Reduce deps (#8)

* pkg

* rm test

* wip

* pkg

* reduce pkg

Manifest.toml

@@ -2,7 +2,7 @@
 
 julia_version = "1.10.3"
 manifest_format = "2.0"
-project_hash = "0a3868209e1e06fd4815a1a4d0fb70163c2c4609"
+project_hash = "c31fe08d86ec107a97ce2f38a0768055cf0cb993"
 
 [[deps.ADTypes]]
 git-tree-sha1 = "016833eb52ba2d6bea9fcb50ca295980e728ee24"
@@ -102,16 +102,6 @@ weakdeps = ["SparseArrays"]
 [[deps.Artifacts]]
 uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33"
 
-[[deps.BandedMatrices]]
-deps = ["ArrayLayouts", "FillArrays", "LinearAlgebra", "PrecompileTools"]
-git-tree-sha1 = "30b7ea34abc4fe816eb1a5f434a43da804836163"
-uuid = "aae01518-5342-5314-be14-df237901396f"
-version = "1.7.0"
-weakdeps = ["SparseArrays"]
-
-    [deps.BandedMatrices.extensions]
-    BandedMatricesSparseArraysExt = "SparseArrays"
-
 [[deps.Base64]]
 uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"
 
@@ -131,29 +121,12 @@ git-tree-sha1 = "0c5f81f47bbbcf4aea7b2959135713459170798b"
 uuid = "62783981-4cbd-42fc-bca8-16325de8dc4b"
 version = "0.1.5"
 
-[[deps.BoundaryValueDiffEq]]
-deps = ["ADTypes", "Adapt", "ArrayInterface", "BandedMatrices", "ConcreteStructs", "DiffEqBase", "FastAlmostBandedMatrices", "FastClosures", "ForwardDiff", "LinearAlgebra", "LinearSolve", "Logging", "NonlinearSolve", "OrdinaryDiffEq", "PreallocationTools", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "Setfield", "SparseArrays", "SparseDiffTools"]
-git-tree-sha1 = "005b55fa2eebaa4d7bf3cfb8097807f47116175f"
-uuid = "764a87c0-6b3e-53db-9096-fe964310641d"
-version = "5.7.1"
-
-    [deps.BoundaryValueDiffEq.extensions]
-    BoundaryValueDiffEqODEInterfaceExt = "ODEInterface"
-
-    [deps.BoundaryValueDiffEq.weakdeps]
-    ODEInterface = "54ca160b-1b9f-5127-a996-1867f4bc2a2c"
-
 [[deps.Bzip2_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
 git-tree-sha1 = "9e2a6b69137e6969bab0152632dcb3bc108c8bdd"
 uuid = "6e34b625-4abd-537c-b88f-471c36dfa7a0"
 version = "1.0.8+1"
 
-[[deps.CEnum]]
-git-tree-sha1 = "389ad5c84de1ae7cf0e28e381131c98ea87d54fc"
-uuid = "fa961155-64e5-5f13-b03f-caf6b980ea82"
-version = "0.5.0"
-
 [[deps.CPUSummary]]
 deps = ["CpuId", "IfElse", "PrecompileTools", "Static"]
 git-tree-sha1 = "585a387a490f1c4bd88be67eea15b93da5e85db7"
@@ -337,12 +310,6 @@ version = "1.0.0"
 deps = ["Printf"]
 uuid = "ade2ca70-3891-5945-98fb-dc099432e06a"
 
-[[deps.DelayDiffEq]]
-deps = ["ArrayInterface", "DataStructures", "DiffEqBase", "LinearAlgebra", "Logging", "OrdinaryDiffEq", "Printf", "RecursiveArrayTools", "Reexport", "SciMLBase", "SimpleNonlinearSolve", "SimpleUnPack"]
-git-tree-sha1 = "5959ae76ebd198f70e9af81153644543da0cfaf2"
-uuid = "bcd4f6db-9728-5f36-b5f7-82caef46ccdb"
-version = "5.47.3"
-
 [[deps.DelimitedFiles]]
 deps = ["Mmap"]
 git-tree-sha1 = "9e2f36d3c96a820c678f2f1f1782582fcf685bae"
@@ -351,11 +318,12 @@ version = "1.9.1"
 
