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Support Oceananigans v0.95 and bump v0.13.4 #233

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Support Oceananigans v0.95 and bump v0.13.4 #233

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2a21879
Support Oceananigans v0.94 and bump v0.13.3
ali-ramadhan Nov 16, 2024
28debf1
Update Manifest.toml
ali-ramadhan Nov 16, 2024
4214a93
Add missing import
ali-ramadhan Nov 16, 2024
bb4d712
`flatten_node` now in Oceananigans
ali-ramadhan Nov 16, 2024
2ae249a
Add missing import for `location`
ali-ramadhan Nov 16, 2024
ef5fee6
Need to import `TendencyCallsite`
ali-ramadhan Nov 16, 2024
4851e94
More imports
ali-ramadhan Nov 16, 2024
afd6578
Reorganize `test_sediments.jl` a bit
ali-ramadhan Nov 16, 2024
e0bf937
Mark `test_flat_sediment` as broken just for now
ali-ramadhan Nov 16, 2024
96d1c4f
Upgrade to Oceananigans v0.94.3
ali-ramadhan Nov 23, 2024
474dfbf
No more `ab2_step_free_surface!`
ali-ramadhan Nov 26, 2024
78b89dd
Update packages
ali-ramadhan Dec 4, 2024
8eb2f18
Merge branch 'main' into ali/oceananigans-0.94
ali-ramadhan Dec 4, 2024
2bee6e5
Bump v0.13.4
ali-ramadhan Dec 4, 2024
b73d2d8
Update packages for docs env
ali-ramadhan Dec 4, 2024
52c2125
Need Manifest.toml for docs env
ali-ramadhan Dec 4, 2024
7117855
Try skipping `test_flat_sediment` again
ali-ramadhan Dec 4, 2024
d1ae8ae
Upgrade to Oceananigans v0.95.3
ali-ramadhan Dec 20, 2024
cd6fc4e
Update packages
ali-ramadhan Dec 20, 2024
2755a9c
Also update docs environment
ali-ramadhan Dec 20, 2024
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153 changes: 68 additions & 85 deletions Manifest.toml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,8 +1,8 @@
# This file is machine-generated - editing it directly is not advised

julia_version = "1.10.5"
julia_version = "1.10.6"
manifest_format = "2.0"
project_hash = "b7b68895e3965b7930805d42785ca0f68052cac9"
project_hash = "6711c2855dab6dc90d90db711a2fef6fa66fe405"

[[deps.AbstractFFTs]]
deps = ["LinearAlgebra"]
Expand All @@ -20,9 +20,9 @@ version = "1.5.0"

[[deps.Accessors]]
deps = ["CompositionsBase", "ConstructionBase", "InverseFunctions", "LinearAlgebra", "MacroTools", "Markdown"]
git-tree-sha1 = "b392ede862e506d451fc1616e79aa6f4c673dab8"
git-tree-sha1 = "96bed9b1b57cf750cca50c311a197e306816a1cc"
uuid = "7d9f7c33-5ae7-4f3b-8dc6-eff91059b697"
version = "0.1.38"
version = "0.1.39"

[deps.Accessors.extensions]
AccessorsAxisKeysExt = "AxisKeys"
Expand All @@ -45,9 +45,9 @@ version = "0.1.38"

[[deps.Adapt]]
deps = ["LinearAlgebra", "Requires"]
git-tree-sha1 = "d80af0733c99ea80575f612813fa6aa71022d33a"
git-tree-sha1 = "50c3c56a52972d78e8be9fd135bfb91c9574c140"
uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e"
version = "4.1.0"
version = "4.1.1"
weakdeps = ["StaticArrays"]

[deps.Adapt.extensions]
Expand Down Expand Up @@ -116,9 +116,9 @@ version = "5.5.2"

[[deps.CUDA_Driver_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
git-tree-sha1 = "ccd1e54610c222fadfd4737dac66bff786f63656"
git-tree-sha1 = "14996d716a2eaaeccfc8d7bc854dd87fde720ac1"
uuid = "4ee394cb-3365-5eb0-8335-949819d2adfc"
version = "0.10.3+0"
version = "0.10.4+0"

[[deps.CUDA_Runtime_Discovery]]
deps = ["Libdl"]
Expand All @@ -128,27 +128,33 @@ version = "0.3.5"

