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)
• 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

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

[codecov-commenter]

Codecov Report

All modified and coverable lines are covered by tests ✅

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

Additional details and impacted files

@@             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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[dalonsoa]

The change looks ok, but I would hold on in case we actually need the setup method. Have a look at #373 - and the explanation in #373 (comment)

[davidorme]

This PR is outdated by the development of the static model