 [[deps.DiffEqBase]]
 deps = ["ArrayInterface", "ConcreteStructs", "DataStructures", "DocStringExtensions", "EnumX", "EnzymeCore", "FastBroadcast", "FastClosures", "ForwardDiff", "FunctionWrappers", "FunctionWrappersWrappers", "LinearAlgebra", "Logging", "Markdown", "MuladdMacro", "Parameters", "PreallocationTools", "PrecompileTools", "Printf", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "Setfield", "SparseArrays", "Static", "StaticArraysCore", "Statistics", "Tricks", "TruncatedStacktraces"]
-git-tree-sha1 = "d520d3007de793f4fca16c77a25a9774ebe4ad6d"
+git-tree-sha1 = "03b9555f4c3a7c2f530bb1ae13e85719c632f74e"
 uuid = "2b5f629d-d688-5b77-993f-72d75c75574e"
-version = "6.150.0"
+version = "6.151.1"
 
     [deps.DiffEqBase.extensions]
+    DiffEqBaseCUDAExt = "CUDA"
     DiffEqBaseChainRulesCoreExt = "ChainRulesCore"
     DiffEqBaseDistributionsExt = "Distributions"
     DiffEqBaseEnzymeExt = ["ChainRulesCore", "Enzyme"]
@@ -368,6 +336,7 @@ version = "6.150.0"
     DiffEqBaseUnitfulExt = "Unitful"
 
     [deps.DiffEqBase.weakdeps]
+    CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba"
     ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
     Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
     Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9"
@@ -384,19 +353,10 @@ deps = ["DataStructures", "DiffEqBase", "ForwardDiff", "Functors", "LinearAlgebr
 git-tree-sha1 = "c959cfd2657d16beada157a74d52269e8556500e"
 uuid = "459566f4-90b8-5000-8ac3-15dfb0a30def"
 version = "3.6.2"
-weakdeps = ["OrdinaryDiffEq", "Sundials"]
 
-[[deps.DiffEqNoiseProcess]]
-deps = ["DiffEqBase", "Distributions", "GPUArraysCore", "LinearAlgebra", "Markdown", "Optim", "PoissonRandom", "QuadGK", "Random", "Random123", "RandomNumbers", "RecipesBase", "RecursiveArrayTools", "Requires", "ResettableStacks", "SciMLBase", "StaticArraysCore", "Statistics"]
-git-tree-sha1 = "65cbbe1450ced323b4b17228ccd96349d96795a7"
-uuid = "77a26b50-5914-5dd7-bc55-306e6241c503"
-version = "5.21.0"
-
-    [deps.DiffEqNoiseProcess.extensions]
-    DiffEqNoiseProcessReverseDiffExt = "ReverseDiff"
-
-    [deps.DiffEqNoiseProcess.weakdeps]
-    ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267"
+    [deps.DiffEqCallbacks.weakdeps]
+    OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
+    Sundials = "c3572dad-4567-51f8-b174-8c6c989267f4"
 
 [[deps.DiffResults]]
 deps = ["StaticArraysCore"]
@@ -410,23 +370,6 @@ git-tree-sha1 = "23163d55f885173722d1e4cf0f6110cdbaf7e272"
 uuid = "b552c78f-8df3-52c6-915a-8e097449b14b"
 version = "1.15.1"
 
-[[deps.DifferentialEquations]]
-deps = ["BoundaryValueDiffEq", "DelayDiffEq", "DiffEqBase", "DiffEqCallbacks", "DiffEqNoiseProcess", "JumpProcesses", "LinearAlgebra", "LinearSolve", "NonlinearSolve", "OrdinaryDiffEq", "Random", "RecursiveArrayTools", "Reexport", "SciMLBase", "SteadyStateDiffEq", "StochasticDiffEq", "Sundials"]
-git-tree-sha1 = "81042254a307980b8ab5b67033aca26c2e157ebb"
-uuid = "0c46a032-eb83-5123-abaf-570d42b7fbaa"
-version = "7.13.0"
-
-[[deps.Distances]]
-deps = ["LinearAlgebra", "Statistics", "StatsAPI"]
-git-tree-sha1 = "66c4c81f259586e8f002eacebc177e1fb06363b0"
-uuid = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7"
-version = "0.10.11"
-weakdeps = ["ChainRulesCore", "SparseArrays"]
-
-    [deps.Distances.extensions]
-    DistancesChainRulesCoreExt = "ChainRulesCore"
-    DistancesSparseArraysExt = "SparseArrays"
-
 [[deps.Distributed]]
 deps = ["Random", "Serialization", "Sockets"]
 uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b"
@@ -555,12 +498,6 @@ git-tree-sha1 = "466d45dc38e15794ec7d5d63ec03d776a9aff36e"
 uuid = "b22a6f82-2f65-5046-a5b2-351ab43fb4e5"
 version = "4.4.4+1"
 