[[deps.CUDA_Runtime_jll]]
deps = ["Artifacts", "CUDA_Driver_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"]
git-tree-sha1 = "e43727b237b2879a34391eeb81887699a26f8f2f"
git-tree-sha1 = "17f1536c600133f7c4113bae0a2d98dbf27c7ebc"
uuid = "76a88914-d11a-5bdc-97e0-2f5a05c973a2"
version = "0.15.3+0"
version = "0.15.5+0"

[[deps.ColorTypes]]
deps = ["FixedPointNumbers", "Random"]
git-tree-sha1 = "b10d0b65641d57b8b4d5e234446582de5047050d"
git-tree-sha1 = "c7acce7a7e1078a20a285211dd73cd3941a871d6"
uuid = "3da002f7-5984-5a60-b8a6-cbb66c0b333f"
version = "0.11.5"
version = "0.12.0"

[deps.ColorTypes.extensions]
StyledStringsExt = "StyledStrings"

[deps.ColorTypes.weakdeps]
StyledStrings = "f489334b-da3d-4c2e-b8f0-e476e12c162b"

[[deps.Colors]]
deps = ["ColorTypes", "FixedPointNumbers", "Reexport"]
git-tree-sha1 = "362a287c3aa50601b0bc359053d5c2468f0e7ce0"
git-tree-sha1 = "64e15186f0aa277e174aa81798f7eb8598e0157e"
uuid = "5ae59095-9a9b-59fe-a467-6f913c188581"
version = "0.12.11"
version = "0.13.0"

[[deps.CommonDataModel]]
deps = ["CFTime", "DataStructures", "Dates", "Preferences", "Printf", "Statistics"]
git-tree-sha1 = "d6fb5bf939a2753c74984b11434ea25d6c397a58"
git-tree-sha1 = "98d64d5b9e5263884276656a43c45424b3a645c2"
uuid = "1fbeeb36-5f17-413c-809b-666fb144f157"
version = "0.3.6"
version = "0.3.7"

[[deps.CommonSolve]]
git-tree-sha1 = "0eee5eb66b1cf62cd6ad1b460238e60e4b09400c"
Expand Down Expand Up @@ -233,9 +239,9 @@ uuid = "ade2ca70-3891-5945-98fb-dc099432e06a"

[[deps.DiskArrays]]
deps = ["LRUCache", "OffsetArrays"]
git-tree-sha1 = "ef25c513cad08d7ebbed158c91768ae32f308336"
git-tree-sha1 = "e0e89a60637a62d13aa2107f0acd169b9b9b77e7"
uuid = "3c3547ce-8d99-4f5e-a174-61eb10b00ae3"
version = "0.3.23"
version = "0.4.6"

[[deps.Distances]]
deps = ["LinearAlgebra", "Statistics", "StatsAPI"]
Expand Down Expand Up @@ -285,9 +291,15 @@ version = "3.3.10+1"

[[deps.FileIO]]
deps = ["Pkg", "Requires", "UUIDs"]
git-tree-sha1 = "62ca0547a14c57e98154423419d8a342dca75ca9"
git-tree-sha1 = "2dd20384bf8c6d411b5c7370865b1e9b26cb2ea3"
uuid = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549"
version = "1.16.4"
version = "1.16.6"

[deps.FileIO.extensions]
HTTPExt = "HTTP"

[deps.FileIO.weakdeps]
HTTP = "cd3eb016-35fb-5094-929b-558a96fad6f3"

[[deps.FileWatching]]
uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee"
Expand All @@ -302,11 +314,6 @@ version = "0.8.5"
deps = ["Random"]
uuid = "9fa8497b-333b-5362-9e8d-4d0656e87820"

[[deps.GMP_jll]]
deps = ["Artifacts", "Libdl"]
uuid = "781609d7-10c4-51f6-84f2-b8444358ff6d"
version = "6.2.1+6"

[[deps.GPUArrays]]
deps = ["Adapt", "GPUArraysCore", "LLVM", "LinearAlgebra", "Printf", "Random", "Reexport", "Serialization", "Statistics"]
git-tree-sha1 = "62ee71528cca49be797076a76bdc654a170a523e"
Expand Down Expand Up @@ -342,12 +349,6 @@ git-tree-sha1 = "97285bbd5230dd766e9ef6749b80fc617126d496"
uuid = "c27321d9-0574-5035-807b-f59d2c89b15c"
version = "1.3.1"

[[deps.GnuTLS_jll]]
deps = ["Artifacts", "GMP_jll", "JLLWrappers", "Libdl", "Nettle_jll", "P11Kit_jll", "Zlib_jll"]
git-tree-sha1 = "383db7d3f900f4c1f47a8a04115b053c095e48d3"
uuid = "0951126a-58fd-58f1-b5b3-b08c7c4a876d"
version = "3.8.4+0"

