From 4911d52dc22e203a1c07da7f70eabb2d86e26edf Mon Sep 17 00:00:00 2001
From: "Navid C. Constantinou" <navidcy@users.noreply.github.com>
Date: Tue, 22 Feb 2022 06:09:18 +1100
Subject: [PATCH 01/15] skip perfect catke; catke still in development

---
 docs/make.jl | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/docs/make.jl b/docs/make.jl
index d7e61841..b3757ecd 100644
--- a/docs/make.jl
+++ b/docs/make.jl
@@ -25,7 +25,7 @@ to_be_literated = [
   "intro_to_inverse_problems.jl",
   "exploring_priors.jl",
   "perfect_convective_adjustment_calibration.jl",
-  "perfect_catke_calibration.jl",
+  # "perfect_catke_calibration.jl",
   "lesbrary_catke_calibration.jl",
   "perfect_baroclinic_adjustment_calibration.jl"
 ]
@@ -59,7 +59,7 @@ pages = [
 
     "Examples" => [ 
         "literated/perfect_convective_adjustment_calibration.md",
-        "literated/perfect_catke_calibration.md",
+        # "literated/perfect_catke_calibration.md",
         "literated/lesbrary_catke_calibration.md",
         "literated/perfect_baroclinic_adjustment_calibration.md"
         ],

From e4ad04e540dbc48ad55953ada9190fd2b2846312 Mon Sep 17 00:00:00 2001
From: "Navid C. Constantinou" <navidcy@users.noreply.github.com>
Date: Tue, 22 Feb 2022 06:09:29 +1100
Subject: [PATCH 02/15] update oceananigans to 0.71

---
 Manifest.toml      |  46 ++++++------
 Project.toml       |   2 +-
 docs/Manifest.toml | 179 ++++++++++++++++++++++++++++++++++-----------
 docs/Project.toml  |   4 +-
 4 files changed, 163 insertions(+), 68 deletions(-)

diff --git a/Manifest.toml b/Manifest.toml
index 49e86260..6c3a51f1 100644
--- a/Manifest.toml
+++ b/Manifest.toml
@@ -201,9 +201,9 @@ uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b"
 
 [[Distributions]]
 deps = ["ChainRulesCore", "DensityInterface", "FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SparseArrays", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns", "Test"]
-git-tree-sha1 = "2e97190dfd4382499a4ac349e8d316491c9db341"
+git-tree-sha1 = "9d3c0c762d4666db9187f363a76b47f7346e673b"
 uuid = "31c24e10-a181-5473-b8eb-7969acd0382f"
-version = "0.25.46"
+version = "0.25.49"
 
 [[DocStringExtensions]]
 deps = ["LibGit2"]
@@ -251,9 +251,9 @@ version = "1.13.0"
 
 [[FillArrays]]
 deps = ["LinearAlgebra", "Random", "SparseArrays", "Statistics"]
-git-tree-sha1 = "deed294cde3de20ae0b2e0355a6c4e1c6a5ceffc"
+git-tree-sha1 = "4c7d3757f3ecbcb9055870351078552b7d1dbd2d"
 uuid = "1a297f60-69ca-5386-bcde-b61e274b549b"
-version = "0.12.8"
+version = "0.13.0"
 
 [[FixedPointNumbers]]
 deps = ["Statistics"]
@@ -357,10 +357,10 @@ uuid = "82899510-4779-5014-852e-03e436cf321d"
 version = "1.0.0"
 
 [[JLD2]]
-deps = ["DataStructures", "FileIO", "MacroTools", "Mmap", "Pkg", "Printf", "Reexport", "TranscodingStreams", "UUIDs"]
-git-tree-sha1 = "b528d68220e2aba1d2d0c0461b6f7eda8c5c1e33"
+deps = ["FileIO", "MacroTools", "Mmap", "OrderedCollections", "Pkg", "Printf", "Reexport", "TranscodingStreams", "UUIDs"]
+git-tree-sha1 = "28b114b3279cdbac9a61c57b3e6548a572142b34"
 uuid = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
-version = "0.4.20"
+version = "0.4.21"
 
 [[JLLWrappers]]
 deps = ["Preferences"]
@@ -400,9 +400,9 @@ version = "4.7.1"
 
 [[LLVMExtra_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
-git-tree-sha1 = "62115afed394c016c2d3096c5b85c407b48be96b"
+git-tree-sha1 = "f7f5dd0fb39209f4d28ca59d0d4e24579ad325fe"
 uuid = "dad2f222-ce93-54a1-a47d-0025e8a3acab"
-version = "0.0.13+1"
+version = "0.0.13+2"
 
 [[LazyArtifacts]]
 deps = ["Artifacts", "Pkg"]
@@ -434,7 +434,7 @@ uuid = "29816b5a-b9ab-546f-933c-edad1886dfa8"
 uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb"
 
 [[LinearAlgebra]]
-deps = ["Libdl"]
+deps = ["Libdl", "libblastrampoline_jll"]
 uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 
 [[LogExpFunctions]]
@@ -536,9 +536,9 @@ uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908"
 
 [[Oceananigans]]
 deps = ["Adapt", "CUDA", "CUDAKernels", "Crayons", "CubedSphere", "Dates", "DocStringExtensions", "FFTW", "Glob", "IncompleteLU", "InteractiveUtils", "IterativeSolvers", "JLD2", "KernelAbstractions", "LinearAlgebra", "Logging", "MPI", "NCDatasets", "OffsetArrays", "OrderedCollections", "PencilFFTs", "Pkg", "Printf", "Random", "Rotations", "SafeTestsets", "SeawaterPolynomials", "SparseArrays", "Statistics", "StructArrays", "Tullio"]
-git-tree-sha1 = "0e88ed5b897f7505fee7cfc1f946e7693d2be307"
+git-tree-sha1 = "65341647e2965be55c191442e5a18a964b5e3954"
 uuid = "9e8cae18-63c1-5223-a75c-80ca9d6e9a09"
-version = "0.70.3"
+version = "0.71.1"
 
 [[OffsetArrays]]
 deps = ["Adapt"]
@@ -548,9 +548,9 @@ version = "1.10.8"
 
 [[OpenBLAS32_jll]]
 deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Pkg"]
-git-tree-sha1 = "ba4a8f683303c9082e84afba96f25af3c7fb2436"
+git-tree-sha1 = "9c6c2ed4b7acd2137b878eb96c68e63b76199d0f"
 uuid = "656ef2d0-ae68-5445-9ca0-591084a874a2"
-version = "0.3.12+1"
+version = "0.3.17+0"
 
 [[OpenBLAS_jll]]
 deps = ["Artifacts", "CompilerSupportLibraries_jll", "Libdl"]
@@ -642,7 +642,7 @@ deps = ["InteractiveUtils", "Markdown", "Sockets", "Unicode"]
 uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb"
 
 [[Random]]
-deps = ["Serialization"]
+deps = ["SHA", "Serialization"]
 uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 
 [[Random123]]
@@ -745,9 +745,9 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 
 [[SpecialFunctions]]
 deps = ["ChainRulesCore", "IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"]
-git-tree-sha1 = "f0bccf98e16759818ffc5d97ac3ebf87eb950150"
+git-tree-sha1 = "2735e252e72ee0367ebdb10b6148343fd15c2481"
 uuid = "276daf66-3868-5448-9aa4-cd146d93841b"
-version = "1.8.1"
+version = "1.8.3"
 
 [[StatProfilerHTML]]
 deps = ["DataStructures", "Dates", "FlameGraphs", "HAML", "Profile", "SHA", "Test"]
@@ -802,9 +802,9 @@ version = "1.1.2"
 
 [[StructArrays]]
 deps = ["Adapt", "DataAPI", "StaticArrays", "Tables"]
-git-tree-sha1 = "d21f2c564b21a202f4677c0fba5b5ee431058544"
+git-tree-sha1 = "57617b34fa34f91d536eb265df67c2d4519b8b98"
 uuid = "09ab397b-f2b6-538f-b94a-2f83cf4a842a"
-version = "0.6.4"
+version = "0.6.5"
 
 [[StructTypes]]
 deps = ["Dates", "UUIDs"]
@@ -817,9 +817,9 @@ deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"]
 uuid = "4607b0f0-06f3-5cda-b6b1-a6196a1729e9"
 
 [[Suppressor]]
-git-tree-sha1 = "a819d77f31f83e5792a76081eee1ea6342ab8787"
+git-tree-sha1 = "c6ed566db2fe3931292865b966d6d140b7ef32a9"
 uuid = "fd094767-a336-5f1f-9728-57cf17d0bbfb"
-version = "0.2.0"
+version = "0.2.1"
 
 [[TOML]]
 deps = ["Dates"]
@@ -895,6 +895,10 @@ version = "1.3.0"
 deps = ["Libdl"]
 uuid = "83775a58-1f1d-513f-b197-d71354ab007a"
 
+[[libblastrampoline_jll]]
+deps = ["Artifacts", "Libdl", "OpenBLAS_jll"]
+uuid = "8e850b90-86db-534c-a0d3-1478176c7d93"
+
 [[nghttp2_jll]]
 deps = ["Artifacts", "Libdl"]
 uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d"
diff --git a/Project.toml b/Project.toml
index cf42be5c..1ae54756 100644
--- a/Project.toml
+++ b/Project.toml
@@ -28,7 +28,7 @@ Distributions = "0.25"
 EnsembleKalmanProcesses = "0.3"
 FileIO = "1"
 JLD2 = "0.4"
-Oceananigans = "^0.70.3"
+Oceananigans = "^0.71"
 OffsetArrays = "1"
 OrderedCollections = "1"
 ProgressBars = "1"
diff --git a/docs/Manifest.toml b/docs/Manifest.toml
index e0375ccf..a0ad91b4 100644
--- a/docs/Manifest.toml
+++ b/docs/Manifest.toml
@@ -1,5 +1,11 @@
 # This file is machine-generated - editing it directly is not advised
 