-[[deps.FastAlmostBandedMatrices]]
-deps = ["ArrayInterface", "ArrayLayouts", "BandedMatrices", "ConcreteStructs", "LazyArrays", "LinearAlgebra", "MatrixFactorizations", "PrecompileTools", "Reexport"]
-git-tree-sha1 = "9dc913faf8552fd09b92a0d7fcc25f1d5609d795"
-uuid = "9d29842c-ecb8-4973-b1e9-a27b1157504e"
-version = "0.1.1"
-
 [[deps.FastBroadcast]]
 deps = ["ArrayInterface", "LinearAlgebra", "Polyester", "Static", "StaticArrayInterface", "StrideArraysCore"]
 git-tree-sha1 = "a6e756a880fc419c8b41592010aebe6a5ce09136"
@@ -643,9 +580,9 @@ weakdeps = ["StaticArrays"]
 
 [[deps.FreeType2_jll]]
 deps = ["Artifacts", "Bzip2_jll", "JLLWrappers", "Libdl", "Zlib_jll"]
-git-tree-sha1 = "d8db6a5a2fe1381c1ea4ef2cab7c69c2de7f9ea0"
+git-tree-sha1 = "5c1d8ae0efc6c2e7b1fc502cbe25def8f661b7bc"
 uuid = "d7e528f0-a631-5988-bf34-fe36492bcfd7"
-version = "2.13.1+0"
+version = "2.13.2+0"
 
 [[deps.FriBidi_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl"]
@@ -939,12 +876,6 @@ weakdeps = ["StaticArrays"]
 deps = ["Artifacts", "Pkg"]
 uuid = "4af54fe1-eca0-43a8-85a7-787d91b784e3"
 
-[[deps.LevyArea]]
-deps = ["LinearAlgebra", "Random", "SpecialFunctions"]
-git-tree-sha1 = "56513a09b8e0ae6485f34401ea9e2f31357958ec"
-uuid = "2d8b4e74-eb68-11e8-0fb9-d5eb67b50637"
-version = "1.0.0"
-
 [[deps.LibCURL]]
 deps = ["LibCURL_jll", "MozillaCACerts_jll"]
 uuid = "b27032c2-a3e7-50c8-80cd-2d36dbcbfd21"
@@ -1207,12 +1138,6 @@ git-tree-sha1 = "a0b464d183da839699f4c79e7606d9d186ec172c"
 uuid = "d41bc354-129a-5804-8e4c-c37616107c6c"
 version = "7.8.3"
 
-[[deps.NLsolve]]
-deps = ["Distances", "LineSearches", "LinearAlgebra", "NLSolversBase", "Printf", "Reexport"]
-git-tree-sha1 = "019f12e9a1a7880459d0173c182e6a99365d7ac1"
-uuid = "2774e3e8-f4cf-5e23-947b-6d7e65073b56"
-version = "4.5.1"
-
 [[deps.NaNMath]]
 deps = ["OpenLibm_jll"]
 git-tree-sha1 = "0877504529a3e5c3343c6f8b4c0381e57e4387e4"
@@ -1298,18 +1223,6 @@ git-tree-sha1 = "13652491f6856acfd2db29360e1bbcd4565d04f1"
 uuid = "efe28fd5-8261-553b-a9e1-b2916fc3738e"
 version = "0.5.5+0"
 
