install.sh

#!/bin/bash

# ==============================================================================
# Define usage
#     Sets up usage function, parses and validates arguments
# ==============================================================================
## define usage
function usage {
    echo "----------------------------------------------------------------"
    echo "Runs install scripts in install.d and sets the "
    echo "environment with an environment.d file"
    echo "----------------------------------------------------------------"
    echo ""
    echo "  FINITEFAULT_DIR string  full path to the local repository"
    echo "                          (example: /home/user/neic-finitefault)"
    echo "  --fd-bank string        the location of the fd_bank file"
    echo "                          if not specified it will be downloaded"
    echo "                          default=download"
    echo "                          (example: --fd-bank /home/user/fd_bank)"
    echo "  --lith string        the location of the lith file"
    echo "                          if not specified it will be downloaded"
    echo "                          default=download"
    echo "                          (example: --lith /home/user/LITHO1.0.nc)"
}

## parse arguments
REQUIRED_ARGS=()
while [[ $# -gt 0 ]]; do
    # shellcheck disable=SC2221,SC2222
    case $1 in
        --fd-bank)
            FD_BANK="$2"
            shift
            shift
            ;;
        --lith)
            LITHO1="$2"
            shift
            shift
            ;;
        -h|--help)
            usage
            exit 0
            ;;
        -*|--*)
            echo "Invalid option $1"
            usage
            exit 1
            ;;
        *)
            REQUIRED_ARGS+=("$1")
            shift
            ;;
    esac
done
### set positional arguments
set -- "${REQUIRED_ARGS[@]}" # restore positional parameters
FINITEFAULT_DIR=${1%%/}
if [ -z ${1+x} ]
then 
    echo "Argument FINITEFAULT_DIR must be set";
    exit 1;
fi

### set defaults
FD_BANK=${FD_BANK:-"download"}
LITHO1=${LITHO1:-"download"}

# Running install scripts in install.d/
INSTALL_DIR="${FINITEFAULT_DIR}/install.d"
# shellcheck source=./install.d/miniforge.sh
source "${INSTALL_DIR}/miniforge.sh" "${FINITEFAULT_DIR}";
# shellcheck disable=SC1090
. "${HOME}/miniforge/etc/profile.d/conda.sh"
# shellcheck source=./install.d/ff-env.sh
source "${INSTALL_DIR}/ff-env.sh" "${FINITEFAULT_DIR}";
conda activate ff-env;
conda env list
pip install -e "${FINITEFAULT_DIR}";
# shellcheck source=./install.d/wasp.sh
source "${INSTALL_DIR}/wasp.sh" "${FINITEFAULT_DIR}";
# shellcheck source=./install.d/data_dependencies.sh
source "${INSTALL_DIR}/data_dependencies.sh" "${FINITEFAULT_DIR}" --fd-bank "${FD_BANK}" --lith "${LITHO1}";

# get back to top level directly and message completion of installation
cd "${FINITEFAULT_DIR}" || echo "Failed to return to finite fault top level directly";
echo "Wasp installation completed!";