+[[AMD]]
+deps = ["Libdl", "LinearAlgebra", "SparseArrays", "Test"]
+git-tree-sha1 = "fc66ffc5cff568936649445f58a55b81eaf9592c"
+uuid = "14f7f29c-3bd6-536c-9a0b-7339e30b5a3e"
+version = "0.4.0"
+
 [[ANSIColoredPrinters]]
 git-tree-sha1 = "574baf8110975760d391c710b6341da1afa48d8c"
 uuid = "a4c015fc-c6ff-483c-b24f-f7ea428134e9"
@@ -61,6 +67,12 @@ version = "0.1.0"
 [[Base64]]
 uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"
 
+[[BenchmarkTools]]
+deps = ["JSON", "Logging", "Printf", "Profile", "Statistics", "UUIDs"]
+git-tree-sha1 = "4c10eee4af024676200bc7752e536f858c6b8f93"
+uuid = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"
+version = "1.3.1"
+
 [[BinaryProvider]]
 deps = ["Libdl", "Logging", "SHA"]
 git-tree-sha1 = "ecdec412a9abc8db54c0efc5548c64dfce072058"
@@ -104,9 +116,9 @@ version = "1.0.5"
 
 [[CairoMakie]]
 deps = ["Base64", "Cairo", "Colors", "FFTW", "FileIO", "FreeType", "GeometryBasics", "LinearAlgebra", "Makie", "SHA", "StaticArrays"]
-git-tree-sha1 = "90fe6622efbb627e7c962e9bd6f5c4228680b7ca"
+git-tree-sha1 = "b1d884ee7dae11985314192270eb5762b9ed09ae"
 uuid = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
-version = "0.7.2"
+version = "0.7.3"
 
 [[Cairo_jll]]
 deps = ["Artifacts", "Bzip2_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "JLLWrappers", "LZO_jll", "Libdl", "Pixman_jll", "Pkg", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Zlib_jll", "libpng_jll"]
@@ -127,9 +139,9 @@ version = "0.3.9"
 
 [[ChainRulesCore]]
 deps = ["Compat", "LinearAlgebra", "SparseArrays"]
-git-tree-sha1 = "f9982ef575e19b0e5c7a98c6e75ee496c0f73a93"
+git-tree-sha1 = "7dd38532a1115a215de51775f9891f0f3e1bac6a"
 uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
-version = "1.12.0"
+version = "1.12.1"
 
 [[ChangesOfVariables]]
 deps = ["ChainRulesCore", "LinearAlgebra", "Test"]
@@ -137,6 +149,18 @@ git-tree-sha1 = "bf98fa45a0a4cee295de98d4c1462be26345b9a1"
 uuid = "9e997f8a-9a97-42d5-a9f1-ce6bfc15e2c0"
 version = "0.1.2"
 
+[[CodecBzip2]]
+deps = ["Bzip2_jll", "Libdl", "TranscodingStreams"]
+git-tree-sha1 = "2e62a725210ce3c3c2e1a3080190e7ca491f18d7"
+uuid = "523fee87-0ab8-5b00-afb7-3ecf72e48cfd"
+version = "0.7.2"
+
+[[CodecZlib]]
+deps = ["TranscodingStreams", "Zlib_jll"]
+git-tree-sha1 = "ded953804d019afa9a3f98981d99b33e3db7b6da"
+uuid = "944b1d66-785c-5afd-91f1-9de20f533193"
+version = "0.7.0"
+
 [[ColorBrewer]]
 deps = ["Colors", "JSON", "Test"]
 git-tree-sha1 = "61c5334f33d91e570e1d0c3eb5465835242582c4"
@@ -183,6 +207,12 @@ git-tree-sha1 = "9f02045d934dc030edad45944ea80dbd1f0ebea7"
 uuid = "d38c429a-6771-53c6-b99e-75d170b6e991"
 version = "0.5.7"
 
+[[Convex]]
+deps = ["AbstractTrees", "BenchmarkTools", "LDLFactorizations", "LinearAlgebra", "MathOptInterface", "OrderedCollections", "SparseArrays", "Test"]
+git-tree-sha1 = "145c5e0b3ea3c9dd3bba134a58bab4112aa250c8"
+uuid = "f65535da-76fb-5f13-bab9-19810c17039a"
+version = "0.14.18"
+
 [[Crayons]]
 git-tree-sha1 = "249fe38abf76d48563e2f4556bebd215aa317e15"
 uuid = "a8cc5b0e-0ffa-5ad4-8c14-923d3ee1735f"
@@ -232,9 +262,9 @@ version = "0.4.0"
 
 [[DiffRules]]
 deps = ["IrrationalConstants", "LogExpFunctions", "NaNMath", "Random", "SpecialFunctions"]
-git-tree-sha1 = "84083a5136b6abf426174a58325ffd159dd6d94f"
+git-tree-sha1 = "dd933c4ef7b4c270aacd4eb88fa64c147492acf0"
 uuid = "b552c78f-8df3-52c6-915a-8e097449b14b"
-version = "1.9.1"
+version = "1.10.0"
 
 [[Distributed]]
 deps = ["Random", "Serialization", "Sockets"]
@@ -242,9 +272,9 @@ uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b"
 
 [[Distributions]]
 deps = ["ChainRulesCore", "DensityInterface", "FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SparseArrays", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns", "Test"]
-git-tree-sha1 = "38012bf3553d01255e83928eec9c998e19adfddf"
+git-tree-sha1 = "9d3c0c762d4666db9187f363a76b47f7346e673b"
 uuid = "31c24e10-a181-5473-b8eb-7969acd0382f"
-version = "0.25.48"
+version = "0.25.49"
 
 [[DocStringExtensions]]
 deps = ["LibGit2"]
@@ -286,10 +316,10 @@ uuid = "b305315f-e792-5b7a-8f41-49f472929428"
 version = "1.0.1"
 
 [[EnsembleKalmanProcesses]]
-deps = ["Distributions", "DocStringExtensions", "LinearAlgebra", "Random", "Statistics", "StatsBase"]
-git-tree-sha1 = "4a0fb4cd1831d0cb630c63da0c1f1fbf50670bad"
+deps = ["Convex", "Distributions", "DocStringExtensions", "LinearAlgebra", "Random", "SCS", "SparseArrays", "Statistics", "StatsBase"]
+git-tree-sha1 = "69ee053771ac874dc0e8836e022e9ffd13c0be42"
 uuid = "aa8a2aa5-91d8-4396-bcef-d4f2ec43552d"
-version = "0.1.2"
+version = "0.3.0"
 
 [[Expat_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
@@ -334,9 +364,9 @@ version = "1.13.0"
 
 [[FillArrays]]
 deps = ["LinearAlgebra", "Random", "SparseArrays", "Statistics"]
-git-tree-sha1 = "deed294cde3de20ae0b2e0355a6c4e1c6a5ceffc"
+git-tree-sha1 = "4c7d3757f3ecbcb9055870351078552b7d1dbd2d"
 uuid = "1a297f60-69ca-5386-bcde-b61e274b549b"
-version = "0.12.8"
+version = "0.13.0"
 
 [[FixedPointNumbers]]
 deps = ["Statistics"]
@@ -456,6 +486,12 @@ git-tree-sha1 = "129acf094d168394e80ee1dc4bc06ec835e510a3"
 uuid = "2e76f6c2-a576-52d4-95c1-20adfe4de566"
 version = "2.8.1+1"
 
+[[HypergeometricFunctions]]
+deps = ["DualNumbers", "LinearAlgebra", "SpecialFunctions", "Test"]
+git-tree-sha1 = "65e4589030ef3c44d3b90bdc5aac462b4bb05567"
+uuid = "34004b35-14d8-5ef3-9330-4cdb6864b03a"
+version = "0.3.8"
+
 [[IOCapture]]
 deps = ["Logging", "Random"]
 git-tree-sha1 = "f7be53659ab06ddc986428d3a9dcc95f6fa6705a"
@@ -563,10 +599,10 @@ uuid = "82899510-4779-5014-852e-03e436cf321d"
 version = "1.0.0"
 
 [[JLD2]]
-deps = ["DataStructures", "FileIO", "MacroTools", "Mmap", "Pkg", "Printf", "Reexport", "TranscodingStreams", "UUIDs"]
-git-tree-sha1 = "b528d68220e2aba1d2d0c0461b6f7eda8c5c1e33"
+deps = ["FileIO", "MacroTools", "Mmap", "OrderedCollections", "Pkg", "Printf", "Reexport", "TranscodingStreams", "UUIDs"]
+git-tree-sha1 = "28b114b3279cdbac9a61c57b3e6548a572142b34"
 uuid = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
-version = "0.4.20"
+version = "0.4.21"
 
 [[JLLWrappers]]
 deps = ["Preferences"]
@@ -616,6 +652,12 @@ git-tree-sha1 = "f6250b16881adf048549549fba48b1161acdac8c"
 uuid = "c1c5ebd0-6772-5130-a774-d5fcae4a789d"
 version = "3.100.1+0"
 
