Merge pull request #46 from ReactionMechanismGenerator/sens

Add Adjoint and Forward Sensitivity Analysis

Author: mjohnson541

.travis.yml

@@ -4,7 +4,7 @@ env:
 os:
   - linux
 julia:
-  - 1.0
+  - 1.3
 before_install:
   - cd ..
   # Install miniconda

Manifest.toml

@@ -30,6 +30,12 @@ git-tree-sha1 = "066d1e7a9eb4873660791db7f0d8c7902600b81c"
 uuid = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9"
 version = "2.11.0"
 
+[[ArrayLayouts]]
+deps = ["FillArrays", "LinearAlgebra"]
+git-tree-sha1 = "6f6e33efac70fc24c1f2a654a090b7af01690ffe"
+uuid = "4c555306-a7a7-4459-81d9-ec55ddd5c99a"
+version = "0.3.7"
+
 [[AxisAlgorithms]]
 deps = ["LinearAlgebra", "Random", "SparseArrays", "WoodburyMatrices"]
 git-tree-sha1 = "a4d07a1c313392a77042855df46c5f534076fab9"
@@ -74,6 +80,12 @@ git-tree-sha1 = "a6c17353ee38ddab30e73dcfaa1107752de724ec"
 uuid = "324d7699-5711-5eae-9e2f-1d82baa6b597"
 version = "0.8.1"
 
+[[ChainRules]]
+deps = ["ChainRulesCore", "LinearAlgebra", "Random", "Reexport", "Requires", "Statistics"]
+git-tree-sha1 = "f54401294c1ed68d7cc2a7ea280ec101bca722bc"
+uuid = "082447d4-558c-5d27-93f4-14fc19e9eca2"
+version = "0.7.12"
+
 [[ChainRulesCore]]
 deps = ["MuladdMacro"]
 git-tree-sha1 = "971b03f25bdf2acab79f1c51afc717f9dccf43c2"
@@ -191,6 +203,30 @@ git-tree-sha1 = "3b9c743d3e789cedb01063871241b5cbb873fcef"
 uuid = "2b5f629d-d688-5b77-993f-72d75c75574e"
 version = "6.41.0"
 
+[[DiffEqCallbacks]]
+deps = ["DataStructures", "DiffEqBase", "ForwardDiff", "LinearAlgebra", "NLsolve", "OrdinaryDiffEq", "RecipesBase", "RecursiveArrayTools", "StaticArrays"]
+git-tree-sha1 = "1b7d2b06490bd917c3c5e7bf65e6490537bb1652"
+uuid = "459566f4-90b8-5000-8ac3-15dfb0a30def"
+version = "2.13.4"
+
+[[DiffEqJump]]
+deps = ["ArrayInterface", "Compat", "DataStructures", "DiffEqBase", "FunctionWrappers", "LinearAlgebra", "Parameters", "PoissonRandom", "Random", "RandomNumbers", "RecursiveArrayTools", "StaticArrays", "Statistics", "TreeViews"]
+git-tree-sha1 = "c9baaba9b1ee1407473a2daac1ca0ffdcb72253d"
+uuid = "c894b116-72e5-5b58-be3c-e6d8d4ac2b12"
+version = "6.9.3"
+
+[[DiffEqNoiseProcess]]
+deps = ["DataStructures", "DiffEqBase", "Distributions", "LinearAlgebra", "PoissonRandom", "Random", "RandomNumbers", "RecipesBase", "RecursiveArrayTools", "Requires", "ResettableStacks", "StaticArrays", "Statistics"]
+git-tree-sha1 = "eee0959f49af807fb79b6800b6cbeafddc4d0b72"
+uuid = "77a26b50-5914-5dd7-bc55-306e6241c503"
+version = "5.1.0"
+
+[[DiffEqSensitivity]]
+deps = ["Adapt", "DiffEqBase", "DiffEqCallbacks", "DiffEqNoiseProcess", "Distributions", "FFTW", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "Parameters", "QuadGK", "QuasiMonteCarlo", "RecursiveArrayTools", "Requires", "ReverseDiff", "Statistics", "StochasticDiffEq", "Tracker", "Zygote", "ZygoteRules"]
+git-tree-sha1 = "c071a0d9893e8b6ec6e8db58ac4eca4ce32672f1"
+uuid = "41bf760c-e81c-5289-8e54-58b1f1f8abe2"
+version = "6.26.0"
+
 [[DiffResults]]
 deps = ["StaticArrays"]
 git-tree-sha1 = "da24935df8e0c6cf28de340b958f6aac88eaa0cc"
@@ -213,6 +249,12 @@ version = "0.8.2"
 deps = ["Random", "Serialization", "Sockets"]
 uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b"
 