[[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 = "38c8874692d48d5440d5752d6c74b0c6b0b60739"
Expand All @@ -356,9 +357,9 @@ version = "1.14.2+1"

[[deps.Hwloc_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl"]
git-tree-sha1 = "dd3b49277ec2bb2c6b94eb1604d4d0616016f7a6"
git-tree-sha1 = "50aedf345a709ab75872f80a2779568dc0bb461b"
uuid = "e33a78d0-f292-5ffc-b300-72abe9b543c8"
version = "2.11.2+0"
version = "2.11.2+1"

[[deps.IncompleteLU]]
deps = ["LinearAlgebra", "SparseArrays"]
Expand Down Expand Up @@ -400,9 +401,9 @@ weakdeps = ["Dates", "Test"]
InverseFunctionsTestExt = "Test"

[[deps.InvertedIndices]]
git-tree-sha1 = "0dc7b50b8d436461be01300fd8cd45aa0274b038"
git-tree-sha1 = "6da3c4316095de0f5ee2ebd875df8721e7e0bdbe"
uuid = "41ab1584-1d38-5bbf-9106-f11c6c58b48f"
version = "1.3.0"
version = "1.3.1"

[[deps.IterativeSolvers]]
deps = ["LinearAlgebra", "Printf", "Random", "RecipesBase", "SparseArrays"]
Expand All @@ -417,9 +418,9 @@ version = "1.0.0"

[[deps.JLD2]]
deps = ["FileIO", "MacroTools", "Mmap", "OrderedCollections", "PrecompileTools", "Requires", "TranscodingStreams"]
git-tree-sha1 = "783c1be5213a09609b23237a0c9e5dfd258ae6f2"
git-tree-sha1 = "f1a1c1037af2a4541ea186b26b0c0e7eeaad232b"
uuid = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
version = "0.5.7"
version = "0.5.10"

[[deps.JLLWrappers]]
deps = ["Artifacts", "Preferences"]
Expand All @@ -434,10 +435,10 @@ uuid = "9c1d0b0a-7046-5b2e-a33f-ea22f176ac7e"
version = "0.2.1+0"

[[deps.KernelAbstractions]]
deps = ["Adapt", "Atomix", "InteractiveUtils", "MacroTools", "PrecompileTools", "Requires", "StaticArrays", "UUIDs", "UnsafeAtomics", "UnsafeAtomicsLLVM"]
git-tree-sha1 = "e73a077abc7fe798fe940deabe30ef6c66bdde52"
deps = ["Adapt", "Atomix", "InteractiveUtils", "MacroTools", "PrecompileTools", "Requires", "StaticArrays", "UUIDs"]
git-tree-sha1 = "b9a838cd3028785ac23822cded5126b3da394d1a"
uuid = "63c18a36-062a-441e-b654-da1e3ab1ce7c"
version = "0.9.29"
version = "0.9.31"

[deps.KernelAbstractions.extensions]
EnzymeExt = "EnzymeCore"
Expand Down Expand Up @@ -595,9 +596,9 @@ version = "2.28.2+1"

[[deps.MicrosoftMPI_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
git-tree-sha1 = "f12a29c4400ba812841c6ace3f4efbb6dbb3ba01"
git-tree-sha1 = "bc95bf4149bf535c09602e3acdf950d9b4376227"
uuid = "9237b28f-5490-5468-be7b-bb81f5f5e6cf"
version = "10.1.4+2"
version = "10.1.4+3"

[[deps.Missings]]
deps = ["DataAPI"]
Expand All @@ -614,15 +615,15 @@ version = "2023.1.10"

[[deps.NCDatasets]]
deps = ["CFTime", "CommonDataModel", "DataStructures", "Dates", "DiskArrays", "NetCDF_jll", "NetworkOptions", "Printf"]
git-tree-sha1 = "77df6d3708ec0eb3441551e1f20f7503b37c2393"
git-tree-sha1 = "2c9dc92001ac06d432f363f37ff5552954d9947c"
uuid = "85f8d34a-cbdd-5861-8df4-14fed0d494ab"
version = "0.14.5"
version = "0.14.6"

[[deps.NVTX]]
deps = ["Colors", "JuliaNVTXCallbacks_jll", "Libdl", "NVTX_jll"]
git-tree-sha1 = "53046f0483375e3ed78e49190f1154fa0a4083a1"
git-tree-sha1 = "6a6f8bfaa91bb2e40ff562ab9f30dc827741daef"
uuid = "5da4648a-3479-48b8-97b9-01cb529c0a1f"
version = "0.3.4"
version = "0.3.5"

