Add a Kernel in a Jupyter Environment

add_kernel.sh

#!/bin/bash
def_yes=n
while getopts ":hy" opt; do
  case ${opt} in
    h ) # process option h
      PRINT_HELP=y
      ;;
    y ) # process option y
      def_yes=y
      ;;
    \? )
      PRINT_HELP=y
      ;;
  esac
done
if [[ $# == 0 || $PRINT_HELP == "y" ]]; then
 echo "Usage $0 [-h] [-y] ENV_DIR [ENV_NAME [REQUIREMENTS]]"
 echo "   Install a Python virtual environment for use as a Jupyter Kernel"
 echo ""
 echo "   -h : print usage help"
 echo "   -y : answer yes to confirmation prompt"
 echo "   ENV_DIR : required path to create a new environment"
 echo "   ENV_NAME : optional str for the name of the kernel"
 echo "   REQUIREMENTS : optional path for required libraries."
 echo
 echo "PYTHON environment variable influences which version is used"
 echo "By default, this uses python3.6 to be consistent with RHEL7"
 echo "JupyterHub on Atmos. On RHEL8, update to python3.8"
 echo
 echo "PYTHON=/usr/bin/python3.6"
 exit
fi
shift $(($OPTIND - 1))


ENV_DIR=${1?Required ENV_DIR of where to make your new kernel}
ENV_NAME_DEF=$(basename ${ENV_DIR})
ENV_NAME=${2:-${ENV_NAME_DEF}}
REQPATH=${3}
PYTHON=${PYTHON:=/usr/bin/python3.6}
echo "Create ${ENV_NAME} at $ENV_DIR with ${PYTHON}"
if [[ ${REQPATH} != "" ]]; then
echo "and packages in ${REQPATH}"
fi
if [[ $def_yes == y ]]; then
  REPLY=y
else
  read -p "Are you sure? " -n 1 -r
fi
echo

# Optionally, modify environment before running
# module purge
# module load netcdf-4.8.1/intel-19.0
# module load hdf5-1.10.8/intel-19.0
if [[ $REPLY =~ ^[Yy]$ ]]
then
  # Create a "virtual environment" called "tempo_env" for this training
  ${PYTHON} -m venv ${ENV_DIR}
  # Upgrade pip
  ${ENV_DIR}/bin/python -m pip install --upgrade pip
  # Install ipykernel
  ${ENV_DIR}/bin/python -m pip install ipykernel
  # Install optional additional libraries
  if [[ ${REQPATH} != "" ]]; then
    ${ENV_DIR}/bin/python -m pip install -r $3
  fi
  # Register kernel
  ${ENV_DIR}/bin/python -m ipykernel install --user --name=${ENV_NAME}
fi

Download and run. For more details on how, run bash ./add_kernel.sh -h