Merge pull request #117 from gaelforget/v0p4p4a

V0p4p4a
JuliaClimate · Aug 21, 2023 · d6e0383 · d6e0383
2 parents 9b73cb0 + 44929bd
commit d6e0383
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diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -51,7 +51,7 @@ jobs:
       - uses: actions/checkout@v2
       - uses: julia-actions/setup-julia@v1
         with:
-          version: '1.7'
+          version: '1.9'
       - run: |
           julia --project=docs -e '
             using Pkg

diff --git a/Project.toml b/Project.toml
@@ -1,23 +1,18 @@
 name = "IndividualDisplacements"
 uuid = "b92f0c32-5b7e-11e9-1d7b-238b2da8b0e6"
 authors = ["gaelforget <gforget@mit.edu>"]
-version = "0.4.3"
+version = "0.4.4"
 
 [deps]
 Artifacts = "56f22d72-fd6d-98f1-02f0-08ddc0907c33"
-CFTime = "179af706-886a-5703-950a-314cd64e0468"
-CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
 CyclicArrays = "6023044f-b3ef-4c22-8399-3ec90a0c9b75"
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
-Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
 LazyArtifacts = "4af54fe1-eca0-43a8-85a7-787d91b784e3"
 MeshArrays = "cb8c808f-1acf-59a3-9d2b-6e38d009f683"
 OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 
 [compat]
-CFTime = "0.1"
-CSV = "0.6, 0.7, 0.8, 0.9, 0.10"
 CyclicArrays = "0.2, 0.3, 0.4, 0.5"
 DataFrames = "0.21, 0.22, 1"
 MeshArrays = "0.2.19, 0.2"

diff --git a/examples/basics/random_flow_field.jl b/examples/basics/random_flow_field.jl
@@ -178,6 +178,7 @@ begin
 end
 
 
+
 # ╔═╡ 00000000-0000-0000-0000-000000000001
 PLUTO_PROJECT_TOML_CONTENTS = """
 [deps]
@@ -965,9 +966,9 @@ version = "1.0.0"
 
 [[deps.IndividualDisplacements]]
 deps = ["Artifacts", "CFTime", "CSV", "CyclicArrays", "DataFrames", "Dates", "LazyArtifacts", "MeshArrays", "OrdinaryDiffEq", "Random"]
-git-tree-sha1 = "c8311939c810c15f7f3dd2f1500adb02e90429b2"
+git-tree-sha1 = "480c518777afde08580d8164edae17da92e080e3"
 uuid = "b92f0c32-5b7e-11e9-1d7b-238b2da8b0e6"
-version = "0.4.2"
+version = "0.4.3"
 
 [[deps.Inflate]]
 git-tree-sha1 = "5cd07aab533df5170988219191dfad0519391428"
@@ -1044,10 +1045,10 @@ uuid = "82899510-4779-5014-852e-03e436cf321d"
 version = "1.0.0"
 
 [[deps.JLLWrappers]]
-deps = ["Preferences"]
-git-tree-sha1 = "abc9885a7ca2052a736a600f7fa66209f96506e1"
+deps = ["Artifacts", "Preferences"]
+git-tree-sha1 = "7e5d6779a1e09a36db2a7b6cff50942a0a7d0fca"
 uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210"
-version = "1.4.1"
+version = "1.5.0"
 
 [[deps.JSON]]
 deps = ["Dates", "Mmap", "Parsers", "Unicode"]
@@ -1233,9 +1234,9 @@ version = "2.5.0"
 
 [[deps.LogExpFunctions]]
 deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"]
-git-tree-sha1 = "c3ce8e7420b3a6e071e0fe4745f5d4300e37b13f"
+git-tree-sha1 = "5ab83e1679320064c29e8973034357655743d22d"
 uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688"
-version = "0.3.24"
+version = "0.3.25"
 
     [deps.LogExpFunctions.extensions]
     LogExpFunctionsChainRulesCoreExt = "ChainRulesCore"
@@ -1274,9 +1275,9 @@ version = "2023.2.0+0"
 
 [[deps.MacroTools]]
 deps = ["Markdown", "Random"]
-git-tree-sha1 = "42324d08725e200c23d4dfb549e0d5d89dede2d2"
+git-tree-sha1 = "9ee1618cbf5240e6d4e0371d6f24065083f60c48"
 uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09"
-version = "0.5.10"
+version = "0.5.11"
 
