Update Documenter + some polishing #146

navidcy · 2023-09-20T09:59:17Z

This PR updates Documenter to v1 + does some polishing in the docs.

jagoosw · 2023-09-20T10:18:45Z

I tried building the docs in a different PR with 1.0 and there were a lot of breaking changes

navidcy · 2023-09-20T10:21:17Z

oh I see.. which PR?

jagoosw · 2023-09-20T10:35:50Z

#138 I ended up pinning Documenter to the version pre 1.0 to get them to build. Some of the commits will still have the error messages I think

Edit: the errors here are the same as what I was getting before

jagoosw · 2023-10-05T18:00:22Z

Do you think we should try to update documenter?

navidcy · 2023-10-10T12:00:22Z

Yeap! I'll give it a go

navidcy · 2023-10-10T12:18:29Z

(Patch release is not necessary, but I thought it would be good to have the "stable" version mentioning the citation info in the docs.)

navidcy · 2023-10-10T12:27:05Z

Let's see if the docs build now. If they do, ideally we'd wanna fix the cross_references error which I bypassed with 92d84c6.

(The docs built successfully locally with draft = true.)

navidcy · 2023-10-10T12:35:09Z

This "oceananigans" here:

OceanBioME.jl/docs/src/contributing.md

Line 117 in b413571

git remote add oceananigans https://github.com/OceanBioME/OceanBioME.jl.git

seems wrong, right @jagoosw?

jagoosw · 2023-10-10T13:07:04Z

This "oceananigans" here:

OceanBioME.jl/docs/src/contributing.md

Line 117 in b413571

git remote add oceananigans https://github.com/OceanBioME/OceanBioME.jl.git

seems wrong, right @jagoosw?

Indeed, I guess we should change it to oceanbiome

navidcy · 2023-10-10T13:42:03Z

@jagoosw I see this:

![Diagram of PISCES architecture](assets/PISCES_architecture.png)

but I don't see this PISCES_architecture.png file.

This is one of Documenter's complaints. ;)

navidcy · 2023-10-10T14:53:56Z

@jagoosw does this ring a bell??
Was there any change in OceanBioME.jl or Oceananigans? I'm using Oceananigans v0.89.1...

