Unverified Commit 242f3629 authored by Michael Aye's avatar Michael Aye Committed by GitHub
Browse files

Cleaning up the Markdown a bit 

I saw that some sections had wrong section numbers as they were hardcoded instead of making use of Markdown's auto-numbering.
I repaired the indents for auto-numbering to work in the first half of the document and didn't touch the 2nd half where things looked okay.
parent 904956da

README.md

+73 −68
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@@ -41,18 +41,19 @@ This installation guide is for ISIS users interested in installing ISIS (3.6.0)+ 
### ISIS Installation With Conda



1. 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: [Anaconda installer](https://www.anaconda.com/download), [Miniconda installer](https://conda.io/miniconda.html)

2.  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.

1. 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.

    

    ```bash

    chmod +x Anaconda3-5.3.0-Linux-x86_64.sh

    ./Anaconda3-5.3.0-Linux-x86_64.sh





    ```

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



3.  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.

4.  After the installation has finished, open up a bash prompt in your terminal window.

5.  Next setup your Anaconda environment for ISIS. In the bash prompt, run the following commands:

1. 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.

1. After the installation has finished, open up a bash prompt in your terminal window.

1. Next setup your Anaconda environment for ISIS. In the bash prompt, run the following commands:



    ```bash

    #Create a new conda environment to install ISIS in

    conda create -n isis python=3.6
@@ -82,22 +83,27 @@ This installation guide is for ISIS users interested in installing ISIS (3.6.0)+ 
    #The order is important.  If conda-forge is before usgs-astrogeology, you will need to run:



    conda config --env --add channels usgs-astrogeology

    ```

    

6.  Download [Mamba](https://github.com/mamba-org/mamba). The ISIS environment is quite large and the Conda solver can take hours to resolve it. Instead, we recommend you use the much faster [Mamba](https://github.com/mamba-org/mamba) solver:

1. Download [Mamba](https://github.com/mamba-org/mamba). The ISIS environment is quite large and the Conda solver can take hours to resolve it. Instead, we recommend you use the much faster [Mamba](https://github.com/mamba-org/mamba) solver:

    

    ```bash

    conda install -n base -c conda-forge mamba

    ```

1. The environment is now ready to download ISIS and its dependencies:



7.  The environment is now ready to download ISIS and its dependencies:



    ```bash

    mamba install -c usgs-astrogeology isis

    ```

    

    If you would like to work with our latest ISIS version 3, rather than updating

    to ISIS 4, instead run:



    ```bash

    mamba install -c usgs-astrogeology isis=3.10.0

    ```





8.  Finally, setup the environment variables:

1. Finally, setup the environment variables:



    ISIS requires several environment variables to be set in order to run correctly.

    The variables include: ISISROOT and ISISDATA.
@@ -109,7 +115,7 @@ This installation guide is for ISIS users interested in installing ISIS (3.6.0)+ 


    There are two methods to configure the environment variables for ISIS:



    7.1 Using `conda env config vars` *preferred*

    1. Using `conda env config vars` *preferred*



       Conda has a built in method for configuring environment variables that are specific to a conda environment since version 4.8.

       This version number applies only to the conda package, not to the version of miniconda or anaconda that was installed.
@@ -142,7 +148,7 @@ This installation guide is for ISIS users interested in installing ISIS (3.6.0)+ 
       **Note** This method will not enable tab completion for arguments in C-Shell.





    7.2 Using the provided isisVarInit.py script:

    1. Using the provided isisVarInit.py script:



       To use the default values for: `$ISISROOT` and `$ISISDATA`, run the ISIS variable initialization script with default arguments:
@@ -159,7 +165,6 @@ This installation guide is for ISIS users interested in installing ISIS (3.6.0)+ 
           prior to Anaconda 3.4 - source activate isis







### Installation with Docker

The ISIS production Dockerfile automates the conda installation process above.

You can either build the Dockerfile yourself or use the