 [[deps.Makie]]
 deps = ["Animations", "Base64", "ColorBrewer", "ColorSchemes", "ColorTypes", "Colors", "Contour", "DelaunayTriangulation", "Distributions", "DocStringExtensions", "Downloads", "FFMPEG", "FileIO", "FixedPointNumbers", "Formatting", "FreeType", "FreeTypeAbstraction", "GeometryBasics", "GridLayoutBase", "ImageIO", "InteractiveUtils", "IntervalSets", "Isoband", "KernelDensity", "LaTeXStrings", "LinearAlgebra", "MacroTools", "MakieCore", "Markdown", "Match", "MathTeXEngine", "Observables", "OffsetArrays", "Packing", "PlotUtils", "PolygonOps", "PrecompileTools", "Printf", "REPL", "Random", "RelocatableFolders", "Setfield", "ShaderAbstractions", "Showoff", "SignedDistanceFields", "SparseArrays", "StableHashTraits", "Statistics", "StatsBase", "StatsFuns", "StructArrays", "TriplotBase", "UnicodeFun"]
@@ -1322,9 +1323,9 @@ version = "2.28.2+0"
 
 [[deps.MeshArrays]]
 deps = ["CatViews", "Dates", "LazyArtifacts", "NearestNeighbors", "Pkg", "Printf", "SparseArrays", "Statistics", "Unitful"]
-git-tree-sha1 = "8aa22a1e308edf2d6120871c67c2b1bde8b695cf"
+git-tree-sha1 = "a70763dc0dae3b7ce8c13ad63e4f22ebfbc30f19"
 uuid = "cb8c808f-1acf-59a3-9d2b-6e38d009f683"
-version = "0.2.37"
+version = "0.2.38"
 
 [[deps.Missings]]
 deps = ["DataAPI"]
@@ -1453,9 +1454,9 @@ version = "0.5.5+0"
 
 [[deps.Optim]]
 deps = ["Compat", "FillArrays", "ForwardDiff", "LineSearches", "LinearAlgebra", "NLSolversBase", "NaNMath", "Parameters", "PositiveFactorizations", "Printf", "SparseArrays", "StatsBase"]
-git-tree-sha1 = "e3a6546c1577bfd701771b477b794a52949e7594"
+git-tree-sha1 = "963b004d15216f8129f6c0f7d187efa136570be0"
 uuid = "429524aa-4258-5aef-a3af-852621145aeb"
-version = "1.7.6"
+version = "1.7.7"
 
 [[deps.Opus_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
@@ -1470,9 +1471,9 @@ version = "1.6.2"
 
 [[deps.OrdinaryDiffEq]]
 deps = ["ADTypes", "Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "ExponentialUtilities", "FastBroadcast", "FastClosures", "FiniteDiff", "ForwardDiff", "FunctionWrappersWrappers", "IfElse", "InteractiveUtils", "LineSearches", "LinearAlgebra", "LinearSolve", "Logging", "LoopVectorization", "MacroTools", "MuladdMacro", "NLsolve", "NonlinearSolve", "Polyester", "PreallocationTools", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLNLSolve", "SciMLOperators", "SimpleNonlinearSolve", "SimpleUnPack", "SparseArrays", "SparseDiffTools", "StaticArrayInterface", "StaticArrays", "TruncatedStacktraces"]
-git-tree-sha1 = "47c560dcb059570bdbd9f887a6b8958190e498a4"
+git-tree-sha1 = "2758190d4b01182e2278b772339daa83e209d45a"
 uuid = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
-version = "6.53.4"
+version = "6.54.0"
 
 [[deps.PCRE2_jll]]
 deps = ["Artifacts", "Libdl"]

diff --git a/examples/basics/solid_body_rotation.jl b/examples/basics/solid_body_rotation.jl
@@ -1,5 +1,5 @@
 ### A Pluto.jl notebook ###
-# v0.19.24
+# v0.19.27
 
 using Markdown
 using InteractiveUtils
@@ -178,6 +178,7 @@ begin
 end
 
 
+
 # ╔═╡ 00000000-0000-0000-0000-000000000001
 PLUTO_PROJECT_TOML_CONTENTS = """
 [deps]
@@ -189,7 +190,7 @@ PlutoUI = "7f904dfe-b85e-4ff6-b463-dae2292396a8"
 
