Merge pull request #44 from ReactionMechanismGenerator/splines

Replace Dierckx with SmoothingSplines

Author: mjohnson541

.travis.yml

@@ -13,17 +13,13 @@ before_install:
   - bash miniconda.sh -b -p $HOME/miniconda
   - export PATH=$HOME/miniconda/bin:$PATH
   #create julia conda enviornment
-  - conda create -n conda_jl --yes python=2.7 conda
+  - conda create -n conda_jl --yes python=3.7 conda
   - source activate conda_jl
-  #install used packages
   - conda install -c rmg --yes rmg
-  - conda install -c rmg --yes rdkit
-  - conda install --yes pydot
-  - conda install --yes yaml
   - conda update --yes conda
 script:
   - if [[ -a .git/shallow ]]; then git fetch --unshallow; fi
-  - travis_wait julia -e 'using Pkg; Pkg.clone("https://github.com/ReactionMechanismGenerator/ReactionMechanismSimulator.jl.git");'
+  - travis_wait julia -e 'using Pkg; Pkg.add(PackageSpec(path="ReactionMechanismSimulator.jl"));'
   - travis_wait julia -e 'using Pkg; Pkg.build("ReactionMechanismSimulator"); Pkg.test("ReactionMechanismSimulator"; coverage=true);'
 after_success: 
   - julia -e 'cd(Pkg.dir("ReactionMechanismSimulator")); Pkg.add("Coverage"); using Coverage; Codecov.submit(Codecov.process_folder())'

Manifest.toml

@@ -26,9 +26,9 @@ version = "0.0.4"
 
 [[ArrayInterface]]
 deps = ["LinearAlgebra", "Requires", "SparseArrays"]
-git-tree-sha1 = "0eccdcbe27fd6bd9cba3be31c67bdd435a21e865"
+git-tree-sha1 = "066d1e7a9eb4873660791db7f0d8c7902600b81c"
 uuid = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9"
-version = "2.9.1"
+version = "2.11.0"
 
 [[AxisAlgorithms]]
 deps = ["LinearAlgebra", "Random", "SparseArrays", "WoodburyMatrices"]
@@ -45,22 +45,16 @@ version = "0.4.3"
 [[Base64]]
 uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"
 
-[[BinaryProvider]]
-deps = ["Libdl", "Logging", "SHA"]
-git-tree-sha1 = "ecdec412a9abc8db54c0efc5548c64dfce072058"
-uuid = "b99e7846-7c00-51b0-8f62-c81ae34c0232"
-version = "0.5.10"
-
 [[CEnum]]
 git-tree-sha1 = "215a9aa4a1f23fbd05b92769fdd62559488d70e9"
 uuid = "fa961155-64e5-5f13-b03f-caf6b980ea82"
 version = "0.4.1"
 
 [[CSV]]
 deps = ["CategoricalArrays", "DataFrames", "Dates", "Mmap", "Parsers", "PooledArrays", "SentinelArrays", "Tables", "Unicode"]
-git-tree-sha1 = "a100a1dd6ab63fc49e79c90dae67e5bc126419ff"
+git-tree-sha1 = "f095e44feec53d0ae809714a78c25908d1f370e6"
 uuid = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
-version = "0.7.3"
+version = "0.7.4"
 
 [[Calculus]]
 deps = ["LinearAlgebra"]
@@ -82,9 +76,9 @@ version = "0.8.1"
 
 [[ChainRulesCore]]
 deps = ["MuladdMacro"]
-git-tree-sha1 = "87e289253a5fc690c4860a41bbd427e16576f716"
+git-tree-sha1 = "9907341fe861268ddd0fc60be260633756b126a2"
 uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
-version = "0.9.3"
+version = "0.9.4"
 
 [[ColorTypes]]
 deps = ["FixedPointNumbers", "Random"]
@@ -191,17 +185,11 @@ uuid = "ade2ca70-3891-5945-98fb-dc099432e06a"
 deps = ["Mmap"]
 uuid = "8bb1440f-4735-579b-a4ab-409b98df4dab"
 
-[[Dierckx]]
-deps = ["BinaryProvider", "Libdl", "Random", "Test"]
-git-tree-sha1 = "956bfe5c4f9b794545f6527424fc0294cc5decbe"
-uuid = "39dd38d3-220a-591b-8e3c-4c3a8c710a94"
-version = "0.4.2"
-
 [[DiffEqBase]]
 deps = ["ArrayInterface", "ChainRulesCore", "ConsoleProgressMonitor", "DataStructures", "Distributed", "DocStringExtensions", "FunctionWrappers", "IterativeSolvers", "IteratorInterfaceExtensions", "LabelledArrays", "LinearAlgebra", "Logging", "LoggingExtras", "MuladdMacro", "Parameters", "Printf", "ProgressLogging", "RecipesBase", "RecursiveArrayTools", "RecursiveFactorization", "Requires", "Roots", "SparseArrays", "StaticArrays", "Statistics", "SuiteSparse", "TableTraits", "TerminalLoggers", "TreeViews", "ZygoteRules"]
-git-tree-sha1 = "71499ee24ffe00892a9e80cc953fe0421a54b552"
+git-tree-sha1 = "7f241c049129a0e765ef449b634990409286ed75"
 uuid = "2b5f629d-d688-5b77-993f-72d75c75574e"
-version = "6.40.8"
+version = "6.40.9"
 
