Fix package name

Project.toml

@@ -1,26 +1,21 @@
-name = "Solus"
-uuid = "16b9c28e-565c-11e9-13a9-53e2645fa95d"
-authors = ["Simon Byrne <simonbyrne@gmail.com>"]
+name = "CES"
+uuid = "57e54526-abb8-4cd3-a48f-48a815226fdb"
+authors = ["Charles_Kawczynski <kawczynski.charles@gmail.com>"]
 version = "0.1.0"
 
 [deps]
 ArgParse = "c7e460c6-2fb9-53a9-8c5b-16f535851c63"
 ConfParser = "88353bc9-fd38-507d-a820-d3b43837d6b9"
+DifferentialEquations = "0c46a032-eb83-5123-abaf-570d42b7fbaa"
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
 DocStringExtensions = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
 EllipsisNotation = "da5c29d0-fa7d-589e-88eb-ea29b0a81949"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+NPZ = "15e1cf62-19b3-5cfa-8e77-841668bca605"
 Parameters = "d96e819e-fc66-5662-9728-84c9c7592b0a"
 PyCall = "438e738f-606a-5dbb-bf0a-cddfbfd45ab0"
+PyPlot = "d330b81b-6aea-500a-939a-2ce795aea3ee"
 ScikitLearn = "3646fa90-6ef7-5e7e-9f22-8aca16db6324"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
-
-[extras]
-DifferentialEquations = "0c46a032-eb83-5123-abaf-570d42b7fbaa"
-NPZ = "15e1cf62-19b3-5cfa-8e77-841668bca605"
-Parameters = "d96e819e-fc66-5662-9728-84c9c7592b0a"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
-
-[targets]
-test = ["DifferentialEquations", "NPZ", "Parameters", "Test"]

README.md

@@ -1,5 +1,12 @@
-# Solus.jl
+# CES.jl
 
-[![Travis Build Status](https://travis-ci.org/climate-machine/Solus.jl.svg?branch=master)](https://travis-ci.org/climate-machine/Solus.jl)
-[![Appveyor Build Status](https://ci.appveyor.com/api/projects/status/uslnruyhehva7bbv/branch/master?svg=true)](https://ci.appveyor.com/project/climate-machine/solus-jl/branch/master)
+| **Build Status**                                                              |
+|:------------------------------------------------------------------------------|
+| [![appveyor][appveyor-img]][appveyor-url] [![travis][travis-img]][travis-url] |
+
+[travis-img]: https://travis-ci.org/climate-machine/CES.jl.svg?branch=master
+[travis-url]: https://travis-ci.org/climate-machine/CES.jl
+
+[appveyor-img]: https://ci.appveyor.com/api/projects/status/uslnruyhehva7bbv/branch/master?svg=true
+[appveyor-url]: https://ci.appveyor.com/project/climate-machine/CES.jl/branch/master
 

docs/Project.toml

@@ -0,0 +1,18 @@
+[deps]
+ArgParse = "c7e460c6-2fb9-53a9-8c5b-16f535851c63"
+CES = "57e54526-abb8-4cd3-a48f-48a815226fdb"
+ConfParser = "88353bc9-fd38-507d-a820-d3b43837d6b9"
+DifferentialEquations = "0c46a032-eb83-5123-abaf-570d42b7fbaa"
+Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
+DocStringExtensions = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
+Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+EllipsisNotation = "da5c29d0-fa7d-589e-88eb-ea29b0a81949"
+LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+NPZ = "15e1cf62-19b3-5cfa-8e77-841668bca605"
+Parameters = "d96e819e-fc66-5662-9728-84c9c7592b0a"
+PyCall = "438e738f-606a-5dbb-bf0a-cddfbfd45ab0"
+PyPlot = "d330b81b-6aea-500a-939a-2ce795aea3ee"
+ScikitLearn = "3646fa90-6ef7-5e7e-9f22-8aca16db6324"
+Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
+StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"

docs/make.jl

@@ -0,0 +1,28 @@
+Base.HOME_PROJECT[] = abspath(Base.HOME_PROJECT[]) # JuliaLang/julia/pull/28625
+
+using CES, Documenter
+
+makedocs(
+  sitename = "CES.jl",
+  doctest = false,
+  strict = false,
+  format = Documenter.HTML(
+        prettyurls = get(ENV, "CI", nothing) == "true",
+        mathengine = MathJax(Dict(
+            :TeX => Dict(
+                :equationNumbers => Dict(:autoNumber => "AMS"),
+                :Macros => Dict()
+            )
+        ))
+  ),
+  clean = false,
+  modules = [Documenter, CES],
+  pages = Any[
+    "Home" => "index.md",
+  ],
+)
+
+deploydocs(
+           repo = "github.com/climate-machine/CES.jl.git",
+           target = "build",
+          )

docs/src/index.md

@@ -0,0 +1,3 @@
+# CES.jl
+
+Stochastic Optimization, Learning, Uncertainty and Sampling

examples/Manifest.toml

@@ -538,7 +538,7 @@ git-tree-sha1 = "012661b70364840fcd380912d878d96f7bf95ff3"
 uuid = "b85f4697-e234-5449-a836-ec8e2f98b302"
 version = "1.0.10"
 
