Merge pull request #176 from OceanBioME/jsw/update-dependencies

Attempt to bump compats
OceanBioME · Jul 1, 2024 · 9645c15 · 9645c15 · jagoosw · Jul 1, 2024
2 parents 12cfa7f + 05477fe
commit 9645c15
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Showing 16 changed files with 185 additions and 163 deletions.
diff --git a/Manifest.toml b/Manifest.toml
diff --git a/Project.toml b/Project.toml
@@ -1,7 +1,7 @@
 name = "OceanBioME"
 uuid = "a49af516-9db8-4be4-be45-1dad61c5a376"
 authors = ["Jago Strong-Wright <[email protected]> and contributors"]
-version = "0.10.2"
+version = "0.10.3"
 
 [deps]
 Adapt = "79e6a3ab-5dfb-504d-930d-738a2a938a0e"
@@ -19,10 +19,10 @@ Documenter = "1"
 EnsembleKalmanProcesses = "1"
 JLD2 = "0.4"
 KernelAbstractions = "0.9"
-Oceananigans = "0.90.11"
+Oceananigans = "0.91"
 Roots = "2"
 StructArrays = "0.4, 0.5, 0.6"
-julia = "1.9"
+julia = "1.10"
 
 [extras]
 CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba"

diff --git a/docs/Project.toml b/docs/Project.toml
@@ -21,4 +21,4 @@ Documenter = "1"
 DocumenterCitations = "1"
 JLD2 = "0.4.38"
 Literate = "≥2.9.0"
-Oceananigans = "0.90.11"
+Oceananigans = "0.91.3"
diff --git a/src/Boundaries/Sediments/coupled_timesteppers.jl b/src/Boundaries/Sediments/coupled_timesteppers.jl
@@ -8,11 +8,12 @@ using Oceananigans.Architectures: AbstractArchitecture
 
 import Oceananigans.TimeSteppers: ab2_step!, rk3_substep!
 
-@inline function ab2_step!(model::NonhydrostaticModel{<:Any, <:Any, <:Any, <:Any, <:Any, <:Any, <:Any, <:Any, <:Any, <:Any, <:Any, <:Any, <:Any, <:Any, <:Any, <:Any, <:Any, <:Biogeochemistry{<:Any, <:Any, <:FlatSediment}}, Δt, χ)
+@inline function ab2_step!(model::NonhydrostaticModel{<:Any, <:Any, <:Any, <:Any, <:Any, <:Any, <:Any, <:Any, <:Any, <:Any, <:Any, <:Any, <:Any, <:Any, <:Any, <:Any, <:Any, <:Biogeochemistry{<:Any, <:Any, <:FlatSediment}}, Δt)
     workgroup, worksize = work_layout(model.grid, :xyz)
     arch = model.architecture
     step_field_kernel! = ab2_step_field!(device(arch), workgroup, worksize)
     model_fields = prognostic_fields(model)
+    χ = model.timestepper.χ
 
     for (i, field) in enumerate(model_fields)
 
@@ -45,7 +46,9 @@ import Oceananigans.TimeSteppers: ab2_step!, rk3_substep!
     return nothing
 end
 
-@inline function ab2_step!(model::HydrostaticFreeSurfaceModel{<:Any, <:Any, <:AbstractArchitecture, <:Any, <:Any, <:Any, <:Any, <:Any, <:Any, <:Any, <:Any, <:Biogeochemistry{<:Any, <:Any, <:FlatSediment}}, Δt, χ)
+@inline function ab2_step!(model::HydrostaticFreeSurfaceModel{<:Any, <:Any, <:AbstractArchitecture, <:Any, <:Any, <:Any, <:Any, <:Any, <:Any, <:Any, <:Any, <:Biogeochemistry{<:Any, <:Any, <:FlatSediment}}, Δt)
+    χ = model.timestepper.χ
+
     # Step locally velocity and tracers
     @apply_regionally local_ab2_step!(model, Δt, χ)
 
