Fixed some show methods

[jagoosw]

When I went to update Oceananigans I found these changes I made so thought we might as well merge them first too.

[navidcy]

Some doctests are failing.

[navidcy]

lgtm

[navidcy]

We dropped showing "Optional components" and "Sinking velocities" from model's show methods?

[codecov]

Codecov Report

Attention: 10 lines in your changes are missing coverage. Please review.

Comparison is base (37530fc) 65.84% compared to head (1658ddf) 64.18%.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #156      +/-   ##
==========================================
- Coverage   65.84%   64.18%   -1.66%     
==========================================
  Files          27       27              
  Lines        1054     1061       +7     
==========================================
- Hits          694      681      -13     
- Misses        360      380      +20     

Files	Coverage Δ
src/Light/2band.jl	88.57% <ø> (ø)
src/Models/AdvectedPopulations/NPZD.jl	87.65% <50.00%> (-1.24%)	⬇️
src/OceanBioME.jl	68.75% <0.00%> (-2.22%)	⬇️
src/Utils/negative_tracers.jl	70.96% <0.00%> (-4.90%)	⬇️
src/Models/AdvectedPopulations/LOBSTER/LOBSTER.jl	70.49% <14.28%> (-6.71%)	⬇️

... and 1 file with indirect coverage changes

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[jagoosw]

We dropped showing "Optional components" and "Sinking velocities" from model's show methods?

Where is this? It still shows them here:

OceanBioME.jl/src/Models/AdvectedPopulations/LOBSTER/LOBSTER.jl

Lines 430 to 435 in c6e098f

	show(io::IO, model::LOBSTER{FT, Val{B}, W}) where {FT, B, W} = print(io, string(summary(model), " \n",
	" Optional components:", "\n",
	" ├── Carbonates $(B[1] ? :✅ : :❌) \n",
	" ├── Oxygen $(B[2] ? :✅ : :❌) \n",
	" └── Variable Redfield Ratio $(B[3] ? :✅ : :❌)", "\n",
	" Sinking Velocities:", "\n", show_sinking_velocities(model.sinking_velocities)))

[navidcy]

E.g., look at the changes in docs/src/model_components/biogeochemical/LOBSTER.md I had to do so that the doctests pass. That's what I meant.

[jagoosw]

Ah I see, that's because there LOBSTER is wrapped in Biogeochemistry so its only showing the summary of the underlying model:

julia> bgc_model
Lodyc-DAMTP Ocean Biogeochemical Simulation Tools for Ecosystem and Resources (LOBSTER) model (Float64) 
 Light attenuation: Two-band light attenuation model (Float64)
 Sediment: Nothing
 Particles: Nothing

julia> bgc_model.underlying_biogeochemistry
Lodyc-DAMTP Ocean Biogeochemical Simulation Tools for Ecosystem and Resources (LOBSTER) model (Float64) 
 Optional components:
    ├── Carbonates ✅ 
    ├── Oxygen ❌ 
    └── Variable Redfield Ratio ❌
 Sinking Velocities:
    ├── sPOM: 0.0 to -3.47e-5 m/s 
    └── bPOM: 0.0 to -0.0023148148148148147 m/s

Perhaps the summary should include slightly more information? I could change it so the summary includes:

summary(::LOBSTER{FT, Val{B}, W}) where {FT, B, W} = string("Lodyc-DAMTP Ocean Biogeochemical Simulation Tools for Ecosystem and Resources (LOBSTER) model ($FT)\n Optional components: carbonates $(B[1] ? :✅ : :❌), oxygen $(B[2] ? :✅ : :❌), variable Redfield ratio $(B[3] ? :✅ : :❌)")

But then it is quite long. I don't think we really need the sinking velocities in the summary since the details are a lot less important.

[navidcy]

I think it’s fine. Just wanted to ensure it wasn’t by accident.

Merge at your convenience.

[jagoosw]

I think it’s fine. Just wanted to ensure it wasn’t by accident.

Merge at your convenience.

Ah thank you, just saw this and have changed them a bit so will need to update docstrings