Automatic Jupyter setup with kernel culling

setup_jupyter.sh

#!/bin/bash

if [[ "$1" == "-h" ]]; then
  echo "**Usage:** ./setup_jupyter.sh <environment> <port>"
  echo ""
  echo "  environment (required): The name of the conda environment to create. Use base to only provide the configuration and conda is already set-up."
  echo "  port (required): The port number on which to run the Jupyter server (integer >= 5000)."
  exit 0
fi

# Check for at least two arguments (environment and port)
if [[ $# -lt 2 ]]; then
  echo "Error: Please provide both environment name (optional) and port number."
  echo "Run './setup_jupyter.sh -h' for help."
  exit 1
fi

# Check if port number is an integer greater than or equal to 5000
if [[ ! "$2" =~ ^[0-9]+$ ]] || [[ "$2" -lt 5000 ]]; then
  echo "Error: Port number must be an integer greater than or equal to 5000."
  echo "Run './setup_jupyter.sh -h' for help."
  exit 1
fi

if command -v conda >/dev/null 2>&1; then
  condapath=$(which conda)
  echo "Conda is found in $condapath"
else
  echo "Conda is not found. Downloading..."
  wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
  chmod +x Miniconda3-latest-Linux-x86_64.sh
  ./Miniconda3-latest-Linux-x86_64.sh
  rm Miniconda3-latest-Linux-x86_64.sh
  source "$HOME/.bashrc"
fi

if ! command -v conda &> /dev/null; then
  echo "conda is not available in the path. Exiting."
  exit 1
fi 

conda_env_name=$1
config_file="$HOME/.jupyter/jupyter_server_config.py"
if [ -f "$config_file" ]; then 
  exists=1
else
  exists=0
fi

if conda env list | grep -q "^$conda_env_name"; then
  echo "Environment '$conda_env_name' already exists. Not creating another one"
else
  echo "Creating conda environment $conda_env_name..."
  conda create --name "$conda_env_name" python=3.12
fi

#activate the environment
#source activate "$conda_env_name"
eval "$(conda shell.bash hook)"
conda activate "$conda_env_name"

#echo "Done! Installing pytorch torchvision torchaudio matplotlib numpy jupyter notebook"
conda install pytorch torchvision torchaudio matplotlib numpy jupyter notebook pytorch-cuda=12.1 -c pytorch -c nvidia
#conda install jupyter notebook

echo "Done! Generating jupyter configuration"
jupyter server --generate-config

if [ -f "$HOME/.jupyter/jupyter_server_config.json" ] && grep "password" "$HOME/.jupyter/jupyter_server_config.json" >/dev/null 2>&1; then
  echo "It seems you already have a Jupyter password. Skipping..."
else
  echo "Pick a password"
  jupyter notebook password
fi

edit_file_with_pattern() {

  # Function arguments
  local file_path="$1"
  local search_pattern="$2"
  local new_line="$3"

  # Check if required arguments are provided
  if [[ -z "$file_path" || -z "$search_pattern" || -z "$new_line" ]]; then
    echo "Error: Please provide all required arguments: file_path, search_pattern, new_line"
    return 1
  fi

  # Use sed to edit the file in-place
  sed -i "/$search_pattern/c\\$new_line" "$file_path"

}

echo "Done! Setting Jupyter notebook defaults"
edit_file_with_pattern "$config_file" "^\s*#\?\s*c\.ServerApp\.port\s*=\s*" "c.ServerApp.port = $2"
edit_file_with_pattern "$config_file" "^\s*#\?\s*c\.ServerApp\.ip\s*=\s*" "c.ServerApp.ip = '*'"
edit_file_with_pattern "$config_file" "^\s*#\?\s*c\.ServerApp\.open_browser\s*=\s*" "c.ServerApp.open_browser = False"
edit_file_with_pattern "$config_file" "^\s*#\?\s*c\.ServerApp\.allow_remote_access\s*=\s*" "c.ServerApp.allow_remote_access = True"

edit_file_with_pattern "$config_file" "^\s*#\?\s*c\.ServerApp\.shutdown_no_activity_timeout\s*=\s*" "c.ServerApp.shutdown_no_activity_timeout = 3*24*60*60"
edit_file_with_pattern "$config_file" "^\s*#\?\s*c\.MappingKernelManager\.cull_connected\s*=\s*" "c.MappingKernelManager.cull_connected = True"
edit_file_with_pattern "$config_file" "^\s*#\?\s*c\.MappingKernelManager\.cull_idle_timeout\s*=\s*" "c.MappingKernelManager.cull_idle_timeout = 24*60*60"
edit_file_with_pattern "$config_file" "^\s*#\?\s*c\.AsyncMappingKernelManager\.cull_connected\s*=\s*" "c.AsyncMappingKernelManager.cull_connected = True"
edit_file_with_pattern "$config_file" "^\s*#\?\s*c\.AsyncMappingKernelManager\.cull_idle_timeout\s*=\s*" "c.AsyncMappingKernelManager.cull_idle_timeout = 24*60*60"
edit_file_with_pattern "$config_file" "^\s*#\?\s*c\.GatewayMappingKernelManager\.cull_connected\s*=\s*" "c.GatewayMappingKernelManager.cull_connected = True"
edit_file_with_pattern "$config_file" "^\s*#\?\s*c\.GatewayMappingKernelManager\.cull_idle_timeout\s*=\s*" "c.GatewayMappingKernelManager.cull_idle_timeout = 24*60*60"