ISIS in other conda Envs (#126)

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:

# 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.)

 No newline at end of file

    - 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