│ using Oceananigans
│
│ grid = RectilinearGrid(size=(3, 3, 30), extent=(10, 10, 200));
│
│ model = NonhydrostaticModel(; grid,
│                               biogeochemistry = LOBSTER(; grid, carbonates = true),
│                               boundary_conditions = (DIC = FieldBoundaryConditions(top = CO₂_flux), ))
│ ```
│   exception =
│    MethodError: no method matching field_arguments(::Int64, ::Int64, ::Int64, ::Oceananigans.Grids.RectilinearGrid{Float64, Oceananigans.Grids.Periodic, Oceananigans.Grids.Periodic, Oceananigans.Grids.Bounded, Float64, Float64, Float64, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, Oceananigans.Architectures.CPU}, ::NamedTuple{(:u, :v, :w, :NO₃, :NH₄, :P, :Z, :sPOM, :bPOM, :DOM, :DIC, :Alk, :PAR), Tuple{Oceananigans.Fields.Field{Oceananigans.Grids.Face, Oceananigans.Grids.Center, Oceananigans.Grids.Center, Nothing, Oceananigans.Grids.RectilinearGrid{Float64, Oceananigans.Grids.Periodic, Oceananigans.Grids.Periodic, Oceananigans.Grids.Bounded, Float64, Float64, Float64, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, Oceananigans.Architectures.CPU}, Tuple{Colon, Colon, Colon}, OffsetArrays.OffsetArray{Float64, 3, Array{Float64, 3}}, Float64, Oceananigans.BoundaryConditions.FieldBoundaryConditions{Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}}, Nothing, Oceananigans.Fields.FieldBoundaryBuffers{Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing}}, Oceananigans.Fields.Field{Oceananigans.Grids.Center, Oceananigans.Grids.Face, Oceananigans.Grids.Center, Nothing, Oceananigans.Grids.RectilinearGrid{Float64, Oceananigans.Grids.Periodic, Oceananigans.Grids.Periodic, Oceananigans.Grids.Bounded, Float64, Float64, Float64, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, Oceananigans.Architectures.CPU}, Tuple{Colon, Colon, Colon}, OffsetArrays.OffsetArray{Float64, 3, Array{Float64, 3}}, Float64, Oceananigans.BoundaryConditions.FieldBoundaryConditions{Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}}, Nothing, Oceananigans.Fields.FieldBoundaryBuffers{Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing}}, Oceananigans.Fields.Field{Oceananigans.Grids.Center, Oceananigans.Grids.Center, Oceananigans.Grids.Face, Nothing, Oceananigans.Grids.RectilinearGrid{Float64, Oceananigans.Grids.Periodic, Oceananigans.Grids.Periodic, Oceananigans.Grids.Bounded, Float64, Float64, Float64, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, Oceananigans.Architectures.CPU}, Tuple{Colon, Colon, Colon}, OffsetArrays.OffsetArray{Float64, 3, Array{Float64, 3}}, Float64, Oceananigans.BoundaryConditions.FieldBoundaryConditions{Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Open, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Open, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}}, Nothing, Oceananigans.Fields.FieldBoundaryBuffers{Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing}}, Oceananigans.Fields.Field{Oceananigans.Grids.Center, Oceananigans.Grids.Center, Oceananigans.Grids.Center, Nothing, Oceananigans.Grids.RectilinearGrid{Float64, Oceananigans.Grids.Periodic, Oceananigans.Grids.Periodic, Oceananigans.Grids.Bounded, Float64, Float64, Float64, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, Oceananigans.Architectures.CPU}, Tuple{Colon, Colon, Colon}, OffsetArrays.OffsetArray{Float64, 3, Array{Float64, 3}}, Float64, Oceananigans.BoundaryConditions.FieldBoundaryConditions{Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}}, Nothing, Oceananigans.Fields.FieldBoundaryBuffers{Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing}}, Oceananigans.Fields.Field{Oceananigans.Grids.Center, Oceananigans.Grids.Center, Oceananigans.Grids.Center, Nothing, Oceananigans.Grids.RectilinearGrid{Float64, Oceananigans.Grids.Periodic, Oceananigans.Grids.Periodic, Oceananigans.Grids.Bounded, Float64, Float64, Float64, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, Oceananigans.Architectures.CPU}, Tuple{Colon, Colon, Colon}, OffsetArrays.OffsetArray{Float64, 3, Array{Float64, 3}}, Float64, Oceananigans.BoundaryConditions.FieldBoundaryConditions{Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}}, Nothing, Oceananigans.Fields.FieldBoundaryBuffers{Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing}}, Oceananigans.Fields.Field{Oceananigans.Grids.Center, Oceananigans.Grids.Center, Oceananigans.Grids.Center, Nothing, Oceananigans.Grids.RectilinearGrid{Float64, Oceananigans.Grids.Periodic, Oceananigans.Grids.Periodic, Oceananigans.Grids.Bounded, Float64, Float64, Float64, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, Oceananigans.Architectures.CPU}, Tuple{Colon, Colon, Colon}, OffsetArrays.OffsetArray{Float64, 3, Array{Float64, 3}}, Float64, Oceananigans.BoundaryConditions.FieldBoundaryConditions{Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}}, Nothing, Oceananigans.Fields.FieldBoundaryBuffers{Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing}}, Oceananigans.Fields.Field{Oceananigans.Grids.Center, Oceananigans.Grids.Center, Oceananigans.Grids.Center, Nothing, Oceananigans.Grids.RectilinearGrid{Float64, Oceananigans.Grids.Periodic, Oceananigans.Grids.Periodic, Oceananigans.Grids.Bounded, Float64, Float64, Float64, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, Oceananigans.Architectures.CPU}, Tuple{Colon, Colon, Colon}, OffsetArrays.OffsetArray{Float64, 3, Array{Float64, 3}}, Float64, Oceananigans.BoundaryConditions.FieldBoundaryConditions{Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}}, Nothing, Oceananigans.Fields.FieldBoundaryBuffers{Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing}}, Oceananigans.Fields.Field{Oceananigans.Grids.Center, Oceananigans.Grids.Center, Oceananigans.Grids.Center, Nothing, Oceananigans.Grids.RectilinearGrid{Float64, Oceananigans.Grids.Periodic, Oceananigans.Grids.Periodic, Oceananigans.Grids.Bounded, Float64, Float64, Float64, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, Oceananigans.Architectures.CPU}, Tuple{Colon, Colon, Colon}, OffsetArrays.OffsetArray{Float64, 