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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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Minor docs cleanup #114

Closed navidcy closed 1 year ago

navidcy commented 1 year ago

I noticed that there were a few docstrings that had an empty line between them and the method they were documenting. This empty line detaches the docstring from the method so Documented does not include it in the Library (Documenter does not know that those docstrings belong to those methods).

I removed the disclaimer from the Docs/Appendix/Library page. @jagoosw is there still methods/types whose docs don't appear in the library page? Note that since we have private = false, only exported methods/types should appear here.

navidcy commented 1 year ago

I also removed the tilmestep wizard from the first example. I thought it's better to keep it as simple as possible for the first example one sees. The particular buoyancy front example keeps CFL < 0.3 with Δt = 2sec.

codecov[bot] commented 1 year ago

Codecov Report

Patch coverage: 50.00% and project coverage change: +0.06 :tada:

Comparison is base (61c0120) 61.40% compared to head (8bc2d6e) 61.46%.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #114 +/- ## ========================================== + Coverage 61.40% 61.46% +0.06% ========================================== Files 26 26 Lines 969 968 -1 ========================================== Hits 595 595 + Misses 374 373 -1 ``` | [Impacted Files](https://app.codecov.io/gh/OceanBioME/OceanBioME.jl/pull/114?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=OceanBioME) | Coverage Δ | | |---|---|---| | [src/Boundaries/Sediments/Sediments.jl](https://app.codecov.io/gh/OceanBioME/OceanBioME.jl/pull/114?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=OceanBioME#diff-c3JjL0JvdW5kYXJpZXMvU2VkaW1lbnRzL1NlZGltZW50cy5qbA==) | `61.53% <ø> (ø)` | | | [src/Boundaries/Sediments/coupled\_timesteppers.jl](https://app.codecov.io/gh/OceanBioME/OceanBioME.jl/pull/114?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=OceanBioME#diff-c3JjL0JvdW5kYXJpZXMvU2VkaW1lbnRzL2NvdXBsZWRfdGltZXN0ZXBwZXJzLmps) | `80.95% <ø> (ø)` | | | [src/Boundaries/Sediments/simple\_multi\_G.jl](https://app.codecov.io/gh/OceanBioME/OceanBioME.jl/pull/114?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=OceanBioME#diff-c3JjL0JvdW5kYXJpZXMvU2VkaW1lbnRzL3NpbXBsZV9tdWx0aV9HLmps) | `92.10% <ø> (ø)` | | | [src/Boundaries/gasexchange.jl](https://app.codecov.io/gh/OceanBioME/OceanBioME.jl/pull/114?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=OceanBioME#diff-c3JjL0JvdW5kYXJpZXMvZ2FzZXhjaGFuZ2Uuamw=) | `84.48% <ø> (ø)` | | | [src/BoxModel/boxmodel.jl](https://app.codecov.io/gh/OceanBioME/OceanBioME.jl/pull/114?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=OceanBioME#diff-c3JjL0JveE1vZGVsL2JveG1vZGVsLmps) | `0.00% <ø> (ø)` | | | [src/BoxModel/timesteppers.jl](https://app.codecov.io/gh/OceanBioME/OceanBioME.jl/pull/114?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=OceanBioME#diff-c3JjL0JveE1vZGVsL3RpbWVzdGVwcGVycy5qbA==) | `0.00% <ø> (ø)` | | | [src/Light/Light.jl](https://app.codecov.io/gh/OceanBioME/OceanBioME.jl/pull/114?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=OceanBioME#diff-c3JjL0xpZ2h0L0xpZ2h0Lmps) | `0.00% <ø> (ø)` | | | [src/Light/morel.jl](https://app.codecov.io/gh/OceanBioME/OceanBioME.jl/pull/114?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=OceanBioME#diff-c3JjL0xpZ2h0L21vcmVsLmps) | `0.00% <0.00%> (ø)` | | | [src/Models/AdvectedPopulations/LOBSTER/LOBSTER.jl](https://app.codecov.io/gh/OceanBioME/OceanBioME.jl/pull/114?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=OceanBioME#diff-c3JjL01vZGVscy9BZHZlY3RlZFBvcHVsYXRpb25zL0xPQlNURVIvTE9CU1RFUi5qbA==) | `81.25% <ø> (ø)` | | | [...AdvectedPopulations/LOBSTER/carbonate\_chemistry.jl](https://app.codecov.io/gh/OceanBioME/OceanBioME.jl/pull/114?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=OceanBioME#diff-c3JjL01vZGVscy9BZHZlY3RlZFBvcHVsYXRpb25zL0xPQlNURVIvY2FyYm9uYXRlX2NoZW1pc3RyeS5qbA==) | `100.00% <ø> (ø)` | | | ... and [13 more](https://app.codecov.io/gh/OceanBioME/OceanBioME.jl/pull/114?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=OceanBioME) | |

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navidcy commented 1 year ago

@jagoosw I don't know if I messed up with the edits in eea66e9. Have a look.

navidcy commented 1 year ago

cool, feel free to merge :)

jagoosw commented 1 year ago

I just thought, given that the Eady problem example has random initial conditions, it might stop it from intermittently failing if we set a random seed (and this seed produces an okay looking result).