ISIS in other conda Envs (#126)

* ISIS in other conda Envs

* downloadIsisData for isis <= 7

docs/how-to-guides/environment-setup-and-maintenance/isis-data-area.md

@@ -97,6 +97,23 @@ downloadIsisData [mission] [download destination] [optional flags]
 downloadIsisData --help
 ```
 
+??? "downloadIsisData script for ISIS 7.0.0 and earlier"
+
+    The `downloadIsisData` was not included with earlier versions of ISIS.  To use it for those versions, download three things first: rclone, the `downloadIsisData` script and the `rclone.conf` file.
+
+    ```sh
+    # Install rclone 
+    conda install -c conda-forge rclone
+
+    # Download the script and rclone config file
+    curl -LJO https://github.com/USGS-Astrogeology/ISIS3/raw/dev/isis/scripts/downloadIsisData
+    curl -LJO https://github.com/USGS-Astrogeology/ISIS3/raw/dev/isis/config/rclone.conf
+
+    # Use python 3 when you run the script,
+    # and use --config to point to where you downloaded the config file 
+    python3 downloadIsisData --config rclone.conf <mission> $ISISDATA
+    ```
+
 ### Full Download
 
 To download **ALL** Isis data, including the base and all of the mission data areas:

docs/how-to-guides/environment-setup-and-maintenance/using-isis-in-other-conda-envs.md

@@ -0,0 +1,124 @@
+# Using ISIS in other Conda Environments
+
+The ISIS conda package pins some of its requirements, 
+which may clash with other packages. 
+
+Therefore, if you want to use ISIS in conjunction with other conda packages, 
+we recommend that you ***avoid*** adding other packages to the environment 
+you create when you 
+[install ISIS](../../how-to-guides/environment-setup-and-maintenance/installing-isis-via-anaconda.md). 
+This is similar to the best-practice of keeping your 
+`base` conda environment free of extra conda packages.
+
+Instead, when you need to run ISIS programs in other conda environments, try **Stacking**.  Or, for some more complex scenarios, you can try *editing the activation script*.
+
+-----
+
+## Stacking (Easy)
+
+Create a working environment (we call ours `working` in this tutorial) and add the conda packages you need.
+
+To stack environments, first activate your `isis` environment.  Then activate your `working` env on top of your isis env with the `--stack` argument.
+
+```sh
+conda activate isis
+conda activate --stack working
+```
+
+That's it, your `working` env is now stacked on top of your `isis` env.
+
+!!! note "Exiting stacked environments: run `conda deactivate` twice"
+
+    You'll have to run `conda deactivate` two times to exit your conda environments: once to get out of `working`, and then once more to get out of `isis`.
+
+-----
+
+## Editing the Activation Script (Hard)
+
+Stacking might not work if you have 
+a complex set of packages/dependencies,
+so here's one alternative: editing the activation script.
+
+!!! warning
+
+    If you aren't comfortable following these steps
+    for editing the activation script, contact your
+    system administrator.
+
+In theory, all you really need in your `working` env are the
+ISIS environmental variables and the path to the ISIS apps.  You can set those up by customizing your conda env's `activate.d/` and `deactivate.d/` directories.
+
+1.  **Working Env**  
+    Create your `working` conda env and add the packages you need.  
+    </br>
+
+1.  **Base Conda Prefix**  
+    Locate the path to your base conda environment.
+
+        echo $CONDA_PREFIX
+
+    Our Result: `~/miniconda3`.  
+    You should use your own result from the above command.  
+    </br>
+
+1.  **ISIS Conda Prefix**  
+    Locate the path to your ISIS conda environment:
+
+        conda activate isis
+        echo $CONDA_PREFIX
+
+    Our Result: `~/miniconda3/envs/isis`.  
+
+    You can do the same thing to find the path to your `working`
+    environment, our result being `~/miniconda3/envs/working`.  
+    </br>
+
+1.  **Copy Scripts**  
+    Copy the ISIS activation and deactivation scripts to your new
+    environment.
+
+    !!! warning "Don't just copy & paste our commands, use your own system details."
+
+        For steps 4-6, use your own **env names** and **folder names**, don't just copy and paste.  If your shell *doesn't use bash*, you may need to use a different `env_vars.*` file, and/or different command syntax.
+
+    ```sh
+    # Go to your conda envs folder
+    cd ~/miniconda3/envs/
+
+    # create activate.d and deactivate.d folders in your 'working' env
+    mkdir -p working/etc/conda/activate.d/
+    mkdir -p working/etc/conda/deactivate.d/
+
+    # Copy activation and deactivation scripts
+    # from your 'isis' env to your 'working' env.
+    cp isis/etc/conda/activate.d/env_vars.sh working/etc/conda/activate.d/env_vars.sh
+    cp isis/etc/conda/deactivate.d/env_vars.sh working/etc/conda/deactivate.d/env_vars.sh
+    ```  
+    </br>
+
+
+1.  **Add /bin to path at Activation**  
+    Edit the copied activation file in
+    `~/miniconda3/envs/working/etc/conda/activate.d/` to add the
+    ISIS executable directory to the path, by adding this line at the
+    end:
+
+    ```sh
+    export PATH=$PATH:$ISISROOT/bin
+    ```
+
+    It's important to add `$ISISROOT/bin` to the end of the path in your
+    working environment, not the beginning.  
+    </br>
+
+1.  **Remove /bin from path at Deactivation**  
+    Edit the copied deactivation file in
+    `$HOME/anaconda3/envs/working/etc/conda/deactivate.d/` to remove
+    the path, by adding this line at the end:
+
+    ```sh
+    export PATH=`echo -n $PATH | awk -v RS=: -v ORS=: '/isis/ {next} {print}' | sed 's/:$//'`;`
+    ```
+
+    (`isis` here being the name of your isis env.  You can look in
+    the `activate.d/env_vars.sh` file to see what it should be.)

mkdocs.yml

@@ -57,6 +57,7 @@ nav:
     - Environment Setup and Maintenance:
       - Installing ISIS:                   how-to-guides/environment-setup-and-maintenance/installing-isis-via-anaconda.md
       - Setting up the ISIS Data Area:     how-to-guides/environment-setup-and-maintenance/isis-data-area.md
+      - Using ISIS in other Conda Envs:    how-to-guides/environment-setup-and-maintenance/using-isis-in-other-conda-envs.md
       - Anaconda in a Network Environment: how-to-guides/environment-setup-and-maintenance/anaconda-in-a-network-environment.md
       - SPICE Kernel Updates in ISIS:      how-to-guides/environment-setup-and-maintenance/spice-kernel-updates-in-isis.md
       - Adding USGSCSM Plugin to ISIS:     how-to-guides/environment-setup-and-maintenance/adding-usgscsm-plugin-to-isis.md