install.sh

# note: make sure conda srbench environment is installed 
set -e

# script to read yaml
function parse_yaml {
   local prefix=$2
   local s='[[:space:]]*' w='[a-zA-Z0-9_]*' fs=$(echo @|tr @ '\034')
   sed -ne "s|^\($s\):|\1|" \
        -e "s|^\($s\)\($w\)$s:$s[\"']\(.*\)[\"']$s\$|\1$fs\2$fs\3|p" \
        -e "s|^\($s\)\($w\)$s:$s\(.*\)$s\$|\1$fs\2$fs\3|p"  $1 |
   awk -F$fs '{
      indent = length($1)/2;
      vname[indent] = $2;
      for (i in vname) {if (i > indent) {delete vname[i]}}
      if (length($3) > 0) {
         vn=""; for (i=0; i<indent; i++) {vn=(vn)(vname[i])("_")}
         printf("%s%s%s=\"%s\"\n", "'$prefix'",vn, $2, $3);
      }
   }'
}

# install base srbench environment if it doesn't exist
if conda info --envs | grep srbench | grep -v "srbench-"; then 
    echo "existing base srbench environment (not installing)"; 
else 
    echo "installing base srbench environment"

    mamba env create -f base_environment.yml

    eval "$(conda shell.bash hook)"

    conda init bash
fi



if (($#==1)); #check if number of arguments is 1 
then
    subnames=($1)
else
    subnames=$(ls algorithms/)
fi

failed=()
succeeded=()

# install methods
echo "////////////////////////////////////////"
echo "installing these SR methods:"
echo ${subnames}
echo "////////////////////////////////////////"

# install all methods
for SUBNAME in ${subnames[@]} ; do

    build_clone_base_env="yes"

    echo "vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv"
    echo ".................... Installing $SUBNAME ..."

    SUBFOLDER="./algorithms/$SUBNAME"
    SUBENV="srbench-$SUBNAME"

    ########################################
    # read yaml
    eval $(parse_yaml $SUBFOLDER/metadata.yml)
    ########################################

    echo "build_clone_base_env: ${build_clone_base_env}"
    if [ ${build_clone_base_env} == "yes" ] ; then

        echo "........................................"
        echo "Cloning base environment"
        echo "........................................"

        if conda info --envs | grep -q $SUBENV ; then 
            echo "not cloning base because ${SUBENV} already exists"
        else
            conda create --name $SUBENV --clone srbench
            # update from base environment
            if test -f "${SUBFOLDER}/environment.yml" ; then
                echo "Update alg env from environment.yml"
                echo "........................................"
                mamba env update -n $SUBENV -f ${SUBFOLDER}/environment.yml
            fi
        fi
    else

        echo "........................................"
        echo "Creating environment ${SUBENV} from scratch"
        echo "........................................"
        mamba create -n $SUBENV -f ${SUBFOLDER}/environment.yml
    fi


    if test -f "${SUBFOLDER}/requirements.txt" ; then
        echo "Update alg env from requirements.txt"
        echo "........................................"
        mamba run -n ${SUBENV} pip install -r ${SUBFOLDER}/requirements.txt
    fi

    # eval "$(conda shell.bash hook)"
    # conda init bash
    # conda activate $SUBENV
    cd $SUBFOLDER
    if test -f "install.sh" ; then
        echo "running install.sh..."
        echo "........................................"
        mamba run -n $SUBENV bash install.sh
    else
        echo "::warning::No install.sh file found in ${SUBFOLDER}."
        echo " Assuming the method is a conda package specified in environment.yml."
    fi
    cd ../../

    # Copy files and environment
    bash scripts/copy_algorithm_files.sh $SUBNAME

    # export env
    echo "Exporting environment"
    echo "........................................"
    # conda env export -n $SUBENV > $SUBFOLDER/environment.lock.yml
    conda env export -n $SUBENV > $SUBFOLDER/environment.lock.yml
    conda env export -n $SUBENV 
    echo "^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^"
done