AtlantisCmd Package Installation

AtlantisCmd is a Python package that provides the atlantis command-line tool for managing runs of the CSIRO Atlantis ecosystem model.

Installation of AtlantisCmd is a 3 step process:

  1. Clone the SS-Atlantis/AtlantisCmd and SalishSeaCast/NEMO-Cmd repositories from GitHub

  2. Create the atlantis-cmd conda environment

  3. Install the NEMO-Cmd and AtlantisCmd packages in the atlantis-cmd environment

The following sections assume that the base directory for your Atlantis work is /ocean/$USER/Atlantis/.

Once you have completed the installation, please see atlantis Sub-Commands for information about how to use the atlantis command, and Run Description File Structure for information about how to construct the run description YAML files that it uses.

Clone Repositories

The AtlantisCmd package relies on the NEMO-Cmd package for some of its functionality.

Clone the repositories from GitHub with:

$ cd /ocean/$USER/Atlantis/
$ git clone git@github.com:SalishSeaCast/NEMO-Cmd.git
$ git clone git@github.com:SS-Atlantis/AtlantisCmd.git

Note

The git clone command above assumes that you are connecting to GitHub using SSH. If it fails, please follow the instructions in our Secure Remote Access docs to set up your SSH keys and Copy Your Public ssh Key to GitHub.

Create Conda Environment

Create an isolated Conda environment for AtlantisCmd to avoid conflicts with other Python packages installed on your system. Assuming that you have Miniconda3 installed, you can create and activate an environment called atlantis-cmd that will have all of the Python packages necessary to use the atlantis command that is provided by the AtlantisCmd package. The environment will also include additional packages that are used for development, testing, and building the package documentation.

$ cd AtlantisCmd
$ conda env create -f envs/environment-dev.yaml

Whenever you want to use the atlantis command you will need to activate the atlantis-cmd environment with the command:

$ conda activate atlantis-cmd

You can tell that the environment is activated because your command-line prompt changes to includes the environment name in parenthesis like:

(atlantis-cmd)$

To deactivate the environment use:

(atlantis-cmd)$ conda deactivate

Install Packages

Activate your atlantis-cmd environment and install the NEMO-Cmd and AtlantisCmd packages in it. You only need to do this once when you are setting things up. After that, activating the atlantis-cmd environment makes the atlantis command available for use.

$ cd AtlantisCmd
$ conda activate atlantis-cmd
(atlantis-cmd)$ pip install --editable ../NEMO-Cmd
(atlantis-cmd)$ pip install --editable .

The --editable option in the pip install commands above install the packages from the cloned repos via symlinks so that the installed packages will be automatically updated as their repos evolve.

You can confirm that the AtlantisCmd package is installed and learn which version it is using with the command:

(atlantis-cmd)$ atlantis --version

The output of that command should be something like:

atlantis 21.1.dev0