Updating documentation of static models on config page.

[sallymatson]

Description

Documentation update for the static model.

The overview is built here and the example is built here.

A few notes:

• The config files are built programmatically, assuming that the combination of models in the example does not change. The code can be viewed if wanted.
• The path setting is still not universal for as os but I have added a note about that at the start.
• I collapsed the output of ve_run so it does not clutter the documentation, and I also collapsed the code for the plots.

@sallymatson I cannot add you as a reviewer, please feel free to comment :-)

Fixes #686

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

[codecov-commenter]

Codecov Report

❌ Patch coverage is 91.00529% with 17 lines in your changes missing coverage. Please review.
✅ Project coverage is 93.89%. Comparing base (2c08828) to head (f7c8ac3).
⚠️ Report is 1925 commits behind head on develop.

Files with missing lines	Patch %	Lines
virtual_ecosystem/models/animal/animal_cohorts.py	66.66%	5 Missing ⚠️
virtual_ecosystem/models/testing/testing_model.py	75.00%	5 Missing ⚠️
virtual_ecosystem/models/abiotic/energy_balance.py	92.68%	3 Missing ⚠️
virtual_ecosystem/models/abiotic/microclimate.py	92.85%	3 Missing ⚠️
virtual_ecosystem/models/plants/plants_model.py	95.83%	1 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           develop     #702      +/-   ##
===========================================
- Coverage    93.96%   93.89%   -0.07%     
===========================================
  Files           75       77       +2     
  Lines         5828     5912      +84     
===========================================
+ Hits          5476     5551      +75     
- Misses         352      361       +9     

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[vgro]

@sallymatson I put together some ideas for an example, please let me know if you think this makes sense and I can create the new input file and add the plotting bits. I'll fix the numbering item issue.

[sallymatson]

@sallymatson I put together some ideas for an example, please let me know if you think this makes sense and I can create the new input file and add the plotting bits. I'll fix the numbering item issue.

I think it's a great approach!! I think it would be helpful for us to figure out the best way to "name" the two approaches because then we can use them in the documentation (on the config page that I've been working on) and here, so that users can quickly understand how the two documents relate to eachother. Otherwise, I think it's clear and thorough !!

[vgro]

@sallymatson I updated the example to make it a bit simpler and focus only on the static setting that starts from scratch for now, not the option to provide all the variables at the start (I think it was a bit confusing and might be better in a separate example, for instance an experiment 3).
My question is do you know how to make changes to the config files in the notebook, or no we need to somehow provide the alternative config files with the example?

[sallymatson]

@sallymatson I updated the example to make it a bit simpler and focus only on the static setting that starts from scratch for now, not the option to provide all the variables at the start (I think it was a bit confusing and might be better in a separate example, for instance an experiment 3). My question is do you know how to make changes to the config files in the notebook, or no we need to somehow provide the alternative config files with the example?

I think that we would need to create a separate example config for the run. If we load the config first, then we could so something like this like I just did for some testing in the plants model:

fixture_config["plants"]["constants"] = {"PlantsConsts": {"leaf_lignin": 100.0}}

Or, you could open the file in the jupyter notebook and edit it (and just explain that this code does not need to be copied.) But I generally think it would be easier and better practice to have its own config, especially since we wouldn't then know if the config changed for other reasons, if it would impact this tutorial.

Does that make sense? If you want to upload the example you have and then I can play around with the config, happy to help more!!

[davidorme]

This is good. I've suggested a few changes:

• Some technical changes to the setup of the worked example (not using the toml package, syntax and hiding the programmatic config creation).

  I ran those changes locally to check I wasn't breaking it, so have a commit I can push if those sound sensible. Let me know if you want me to do that.

• Some styling suggestions for accessibility and tweaks to wording.

• I think the overview of static mode is a little hard hitting. Again - I have a revised version which I'm happy to push if that is ok.

[davidorme]

Suggested change

	```{code-cell} ipython3
	```{code-cell} bash

Here and elsewhere, these cells should not be styled as python.

[davidorme]

Oh bugger. We can't do this, because our use of jupytext dictates a single {code-cell} language and it automatically enforces this. See mwouts/jupytext#1267 (comment)

[davidorme]

I think all the relevant information is here but it goes in hard with technical details and repeats quite a lot - I think it would be easier to follow if it builds up a bit more from first principles.

[davidorme]

@vgro and @sallymatson I've pushed my suggestions to a new PR subbranch off this one #905 and asked for a review.

[arne-exe]

Hi @vgro, a very nice applied example of how to run the model in static mode. I only had suggestions in 2 places where you repeated the same words.

[davidorme]

LGTM