From 1b17502f60ee6113924d2bbaca30da243fe1c3ab Mon Sep 17 00:00:00 2001 From: "Navid C. Constantinou" Date: Tue, 24 Oct 2023 21:33:25 -0600 Subject: [PATCH 1/9] add Siegelman & Young 2023 --- docs/src/index.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/docs/src/index.md b/docs/src/index.md index 2a37692e..9b29ab35 100644 --- a/docs/src/index.md +++ b/docs/src/index.md @@ -84,6 +84,8 @@ The bibtex entry for the paper is: ## Papers using `GeophysicalFlows.jl` +1. Siegelman, L. and Young, W. R. (2023). Two-dimensional turbulence above topography: Vortices and potential vorticity homogenization. _Proceedings of the National Academy of Sciences_, **120(44)**, e2308018120, doi:[10.1073/pnas.2308018120](https://doi.org/10.1073/pnas.2308018120). + 1. Bisits, J. I., Stanley G. J., and Zika, J. D. (2023). Can we accurately quantify a lateral diffusivity using a single tracer release? _Journal of Physical Oceanography_, **53(2)**, 647–659, doi:[10.1175/JPO-D-22-0145.1](https://doi.org/10.1175/JPO-D-22-0145.1). 1. Siegelman, L., Young, W. R., and Ingersoll, A. P. (2022). Polar vortex crystals: Emergence and structure _Proceedings of the National Academy of Sciences_, **119(17)**, e2120486119. doi:[10.1073/pnas.2120486119](https://doi.org/10.1073/pnas.2120486119). From 7c58b2f12d96a724fa5d6f77c6e6870fa0c1ecb5 Mon Sep 17 00:00:00 2001 From: "Navid C. Constantinou" Date: Tue, 24 Oct 2023 21:38:18 -0600 Subject: [PATCH 2/9] add compat for Documenter v0.27 --- docs/Project.toml | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/Project.toml b/docs/Project.toml index fb9b20b4..317883a4 100644 --- a/docs/Project.toml +++ b/docs/Project.toml @@ -9,4 +9,5 @@ Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7" [compat] CairoMakie = "< 0.10.5" CUDA = "1, 2.4.2, 3.0.0 - 3.6.4, 3.7.1, 4" +Documenter = "0.27" Literate = "≥2.9.0" From 75beecaa556bcd2a6eaacfc8346f2c399ed3ff17 Mon Sep 17 00:00:00 2001 From: "Navid C. Constantinou" Date: Wed, 25 Oct 2023 10:10:51 -0600 Subject: [PATCH 3/9] fix code + drop remark for julia v1.0.5 --- docs/src/installation_instructions.md | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/docs/src/installation_instructions.md b/docs/src/installation_instructions.md index f4070152..48a6ed85 100644 --- a/docs/src/installation_instructions.md +++ b/docs/src/installation_instructions.md @@ -5,7 +5,7 @@ You can install the latest version of GeophysicalFlows.jl via the built-in packa instantiate/build all the required dependencies ```julia -julia>] +julia> ] (v1.6) pkg> add GeophysicalFlows (v1.6) pkg> instantiate ``` @@ -30,6 +30,3 @@ more than happy to help with getting your simulations up and running. Last version compatible with Julia v1.5: GeophysicalFlows.jl v0.13.1 - Last version compatible with Julia v1.0.5 (the current long-term-release): GeophysicalFlows.jl v0.5.1 - - From d6102d0433aece9def00c74e29d16def4786352c Mon Sep 17 00:00:00 2001 From: "Navid C. Constantinou" Date: Wed, 25 Oct 2023 10:11:18 -0600 Subject: [PATCH 4/9] run gh actions on julia v1.9 --- .github/workflows/{main.yml => CompatHelper.yml} | 2 +- .github/workflows/Documenter.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) rename .github/workflows/{main.yml => CompatHelper.yml} (95%) diff --git a/.github/workflows/main.yml b/.github/workflows/CompatHelper.yml similarity index 95% rename from .github/workflows/main.yml rename to .github/workflows/CompatHelper.yml index a26db5b5..e60e2dc7 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/CompatHelper.yml @@ -10,7 +10,7 @@ jobs: steps: - uses: julia-actions/setup-julia@latest with: - version: 1.6 + version: 1.9 - name: Pkg.add("CompatHelper") run: julia -e 'using Pkg; Pkg.add("CompatHelper")' - name: CompatHelper.main() diff --git a/.github/workflows/Documenter.yml b/.github/workflows/Documenter.yml index d140b8a1..612779ef 100644 --- a/.github/workflows/Documenter.yml +++ b/.github/workflows/Documenter.yml @@ -18,7 +18,7 @@ jobs: - uses: actions/checkout@v3 - uses: julia-actions/setup-julia@latest with: - version: '1.8' + version: '1.9' - name: Install dependencies run: julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()' - name: Build and deploy From ea40233328c3af96d54792f54d890bfad905f92c Mon Sep 17 00:00:00 2001 From: "Navid C. Constantinou" Date: Wed, 25 Oct 2023 10:11:34 -0600 Subject: [PATCH 5/9] use Documenter v1 --- docs/Project.toml | 4 +- docs/make.jl | 94 +++++++++++++++++++++++------------------------ 2 files changed, 49 insertions(+), 49 deletions(-) diff --git a/docs/Project.toml b/docs/Project.toml index 317883a4..0ce61883 100644 --- a/docs/Project.toml +++ b/docs/Project.toml @@ -7,7 +7,7 @@ Literate = "98b081ad-f1c9-55d3-8b20-4c87d4299306" Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7" [compat] -CairoMakie = "< 0.10.5" CUDA = "1, 2.4.2, 3.0.0 - 3.6.4, 3.7.1, 4" -Documenter = "0.27" +CairoMakie = "< 0.10.5" +Documenter = "1" Literate = "≥2.9.0" diff --git a/docs/make.jl b/docs/make.jl index 7076619f..41428bc8 100644 --- a/docs/make.jl +++ b/docs/make.jl @@ -48,55 +48,55 @@ format = Documenter.HTML( ) makedocs( - modules = [GeophysicalFlows], - doctest = true, - clean = true, + modules = [GeophysicalFlows], + doctest = true, + clean = true, checkdocs = :all, - format = format, - authors = "Navid C. Constantinou, Gregory L. Wagner, and contributors", -sitename = "GeophysicalFlows.jl", - pages = Any[ - "Home" => "index.md", - "Installation instructions" => "installation_instructions.md", - "Aliasing" => "aliasing.md", - "GPU" => "gpu.md", - "Visualize output" => "visualize.md", - "Examples" => [ - "TwoDNavierStokes" => Any[ - "literated/twodnavierstokes_decaying.md", - "literated/twodnavierstokes_stochasticforcing.md", - "literated/twodnavierstokes_stochasticforcing_budgets.md", - ], - "SingleLayerQG" => Any[ - "literated/singlelayerqg_betadecay.md", - "literated/singlelayerqg_betaforced.md", - "literated/singlelayerqg_decaying_topography.md", - "literated/singlelayerqg_decaying_barotropic_equivalentbarotropic.md" - ], - "BarotropicQGQL" => Any[ - "literated/barotropicqgql_betaforced.md", - ], - "MultiLayerQG" => Any[ - "literated/multilayerqg_2layer.md" - ], - "SurfaceQG" => Any[ - "literated/surfaceqg_decaying.md" + format = format, + authors = "Navid C. Constantinou, Gregory L. Wagner, and contributors", + sitename = "GeophysicalFlows.jl", + pages = Any[ + "Home" => "index.md", + "Installation instructions" => "installation_instructions.md", + "Aliasing" => "aliasing.md", + "GPU" => "gpu.md", + "Visualize output" => "visualize.md", + "Examples" => [ + "TwoDNavierStokes" => Any[ + "literated/twodnavierstokes_decaying.md", + "literated/twodnavierstokes_stochasticforcing.md", + "literated/twodnavierstokes_stochasticforcing_budgets.md", + ], + "SingleLayerQG" => Any[ + "literated/singlelayerqg_betadecay.md", + "literated/singlelayerqg_betaforced.md", + "literated/singlelayerqg_decaying_topography.md", + "literated/singlelayerqg_decaying_barotropic_equivalentbarotropic.md" + ], + "BarotropicQGQL" => Any[ + "literated/barotropicqgql_betaforced.md", + ], + "MultiLayerQG" => Any[ + "literated/multilayerqg_2layer.md" + ], + "SurfaceQG" => Any[ + "literated/surfaceqg_decaying.md" + ] + ], + "Modules" => Any[ + "modules/twodnavierstokes.md", + "modules/singlelayerqg.md", + "modules/barotropicqgql.md", + "modules/multilayerqg.md", + "modules/surfaceqg.md" + ], + "Stochastic forcing" => "stochastic_forcing.md", + "Contributor's guide" => "contributing.md", + "Library" => Any[ + "lib/types.md", + "lib/functions.md" ] - ], - "Modules" => Any[ - "modules/twodnavierstokes.md", - "modules/singlelayerqg.md", - "modules/barotropicqgql.md", - "modules/multilayerqg.md", - "modules/surfaceqg.md" - ], - "Stochastic forcing" => "stochastic_forcing.md", - "Contributor's guide" => "contributing.md", - "Library" => Any[ - "lib/types.md", - "lib/functions.md" - ] - ] + ] ) @info "Clean up temporary .jld2 and .nc output created by doctests or literated examples..." From a2f6c38da883264b48816636de3e5072855a9d11 Mon Sep 17 00:00:00 2001 From: "Navid C. Constantinou" Date: Wed, 25 Oct 2023 10:17:43 -0600 Subject: [PATCH 6/9] a few more frames --- examples/singlelayerqg_betadecay.jl | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/examples/singlelayerqg_betadecay.jl b/examples/singlelayerqg_betadecay.jl index 0f03c624..23002021 100644 --- a/examples/singlelayerqg_betadecay.jl +++ b/examples/singlelayerqg_betadecay.jl @@ -31,7 +31,7 @@ nothing #hide stepper = "FilteredRK4" # timestepper dt = 0.04 # timestep nsteps = 2000 # total number of time-steps - nsubs = 20 # number of time-steps for intermediate logging/plotting (nsteps must be multiple of nsubs) + nsubs = 10 # number of time-steps for intermediate logging/plotting (nsteps must be multiple of nsubs) nothing #hide @@ -201,7 +201,7 @@ startwalltime = time() frames = 0:round(Int, nsteps / nsubs) -record(fig, "singlelayerqg_betadecay.mp4", frames, framerate = 8) do j +record(fig, "singlelayerqg_betadecay.mp4", frames, framerate = 12) do j if j % round(Int, nsteps/nsubs / 4) == 0 cfl = clock.dt * maximum([maximum(vars.u) / grid.dx, maximum(vars.v) / grid.dy]) From 390a99aa6cf8a7782e042e236146381b6b2a15b1 Mon Sep 17 00:00:00 2001 From: "Navid C. Constantinou" Date: Wed, 25 Oct 2023 10:22:32 -0600 Subject: [PATCH 7/9] add palinstrophy --- docs/src/lib/functions.md | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/src/lib/functions.md b/docs/src/lib/functions.md index 01639f16..92b5058d 100644 --- a/docs/src/lib/functions.md +++ b/docs/src/lib/functions.md @@ -22,6 +22,7 @@ GeophysicalFlows.TwoDNavierStokes.energy_work GeophysicalFlows.TwoDNavierStokes.enstrophy_dissipation_hyperviscosity GeophysicalFlows.TwoDNavierStokes.enstrophy_dissipation_hypoviscosity GeophysicalFlows.TwoDNavierStokes.enstrophy_work +GeophysicalFlows.TwoDNavierStokes.palinstrophy ``` ### Private functions From 066c0e7c6b43b6b5795e3c089a898bc0891e6f5f Mon Sep 17 00:00:00 2001 From: "Navid C. Constantinou" Date: Wed, 25 Oct 2023 10:31:27 -0600 Subject: [PATCH 8/9] add main module docs --- docs/src/lib/functions.md | 3 +++ 1 file changed, 3 insertions(+) diff --git a/docs/src/lib/functions.md b/docs/src/lib/functions.md index 92b5058d..af0fe0d5 100644 --- a/docs/src/lib/functions.md +++ b/docs/src/lib/functions.md @@ -1,6 +1,9 @@ # Functions ## `GeophysicalFlows` +```@docs +GeophysicalFlows.GeophysicalFlows +``` ### Exported functions From 39a0c5e71740bab2766aa1b18b5d8d8e8cc9c99a Mon Sep 17 00:00:00 2001 From: "Navid C. Constantinou" Date: Fri, 27 Oct 2023 08:19:05 -0600 Subject: [PATCH 9/9] fix ref id --- examples/singlelayerqg_decaying_topography.jl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/examples/singlelayerqg_decaying_topography.jl b/examples/singlelayerqg_decaying_topography.jl index 29532dc0..fc4585a7 100644 --- a/examples/singlelayerqg_decaying_topography.jl +++ b/examples/singlelayerqg_decaying_topography.jl @@ -1,4 +1,4 @@ -# # [Decaying barotropic QG turbulence over topography](@id singlelayerqg_decaying_topography) +# # [Decaying barotropic QG turbulence over topography](@id singlelayerqg_decay_topography_example) # # An example of decaying barotropic quasi-geostrophic turbulence over topography. #