+[[LDLFactorizations]]
+deps = ["AMD", "LinearAlgebra", "SparseArrays", "Test"]
+git-tree-sha1 = "399bbe845e06e1c2d44ebb241f554d45eaf66788"
+uuid = "40e66cde-538c-5869-a4ad-c39174c6795b"
+version = "0.8.1"
+
 [[LLVM]]
 deps = ["CEnum", "LLVMExtra_jll", "Libdl", "Printf", "Unicode"]
 git-tree-sha1 = "f8dcd7adfda0dddaf944e62476d823164cccc217"
@@ -624,9 +666,9 @@ version = "4.7.1"
 
 [[LLVMExtra_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
-git-tree-sha1 = "62115afed394c016c2d3096c5b85c407b48be96b"
+git-tree-sha1 = "f7f5dd0fb39209f4d28ca59d0d4e24579ad325fe"
 uuid = "dad2f222-ce93-54a1-a47d-0025e8a3acab"
-version = "0.0.13+1"
+version = "0.0.13+2"
 
 [[LZO_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
@@ -699,14 +741,14 @@ uuid = "38a345b3-de98-5d2b-a5d3-14cd9215e700"
 version = "2.36.0+0"
 
 [[LinearAlgebra]]
-deps = ["Libdl"]
+deps = ["Libdl", "libblastrampoline_jll"]
 uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 
 [[Literate]]
 deps = ["Base64", "IOCapture", "JSON", "REPL"]
-git-tree-sha1 = "32b914d8654e945e1076bab58b02dad479ceffcd"
+git-tree-sha1 = "b856be4fe3dfa4146e5c890f1d9865f4e2e4779d"
 uuid = "98b081ad-f1c9-55d3-8b20-4c87d4299306"
-version = "2.12.1"
+version = "2.13.0"
 
 [[LogExpFunctions]]
 deps = ["ChainRulesCore", "ChangesOfVariables", "DocStringExtensions", "InverseFunctions", "IrrationalConstants", "LinearAlgebra"]
@@ -743,9 +785,9 @@ version = "0.5.9"
 
 [[Makie]]
 deps = ["Animations", "Base64", "ColorBrewer", "ColorSchemes", "ColorTypes", "Colors", "Contour", "Distributions", "DocStringExtensions", "FFMPEG", "FileIO", "FixedPointNumbers", "Formatting", "FreeType", "FreeTypeAbstraction", "GeometryBasics", "GridLayoutBase", "ImageIO", "IntervalSets", "Isoband", "KernelDensity", "LaTeXStrings", "LinearAlgebra", "MakieCore", "Markdown", "Match", "MathTeXEngine", "Observables", "OffsetArrays", "Packing", "PlotUtils", "PolygonOps", "Printf", "Random", "RelocatableFolders", "Serialization", "Showoff", "SignedDistanceFields", "SparseArrays", "StaticArrays", "Statistics", "StatsBase", "StatsFuns", "StructArrays", "UnicodeFun"]
-git-tree-sha1 = "0aafd5121c6e1b6a83bd3bb341da45f058225a9b"
+git-tree-sha1 = "475b854bff7867c37687d65f7b9498401ac6536d"
 uuid = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a"
-version = "0.16.3"
+version = "0.16.4"
 
 [[MakieCore]]
 deps = ["Observables"]
@@ -767,6 +809,12 @@ git-tree-sha1 = "1d9bc5c1a6e7ee24effb93f175c9342f9154d97f"
 uuid = "7eb4fadd-790c-5f42-8a69-bfa0b872bfbf"
 version = "1.2.0"
 
+[[MathOptInterface]]
+deps = ["BenchmarkTools", "CodecBzip2", "CodecZlib", "JSON", "LinearAlgebra", "MutableArithmetics", "OrderedCollections", "Printf", "SparseArrays", "Test", "Unicode"]
+git-tree-sha1 = "e8c9653877adcf8f3e7382985e535bb37b083598"
+uuid = "b8f27783-ece8-5eb3-8dc8-9495eed66fee"
+version = "0.10.9"
+
 [[MathTeXEngine]]
 deps = ["AbstractTrees", "Automa", "DataStructures", "FreeTypeAbstraction", "GeometryBasics", "LaTeXStrings", "REPL", "RelocatableFolders", "Test"]
 git-tree-sha1 = "70e733037bbf02d691e78f95171a1fa08cdc6332"
@@ -807,6 +855,12 @@ version = "0.3.3"
 [[MozillaCACerts_jll]]
 uuid = "14a3606d-f60d-562e-9121-12d972cd8159"
 
+[[MutableArithmetics]]
+deps = ["LinearAlgebra", "SparseArrays", "Test"]
+git-tree-sha1 = "842b5ccd156e432f369b204bb704fd4020e383ac"
+uuid = "d8a4904e-b15c-11e9-3269-09a3773c0cb0"
+version = "0.3.3"
+
 [[NCDatasets]]
 deps = ["CFTime", "DataStructures", "Dates", "NetCDF_jll", "Printf"]
 git-tree-sha1 = "17e39eb5bbe564f48bdbefbd103bd3f49fcfcb9b"
@@ -840,9 +894,9 @@ version = "0.4.0"
 
 [[Oceananigans]]
 deps = ["Adapt", "CUDA", "CUDAKernels", "Crayons", "CubedSphere", "Dates", "DocStringExtensions", "FFTW", "Glob", "IncompleteLU", "InteractiveUtils", "IterativeSolvers", "JLD2", "KernelAbstractions", "LinearAlgebra", "Logging", "MPI", "NCDatasets", "OffsetArrays", "OrderedCollections", "PencilFFTs", "Pkg", "Printf", "Random", "Rotations", "SafeTestsets", "SeawaterPolynomials", "SparseArrays", "Statistics", "StructArrays", "Tullio"]
-git-tree-sha1 = "0e88ed5b897f7505fee7cfc1f946e7693d2be307"
+git-tree-sha1 = "65341647e2965be55c191442e5a18a964b5e3954"
 uuid = "9e8cae18-63c1-5223-a75c-80ca9d6e9a09"
-version = "0.70.3"
+version = "0.71.1"
 
 [[OffsetArrays]]
 deps = ["Adapt"]
@@ -856,6 +910,16 @@ git-tree-sha1 = "887579a3eb005446d514ab7aeac5d1d027658b8f"
 uuid = "e7412a2a-1a6e-54c0-be00-318e2571c051"
 version = "1.3.5+1"
 
+[[OpenBLAS32_jll]]
+deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Pkg"]
+git-tree-sha1 = "9c6c2ed4b7acd2137b878eb96c68e63b76199d0f"
+uuid = "656ef2d0-ae68-5445-9ca0-591084a874a2"
+version = "0.3.17+0"
+
+[[OpenBLAS_jll]]
+deps = ["Artifacts", "CompilerSupportLibraries_jll", "Libdl"]
+uuid = "4536629a-c528-5b80-bd46-f80d51c5b363"
+
 [[OpenEXR]]
 deps = ["Colors", "FileIO", "OpenEXR_jll"]
 git-tree-sha1 = "327f53360fdb54df7ecd01e96ef1983536d1e633"
@@ -951,9 +1015,9 @@ version = "0.15.2"
 
 [[PencilFFTs]]
 deps = ["AbstractFFTs", "FFTW", "LinearAlgebra", "MPI", "PencilArrays", "Reexport", "TimerOutputs"]
-git-tree-sha1 = "323bc75909576d8c660696d12f39bfec49b7223a"
+git-tree-sha1 = "47808b022d4a1568745421239db6366c8dceeee7"
 uuid = "4a48f351-57a6-4416-9ec4-c37015456aae"
-version = "0.13.2"
+version = "0.13.3"
 
 [[Pixman_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
@@ -992,6 +1056,10 @@ version = "1.2.3"
 deps = ["Unicode"]
 uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7"
 
+[[Profile]]
+deps = ["Printf"]
+uuid = "9abbd945-dff8-562f-b5e8-e1ebf5ef1b79"
+
 [[ProgressMeter]]
 deps = ["Distributed", "Printf"]
 git-tree-sha1 = "afadeba63d90ff223a6a48d2009434ecee2ec9e8"
@@ -1011,17 +1079,17 @@ uuid = "1fd47b50-473d-5c70-9696-f719f8f3bcdc"
 version = "2.4.2"
 
 [[Quaternions]]
-deps = ["DualNumbers", "LinearAlgebra"]
-git-tree-sha1 = "adf644ef95a5e26c8774890a509a55b7791a139f"
+deps = ["DualNumbers", "LinearAlgebra", "Random"]
+git-tree-sha1 = "abe487c51089a229e2f004f8bee0b057a03ade21"
 uuid = "94ee1d12-ae83-5a48-8b1c-48b8ff168ae0"
-version = "0.4.2"
+version = "0.4.8"
 
 [[REPL]]
 deps = ["InteractiveUtils", "Markdown", "Sockets", "Unicode"]
 uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb"
 
 [[Random]]
-deps = ["Serialization"]
+deps = ["SHA", "Serialization"]
 uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 
 [[Random123]]
@@ -1082,6 +1150,24 @@ git-tree-sha1 = "405148000e80f70b31e7732ea93288aecb1793fa"
 uuid = "6038ab10-8711-5258-84ad-4b1120ba62dc"
 version = "1.2.0"
 
