install_script.sh

#!/usr/bin/env bash

# References
# http://kvz.io/blog/2013/11/21/bash-best-practices/
# http://jvns.ca/blog/2017/03/26/bash-quirks/

# default logfile name
FILENAME="jupyter-vcdat_logfile.txt"

# dev conda channels to use
DEV_CHANNELS="-c cdat/label/v8.2.1 -c conda-forge"

# user conda channels (stable)
USER_CHANNELS="-c cdat/label/v8.2.1 -c conda-forge"

# choose base packages based on OS
if [[ "$OSTYPE" == "linux-gnu"* ]]; then
  BASE_CONDA_PKGS="pip cdms2 vcs tqdm nodejs 'python=3.7' jupyterlab jupyterhub ipywidgets numpy 'mesalib=18.3.1'"
elif [[ "$OSTYPE" == "darwin"* ]]; then
  BASE_CONDA_PKGS="pip cdms2 vcs tqdm nodejs 'python=3.7' jupyterlab jupyterhub ipywidgets numpy 'mesalib=17.3.9'"
fi

# dev and test packages
DEV_CONDA_PKGS="testsrunner cdat_info"

# default env name
REQUESTED_ENV_NAME="jupyter-vcdat"

# NOT VERBOSE by default
VERBOSE=0

# installation mode (USER or DEV)
INSTALL_MODE="USER"

# conda channels to use
CONDA_CHANNELS="$USER_CHANNELS"
CONDA_PACKAGES=$BASE_CONDA_PKGS

function usage() {
  cat <<EOF
usage: Install vcdat jupyter-lab extension

optional arguments:
  -h, --help            
                        show this help message and exit
  -f FILENAME, --FILENAME FILENAME
                        name of file where to log output
  -v VERBOSE
                        Also prints output to screen
  -d DEVELOPER
                        Installs developer version with developer tools
  -n CONDA_ENV_NAME, --name CONDA_ENV_NAME
                        Name of the conda environment to install in (will create if not existing)
EOF
  exit 0
}

# Figure out command line arguments: http://linuxcommand.org/lc3_wss0120.php
while [ "$1" != "" ]; do
  case $1 in
  -f | --file)
    shift
    FILENAME=$1
    ;;
  -v | --VERBOSE)
    VERBOSE=1
    ;;
  -n | --name)
    shift
    REQUESTED_ENV_NAME=$1
    ;;
  -d | --dev)
    INSTALL_MODE="DEV"
    ;;
  -h | --help)
    usage
    ;;
  *)
    usage
    exit 1
    ;;
  esac
  shift
done

echo "Installing jupyter-vcdat extension in conda env: '${REQUESTED_ENV_NAME}' (you can change this via -c option)"

# Choose conda channels and packages based on installion mode
if [ $INSTALL_MODE == "DEV" ]; then
  CONDA_CHANNELS="$DEV_CHANNELS $BASE_CHANNELS"
  CONDA_PACKAGES="$BASE_CONDA_PKGS $DEV_CONDA_PKGS"
fi

echo "Using following conda channels: '${CONDA_CHANNELS}'"
echo "Output will be redirected to: '$FILENAME' (you can control the FILENAME with -f option)"
# Redirect to logfile and possibly screen if verbose
if [ $VERBOSE == 1 ]; then
  # Redirect stdout ( > ) into a named pipe ( >() ) running "tee"
  exec > >(tee -i $FILENAME)
else
  echo "Going into quiet mode, suppressing output"
  echo "For verbose mode run with -v option"
  # https://stackoverflow.com/questions/637827/redirect-stderr-and-stdout-in-bash
  # Close STDOUT file descriptor
  exec 1<&-
  # Close STDERR FD
  exec 2<&-

  # Open STDOUT as $LOG_FILE file for read and write.
  exec 1<>$FILENAME
fi

# Without this, only stdout would be captured - i.e. your
# log file would not contain any error messages.
exec 2>&1

# exit when a command fails
set -o errexit

# exit if any pipe commands fail
set -o pipefail

set -E
set -o functrace
function handle_error() {
  local retval=$?
  local line=${last_lineno:-$1}
  echo "Failed at $line: $BASH_COMMAND"
  echo "Trace: " "$@"
  echo "return code: " "$?"
  exit $retval
}
trap 'handle_error $LINENO ${BASH_LINENO[@]}' ERR

CONDA_EXE="$(which conda)"

# Activate requested conda environment
if [ ${CONDA_DEFAULT_ENV:-"NA"} != ${REQUESTED_ENV_NAME} ]; then
  echo "Current conda does not match requested conda: ${CONDA_DEFAULT_ENV:-'NA'} vs ${REQUESTED_ENV_NAME}"
  envs=$(${CONDA_EXE} env list | cut -d ' ' -f1)
  found=0
  for a_env in $envs; do
    if [ $a_env == ${REQUESTED_ENV_NAME} ]; then
      found=1
    fi
  done
  if [ $found == 1 ]; then
    echo "ACTIVATING existing env: ${REQUESTED_ENV_NAME}"
    conda activate ${REQUESTED_ENV_NAME}
  else
    echo "The requested env ${REQUESTED_ENV_NAME} does not seem to exist we will create it."
  fi
fi

if [ ${CONDA_DEFAULT_ENV:-"NA"} != ${REQUESTED_ENV_NAME} ]; then
  # If requested conda environment doesn't exist, create it
  echo "Creating conda env: ${REQUESTED_ENV_NAME}"
  conda config --set channel_priority strict
  echo "conda create -y -n ${REQUESTED_ENV_NAME} $CONDA_CHANNELS $CONDA_PACKAGES"
  conda create -y -n ${REQUESTED_ENV_NAME} $CONDA_CHANNELS $CONDA_PACKAGES
  CONDA_BASE=$(conda info --base)
  source $CONDA_BASE/etc/profile.d/conda.sh
  conda activate ${REQUESTED_ENV_NAME}
else
  # Install required conda packages into existing environment
  echo "Installing conda packages in  environment: ${REQUESTED_ENV_NAME}"
  conda config --set channel_priority strict
  echo "conda install -y $CONDA_CHANNELS $CONDA_PACKAGES"
  conda create -y $CONDA_CHANNELS $CONDA_PACKAGES
fi

# Install sidecar
python -m pip install sidecar || pip install sidecar

# Install dev packages if needed
if [ $INSTALL_MODE == "DEV" ]; then
	python -m pip install flake8 || pip install flake8
	python -m pip install selenium || pip install selenium
	python -m pip install pyvirtualdisplay || pip install pyvirtualdisplay
fi

# Install extensions
jupyter labextension install @jupyter-widgets/jupyterlab-manager --no-build
jupyter labextension install @jupyter-widgets/jupyterlab-sidecar --no-build
jupyter labextension install jupyterlab-tutorial-extension --no-build
jupyter labextension install @jupyterlab/hub-extension --no-build

# Install jupyter-vcdat extension
npm install
jupyter lab build
jupyter labextension install .

# Success message
echo Jupyter VCDAT has been successfully installed!
echo "To run: conda activate ${REQUESTED_ENV_NAME} && jupyter lab"