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://docs.jupyter-jsc.fz-juelich.de/github/FZJ-JSC/jupyter-jsc-notebooks/blob/documentation/index.ipynb) -> 'Install kernel with conda'
##
## The steps performed here are only the lsat ones after installing an own conda environment.
##


CONDA_TARGET_DIR=/p/project/<PROJECTNAME>/<USERNAME>/miniconda3

CONDA_ENV=picongpu

echo '#!/bin/bash

# module 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=${CONDA_PREFIX}/lib/python3.10/site-packages:${PYTHONPATH}
    
exec python -m ipykernel $@' > ${CONDA_TARGET_DIR}/envs/${CONDA_ENV}/kernel.sh

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

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"
}' > $HOME/.local/share/jupyter/kernels/conda_${CONDA_ENV}/kernel.json