3, Array{Float64, 3}}, Float64, Oceananigans.BoundaryConditions.FieldBoundaryConditions{Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}}, Nothing, Oceananigans.Fields.FieldBoundaryBuffers{Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing}}, Oceananigans.Fields.Field{Oceananigans.Grids.Center, Oceananigans.Grids.Center, Oceananigans.Grids.Center, Nothing, Oceananigans.Grids.RectilinearGrid{Float64, Oceananigans.Grids.Periodic, Oceananigans.Grids.Periodic, Oceananigans.Grids.Bounded, Float64, Float64, Float64, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, Oceananigans.Architectures.CPU}, Tuple{Colon, Colon, Colon}, OffsetArrays.OffsetArray{Float64, 3, Array{Float64, 3}}, Float64, Oceananigans.BoundaryConditions.FieldBoundaryConditions{Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}}, Nothing, Oceananigans.Fields.FieldBoundaryBuffers{Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing}}, Oceananigans.Fields.Field{Oceananigans.Grids.Center, Oceananigans.Grids.Center, Oceananigans.Grids.Center, Nothing, Oceananigans.Grids.RectilinearGrid{Float64, Oceananigans.Grids.Periodic, Oceananigans.Grids.Periodic, Oceananigans.Grids.Bounded, Float64, Float64, Float64, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, Oceananigans.Architectures.CPU}, Tuple{Colon, Colon, Colon}, OffsetArrays.OffsetArray{Float64, 3, Array{Float64, 3}}, Float64, Oceananigans.BoundaryConditions.FieldBoundaryConditions{Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}}, Nothing, Oceananigans.Fields.FieldBoundaryBuffers{Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing}}, Oceananigans.Fields.Field{Oceananigans.Grids.Center, Oceananigans.Grids.Center, Oceananigans.Grids.Center, Nothing, Oceananigans.Grids.RectilinearGrid{Float64, Oceananigans.Grids.Periodic, Oceananigans.Grids.Periodic, Oceananigans.Grids.Bounded, Float64, Float64, Float64, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, Oceananigans.Architectures.CPU}, Tuple{Colon, Colon, Colon}, OffsetArrays.OffsetArray{Float64, 3, Array{Float64, 3}}, Float64, Oceananigans.BoundaryConditions.FieldBoundaryConditions{Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Oceananigans.BoundaryConditions.ContinuousBoundaryFunction{Oceananigans.Grids.Center, Oceananigans.Grids.Center, Nothing, Oceananigans.BoundaryConditions.RightBoundary, typeof(OceanBioME.Boundaries.gasexchange_function), GasExchange{Val{:CO₂}, NamedTuple{(:A, :B, :C, :D), NTuple{4, Float64}}, NamedTuple{(:A₁, :A₂, :A₃, :B₁, :B₂, :B₃), NTuple{6, Float64}}, Float64, Float64, Float64, Nothing, Nothing, OceanBioME.Boundaries.pCO₂{NamedTuple{(:C, :invT, :logCT, :ClogT, :T², :ST², :ST, :S), NTuple{8, Float64}}, NamedTuple{(:C, :S, :S², :invT, :logT), NTuple{5, Float64}}, NamedTuple{(:C, :S, :S², :invT, :logT), NTuple{5, Float64}}, NamedTuple{(:C, :invT, :invTsqrtS, :invTS, :invTS¹⁵, :invTS², :sqrtS, :S, :logT, :logTsqrtS, :logTS, :TsqrtS), NTuple{12, Float64}}, NamedTuple{(:C, :invT, :logT, :sqrtSinvT, :sqrtS, :sqrtSlogT, :S), NTuple{7, Float64}}, Float64}}, NTuple{4, Symbol}, Tuple{Int64, Int64, Nothing, Nothing}, Tuple{typeof(Oceananigans.Operators.identity3), typeof(Oceananigans.Operators.identity4), typeof(Oceananigans.Operators.identity5), typeof(Oceananigans.Operators.identity1)}}}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}}, Nothing, Oceananigans.Fields.FieldBoundaryBuffers{Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing}}, Oceananigans.Fields.Field{Oceananigans.Grids.Center, Oceananigans.Grids.Center, Oceananigans.Grids.Center, Nothing, Oceananigans.Grids.RectilinearGrid{Float64, Oceananigans.Grids.Periodic, Oceananigans.Grids.Periodic, Oceananigans.Grids.Bounded, Float64, Float64, Float64, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, Oceananigans.Architectures.CPU}, Tuple{Colon, Colon, Colon}, OffsetArrays.OffsetArray{Float64, 3, Array{Float64, 3}}, Float64, Oceananigans.BoundaryConditions.FieldBoundaryConditions{Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}}, Nothing, Oceananigans.Fields.FieldBoundaryBuffers{Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing}}, Oceananigans.Fields.Field{Oceananigans.Grids.Center, Oceananigans.Grids.Center, Oceananigans.Grids.Center, Nothing, Oceananigans.Grids.RectilinearGrid{Float64, Oceananigans.Grids.Periodic, Oceananigans.Grids.Periodic, Oceananigans.Grids.Bounded, Float64, Float64, Float64, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, Oceananigans.Architectures.CPU}, Tuple{Colon, Colon, Colon}, OffsetArrays.OffsetArray{Float64, 3, Array{Float64, 3}}, Float64, Oceananigans.BoundaryConditions.FieldBoundaryConditions{Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Value, Oceananigans.BoundaryConditions.ContinuousBoundaryFunction{Oceananigans.Grids.Center, Oceananigans.Grids.Center, Nothing, Oceananigans.BoundaryConditions.RightBoundary, OceanBioME.LOBSTERModel.var"#3#5", Nothing, Tuple{}, Tuple{}, Tuple{}}}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}}, Nothing, Oceananigans.Fields.FieldBoundaryBuffers{Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing}}}}, ::Tuple{typeof(Oceananigans.Operators.identity3), typeof(Oceananigans.Operators.identity4), typeof(Oceananigans.Operators.identity5), typeof(Oceananigans.Operators.identity1)}, ::Tuple{Int64, Int64, Nothing, Nothing})
│
│    Closest candidates are:
│      field_arguments(::Any, ::Any, ::Any, ::Any, ::Any, ::Any, ::Tuple{T, T} where T)
│       @ Oceananigans ~/.julia/packages/Oceananigans/1LLCG/src/Utils/user_function_arguments.jl:4
│      field_arguments(::Any, ::Any, ::Any, ::Any, ::Any, ::Any, ::Tuple{T, T, T} where T)
│       @ Oceananigans ~/.julia/packages/Oceananigans/1LLCG/src/Utils/user_function_arguments.jl:8
│      field_arguments(::Any, ::Any, ::Any, ::Any, ::Any, ::Any, ::Tuple{Any})
│       @ Oceananigans ~/.julia/packages/Oceananigans/1LLCG/src/Utils/user_function_arguments.jl:1
│      ...