@@ -54,6 +57,7 @@ end
 
     sediment = model.biogeochemistry.sediment
     arch = model.architecture
+
 
     for (i, field) in enumerate(sediment_fields(sediment))
         launch!(arch, model.grid, :xy, ab2_step_flat_field!, 

diff --git a/src/BoxModel/boxmodel.jl b/src/BoxModel/boxmodel.jl
@@ -44,7 +44,7 @@ end
     BoxModel(; biogeochemistry::B,
                forcing = NamedTuple(),
                timestepper = :RungeKutta3,
-               clock::C = Clock(0.0, 0, 1),
+               clock::C = Clock(; time = 0.0),
                prescribed_fields::PF = (:T, :PAR))
 
 Constructs a box model of a `biogeochemistry` model. Once this has been constructed you can set initial condiitons by `set!(model, X=1.0...)` and then `run!(model)`.
@@ -61,7 +61,7 @@ Keyword Arguments
 function BoxModel(; biogeochemistry::B,
                     forcing = NamedTuple(),
                     timestepper = :RungeKutta3,
-                    clock::C = Clock(0.0, 0, 1),
+                    clock::C = Clock(; time = 0.0),
                     prescribed_fields::PF = (:T, :PAR)) where {B, C, PF}
 
     variables = (required_biogeochemical_tracers(biogeochemistry)..., required_biogeochemical_auxiliary_fields(biogeochemistry)...)

diff --git a/src/Models/Individuals/SLatissima.jl b/src/Models/Individuals/SLatissima.jl
@@ -24,6 +24,7 @@ using Oceananigans.Units
 using Oceananigans: Center, CPU
 using Oceananigans.Architectures: on_architecture, device, architecture
 using Oceananigans.Biogeochemistry: required_biogeochemical_tracers, biogeochemical_auxiliary_fields
+using Oceananigans.Models.LagrangianParticleTracking: _advect_particles!
 
 using Oceananigans.Operators: volume
 using Oceananigans.Grids: AbstractGrid, Flat
@@ -32,7 +33,7 @@ using Oceananigans.Models: total_velocities
 
 import Adapt: adapt_structure, adapt
 import Oceananigans.Biogeochemistry: update_tendencies!
-import Oceananigans.Models.LagrangianParticleTracking: update_lagrangian_particle_properties!, _advect_particles!
+import Oceananigans.Models.LagrangianParticleTracking: update_lagrangian_particle_properties!
 
 @inline no_dynamics(args...) = nothing
 
@@ -333,10 +334,7 @@ function update_lagrangian_particle_properties!(particles::SLatissima, model, bg
     # Advect particles
     advect_particles_kernel! = _advect_particles!(device(arch), workgroup, worksize)
 
-    advect_particles_kernel!((x = particles.x, y = particles.y, z = particles.z), 
-                             1.0, model.grid, Δt,
-                             total_velocities(model))
-
+    advect_particles_kernel!(particles, 1.0, model.grid, Δt, total_velocities(model))
 
     update_particle_properties_kernel! = _update_lagrangian_particle_properties!(device(arch), workgroup, worksize)
 

diff --git a/src/Particles/Particles.jl b/src/Particles/Particles.jl
@@ -26,7 +26,7 @@ abstract type BiogeochemicalParticles end
 @inline update_lagrangian_particle_properties!(model, bgc::Biogeochemistry{<:Any, <:Any, <:Any, <:BiogeochemicalParticles}, Δt) = 
     update_lagrangian_particle_properties!(bgc.particles, model, bgc, Δt)
 
-update_lagrangian_particle_properties!(::BiogeochemicalParticles, model, bgc, Δt) = nothing
+@inline update_lagrangian_particle_properties!(::BiogeochemicalParticles, model, bgc, Δt) = nothing
 
 size(particles::BiogeochemicalParticles) = size(particles.x)
 length(particles::BiogeochemicalParticles) = length(particles.x)

diff --git a/test/dependencies_for_runtests.jl b/test/dependencies_for_runtests.jl
@@ -0,0 +1,3 @@
+using OceanBioME, Test, CUDA, Oceananigans, JLD2, Documenter
+
+architecture = CUDA.has_cuda() ? GPU() : CPU()
diff --git a/test/runtests.jl b/test/runtests.jl
@@ -1,13 +1,11 @@
-using OceanBioME, Documenter, Test, CUDA, Oceananigans
-
-architecture = CUDA.has_cuda() ? GPU() : CPU()
+include("dependencies_for_runtests.jl")
 