-[[Solus]]
+[[CES]]
 deps = ["Distributions", "DocStringExtensions", "LinearAlgebra", "Statistics", "Test"]
 path = ".."
 uuid = "16b9c28e-565c-11e9-13a9-53e2645fa95d"

examples/Project.toml

@@ -6,4 +6,4 @@ LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 Parameters = "d96e819e-fc66-5662-9728-84c9c7592b0a"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
 PyPlot = "d330b81b-6aea-500a-939a-2ce795aea3ee"
-Solus = "16b9c28e-565c-11e9-13a9-53e2645fa95d"
+CES = "16b9c28e-565c-11e9-13a9-53e2645fa95d"

src/Solus.jl → src/CES.jl

@@ -1,4 +1,4 @@
-module Solus
+module CES
 
 using Distributions, Statistics, LinearAlgebra, DocStringExtensions
 

src/GPR.jl

@@ -1,6 +1,6 @@
 module GPR
 """
-For the time being, please use `include("src/GPR.jl")` and not `using Solus.GPR`
+For the time being, please use `include("src/GPR.jl")` and not `using CES.GPR`
 since there are precompile issues with the backend (scikit-learn)
 """
 

src/neki.jl

@@ -1,11 +1,11 @@
 """
-    neki_iter(prob::SolusProblem, θs, fθs)
+    neki_iter(prob::CESProblem, θs, fθs)
 
 Peform an iteration of NEKI, returning a new set of proposed `θs`.
 
 See eqs. (5.4a-b) from https://arxiv.org/abs/1903.08866.
 """
-function neki_iter(prob::SolusProblem, θs, fθs)
+function neki_iter(prob::CESProblem, θs, fθs)
     covθ = cov(θs)
     meanθ = mean(θs)
 

src/problems.jl

@@ -1,13 +1,13 @@
 """
-    SolusProblem
+    CESProblem
 
 An uncertainty quantification problem.
 
 # Fields
 
 $(DocStringExtensions.FIELDS)
 """
-struct SolusProblem{P,M,O,S<:HilbertSpace}
+struct CESProblem{P,M,O,S<:HilbertSpace}
     """
     The prior distribution for the parameters ``θ``. Currently only `MvNormal` objects are supported.
     """
@@ -28,15 +28,15 @@ struct SolusProblem{P,M,O,S<:HilbertSpace}
     """
     space::S
 end
-SolusProblem(prior, forwardmodel, obs) = SolusProblem(prior, forwardmodel, obs, DefaultSpace())
+CESProblem(prior, forwardmodel, obs) = CESProblem(prior, forwardmodel, obs, DefaultSpace())
 
 
 struct FlatPrior
 end
 
 Distributions.logpdf(::FlatPrior, x) = 0.0
 
-function neglogposteriordensity(s::SolusProblem, θ)
+function neglogposteriordensity(s::CESProblem, θ)
     -logpdf(s.prior, θ) + norm(s.forwardmodel(θ) - s.obs, s.space)
 end
 

test/neki.jl

@@ -1,5 +1,5 @@
 using Test
-using Solus
+using CES
 using LinearAlgebra, Distributions
 
 @testset "NEKI" begin
@@ -16,14 +16,14 @@ using LinearAlgebra, Distributions
 
     Γ = 0.1*Matrix{Float64}(I,10,10)
 
-    prob = Solus.SolusProblem(prior, f, y_obs, Solus.CovarianceSpace(Γ))
+    prob = CES.CESProblem(prior, f, y_obs, CES.CovarianceSpace(Γ))
 
     J = 50
     θs = [rand(2) for i in 1:J]
 
     for i = 1:20
         fθs = map(f, θs)
-        θs = Solus.neki_iter(prob, θs, fθs)
+        θs = CES.neki_iter(prob, θs, fθs)
     end
 
     postΣ = inv(inv(Σ) + A'*inv(Γ)*A)

test/runtests.jl

@@ -1,5 +1,5 @@
 using Test
-using Solus
+using CES
 ENV["JULIA_LOG_LEVEL"] = "WARN"
 
 include("neki.jl")