setup_PreFRBLE.sh

#!/bin/bash

## exit if any command fails
set -e

## path of thi bash script, should be placed in top folder of PreFRBLE
BASE_DIR=$(dirname $0)

## directiories for virtual environment and where source code is found
DIR=$BASE_DIR/venv_PreFRBLE
PACKAGE=$BASE_DIR/PreFRBLE

read -p "Do you want to create a new virtual environment? " -n 1 -r
echo    # (optional) move to a new line
if [[ $REPLY =~ ^[Yy]$ ]]
then
    ## create directory of virtual environment (delete old version)
    rm -rf $DIR
    mkdir $DIR
    virtualenv -p python3 $DIR

    source $DIR/bin/activate

    ### IF INSTALLATION FAILS
    ###   due to missing lapack/blas package:
    ###       install openBLAS locally:
    cd $DIR && git clone https://github.com/xianyi/OpenBLAS
    cd OpenBLAS && make FC=gfortran && make PREFIX=$DIR install
    export LD_LIBRARY_PATH=$DIR/OpenBLAS/lib:$LD_LIBRARY_PATH  ## also copy to .source_activate
    export BLAS=$DIR/OpenBLAS/libopenblas.a
    export ATLAS=$DIR/OpenBLAS/libopenblas.a
    pip3 install numpy cython  ## install critical packages
    pip3 install pandas
    ###       if following still fails duw to missing lapack/blas, simply run bash install_PreFRBLE.sh  it will work now
    
    ## install python packages used not by PreFRBLE, but by notebooks. If this fails, continue with install_PreFRBLE.sh
    pip3 install numpy cython ipython jupyter scipy pandas statsmodels    
    echo "environment is created. If following fails, run setup again and skip creating new environment"
fi



## install PreFRBLE
bash $BASE_DIR/install_PreFRBLE.sh


## PreFRBLE can now be used in python within the virtual environment
## activate environment by changing into parent folder and execute
##
##    source .activate_PreFRBLE
##
## in python, you can now use PreFRBLE functions by calling
##
##    import PreFRBLE
##