+[[SCS]]
+deps = ["LinearAlgebra", "MathOptInterface", "Requires", "SCS_GPU_jll", "SCS_jll", "SparseArrays"]
+git-tree-sha1 = "5982566c8db974ab2294c8172f3a00f6e6264fa8"
+uuid = "c946c3f1-0d1f-5ce8-9dea-7daa1f7e2d13"
+version = "0.9.0"
+
+[[SCS_GPU_jll]]
+deps = ["Artifacts", "JLLWrappers", "Libdl", "OpenBLAS_jll", "Pkg"]
+git-tree-sha1 = "d73211cbae51a6e30338e26e5919bc48a8a95736"
+uuid = "af6e375f-46ec-5fa0-b791-491b0dfa44a4"
+version = "3.0.0+0"
+
+[[SCS_jll]]
+deps = ["Artifacts", "JLLWrappers", "Libdl", "OpenBLAS32_jll", "Pkg"]
+git-tree-sha1 = "085fee3a6e5790b198c820140e75f790008c642d"
+uuid = "f4f2fc5b-1d94-523c-97ea-2ab488bedf4b"
+version = "3.0.1+0"
+
 [[SHA]]
 uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce"
 
@@ -1153,9 +1239,9 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 
 [[SpecialFunctions]]
 deps = ["ChainRulesCore", "IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"]
-git-tree-sha1 = "f0bccf98e16759818ffc5d97ac3ebf87eb950150"
+git-tree-sha1 = "2735e252e72ee0367ebdb10b6148343fd15c2481"
 uuid = "276daf66-3868-5448-9aa4-cd146d93841b"
-version = "1.8.1"
+version = "1.8.3"
 
 [[StackViews]]
 deps = ["OffsetArrays"]
@@ -1171,9 +1257,9 @@ version = "0.5.5"
 
 [[StaticArrays]]
 deps = ["LinearAlgebra", "Random", "Statistics"]
-git-tree-sha1 = "a635a9333989a094bddc9f940c04c549cd66afcf"
+git-tree-sha1 = "95c6a5d0e8c69555842fc4a927fc485040ccc31c"
 uuid = "90137ffa-7385-5640-81b9-e52037218182"
-version = "1.3.4"
+version = "1.3.5"
 
 [[StaticPermutations]]
 git-tree-sha1 = "193c3daa18ff3e55c1dae66acb6a762c4a3bdb0b"
@@ -1185,21 +1271,22 @@ deps = ["LinearAlgebra", "SparseArrays"]
 uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 
 [[StatsAPI]]
-git-tree-sha1 = "d88665adc9bcf45903013af0982e2fd05ae3d0a6"
+deps = ["LinearAlgebra"]
+git-tree-sha1 = "c3d8ba7f3fa0625b062b82853a7d5229cb728b6b"
 uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0"
-version = "1.2.0"
+version = "1.2.1"
 
 [[StatsBase]]
 deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"]
-git-tree-sha1 = "118e8411d506d583fbbcf4f3a0e3c5a9e83370b8"
+git-tree-sha1 = "8977b17906b0a1cc74ab2e3a05faa16cf08a8291"
 uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
-version = "0.33.15"
+version = "0.33.16"
 
 [[StatsFuns]]
-deps = ["ChainRulesCore", "InverseFunctions", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"]
-git-tree-sha1 = "f35e1879a71cca95f4826a14cdbf0b9e253ed918"
+deps = ["ChainRulesCore", "HypergeometricFunctions", "InverseFunctions", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"]
+git-tree-sha1 = "25405d7016a47cf2bd6cd91e66f4de437fd54a07"
 uuid = "4c63d2b9-4356-54db-8cca-17b64c39e42c"
-version = "0.9.15"
+version = "0.9.16"
 
 [[Strided]]
 deps = ["LinearAlgebra", "TupleTools"]
@@ -1209,9 +1296,9 @@ version = "1.1.2"
 
 [[StructArrays]]
 deps = ["Adapt", "DataAPI", "StaticArrays", "Tables"]
-git-tree-sha1 = "d21f2c564b21a202f4677c0fba5b5ee431058544"
+git-tree-sha1 = "57617b34fa34f91d536eb265df67c2d4519b8b98"
 uuid = "09ab397b-f2b6-538f-b94a-2f83cf4a842a"
-version = "0.6.4"
+version = "0.6.5"
 
 [[StructTypes]]
 deps = ["Dates", "UUIDs"]
@@ -1393,6 +1480,10 @@ git-tree-sha1 = "5982a94fcba20f02f42ace44b9894ee2b140fe47"
 uuid = "0ac62f75-1d6f-5e53-bd7c-93b484bb37c0"
 version = "0.15.1+0"
 
+[[libblastrampoline_jll]]
+deps = ["Artifacts", "Libdl", "OpenBLAS_jll"]
+uuid = "8e850b90-86db-534c-a0d3-1478176c7d93"
+
 [[libfdk_aac_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
 git-tree-sha1 = "daacc84a041563f965be61859a36e17c4e4fcd55"
diff --git a/docs/Project.toml b/docs/Project.toml
index 4a4a216e..b52274d8 100644
--- a/docs/Project.toml
+++ b/docs/Project.toml
@@ -8,5 +8,5 @@ Literate = "98b081ad-f1c9-55d3-8b20-4c87d4299306"
 Oceananigans = "9e8cae18-63c1-5223-a75c-80ca9d6e9a09"
 
 [compat]
-EnsembleKalmanProcesses = "0.1"
-Oceananigans = "^0.70.3"
+EnsembleKalmanProcesses = "0.3"
+Oceananigans = "^0.71"

From 235f70ee2bfd34c1ace203decadc572ed9169fb9 Mon Sep 17 00:00:00 2001
From: "Navid C. Constantinou" <navidcy@users.noreply.github.com>
Date: Tue, 22 Feb 2022 06:11:01 +1100
Subject: [PATCH 03/15] ExplicitTimeDiscretization -> Explicit

---
 src/Parameters.jl | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/Parameters.jl b/src/Parameters.jl
index cf508b78..96599977 100644
--- a/src/Parameters.jl
+++ b/src/Parameters.jl
@@ -4,7 +4,7 @@ export FreeParameters, lognormal, ScaledLogitNormal
 
 using Oceananigans.Architectures: CPU, arch_array, architecture
 using Oceananigans.TurbulenceClosures: AbstractTurbulenceClosure
-using Oceananigans.TurbulenceClosures: AbstractTimeDiscretization, ExplicitTimeDiscretization
+using Oceananigans.TurbulenceClosures: AbstractTimeDiscretization, Explicit
 
 using Printf
 using Distributions
@@ -445,7 +445,7 @@ Closure(ClosureSubModel(12, 2), 3)
 """
 closure_with_parameters(closure, parameters) = construct_object(dict_properties(closure), parameters)
 
-closure_with_parameters(closure::AbstractTurbulenceClosure{ExplicitTimeDiscretization}, parameters) =
+closure_with_parameters(closure::AbstractTurbulenceClosure{Explicit}, parameters) =
     construct_object(dict_properties(closure), parameters, type_parameter=nothing)
 
 closure_with_parameters(closure::AbstractTurbulenceClosure{TD}, parameters) where {TD <: AbstractTimeDiscretization} =

From 27ef3359cde91b59398ca6a4aff250e2fa194ba5 Mon Sep 17 00:00:00 2001
From: "Navid C. Constantinou" <navidcy@users.noreply.github.com>
Date: Tue, 22 Feb 2022 06:11:15 +1100
Subject: [PATCH 04/15] bump patch release

---
 Project.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Project.toml b/Project.toml
index 1ae54756..c21a2d16 100644
--- a/Project.toml
+++ b/Project.toml
@@ -2,7 +2,7 @@ name = "OceanTurbulenceParameterEstimation"
 uuid = "eca81dc5-87a6-4430-aec8-c76695404a43"
 license = "MIT"
 authors = ["Adeline Hillier <adelineh2000@gmail.com>", "Gregory L. Wagner <wagner.greg@gmail.com>", "Navid C. Constantinou <navidcy@gmail.com>", "and co-contributors"]
-version = "0.10.0"
+version = "0.10.1"
 
 [deps]
 DataDeps = "124859b0-ceae-595e-8997-d05f6a7a8dfe"

From e3b2b24b92f38913774c81d2a7f0925dfbab767b Mon Sep 17 00:00:00 2001
From: "Navid C. Constantinou" <navidcy@users.noreply.github.com>
Date: Tue, 22 Feb 2022 06:34:39 +1100
Subject: [PATCH 05/15] build manifests with julia 1.6

---
 Manifest.toml      | 12 ++++--------
 docs/Manifest.toml | 12 ++++--------
 2 files changed, 8 insertions(+), 16 deletions(-)

diff --git a/Manifest.toml b/Manifest.toml
index 6c3a51f1..a5313ebe 100644
--- a/Manifest.toml
+++ b/Manifest.toml
@@ -434,7 +434,7 @@ uuid = "29816b5a-b9ab-546f-933c-edad1886dfa8"
 uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb"
 
 [[LinearAlgebra]]
-deps = ["Libdl", "libblastrampoline_jll"]
+deps = ["Libdl"]
 uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 
 [[LogExpFunctions]]
@@ -548,9 +548,9 @@ version = "1.10.8"
 
 [[OpenBLAS32_jll]]
 deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Pkg"]
-git-tree-sha1 = "9c6c2ed4b7acd2137b878eb96c68e63b76199d0f"
+git-tree-sha1 = "ba4a8f683303c9082e84afba96f25af3c7fb2436"
 uuid = "656ef2d0-ae68-5445-9ca0-591084a874a2"
-version = "0.3.17+0"
+version = "0.3.12+1"
 
 [[OpenBLAS_jll]]
 deps = ["Artifacts", "CompilerSupportLibraries_jll", "Libdl"]
@@ -642,7 +642,7 @@ deps = ["InteractiveUtils", "Markdown", "Sockets", "Unicode"]
 uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb"
 
 [[Random]]
-deps = ["SHA", "Serialization"]
+deps = ["Serialization"]
 uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 
 [[Random123]]
@@ -895,10 +895,6 @@ version = "1.3.0"
 deps = ["Libdl"]
 uuid = "83775a58-1f1d-513f-b197-d71354ab007a"
 
