Install Jupyter kernel in custom conda environment on JUWELS

installJupyKernel.sh

## Install a kernel for the picongpu analysis environment
## 
## Before runnign this script, see JSC documentation at
##     (https://jupyterjsc.pages.jsc.fz-juelich.de/docs/jupyterjsc/users/jupyterlab/4.3/kernels_hpc_conda/)
##
## The steps performed here are only the last ones after installing an own conda environment.
## For installing a suitable conda environment see
##     (https://gist.github.com/steindev/c1d678375fd0f974f4b9cb1480b3da03)
##


CONDA_ENV=picongpu
export PROJECT=${PROJECT_jureap18}

export CONDA_ENV=$(echo "${CONDA_ENV}" | awk '{print tolower($0)}')
echo ${CONDA_ENV} # double check

export CONDA_TARGET_DIR=${PROJECT}/${USER}/miniforge3
echo ${CONDA_TARGET_DIR} # double check


echo '#!/bin/bash

module --force purge # optional to disable the external environment, necessary, if python version is different
 
# Activate your Python virtual environment
source '"${CONDA_TARGET_DIR}"'/bin/activate '"${CONDA_ENV}"'
    
# Ensure python packages installed in conda are always prefered, not necessary if module purge is used
export PYTHONPATH=${CONDA_PREFIX}/lib/python3.13/site-packages:${PYTHONPATH}
    
exec python -m ipykernel $@' > ${CONDA_TARGET_DIR}/envs/${CONDA_ENV}/kernel.sh

chmod +x ${CONDA_TARGET_DIR}/envs/${CONDA_ENV}/kernel.sh

echo ${CONDA_TARGET_DIR}/envs/${CONDA_ENV}/kernel.sh

mkdir -p $HOME/.local/share/jupyter/kernels/conda_${CONDA_ENV}

echo '{
 "argv": [
  "'"${CONDA_TARGET_DIR}"'/envs/'"${CONDA_ENV}"'/kernel.sh",
  "-f",
  "{connection_file}"
 ],
 "display_name": "conda_'"${CONDA_ENV}"'",
 "language": "python",
 "metadata": {
   "debugger": true
 }
}' > $HOME/.local/share/jupyter/kernels/conda_${CONDA_ENV}/kernel.json