Switch core over to new configuration

[davidorme]

Description

This PR updates the whole of the core model to using the new configuration system.

The big changes are:

• The core.core_component and core.grid modules have been updated to use data provided from core.model_config classes, removing all usage of the old Config dictionary.
• The core.model_config module has been updated to improve the docstrings and to provide better validation and class structure.
• The soil.model_config has been updated. I'd been planning to move forward with moving soil config into CSV files and had left a lot of structure out of this file, which is now provided. I still think we should move to CSV, but not within the [META] Replacing the configuration system. #1085 meta PR

The other changes are utility fixes, improvements

• Made the new configuration classes frozen and also stopped them silently ignoring unknown inputs.
• Added a TOML output method to CompiledConfiguration
• Some of the core tests were config validation within the setup - these tests are all now more appropriate at the level of the core.model_config classes since that is one of the key advantages of the new system. Bad configs basically can't be created.

Everything else is test fixes:

• Core stuff and the core fixtures all swap out the old style Config dict for the new classes.
• Other model tests are updated to fix. These mostly maintain a dual system for now until they can be swapped over. Several of the Model.from_config tests currently throw in a test case with bad config inputs. As noted above - this is no longer a thing under the new system - the configuration classes auto-validate on loading before they even get near a from_config method, so a bad Configuration object is no longer possible. I've propped these tests up for now but those test cases can be retired as models are updated.

Fixes #1101

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

❌ Patch coverage is 98.10127% with 3 lines in your changes missing coverage. Please review.
✅ Project coverage is 94.56%. Comparing base (8ad15e1) to head (18e8967).

Files with missing lines	Patch %	Lines
virtual_ecosystem/core/configuration.py	60.00%	2 Missing ⚠️
virtual_ecosystem/core/model_config.py	98.59%	1 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #1103      +/-   ##
===========================================
+ Coverage    94.55%   94.56%   +0.01%     
===========================================
  Files           90       90              
  Lines         7882     7916      +34     
===========================================
+ Hits          7453     7486      +33     
- Misses         429      430       +1     

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[davidorme]

@jacobcook1995 Do you think you'd have time to look at this before you leave? There are quite a lot of files, but it is basically swapping out configuration settings to maintain the same set of tests.

I've edited tests that incorporated config validation, since that now all happens much earlier.

[jacobcook1995]

@davidorme if it's ready to review now I can take a look today

[jacobcook1995]

LGTM! A few minor comments + queries but nothing that should prevent merging