Theory documentation for the soil microbial community

[jacobcook1995]

Description

I've added the details of how the microbial community is implemented in the model to the soil theory documentation. @hrlai let me know what you think, and feel free to make edits as you see fit. The documentation for the branch associated with this pull request can be found here

I'm setting this as a draft for now as I haven't added any documentation of the microbial group or enzyme parameters, as I wasn't sure where this best fitted. (This would be something similar to how the model constants are currently documented). If you have any suggestions for where this could fit let me know!

Fixes #814

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)
• Documentation improvement

[codecov-commenter]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 94.31%. Comparing base (0861c95) to head (399c54c).
⚠️ Report is 1452 commits behind head on develop.

Additional details and impacted files

@@           Coverage Diff            @@
##           develop     #947   +/-   ##
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  Coverage    94.31%   94.31%           
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  Files           79       79           
  Lines         6576     6576           
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  Hits          6202     6202           
  Misses         374      374           

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[hrlai]

Looks good to me overall!

Just a side note that we should have a chat about build_microbial_group sometime later for me to better understand data needs.

[jacobcook1995]

Thanks for the suggested changes, I have implemented them!

Just a side note that we should have a chat about build_microbial_group sometime later for me to better understand data needs.

Yes I think we should discuss this when we next meet. I'll keep this PR as a draft until then, as I think our discussion probably will give pointers for how to improve these docs further.

[jacobcook1995]

@hrlai , if it works for you I might merge this now, and make a separate issue for the documenting microbial constants issue

[hrlai]

Yeap, it looks good and time to move on!

[jacobcook1995]

Okay, I've made an issue for the lack of default value documentation (#987). Might be worth discussing this at our next meeting