-[[libblastrampoline_jll]]
-deps = ["Artifacts", "Libdl", "OpenBLAS_jll"]
-uuid = "8e850b90-86db-534c-a0d3-1478176c7d93"
-
 [[nghttp2_jll]]
 deps = ["Artifacts", "Libdl"]
 uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d"
diff --git a/docs/Manifest.toml b/docs/Manifest.toml
index a0ad91b4..17518a7c 100644
--- a/docs/Manifest.toml
+++ b/docs/Manifest.toml
@@ -741,7 +741,7 @@ uuid = "38a345b3-de98-5d2b-a5d3-14cd9215e700"
 version = "2.36.0+0"
 
 [[LinearAlgebra]]
-deps = ["Libdl", "libblastrampoline_jll"]
+deps = ["Libdl"]
 uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 
 [[Literate]]
@@ -912,9 +912,9 @@ version = "1.3.5+1"
 
 [[OpenBLAS32_jll]]
 deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Pkg"]
-git-tree-sha1 = "9c6c2ed4b7acd2137b878eb96c68e63b76199d0f"
+git-tree-sha1 = "ba4a8f683303c9082e84afba96f25af3c7fb2436"
 uuid = "656ef2d0-ae68-5445-9ca0-591084a874a2"
-version = "0.3.17+0"
+version = "0.3.12+1"
 
 [[OpenBLAS_jll]]
 deps = ["Artifacts", "CompilerSupportLibraries_jll", "Libdl"]
@@ -1089,7 +1089,7 @@ deps = ["InteractiveUtils", "Markdown", "Sockets", "Unicode"]
 uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb"
 
 [[Random]]
-deps = ["SHA", "Serialization"]
+deps = ["Serialization"]
 uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 
 [[Random123]]
@@ -1480,10 +1480,6 @@ git-tree-sha1 = "5982a94fcba20f02f42ace44b9894ee2b140fe47"
 uuid = "0ac62f75-1d6f-5e53-bd7c-93b484bb37c0"
 version = "0.15.1+0"
 
-[[libblastrampoline_jll]]
-deps = ["Artifacts", "Libdl", "OpenBLAS_jll"]
-uuid = "8e850b90-86db-534c-a0d3-1478176c7d93"
-
 [[libfdk_aac_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
 git-tree-sha1 = "daacc84a041563f965be61859a36e17c4e4fcd55"

From fbd2b8765990d3514ff86d476380b1ef69b588a7 Mon Sep 17 00:00:00 2001
From: "Navid C. Constantinou" <navidcy@users.noreply.github.com>
Date: Tue, 22 Feb 2022 07:48:31 +1100
Subject: [PATCH 06/15] update diffusivity construction

---
 examples/perfect_baroclinic_adjustment_calibration.jl | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/examples/perfect_baroclinic_adjustment_calibration.jl b/examples/perfect_baroclinic_adjustment_calibration.jl
index 00c35adb..75c88ec4 100644
--- a/examples/perfect_baroclinic_adjustment_calibration.jl
+++ b/examples/perfect_baroclinic_adjustment_calibration.jl
@@ -56,7 +56,8 @@ save_interval = 0.25days  # save observation every so often
 force_generate_observations = false
 nothing # hide
 
-anisotropic_diffusivity = AnisotropicDiffusivity(κh=100, κz=1e-2)
+horizontal_diffusivity = ScalarDiffusivity(κ=100, isotropy=Horizontal())
+vertical_diffusivity = ScalarDiffusivity(κ=1e-2, isotropy=Vertical())
 
 # The isopycnal skew-symmetric diffusivity closure.
 gerdes_koberle_willebrand_tapering = FluxTapering(1e-2)
@@ -74,7 +75,7 @@ if force_generate_observations || !(isfile(data_path))
                            z = (-Lz, 0),
                            halo = (3, 3))
 
-    closures = (gent_mcwilliams_diffusivity, anisotropic_diffusivity)
+    closures = (gent_mcwilliams_diffusivity, horizontal_diffusivity, vertical_diffusivity)
     
     model = HydrostaticFreeSurfaceModel(grid = grid,
                                         tracers = (:b, :c),

From 8a17e6c57cb890da77638728cb976b3371f84c3b Mon Sep 17 00:00:00 2001
From: "Navid C. Constantinou" <navidcy@users.noreply.github.com>
Date: Tue, 22 Feb 2022 07:49:59 +1100
Subject: [PATCH 07/15] some imports for diffusivity isotropies

---
 examples/perfect_baroclinic_adjustment_calibration.jl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/examples/perfect_baroclinic_adjustment_calibration.jl b/examples/perfect_baroclinic_adjustment_calibration.jl
index 75c88ec4..47056d2f 100644
--- a/examples/perfect_baroclinic_adjustment_calibration.jl
+++ b/examples/perfect_baroclinic_adjustment_calibration.jl
@@ -20,7 +20,7 @@ using OceanTurbulenceParameterEstimation
 
 using Oceananigans
 using Oceananigans.Units
-using Oceananigans.TurbulenceClosures: FluxTapering
+using Oceananigans.TurbulenceClosures: FluxTapering, Vertical, Horizontal
 using Oceananigans.Models.HydrostaticFreeSurfaceModels: SliceEnsembleSize
 using Distributions
 using Printf

From 5081b8df1aae39df59dce69653f4c82086972db3 Mon Sep 17 00:00:00 2001
From: "Navid C. Constantinou" <navidcy@users.noreply.github.com>
Date: Tue, 22 Feb 2022 09:40:41 +1100
Subject: [PATCH 08/15] fix closures

---
 examples/perfect_baroclinic_adjustment_calibration.jl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/examples/perfect_baroclinic_adjustment_calibration.jl b/examples/perfect_baroclinic_adjustment_calibration.jl
index 47056d2f..e9c8aebb 100644
--- a/examples/perfect_baroclinic_adjustment_calibration.jl
+++ b/examples/perfect_baroclinic_adjustment_calibration.jl
@@ -156,7 +156,7 @@ slice_ensemble_size = SliceEnsembleSize(size=(Ny, Nz), ensemble=ensemble_size)
                                       halo=(3, 3))
 
 gm_ensemble = [deepcopy(gent_mcwilliams_diffusivity) for i = 1:ensemble_size] 
-closures = (gm_ensemble, anisotropic_diffusivity)
+closures = (gm_ensemble, horizontal_diffusivity, vertical_diffusivity)
 
 @show ensemble_model = HydrostaticFreeSurfaceModel(grid = ensemble_grid,
                                                    tracers = (:b, :c),

From ba3ac113e339d17a621b8502ead3f7ac14822778 Mon Sep 17 00:00:00 2001
From: "Navid C. Constantinou" <navidcy@users.noreply.github.com>
Date: Mon, 28 Feb 2022 11:52:37 +1100
Subject: [PATCH 09/15] update to Oceananigans v0.71.4

---
 Manifest.toml      | 45 ++++++++++++++--------------
 docs/Manifest.toml | 75 +++++++++++++++++++++++-----------------------
 src/Parameters.jl  |  4 +--
 3 files changed, 61 insertions(+), 63 deletions(-)

diff --git a/Manifest.toml b/Manifest.toml
index cfa35b83..f3662730 100644
--- a/Manifest.toml
+++ b/Manifest.toml
@@ -92,9 +92,9 @@ version = "0.3.9"
 
 [[ChainRulesCore]]
 deps = ["Compat", "LinearAlgebra", "SparseArrays"]
-git-tree-sha1 = "7dd38532a1115a215de51775f9891f0f3e1bac6a"
+git-tree-sha1 = "c9a6160317d1abe9c44b3beb367fd448117679ca"
 uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
-version = "1.12.1"
+version = "1.13.0"
 
 [[ChangesOfVariables]]
 deps = ["ChainRulesCore", "LinearAlgebra", "Test"]
@@ -292,9 +292,9 @@ version = "0.3.5"
 
 [[HDF5_jll]]
 deps = ["Artifacts", "JLLWrappers", "LibCURL_jll", "Libdl", "OpenSSL_jll", "Pkg", "Zlib_jll"]
-git-tree-sha1 = "fd83fa0bde42e01952757f01149dd968c06c4dba"
+git-tree-sha1 = "bab67c0d1c4662d2c4be8c6007751b0b6111de5c"
 uuid = "0234f1f7-429e-5d53-9886-15a909be8d59"
-version = "1.12.0+1"
+version = "1.12.1+0"
 
 [[HTTP]]
 deps = ["Base64", "Dates", "IniFile", "Logging", "MbedTLS", "NetworkOptions", "Sockets", "URIs"]
@@ -319,10 +319,9 @@ uuid = "9b13fd28-a010-5f03-acff-a1bbcff69959"
 version = "1.0.0"
 
 [[IniFile]]
-deps = ["Test"]
-git-tree-sha1 = "098e4d2c533924c921f9f9847274f2ad89e018b8"
+git-tree-sha1 = "f550e6e32074c939295eb5ea6de31849ac2c9625"
 uuid = "83e8ac13-25f8-5344-8a64-a9f2b223428f"
-version = "0.5.0"
+version = "0.5.1"
 
 [[IntelOpenMP_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
@@ -394,15 +393,15 @@ version = "0.8.1"
 
 [[LLVM]]
 deps = ["CEnum", "LLVMExtra_jll", "Libdl", "Printf", "Unicode"]
-git-tree-sha1 = "f8dcd7adfda0dddaf944e62476d823164cccc217"
+git-tree-sha1 = "761c362ede582d358026e22d08695231dd25242e"
 uuid = "929cbde3-209d-540e-8aea-75f648917ca0"
-version = "4.7.1"
+version = "4.8.0"
 
