Fluxnet and global run documentation

[kmdeck]

Purpose

Improve documentation for fluxnet and global runs; simplify table of contents in docs
preview: https://clima.github.io/ClimaLand.jl/previews/PR1288/

Bucket Plots:
bucket_figures.pdf
bucket_annual_timeseries.pdf

Snow land fluxnet:
US_NR1_variable_timeseries.pdf
US_NR1_diurnal_timeseries.pdf

Soil canopy
US_MOz_diurnal_timeseries.pdf

To-do

Future PRs
- Change default plotting to png - otherwise we cannot show pdf in doc markdown

Content

docs:

• Rearrange docs a bit: create a fluxnet simulation group, and a global sim group, in addition to standalone model group
• add fluxnet documentation (soil canopy and snowy land runs, visualization, forcing data)
• add global run documentation (bucket + snowy land)
• added stand in pages for things we know we need to add
  To review: @juliasloan25 all docs/ changes and src/integrated/soil_canopy_model.jl
  @AlexisRenchon all docs/ changes and src/integrated/soil_canopy_model.jl

fluxnet and simulations:

• Add make_set_fluxnet_ic function to hide closure from user and be more in line with how we create the ic function in the global case
• added start_date to Simulation struct (used in plotting fluxnet runs)
• small other changes
• @imreddyTeja could review: - ozark_pft.jl
• ozark_soilsnow.jl
• run_fluxnet.jl
• ozark_conservation.jl
• ext/FluxnetSimulationsExt.jl
• ext/LandSimulationVisualizationExt.jl
• ext/fluxnet_simulations/initial_conditions.jl
• ext/land_sim_vis/plotting_utils.jl
• src/simulations/Simulations.jl

Moved to PR 1315:

• src/standalone/Vegetation/Canopy.jl
• test/integrated/full_land.jl
  -test/integrated/full_land_utils.jl
• test/standalone/Soil/Biogeochemistry/biogeochemistry_module.jl

---

• I have read and checked the items on the review checklist.

[juliasloan25]

We should support periodic BC for fluxnet forcing - can we do that?

I don't completely understand how we read in the fluxnet forcing. We can have periodic BCs if we use the TVI constructor we use for prescribed_forcing_era5 instead of the one we use for prescribed_forcing_fluxnet, but I'm not sure if there's something prohibiting us from using that.

[kmdeck]

We should support periodic BC for fluxnet forcing - can we do that?

I don't completely understand how we read in the fluxnet forcing. We can have periodic BCs if we use the TVI constructor we use for prescribed_forcing_era5 instead of the one we use for prescribed_forcing_fluxnet, but I'm not sure if there's something prohibiting us from using that.

I wasnt sure because when I worked on this the time for the TimeVaryingInput0D had to be a float, in which case a periodic calendar doesnt make sense...but perhaps we can do this now. Ill try in a later PR

[AlexisRenchon]

This is a dramatic improvement of ClimaLand documentation, thank you Kat!
I left a bunch of comments below, I don't think we need to address them all in this PR, I leave it up to you.
I can go through another review later on today if needed, let me know when you think it is ready to merge!

Note: the getting_started.md page (not modified in this PR) has a typo, we could correct it here. Line 17, "journet" instead of "journey".

In getting_started.md, there's an error due to "About.jl" not being installed. I know we removed it a while ago because of a bug. Maybe it's been fixed now? (I can do this in another PR)

the getting_started.md page is called "running your first simulation" yet doesn't have code to run a simulation (also for another PR maybe - I thought Julia had a PR for it but I can't find it anymore)

The file structure in the code doesn't match the menu structure of the docs. it makes it a bit hard to navigate.
docs menu:

docs code:

The page changing_canopy_parameterizations is empty

Maybe we don't want to show the output (or silence warning) of some box of code, e.g., running fluxnet simulations:

Note this seems quite important - some box of warnings are very long... (if needed I can help with this)

The driver_tutorial page has a long return box that should be hidden

Can we rename "Leaderboard" to "Benchmark"? Benchmark is a well known modelling exercise, to compare model output to observation. Leaderboard is more an internal CliMA goal of showing we're the best model...

Note: I see that Kevin added warning boxes in the calibration docs. I think this is pretty neat and we should use it throughout the docs

APIs/shared_utilities, simulations, has a blank name (-) (which should be "LandSimulations" I believe)

APIs/Soil_Albedo rendering is bugged. It seems to be full of titles (hashtags)

[AlexisRenchon]

APIs currently has two nested ClimaLand

we should remove the ClimaLand fold (there's only one fold)

[imreddyTeja]

The new make_set_fluxnet_initial_conditions is much cleaner than defining it is the simulation script!

I left a few comments, mostly about the assumption that start_date = t0.epoch (which is almost always the case).

[juliasloan25]

I had the same HTTP error in the ubuntu tests - I retried and it ran ok