 [[DiffResults]]
 deps = ["StaticArrays"]
@@ -262,15 +250,15 @@ version = "3.3.9+5"
 
 [[FileIO]]
 deps = ["Pkg"]
-git-tree-sha1 = "202335fd24c2776493e198d6c66a6d910400a895"
+git-tree-sha1 = "f354b2087a3b01c1d7152c19f45886c8a036fa5e"
 uuid = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549"
-version = "1.3.0"
+version = "1.4.0"
 
 [[FiniteDiff]]
 deps = ["ArrayInterface", "LinearAlgebra", "Requires", "SparseArrays", "StaticArrays"]
-git-tree-sha1 = "b02b6f6ea2c33f86a444f9cf132c1d1180a66cfd"
+git-tree-sha1 = "80becc23db3942d9e5eb8d0d42e725b9c46616f8"
 uuid = "6a86dc24-6348-571c-b903-95158fe2bd41"
-version = "2.4.1"
+version = "2.5.0"
 
 [[FixedPointNumbers]]
 git-tree-sha1 = "4aaea64dd0c30ad79037084f8ca2b94348e65eaa"
@@ -486,9 +474,9 @@ version = "0.4.2"
 
 [[LoopVectorization]]
 deps = ["DocStringExtensions", "LinearAlgebra", "OffsetArrays", "SIMDPirates", "SLEEFPirates", "UnPack", "VectorizationBase"]
-git-tree-sha1 = "4c002de66221639174e081ec74c156e9013e4afa"
+git-tree-sha1 = "8c19b0c629dae1cea52a990d6303d03fe4328795"
 uuid = "bdcacae8-1622-11e9-2a5c-532679323890"
-version = "0.8.17"
+version = "0.8.19"
 
 [[METIS_jll]]
 deps = ["Libdl", "Pkg"]
@@ -720,9 +708,9 @@ version = "0.5.4"
 
 [[SentinelArrays]]
 deps = ["Dates", "Random"]
-git-tree-sha1 = "41e78a6419de2279b23cc70342c7147dc4c98860"
+git-tree-sha1 = "cd9dccb026262a46d5a81ef1ce1e595150b2b8d2"
 uuid = "91c51154-3ec4-41a3-a24f-3f23e20d615c"
-version = "1.2.8"
+version = "1.2.9"
 
 [[Serialization]]
 uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b"
@@ -737,6 +725,12 @@ git-tree-sha1 = "2ee666b24ab8be6a922f9d6c11a86e1a703a7dda"
 uuid = "699a6c99-e7fa-54fc-8d76-47d257e15c1d"
 version = "0.9.2"
 
+[[SmoothingSplines]]
+deps = ["LinearAlgebra", "Random", "Reexport", "StatsBase", "Test"]
+git-tree-sha1 = "9e47150ea38107ba762fb26bd5c2a000b27ecf94"
+uuid = "102930c3-cf33-599f-b3b1-9a29a5acab30"
+version = "0.2.1"
+
 [[Sockets]]
 uuid = "6462fe0b-24de-5631-8697-dd941f90decc"
 

Project.toml

@@ -1,13 +1,12 @@
 name = "ReactionMechanismSimulator"
 uuid = "c2d78dd2-25c4-5b79-bebc-be6c69dd440f"
 authors = ["Matt Johnson <mjohnson541@gmail.com>"]
-version = "0.2.0"
+version = "0.2.1"
 
 [deps]
 CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
 Calculus = "49dc2e85-a5d0-5ad3-a950-438e2897f1b9"
 Colors = "5ae59095-9a9b-59fe-a467-6f913c188581"
-Dierckx = "39dd38d3-220a-591b-8e3c-4c3a8c710a94"
 DiffEqBase = "2b5f629d-d688-5b77-993f-72d75c75574e"
 ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
 Images = "916415d5-f1e6-5110-898d-aaa5f9f070e0"
@@ -18,6 +17,7 @@ Parameters = "d96e819e-fc66-5662-9728-84c9c7592b0a"
 PyCall = "438e738f-606a-5dbb-bf0a-cddfbfd45ab0"
 PyPlot = "d330b81b-6aea-500a-939a-2ce795aea3ee"
 QuartzImageIO = "dca85d43-d64c-5e67-8c65-017450d5d020"
+SmoothingSplines = "102930c3-cf33-599f-b3b1-9a29a5acab30"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b"
 StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
@@ -27,22 +27,22 @@ Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
 YAML = "ddb6d928-2868-570f-bddf-ab3f9cf99eb6"
 
