

echo -n "[2/4] Installing C dependencies... "
silent_run install_deps
[ $? == 0 ] && echo "done." || failed

echo -n "[3/4] Installing Python dependencies... "
if [[ $USE_CONDA == "yes" ]]
then
    silent_run conda install --yes numpy scipy matplotlib netcdf4 h5py xarray
else
    silent_run pip install numpy
fi
silent_run pip install -r requirements.txt
[ $? == 0 ] && echo "done." || failed

echo -n "[4/4] Installing limix itself... "
silent_run pip install .
[ $? == 0 ] && echo "done." || failed

rm "$logfile" || true