 [[LLVMExtra_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
-git-tree-sha1 = "f7f5dd0fb39209f4d28ca59d0d4e24579ad325fe"
+git-tree-sha1 = "67cc5406b15bd04ff72a45f628bec61d36078908"
 uuid = "dad2f222-ce93-54a1-a47d-0025e8a3acab"
-version = "0.0.13+2"
+version = "0.0.13+3"
 
 [[LazyArtifacts]]
 deps = ["Artifacts", "Pkg"]
@@ -460,9 +459,9 @@ version = "0.19.2"
 
 [[MPICH_jll]]
 deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Pkg"]
-git-tree-sha1 = "4b754a51cec47b0366056efcf6e19d95b2ecb54c"
+git-tree-sha1 = "8eed51eb836c8f47781cdb493ffd5f56370c0496"
 uuid = "7cb0a576-ebde-5e09-9194-50597f1243b4"
-version = "4.0.0+0"
+version = "4.0.1+0"
 
 [[MacroTools]]
 deps = ["Markdown", "Random"]
@@ -527,18 +526,18 @@ version = "1.0.0"
 
 [[NetCDF_jll]]
 deps = ["Artifacts", "HDF5_jll", "JLLWrappers", "LibCURL_jll", "LibSSH2_jll", "Libdl", "MbedTLS_jll", "Pkg", "Zlib_jll", "nghttp2_jll"]
-git-tree-sha1 = "0cf4d1bf2ef45156aed85c9ac5f8c7e697d9288c"
+git-tree-sha1 = "598f1a5e9829b3e57f233f98b34a22b376dff373"
 uuid = "7243133f-43d8-5620-bbf4-c2c921802cf3"
-version = "400.702.400+0"
+version = "400.702.402+0"
 
 [[NetworkOptions]]
 uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908"
 
 [[Oceananigans]]
 deps = ["Adapt", "CUDA", "CUDAKernels", "Crayons", "CubedSphere", "Dates", "DocStringExtensions", "FFTW", "Glob", "IncompleteLU", "InteractiveUtils", "IterativeSolvers", "JLD2", "KernelAbstractions", "LinearAlgebra", "Logging", "MPI", "NCDatasets", "OffsetArrays", "OrderedCollections", "PencilFFTs", "Pkg", "Printf", "Random", "Rotations", "SafeTestsets", "SeawaterPolynomials", "SparseArrays", "Statistics", "StructArrays", "Tullio"]
-git-tree-sha1 = "65341647e2965be55c191442e5a18a964b5e3954"
+git-tree-sha1 = "a0f4e9f4dfe2626ec76748f713b1a931f1fda149"
 uuid = "9e8cae18-63c1-5223-a75c-80ca9d6e9a09"
-version = "0.71.1"
+version = "0.71.4"
 
 [[OffsetArrays]]
 deps = ["Adapt"]
@@ -585,9 +584,9 @@ version = "1.4.1"
 
 [[PDMats]]
 deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"]
-git-tree-sha1 = "ee26b350276c51697c9c2d88a072b339f9f03d73"
+git-tree-sha1 = "7e2166042d1698b6072352c74cfd1fca2a968253"
 uuid = "90014a1f-27ba-587c-ab20-58faa44d9150"
-version = "0.11.5"
+version = "0.11.6"
 
 [[Parsers]]
 deps = ["Dates"]
@@ -613,9 +612,9 @@ uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
 
 [[Preferences]]
 deps = ["TOML"]
-git-tree-sha1 = "2cf929d64681236a2e074ffafb8d568733d2e6af"
+git-tree-sha1 = "de893592a221142f3db370f48290e3a2ef39998f"
 uuid = "21216c6a-2e73-6563-6e65-726566657250"
-version = "1.2.3"
+version = "1.2.4"
 
 [[Printf]]
 deps = ["Unicode"]
@@ -745,9 +744,9 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 
 [[SpecialFunctions]]
 deps = ["ChainRulesCore", "IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"]
-git-tree-sha1 = "2735e252e72ee0367ebdb10b6148343fd15c2481"
+git-tree-sha1 = "cbf21db885f478e4bd73b286af6e67d1beeebe4c"
 uuid = "276daf66-3868-5448-9aa4-cd146d93841b"
-version = "1.8.3"
+version = "1.8.4"
 
 [[StatProfilerHTML]]
 deps = ["DataStructures", "Dates", "FlameGraphs", "HAML", "Profile", "SHA", "Test"]
diff --git a/docs/Manifest.toml b/docs/Manifest.toml
index 522908a1..33de7b1f 100644
--- a/docs/Manifest.toml
+++ b/docs/Manifest.toml
@@ -116,9 +116,9 @@ version = "1.0.5"
 
 [[CairoMakie]]
 deps = ["Base64", "Cairo", "Colors", "FFTW", "FileIO", "FreeType", "GeometryBasics", "LinearAlgebra", "Makie", "SHA", "StaticArrays"]
-git-tree-sha1 = "b1d884ee7dae11985314192270eb5762b9ed09ae"
+git-tree-sha1 = "aedc7c910713eb616391cf95218277b714a7913f"
 uuid = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
-version = "0.7.3"
+version = "0.7.4"
 
 [[Cairo_jll]]
 deps = ["Artifacts", "Bzip2_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "JLLWrappers", "LZO_jll", "Libdl", "Pixman_jll", "Pkg", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Zlib_jll", "libpng_jll"]
@@ -139,9 +139,9 @@ version = "0.3.9"
 
 [[ChainRulesCore]]
 deps = ["Compat", "LinearAlgebra", "SparseArrays"]
-git-tree-sha1 = "7dd38532a1115a215de51775f9891f0f3e1bac6a"
+git-tree-sha1 = "c9a6160317d1abe9c44b3beb367fd448117679ca"
 uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
-version = "1.12.1"
+version = "1.13.0"
 
 [[ChangesOfVariables]]
 deps = ["ChainRulesCore", "LinearAlgebra", "Test"]
@@ -284,9 +284,9 @@ version = "0.8.6"
 
 [[Documenter]]
 deps = ["ANSIColoredPrinters", "Base64", "Dates", "DocStringExtensions", "IOCapture", "InteractiveUtils", "JSON", "LibGit2", "Logging", "Markdown", "REPL", "Test", "Unicode"]
-git-tree-sha1 = "75c6cf9d99e0efc79b724f5566726ad3ad010a01"
+git-tree-sha1 = "2c023382ab49c40475fcf59b90ba1c8edd9ff45e"
 uuid = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
-version = "0.27.12"
+version = "0.27.13"
 
 [[Downloads]]
 deps = ["ArgTools", "LibCURL", "NetworkOptions"]
@@ -459,9 +459,9 @@ version = "1.3.14+0"
 
 [[GridLayoutBase]]
 deps = ["GeometryBasics", "InteractiveUtils", "Observables"]
-git-tree-sha1 = "70938436e2720e6cb8a7f2ca9f1bbdbf40d7f5d0"
+git-tree-sha1 = "169c3dc5acae08835a573a8a3e25c62f689f8b5c"
 uuid = "3955a311-db13-416c-9275-1d80ed98e5e9"
-version = "0.6.4"
+version = "0.6.5"
 
 [[Grisu]]
 git-tree-sha1 = "53bb909d1151e57e2484c3d1b53e19552b887fb2"
@@ -470,9 +470,9 @@ version = "1.0.2"
 
 [[HDF5_jll]]
 deps = ["Artifacts", "JLLWrappers", "LibCURL_jll", "Libdl", "OpenSSL_jll", "Pkg", "Zlib_jll"]
-git-tree-sha1 = "fd83fa0bde42e01952757f01149dd968c06c4dba"
+git-tree-sha1 = "bab67c0d1c4662d2c4be8c6007751b0b6111de5c"
 uuid = "0234f1f7-429e-5d53-9886-15a909be8d59"
-version = "1.12.0+1"
+version = "1.12.1+0"
 
 [[HTTP]]
 deps = ["Base64", "Dates", "IniFile", "Logging", "MbedTLS", "NetworkOptions", "Sockets", "URIs"]
@@ -538,10 +538,9 @@ uuid = "d25df0c9-e2be-5dd7-82c8-3ad0b3e990b9"
 version = "0.1.2"
 
 [[IniFile]]
-deps = ["Test"]
-git-tree-sha1 = "098e4d2c533924c921f9f9847274f2ad89e018b8"
+git-tree-sha1 = "f550e6e32074c939295eb5ea6de31849ac2c9625"
 uuid = "83e8ac13-25f8-5344-8a64-a9f2b223428f"
-version = "0.5.0"
+version = "0.5.1"
 
 [[IntelOpenMP_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
@@ -660,15 +659,15 @@ version = "0.8.1"
 
 [[LLVM]]
 deps = ["CEnum", "LLVMExtra_jll", "Libdl", "Printf", "Unicode"]
-git-tree-sha1 = "f8dcd7adfda0dddaf944e62476d823164cccc217"
+git-tree-sha1 = "761c362ede582d358026e22d08695231dd25242e"
 uuid = "929cbde3-209d-540e-8aea-75f648917ca0"
-version = "4.7.1"
+version = "4.8.0"
 
 [[LLVMExtra_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
-git-tree-sha1 = "f7f5dd0fb39209f4d28ca59d0d4e24579ad325fe"
+git-tree-sha1 = "67cc5406b15bd04ff72a45f628bec61d36078908"
 uuid = "dad2f222-ce93-54a1-a47d-0025e8a3acab"
-version = "0.0.13+2"
+version = "0.0.13+3"
 