+[[Distributions]]
+deps = ["FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns"]
+git-tree-sha1 = "21fe8727469b4eeb5a006e0399588180f5dc9db4"
+uuid = "31c24e10-a181-5473-b8eb-7969acd0382f"
+version = "0.23.5"
+
 [[DocStringExtensions]]
 deps = ["LibGit2", "Markdown", "Pkg", "Test"]
 git-tree-sha1 = "c5714d9bcdba66389612dc4c47ed827c64112997"
@@ -254,6 +296,12 @@ git-tree-sha1 = "f354b2087a3b01c1d7152c19f45886c8a036fa5e"
 uuid = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549"
 version = "1.4.0"
 
+[[FillArrays]]
+deps = ["LinearAlgebra", "Random", "SparseArrays"]
+git-tree-sha1 = "be4180bdb27a11188d694ee3773122f4921f1a62"
+uuid = "1a297f60-69ca-5386-bcde-b61e274b549b"
+version = "0.8.13"
+
 [[FiniteDiff]]
 deps = ["ArrayInterface", "LinearAlgebra", "Requires", "SparseArrays", "StaticArrays"]
 git-tree-sha1 = "43b397bf66d07d113cc2cc012dd2029d336c3894"
@@ -293,6 +341,12 @@ git-tree-sha1 = "45d684ead5b65c043ad46bd5be750d61c39d7ef8"
 uuid = "a2bd30eb-e257-5431-a919-1863eab51364"
 version = "1.0.2"
 
+[[IRTools]]
+deps = ["InteractiveUtils", "MacroTools", "Test"]
+git-tree-sha1 = "6875ae3cfcb9a50af80553d5cc825f406e8d13bc"
+uuid = "7869d1d1-7146-5819-86e3-90919afe41df"
+version = "0.4.0"
+
 [[IdentityRanges]]
 deps = ["OffsetArrays"]
 git-tree-sha1 = "be8fcd695c4da16a1d6d0cd213cb88090a150e3b"
@@ -436,6 +490,12 @@ git-tree-sha1 = "5e04374019448f8509349948ab504f117e3b575a"
 uuid = "2ee39098-c373-598a-b85f-a56591580800"
 version = "1.3.0"
 
+[[LatinHypercubeSampling]]
+deps = ["Random", "StatsBase", "Test"]
+git-tree-sha1 = "f6df9a2cd3c2ee1123c39fac3cca18993fc88247"
+uuid = "a5e1c1ea-c99a-51d3-a14d-a9a37257b02d"
+version = "1.6.4"
+
 [[LeftChildRightSiblingTrees]]
 deps = ["AbstractTrees"]
 git-tree-sha1 = "71be1eb5ad19cb4f61fa8c73395c0338fd092ae0"
@@ -584,6 +644,12 @@ git-tree-sha1 = "b3e9e9a0bdd8e0ac3703e8c4be3cb504d1ebd312"
 uuid = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
 version = "5.42.0"
 
+[[PDMats]]
+deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse", "Test"]
+git-tree-sha1 = "b3405086eb6a974eba1958923d46bc0e1c2d2d63"
+uuid = "90014a1f-27ba-587c-ab20-58faa44d9150"
+version = "0.10.0"
+
 [[PaddedViews]]
 deps = ["OffsetArrays"]
 git-tree-sha1 = "100195a79b577d5747db98bf1732c3686285fa1e"
@@ -606,6 +672,12 @@ version = "1.0.7"
 deps = ["Dates", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "UUIDs"]
 uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
 
