Merge pull request #5 from simone-silvestri/ss-hl-lb-as/strandardizin…

…g-weno-neverworld

Cleanup simulation

.github/workflows/CI.yaml

@@ -0,0 +1,34 @@
+name: CI
+on:
+  push:
+    branches:
+      - main
+    tags: ['*']
+  pull_request:
+concurrency:
+  # Skip intermediate builds: always.
+  # Cancel intermediate builds: only if it is a pull request build.
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: ${{ startsWith(github.ref, 'refs/pull/') }}
+jobs:
+  test:
+    name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        version:
+          - '1.8'
+        os:
+          - ubuntu-latest
+        arch:
+          - x64
+    steps:
+      - uses: actions/checkout@v2
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: ${{ matrix.version }}
+          arch: ${{ matrix.arch }}
+      - uses: julia-actions/cache@v1
+      - uses: julia-actions/julia-buildpkg@v1
+      - uses: julia-actions/julia-runtest@v1

.github/workflows/TagBot.yaml

@@ -0,0 +1,15 @@
+name: TagBot
+on:
+  issue_comment:
+    types:
+      - created
+  workflow_dispatch:
+jobs:
+  TagBot:
+    if: github.event_name == 'workflow_dispatch' || github.actor == 'JuliaTagBot'
+    runs-on: ubuntu-latest
+    steps:
+      - uses: JuliaRegistries/TagBot@v1
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          ssh: ${{ secrets.DOCUMENTER_KEY }}

Manifest.toml

@@ -2,19 +2,21 @@
 
 julia_version = "1.9.2"
 manifest_format = "2.0"
-project_hash = "5411c641a7bad65eba10b4657191742605d0069c"
+project_hash = "e43aeb692041b95ca8b35784687ca34ab003a8f5"
 
 [[deps.AbstractFFTs]]
 deps = ["LinearAlgebra"]
-git-tree-sha1 = "cad4c758c0038eea30394b1b671526921ca85b21"
+git-tree-sha1 = "d92ad398961a3ed262d8bf04a1a2b8340f915fef"
 uuid = "621f4979-c628-5d54-868e-fcf4e3e8185c"
-version = "1.4.0"
+version = "1.5.0"
 
     [deps.AbstractFFTs.extensions]
     AbstractFFTsChainRulesCoreExt = "ChainRulesCore"
+    AbstractFFTsTestExt = "Test"
 
     [deps.AbstractFFTs.weakdeps]
     ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
+    Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [[deps.Adapt]]
 deps = ["LinearAlgebra", "Requires"]
@@ -119,9 +121,9 @@ version = "0.2.4"
 
 [[deps.Compat]]
 deps = ["UUIDs"]
-git-tree-sha1 = "4e88377ae7ebeaf29a047aa1ee40826e0b708a5d"
+git-tree-sha1 = "e460f044ca8b99be31d35fe54fc33a5c33dd8ed7"
 uuid = "34da2185-b29b-5c13-b0c7-acf172513d20"
-version = "4.7.0"
+version = "4.9.0"
 weakdeps = ["Dates", "LinearAlgebra"]
 
     [deps.Compat.extensions]
@@ -150,9 +152,9 @@ version = "1.15.0"
 
 [[deps.DataStructures]]
 deps = ["Compat", "InteractiveUtils", "OrderedCollections"]
-git-tree-sha1 = "cf25ccb972fec4e4817764d01c82386ae94f77b4"
+git-tree-sha1 = "3dbd312d370723b6bb43ba9d02fc36abade4518d"
 uuid = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
-version = "0.18.14"
+version = "0.18.15"
 
 [[deps.DataValueInterfaces]]
 git-tree-sha1 = "bfc1187b79289637fa0ef6d4436ebdfe6905cbd6"
@@ -163,6 +165,16 @@ version = "1.0.0"
 deps = ["Printf"]
 uuid = "ade2ca70-3891-5945-98fb-dc099432e06a"
 
+[[deps.Distances]]
+deps = ["LinearAlgebra", "Statistics", "StatsAPI"]
+git-tree-sha1 = "b6def76ffad15143924a2199f72a5cd883a2e8a9"
+uuid = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7"
+version = "0.10.9"
+weakdeps = ["SparseArrays"]
+
+    [deps.Distances.extensions]
+    DistancesSparseArraysExt = "SparseArrays"
+
 [[deps.Distributed]]
 deps = ["Random", "Serialization", "Sockets"]
 uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b"
@@ -184,9 +196,9 @@ uuid = "b305315f-e792-5b7a-8f41-49f472929428"
 version = "1.0.1"
 
