Merge pull request #155 from tomchor/compathelper/new_version/2023-09…

…-21-01-06-42-858-03230177406

CompatHelper: bump compat for Oceananigans to 0.88, (keep existing compat)

Manifest.toml

@@ -2,7 +2,7 @@
 
 julia_version = "1.9.2"
 manifest_format = "2.0"
-project_hash = "499db9e8a647dd4085244c2217886e12b219e87a"
+project_hash = "ec6ea1621ee15ad706cd9132940939cbe9c1fe63"
 
 [[deps.AbstractFFTs]]
 deps = ["LinearAlgebra"]
@@ -474,9 +474,9 @@ version = "1.2.0"
 
 [[deps.Oceananigans]]
 deps = ["Adapt", "CUDA", "Crayons", "CubedSphere", "Dates", "Distances", "DocStringExtensions", "FFTW", "Glob", "IncompleteLU", "InteractiveUtils", "IterativeSolvers", "JLD2", "KernelAbstractions", "LinearAlgebra", "Logging", "MPI", "NCDatasets", "OffsetArrays", "OrderedCollections", "PencilArrays", "PencilFFTs", "Pkg", "Printf", "Random", "Rotations", "SeawaterPolynomials", "SparseArrays", "Statistics", "StructArrays"]
-git-tree-sha1 = "20b9c143de93ef4bc4322ce5f888dcfa8113c151"
+git-tree-sha1 = "1821dce5269caa6f9dc3df3e1b97928b39f233b5"
 uuid = "9e8cae18-63c1-5223-a75c-80ca9d6e9a09"
-version = "0.87.3"
+version = "0.88.0"
 
 [[deps.OffsetArrays]]
 deps = ["Adapt"]

Project.toml

@@ -1,7 +1,7 @@
 name = "Oceanostics"
 uuid = "d0ccf422-c8fb-49b5-a76d-74acdde946ac"
 authors = ["tomchor <tomaschor@gmail.com>"]
-version = "0.12.1"
+version = "0.13.0"
 
 [deps]
 DocStringExtensions = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
@@ -10,7 +10,7 @@ Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
 
 [compat]
 DocStringExtensions = "0.9"
-Oceananigans = "0.85, 0.86, 0.87"
+Oceananigans = "0.85, 0.86, 0.87, 0.88"
 julia = "1.9"
 
 [extras]

docs/Project.toml

@@ -3,3 +3,6 @@ CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 Literate = "98b081ad-f1c9-55d3-8b20-4c87d4299306"
 Rasters = "a3a2b9e3-a471-40c9-b274-f788e487c689"
+
+[compat]
+Documenter = "1"

docs/examples/tilted_bottom_boundary_layer.jl

@@ -137,7 +137,7 @@ simulation.callbacks[:wizard] = Callback(wizard, IterationInterval(4))
 using Oceanostics.ProgressMessengers
 
 walltime_per_timestep = StepDuration() # This needs to instantiated here, and not in the function below
-progress(simulation) = @info (PercentageProgress(with_prefix=false, with_units=false) + Time() + TimeStep() + MaxVelocities() + AdvectiveCFLNumber() + walltime_per_timestep)(simulation)
+progress(simulation) = @info (PercentageProgress(with_prefix=false, with_units=false) + SimulationTime() + TimeStep() + MaxVelocities() + AdvectiveCFLNumber() + walltime_per_timestep)(simulation)
 
 simulation.callbacks[:progress] = Callback(progress, IterationInterval(400))
 

docs/make.jl

@@ -46,7 +46,6 @@ makedocs(sitename = "Oceanostics.jl",
          pages = pages,
          modules = [Oceanostics],
          doctest = true,
-         strict = :doctest,
          clean = true,
          format = format,
          checkdocs = :exports

src/Oceanostics.jl

@@ -67,22 +67,17 @@ end
 #---
 
 #+++ A few utils for closure tuples:
-using Oceananigans.TurbulenceClosures: νᶜᶜᶜ, calc_nonlinear_κᶜᶜᶜ
+using Oceananigans.TurbulenceClosures: νᶜᶜᶜ
 
 # Fallbacks that capture "single closure" case
 @inline _νᶜᶜᶜ(args...) = νᶜᶜᶜ(args...)
-@inline _calc_nonlinear_κᶜᶜᶜ(args...) = calc_nonlinear_κᶜᶜᶜ(args...)
 
