OceanBioME / OceanBioME.jl

🌊 🦠 🌿 A fast and flexible modelling environment written in Julia for modelling the coupled interactions between ocean biogeochemistry, carbonate chemistry, and physics
https://oceanbiome.github.io/OceanBioME.jl/
MIT License
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Add default parameters table to docs #101

Closed jagoosw closed 1 year ago

jagoosw commented 1 year ago

This adds the automatic generation of pages showing the default parameter values for models. I think this is quite important because I've often struggled trying to find parameter values for BGC models because often a couple are missed in papers, but with this we know the defaults in some version and can just detail variations from default.

Fixes #98

jagoosw commented 1 year ago

Let’s see the preview before approving

Yeah, seems to work locally but lets see

codecov[bot] commented 1 year ago

Codecov Report

Patch coverage has no change and project coverage change: -0.21 :warning:

Comparison is base (888a107) 52.78% compared to head (461724c) 52.58%.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #101 +/- ## ========================================== - Coverage 52.78% 52.58% -0.21% ========================================== Files 26 26 Lines 1023 1027 +4 ========================================== Hits 540 540 - Misses 483 487 +4 ``` | [Impacted Files](https://app.codecov.io/gh/OceanBioME/OceanBioME.jl/pull/101?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=OceanBioME) | Coverage Δ | | |---|---|---| | [src/Utils/sinking\_velocity\_fields.jl](https://app.codecov.io/gh/OceanBioME/OceanBioME.jl/pull/101?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=OceanBioME#diff-c3JjL1V0aWxzL3NpbmtpbmdfdmVsb2NpdHlfZmllbGRzLmps) | `43.33% <0.00%> (-6.67%)` | :arrow_down: |

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jagoosw commented 1 year ago

Not sure whats caused this docs error, other people seem to have been getting the same recently: https://github.com/trixi-framework/Trixi.jl/issues/1475

navidcy commented 1 year ago

I can dig in. I think I was getting this yesterday snd fixed it. It because eg there are two doc sections with name LOBSTER so [LOBSTER](@ref) becomes ambiguous

jagoosw commented 1 year ago

Ah I see, I though they had to be names like (@id LOBSTER) to be referenced. I imagine this is coming from the page titles and the new parameter pages so I will try changing the automatic title to X default parameters rather than just X.

navidcy commented 1 year ago

This is one way to reference them. But also module or methods names. And eg because the LOBSTER constructor is in the docs library then if you make another page with @id LOBSTER you run into trouble. 🦞

jagoosw commented 1 year ago

Ah I see, thank you

navidcy commented 1 year ago

This is one way to reference them. But also module or methods names. And eg because the LOBSTER constructor is in the docs library then if you make another page with @id LOBSTER you run into trouble. 🦞

(i think that’s the culprit)

jagoosw commented 1 year ago

lgtm

it'd be nice if units appeared... but it's definitely good for now!

Yeah that would be good, I'm not sure how, maybe with something like Unitful.