SalishSeaCmd Package Installation

SalishSeaCmd is a Python package that provides the salishsea command-line tool for doing various operations associated with the Salish Sea NEMO model. It is an extension of the NEMO-Cmd package customized for working with the SalishSeaCast NEMO model.

These instructions assume that:

• You have an up to date clone of the SalishSeaCmd repository.

• You have installed the Pixi package and environments manager (installation instructions).

Use Pixi to create an isolated environment for SalishSeaCmd to avoid conflicts with other Python packages installed on your system. That environment will have all of the Python packages necessary to use the salishsea command that is provided by the SalishSeaCmd package.

$ cd SalishSeaCmd
$ pixi install

When you are in the SalishSeaCmd/ directory (or a sub-directory) you can run the salishsea command with with the pixi run command. Example:

$ pixi run salishsea help

A common use-case is to execute the salishsea run command in the directory containing your run description YAML file. To accomplish that, you have to tell Pixi where to find the SalishSeaCmd/ directory so that it can use the correct environment. You do that by using the -m or --manifest option of pixi run. Example:

$ cd SS-run-sets/SalishSea/sea/Carbon_v202111/
$ pixi run -m $HOME/MEOPAR/SalishSeaCmd salishsea run 01jan11_Lb80.yaml \
    /scratch/allen/Carbon/MoreSens/Now/01jan11/

For doing development, testing, and documentation of the SalishSeaCmd package, please see the SalishSeaCmd Package Development section.