 include("test_utils.jl")
 include("test_light.jl")
+include("test_slatissima.jl")
 include("test_LOBSTER.jl")
 include("test_NPZD.jl")
 include("test_gasexchange.jl")
-include("test_slatissima.jl")
 include("test_sediments.jl")
 
 architecture == CPU() && @testset "Doctests" begin

diff --git a/test/test_LOBSTER.jl b/test/test_LOBSTER.jl
@@ -1,4 +1,5 @@
-using Test
+include("dependencies_for_runtests.jl")
+
 using OceanBioME: LOBSTER, conserved_tracers, redfield
 using Oceananigans, CUDA
 

diff --git a/test/test_NPZD.jl b/test/test_NPZD.jl
@@ -1,4 +1,5 @@
-using Test
+include("dependencies_for_runtests.jl")
+
 using OceanBioME: NutrientPhytoplanktonZooplanktonDetritus
 using Oceananigans
 

diff --git a/test/test_gasexchange.jl b/test/test_gasexchange.jl
@@ -1,4 +1,5 @@
-using Test
+include("dependencies_for_runtests.jl")
+
 using OceanBioME: Boundaries, GasExchange, LOBSTER
 using Oceananigans, DataDeps, JLD2, Statistics
 using Oceananigans.Units

diff --git a/test/test_light.jl b/test/test_light.jl
@@ -1,4 +1,5 @@
-using Oceananigans, Test
+include("dependencies_for_runtests.jl")
+
 using OceanBioME: TwoBandPhotosyntheticallyActiveRadiation, LOBSTER, NutrientPhytoplanktonZooplanktonDetritus
 using Oceananigans.Biogeochemistry: update_biogeochemical_state!, required_biogeochemical_tracers, biogeochemical_auxiliary_fields
 
@@ -50,7 +51,7 @@ end
         bgc in (LOBSTER, NutrientPhytoplanktonZooplanktonDetritus) # this is now redundant since each model doesn't deal with the light separatly
 
         if !((model == NonhydrostaticModel) && ((grid isa LatitudeLongitudeGrid) | (grid isa OrthogonalSphericalShellGrid)))
-            @info "Testing $bgc in $model on $grid..."
+            @info "Testing light with $bgc in $model on $grid..."
             @test test_two_band(grid, bgc, model)
         end
     end

diff --git a/test/test_sediments.jl b/test/test_sediments.jl
@@ -1,4 +1,4 @@
-using OceanBioME, Oceananigans, Test, JLD2
+include("dependencies_for_runtests.jl")
 
 using OceanBioME.Sediments: SimpleMultiG, InstantRemineralisation
 using Oceananigans.Units

diff --git a/test/test_slatissima.jl b/test/test_slatissima.jl
@@ -1,4 +1,5 @@
-using Test, OceanBioME, Oceananigans
+include("dependencies_for_runtests.jl")
+
 using OceanBioME.SLatissimaModel: SLatissima
 using Oceananigans.Units
 using Oceananigans.Fields: TracerFields
@@ -31,7 +32,9 @@ sum_tracer_carbon(tracers, redfield, organic_carbon_calcate_ratio) =
     # Initial properties
 
     particles = SLatissima(; architecture,
-                             x = on_architecture(architecture, ones(Float64, 2)),
+                             x = on_architecture(architecture,   ones(Float64, 2) .* .5),
+                             y = on_architecture(architecture,   ones(Float64, 2) .* .5),
+                             z = on_architecture(architecture, - ones(Float64, 2) .* .5),
                              A = on_architecture(architecture, ones(Float64, 2) .* 5),
                              N = on_architecture(architecture, ones(Float64, 2)),
                              C = on_architecture(architecture, ones(Float64, 2)),
@@ -60,7 +63,7 @@ sum_tracer_carbon(tracers, redfield, organic_carbon_calcate_ratio) =
     model.clock.time = 60days # get to a high growth phase
 
     for _ in 1:10
-        time_step!(model, 1.0)
+        time_step!(model, 1)
     end
 
     final_tracer_N = sum_tracer_nitrogen(model.tracers)

diff --git a/test/test_utils.jl b/test/test_utils.jl
@@ -1,4 +1,4 @@
-using Test, OceanBioME, Oceananigans
+include("dependencies_for_runtests.jl")
 
 function test_negative_scaling(arch)
     grid = RectilinearGrid(arch, size = (1, 1, 1), extent = (1, 1, 1))