py_env_create

#!/bin/bash
#
# py_env_create -- setup the python environment in order to use SLIM python tools
#
# Simple bash script to setup the python environment for the user so they can run the SLIM
# python tools using "conda".
#
dir=${0%/*}
if [ "$dir" = "$0" ];then
  dir="."
fi

# Check if conda is in your path
conda --help >& condahelp.txt
error=$?
if [ $error != 0 ]; then
   echo "conda is NOT in your path for the bash shell add it with modules or whatever is required on your system to get it in your path"
   echo "on cheyenne/capser/etc use -- module load conda"
   echo "on izumi/CGD systems use -- module load lang/python"
   echo "For notes on installing on a user system see: https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html"
   echo "Error code was $error"
   cat condahelp.txt
   exit -1
fi
rm condahelp.txt
python_env=slim_pylib


condadir="$dir/python"

domain=`domainname`
if [[ $domain =~ cgd.* ]]; then
   condafile="conda_env_slim_py_cgd.txt"
else
   condafile="conda_env_slim_py.txt"
fi
#----------------------------------------------------------------------
# Usage subroutine
usage() {
  echo ""
  echo "***********************************************************************"
  echo "usage:"
  echo "./py_env_create"
  echo ""
  echo "valid arguments: "
  echo "[-h|--help]  "
  echo "     Displays this help message"
  echo "[-v|--verbose]  "
  echo "     Run with verbose mode for the install so you see the progress bar"
  echo "[-f|--file <file>]  "
  echo "     Conda environment file to use (can be a text format or YAML format)"
  echo "     Assumed to be under the directory: $condadir"
  echo "     Default is: $condafile"
  echo "[--option <option>]  "
  echo "     Option(s) to pass to 'conda install' step"
  echo "***********************************************************************"
}

verbose="No"
option=""
while [ $# -gt 0 ]; do
   case $1 in
       -h|--help )
           usage
           exit 0
           ;;
       -v|--verbose )
           verbose="Yes"
           ;;
       -f|--file )
           condafile=$2
           shift
           ;;
       --option )
           option=$2
           shift
           ;;
       * )
           echo "ERROR:: invalid argument sent in: $2"
           usage
           exit 1
           ;;
   esac
   shift
done

if [ ! -f $condadir/$condafile ]; then
   echo "$condadir/$condafile does NOT exist"
   echo "Use the --file option with a valid filename"
   exit -1
fi

echo "Use conda to install the python environment needed to run the SLIM python tools in the conda environment: $python_env"
echo "Using the file: $condadir/$condafile"

# Check if the environment already exists, if it does continue, if not create it
conda list -n $python_env >& /dev/null
if [ $? != 0 ]; then
   echo "Create $python_env"
   cmd="conda create --force -n $python_env -q"
   echo "$cmd"
   $cmd
   if [ $? != 0 ]; then
      echo "Error creating conda environment $python_env"
      exit -1
   fi
else
   echo "$python_env environment already exists"
fi
echo "Install $python_env this can take a long time, be patient...."
verbosity="-q"
if [ "$verbose" == "Yes" ]; then
  verbosity="-v"
fi
cmd="conda install --yes $verbosity -c conda-forge -n $python_env --file $condadir/$condafile $option"
echo "$cmd"
$cmd
if [ $? != 0 ]; then
   echo "Trouble installing the $python_env python environment"
   echo "There must be a problem in the $condadir/$condafile conda specification environment file"
   echo "Change the file and try again"
   if [[ $domain =~ cgd.* ]]; then
       pythonpath=`which python`
       echo
       echo "On CGD systems you may need to do the following..."
       echo "Create a bin subdirectory and then link the python version into it..."
       echo "   mkdir $HOME/.conda/envs/$python_env/bin/"
       echo "   ln -s $pythonpath $HOME/.conda/envs/$python_env/bin/python3.7"
       echo
   fi
   exit -2
fi
echo "Successfully installed the $python_env python environment"
echo
echo "activate the environment by doing the following..."
echo "conda activate $python_env"