Merge pull request #110 from OceanBioME/jsw/update-dependencies

Update Oceananigans/KernelAbstractions versions
OceanBioME · Jun 24, 2023 · f83a4df · f83a4df · jagoosw · Jun 24, 2023
2 parents d6c6132 + 2207525
commit f83a4df
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Showing 23 changed files with 345 additions and 838 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 <js2430@damtp.cam.ac.uk>", "John R Taylor <j.r.taylor@damtp.cam.ac.uk>", "Si Chen <sc2350@damtp.cam.ac.uk>"]
-version = "0.1.2"
+version = "0.2.0"
 
 [deps]
 Adapt = "79e6a3ab-5dfb-504d-930d-738a2a938a0e"
@@ -16,8 +16,8 @@ StructArrays = "09ab397b-f2b6-538f-b94a-2f83cf4a842a"
 Adapt = "^3.4"
 DiffEqBase = "^6.100"
 JLD2 = "^0.4.31"
-KernelAbstractions = "^0.8.6"
-Oceananigans = "^0.81.0"
+KernelAbstractions = "^0.9.0"
+Oceananigans = "^0.83.0"
 Roots = "^2.0.0"
 StructArrays = "^0.6.15"
 julia = "^1.8.0"

diff --git a/docs/Project.toml b/docs/Project.toml
@@ -17,4 +17,4 @@ Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 [compat]
 CairoMakie = "0.10"
 Literate = "≥2.9.0"
-Oceananigans = "^0.81.0"
+Oceananigans = "^0.83.0"
diff --git a/docs/display_parameters.jl b/docs/display_parameters.jl
@@ -12,7 +12,7 @@ function parameter_table(labels, values)
     return output 
 end
 
-function show_parameters(model; exclude = (:advection_schemes, :optionals, :light_attenuation_model, :particles, :sediment_model, # usually bgc models
+function show_parameters(model; exclude = (:optionals, :light_attenuation_model, :particles, :sediment_model, # usually bgc models
                                            :architecture, :x, :y, :z, :A, :N, :C, :nitrate_uptake, :ammonia_uptake, 
                                            :primary_production, :frond_exudation, :nitrogen_erosion, :carbon_erosion, :scalefactor, :custom_dynamics,
                                            :pescribed_temperature, :pescribed_salinity, # usually particles

diff --git a/docs/src/model_components/individuals/index.md b/docs/src/model_components/individuals/index.md
@@ -23,15 +23,15 @@ You then need to overload particular functions to integrate the growth, so they
 
 ```@example particles
 import Oceananigans.Biogeochemistry: update_tendencies!
-import Oceananigans.LagrangianParticleTracking: update_particle_properties!, _advect_particles!
+import Oceananigans.Models.LagrangianParticleTracking: update_lagrangian_particle_properties!, _advect_particles!
 ```
 
 First, to integrate the particles properties we overload `update_particle_properties`, in this fictitious case we will have a Mondo-quota nutrient uptake and growth:
 
 ```@example particles
 using Oceananigans.Fields: interpolate
 
-function update_particle_properties!(particles::GrowingParticles, model, bgc, Δt)
+function update_lagrangian_particle_properties!(particles::GrowingParticles, model, bgc, Δt)
     @inbounds for p in 1:length(particles)
         nutrients = @inbounds interpolate(model.tracers.NO₃, particle.x[p], particle.y[p], particle.z[p])
 

diff --git a/examples/NPZD.jl b/examples/NPZD.jl