Atlantis Code Development Environment

The AtlantisCmd package includes an environment called atlantis-code for doing development and debugging of the Atlantis code, as well as analysis of model run results using R via the CSIRO Shiny apps and Python using Jupyter Lab.

These instructions assume that you have installed the Pixi package and environments manager (installation instructions), and that you have already set up the Atlantis command processor package (AtlantisCmd Package Installation).

Use Pixi to create the isolated atlantis-code environment to avoid conflicts the AtlantisCmd environment or with other Python packages installed on your system.

$ cd AtlantisCmd
$ pixi install -e atlantis-code

You can then run commands that use the atlantis-code environment by prefixing them with pixi run -m /ocean/$USER/Atlantis/AtlantisCmd -e atlantis-code. Alternatively, you can launch a sub-shell in the atlantis-code environment with pixi shell -e atlantis-code. In the sub-shell, you can use commands without the pixi run ... prefix. That can be convenient when you are working in the edit-make-run-evaluate cycle. Use exit to end the sub-shell.