+[[PoissonRandom]]
+deps = ["Random", "Statistics", "Test"]
+git-tree-sha1 = "44d018211a56626288b5d3f8c6497d28c26dc850"
+uuid = "e409e4f3-bfea-5376-8464-e040bb5c01ab"
+version = "0.4.0"
+
 [[PooledArrays]]
 deps = ["DataAPI"]
 git-tree-sha1 = "b1333d4eced1826e15adbdf01a4ecaccca9d353c"
@@ -640,12 +712,24 @@ git-tree-sha1 = "67dde2482fe1a72ef62ed93f8c239f947638e5a2"
 uuid = "d330b81b-6aea-500a-939a-2ce795aea3ee"
 version = "2.9.0"
 
+[[QuadGK]]
+deps = ["DataStructures", "LinearAlgebra"]
+git-tree-sha1 = "0ab8a09d4478ebeb99a706ecbf8634a65077ccdc"
+uuid = "1fd47b50-473d-5c70-9696-f719f8f3bcdc"
+version = "2.4.0"
+
 [[QuartzImageIO]]
 deps = ["ColorVectorSpace", "FileIO", "ImageCore", "Libdl"]
 git-tree-sha1 = "021906af4af85b96489c45c12a490ae886a17fea"
 uuid = "dca85d43-d64c-5e67-8c65-017450d5d020"
 version = "0.7.2"
 
+[[QuasiMonteCarlo]]
+deps = ["Distributions", "LatinHypercubeSampling", "Sobol"]
+git-tree-sha1 = "b90f9ff53b4c1f14eee512626cd8e7f9791b20a2"
+uuid = "8a4e6c94-4038-4cdc-81c3-7e6ffdb2a71b"
+version = "0.2.0"
+
 [[REPL]]
 deps = ["InteractiveUtils", "Markdown", "Sockets"]
 uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb"
@@ -654,6 +738,12 @@ uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb"
 deps = ["Serialization"]
 uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 
+[[RandomNumbers]]
+deps = ["Random", "Requires"]
+git-tree-sha1 = "441e6fc35597524ada7f85e13df1f4e10137d16f"
+uuid = "e6cf234a-135c-5ec9-84dd-332b85af5143"
+version = "1.4.0"
+
 [[RangeArrays]]
 git-tree-sha1 = "b9039e93773ddcfc828f12aadf7115b4b4d225f5"
 uuid = "b3c3ace0-ae52-54e7-9d0b-2c1406fd6b9d"
@@ -693,12 +783,30 @@ git-tree-sha1 = "d37400976e98018ee840e0ca4f9d20baa231dc6b"
 uuid = "ae029012-a4dd-5104-9daa-d747884805df"
 version = "1.0.1"
 
+[[ResettableStacks]]
+deps = ["StaticArrays"]
+git-tree-sha1 = "d19e9c93de6020a96dbb2820567c78d0ab8f7248"
+uuid = "ae5879a3-cd67-5da8-be7f-38c6eb64a37b"
+version = "1.0.0"
+
 [[ReverseDiff]]
 deps = ["DiffResults", "DiffRules", "ForwardDiff", "FunctionWrappers", "LinearAlgebra", "MacroTools", "NaNMath", "Random", "SpecialFunctions", "StaticArrays", "Statistics"]
 git-tree-sha1 = "d10f33d434e920442cc6e88fdd5bbc8a5b54494f"
 uuid = "37e2e3b7-166d-5795-8a7a-e32c996b4267"
 version = "1.4.1"
 
+[[Rmath]]
+deps = ["Random", "Rmath_jll"]
+git-tree-sha1 = "86c5647b565873641538d8f812c04e4c9dbeb370"
+uuid = "79098fc4-a85e-5d69-aa6a-4863f24498fa"
+version = "0.6.1"
+
+[[Rmath_jll]]
+deps = ["Libdl", "Pkg"]
+git-tree-sha1 = "d76185aa1f421306dec73c057aa384bad74188f0"
+uuid = "f50d1b31-88e8-58de-be2c-1cc44531875f"
+version = "0.2.2+1"
+
 [[Roots]]
 deps = ["Printf"]
 git-tree-sha1 = "069e68c2173b4e4d0c37ffb3268d37f168ad719c"
@@ -751,6 +859,12 @@ git-tree-sha1 = "9e47150ea38107ba762fb26bd5c2a000b27ecf94"
 uuid = "102930c3-cf33-599f-b3b1-9a29a5acab30"
 version = "0.2.1"
 