 [[LZO_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
@@ -773,9 +772,9 @@ version = "0.19.2"
 
 [[MPICH_jll]]
 deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Pkg"]
-git-tree-sha1 = "4b754a51cec47b0366056efcf6e19d95b2ecb54c"
+git-tree-sha1 = "8eed51eb836c8f47781cdb493ffd5f56370c0496"
 uuid = "7cb0a576-ebde-5e09-9194-50597f1243b4"
-version = "4.0.0+0"
+version = "4.0.1+0"
 
 [[MacroTools]]
 deps = ["Markdown", "Random"]
@@ -785,9 +784,9 @@ version = "0.5.9"
 
 [[Makie]]
 deps = ["Animations", "Base64", "ColorBrewer", "ColorSchemes", "ColorTypes", "Colors", "Contour", "Distributions", "DocStringExtensions", "FFMPEG", "FileIO", "FixedPointNumbers", "Formatting", "FreeType", "FreeTypeAbstraction", "GeometryBasics", "GridLayoutBase", "ImageIO", "IntervalSets", "Isoband", "KernelDensity", "LaTeXStrings", "LinearAlgebra", "MakieCore", "Markdown", "Match", "MathTeXEngine", "Observables", "OffsetArrays", "Packing", "PlotUtils", "PolygonOps", "Printf", "Random", "RelocatableFolders", "Serialization", "Showoff", "SignedDistanceFields", "SparseArrays", "StaticArrays", "Statistics", "StatsBase", "StatsFuns", "StructArrays", "UnicodeFun"]
-git-tree-sha1 = "475b854bff7867c37687d65f7b9498401ac6536d"
+git-tree-sha1 = "cd0fd02ab0d129f03515b7b68ca77fb670ef2e61"
 uuid = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a"
-version = "0.16.4"
+version = "0.16.5"
 
 [[MakieCore]]
 deps = ["Observables"]
@@ -874,9 +873,9 @@ version = "0.3.7"
 
 [[NetCDF_jll]]
 deps = ["Artifacts", "HDF5_jll", "JLLWrappers", "LibCURL_jll", "LibSSH2_jll", "Libdl", "MbedTLS_jll", "Pkg", "Zlib_jll", "nghttp2_jll"]
-git-tree-sha1 = "0cf4d1bf2ef45156aed85c9ac5f8c7e697d9288c"
+git-tree-sha1 = "598f1a5e9829b3e57f233f98b34a22b376dff373"
 uuid = "7243133f-43d8-5620-bbf4-c2c921802cf3"
-version = "400.702.400+0"
+version = "400.702.402+0"
 
 [[Netpbm]]
 deps = ["FileIO", "ImageCore"]
@@ -894,9 +893,9 @@ version = "0.4.0"
 
 [[Oceananigans]]
 deps = ["Adapt", "CUDA", "CUDAKernels", "Crayons", "CubedSphere", "Dates", "DocStringExtensions", "FFTW", "Glob", "IncompleteLU", "InteractiveUtils", "IterativeSolvers", "JLD2", "KernelAbstractions", "LinearAlgebra", "Logging", "MPI", "NCDatasets", "OffsetArrays", "OrderedCollections", "PencilFFTs", "Pkg", "Printf", "Random", "Rotations", "SafeTestsets", "SeawaterPolynomials", "SparseArrays", "Statistics", "StructArrays", "Tullio"]
-git-tree-sha1 = "65341647e2965be55c191442e5a18a964b5e3954"
+git-tree-sha1 = "a0f4e9f4dfe2626ec76748f713b1a931f1fda149"
 uuid = "9e8cae18-63c1-5223-a75c-80ca9d6e9a09"
-version = "0.71.1"
+version = "0.71.4"
 
 [[OffsetArrays]]
 deps = ["Adapt"]
@@ -973,9 +972,9 @@ version = "8.44.0+0"
 
 [[PDMats]]
 deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"]
-git-tree-sha1 = "ee26b350276c51697c9c2d88a072b339f9f03d73"
+git-tree-sha1 = "7e2166042d1698b6072352c74cfd1fca2a968253"
 uuid = "90014a1f-27ba-587c-ab20-58faa44d9150"
-version = "0.11.5"
+version = "0.11.6"
 
 [[PNGFiles]]
 deps = ["Base64", "CEnum", "ImageCore", "IndirectArrays", "OffsetArrays", "libpng_jll"]
@@ -1048,9 +1047,9 @@ version = "0.1.2"
 
 [[Preferences]]
 deps = ["TOML"]
-git-tree-sha1 = "2cf929d64681236a2e074ffafb8d568733d2e6af"
+git-tree-sha1 = "de893592a221142f3db370f48290e3a2ef39998f"
 uuid = "21216c6a-2e73-6563-6e65-726566657250"
-version = "1.2.3"
+version = "1.2.4"
 
 [[Printf]]
 deps = ["Unicode"]
@@ -1080,9 +1079,9 @@ version = "2.4.2"
 
 [[Quaternions]]
 deps = ["DualNumbers", "LinearAlgebra", "Random"]
-git-tree-sha1 = "abe487c51089a229e2f004f8bee0b057a03ade21"
+git-tree-sha1 = "d0baaa6bcbac4369f1ecfb4a8c44b96ef3e5acb9"
 uuid = "94ee1d12-ae83-5a48-8b1c-48b8ff168ae0"
-version = "0.4.8"
+version = "0.5.1"
 
 [[REPL]]
 deps = ["InteractiveUtils", "Markdown", "Sockets", "Unicode"]
@@ -1146,9 +1145,9 @@ version = "0.3.0+0"
 
 [[Rotations]]
 deps = ["LinearAlgebra", "Quaternions", "Random", "StaticArrays", "Statistics"]
-git-tree-sha1 = "405148000e80f70b31e7732ea93288aecb1793fa"
+git-tree-sha1 = "a167638e2cbd8ac41f9cd57282cab9b042fa26e6"
 uuid = "6038ab10-8711-5258-84ad-4b1120ba62dc"
-version = "1.2.0"
+version = "1.3.0"
 
 [[SCS]]
 deps = ["LinearAlgebra", "MathOptInterface", "Requires", "SCS_GPU_jll", "SCS_jll", "SparseArrays"]
@@ -1239,9 +1238,9 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 
 [[SpecialFunctions]]
 deps = ["ChainRulesCore", "IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"]
-git-tree-sha1 = "2735e252e72ee0367ebdb10b6148343fd15c2481"
+git-tree-sha1 = "cbf21db885f478e4bd73b286af6e67d1beeebe4c"
 uuid = "276daf66-3868-5448-9aa4-cd146d93841b"
-version = "1.8.3"
+version = "1.8.4"
 
 [[StackViews]]
 deps = ["OffsetArrays"]
@@ -1469,10 +1468,10 @@ deps = ["Libdl"]
 uuid = "83775a58-1f1d-513f-b197-d71354ab007a"
 
 [[isoband_jll]]
-deps = ["Libdl", "Pkg"]
-git-tree-sha1 = "a1ac99674715995a536bbce674b068ec1b7d893d"
+deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
+git-tree-sha1 = "51b5eeb3f98367157a7a12a1fb0aa5328946c03c"
 uuid = "9a68df92-36a6-505f-a73e-abb412b6bfb4"
-version = "0.2.2+0"
+version = "0.2.3+0"
 
 [[libass_jll]]
 deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "HarfBuzz_jll", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"]
diff --git a/src/Parameters.jl b/src/Parameters.jl
index 96599977..cf508b78 100644
--- a/src/Parameters.jl
+++ b/src/Parameters.jl
@@ -4,7 +4,7 @@ export FreeParameters, lognormal, ScaledLogitNormal
 
 using Oceananigans.Architectures: CPU, arch_array, architecture
 using Oceananigans.TurbulenceClosures: AbstractTurbulenceClosure
-using Oceananigans.TurbulenceClosures: AbstractTimeDiscretization, Explicit
+using Oceananigans.TurbulenceClosures: AbstractTimeDiscretization, ExplicitTimeDiscretization
 
 using Printf
 using Distributions
@@ -445,7 +445,7 @@ Closure(ClosureSubModel(12, 2), 3)
 """
 closure_with_parameters(closure, parameters) = construct_object(dict_properties(closure), parameters)
 
-closure_with_parameters(closure::AbstractTurbulenceClosure{Explicit}, parameters) =
+closure_with_parameters(closure::AbstractTurbulenceClosure{ExplicitTimeDiscretization}, parameters) =
     construct_object(dict_properties(closure), parameters, type_parameter=nothing)
 
 closure_with_parameters(closure::AbstractTurbulenceClosure{TD}, parameters) where {TD <: AbstractTimeDiscretization} =

From 3219dc798939db0ca0c74264132bc2e79c9d605a Mon Sep 17 00:00:00 2001
From: "Navid C. Constantinou" <navidcy@users.noreply.github.com>
Date: Mon, 28 Feb 2022 12:02:05 +1100
Subject: [PATCH 10/15] fix diffusivities

---
 examples/perfect_baroclinic_adjustment_calibration.jl | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/examples/perfect_baroclinic_adjustment_calibration.jl b/examples/perfect_baroclinic_adjustment_calibration.jl
index e9c8aebb..cc27a1e3 100644
--- a/examples/perfect_baroclinic_adjustment_calibration.jl
+++ b/examples/perfect_baroclinic_adjustment_calibration.jl
@@ -56,8 +56,8 @@ save_interval = 0.25days  # save observation every so often
 force_generate_observations = false
 nothing # hide
 