 [compat]
-julia = "^1.0.0"
-CSV = "^0.7.3"
-Calculus = "^0.5.1"
-Colors = "^0.12.3"
-Dierckx = "^0.4.2"
-DiffEqBase = "^6.40.8"
-ForwardDiff = "^0.10.12"
-Images = "^0.22.4"
-IterTools = "^1.3.0"
-OrdinaryDiffEq = "^5.41.0"
-Parameters = "^0.12.1"
-PyCall = "^1.91.4"
-PyPlot = "^2.9.0"
-QuartzImageIO = "^0.7.1"
-SpecialFunctions = "^0.10.3"
-StaticArrays = "^0.12.4"
-Sundials = "^4.2.5"
-Unitful = "^1.3.0"
-YAML = "^0.4.0"
+CSV = "<1"
+Calculus = "<1"
+Colors = "<1"
+DiffEqBase = "6.6.0"
+ForwardDiff = "<1"
+Images = "<1"
+IterTools = "1.3.0"
+OrdinaryDiffEq = "<6"
+Parameters = "<1"
+PyCall = "1.91.4"
+PyPlot = "2.9.0"
+QuartzImageIO = "<1"
+SmoothingSplines = "<1"
+SpecialFunctions = "<1"
+StaticArrays = "<1"
+Sundials = "<5"
+Unitful = "1.3.0"
+YAML = "<1"
+julia = "1"

src/Domain.jl

@@ -1,8 +1,8 @@
 using Parameters
 using LinearAlgebra
 using StaticArrays
-using Dierckx
 using Calculus
+using SmoothingSplines
 
 abstract type AbstractDomain end
 export AbstractDomain
@@ -263,16 +263,14 @@ function ParametrizedTPDomain(;phase::Z,initialconds::Dict{X,Any},constantspecie
     end
     @assert V != 0.0 || (T != 0.0 && P != 0.0)
     if isa(T,AbstractArray)
-        q = Spline1D(ts,T;k=3,s=1e-11)
-        Tfcn(x::Float64) = q(x)
+        Tfcn = getspline(ts,T)
     elseif isa(T,Function)
         Tfcn = T
     else
         throw(error("ParametrizedTPDomain must take \"T\" as a function or if an array of times for \"ts\" is supplied as an array of volumes"))
     end
     if isa(P,AbstractArray)
-        v = Spline1D(ts,P;k=3,s=1e-11)
-        Pfcn(x::Float64) = v(x)
+        Pfcn = getspline(ts,P)
     elseif isa(P,Function)
         Pfcn = P
     else
@@ -346,8 +344,7 @@ function ParametrizedVDomain(;phase::Z,initialconds::Dict{X,Any},constantspecies
     end
     @assert isa(V,Function) || isa(V,AbstractArray)
     if isa(V,AbstractArray)
-        q = Spline1D(ts,V;k=3,s=1e-11)
-        Vfcn = f(x::Float64) = q(x)
+        Vfcn = getspline(ts,V)
     elseif isa(V,Function)
         Vfcn = V
     else
@@ -422,8 +419,7 @@ function ParametrizedPDomain(;phase::Z,initialconds::Dict{X,Any},constantspecies
     end
     @assert isa(P,Function) || isa(P,AbstractArray)
     if isa(P,AbstractArray)
-        q = Spline1D(ts,P;k=3,s=1e-11)
-        Pfcn = f(x::Float64) = q(x)
+        Pfcn = getspline(ts,P)
     elseif isa(P,Function)
         Pfcn = P
     else
@@ -577,8 +573,7 @@ function ParametrizedTConstantVDomain(;phase::IdealDiluteSolution,initialconds::
         end
     end
     if isa(T,AbstractArray)
-        q = Spline1D(ts,T;k=3,s=1e-11)
-        Tfcn = f(x::Float64) = q(x)
+        Tfcn = getspline(ts,T)
     elseif isa(T,Function)
         Tfcn = T
     else
@@ -943,3 +938,12 @@ function getreactionindices(ig::Q) where {Q<:AbstractPhase}
     return arr
 end
 export getreactionindices
+
+"""
+fit a cubic spline to data and return a function evaluating that spline
+"""
+function getspline(xs,vals;s=1e-10)
+    smspl = fit(SmoothingSpline,xs,vals,s)
+    F(x::T) where {T} = predict(smspl,x)
+    return F
+end