[SimulationEngine] Disentangle module data sharing in SimulationEngine

[ew3361zh]

Context

Issue(s) closed by this pull request: closes #2855 closes #2858

What

• Moves/creates key feed/ration data structures to allow for disentanglement of Feed and Animal modules
• Creates SimulationType properties to group simulation types by which modules are needed
• Refactors SimulationEngine.initialize_simulation() to only initialize necessary modules based on these SimulationType property groupings
• Disentangles ration formulation from feed degradation processing
• Only runs end-of-simulation reporting for specific modules if they were a part of the simulation.

TODOs remaining:

• Update E2E results - e.g. we should be expecting no results for animal module (and eventually Manure module) when FIELDS_AND_FEEDS simulation type runs
• Move/amend assembling crops_to_get_next_harvest_dates (needs FeedManager) in SimulationEngine._build_harvest_schedule() (a FieldManager operation)
• Figure out how to generate manure application results when there is no manure module initialized
• Move/amend storing harvested crops to FeedManager in SimulationEngine._execute_daily_field_operations() (a FieldManager operation)
• Reinstate check on whether to initialize the manure module in SimulationEngine._initialize_simulation()

Why

This is a key set of steps necessary to be able to isolate each RuFaS biophysical module and allow them all to run individually.

How

See What section and Files changed tab for now.

Test plan

So far have just run example_freestall and example_field_and_feed tasks on this branch but both seem successful.

Input Changes

Output Changes

• N/A

Filter

[github-actions]

Current Coverage: %

Mypy errors on sim-eng-data-disentanglement branch: 1274
Mypy errors on dev branch: 1191
83 more errors on sim-eng-data-disentanglement branch

[github-actions]

🚨 Please update the changelog. This PR cannot be merged until changelog.md is updated.
🚨 Flake8 linting errors were found. Please fix the linting issues.
🚨 Some tests have failed.

[github-actions]

Current Coverage: %

Mypy errors on sim-eng-data-disentanglement branch: 1218
Mypy errors on dev branch: 1191
27 more errors on sim-eng-data-disentanglement branch

[github-actions]

🚨 Please update the changelog. This PR cannot be merged until changelog.md is updated.
🚨 Flake8 linting errors were found. Please fix the linting issues.
🚨 Some tests have failed.

[github-actions]

Current Coverage: %

Mypy errors on sim-eng-data-disentanglement branch: 1218
Mypy errors on dev branch: 1191
27 more errors on sim-eng-data-disentanglement branch

[github-actions]

🚨 Please update the changelog. This PR cannot be merged until changelog.md is updated.
🚨 Flake8 linting errors were found. Please fix the linting issues.
🚨 Some tests have failed.