 [[deps.ExprTools]]
-git-tree-sha1 = "c1d06d129da9f55715c6c212866f5b1bddc5fa00"
+git-tree-sha1 = "27415f162e6028e81c72b82ef756bf321213b6ec"
 uuid = "e2ba6199-217a-4e67-a87a-7c52f15ade04"
-version = "0.1.9"
+version = "0.1.10"
 
 [[deps.FFTW]]
 deps = ["AbstractFFTs", "FFTW_jll", "LinearAlgebra", "MKL_jll", "Preferences", "Reexport"]
@@ -234,9 +246,9 @@ version = "1.3.1"
 
 [[deps.HDF5_jll]]
 deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LLVMOpenMP_jll", "LazyArtifacts", "LibCURL_jll", "Libdl", "MPICH_jll", "MPIPreferences", "MPItrampoline_jll", "MicrosoftMPI_jll", "OpenMPI_jll", "OpenSSL_jll", "TOML", "Zlib_jll", "libaec_jll"]
-git-tree-sha1 = "3b20c3ce9c14aedd0adca2bc8c882927844bd53d"
+git-tree-sha1 = "592e1c427983a465831fc73c5ae0ca5d0ac13a9e"
 uuid = "0234f1f7-429e-5d53-9886-15a909be8d59"
-version = "1.14.0+0"
+version = "1.14.1+0"
 
 [[deps.IfElse]]
 git-tree-sha1 = "debdd00ffef04665ccbb3e150747a77560e8fad1"
@@ -251,9 +263,9 @@ version = "0.2.1"
 
 [[deps.IntelOpenMP_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
-git-tree-sha1 = "0cb9352ef2e01574eeebdb102948a58740dcaf83"
+git-tree-sha1 = "ad37c091f7d7daf900963171600d7c1c5c3ede32"
 uuid = "1d5cc7b8-4909-519e-a0f8-d0f5ad9712d0"
-version = "2023.1.0+0"
+version = "2023.2.0+0"
 
 [[deps.InteractiveUtils]]
 deps = ["Markdown"]
@@ -277,9 +289,9 @@ version = "1.0.0"
 
 [[deps.JLD2]]
 deps = ["FileIO", "MacroTools", "Mmap", "OrderedCollections", "Pkg", "Printf", "Reexport", "Requires", "TranscodingStreams", "UUIDs"]
-git-tree-sha1 = "5df8278ad24772c0c6dbbeb97b162ccf29ced2a9"
+git-tree-sha1 = "aa6ffef1fd85657f4999030c52eaeec22a279738"
 uuid = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
-version = "0.4.32"
+version = "0.4.33"
 
 [[deps.JLLWrappers]]
 deps = ["Preferences"]
@@ -289,9 +301,9 @@ version = "1.4.1"
 
 [[deps.JSON3]]
 deps = ["Dates", "Mmap", "Parsers", "PrecompileTools", "StructTypes", "UUIDs"]
-git-tree-sha1 = "5b62d93f2582b09e469b3099d839c2d2ebf5066d"
+git-tree-sha1 = "95220473901735a0f4df9d1ca5b171b568b2daa3"
 uuid = "0f8b85d8-7281-11e9-16c2-39a750bddbf1"
-version = "1.13.1"
+version = "1.13.2"
 
 [[deps.KernelAbstractions]]
 deps = ["Adapt", "Atomix", "InteractiveUtils", "LinearAlgebra", "MacroTools", "PrecompileTools", "Requires", "SparseArrays", "StaticArrays", "UUIDs", "UnsafeAtomics", "UnsafeAtomicsLLVM"]
@@ -382,15 +394,15 @@ uuid = "56ddb016-857b-54e1-b83d-db4d58db5568"
 
 [[deps.MKL_jll]]
 deps = ["Artifacts", "IntelOpenMP_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "Pkg"]
-git-tree-sha1 = "154d7aaa82d24db6d8f7e4ffcfe596f40bff214b"
+git-tree-sha1 = "eb006abbd7041c28e0d16260e50a24f8f9104913"
 uuid = "856f044c-d86e-5d09-b602-aeab76dc8ba7"
-version = "2023.1.0+0"
+version = "2023.2.0+0"
 
