Updates and edits to InstallGuide.xml, as well as the isis3VarInit script...

#!/usr/bin/env python

import os

#Might need to make these command line args.

isisroot = '$CONDA_PREFIX'

data_dir='$CONDA_PREFIX/..data'

testdata_dir='$CONDA_PREFIX/..testData'

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

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

os.popen("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')

os.popen("echo '#!/bin/sh' >> "+isisroot+ "/etc/conda/activate.d/env_vars.sh")

os.popen("echo 'export ISISROOT="+isisroot+"' >>"+isisroot+"/etc/conda/activate.d/env_vars.sh")

os.popen("echo 'export ISIS3DATA="+data_dir+"' >>"+isisroot+"/etc/conda/activate.d/env_vars.sh")

os.popen("echo 'export ISIS3TESTDATA="+testdata_dir+"' >>"+isisroot+"/etc/conda/activate.d/env_vars.sh")

os.popen("echo '#!/bin/sh' >> "+isisroot+ "/etc/conda/deactivate.d/env_vars.sh")

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

os.popen("echo 'unset ISIS3DATA' >>"+isisroot+"/etc/conda/deactivate.d/env_vars.sh")

os.popen("echo 'unset ISIS3TESTDATA' >>"+isisroot+"/etc/conda/deactivate.d/env_vars.sh")

  <h2>Overview</h2>

  <p>

    This installation guide is for ISIS3 users interested in installing ISIS3 through conda, or compiling on their own systems using cmake.  

    This installation guide is for ISIS3 users interested in installing ISIS3 (3.6.0)+ through conda.  

    If you are a developer, we refer you to our <a href="https://github.com/USGS-Astrogeology/ISIS3">GitHub repository.</a>

  </p>

    <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):</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>

        <pre>

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

          ./Anaconda3-5.2.0-Linux-x86_64.sh          

          conda config --add channels usgs-astrogeology

          #Create a new conda environment to install ISIS3 in

          conda create -n isis3alpha

          conda create -n isis3

          #Activate the environment

          source activate isis3alpha

          source activate isis3

          #Download the ISIS3 version with label alpha

          conda install -c usgs-astrogeology/label/alpha isis3

          conda install -c usgs-astrogeology isis3

          #Execute the ISIS3 variable initialization script.  

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

         ./$CONDA_PREFIX/scripts/isis3VarInit

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

          source activate isis3alpha

          #Set the ISISROOT variable

          export ISISROOT=$CONDA_PREFIX

          #Execute the ISIS3 startup script

          source $CONDA_PREFIX/scripts/isis3Startup.sh

        </pre>

      </li>

<h3>How do I install ISIS3.5.2 or earlier?</h3>

    <p>

         If you are looking for a version of ISIS3 prior to 3.5.3, please

         If you are looking for a version of ISIS3 prior to 3.6.0, please

        <a href="../../documents/LegacyInstallGuide/index.html">refer to the Legacy ISIS3 Installation

        Guide</a> for instructions on downloading and installing ISIS3, version 3.5.2 or earlier.

        Guide</a> for instructions on downloading and installing ISIS3, versions prior to 3.6.0.

    </p>

      </body>

      This document describes how to download/compile and install a

      binary version of ISIS3 as well

    </description>

    <author>ASC Development Team</author>

    <author>Kristin Berry</author>

    <date>2018-08-28</date>

  </bibliography>

</documentation>