Fixing calculate atmospheric layer geometry

[davidorme]

Description

This PR:

• Fixes a bug in calculate_atmospheric_layer_geometry that was calculating heights between cells rather than between canopy layers.
• Reworks the compute_layer_thickness_for_varying_canopy function to use a faster parallelized calculation.
• Adds bottleneck to the package dependencies to speed this calculation up. @dalonsoa I think some of the performance enhancement may be trying to spot where we can use bn

Fixes #1351
Makes partial progress to solving the issues in #1314 (or at least, finds the next bug).

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 94.95%. Comparing base (37d98b2) to head (129f619).

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #1352      +/-   ##
===========================================
- Coverage    94.96%   94.95%   -0.01%     
===========================================
  Files           71       71              
  Lines         7382     7371      -11     
===========================================
- Hits          7010     6999      -11     
  Misses         372      372              

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[davidorme]

@vgro - as you're on leave, I've asked @jacobcook1995 to review this to get the fix down into develop, but you probably want to review this PR!

[jacobcook1995]

LGTM, but yes agree @vgro should look at this once she is back