666 repair model attribute typing and docstrings

[sallymatson]

Description

Move attribute declarations out of _setup to subclass __init__ functions. The attributes are now defined and documented in the proper place (e.g. see updated hydrology docs as compared to old hydrology docs).

It would be great to get general feedback, as well as everyone looking over the changes to their modules in order to make sure the variables are all typed correctly etc @vgro @davidorme @jacobcook1995 @TaranRallings.

Fixes #666

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
• Relevant documentation reviewed and updated

[codecov-commenter]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 94.66%. Comparing base (7838fa8) to head (1dabb2a).

Additional details and impacted files

@@             Coverage Diff             @@
##           develop     #692      +/-   ##
===========================================
+ Coverage    94.60%   94.66%   +0.05%     
===========================================
  Files           73       73              
  Lines         4800     4833      +33     
===========================================
+ Hits          4541     4575      +34     
+ Misses         259      258       -1     

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[dalonsoa]

The changes look good, and indeed this is a more canonical approach than using fake class variables.

Probably the docs should be updated to explain what goes in __init__ and what in _setup when creating a new model.

[davidorme]

This is looking good. Can you update the doc API files for the models to include inherited members? I think that's what we want as we currently can't see anything being inherited from the base class.

For example:

virtual_ecosystem/docs/source/api/models/plants/plants_model.md

Lines 29 to 36 in 7838fa8

	## The {mod}`~virtual_ecosystem.models.plants.plants_model` module
	```{eval-rst}
	.. automodule:: virtual_ecosystem.models.plants.plants_model
	:autosummary:
	:members:
	:exclude-members: model_name
	```

should go to (I think):

```{eval-rst}
.. automodule:: virtual_ecosystem.models.plants.plants_model
    :autosummary:
    :members:
    :exclude-members: model_name
    :inherited_members:
```

[sallymatson]

This is looking good. Can you update the doc API files for the models to include inherited members? I think that's what we want as we currently can't see anything being inherited from the base class.

For example:

virtual_ecosystem/docs/source/api/models/plants/plants_model.md

Lines 29 to 36 in 7838fa8

	## The {mod}`~virtual_ecosystem.models.plants.plants_model` module
	```{eval-rst}
	.. automodule:: virtual_ecosystem.models.plants.plants_model
	:autosummary:
	:members:
	:exclude-members: model_name
	```

should go to (I think):

```{eval-rst}
.. automodule:: virtual_ecosystem.models.plants.plants_model
    :autosummary:
    :members:
    :exclude-members: model_name
    :inherited_members:

I added this. I'm a bit confused about how the docs work TBH because in the version that I built and linked in the description above, it does seem to be showing? Is that in a different place? Anyways, added :inherited-members: to all of them !

[davidorme]

This looks good - we really need to update the model creation docs, but we also need to do that to reflect the static model changes as well, so lets do that separately under #676