-[[deps.Optim]]
-deps = ["Compat", "FillArrays", "ForwardDiff", "LineSearches", "LinearAlgebra", "NLSolversBase", "NaNMath", "Parameters", "PositiveFactorizations", "Printf", "SparseArrays", "StatsBase"]
-git-tree-sha1 = "d9b79c4eed437421ac4285148fcadf42e0700e89"
-uuid = "429524aa-4258-5aef-a3af-852621145aeb"
-version = "1.9.4"
-
-    [deps.Optim.extensions]
-    OptimMOIExt = "MathOptInterface"
-
-    [deps.Optim.weakdeps]
-    MathOptInterface = "b8f27783-ece8-5eb3-8dc8-9495eed66fee"
-
 [[deps.Opus_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
 git-tree-sha1 = "51a08fb14ec28da2ec7a927c4337e4332c2a4720"
@@ -1323,9 +1236,9 @@ version = "1.6.3"
 
 [[deps.OrdinaryDiffEq]]
 deps = ["ADTypes", "Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "ExponentialUtilities", "FastBroadcast", "FastClosures", "FillArrays", "FiniteDiff", "ForwardDiff", "FunctionWrappersWrappers", "IfElse", "InteractiveUtils", "LineSearches", "LinearAlgebra", "LinearSolve", "Logging", "MacroTools", "MuladdMacro", "NonlinearSolve", "Polyester", "PreallocationTools", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SciMLStructures", "SimpleNonlinearSolve", "SimpleUnPack", "SparseArrays", "SparseDiffTools", "StaticArrayInterface", "StaticArrays", "TruncatedStacktraces"]
-git-tree-sha1 = "4cf03bfe9c6159f66b57cda85f169cd0eff0818d"
+git-tree-sha1 = "a6ef55f6ce8a64e2d3c804d1c56fdafdd1528f86"
 uuid = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
-version = "6.76.0"
+version = "6.77.1"
 
 [[deps.PCRE2_jll]]
 deps = ["Artifacts", "Libdl"]
@@ -1422,12 +1335,6 @@ git-tree-sha1 = "240d7170f5ffdb285f9427b92333c3463bf65bf6"
 uuid = "1d0040c9-8b98-4ee7-8388-3f51789ca0ad"
 version = "0.2.1"
 
-[[deps.PositiveFactorizations]]
-deps = ["LinearAlgebra"]
-git-tree-sha1 = "17275485f373e6673f7e7f97051f703ed5b15b20"
-uuid = "85a6dd25-e78a-55b7-8502-1745935b8125"
-version = "0.2.4"
-
 [[deps.PreallocationTools]]
 deps = ["Adapt", "ArrayInterface", "ForwardDiff"]
 git-tree-sha1 = "a660e9daab5db07adf3dedfe09b435cc530d855e"
@@ -1481,12 +1388,6 @@ uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb"
 deps = ["SHA"]
 uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 
-[[deps.Random123]]
-deps = ["Random", "RandomNumbers"]
-git-tree-sha1 = "4743b43e5a9c4a2ede372de7061eed81795b12e7"
-uuid = "74087812-796a-5b5d-8853-05524746bad3"
-version = "1.7.0"
-
 [[deps.RandomNumbers]]
 deps = ["Random", "Requires"]
 git-tree-sha1 = "043da614cc7e95c703498a491e2c21f58a2b8111"
@@ -1552,12 +1453,6 @@ git-tree-sha1 = "838a3a4188e2ded87a4f9f184b4b0d78a1e91cb7"
 uuid = "ae029012-a4dd-5104-9daa-d747884805df"
 version = "1.3.0"
 
-[[deps.ResettableStacks]]
-deps = ["StaticArrays"]
-git-tree-sha1 = "256eeeec186fa7f26f2801732774ccf277f05db9"
-uuid = "ae5879a3-cd67-5da8-be7f-38c6eb64a37b"
-version = "1.1.1"
-
 [[deps.Rmath]]
 deps = ["Random", "Rmath_jll"]
 git-tree-sha1 = "f65dcb5fa46aee0cf9ed6274ccbd597adc49aa7b"
@@ -1801,18 +1696,6 @@ weakdeps = ["ChainRulesCore", "InverseFunctions"]
     StatsFunsChainRulesCoreExt = "ChainRulesCore"
     StatsFunsInverseFunctionsExt = "InverseFunctions"
 
