Added setup step to main function flow

[jacobcook1995]

Description

This adds a setup step to the main function flow (which the abiotic_simple model needs to run correctly). This was added in before but seems to have been overwritten (potentially due to bad git merging on my part).

There's no testing of it as it's pretty hard to test things in vr_run in a sane manner.

Type of change

• New feature (non-breaking change which adds functionality)
• Optimization (back-end change that speeds up the code)
• Bug fix (non-breaking change which fixes an issue)

Key checklist

• Make sure you've run the pre-commit checks: $ pre-commit run -a
• All tests pass: $ poetry run pytest

Further checks

• Code is commented, particularly in hard-to-understand areas
• Tests added that prove fix is effective or that feature works

[vgro]

LGTM