Clean cloning of a conda env (and add it to jupyter kernel list)

clone.sh

#!/bin/sh
#
# Clone a conda env and add it to jupyter kernel list
#
# This is basicaly a nice shortcut for:
# 	mamba create --name argopy-pull208 --clone argopy-py38-all-pinned
# 	python -m ipykernel install --user --name=argopy-pull208
#
# 
# Created by G. Maze on 2023-06-21.


#########################
# FUNCTIONS
#########################
Help() {
   # Display Help
   echo "Clone Conda environments nicely"
   echo
   echo "Syntax: clone -o <origin> -c <clone>"
   echo "options:"
   echo "h     Print this Help"
   echo "o     Name of the environment to clone, default is 'argopy-py38-all-pinned'"
   echo "c     Name of the cloned environment"
   echo
}

fix_kernel_path (){
  ENV=${1}

  kernelspec="$(jupyter kernelspec list | grep ${ENV})"
  echo "${kernelspec}"
  IFS=' ' read -ra ADDR <<< "$kernelspec"
  kernel_path="${ADDR[1]}"
  kernel_cfg_file="${kernel_path}/kernel.json"
  python_path="$(more ${kernel_cfg_file} | jq .argv[0] | sed 's/\"//g')"
  DIR="$(dirname ${python_path})"
  FILE="$(basename ${python_path})"
  #echo "[${DIR}] [${FILE}]"
  IFS='/' read -r -a parts <<< "$DIR"
  # We expect: /Users/gmaze/miniconda3/envs/<ENV>/bin
  if [ "${parts[-2]}" = ${ENV} ]; then
    echo "kernel spec OK"
  else
    parts[-2]=${ENV}  # update with appropriate python path
    NEW_DIR=$(IFS='/' ; echo "${parts[*]}")
    new_python_path="${NEW_DIR}/${FILE}"

    while true; do
      printf "Replace: \n${python_path} \nwith: \n${new_python_path}\n"
      read -p "Do you confirm ? [Yy/Nn] " yn
      case $yn in
          [Yy]* )
            cp -f ${kernel_cfg_file} "${kernel_cfg_file}.bak"
            tmp=$(mktemp)
            jq --arg a "$new_python_path" '.argv[0] = $a' ${kernel_cfg_file} > "$tmp" && mv "$tmp" ${kernel_cfg_file}
            break;;
          [Nn]* ) exit;;
          * ) echo "Please answer yes [Yy] or no [Nn]";;
      esac
    done

  fi
}

add_ipykernel () {
  # Possibly add it the Jupyter kernels:

   python -m ipykernel install --user --name=$1

   # Check installation of the kernel:
   fix_kernel_path ${1}
}


clone_conda_env () {
	# $1 is the name of the new environment
	# $2 is the name of the environment to clone

	# Eventually remove environment if exists:
	if conda env list | grep $1; then
	    printf "$1 already exists, removing this environment...\n"
		  mamba remove --quiet --name $1 --all --yes --json > /dev/null 2>&1
	fi

	# Create the environment from file
    printf "Creating conda environment $1 ...\n"
	mamba create --name $1 --clone $2 > /dev/null 2>&1

}


#########################
# PROCESS OPTIONS
#########################

# Set variables
envname_to_clone="argopy-py38-all-pinned"
envname_to_install=""

# Get the options
while getopts "ho:c:" option; do
   case $option in
      h) # display Help
         Help
         exit 0
         ;;
      o) # Enter an action to perform
         envname_to_clone=$OPTARG
         ;;
      c) # Enter an action to perform
         envname_to_install=$OPTARG
         ;;
   esac
done


#########################
# ACTIONS
#########################

if [ -n "$envname_to_install" ]; then
	clone_conda_env $envname_to_install $envname_to_clone
	add_ipykernel $envname_to_clone
fi