navidcy · 2023-10-10T15:00:43Z

This error seems to appear at Oceananigans v0.88 and later.
The docs are currently using Oceananigans v0.87 and that's why all is ok; see

OceanBioME.jl/docs/Project.toml

Line 21 in b413571

Oceananigans = "0.84.1, 0.85, 0.86, 0.87"

navidcy · 2023-10-10T15:01:16Z

cc @simone-silvestri, any idea whether v0.88 changed something that might be creating the above?

navidcy · 2023-10-10T15:57:25Z

I'm going back to Oceananigans v0.87 and leave upgrading Oceananigans for a different PR.

jagoosw · 2023-10-10T16:12:16Z

@jagoosw does this ring a bell?? Was there any change in OceanBioME.jl or Oceananigans? I'm using Oceananigans v0.89.1...

│ using Oceananigans
│
│ grid = RectilinearGrid(size=(3, 3, 30), extent=(10, 10, 200));
│
│ model = NonhydrostaticModel(; grid,
│                               biogeochemistry = LOBSTER(; grid, carbonates = true),
│                               boundary_conditions = (DIC = FieldBoundaryConditions(top = CO₂_flux), ))
│ ```
│   exception =
│    MethodError: no method matching field_arguments(::Int64, ::Int64, ::Int64, ::Oceananigans.Grids.RectilinearGrid{Float64, Oceananigans.Grids.Periodic, Oceananigans.Grids.Periodic, Oceananigans.Grids.Bounded, Float64, Float64, Float64, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, Oceananigans.Architectures.CPU}, ::NamedTuple{(:u, :v, :w, :NO₃, :NH₄, :P, :Z, :sPOM, :bPOM, :DOM, :DIC, :Alk, :PAR), Tuple{Oceananigans.Fields.Field{Oceananigans.Grids.Face, Oceananigans.Grids.Center, Oceananigans.Grids.Center, Nothing, Oceananigans.Grids.RectilinearGrid{Float64, Oceananigans.Grids.Periodic, Oceananigans.Grids.Periodic, Oceananigans.Grids.Bounded, Float64, Float64, Float64, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, Oceananigans.Architectures.CPU}, Tuple{Colon, Colon, Colon}, OffsetArrays.OffsetArray{Float64, 3, Array{Float64, 3}}, Float64, Oceananigans.BoundaryConditions.FieldBoundaryConditions{Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}}, Nothing, Oceananigans.Fields.FieldBoundaryBuffers{Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing}}, Oceananigans.Fields.Field{Oceananigans.Grids.Center, Oceananigans.Grids.Face, Oceananigans.Grids.Center, Nothing, Oceananigans.Grids.RectilinearGrid{Float64, Oceananigans.Grids.Periodic, Oceananigans.Grids.Periodic, Oceananigans.Grids.Bounded, Float64, Float64, Float64, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, Oceananigans.Architectures.CPU}, Tuple{Colon, Colon, Colon}, OffsetArrays.OffsetArray{Float64, 3, Array{Float64, 3}}, Float64, Oceananigans.BoundaryConditions.FieldBoundaryConditions{Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}}, Nothing, Oceananigans.Fields.FieldBoundaryBuffers{Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing}}, Oceananigans.Fields.Field{Oceananigans.Grids.Center, Oceananigans.Grids.Center, Oceananigans.Grids.Face, Nothing, Oceananigans.Grids.RectilinearGrid{Float64, Oceananigans.Grids.Periodic, Oceananigans.Grids.Periodic, Oceananigans.Grids.Bounded, Float64, Float64, Float64, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, Oceananigans.Architectures.CPU}, Tuple{Colon, Colon, Colon}, OffsetArrays.OffsetArray{Float64, 3, Array{Float64, 3}}, Float64, Oceananigans.BoundaryConditions.FieldBoundaryConditions{Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Open, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Open, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}}, Nothing, Oceananigans.Fields.FieldBoundaryBuffers{Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing}}, Oceananigans.Fields.Field{Oceananigans.Grids.Center, Oceananigans.Grids.Center, Oceananigans.Grids.Center, Nothing, Oceananigans.Grids.RectilinearGrid{Float64, Oceananigans.Grids.Periodic, Oceananigans.Grids.Periodic, Oceananigans.Grids.Bounded, Float64, Float64, Float64, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, Oceananigans.Architectures.CPU}, Tuple{Colon, Colon, Colon}, OffsetArrays.OffsetArray{Float64, 3, Array{Float64, 