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 up to date clones of the SalishSeaCmd and NEMO-Cmd repositories

• You have a Conda Python environment and package manager (Miniforge or Miniconda3) installed

To install the SalishSeaCmd package so that the salishsea command is available in your $HOME/.local/bin/ directory, go to the directory in which you cloned the SalishSeaCmd and NEMO-Cmd repositories, then do:

$ conda env create -f SalishSeaCmd/envs/environment-hpc.yaml
$ conda activate salishsea-cmd
(salishsea-cmd)$ python3 -m pip install --user --editable NEMO-Cmd
(salishsea-cmd)$ python3 -m pip install --user --editable SalishSeaCmd

The --editable option in the pip install commands installs the packages in a way that they can be updated when new features are pushed to GitHub by simply doing a git pull in the package clone directories.

The --user option in the pip install ... SalishSeaCmd command installs the salishsea command in your $HOME/.local/bin/ directory which is where the SalishSeaNEMO.sh shell scripts generated by the salishsea run command expect to find it.

The SalishSeaCmd package can also be installed in an isolated conda environment. The common use case for doing so it development, testing, and documentation of the package; please see the SalishSeaCmd Package Development section for details.