[[deps.NVTX_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
Expand All @@ -636,21 +637,15 @@ git-tree-sha1 = "a8af1798e4eb9ff768ce7fdefc0e957097793f15"
uuid = "7243133f-43d8-5620-bbf4-c2c921802cf3"
version = "400.902.209+0"

[[deps.Nettle_jll]]
deps = ["Artifacts", "GMP_jll", "JLLWrappers", "Libdl", "Pkg"]
git-tree-sha1 = "eca63e3847dad608cfa6a3329b95ef674c7160b4"
uuid = "4c82536e-c426-54e4-b420-14f461c4ed8b"
version = "3.7.2+0"

[[deps.NetworkOptions]]
uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908"
version = "1.2.0"

[[deps.Oceananigans]]
deps = ["Adapt", "CUDA", "Crayons", "CubedSphere", "Dates", "Distances", "DocStringExtensions", "FFTW", "Glob", "IncompleteLU", "InteractiveUtils", "IterativeSolvers", "JLD2", "KernelAbstractions", "LinearAlgebra", "Logging", "MPI", "NCDatasets", "OffsetArrays", "OrderedCollections", "Pkg", "Printf", "Random", "Rotations", "SeawaterPolynomials", "SparseArrays", "Statistics", "StructArrays"]
git-tree-sha1 = "cddb567fbab1c40b22914e24ad2fe917ff00d8c9"
git-tree-sha1 = "ae24fa7b83f5e6227a8768e0fe24c2bf9ba1e4d7"
uuid = "9e8cae18-63c1-5223-a75c-80ca9d6e9a09"
version = "0.93.1"
version = "0.95.3"

[deps.Oceananigans.extensions]
OceananigansEnzymeExt = "Enzyme"
Expand All @@ -662,9 +657,9 @@ version = "0.93.1"
MakieCore = "20f20a25-4f0e-4fdf-b5d1-57303727442b"

[[deps.OffsetArrays]]
git-tree-sha1 = "1a27764e945a152f7ca7efa04de513d473e9542e"
git-tree-sha1 = "5e1897147d1ff8d98883cda2be2187dcf57d8f0c"
uuid = "6fe1bfb0-de20-5000-8ca7-80f57d26f881"
version = "1.14.1"
version = "1.15.0"
weakdeps = ["Adapt"]

[deps.OffsetArrays.extensions]
Expand All @@ -677,9 +672,9 @@ version = "0.3.23+4"

[[deps.OpenMPI_jll]]
deps = ["Artifacts", "CompilerSupportLibraries_jll", "Hwloc_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPIPreferences", "TOML", "Zlib_jll"]
git-tree-sha1 = "bfce6d523861a6c562721b262c0d1aaeead2647f"
git-tree-sha1 = "2dace87e14256edb1dd0724ab7ba831c779b96bd"
uuid = "fe0851c0-eecd-5654-98d4-656369965a5c"
version = "5.0.5+0"
version = "5.0.6+0"

[[deps.OpenSSL_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl"]
Expand All @@ -688,15 +683,9 @@ uuid = "458c3c95-2e84-50aa-8efc-19380b2a3a95"
version = "3.0.15+1"

[[deps.OrderedCollections]]
git-tree-sha1 = "dfdf5519f235516220579f949664f1bf44e741c5"
git-tree-sha1 = "12f1439c4f986bb868acda6ea33ebc78e19b95ad"
uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
version = "1.6.3"

[[deps.P11Kit_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
git-tree-sha1 = "2cd396108e178f3ae8dedbd8e938a18726ab2fbf"
uuid = "c2071276-7c44-58a7-b746-946036e04d0a"
version = "0.24.1+0"
version = "1.7.0"

[[deps.Pkg]]
deps = ["Artifacts", "Dates", "Downloads", "FileWatching", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"]
Expand Down Expand Up @@ -788,9 +777,9 @@ version = "1.3.0"

[[deps.Roots]]
deps = ["Accessors", "CommonSolve", "Printf"]
git-tree-sha1 = "3a7c7e5c3f015415637f5debdf8a674aa2c979c4"
git-tree-sha1 = "8e3694d669323cdfb560e344dc872b984de23b71"
uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665"
version = "2.2.1"
version = "2.2.2"

[deps.Roots.extensions]
RootsChainRulesCoreExt = "ChainRulesCore"
Expand Down Expand Up @@ -833,9 +822,9 @@ version = "0.3.5"

