Retiring `BaseModel.setup`

[davidorme]

Description

This PR:

• Moves AnimalModel.setup to AnimalModel._setup, keeping the same organisation. This is called from within __init__, as before.
• Removes BaseModel.setup from the BaseModel definition
• Removes calls to model setup methods in the main runner.
• Updates docs
• Fixes tests.

Fixes #540 (issue)

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)
• [x] None of the above! A breaking change (API change) to remove unneeded complexity.

Key checklist

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

Further checks

• [x] Code is commented, particularly in hard-to-understand areas
• [x] Tests added that prove fix is effective or that feature works
• [x] Relevant documentation reviewed and updated

[codecov-commenter]

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 94.96%. Comparing base (f3c6f53) to head (d2abee5).

Additional details and impacted files

```diff @@ Coverage Diff @@ ## develop #541 +/- ## =========================================== - Coverage 94.98% 94.96% -0.02% =========================================== Files 74 74 Lines 4145 4135 -10 =========================================== - Hits 3937 3927 -10 Misses 208 208 ```

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