Trophic record exporter

[TaranRallings]

Description

This PR builds on the existing cohort exporter to export a second csv file detailing every trophic interaction that occurs over the course of the model run. The purpose of this data export is so that the data team can build food web time-series.

The way it works is that each cohort has a new dict attribute called trophic_record. Every trophic interaction the cohort has is stored in this dict. At the end of each time step, this information is dumped into the csv and then the attribute is reset.

New additions:

• trophic_record cohort attribute
• write-to-record functionality built into foraging system
• trophic_output system built into exporter, mirroring the existing cohort_output system
• supporting tests

Fixes # (issue)

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 93.61702% with 6 lines in your changes missing coverage. Please review.
✅ Project coverage is 94.97%. Comparing base (40d4456) to head (1af2cc4).

Files with missing lines	Patch %	Lines
virtual_ecosystem/models/animal/exporter.py	92.75%	5 Missing ⚠️
virtual_ecosystem/models/animal/animal_cohorts.py	94.11%	1 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #1270      +/-   ##
===========================================
- Coverage    95.02%   94.97%   -0.05%     
===========================================
  Files           71       71              
  Lines         7274     7344      +70     
===========================================
+ Hits          6912     6975      +63     
- Misses         362      369       +7     

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

🚀 New features to boost your workflow:

• ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

[davidorme]

LGTM - just one question.

[davidorme]

Are these separated because it is possible that you might start outputting only to cohorts and not get interactions until later. For example, if you only had adult varanids in the simulation, and they just get hungrier and hungrier until some baby varanids turn up to eat?

[TaranRallings]

My thinking at the time was simply that keeping them distinct helps with debugging and updating down the road. I suppose it could be used for that as well.