 [compat]
 CairoMakie = "~0.10.4"
-DataFrames = "~1.5.0"
+DataFrames = "~1.6.0"
 IndividualDisplacements = "~0.4.2"
 MeshArrays = "~0.2.36"
 PlutoUI = "~0.7.50"
@@ -201,7 +202,7 @@ PLUTO_MANIFEST_TOML_CONTENTS = """
 
 julia_version = "1.9.1"
 manifest_format = "2.0"
-project_hash = "173d400d08eb78b2998f88a6415add9e29afdc80"
+project_hash = "fb2a0616f29efd4246315bd0acc249d8ce934f01"
 
 [[deps.ADTypes]]
 git-tree-sha1 = "f5c25e8a5b29b5e941b7408bc8cc79fea4d9ef9a"
@@ -510,10 +511,10 @@ uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a"
 version = "1.15.0"
 
 [[deps.DataFrames]]
-deps = ["Compat", "DataAPI", "Future", "InlineStrings", "InvertedIndices", "IteratorInterfaceExtensions", "LinearAlgebra", "Markdown", "Missings", "PooledArrays", "PrettyTables", "Printf", "REPL", "Random", "Reexport", "SentinelArrays", "SnoopPrecompile", "SortingAlgorithms", "Statistics", "TableTraits", "Tables", "Unicode"]
-git-tree-sha1 = "aa51303df86f8626a962fccb878430cdb0a97eee"
+deps = ["Compat", "DataAPI", "DataStructures", "Future", "InlineStrings", "InvertedIndices", "IteratorInterfaceExtensions", "LinearAlgebra", "Markdown", "Missings", "PooledArrays", "PrecompileTools", "PrettyTables", "Printf", "REPL", "Random", "Reexport", "SentinelArrays", "SortingAlgorithms", "Statistics", "TableTraits", "Tables", "Unicode"]
+git-tree-sha1 = "04c738083f29f86e62c8afc341f0967d8717bdb8"
 uuid = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
-version = "1.5.0"
+version = "1.6.1"
 
 [[deps.DataStructures]]
 deps = ["Compat", "InteractiveUtils", "OrderedCollections"]
@@ -969,9 +970,9 @@ version = "1.0.0"
 
 [[deps.IndividualDisplacements]]
 deps = ["Artifacts", "CFTime", "CSV", "CyclicArrays", "DataFrames", "Dates", "LazyArtifacts", "MeshArrays", "OrdinaryDiffEq", "Random"]
-git-tree-sha1 = "c8311939c810c15f7f3dd2f1500adb02e90429b2"
+git-tree-sha1 = "480c518777afde08580d8164edae17da92e080e3"
 uuid = "b92f0c32-5b7e-11e9-1d7b-238b2da8b0e6"
-version = "0.4.2"
+version = "0.4.3"
 
 [[deps.Inflate]]
 git-tree-sha1 = "5cd07aab533df5170988219191dfad0519391428"
@@ -1048,10 +1049,10 @@ uuid = "82899510-4779-5014-852e-03e436cf321d"
 version = "1.0.0"
 
 [[deps.JLLWrappers]]
-deps = ["Preferences"]
-git-tree-sha1 = "abc9885a7ca2052a736a600f7fa66209f96506e1"
+deps = ["Artifacts", "Preferences"]
+git-tree-sha1 = "7e5d6779a1e09a36db2a7b6cff50942a0a7d0fca"
 uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210"
-version = "1.4.1"
+version = "1.5.0"
 
 [[deps.JSON]]
 deps = ["Dates", "Mmap", "Parsers", "Unicode"]
@@ -1237,9 +1238,9 @@ version = "2.5.0"
 
 [[deps.LogExpFunctions]]
 deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"]
-git-tree-sha1 = "c3ce8e7420b3a6e071e0fe4745f5d4300e37b13f"
+git-tree-sha1 = "5ab83e1679320064c29e8973034357655743d22d"
 uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688"
-version = "0.3.24"
+version = "0.3.25"
 
     [deps.LogExpFunctions.extensions]
     LogExpFunctionsChainRulesCoreExt = "ChainRulesCore"
@@ -1278,9 +1279,9 @@ version = "2023.2.0+0"
 
 [[deps.MacroTools]]
 deps = ["Markdown", "Random"]
-git-tree-sha1 = "42324d08725e200c23d4dfb549e0d5d89dede2d2"
+git-tree-sha1 = "9ee1618cbf5240e6d4e0371d6f24065083f60c48"
 uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09"
-version = "0.5.10"
+version = "0.5.11"
 
