Updated grid implementation

[davidorme]

Description

This updates the grid system in line with the discussion in #79 and implements a first draft of neighbour lists and cell to cell distance calculations

Closes #79

Also:

• Closes Convert TODOs in grid.py to GitHub issues #37
• Closes Add tests for functions/methods in grid.py #31

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

[codecov-commenter]

Codecov Report

Merging #84 (f8f725e) into develop (2ba90a3) will increase coverage by 0.34%.
The diff coverage is 100.00%.

@@             Coverage Diff             @@
##           develop      #84      +/-   ##
===========================================
+ Coverage    95.07%   95.41%   +0.34%     
===========================================
  Files            6        6              
  Lines          264      262       -2     
===========================================
- Hits           251      250       -1     
+ Misses          13       12       -1     

Impacted Files	Coverage Δ
virtual_rainforest/core/grid.py	93.20% <100.00%> (+0.82%)	⬆️

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[davidorme]

This clashes with #83 as it stands because the testing isn't typed. We should resolve that PR first.

[davidorme]

That is now resolved - tests do not require mypy annotation and so this PR is in line with develop

[davidorme]

@dalonsoa - could you review this PR. It is pretty much as we discussed. The distances[idx, idx] style interface isn't implemented because the full distance matrix isn't stored by default. I guess we could use a custom DistanceMatrix class with a __getitem__ method to set that up?

[dalonsoa]

It looks good. I've just made a couple of comments in relation to the GridStructure class that need to be address - either way.

[davidorme]

OK - I have run git revert HEAD on #74 and then used git cherry-pick to bring those changes across here. Mostly as an exercise in figuring out how to do it 😄

This is much cleaner - I've added a test for the two current Grid init failure modes.

[davidorme]

Also

• Closes Convert TODOs in grid.py to GitHub issues #37
• Closes Add tests for functions/methods in grid.py #31