Defining the CoreComponents, LayerStructure and ModelTiming classes

[davidorme]

Description

Following the discussion in #369, we've aligned on a solution that tries to strike a balance between the original completely identical BaseModel subclass signatures and something that retains some of the model to model differences. See
#369 (comment) for a sketch of this solution.

That requires a dataclass of core details that can be created once and then passed to all model initialisations. Models will then share a genuine single copy of those details - not individual identical copies - and model signatures can avoid the more opaque Config objects while still inheriting core components.

This PR implements that by creating CoreComponents which includes nested classes for LayerStructure and ModelTiming. Those borrow heavily from existing code for generating layer_roles and the extract_timing_details function. Once this is accepted, those functions will disappear and an instance of CoreComponents can be used in their place.

Issue #369 is not completed by this PR, but it would be good to agree on this structure and I can then adopt this structure in a second PR onto this, so we can break up the review a little bit!

Edited to add: That second WIP PR (#375) is now in progress - I wanted to see if implementing the changes here threw up anything unexpected. They did not.

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

[codecov-commenter]

Codecov Report

Attention: 7 lines in your changes are missing coverage. Please review.

Comparison is base (e9365f0) 93.30% compared to head (42bd787) 93.18%.

Files	Patch %	Lines
virtual_rainforest/core/core_components.py	94.21%	7 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           develop     #374      +/-   ##
===========================================
- Coverage    93.30%   93.18%   -0.13%     
===========================================
  Files           59       60       +1     
  Lines         2866     2918      +52     
===========================================
+ Hits          2674     2719      +45     
- Misses         192      199       +7     

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[davidorme]

Something odd going on with sphinx (what a surprise) that means it can't seem to find references for imported objects like InitVar and np abbreviations.

[jacobcook1995]

Looks sensible to me, just one small query.

Also I can't work out why codecov is claiming that your changes have 0% test coverage, despite the fact you've written quite a few unit tests?

[vgro]

LGTM. My only concern is that we maybe overdo it with the wrapping and lose transparency.

[dalonsoa]

Looks good!

[dalonsoa]

By the time this is called, the config has already validated to ensure there's a core and a timing, right? I think so, but just cross checking.

[davidorme]

I've merged #375 into this branch, ready to merge the whole thing down into develop.