-horizontal_diffusivity = ScalarDiffusivity(κ=100, isotropy=Horizontal())
-vertical_diffusivity = ScalarDiffusivity(κ=1e-2, isotropy=Vertical())
+horizontal_diffusivity = HorizontalScalarDiffusivity(κ=100)
+vertical_diffusivity = VerticalScalarDiffusivity(κ=1e-2)
 
 # The isopycnal skew-symmetric diffusivity closure.
 gerdes_koberle_willebrand_tapering = FluxTapering(1e-2)

From 09246198b8c32edd43c45e1b282cfc7a28116605 Mon Sep 17 00:00:00 2001
From: "Navid C. Constantinou" <navidcy@users.noreply.github.com>
Date: Mon, 28 Feb 2022 12:44:42 +1100
Subject: [PATCH 11/15] remove deprecated Vertical/Horizontal

---
 examples/perfect_baroclinic_adjustment_calibration.jl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/examples/perfect_baroclinic_adjustment_calibration.jl b/examples/perfect_baroclinic_adjustment_calibration.jl
index cc27a1e3..4cb6d810 100644
--- a/examples/perfect_baroclinic_adjustment_calibration.jl
+++ b/examples/perfect_baroclinic_adjustment_calibration.jl
@@ -20,7 +20,7 @@ using OceanTurbulenceParameterEstimation
 
 using Oceananigans
 using Oceananigans.Units
-using Oceananigans.TurbulenceClosures: FluxTapering, Vertical, Horizontal
+using Oceananigans.TurbulenceClosures: FluxTapering
 using Oceananigans.Models.HydrostaticFreeSurfaceModels: SliceEnsembleSize
 using Distributions
 using Printf

From ce5c017d7b218b96ebdf2d6c5071fdee5c4ceb94 Mon Sep 17 00:00:00 2001
From: "Navid C. Constantinou" <navidcy@users.noreply.github.com>
Date: Tue, 1 Mar 2022 12:41:19 +1100
Subject: [PATCH 12/15] use Oceananigans#ncc/fix-bug-otpe

---
 Manifest.toml                                         | 4 +++-
 docs/Manifest.toml                                    | 4 +++-
 examples/perfect_baroclinic_adjustment_calibration.jl | 6 +++---
 3 files changed, 9 insertions(+), 5 deletions(-)

diff --git a/Manifest.toml b/Manifest.toml
index f3662730..92d77ea4 100644
--- a/Manifest.toml
+++ b/Manifest.toml
@@ -535,7 +535,9 @@ uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908"
 
 [[Oceananigans]]
 deps = ["Adapt", "CUDA", "CUDAKernels", "Crayons", "CubedSphere", "Dates", "DocStringExtensions", "FFTW", "Glob", "IncompleteLU", "InteractiveUtils", "IterativeSolvers", "JLD2", "KernelAbstractions", "LinearAlgebra", "Logging", "MPI", "NCDatasets", "OffsetArrays", "OrderedCollections", "PencilFFTs", "Pkg", "Printf", "Random", "Rotations", "SafeTestsets", "SeawaterPolynomials", "SparseArrays", "Statistics", "StructArrays", "Tullio"]
-git-tree-sha1 = "a0f4e9f4dfe2626ec76748f713b1a931f1fda149"
+git-tree-sha1 = "dc22cce4a0645420cca327e40c795a77f0876c92"
+repo-rev = "ncc/fix-bug-otpe"
+repo-url = "https://github.com/CliMA/Oceananigans.jl.git"
 uuid = "9e8cae18-63c1-5223-a75c-80ca9d6e9a09"
 version = "0.71.4"
 
diff --git a/docs/Manifest.toml b/docs/Manifest.toml
index 33de7b1f..9c8e6058 100644
--- a/docs/Manifest.toml
+++ b/docs/Manifest.toml
@@ -893,7 +893,9 @@ version = "0.4.0"
 
 [[Oceananigans]]
 deps = ["Adapt", "CUDA", "CUDAKernels", "Crayons", "CubedSphere", "Dates", "DocStringExtensions", "FFTW", "Glob", "IncompleteLU", "InteractiveUtils", "IterativeSolvers", "JLD2", "KernelAbstractions", "LinearAlgebra", "Logging", "MPI", "NCDatasets", "OffsetArrays", "OrderedCollections", "PencilFFTs", "Pkg", "Printf", "Random", "Rotations", "SafeTestsets", "SeawaterPolynomials", "SparseArrays", "Statistics", "StructArrays", "Tullio"]
-git-tree-sha1 = "a0f4e9f4dfe2626ec76748f713b1a931f1fda149"
+git-tree-sha1 = "dc22cce4a0645420cca327e40c795a77f0876c92"
+repo-rev = "ncc/fix-bug-otpe"
+repo-url = "https://github.com/CliMA/Oceananigans.jl.git"
 uuid = "9e8cae18-63c1-5223-a75c-80ca9d6e9a09"
 version = "0.71.4"
 
diff --git a/examples/perfect_baroclinic_adjustment_calibration.jl b/examples/perfect_baroclinic_adjustment_calibration.jl
index 4cb6d810..22fca51c 100644
--- a/examples/perfect_baroclinic_adjustment_calibration.jl
+++ b/examples/perfect_baroclinic_adjustment_calibration.jl
@@ -37,7 +37,7 @@ nothing # hide
 
 # We gather the "true" parameters in a named tuple ``θ_*``:
 
-θ★ = (κ_skew = κ_skew, κ_symmetric = κ_symmetric)
+θ★ = (; κ_skew, κ_symmetric)
 
 # The experiment name and where the synthetic observations will be saved.
 experiment_name = "baroclinic_adjustment"
@@ -113,9 +113,9 @@ if force_generate_observations || !(isfile(data_path))
     cᵢ(x, y, z) = exp(-y^2 / 2Δc_y^2) * exp(-(z + Lz/2)^2 / (2Δc_z^2))
 
     set!(model, b=bᵢ, c=cᵢ)
-    
+
     simulation = Simulation(model, Δt=Δt, stop_time=stop_time)
-    
+
     simulation.output_writers[:fields] = JLD2OutputWriter(model, merge(model.velocities, model.tracers),
                                                           schedule = TimeInterval(save_interval),
                                                           prefix = experiment_name,

From f1323713d14487cf75d1cebf35b33463da458a0e Mon Sep 17 00:00:00 2001
From: "Navid C. Constantinou" <navidcy@users.noreply.github.com>
Date: Tue, 1 Mar 2022 13:49:04 +1100
Subject: [PATCH 13/15] converge faster

---
 examples/perfect_baroclinic_adjustment_calibration.jl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/examples/perfect_baroclinic_adjustment_calibration.jl b/examples/perfect_baroclinic_adjustment_calibration.jl
index 22fca51c..d26f1eab 100644
--- a/examples/perfect_baroclinic_adjustment_calibration.jl
+++ b/examples/perfect_baroclinic_adjustment_calibration.jl
@@ -234,7 +234,7 @@ mean(G, dims=2) ≈ y
 
 # Next, we construct an `EnsembleKalmanInversion` (EKI) object,
 
-eki = EnsembleKalmanInversion(calibration; convergence_rate = 0.5)
+eki = EnsembleKalmanInversion(calibration; convergence_rate = 0.4)
 
 # and perform few iterations to see if we can converge to the true parameter values.
 

From 7cbad1e07b79496a9e7d6fb3009756901f35e884 Mon Sep 17 00:00:00 2001
From: "Navid C. Constantinou" <navidcy@users.noreply.github.com>
Date: Tue, 1 Mar 2022 13:51:35 +1100
Subject: [PATCH 14/15] converge faster

---
 examples/perfect_convective_adjustment_calibration.jl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/examples/perfect_convective_adjustment_calibration.jl b/examples/perfect_convective_adjustment_calibration.jl
index 0272ed88..f2b708a7 100644
--- a/examples/perfect_convective_adjustment_calibration.jl
+++ b/examples/perfect_convective_adjustment_calibration.jl
@@ -65,7 +65,7 @@ calibration = InverseProblem(observations, ensemble_simulation, free_parameters)
 # algorithm refer to
 # [EnsembleKalmanProcesses.jl documentation](https://clima.github.io/EnsembleKalmanProcesses.jl/stable/ensemble_kalman_inversion/).
 
-eki = EnsembleKalmanInversion(calibration; noise_covariance = 1e-2)
+eki = EnsembleKalmanInversion(calibration; convergence_rate = 0.5)
 
 # and perform few iterations to see if we can converge to the true parameter values.
 

From 28963fcbb87b16a0c582716f528ca12ca6859608 Mon Sep 17 00:00:00 2001
From: "Navid C. Constantinou" <navidcy@users.noreply.github.com>
Date: Tue, 1 Mar 2022 14:47:32 +1100
Subject: [PATCH 15/15] better axis lims

---
 examples/perfect_baroclinic_adjustment_calibration.jl | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/examples/perfect_baroclinic_adjustment_calibration.jl b/examples/perfect_baroclinic_adjustment_calibration.jl
index d26f1eab..aa57277a 100644
--- a/examples/perfect_baroclinic_adjustment_calibration.jl
+++ b/examples/perfect_baroclinic_adjustment_calibration.jl
@@ -327,8 +327,8 @@ xlims!(axmain, 350, 1350)
 xlims!(axtop, 350, 1350)
 ylims!(axmain, 650, 1750)
 ylims!(axright, 650, 1750)
-xlims!(axright, 0, 0.02)
-ylims!(axtop, 0, 0.02)
+xlims!(axright, 0, 0.015)
+ylims!(axtop, 0, 0.015)
 
 save("distributions_baroclinic_adjustment.svg", f); nothing #hide