Animal Foragin Debug - Cumulative prey densities and handling time

[TaranRallings]

Description

This PR fixes some bugs in the animal foraging system.

• H_i_j (handling time calculator) was keying off predator mass instead of prey mass
• cumulative prey density was not being calculated or used

H_i_j, now correctly uses prey mass in the calculation.
The cohort method calculate_total_handling_time_for_predation, now correctly sums over available prey for determining density.

Fixes #1317

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

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 94.84%. Comparing base (8a26398) to head (4962fea).
⚠️ Report is 45 commits behind head on develop.

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #1401      +/-   ##
===========================================
- Coverage    94.85%   94.84%   -0.01%     
===========================================
  Files           71       71              
  Lines         7387     7455      +68     
===========================================
+ Hits          7007     7071      +64     
- Misses         380      384       +4     

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[dalonsoa]

The code looks correct - obviously, no idea about the science.

Having said that, having variables that include subindices (i, j) is very confusing. It feels they should be 2D arrays and not variable of function names. They are not informative of what they represent. what is i? and j? I know that was not implemented in this PR, but I have just seen it, so thought mentioning it.

[TaranRallings]

Having said that, having variables that include subindices (i, j) is very confusing. It feels they should be 2D arrays and not variable of function names. They are not informative of what they represent. what is i? and j? I know that was not implemented in this PR, but I have just seen it, so thought mentioning it.

Totally agree. A round of naming updates is on my to-do list for exactly that reason. The names they have currently are there to make it easy to compare to the paper they are drawn from. In the fairly near future I'll be changing them all.