-[[deps.SteadyStateDiffEq]]
-deps = ["ConcreteStructs", "DiffEqBase", "DiffEqCallbacks", "LinearAlgebra", "Reexport", "SciMLBase"]
-git-tree-sha1 = "1158cfdf0da5b0eacdfcfba7c16b174a37bdf6c7"
-uuid = "9672c7b4-1e72-59bd-8a11-6ac3964bc41f"
-version = "2.2.0"
-
-[[deps.StochasticDiffEq]]
-deps = ["Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DiffEqNoiseProcess", "DocStringExtensions", "FiniteDiff", "ForwardDiff", "JumpProcesses", "LevyArea", "LinearAlgebra", "Logging", "MuladdMacro", "NLsolve", "OrdinaryDiffEq", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SparseArrays", "SparseDiffTools", "StaticArrays", "UnPack"]
-git-tree-sha1 = "97e5d0b7e5ec2e68eec6626af97c59e9f6b6c3d0"
-uuid = "789caeaf-c7a9-5a7d-9973-96adeb23e2a0"
-version = "6.65.1"
-
 [[deps.StrideArraysCore]]
 deps = ["ArrayInterface", "CloseOpenIntervals", "IfElse", "LayoutPointers", "LinearAlgebra", "ManualMemory", "SIMDTypes", "Static", "StaticArrayInterface", "ThreadingUtilities"]
 git-tree-sha1 = "25349bf8f63aa36acbff5e3550a86e9f5b0ef682"
@@ -1828,18 +1711,6 @@ deps = ["Artifacts", "Libdl", "libblastrampoline_jll"]
 uuid = "bea87d4a-7f5b-5778-9afe-8cc45184846c"
 version = "7.2.1+1"
 
-[[deps.Sundials]]
-deps = ["CEnum", "DataStructures", "DiffEqBase", "Libdl", "LinearAlgebra", "Logging", "PrecompileTools", "Reexport", "SciMLBase", "SparseArrays", "Sundials_jll"]
-git-tree-sha1 = "e15f5a73f0d14b9079b807a9d1dac13e4302e997"
-uuid = "c3572dad-4567-51f8-b174-8c6c989267f4"
-version = "4.24.0"
-
-[[deps.Sundials_jll]]
-deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "SuiteSparse_jll", "libblastrampoline_jll"]
-git-tree-sha1 = "ba4d38faeb62de7ef47155ed321dce40a549c305"
-uuid = "fb77eaff-e24c-56d4-86b1-d163f2edb164"
-version = "5.2.2+0"
-
 [[deps.SymbolicIndexingInterface]]
 deps = ["Accessors", "ArrayInterface", "RuntimeGeneratedFunctions", "StaticArraysCore"]
 git-tree-sha1 = "b479c7a16803f08779ac5b7f9844a42621baeeda"
@@ -2039,9 +1910,9 @@ version = "1.31.0+0"
 
 [[deps.XML2_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Zlib_jll"]
-git-tree-sha1 = "532e22cf7be8462035d092ff21fada7527e2c488"
+git-tree-sha1 = "52ff2af32e591541550bd753c0da8b9bc92bb9d9"
 uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a"
-version = "2.12.6+0"
+version = "2.12.7+0"
 
 [[deps.XSLT_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Libgpg_error_jll", "Libiconv_jll", "Pkg", "XML2_jll", "Zlib_jll"]

Project.toml

@@ -4,7 +4,8 @@ authors = ["Wen-Wei Tseng <[email protected]>"]
 version = "0.1.0"
 
 [deps]
-DifferentialEquations = "0c46a032-eb83-5123-abaf-570d42b7fbaa"
+DiffEqCallbacks = "459566f4-90b8-5000-8ac3-15dfb0a30def"
 ModelingToolkit = "961ee093-0014-501f-94e3-6117800e7a78"
 NaNMath = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3"
+OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"

docs/camkii_calwave.jl

@@ -1,7 +1,8 @@
 #===
 # Smooth calcium wave
 ===#
-using DifferentialEquations
+using OrdinaryDiffEq
+using DiffEqCallbacks
 using ModelingToolkit
 using Plots
 using CaMKIIModel: get_camkii_eqs, μM, nM, second

docs/camkii_catalyst.jl

@@ -1,6 +1,7 @@
 # # Isolated CaMKII response
 using ModelingToolkit
-using DifferentialEquations
+using OrdinaryDiffEq
+using DiffEqCallbacks
 using Plots
 using CaMKIIModel: nM, μM, Hz, get_camkii_eqs