Review the implementation section of the docs

[davidorme]

Description

This PR improves the implementation section of the documents. The docs for the PR are being built here:

https://virtual-ecosystem.readthedocs.io/en/514-review-the-implementation-section-of-the-docs/virtual_ecosystem/implementation/implementation.html

Broadly:

• remove code and methods etc. from the section and provide overview and conceptual text with some nice diagrams.
• add some stubs for missing work
• provide some simple functions to use the new variables system to generate nice markdown tables of variables for use in model implementations and in the variables listing. These functions are currently just floating in the sphinx tree but possibly should move into core.variables when they mature!

This PR also fiddles with sphinx:

• I've turned off the RemovedInSphinx80Warning warnings from sphinx.deprecation that are spamming the sphinx output and making it unreadable.

• I've added sphinx.ext.viewcode to provide links to the source code from the API docs. That does add some time, as the sphinx run has to highlight and include the module code in the docs, but it is a useful feature. See the [source] tag here:

  https://virtual-ecosystem.readthedocs.io/en/514-review-the-implementation-section-of-the-docs/api/core/config.html#virtual_ecosystem.core.config.Config

• I've turned on figure numbering using numref. That adds time for... reasons?

Fixes #514

Type of change

• [x] 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 :white_check_mark:

Project coverage is 94.93%. Comparing base (62ebb70) to head (ae99383).

Additional details and impacted files

```diff @@ Coverage Diff @@ ## develop #516 +/- ## ======================================== Coverage 94.93% 94.93% ======================================== Files 73 73 Lines 4050 4050 ======================================== Hits 3845 3845 Misses 205 205 ```

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[davidorme]

@dalonsoa and @jacobcook1995

I realised I was starting to run away with a grand documentation PR so I'm giving myself a stern talking to and stopping. Could you have another quick look and see if anything is wildly bad? The documentation stuff is quite 'dynamic' right now, so I think we'll likely have a tidy up phase once all of this has settled down.

[davidorme]

@dalonsoa Yup - we've got a lot of movement and it seems better to keep everything up to date in develop and use small PRs rather than spinning off into deep parallel PRs!