3}}, Float64, Oceananigans.BoundaryConditions.FieldBoundaryConditions{Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}}, Nothing, Oceananigans.Fields.FieldBoundaryBuffers{Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing}}, Oceananigans.Fields.Field{Oceananigans.Grids.Center, Oceananigans.Grids.Center, Oceananigans.Grids.Center, Nothing, Oceananigans.Grids.RectilinearGrid{Float64, Oceananigans.Grids.Periodic, Oceananigans.Grids.Periodic, Oceananigans.Grids.Bounded, Float64, Float64, Float64, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, Oceananigans.Architectures.CPU}, Tuple{Colon, Colon, Colon}, OffsetArrays.OffsetArray{Float64, 3, Array{Float64, 3}}, Float64, Oceananigans.BoundaryConditions.FieldBoundaryConditions{Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}}, Nothing, Oceananigans.Fields.FieldBoundaryBuffers{Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing}}, Oceananigans.Fields.Field{Oceananigans.Grids.Center, Oceananigans.Grids.Center, Oceananigans.Grids.Center, Nothing, Oceananigans.Grids.RectilinearGrid{Float64, Oceananigans.Grids.Periodic, Oceananigans.Grids.Periodic, Oceananigans.Grids.Bounded, Float64, Float64, Float64, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, Oceananigans.Architectures.CPU}, Tuple{Colon, Colon, Colon}, OffsetArrays.OffsetArray{Float64, 3, Array{Float64, 3}}, Float64, Oceananigans.BoundaryConditions.FieldBoundaryConditions{Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}}, Nothing, Oceananigans.Fields.FieldBoundaryBuffers{Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing}}, Oceananigans.Fields.Field{Oceananigans.Grids.Center, Oceananigans.Grids.Center, Oceananigans.Grids.Center, Nothing, Oceananigans.Grids.RectilinearGrid{Float64, Oceananigans.Grids.Periodic, Oceananigans.Grids.Periodic, Oceananigans.Grids.Bounded, Float64, Float64, Float64, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, Oceananigans.Architectures.CPU}, Tuple{Colon, Colon, Colon}, OffsetArrays.OffsetArray{Float64, 3, Array{Float64, 3}}, Float64, Oceananigans.BoundaryConditions.FieldBoundaryConditions{Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}}, Nothing, Oceananigans.Fields.FieldBoundaryBuffers{Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing}}, Oceananigans.Fields.Field{Oceananigans.Grids.Center, Oceananigans.Grids.Center, Oceananigans.Grids.Center, Nothing, Oceananigans.Grids.RectilinearGrid{Float64, Oceananigans.Grids.Periodic, Oceananigans.Grids.Periodic, Oceananigans.Grids.Bounded, Float64, Float64, Float64, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, Oceananigans.Architectures.CPU}, Tuple{Colon, Colon, Colon}, OffsetArrays.OffsetArray{Float64, 3, Array{Float64, 3}}, Float64, Oceananigans.BoundaryConditions.FieldBoundaryConditions{Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}}, Nothing, Oceananigans.Fields.FieldBoundaryBuffers{Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing}}, Oceananigans.Fields.Field{Oceananigans.Grids.Center, Oceananigans.Grids.Center, Oceananigans.Grids.Center, Nothing, Oceananigans.Grids.RectilinearGrid{Float64, Oceananigans.Grids.Periodic, Oceananigans.Grids.Periodic, Oceananigans.Grids.Bounded, Float64, Float64, Float64, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, Oceananigans.Architectures.CPU}, Tuple{Colon, Colon, Colon}, OffsetArrays.OffsetArray{Float64, 3, Array{Float64, 3}}, Float64, Oceananigans.BoundaryConditions.FieldBoundaryConditions{Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}}, Nothing, Oceananigans.Fields.FieldBoundaryBuffers{Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing}}, Oceananigans.Fields.Field{Oceananigans.Grids.Center, Oceananigans.Grids.Center, Oceananigans.Grids.Center, Nothing, Oceananigans.Grids.RectilinearGrid{Float64, Oceananigans.Grids.Periodic, Oceananigans.Grids.Periodic, Oceananigans.Grids.Bounded, Float64, Float64, Float64, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, Oceananigans.Architectures.CPU}, Tuple{Colon, Colon, Colon}, OffsetArrays.OffsetArray{Float64, 3, Array{Float64, 3}}, Float64, Oceananigans.BoundaryConditions.FieldBoundaryConditions{Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}}, Nothing, Oceananigans.Fields.FieldBoundaryBuffers{Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing}}, Oceananigans.Fields.Field{Oceananigans.Grids.Center, Oceananigans.Grids.Center, Oceananigans.Grids.Center, Nothing, Oceananigans.Grids.RectilinearGrid{Float64, Oceananigans.Grids.Periodic, Oceananigans.Grids.Periodic, Oceananigans.Grids.Bounded, Float64, Float64, Float64, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, Oceananigans.Architectures.CPU}, Tuple{Colon, Colon, Colon}, OffsetArrays.OffsetArray{Float64, 