 [[deps.MPI]]
 deps = ["Distributed", "DocStringExtensions", "Libdl", "MPICH_jll", "MPIPreferences", "MPItrampoline_jll", "MicrosoftMPI_jll", "OpenMPI_jll", "PkgVersion", "PrecompileTools", "Requires", "Serialization", "Sockets"]
-git-tree-sha1 = "98fc280a56d3b5cc218435f82df60e05771fefa6"
+git-tree-sha1 = "49579593ac2c5f9213c61eead3e39606d22a2a04"
 uuid = "da04e1cc-30fd-572f-bb4f-1f8673147195"
-version = "0.20.12"
+version = "0.20.13"
 
     [deps.MPI.extensions]
     AMDGPUExt = "AMDGPU"
@@ -408,9 +420,9 @@ version = "4.1.2+0"
 
 [[deps.MPIPreferences]]
 deps = ["Libdl", "Preferences"]
-git-tree-sha1 = "d86a788b336e8ae96429c0c42740ccd60ac0dfcc"
+git-tree-sha1 = "781916a2ebf2841467cda03b6f1af43e23839d85"
 uuid = "3da0fdf6-3ccc-4f1b-acd9-58baa6c99267"
-version = "0.1.8"
+version = "0.1.9"
 
 [[deps.MPItrampoline_jll]]
 deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPIPreferences", "TOML"]
@@ -463,12 +475,12 @@ uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908"
 version = "1.2.0"
 
 [[deps.Oceananigans]]
-deps = ["Adapt", "CUDA", "Crayons", "CubedSphere", "Dates", "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 = "0cbd8f251530630509958cfb7a155d19ddce0039"
+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 = "62c7f218c9bcddfee05ab89f218440781a03a692"
 repo-rev = "ss/load-balance-and-corners"
 repo-url = "https://github.com/CliMA/Oceananigans.jl.git"
 uuid = "9e8cae18-63c1-5223-a75c-80ca9d6e9a09"
-version = "0.85.0"
+version = "0.86.0"
 
 [[deps.OffsetArrays]]
 deps = ["Adapt"]
@@ -494,9 +506,9 @@ version = "4.1.5+0"
 
 [[deps.OpenSSL_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl"]
-git-tree-sha1 = "cae3153c7f6cf3f069a853883fd1919a6e5bab5b"
+git-tree-sha1 = "e78db7bd5c26fc5a6911b50a47ee302219157ea8"
 uuid = "458c3c95-2e84-50aa-8efc-19380b2a3a95"
-version = "3.0.9+0"
+version = "3.0.10+0"
 
 [[deps.OpenSpecFun_jll]]
 deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Pkg"]
@@ -505,21 +517,21 @@ uuid = "efe28fd5-8261-553b-a9e1-b2916fc3738e"
 version = "0.5.5+0"
 
 [[deps.OrderedCollections]]
-git-tree-sha1 = "d321bf2de576bf25ec4d3e4360faca399afca282"
+git-tree-sha1 = "2e73fe17cac3c62ad1aebe70d44c963c3cfdc3e3"
 uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
-version = "1.6.0"
+version = "1.6.2"
 
 [[deps.Parsers]]
 deps = ["Dates", "PrecompileTools", "UUIDs"]
-git-tree-sha1 = "4b2e829ee66d4218e0cef22c0a64ee37cf258c29"
+git-tree-sha1 = "716e24b21538abc91f6205fd1d8363f39b442851"
 uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0"
-version = "2.7.1"
+version = "2.7.2"
 
 [[deps.PencilArrays]]
 deps = ["Adapt", "JSON3", "LinearAlgebra", "MPI", "OffsetArrays", "Random", "Reexport", "StaticArrayInterface", "StaticArrays", "StaticPermutations", "Strided", "TimerOutputs", "VersionParsing"]
-git-tree-sha1 = "c1d2b659ce423897de45e998f49f77e789e1859d"
+git-tree-sha1 = "c30a7fb1e424ea572962dac493ad6c3f556695e0"
 uuid = "0e08944d-e94e-41b1-9406-dcf66b6a9d2e"
-version = "0.18.1"
+version = "0.19.0"
 
     [deps.PencilArrays.extensions]
     PencilArraysDiffEqExt = ["DiffEqBase"]
@@ -531,9 +543,9 @@ version = "0.18.1"
 
 [[deps.PencilFFTs]]
 deps = ["AbstractFFTs", "FFTW", "LinearAlgebra", "MPI", "PencilArrays", "Reexport", "TimerOutputs"]
-git-tree-sha1 = "af200cef52069f3428127b237919d7c69eb6b10d"
+git-tree-sha1 = "bd69f3f0ee248cfb4241800aefb705b5ded592ff"
 uuid = "4a48f351-57a6-4416-9ec4-c37015456aae"
-version = "0.15.0"
+version = "0.15.1"
 