+[[Sobol]]
+deps = ["DelimitedFiles", "Random"]
+git-tree-sha1 = "c267048df70f47d47d5272fe1a63a66c51c53014"
+uuid = "ed01d8cd-4d21-5b2a-85b4-cc3bdc58bad4"
+version = "1.4.0"
+
 [[Sockets]]
 uuid = "6462fe0b-24de-5631-8697-dd941f90decc"
 
@@ -792,6 +906,18 @@ git-tree-sha1 = "a6102b1f364befdb05746f386b67c6b7e3262c45"
 uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
 version = "0.33.0"
 
+[[StatsFuns]]
+deps = ["Rmath", "SpecialFunctions"]
+git-tree-sha1 = "04a5a8e6ab87966b43f247920eab053fd5fdc925"
+uuid = "4c63d2b9-4356-54db-8cca-17b64c39e42c"
+version = "0.9.5"
+
+[[StochasticDiffEq]]
+deps = ["ArrayInterface", "DataStructures", "DiffEqBase", "DiffEqJump", "DiffEqNoiseProcess", "FillArrays", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "Logging", "MuladdMacro", "NLsolve", "OrdinaryDiffEq", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "SparseArrays", "SparseDiffTools", "StaticArrays", "UnPack"]
+git-tree-sha1 = "a6bd84689c76ad649fcb9c994a7bdb20802846ac"
+uuid = "789caeaf-c7a9-5a7d-9973-96adeb23e2a0"
+version = "6.24.0"
+
 [[SuiteSparse]]
 deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"]
 uuid = "4607b0f0-06f3-5cda-b6b1-a6196a1729e9"
@@ -901,6 +1027,12 @@ git-tree-sha1 = "c5e2eaa5ce818c5277388377d592eb4c81f27c00"
 uuid = "ddb6d928-2868-570f-bddf-ab3f9cf99eb6"
 version = "0.4.0"
 
+[[Zygote]]
+deps = ["AbstractFFTs", "ArrayLayouts", "ChainRules", "DiffRules", "Distributed", "FillArrays", "ForwardDiff", "Future", "IRTools", "InteractiveUtils", "LinearAlgebra", "LoopVectorization", "MacroTools", "NNlib", "NaNMath", "Random", "Requires", "SpecialFunctions", "Statistics", "ZygoteRules"]
+git-tree-sha1 = "16a7228209e6f457e9d71c39a58965616425384e"
+uuid = "e88e6eb3-aa80-5325-afca-941959d7151f"
+version = "0.5.3"
+
 [[ZygoteRules]]
 deps = ["MacroTools"]
 git-tree-sha1 = "b3b4882cc9accf6731a08cc39543fbc6b669dca8"

Project.toml

@@ -8,6 +8,7 @@ CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
 Calculus = "49dc2e85-a5d0-5ad3-a950-438e2897f1b9"
 Colors = "5ae59095-9a9b-59fe-a467-6f913c188581"
 DiffEqBase = "2b5f629d-d688-5b77-993f-72d75c75574e"
+DiffEqSensitivity = "41bf760c-e81c-5289-8e54-58b1f1f8abe2"
 ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
 Images = "916415d5-f1e6-5110-898d-aaa5f9f070e0"
 IterTools = "c8e1da08-722c-5040-9ed9-7db0dc04731e"
@@ -32,14 +33,15 @@ YAML = "ddb6d928-2868-570f-bddf-ab3f9cf99eb6"
 CSV = "<1"
 Calculus = "<1"
 Colors = "<1"
-DiffEqBase = "6.6.0"
+DiffEqBase = "<7"
+DiffEqSensitivity = "6.22.0"
 ForwardDiff = "<1"
 Images = "<1"
 IterTools = "1.3.0"
 OrdinaryDiffEq = "<6"
 Parameters = "<1"
-PyCall = "1.91.4"
-PyPlot = "2.9.0"
+PyCall = "<2"
+PyPlot = "<3"
 QuartzImageIO = "<1"
 ReverseDiff = "<2"
 SmoothingSplines = "<1"
@@ -49,4 +51,4 @@ Sundials = "<5"
 Tracker = "0.2"
 Unitful = "1.3.0"
 YAML = "<1"
-julia = "1"
+julia = "1.3"