3, Array{Float64, 3}}, Float64, Oceananigans.BoundaryConditions.FieldBoundaryConditions{Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Oceananigans.BoundaryConditions.ContinuousBoundaryFunction{Oceananigans.Grids.Center, Oceananigans.Grids.Center, Nothing, Oceananigans.BoundaryConditions.RightBoundary, typeof(OceanBioME.Boundaries.gasexchange_function), GasExchange{Val{:CO₂}, NamedTuple{(:A, :B, :C, :D), NTuple{4, Float64}}, NamedTuple{(:A₁, :A₂, :A₃, :B₁, :B₂, :B₃), NTuple{6, Float64}}, Float64, Float64, Float64, Nothing, Nothing, OceanBioME.Boundaries.pCO₂{NamedTuple{(:C, :invT, :logCT, :ClogT, :T², :ST², :ST, :S), NTuple{8, Float64}}, NamedTuple{(:C, :S, :S², :invT, :logT), NTuple{5, Float64}}, NamedTuple{(:C, :S, :S², :invT, :logT), NTuple{5, Float64}}, NamedTuple{(:C, :invT, :invTsqrtS, :invTS, :invTS¹⁵, :invTS², :sqrtS, :S, :logT, :logTsqrtS, :logTS, :TsqrtS), NTuple{12, Float64}}, NamedTuple{(:C, :invT, :logT, :sqrtSinvT, :sqrtS, :sqrtSlogT, :S), NTuple{7, Float64}}, Float64}}, NTuple{4, Symbol}, Tuple{Int64, Int64, Nothing, Nothing}, Tuple{typeof(Oceananigans.Operators.identity3), typeof(Oceananigans.Operators.identity4), typeof(Oceananigans.Operators.identity5), typeof(Oceananigans.Operators.identity1)}}}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}}, Nothing, Oceananigans.Fields.FieldBoundaryBuffers{Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing}}, Oceananigans.Fields.Field{Oceananigans.Grids.Center, Oceananigans.Grids.Center, Oceananigans.Grids.Center, Nothing, Oceananigans.Grids.RectilinearGrid{Float64, Oceananigans.Grids.Periodic, Oceananigans.Grids.Periodic, Oceananigans.Grids.Bounded, Float64, Float64, Float64, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, Oceananigans.Architectures.CPU}, Tuple{Colon, Colon, Colon}, OffsetArrays.OffsetArray{Float64, 3, Array{Float64, 3}}, Float64, Oceananigans.BoundaryConditions.FieldBoundaryConditions{Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}}, Nothing, Oceananigans.Fields.FieldBoundaryBuffers{Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing}}, Oceananigans.Fields.Field{Oceananigans.Grids.Center, Oceananigans.Grids.Center, Oceananigans.Grids.Center, Nothing, Oceananigans.Grids.RectilinearGrid{Float64, Oceananigans.Grids.Periodic, Oceananigans.Grids.Periodic, Oceananigans.Grids.Bounded, Float64, Float64, Float64, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, Oceananigans.Architectures.CPU}, Tuple{Colon, Colon, Colon}, OffsetArrays.OffsetArray{Float64, 3, Array{Float64, 3}}, Float64, Oceananigans.BoundaryConditions.FieldBoundaryConditions{Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Value, Oceananigans.BoundaryConditions.ContinuousBoundaryFunction{Oceananigans.Grids.Center, Oceananigans.Grids.Center, Nothing, Oceananigans.BoundaryConditions.RightBoundary, OceanBioME.LOBSTERModel.var"#3#5", Nothing, Tuple{}, Tuple{}, Tuple{}}}, Oceananigans.BoundaryConditions.BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}}, Nothing, Oceananigans.Fields.FieldBoundaryBuffers{Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing}}}}, ::Tuple{typeof(Oceananigans.Operators.identity3), typeof(Oceananigans.Operators.identity4), typeof(Oceananigans.Operators.identity5), typeof(Oceananigans.Operators.identity1)}, ::Tuple{Int64, Int64, Nothing, Nothing})
│
│    Closest candidates are:
│      field_arguments(::Any, ::Any, ::Any, ::Any, ::Any, ::Any, ::Tuple{T, T} where T)
│       @ Oceananigans ~/.julia/packages/Oceananigans/1LLCG/src/Utils/user_function_arguments.jl:4
│      field_arguments(::Any, ::Any, ::Any, ::Any, ::Any, ::Any, ::Tuple{T, T, T} where T)
│       @ Oceananigans ~/.julia/packages/Oceananigans/1LLCG/src/Utils/user_function_arguments.jl:8
│      field_arguments(::Any, ::Any, ::Any, ::Any, ::Any, ::Any, ::Tuple{Any})
│       @ Oceananigans ~/.julia/packages/Oceananigans/1LLCG/src/Utils/user_function_arguments.jl:1
│      ...

