Skip to content
Snippets Groups Projects
Select Git revision
  • 3d3e240181dd9567976e57d8290e58d0c94462bf
  • main default protected
  • 1.0.0
3 results

code.json

Blame
  • README.md 25.73 KiB

    ISIS

    Join the chat at https://gitter.im/USGS-Astrogeology/isis3_cmake Join the discourse at https://astrodiscuss.usgs.gov Anaconda-Server Badge Anaconda-Server Badge DOI

    Table of Contents

    Requests for Comment

    The ISIS project uses a Request for Comment (RFC) model whereby major potential changes to the code base, data area, or binary delivery process are proposed, iterated on by any interested parties, and potentially adopted. Right now, RFCs are being housed in this repository's wiki with associated discussions occurring on astrodiscuss.

    Current open RFCs:

    • No Requests for Comment are currently open

    We encourage all contributors and users to review open RFCs and comment as these proposed changes will impact use of the software.

    FAQ

    We maintain a list of frequently encountered questions and issues. Before opening a new issue, please take a look at the FAQ.

    Installation

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

    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, Miniconda installer

    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.

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

      #Create a new conda environment to install ISIS in
      conda create -n isis python=3.6
      
      #Activate the environment
      #Depending on your version of Anaconda use one of the following:
      
      #Anaconda 3.4 and up:
      conda activate isis
      
      #Prior to Anaconda 3.4:
      source activate isis
      
      #Add the following channels to the environment
      conda config --env --add channels conda-forge
      conda config --env --add channels usgs-astrogeology
      
      #Verify you have the correct channels:
      conda config --show channels
      
      #You should see:
      
      channels:
          - usgs-astrogeology
          - conda-forge
          - defaults
      
      #The order is important.  If conda-forge is before usgs-astrogeology, you will need to run:
      
      conda config --env --add channels usgs-astrogeology
    6. The environment is now ready to download ISIS and its dependencies:

      conda 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:

      conda install -c usgs-astrogeology isis=3.10.0
    7. Finally, setup the environment variables:

      To use the default values for: $ISISROOT, $ISISDATA, $ISISTESTDATA, run the ISIS variable initialization script with default arguments.

      To do this, for versions of ISIS 4.2.0 and earlier, use:

      python $CONDA_PREFIX/scripts/isis3VarInit.py

      For versions of ISIS after 4.2.0, use:

      python $CONDA_PREFIX/scripts/isisVarInit.py

      Executing this script with no arguments will result in ISISDATA=CONDA_PREFIX/data, and ISISTESTDATA=CONDA_PREFIX/testdata. The user can specify different directories for both of these optional values:

      For ISIS 4.2.0 and earlier, use:

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

      For versions of ISIS after 4.2.0, use:

      python $CONDA_PREFIX/scripts/isisVarInit.py --data-dir=[path to data directory]  --test-dir=[path to test data directory]

      More information about the ISISDATA environment variable and the ISIS Data Area can be found here. Now everytime the isis environment is activated, $ISISROOT, $ISISDATA, and $ISISTESTDATA will be set to the values passed to isisVarInit.py. This does not happen retroactively, so re-activate the isis envionment with one of the following commands:

      for Anaconda 3.4 and up - conda activate isis
      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 usgsastro/isis image from DockerHub.

    To build the Dockerfile

    1. Download the production Docker file
    2. Build the Dockerfile
    docker build -t isis -f production.dockerfile .