 [[deps.Makie]]
 deps = ["Animations", "Base64", "ColorBrewer", "ColorSchemes", "ColorTypes", "Colors", "Contour", "DelaunayTriangulation", "Distributions", "DocStringExtensions", "Downloads", "FFMPEG", "FileIO", "FixedPointNumbers", "Formatting", "FreeType", "FreeTypeAbstraction", "GeometryBasics", "GridLayoutBase", "ImageIO", "InteractiveUtils", "IntervalSets", "Isoband", "KernelDensity", "LaTeXStrings", "LinearAlgebra", "MacroTools", "MakieCore", "Markdown", "Match", "MathTeXEngine", "Observables", "OffsetArrays", "Packing", "PlotUtils", "PolygonOps", "PrecompileTools", "Printf", "REPL", "Random", "RelocatableFolders", "Setfield", "ShaderAbstractions", "Showoff", "SignedDistanceFields", "SparseArrays", "StableHashTraits", "Statistics", "StatsBase", "StatsFuns", "StructArrays", "TriplotBase", "UnicodeFun"]
@@ -1326,9 +1327,9 @@ version = "2.28.2+0"
 
 [[deps.MeshArrays]]
 deps = ["CatViews", "Dates", "LazyArtifacts", "NearestNeighbors", "Pkg", "Printf", "SparseArrays", "Statistics", "Unitful"]
-git-tree-sha1 = "8aa22a1e308edf2d6120871c67c2b1bde8b695cf"
+git-tree-sha1 = "a70763dc0dae3b7ce8c13ad63e4f22ebfbc30f19"
 uuid = "cb8c808f-1acf-59a3-9d2b-6e38d009f683"
-version = "0.2.37"
+version = "0.2.38"
 
 [[deps.Missings]]
 deps = ["DataAPI"]
@@ -1457,9 +1458,9 @@ version = "0.5.5+0"
 
 [[deps.Optim]]
 deps = ["Compat", "FillArrays", "ForwardDiff", "LineSearches", "LinearAlgebra", "NLSolversBase", "NaNMath", "Parameters", "PositiveFactorizations", "Printf", "SparseArrays", "StatsBase"]
-git-tree-sha1 = "e3a6546c1577bfd701771b477b794a52949e7594"
+git-tree-sha1 = "963b004d15216f8129f6c0f7d187efa136570be0"
 uuid = "429524aa-4258-5aef-a3af-852621145aeb"
-version = "1.7.6"
+version = "1.7.7"
 
 [[deps.Opus_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
@@ -1474,9 +1475,9 @@ version = "1.6.2"
 
 [[deps.OrdinaryDiffEq]]
 deps = ["ADTypes", "Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "ExponentialUtilities", "FastBroadcast", "FastClosures", "FiniteDiff", "ForwardDiff", "FunctionWrappersWrappers", "IfElse", "InteractiveUtils", "LineSearches", "LinearAlgebra", "LinearSolve", "Logging", "LoopVectorization", "MacroTools", "MuladdMacro", "NLsolve", "NonlinearSolve", "Polyester", "PreallocationTools", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLNLSolve", "SciMLOperators", "SimpleNonlinearSolve", "SimpleUnPack", "SparseArrays", "SparseDiffTools", "StaticArrayInterface", "StaticArrays", "TruncatedStacktraces"]
-git-tree-sha1 = "47c560dcb059570bdbd9f887a6b8958190e498a4"
+git-tree-sha1 = "2758190d4b01182e2278b772339daa83e209d45a"
 uuid = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
-version = "6.53.4"
+version = "6.54.0"
 
 [[deps.PCRE2_jll]]
 deps = ["Artifacts", "Libdl"]

diff --git a/examples/worldwide/ECCO_FlowFields.jl b/examples/worldwide/ECCO_FlowFields.jl
@@ -1,13 +1,10 @@
 module ECCO_FlowFields
 
-using IndividualDisplacements, OceanStateEstimation, MITgcmTools
+using IndividualDisplacements, OceanStateEstimation, MITgcmTools, CSV, JLD2
 
 import IndividualDisplacements.DataFrames: DataFrame
 import IndividualDisplacements.MeshArrays as MeshArrays
 import IndividualDisplacements.MeshArrays: gcmgrid, MeshArray
-import IndividualDisplacements.CSV as CSV
-
-import OceanStateEstimation.ECCO_helpers.JLD2 as JLD2
 
 """
     init_from_file(np ::Int)