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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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Bump Oceananigans to 0.90 #157

Closed jagoosw closed 10 months ago

jagoosw commented 10 months ago

Some (internal) fixes required for light attenuation.

navidcy commented 10 months ago

We need to update the example in the README.md + docs landing page.

codecov[bot] commented 10 months ago

Codecov Report

Attention: 1 lines in your changes are missing coverage. Please review.

Comparison is base (1658ddf) 64.18% compared to head (f610b33) 64.19%. Report is 1 commits behind head on main.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #157 +/- ## ======================================= Coverage 64.18% 64.19% ======================================= Files 27 27 Lines 1061 1064 +3 ======================================= + Hits 681 683 +2 - Misses 380 381 +1 ``` | [Files](https://app.codecov.io/gh/OceanBioME/OceanBioME.jl/pull/157?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=OceanBioME) | Coverage Δ | | |---|---|---| | [src/Light/2band.jl](https://app.codecov.io/gh/OceanBioME/OceanBioME.jl/pull/157?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=OceanBioME#diff-c3JjL0xpZ2h0LzJiYW5kLmps) | `89.18% <100.00%> (+0.61%)` | :arrow_up: | | [src/Models/AdvectedPopulations/LOBSTER/LOBSTER.jl](https://app.codecov.io/gh/OceanBioME/OceanBioME.jl/pull/157?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=OceanBioME#diff-c3JjL01vZGVscy9BZHZlY3RlZFBvcHVsYXRpb25zL0xPQlNURVIvTE9CU1RFUi5qbA==) | `70.00% <ø> (-0.50%)` | :arrow_down: | | [src/Models/AdvectedPopulations/NPZD.jl](https://app.codecov.io/gh/OceanBioME/OceanBioME.jl/pull/157?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=OceanBioME#diff-c3JjL01vZGVscy9BZHZlY3RlZFBvcHVsYXRpb25zL05QWkQuamw=) | `87.50% <ø> (-0.16%)` | :arrow_down: | | [src/Light/Light.jl](https://app.codecov.io/gh/OceanBioME/OceanBioME.jl/pull/157?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=OceanBioME#diff-c3JjL0xpZ2h0L0xpZ2h0Lmps) | `75.00% <66.66%> (-25.00%)` | :arrow_down: |

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jagoosw commented 10 months ago

This is now failing from a bug in Oceananigans, I'll make a PR there (https://github.com/CliMA/Oceananigans.jl/pull/3383) and maybe just change how the temperature is set in this example for now (since it doesn't have any movement it can just be a function field instead).

jagoosw commented 10 months ago

Actually changing this example to have a function field makes it quite messy since T is a tracer required by the bgc model so we would have to predefined all of the tracers like:

clock = Clock(; time = 0.0)
T = FunctionField{Center, Center, Center}(temp, grid; clock)
P = CenterField(grid)
N = CenterField(grid)

model = NonhydrostaticModel(..., tracers = (; N, P, T))

Which takes away from our demonstration of the automatic setup. I am going to try and run the example with a temperature forcing that is the derivative of the prescribed temperature and see if the time resolution is sufficient for it to work correctly.

jagoosw commented 10 months ago

Should we merge #156 then this with a minorpatch version update, then #155 then minor release?

navidcy commented 10 months ago

We can just do a minor update when all three are merged?

jagoosw commented 10 months ago

Oh yeah I meant patch but we can just merge them all and do a minor release when #155 is merged