I'm not sure, where is this from?

I've been using Oceananigans 0.88 and 0.89 with OceanBioME and its been fine? I just tried running the tests and the above snipped (admittedly on a slightly different version, but will change to main now) and they run with 0.88.

I have some small changes I want to make to the gas exchange stuff anyway so I'll make a new PR and solve this there.

navidcy · 2023-10-10T16:14:09Z

This

using Oceananigans, OceanBioME

grid = RectilinearGrid(size=(3, 3, 30), extent=(10, 10, 200));

model = NonhydrostaticModel(; grid,
                              biogeochemistry = LOBSTER(; grid, carbonates = true),
                              boundary_conditions = (DIC = FieldBoundaryConditions(top = CO₂_flux), ))

works for you in Oceananigans v0.88 or later? For me it doesn't...

navidcy · 2023-10-10T16:21:33Z

@jagoosw the PISCES.md does not appear in the Docs. Do we want to include it? Or delete it completely? (There is no point of it being there and just create errors in the Doc builds)

docs/src/model_components/biogeochemical/PISCES.md

jagoosw · 2023-10-10T16:24:54Z

using Oceananigans, OceanBioME

grid = RectilinearGrid(size=(3, 3, 30), extent=(10, 10, 200));

CO₂_flux = GasExchange(; air_concentration, gas = :CO₂) 

model = NonhydrostaticModel(; grid,
                              biogeochemistry = LOBSTER(; grid, carbonates = true),
                              boundary_conditions = (DIC = FieldBoundaryConditions(top = CO₂_flux), ))

works for me in 0.88.

jagoosw · 2023-10-10T16:25:15Z

@jagoosw the PISCES.md does not appear in the Docs. Do we want to include it? Or delete it completely? (There is no point of it being there and just create errors in the Doc builds)

I agree delete

navidcy · 2023-10-10T16:28:57Z

using Oceananigans, OceanBioME

grid = RectilinearGrid(size=(3, 3, 30), extent=(10, 10, 200));

CO₂_flux = GasExchange(; gas = :CO₂)

model = NonhydrostaticModel(; grid,
                              biogeochemistry = LOBSTER(; grid, carbonates = true),
                              boundary_conditions = (DIC = FieldBoundaryConditions(top = CO₂_flux), ))

works for me in 0.88.

Not for me! Weird!

Actually,

julia> CO₂_flux = GasExchange(; air_concentration, gas = :CO₂)
ERROR: UndefVarError: `air_concentration` not defined
Stacktrace:
 [1] top-level scope
   @ REPL[13]:1

so I tried this:

julia> using Oceananigans, OceanBioME

julia> grid = RectilinearGrid(size=(3, 3, 30), extent=(10, 10, 200));

julia> CO₂_flux = GasExchange(; gas = :CO₂)
FluxBoundaryCondition: ContinuousBoundaryFunction gasexchange_function at (Nothing, Nothing, Nothing)

julia> model = NonhydrostaticModel(; grid,
                                     biogeochemistry = LOBSTER(; grid, carbonates = true),
                                     boundary_conditions = (DIC = FieldBoundaryConditions(top = CO₂_flux), ))

and for me it errors!

jagoosw · 2023-10-10T16:30:57Z

I've just got the same error trying todo something slightly different so even weirder

jagoosw · 2023-10-10T16:34:23Z

Oh, I've worked out what the original error is. Its because the model doesn't have T and S tracers. This should work:

using Oceananigans, OceanBioME

grid = RectilinearGrid(size=(3, 3, 30), extent=(10, 10, 200));

