Updated the Installation instructions based on user feedback. Also fixed a...

#!/usr/bin/env python

import argparse

import os

import sys

##########################################################################################################

#Author:  Tyler Wilson

#Date  :  2018-10-05

#Description:  This script sets ISISROOT/ISIS3DATA/ISIS3TESTDATA for the user and is executed

#The data directory and test directory are optional command line arguments.  If the user chooses

#not to set them, they will both be placed created on the same level as the $ISISROOT directory

#within the conda environment.

#History:

#   Author:  Tyler Wilson

#   Date:    2018-11-01

#   Description:  Removed a pair of lines which were causing output errors on Mac OS X and were note

#                 needed anyway.

#

##########################################################################################################

parser = argparse.ArgumentParser(description='Usage:  ./isis3VarInit --data_dir <data dir path> --test_dir <test dir path')

os.popen('mkdir -p '+isisroot+'/etc/conda/activate.d')

os.popen('mkdir -p '+isisroot+'/etc/conda/deactivate.d')

os.system("echo -n '' >"+isisroot+"/etc/conda/activate.d/env_vars.sh")

os.popen("echo -n '' >"+isisroot+"/etc/conda/deactivate.d/env_vars.sh")

os.popen('touch '+isisroot+'/etc/conda/activate.d/env_vars.sh')

os.popen('touch '+isisroot+'/etc/conda/activate.d/env_vars.sh')

    <ol>

      <li>Download either the Anaconda or Miniconda installation script for your OS platform.  Anaconda is a much larger distribtion of packages supporting scientific python, while Miniconda is a minimal installation and not as large: 

      <a href="https://www.anaconda.com/download">Anaconda installer</a>, <a href="https://conda.io/miniconda.html">Miniconda installer</a></li>

      <li>Open a terminal window in the directory where you downloaded the script, and run the following commands.  In this example, we chose to do a full install of Anaconda, and our OS is Linux-based.  Your file name may be different depending on your environment.</li>

      <li>If you are running on some variant of Linux, open a terminal window in the directory where you downloaded the script, and run the following commands.  In this example, we chose to do a full install of Anaconda, and our OS is Linux-based.  Your file name may be different depending on your environment.</li>

        <pre>

          chmod +x Anaconda3-5.2.0-Linux-x86_64.sh

          ./Anaconda3-5.2.0-Linux-x86_64.sh          

          <strong>chmod +x Anaconda3-5.2.0-Linux-x86_64.sh</strong>

          <strong>./Anaconda3-5.2.0-Linux-x86_64.sh</strong>          

        </pre>

        This will start the Anaconda installer which will guide you through the installation process.

      <li>After the installation has finished, open up a bash prompt in your terminal window.</li>

      <li>Create a new environment for your ISIS3 installation:

       <li>If you are running Mac OS X, a pkg file (which looks similar to Anaconda3-5.3.0-MacOSX-x86_64.pkg) will be downloaded.  Double-click on the file to start the installation process.</li>

      <li>Again from within a terminal window, create a new environment for your ISIS3 installation:

        <pre>

          #Add the following channels to the Anaconda installation

          conda config --add channels conda-forge, usgs-astrogeology

          <em>#Add the following channels to the Anaconda installation</em>

          <strong>conda config --add channels conda-forge</strong>

          <strong>conda config --add channels usgs-astrogeology</strong>

          #Verify you have the correct channels:

          <strong>conda config --show channels</strong>

          <em>#You should see:</em>

          <strong>channels:</strong>

           <strong>   - usgs-astrogeology</strong>

           <strong>   - conda-forge</strong>

           <strong>   - defaults</strong>

           <em>#The order is important.  If conda-forge is before usgs-astrogeology, you will need to run:</em>

           <strong>conda config --add channels usgs-astrogeology</strong>

          #Create a new conda environment to install ISIS3 in

          conda create -n isis3

          <em>#Create a new conda environment to install ISIS3 in.</em>

          <strong>conda create -n isis3</strong>

          #Activate the environment

          source activate isis3

          <em>#Activate the environment</em>

          <strong>source activate isis3</strong>

          #Download the ISIS3 version

          conda install -c usgs-astrogeology isis3

          <em>#Download the ISIS3 version</em>

          <strong>conda install -c usgs-astrogeology isis3</strong>

          #Execute the ISIS3 variable initialization script with default arguments.

          #This script prepares default values for:  $ISISROOT/$ISIS3DATA/$ISIS3TESTDATA

          <em>#Execute the ISIS3 variable initialization script with default arguments.</em>

          <em>#This script prepares default values for:  $ISISROOT/$ISIS3DATA/$ISIS3TESTDATA</em>

          python $CONDA_PREFIX/scripts/isis3VarInit.py

          <strong>python $CONDA_PREFIX/scripts/isis3VarInit.py</strong>

         Executing this script with no arguments will result in $ISIS3DATA=$CONDA_PREFIX/data, 

         and $ISIS3TESTDATA=$CONDA_PREFIX/testdata.  The user can specify different directories

         for both of these optional values:

         ./$CONDA_PREFIX/scripts/isis3VarInit --data-dir=[path to data directory]  --test-dir=[path to test data directory]

         <strong>./$CONDA_PREFIX/scripts/isis3VarInit --data-dir=[path to data directory]  --test-dir=[path to test data directory]</strong>

          <em>#Run the source activate command a second time to process the changes:</em>

          <strong>source activate isis3</strong>

          To avoid having to do this every time you open a new terminal window, we suggest adding the following lines to the end of your .bashrc file

          (to ensure that conda is in your PATH variable):

          <strong>source activate isis3</strong>

          <strong>python $CONDA_PREFIX/scripts/isis3VarInit.py</strong>

          <strong>source activate isis3</strong>

          #Run the source activate command a second time to process the changes:

          source activate isis3

        </pre>

      </li>

  <history>

    <change name="Kristin Berry" date="2018-08-28">Original Version</change>

    <change name ="Tyler Wilson along with the ASC Development Team" date="2018-09-26">Updated version to incorporate installation through Conda</change>

    <change name="Tyler Wilson" date="2018-10-01">Updated version after feedback was received from outside users.</change>

  </history>