[[deps.SentinelArrays]]
deps = ["Dates", "Random"]
git-tree-sha1 = "305becf8af67eae1dbc912ee9097f00aeeabb8d5"
git-tree-sha1 = "712fb0231ee6f9120e005ccd56297abbc053e7e0"
uuid = "91c51154-3ec4-41a3-a24f-3f23e20d615c"
version = "1.4.6"
version = "1.4.8"

[[deps.Serialization]]
uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b"
Expand All @@ -856,9 +845,9 @@ version = "1.10.0"

[[deps.StaticArrays]]
deps = ["LinearAlgebra", "PrecompileTools", "Random", "StaticArraysCore"]
git-tree-sha1 = "777657803913ffc7e8cc20f0fd04b634f871af8f"
git-tree-sha1 = "7c01731da8ab6d3094c4d44c9057b00932459255"
uuid = "90137ffa-7385-5640-81b9-e52037218182"
version = "1.9.8"
version = "1.9.9"

[deps.StaticArrays.extensions]
StaticArraysChainRulesCoreExt = "ChainRulesCore"
Expand Down Expand Up @@ -950,9 +939,9 @@ uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40"

[[deps.TimerOutputs]]
deps = ["ExprTools", "Printf"]
git-tree-sha1 = "3a6f063d690135f5c1ba351412c82bae4d1402bf"
git-tree-sha1 = "d7298ebdfa1654583468a487e8e83fae9d72dac3"
uuid = "a759f4b9-e2f1-59dc-863e-4aeb61b1ea8f"
version = "0.5.25"
version = "0.5.26"

[[deps.TranscodingStreams]]
git-tree-sha1 = "0c45878dcfdcfa8480052b6ab162cdd138781742"
Expand All @@ -971,17 +960,11 @@ git-tree-sha1 = "6331ac3440856ea1988316b46045303bef658278"
uuid = "013be700-e6cd-48c3-b4a1-df204f14c38f"
version = "0.2.1"

[[deps.UnsafeAtomicsLLVM]]
deps = ["LLVM", "UnsafeAtomics"]
git-tree-sha1 = "2d17fabcd17e67d7625ce9c531fb9f40b7c42ce4"
uuid = "d80eeb9a-aca5-4d75-85e5-170c8b632249"
version = "0.2.1"

[[deps.XML2_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Zlib_jll"]
git-tree-sha1 = "6a451c6f33a176150f315726eba8b92fbfdb9ae7"
git-tree-sha1 = "a2fccc6559132927d4c5dc183e3e01048c6dcbd6"
uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a"
version = "2.13.4+0"
version = "2.13.5+0"

[[deps.XZ_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl"]
Expand Down Expand Up @@ -1018,10 +1001,10 @@ uuid = "8e850b90-86db-534c-a0d3-1478176c7d93"
version = "5.11.0+0"

[[deps.libzip_jll]]
deps = ["Artifacts", "Bzip2_jll", "GnuTLS_jll", "JLLWrappers", "Libdl", "XZ_jll", "Zlib_jll", "Zstd_jll"]
git-tree-sha1 = "668ac0297e6bd8f4d53dfdcd3ace71f2e00f4a35"
deps = ["Artifacts", "Bzip2_jll", "JLLWrappers", "Libdl", "OpenSSL_jll", "XZ_jll", "Zlib_jll", "Zstd_jll"]
git-tree-sha1 = "e797fa066eba69f4c0585ffbd81bc780b5118ce2"
uuid = "337d8026-41b4-5cde-a456-74a10e5b31d1"
version = "1.11.1+0"
version = "1.11.2+0"

[[deps.nghttp2_jll]]
deps = ["Artifacts", "Libdl"]
Expand Down
4 changes: 2 additions & 2 deletions Project.toml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
name = "OceanBioME"
uuid = "a49af516-9db8-4be4-be45-1dad61c5a376"
authors = ["Jago Strong-Wright <[email protected]> and contributors"]
version = "0.13.3"
version = "0.13.4"

[deps]
Adapt = "79e6a3ab-5dfb-504d-930d-738a2a938a0e"
Expand All @@ -24,7 +24,7 @@ EnsembleKalmanProcesses = "1"
GibbsSeaWater = "0.1"
JLD2 = "0.4, 0.5"
KernelAbstractions = "0.9"
Oceananigans = "^0.92.1, ^0.93.0"
Oceananigans = "^0.95"
OffsetArrays = "1.14"
Roots = "2"
SeawaterPolynomials = "0.3"
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