 [[deps.Pkg]]
 deps = ["Artifacts", "Dates", "Downloads", "FileWatching", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"]
@@ -668,9 +680,9 @@ version = "2.3.0"
 
 [[deps.Static]]
 deps = ["IfElse"]
-git-tree-sha1 = "dbde6766fc677423598138a5951269432b0fcc90"
+git-tree-sha1 = "f295e0a1da4ca425659c57441bcb59abb035a4bc"
 uuid = "aedffcd0-7271-4cad-89d0-dc628f76c6d3"
-version = "0.8.7"
+version = "0.8.8"
 
 [[deps.StaticArrayInterface]]
 deps = ["ArrayInterface", "Compat", "IfElse", "LinearAlgebra", "Requires", "SnoopPrecompile", "SparseArrays", "Static", "SuiteSparse"]
@@ -685,18 +697,18 @@ weakdeps = ["OffsetArrays", "StaticArrays"]
 
 [[deps.StaticArrays]]
 deps = ["LinearAlgebra", "Random", "StaticArraysCore"]
-git-tree-sha1 = "fffc14c695c17bfdbfa92a2a01836cdc542a1e46"
+git-tree-sha1 = "9cabadf6e7cd2349b6cf49f1915ad2028d65e881"
 uuid = "90137ffa-7385-5640-81b9-e52037218182"
-version = "1.6.1"
+version = "1.6.2"
 weakdeps = ["Statistics"]
 
     [deps.StaticArrays.extensions]
     StaticArraysStatisticsExt = "Statistics"
 
 [[deps.StaticArraysCore]]
-git-tree-sha1 = "1d5708d926c76a505052d0d24a846d5da08bc3a4"
+git-tree-sha1 = "36b3d696ce6366023a0ea192b4cd442268995a0d"
 uuid = "1e83bf80-4336-4d27-bf5d-d5a4f845583c"
-version = "1.4.1"
+version = "1.4.2"
 
 [[deps.StaticPermutations]]
 git-tree-sha1 = "193c3daa18ff3e55c1dae66acb6a762c4a3bdb0b"
@@ -708,11 +720,17 @@ deps = ["LinearAlgebra", "SparseArrays"]
 uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 version = "1.9.0"
 
+[[deps.StatsAPI]]
+deps = ["LinearAlgebra"]
+git-tree-sha1 = "45a7769a04a3cf80da1c1c7c60caf932e6f4c9f7"
+uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0"
+version = "1.6.0"
+
 [[deps.Strided]]
 deps = ["LinearAlgebra", "StridedViews", "TupleTools"]
-git-tree-sha1 = "b32eadf6ac726a790567fdc872b63117712e16a8"
+git-tree-sha1 = "137303f5e0a39f966b462c53ae2c5c6e34c4828b"
 uuid = "5e0ebb24-38b0-5f93-81fe-25c709ecae67"
-version = "2.0.1"
+version = "2.0.3"
 
 [[deps.StridedViews]]
 deps = ["LinearAlgebra"]
@@ -761,7 +779,7 @@ version = "1.10.1"
 [[deps.Tar]]
 deps = ["ArgTools", "SHA"]
 uuid = "a4e569a6-e804-4fa4-b0f3-eef7a1d5b13e"
-version = "1.10.1"
+version = "1.10.0"
 
 [[deps.TaylorSeries]]
 deps = ["LinearAlgebra", "Markdown", "Requires", "SparseArrays"]

Project.toml

@@ -4,6 +4,7 @@ authors = ["Simone Silvestri <[email protected]>"]
 version = "0.1.0"
 
 [deps]
+Adapt = "79e6a3ab-5dfb-504d-930d-738a2a938a0e"
 CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba"
 FFTW = "7a1cc6ca-52ef-59f5-83cd-3a7055c09341"
 JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
@@ -15,3 +16,13 @@ Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
 
 [compat]
 MPI = "0.20.0"
+
+[extras]
+CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
+FFMPEG = "c87230d0-a227-11e9-1b43-d7ebe4e7570a"
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+UnicodePlots = "b8865327-cd53-5732-bb35-84acbb429228"
+
+[targets]
+example = ["UnicodePlots", "FFMPEG", "CairoMakie"]
+test = ["Test"]