CO₂_flux = GasExchange(; air_concentration = 240.0, gas = :CO₂) 

model = NonhydrostaticModel(; grid,
                              biogeochemistry = LOBSTER(; grid, carbonates = true),
                              boundary_conditions = (DIC = FieldBoundaryConditions(top = CO₂_flux), ),
                              tracers = (:T, :S))

What I said before should also have errored in previous versions.

navidcy · 2023-10-10T16:37:01Z

Did the default tracers changed in NonhydrostaticModel?

navidcy · 2023-10-10T16:40:32Z

Well this appears in many places in the examples and docs. Shall we leave it for a different PR?

jagoosw · 2023-10-10T16:59:22Z

I think all of the examples either specify T and S (the eady one) or have functional T and S specified for the boundary (which is something I'm working on dropping because it's made it all a mess).

If it appears as is anywhere then I have no clue how it didn't fail because the default tracers for nonhydrostatic have always been nothing.

In the tests we manually specify T and S:

OceanBioME.jl/test/test_gasexchange.jl

Lines 18 to 21 in b413571

    
           model = NonhydrostaticModel(; grid,  
        
                                         tracers = (:T, :S), 
        
                                         biogeochemistry = LOBSTER(; grid, carbonates = true),  
        
                                         boundary_conditions = (DIC = FieldBoundaryConditions(top = GasExchange(; air_concentration, gas = :CO₂)), ))

I think we can leave for another PR but I guess we should work out a way to check that T and S are present. This is kind of a floor in the Oceanangans regularisation because the error above could be caught earlier when the indices of the fields are determined, I suppose after this:

https://github.com/CliMA/Oceananigans.jl/blob/4f26afb2b509870a5448943198b1b5c404a86430/src/Operators/interpolation_utils.jl#L104-L107

jagoosw · 2023-10-10T17:58:38Z

I've been meaning to drop support for prescribing temperature and salinity in the gas exchange and kelp models as its made a mess of the code and is a hangover from some of our column experiments which isn't needed since they can just be put in the model as a function field much more cleanly.

I've implemented this in #149

codecov · 2023-10-10T18:03:17Z

Codecov Report

All modified lines are covered by tests ✅

Comparison is base (b413571) 65.78% compared to head (3fa303d) 65.69%.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #146      +/-   ##
==========================================
- Coverage   65.78%   65.69%   -0.10%     
==========================================
  Files          27       27              
  Lines        1064     1064              
==========================================
- Hits          700      699       -1     
- Misses        364      365       +1

see 1 file with indirect coverage changes

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navidcy · 2023-10-10T18:24:35Z

Ok. This looks ready. @jagoosw ?

jagoosw

LGTM, thank you!

update dependencies

497efe0

navidcy requested a review from jagoosw September 20, 2023 09:59

navidcy added the package label Sep 20, 2023

navidcy added 2 commits September 20, 2023 13:22

drop strict=true kwarg

6327e08

update deps

d627919

navidcy added 3 commits October 10, 2023 08:03

merge main

f5a1280

update bib syntax

f4176c8

bump patch release

b2fa2c2

don't error for cross_references

92d84c6

navidcy added 3 commits October 10, 2023 08:31

add contributors in authors; clean code

662db63

add missing quote

0e14e4d

remove extra quote

75567d3

navidcy added 2 commits October 10, 2023 08:37

add missing doi

8f5e155

add missing doi

9dc4a02

navidcy changed the title ~~Update dependencies~~ Update dependencies + some polishing Oct 10, 2023

navidcy added 2 commits October 10, 2023 09:21

update git remote instruction

42bf991

some rephrase; use present rather than future for more directness

aa550ea

navidcy added 3 commits October 10, 2023 09:43

fix doc crossrefs

b75bb08

remove unnecessary import

368610c

bit rephrasing

8c3158d

navidcy added 3 commits October 10, 2023 10:43

point to julia docs for import vs using

039ffc6

use present

91e3db5

code cleanup

9e623cb

pin to Oceananigans v0.87

fb16867

navidcy changed the title ~~Update dependencies + some polishing~~ Update Documenter + some polishing Oct 10, 2023

try remove warnonly

b5dc83f

delete PISCES.md

3fa303d

navidcy commented Oct 10, 2023

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jagoosw mentioned this pull request Oct 10, 2023

(0.89.2) Fix various bugs in auto adding bgc tracers and setting up field dependant forcing CliMA/Oceananigans.jl#3323

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navidcy merged commit 0726da1 into main Oct 10, 2023
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navidcy deleted the ncc/update-deps branch October 10, 2023 20:51

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