 # End point
 @inline _νᶜᶜᶜ(i, j, k, grid, closure_tuple::Tuple{}, K::Tuple{}, clock) = zero(grid)
-@inline _calc_nonlinear_κᶜᶜᶜ(i, j, k, grid, closure_tuple::Tuple{}, args...) = zero(grid)
 
 # Unroll the loop over a tuple
 @inline _νᶜᶜᶜ(i, j, k, grid, closure_tuple::Tuple, K::Tuple, clock) = νᶜᶜᶜ(i, j, k, grid, closure_tuple[1],     K[1],     clock) + 
                                                                      _νᶜᶜᶜ(i, j, k, grid, closure_tuple[2:end], K[2:end], clock)
-
-@inline _calc_nonlinear_κᶜᶜᶜ(i, j, k, grid, closure_tuple::Tuple, args...) = calc_nonlinear_κᶜᶜᶜ(i, j, k, grid, closure_tuple[1], args...) +
-                                                                            _calc_nonlinear_κᶜᶜᶜ(i, j, k, grid, closure_tuple[2:end], args...)
 #---
 
 include("TKEBudgetTerms.jl")

src/ProgressMessengers/ProgressMessengers.jl

@@ -9,7 +9,7 @@ export AbstractProgressMessenger
 export FunctionMessenger
 export MaxUVelocity, MaxVVelocity, MaxWVelocity
 export MaxVelocities
-export Iteration, Time, TimeStep, PercentageProgress, Walltime, StepDuration, BasicTimeMessenger, TimeMessenger, StopwatchMessenger
+export Iteration, SimulationTime, TimeStep, PercentageProgress, Walltime, StepDuration, BasicTimeMessenger, TimeMessenger, StopwatchMessenger
 export MaxViscosity, AdvectiveCFLNumber, DiffusiveCFLNumber, BasicStabilityMessenger, StabilityMessenger
 export CourantNumber, NormalizedMaxViscosity
 export BasicMessenger, SingleLineMessenger, TimedMessenger

src/ProgressMessengers/timing.jl

@@ -15,14 +15,14 @@ end
 end
 #---
 
-#+++ Time
-Base.@kwdef struct Time <: AbstractProgressMessenger
+#+++ SimulationTime
+Base.@kwdef struct SimulationTime <: AbstractProgressMessenger
     with_prefix :: Bool = true
     with_units ::  Bool = true
     print       :: Bool = false
 end
 
-@inline function (tm::Time)(simulation)
+@inline function (tm::SimulationTime)(simulation)
     t = time(simulation)
     message = tm.with_units ? prettytime(t) : @sprintf("%.2g", t)
     tm.with_prefix && (message = "time = " * message)
@@ -119,10 +119,10 @@ struct BasicTimeMessenger{PM <: AbstractProgressMessenger} <: AbstractProgressMe
 end
 
 BasicTimeMessenger(; percentage = PercentageProgress(with_prefix = false, with_units = false, print = false),
-                      time = Time(with_prefix = true, with_units = true, print = false),
-                      Δt = TimeStep(with_prefix = true, with_units = true, print = false),
-                      walltime = Walltime(with_prefix = true, with_units = true, print = false),
-                      print = true) = BasicTimeMessenger{AbstractProgressMessenger}(percentage, time, Δt, walltime, print)
+                     time = SimulationTime(with_prefix = true, with_units = true, print = false),
+                     Δt = TimeStep(with_prefix = true, with_units = true, print = false),
+                     walltime = Walltime(with_prefix = true, with_units = true, print = false),
+                     print = true) = BasicTimeMessenger{AbstractProgressMessenger}(percentage, time, Δt, walltime, print)
 
 function (stm::BasicTimeMessenger)(simulation)
     message = ("["*stm.percentage*"] " * stm.time + stm.Δt + stm.walltime)(simulation)

test/runtests.jl

@@ -481,7 +481,7 @@ model_types = (NonhydrostaticModel, HydrostaticFreeSurfaceModel)
         model.clock.iteration = 0
         step_duration = StepDuration()
         progress(simulation) = @info (PercentageProgress(with_prefix=false, with_units=false)
-                                      + Time() + TimeStep() + MaxVelocities()
+                                      + SimulationTime() + TimeStep() + MaxVelocities()
                                       + AdvectiveCFLNumber() + step_duration)(simulation)
         test_progress_messenger(model, progress)
     end