Jupyter conda kernel installer

conda-jupyter-kernel-installer.sh

#!/bin/bash

# Uninstall kernel.

# rm -rf ${HOME}/.local/share/jupyter/kernels/my-pykernel/
# rm -rf ${HOME}/my-pykernel/

# Specify a few targets.

if [[ -f environment.yaml ]]; then

  JUPYTER_KERNEL_NAME=$(grep -e 'name:' environment.yaml | awk '{print $2}')
  CONDA_INSTALL_DIR=${HOME}/${JUPYTER_KERNEL_NAME}

else

  echo "environment.yaml not found..."; exit

fi

# Install "isolated" conda environment.

module purge

mkdir -p "${CONDA_INSTALL_DIR}"

wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh -b -f -p "${CONDA_INSTALL_DIR}"
${CONDA_INSTALL_DIR}/bin/conda env create -f environment.yaml

rm Miniconda3-latest-Linux-x86_64.sh
${CONDA_INSTALL_DIR}/bin/conda clean --all --yes

# Specify Jupyter kernel start-up script.

echo '#!/bin/bash
module purge
source '"${CONDA_INSTALL_DIR}"'/etc/profile.d/conda.sh
conda activate '"${JUPYTER_KERNEL_NAME}"'
exec python "$@"' > "${CONDA_INSTALL_DIR}"/kernel.sh

chmod +x "${CONDA_INSTALL_DIR}"/kernel.sh

# Manually register Jupyter kernel.

JUPYTER_USER_KERNEL_DIR=${HOME}/.local/share/jupyter/kernels/${JUPYTER_KERNEL_NAME}
mkdir -p "${JUPYTER_USER_KERNEL_DIR}"

echo '{
 "argv": [
  "'"$CONDA_INSTALL_DIR"'/kernel.sh",
  "-m",
  "ipykernel_launcher",
  "-f",
  "{connection_file}"
 ],
 "display_name": "my-pykernel",
 "language": "python",
 "metadata": {
  "debugger": true
 }
}' > "${JUPYTER_USER_KERNEL_DIR}"/kernel.json

# $ CONDA_INSTALL_DIR=${HOME}/my-pykernel JUPYTER_KERNEL_NAME=my-pykernel bash -c 'source ${CONDA_INSTALL_DIR}/etc/profile.d/conda.sh; conda activate ${JUPYTER_KERNEL_NAME}; ipython kernel install --name my-pykernel --prefix ${HOME}/tmp'
# $ cat ${HOME}/tmp/share/jupyter/kernels/my-pykernel/kernel.json
#
# {
#  "argv": [
#   "/home/jovyan/my-pykernel/envs/my-pykernel/bin/python",
#   "-m",
#   "ipykernel_launcher",
#   "-f",
#   "{connection_file}"
#  ],
#  "display_name": "my-pykernel",
#  "language": "python",
#  "metadata": {
#   "debugger": true
#  }
# }

# References
# https://docs.jupyter-jsc.fz-juelich.de/github/FZJ-JSC/jupyter-jsc-notebooks/blob/master/001-Jupyter/Create_JupyterKernel_conda.ipynb
# https://github.com/geomar-od/visualize-15-million-trajectories/tree/af46ce2bdfe94af84f2725e74a275d323cd92776/envs
# https://conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html#creating-an-environment-from-an-environment-yml-file
# https://conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html#creating-an-environment-file-manually
# https://ipython.readthedocs.io/en/stable/install/kernel_install.html#kernels-for-different-environments

environment.yaml

name: my-pykernel
channels:
  - conda-forge
dependencies:
  - ipykernel